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Goh Y, Sadikan MZ, Jaiprakash H, Nasir NAA, Agarwal R, Iezhitsa I, Ismail NM. Tocotrienol-rich fraction (TRF) protects against retinal cell apoptosis and preserves visual behavior in rats with streptozotocin-induced diabetic retinopathy. BMC Complement Med Ther 2024; 24:322. [PMID: 39215295 PMCID: PMC11365272 DOI: 10.1186/s12906-024-04614-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Tocotrienol is a vitamin E analogue that is known to exert anti-inflammatory and antioxidant effects. Hence, in the current study, the effects of TRF on the expression of pro- and anti-apoptotic proteins in the streptozotocin-induced diabetic rat retinas were investigated. The effect of TRF on the visual behaviour of rats was also studied. METHODS Diabetes was induced in rats by intraperitoneal injection of streptozotocin and was confirmed by a blood sugar level of at least 20 mmol/L, 48 h, post-injection. Diabetic rats were divided into a group treated with vehicle (DV) and the other treated with TRF (100 mg/kg; DT). A group of non-diabetic rats treated with vehicle (N) served as the control group. All treatments were administered orally for 12 weeks. Rats were then subjected to an assessment of general behaviour in an open field arena and a two-chamber mirror test to assess their visual behaviour. At the end of the experimental period, rats were sacrificed, and their retinas were isolated to measure the expression of pro- (Casp3, Bax) and anti-apoptotic (Bcl2) markers using RT-qPCR and ELISA. TUNEL staining was used to detect the apoptotic retinal cells. RESULTS Treatment with TRF lowered the retinal expression of Casp3 protein by 2.26-folds (p < 0.001) and Bax protein by 2.18-fold (p < 0.001) compared to vehicle-treated rats. The retinal anti-apoptotic protein Bcl2 expression was 1.87-fold higher in DT compared to DV rats (p < 0.001). Accordingly, the Bax/Bcl2 ratio in the TRF-treated group was significantly greater in DT compared to DV rats. Retinal Casp3, Bax, and Bcl2 gene expression, as determined by RT-qPCR, also showed changes corresponding to protein expression. In the open field test, DV rats showed greater anxiety-related behaviour than group N, while the behaviour of DT rats was similar to the N group of rats. DT rats and group N rats preferred the inverse mirror chamber over the mirror-containing chamber in the two-mirror chamber test (p < 0.01). CONCLUSION Oral TRF therapy for 12 weeks lowers retinal cell apoptosis by decreasing pro- and increasing anti-apoptotic markers. The preservation of visual behaviour in a two-chamber mirror test supported these retinal molecular alterations in diabetic rats.
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Affiliation(s)
- You Goh
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Muhammad Zulfiqah Sadikan
- Department of Pharmacology, Faculty of Medicine, Manipal University College Malaysia, Bukit Baru, Melaka, 75150, Malaysia
- Centre for Neuroscience Research (NeuRon), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh, Selangor, 47000, Malaysia
| | - Heethal Jaiprakash
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia.
| | - Nurul Alimah Abdul Nasir
- Centre for Neuroscience Research (NeuRon), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh, Selangor, 47000, Malaysia
| | - Renu Agarwal
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Igor Iezhitsa
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
- Department of Pharmacology and Bioinformatics, Volgograd State Medical University, Pavshikh Bortsov sq. 1, Volgograd, 400131, Russian Federation
| | - Nafeeza Mohd Ismail
- Centre for Neuroscience Research (NeuRon), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh, Selangor, 47000, Malaysia
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D'Souza N, Porter AM, Rose JB, Dreelin E, Peters SE, Nowlin PJ, Carbonell S, Cissell K, Wang Y, Flood MT, Rachmadi AT, Xi C, Song P, Briggs S. Public health use and lessons learned from a statewide SARS-CoV-2 wastewater monitoring program (MiNET). Heliyon 2024; 10:e35790. [PMID: 39220928 PMCID: PMC11363850 DOI: 10.1016/j.heliyon.2024.e35790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/27/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
The global SARS-CoV-2 monitoring effort has been extensive, resulting in many states and countries establishing wastewater-based epidemiology programs to address the spread of the virus during the pandemic. Challenges for programs include concurrently optimizing methods, training new laboratories, and implementing successful surveillance programs that can rapidly translate results for public health, and policy making. Surveillance in Michigan early in the pandemic in 2020 highlights the importance of quality-controlled data and explores correlations with wastewater and clinical case data aggregated at the state level. The lessons learned and potential measures to improve public utilization of results are discussed. The Michigan Network for Environmental Health and Technology (MiNET) established a network of laboratories that partnered with local health departments, universities, wastewater treatment plants (WWTPs) and other stakeholders to monitor SARS-CoV-2 in wastewater at 214 sites in Michigan. MiNET consisted of nineteen laboratories, twenty-nine local health departments, 6 Native American tribes, and 60 WWTPs monitoring sites representing 45 % of Michigan's population from April 6 and December 29, 2020. Three result datasets were created based on quality control criteria. Wastewater results that met all quality assurance criteria (Dataset Mp) produced strongest correlations with reported clinical cases at 16 days lag (rho = 0.866, p < 0.05). The project demonstrated the ability to successfully track SARS-CoV-2 on a large, state-wide scale, particularly data that met the outlined quality criteria and provided an early warning of increasing COVID-19 cases. MiNET is currently poised to leverage its competency to complement public health surveillance networks through environmental monitoring for new and emerging pathogens of concern and provides a valuable resource to state and federal agencies to support future responses.
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Affiliation(s)
- Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Alexis M. Porter
- Annis Water Resources Insititute, Grand Valley State University, Muskegon, MI, USA
| | - Joan B. Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Erin Dreelin
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Susan E. Peters
- Michigan Department of Health and Human Services, Lansing, MI, USA
| | | | - Samantha Carbonell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Yili Wang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew T. Flood
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | | | - Chuanwu Xi
- University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Song
- University of Michigan, Ann Arbor, Michigan, USA
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes, and Energy, Lansing, MI, USA
| | - the Michigan Network for Environmental Health and Technology (MiNET) consortium
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
- Annis Water Resources Insititute, Grand Valley State University, Muskegon, MI, USA
- Michigan Department of Health and Human Services, Lansing, MI, USA
- Northern Michigan Regional Laboratory, Gaylord, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Saginaw Valley State University, Michigan, USA
- University of Michigan, Ann Arbor, Michigan, USA
- Institute of Environmental Science and Research (ESR), New Zealand
- Michigan Department of Environment, Great Lakes, and Energy, Lansing, MI, USA
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Ijatuyi TT, Lawal AO, Akinjiyan MO, Ojo FM, Koledoye OF, Agboola OO, Dahunsi DT, Folorunso IM, Elekofehinti OO. Effects of Bryophyllum pinnatum on Dysfunctional Autophagy in Rats Lungs Exposed to Zinc Oxide Nanoparticles. Int Immunopharmacol 2024; 141:113005. [PMID: 39213874 DOI: 10.1016/j.intimp.2024.113005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/06/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Lung inflammation as a result of exposure to toxicants is a major pathological problem. Autophagy (AP) is a process of cell self-digestion and can be disrupted by environmental toxicants, leading to oxidative stress, inflammation and cellular damage. Bryophyllum pinnatum (Lam.) Oken has been used in folklore medicine to manage pathological abnormalities, including inflammation, but mechanisms remain unclear. This work investigated the effects of Bryophyllum pinnatum ethanol leaf extract (BP) on dysfunctional AP in the lungs of Wistar rats exposed to zinc oxide nanoparticles (ZONPs). The experimental rats were orally administered ZONPs for seven days (10 mg/kg). Some exposed rats were post-treated with BP (62.5 and 125 mg/kg) through oral gavage. Oxidative stress, inflammation, and apoptotic and autophagic parameters were assessed using biochemical assay and gene expression methods. Several indices of pulmonary damage were also evaluated. PCR analysis suggested that ZONP downregulated the expression of pro-autophagy-related genes (Beclin 2, ATG5, DAPK, and FOXP3) and upregulated the expression of the TNF-alpha, NF-Kb, LC3 and Bcl2 genes. In contrast, BP significantly (p < 0.0001) reversed ZONP-induced pulmonary toxicity and oxidative stress. It reduced MDA levels and increased SOD, CAT, GSH and GPxD activities. BP significantly (p < 0.0001) downregulated the expressions of proinflammatory genes (IL-6 and JNK) and upregulated the expressions of IL-10, CAT and SOD genes in ZONP-exposed rats. BP restored the lung's histoarchitectural structure after ZNOP-induced distortion. The results suggested that BP has antioxidant and anti-inflammatory properties, and could effectively restore ZNOP-induced dysfunctional AP in the lungs of Wistar rats.
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Affiliation(s)
- Taiwo Tolulope Ijatuyi
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria
| | - Akeem Olalekan Lawal
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria; Precision Molecular Laboratory, Akure, Ondo State, Nigeria
| | - Moses Orimoloye Akinjiyan
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria; Medical Biochemistry Department, School of Basic Medical Sciences, Federal University of Technology, Akure, Ondo State, Nigeria.
| | - Funmilayo Mercy Ojo
- Medical Biochemistry Department, School of Basic Medical Sciences, Federal University of Technology, Akure, Ondo State, Nigeria
| | - Omowumi Funmilayo Koledoye
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria
| | - Olaoluwa Oladimeji Agboola
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria
| | - Damilola Timothy Dahunsi
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria
| | - Ibukun Mary Folorunso
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria; Precision Molecular Laboratory, Akure, Ondo State, Nigeria
| | - Olusola Olalekan Elekofehinti
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Life Sciences, Federal University of Technology, Akure, P.M.B. 704, Akure, Ondo-State, Nigeria
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Petri FAM, Malcher CS, Mechler-Dreibi ML, Panneitz AK, Braga ER, Aguiar GAD, Toledo LT, Martins TS, Cides-da-Silva LC, Fantini MCA, Sant'Anna OA, Montassier HJ, Oliveira LGD. Shedding reduction and immunity modulation in piglets with an inactivated Mycoplasma hyopneumoniae vaccine encapsulated in nanostructured SBA-15 silica. Vaccine 2024; 42:126268. [PMID: 39208565 DOI: 10.1016/j.vaccine.2024.126268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Mycoplasma (M.) hyopneumoniae is a primary etiological agent of porcine enzootic pneumonia (PEP), a disease that causes significant economic losses to pig farming worldwide. Current commercial M. hyopneumoniae vaccines induce partial protection, decline in preventing transmission of this pathogen or inducing complete immunity, evidencing the need for improving vaccines against PEP. In our study, we aimed to test the effectiveness of the SBA-15 ordered mesoporous silica nanostructured particles as an immune adjuvant of a vaccine composed of M. hyopneumoniae strain 232 proteins encapsulated in SBA-15 and administered by intramuscular route in piglets to evaluate the immune responses and immune-protection against challenge. Forty-eight 24-day-old M. hyopneumoniae-free piglets were divided into four experimental groups with different protocols, encompassing a commercial vaccine against M. hyopneumoniae, SBA-15 vaccine, SBA-15 adjuvant without antigens and a non-immunized group. All piglets were challenged with the virulent strain 232 of M. hyopneumoniae. Piglets that received the SBA-15 and commercial vaccine presented marked immune responses characterized by anti-M. hyopneumoniae IgA and IgG antibodies in serum, anti-M. hyopneumoniae IgA antibodies in nasal mucosa and showed an upregulation of IL-17 and IL-4 cytokines and downregulation of IFN-γ in lungs 35 days post-infection. Piglets immunized with SBA-15 vaccine presented a reduction of bacterial shedding compared to piglets immunized with a commercial bacterin. In addition, piglets from SBA-15 adjuvant suspension group presented increased IL-17 gene expression in the lungs without involvement of Th1 and Th2 responses after challenge. These results indicated that SBA-15 vaccine induced both humoral and cell-mediated responses in the upper respiratory tract and lungs, first site of replication and provided protection against M. hyopneumoniae infection with a homologous strain with reduction of lung lesions and bacterial shedding. Finally, these results enhance the potential use of new technologies such as nanostructured particles applied in vaccines for the pig farming industry.
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Affiliation(s)
| | - Clarisse Sena Malcher
- São Paulo State University (Unesp), School of Agricultural and Veterinary Sciences, Jaboticabal, Brazil
| | | | - Ana Karolina Panneitz
- São Paulo State University (Unesp), School of Agricultural and Veterinary Sciences, Jaboticabal, Brazil
| | - Eduarda Ribeiro Braga
- São Paulo State University (Unesp), School of Agricultural and Veterinary Sciences, Jaboticabal, Brazil
| | | | - Leonardo Teófilo Toledo
- Federal University of Viçosa (UFV), Laboratory of Bacterial Diseases (LDBAC), Viçosa, Brazil
| | - Tereza Silva Martins
- Department of Chemistry, Federal University of São Paulo (UNIFESP), Diadema, São Paulo, Brazil
| | | | | | | | - Hélio J Montassier
- São Paulo State University (Unesp), School of Agricultural and Veterinary Sciences, Jaboticabal, Brazil
| | - Luís Guilherme de Oliveira
- São Paulo State University (Unesp), School of Agricultural and Veterinary Sciences, Jaboticabal, Brazil.
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Mandal D, Datta S, Mitra S, Nag Chaudhuri R. ABSCISIC ACID INSENSITIVE 3 promotes auxin signalling by regulating SHY2 expression to control primary root growth in response to dehydration stress. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5111-5129. [PMID: 38770693 DOI: 10.1093/jxb/erae237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/20/2024] [Indexed: 05/22/2024]
Abstract
Plants combat dehydration stress through different strategies including root architectural changes. Here we show that when exposed to varying levels of dehydration stress, primary root growth in Arabidopsis is modulated by regulating root meristem activity. Abscisic acid (ABA) in concert with auxin signalling adjust primary root growth according to stress levels. ABSCISIC ACID INSENSITIVE 3 (ABI3), an ABA-responsive transcription factor, stands at the intersection of ABA and auxin signalling and fine-tunes primary root growth in response to dehydration stress. Under low ABA or dehydration stress, induction of ABI3 expression promotes auxin signalling by decreasing expression of SHY2, a negative regulator of auxin response. This further enhances the expression of auxin transporter gene PIN1 and cell cycle gene CYCB1;1, resulting in an increase in primary root meristem size and root length. Higher levels of dehydration stress or ABA repress ABI3 expression and promote ABSCISIC ACID INSENSITIVE 5 (ABI5) expression. This elevates SHY2 expression, thereby impairing primary root meristem activity and retarding root growth. Notably, ABI5 can promote SHY2 expression only in the absence of ABI3. Such ABA concentration-dependent expression of ABI3 therefore functions as a regulatory sensor of dehydration stress levels and orchestrates primary root growth by coordinating its downstream regulation.
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Affiliation(s)
- Drishti Mandal
- Department of Biotechnology, St Xavier's College, 30, Mother Teresa Sarani, Kolkata-700016, India
| | - Saptarshi Datta
- Department of Biotechnology, St Xavier's College, 30, Mother Teresa Sarani, Kolkata-700016, India
| | - Sicon Mitra
- Department of Biotechnology, St Xavier's College, 30, Mother Teresa Sarani, Kolkata-700016, India
| | - Ronita Nag Chaudhuri
- Department of Biotechnology, St Xavier's College, 30, Mother Teresa Sarani, Kolkata-700016, India
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56
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Papp H, Tóth E, Bóvári-Biri J, Bánfai K, Juhász P, Mahdi M, Russo LC, Bajusz D, Sipos A, Petri L, Szalai TV, Kemény Á, Madai M, Kuczmog A, Batta G, Mózner O, Vaskó D, Hirsch E, Bohus P, Méhes G, Tőzsér J, Curtin NJ, Helyes Z, Tóth A, Hoch NC, Jakab F, Keserű GM, Pongrácz JE, Bai P. The PARP inhibitor rucaparib blocks SARS-CoV-2 virus binding to cells and the immune reaction in models of COVID-19. Br J Pharmacol 2024. [PMID: 39191429 DOI: 10.1111/bph.17305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND AND PURPOSE To date, there are limited options for severe Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 virus. As ADP-ribosylation events are involved in regulating the life cycle of coronaviruses and the inflammatory reactions of the host; we have, here, assessed the repurposing of registered PARP inhibitors for the treatment of COVID-19. EXPERIMENTAL APPROACH The effects of PARP inhibitors on virus uptake were assessed in cell-based experiments using multiple variants of SARS-CoV-2. The binding of rucaparib to spike protein was tested by molecular modelling and microcalorimetry. The anti-inflammatory properties of rucaparib were demonstrated in cell-based models upon challenging with recombinant spike protein or SARS-CoV-2 RNA vaccine. KEY RESULTS We detected high levels of oxidative stress and strong PARylation in all cell types in the lungs of COVID-19 patients, both of which negatively correlated with lymphocytopaenia. Interestingly, rucaparib, unlike other tested PARP inhibitors, reduced the SARS-CoV-2 infection rate through binding to the conserved 493-498 amino acid region located in the spike-ACE2 interface in the spike protein and prevented viruses from binding to ACE2. In addition, the spike protein and viral RNA-induced overexpression of cytokines was down-regulated by the inhibition of PARP1 by rucaparib at pharmacologically relevant concentrations. CONCLUSION AND IMPLICATIONS These results point towards repurposing rucaparib for treating inflammatory responses in COVID-19.
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Affiliation(s)
- Henrietta Papp
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Emese Tóth
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- HUN-REN-DE Cell Biology and Signaling Research Group, Debrecen, Hungary
| | - Judit Bóvári-Biri
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pécs, Pécs, Hungary
| | - Krisztina Bánfai
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pécs, Pécs, Hungary
| | - Péter Juhász
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Mohamed Mahdi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lilian Cristina Russo
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Adrienn Sipos
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- HUN-REN-DE Cell Biology and Signaling Research Group, Debrecen, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tibor Viktor Szalai
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Ágnes Kemény
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Pharmacology and Pharmacotherapy, Medical School & Centre for Neuroscience, University of Pécs, Pécs, Hungary
- Department of Medical Biology, Medical School, Pécs, Hungary
| | - Mónika Madai
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Anett Kuczmog
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Orsolya Mózner
- Doctoral School of Molecular Medicine, Semmelweis University, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dorottya Vaskó
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Edit Hirsch
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nicola J Curtin
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School & Centre for Neuroscience, University of Pécs, Pécs, Hungary
- Hungarian Research Network, Chronic Pain Research Group, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | - Attila Tóth
- Section of Clinical Physiology, Department of Cardiology, University of Debrecen, Debrecen, Hungary
| | - Nicolas C Hoch
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Ferenc Jakab
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Judit E Pongrácz
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pécs, Pécs, Hungary
| | - Péter Bai
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, Hungary
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Neto IVDS, Pinto AP, de Andrade RV, de Souza FHV, de Souza PEN, Assis V, Tibana RA, Neves RVP, Rosa TDS, Prestes J, da Silva ASR, Marqueti RDC. Paternal exercise induces antioxidant defenses by α-Klotho/Keap1 pathways in the skeletal muscle of offspring exposed to a high fat-diet without changing telomere length. J Nutr Biochem 2024:109747. [PMID: 39197728 DOI: 10.1016/j.jnutbio.2024.109747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 08/01/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
Although previous studies demonstrated that the ancestral lifestyle can enhance the metabolic health of offspring exposed to an obesogenic diet, the specific connections between these positive effects in redox state and telomere length are unknown. We investigated the impact of paternal resistance training (RT) on stress-responsive signaling and the pathways involved in telomere homeostasis in skeletal muscle. This investigation encompassed both the fathers and first-generation litter exposed to a long-term standard diet (24 weeks) and high fat diet (HFD). Wistar rats were randomized into sedentary or trained fathers (8 weeks of resistance training). The offspring were obtained by mating with sedentary females. Upon weaning, male offspring were divided into four groups: offspring of sedentary or trained fathers exposed to either a control diet or HFD. The gastrocnemius was prepared for reverse transcription-quantitative polymerase chain reaction, immunoblotting, ELISA, and electron paramagnetic resonance spectroscopy. RT upregulated shelterin mRNA levels and antioxidant protein, preserving muscle telomere in fathers. Conversely, HFD induced a disturbance in the redox balance, which may have contributed to the offspring telomere shortening from sedentary fathers. Pre-conceptional paternal RT downregulates Kelch-like ECH-associated protein 1 (Keap1) mRNA levels in the skeletal muscle of progeny exposed to HFD, driving an increase in Glutathione reductase mRNA levels, Sod1 and Catalase protein levels to mitigate ROS production. Also, paternal exercise upregulates α-Klotho protein levels, mediating antioxidative responses without altering shelterin mRNA levels and telomere length. We provide the first in-depth analysis that the offspring's redox state seems to be directly associated with the beneficial effects of paternal exercise.
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Affiliation(s)
- Ivo Vieira de Sousa Neto
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.
| | - Ana Paula Pinto
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Rosangela Vieira de Andrade
- Graduate Program in Genomic Science and Biotechnology, Catholic University of Brasília, Taguatinga, DF, Brazil
| | | | | | - Victória Assis
- Molecular Analysis Laboratory, Faculty of Ceilândia, Universidade de Brasília (UNB), Distrito Federal, Brazil
| | - Ramires Alsamir Tibana
- Graduate Program in Health Sciences, Faculdade de Medicine, Universidade Federal do Mato Grosso (UFMT), Cuiabá, MT, Brazil
| | | | | | - Jonato Prestes
- Graduate Program in Physical Education, Universidade Católica de Brasilia, DF, Brazil
| | - Adelino Sanchez Ramos da Silva
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil; Postgraduate Program in Rehabilitation and Functional Performance, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Rita de Cassia Marqueti
- Molecular Analysis Laboratory, Faculty of Ceilândia, Universidade de Brasília (UNB), Distrito Federal, Brazil
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Jung KJ, Cho J, Yang MJ, Hwang JH, Song J. Exposure to polyhexamethyleneguanidine phosphate in early life dampens pulmonary damage compared to adult mice. Chem Biol Interact 2024; 399:111134. [PMID: 38969276 DOI: 10.1016/j.cbi.2024.111134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Polyhexamethyleneguanidine phosphate (PHMG-P) is a biocide of guanidine family that can cause a fatal lung damage if exposed directly to the lungs. No reports exist regarding the toxicity of PHMG-P in neonatal animals. Therefore, this study aimed to determine PHMG-P toxicity in neonatal and 8-week-old mice after they were intranasally instilled with 1.5 mg/kg, 3 mg/kg, and 4.5 mg/kg PHMG-P. PHMG-P lung exposure resulted in more severe pulmonary toxicity in adult mice than in newborn mice. In the high-dose group of newborn mice, a minimal degree of inflammatory cell infiltration and fibrosis in the lung were detected, whereas more severe pathological lesions including granulomatous inflammation, fibrosis, and degeneration of the bronchiolar epithelium were observed in adult mice. At day 4, C-C motif chemokine ligand 2 (CCL2), a potent chemokine for monocytes, was upregulated but recovered to normal levels at day 15 in newborn mice. However, increased CCL2 and IL-6 levels were sustained at day 15 in adult mice. When comparing the differentially expressed genes of newborn and adult mice through RNA-seq analysis, there were expression changes in several genes associated with inflammation in neonates that were similar or different from those in adults. Although no significant lung damage occurred in newborns, growth inhibition was observed which was not reversed until the end of the experiment. Further research is needed to determine how growth inhibition from neonatal exposure to PHMG-P affects adolescent and young adult health.
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Affiliation(s)
- Kyung Jin Jung
- Immunotoxicology Research Group, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Jeonghee Cho
- Center for Vascular Research, Institute for Basci Science, Daejeon, 34126, Republic of Korea
| | - Mi-Jin Yang
- Jeonbuk Pathology Research Group, Korea Institute of Toxicology, Jeonbuk, 56212, Republic of Korea
| | - Jeong Ho Hwang
- Animal Model Research Group, Korea Institute of Toxicology, Jeongeup, 56212, Republic of Korea
| | - Jeongah Song
- Animal Model Research Group, Korea Institute of Toxicology, Jeongeup, 56212, Republic of Korea.
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59
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McCarron A, Ling KM, Montgomery ST, Martinovich KM, Cmielewski P, Rout-Pitt N, Kicic A, Parsons D, Donnelley M. Lentiviral vector gene therapy and CFTR modulators show comparable effectiveness in cystic fibrosis rat airway models. Gene Ther 2024:10.1038/s41434-024-00480-y. [PMID: 39183346 DOI: 10.1038/s41434-024-00480-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
Mutation-agnostic treatments such as airway gene therapy have the potential to treat any individual with cystic fibrosis (CF), irrespective of their CF transmembrane conductance regulator (CFTR) gene variants. The aim of this study was to employ two CF rat models, Phe508del and CFTR knockout (KO), to assess the comparative effectiveness of CFTR modulators and lentiviral (LV) vector-mediated gene therapy. Cells were isolated from the tracheas of rats and used to establish air-liquid interface (ALI) cultures. Phe508del rat ALIs were treated with the modulator combination, elexacaftor-tezacaftor-ivacaftor (ETI), and separate groups of Phe508del and KO tracheal epithelial cells were treated with LV-CFTR followed by differentiation at ALI. Ussing chamber measurements were performed to assess CFTR function. ETI-treated Phe508del ALI cultures demonstrated CFTR function that was 59% of wild-type level, while gene-addition therapy restored Phe508del to 68% and KO to 47% of wild-type level, respectively. Our findings show that rat Phe508del-CFTR protein can be successfully rescued with ETI treatment, and that CFTR gene-addition therapy provides significant CFTR correction in Phe508del and KO ALI cultures to levels that were comparable to ETI. These findings highlight the potential of an LV vector-based gene therapy for the treatment of CF lung disease.
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Affiliation(s)
- Alexandra McCarron
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia.
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, SA, Australia.
| | - Kak-Ming Ling
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Nedlands, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
| | - Samuel T Montgomery
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Nedlands, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
| | - Kelly M Martinovich
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Crawley, WA, Australia
| | - Patricia Cmielewski
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Nathan Rout-Pitt
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Nedlands, WA, Australia
- School of Population Health, Curtin University, Bentley, WA, Australia
- Department of Respiratory and Sleep, Perth Children's Hospital, Nedlands, WA, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - David Parsons
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Martin Donnelley
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, North Adelaide, SA, Australia
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60
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Srinivasan P, Canova CT, Sha S, Nguyen TNT, Joseph J, Sangerman J, Maloney AJ, Katsikis G, Ou RW, Hong MS, Ng J, Yuan A, Antov D, Song S, Chen W, Neufeld C, Wolfrum JM, Barone PW, Sinskey AJ, Springs SL, Braatz RD. Multidose transient transfection of human embryonic kidney 293 cells modulates recombinant adeno-associated virus2/5 Rep protein expression and influences the enrichment fraction of filled capsids. Biotechnol Bioeng 2024. [PMID: 39176568 DOI: 10.1002/bit.28828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/04/2024] [Accepted: 08/04/2024] [Indexed: 08/24/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is a commonly used in vivo gene therapy vector because of its nonpathogenicity, long-term transgene expression, broad tropism, and ability to transduce both dividing and nondividing cells. However, rAAV vector production via transient transfection of mammalian cells typically yields a low fraction of filled-to-total capsids (~1%-30% of total capsids produced). Analysis of our previously developed mechanistic model for rAAV2/5 production attributed these low fill fractions to a poorly coordinated timeline between capsid synthesis and viral DNA replication and the repression of later phase capsid formation by Rep proteins. Here, we extend the model by quantifying the expression dynamics of total Rep proteins and their influence on the key steps of rAAV2/5 production using a multiple dosing transfection of human embryonic kidney 293 (HEK293) cells. We report that the availability of preformed empty capsids and viral DNA copies per cell are not limiting to the capsid-filling reaction. However, optimal expression of Rep proteins (<240 ± 13 ag per cell) enables enrichment of the filled capsid population (>12% of total capsids/cell) upstream. Our analysis suggests increased enrichment of filled capsids via regulating the expression of Rep proteins is possible but at the expense of per cell capsid titer in a triple plasmid transfection. Our study reveals an intrinsic limitation of scaling rAAV2/5 vector genome (vg) production and underscores the need for approaches that allow for regulating the expression of Rep proteins to maximize vg titer per cell upstream.
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Affiliation(s)
- Prasanna Srinivasan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher T Canova
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sha Sha
- Ultragenyx Pharmaceutical Inc., Novato, Cambridge, USA
| | | | - John Joseph
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jose Sangerman
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | | | - Rui Wen Ou
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Moo Sun Hong
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Jaclyn Ng
- Stanford University School of Medicine, Stanford, California, USA
| | - Arella Yuan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel Antov
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sally Song
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wenyu Chen
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Caleb Neufeld
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard D Braatz
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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61
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Liu Z, Liu W, Wang Z, Xie Z, Qi K, Yue D, Li Y, Zhang S, Wu J, Wang P. Molecular characterization of PSEUDO RESPONSE REGULATOR family in Rosaceae and function of PbPRR59a and PbPRR59b in flowering regulation. BMC Genomics 2024; 25:794. [PMID: 39169310 PMCID: PMC11340073 DOI: 10.1186/s12864-024-10720-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND PSEUDO RESPONSE REGULATOR (PRR) genes are essential components of circadian clock, playing vital roles in multiple processes including plant growth, flowering and stress response. Nonetheless, little is known about the evolution and function of PRR family in Rosaceae species. RESULTS In this study, a total of 43 PRR genes in seven Rosaceae species were identified through comprehensive analysis. The evolutionary relationships were analyzed with phylogenetic tree, duplication events and synteny. PRR genes were classified into three groups (PRR1, PRR5/9, PRR3/7). The expansion of PRR family was mainly derived from dispersed and whole-genome duplication events. Purifying selection was the major force for PRR family evolution. Synteny analysis indicated the existence of multiple orthologous PRR gene pairs between pear and other Rosaceae species. Moreover, the conserved motifs of eight PbPRR proteins supported the phylogenetic relationship. PRR genes showed diverse expression pattern in various tissues of pear (Pyrus bretschneideri). Transcript analysis under 12-h light/ dark cycle and constant light conditions revealed that PRR genes exhibited distinct rhythmic oscillations in pear. PbPRR59a and PbPRR59b highly homologous to AtPRR5 and AtPRR9 were cloned for further functional verification. PbPRR59a and PbPRR59b proteins were localized in the nucleus. The ectopic overexpression of PbPRR59a and PbPRR59b significantly delayed flowering in Arabidopsis transgenic plants by repress the expression of AtGI, AtCO and AtFT under long-day conditions. CONCLUSIONS These results provide information for exploring the evolution of PRR genes in plants, and contribute to the subsequent functional studies of PRR genes in pear and other Rosaceae species.
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Affiliation(s)
- Zhe Liu
- School of Pharmacy, Changzhi Medical College, Changzhi, 046000, China
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weijuan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhangqing Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Yue
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Key Laboratory for Horticultural Crop Breeding, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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62
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Claeys M, Al Obaidi S, Bruyland K, Vandecandelaere I, Vandesompele J. Assessment of DNA/RNA Defend Pro: An Inactivating Sample Collection Buffer for Enhanced Stability, Extraction-Free PCR, and Rapid Antigen Testing of Nasopharyngeal Swab Samples. Int J Mol Sci 2024; 25:9097. [PMID: 39201783 PMCID: PMC11354787 DOI: 10.3390/ijms25169097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 09/03/2024] Open
Abstract
This study comprehensively evaluated the DNA/RNA Defend Pro (DRDP) sample collection buffer, designed to inactivate and stabilize patient samples. The primary objectives were to assess DRDP's efficacy in ensuring sample stability, facilitating extraction-free polymerase chain reaction (PCR), and ensuring compatibility with rapid antigen testing (RAT). Ninety-five diagnostic nasopharyngeal swab samples tested for influenza virus (influenza A), respiratory syncytial virus (RSV A), and/or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were 10-fold diluted with DRDP and anonymized. Initial characterization and retesting of these samples using cobas Liat confirmed 88 samples as positive, validating the presence of viral targets. Results from rapid antigen testing showed lower sensitivity compared to nucleic acid amplification testing (NAAT) but maintained perfect specificity, with 40 out of 88 positive samples by cobas Liat also testing positive for RAT. Direct RT-qPCR of DRDP-diluted samples demonstrated robust compatibility, with 72 out of 88 samples positive for cobas Liat also testing positive by direct RT-qPCR. Non-concordant results could be explained by the 200-fold lower input of extraction-free NAAT. Stability testing involved incubating 31 positive samples at 4 °C, 20 °C, and 37 °C for 7 days, with extraction-free NAAT. DRDP guaranteed viral RNA stability at all temperatures for influenza A, SARS-CoV-2, and RSV A, showing stability up to 7 days at 4 °C. In conclusion, DRDP is an effective stabilizing medium compatible with direct RT-qPCR and rapid antigen testing and shows great potential for optimizing diagnostic processes, particularly in resource-limited or time-sensitive scenarios.
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Affiliation(s)
- Mikhail Claeys
- InActiv Blue, Industriepark Oost 2A, 8730 Beernem, Belgium; (M.C.); (S.A.O.)
| | - Saif Al Obaidi
- InActiv Blue, Industriepark Oost 2A, 8730 Beernem, Belgium; (M.C.); (S.A.O.)
- Campus Brugge Station, Howest University of Applied Sciences, Rijselstraat 5, 8200 Brugge, Belgium
| | - Karen Bruyland
- Medisch Labo Bruyland, Beneluxpark 2, 8500 Kortrijk, Belgium (I.V.)
| | | | - Jo Vandesompele
- InActiv Blue, Industriepark Oost 2A, 8730 Beernem, Belgium; (M.C.); (S.A.O.)
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Gent, Belgium
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63
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Schaub A, David SC, Glas I, Klein LK, Violaki K, Terrettaz C, Motos G, Bluvshtein N, Luo B, Pohl M, Hugentobler W, Nenes A, Krieger UK, Peter T, Stertz S, Kohn T. Impact of organic compounds on the stability of influenza A virus in deposited 1-μL droplets. mSphere 2024:e0041424. [PMID: 39171937 DOI: 10.1128/msphere.00414-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/11/2024] [Indexed: 08/23/2024] Open
Abstract
The composition of respiratory fluids influences the stability of viruses in exhaled aerosol particles and droplets, though the role of respiratory organics in modulating virus stability remains poorly understood. This study investigates the effect of organic compounds on the stability of influenza A virus (IAV) in deposited droplets. We compare the infectivity loss of IAV at different relative humidities (RHs) over the course of 1 h in 1-µL droplets consisting of phosphate-buffered saline (without organics), synthetic lung fluid, or nasal mucus (both containing organics). We show that IAV stability increases with increasing organic:salt ratios. Among the various organic species, proteins are identified as the most protective component, with smaller proteins stabilizing IAV more efficiently at the same mass concentration. Organics act by both increasing the efflorescence RH and shortening the drying period until efflorescence at a given RH. This research advances our mechanistic understanding of how organics stabilize exhaled viruses and thus influence their inactivation in respiratory droplets. IMPORTANCE This study investigates how the composition of respiratory fluids affects the stability of viruses in exhaled droplets. Understanding virus stability in droplets is important as it impacts how viruses spread and how we can combat them. We focus on influenza A virus (IAV) and investigate how different organic compounds found in lung fluid and nasal mucus protect the virus from inactivation. We demonstrate that the ratio of organics to salt in the fluid is an indicator of IAV stability. Among organics, small proteins are particularly effective at protecting IAV. Their effect is in part explained by the proteins' influence on the crystallization of salts in the droplets, thereby shielding the viruses from prolonged exposure to harmful salt concentrations. Understanding these mechanisms helps us grasp how viruses sustain their infectivity over time in respiratory droplets, contributing to efforts in controlling infectious diseases.
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Affiliation(s)
- Aline Schaub
- Laboratory of Environmental Virology, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Shannon C David
- Laboratory of Environmental Virology, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Liviana K Klein
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
| | - Kalliopi Violaki
- Laboratory of Atmospheric Processes and Their Impacts, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Céline Terrettaz
- Laboratory of Environmental Virology, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Laboratory of Atmospheric Processes and Their Impacts, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ghislain Motos
- Laboratory of Atmospheric Processes and Their Impacts, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nir Bluvshtein
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
| | - Beiping Luo
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
| | - Marie Pohl
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Walter Hugentobler
- Laboratory of Atmospheric Processes and Their Impacts, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Athanasios Nenes
- Laboratory of Atmospheric Processes and Their Impacts, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Center for The Study of Air Quality and Climate Change, Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas, Patras, Greece
| | - Ulrich K Krieger
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
| | - Thomas Peter
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Virology, School of Architecture, Civil & Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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64
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Gao R, Zhu Q, Huang L, Fan X, Teng X, Miao Y. LEP Gene Promotes Milk Fat Synthesis via the JAK2-STAT3 and mTOR Signaling Pathways in Buffalo Mammary Epithelial Cells. Animals (Basel) 2024; 14:2446. [PMID: 39199979 PMCID: PMC11350831 DOI: 10.3390/ani14162446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024] Open
Abstract
Leptin (LEP), a protein hormone well-known for its role in metabolic regulation, has recently been linked to lipid metabolism in cattle. However, its function in buffalo mammary glands remains unclear. To address this issue, we isolated and identified the LEP gene and conducted experiments to investigate its function in buffalo mammary epithelial cells (BuMECs). In this study, two transcript variants of LEP, designated as LEP_X1 and LEP_X2, were identified. The coding sequences (CDS) of LEP_X1 and LEP_X2 are 504 bp and 579 bp in length, encoding 167 and 192 amino acid residues, respectively. Bioinformatics analysis revealed that LEP_X2 is a hydrophobic protein with an isoelectric point below 7 and contains a signal peptide, while LEP_X1 is hydrophilic and lacks a signal peptide. Our study found that LEP gene expression in lactating BuMECs was significantly higher than in non-lactating cells, with LEP_X2 expression remarkably higher than LEP_X1 in lactating BuMECs. Overexpression of both LEP_X1 and LEP_X2 significantly promoted the expression of genes related to milk fat synthesis in lactating BuMECs, including STAT3, PI3K, mTOR, SCD, and SREBF1, accompanied by an increase in cellular triglycerides (TG). Interestingly, LEP_X2 overexpression significantly suppressed LEP_X1 expression while increasing intracellular TG concentration by 12.10-fold compared to LEP_X1 overexpression, suggesting an antagonistic relationship between the two variants and supposing LEP_X2 plays a dominant role in milk fat synthesis in lactating BuMECs. Additionally, four nucleotide substitutions were identified in the buffalo LEP CDS, including a nonsynonymous substitution c.148C>T (p.Arg50Cys), which was predicted to decrease the stability of the LEP protein without affecting its function. These results collectively underscore the significant role of LEP in milk fat synthesis and can provide a basis for molecular breeding strategies of buffalo.
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Affiliation(s)
| | | | | | | | | | - Yongwang Miao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (R.G.); (Q.Z.); (L.H.); (X.F.); (X.T.)
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65
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Oberreiter V, Gelabert P, Brück F, Franz S, Zelger E, Szedlacsek S, Cheronet O, Cano FT, Exler F, Zagorc B, Karavanić I, Banda M, Gasparyan B, Straus LG, Gonzalez Morales MR, Kappelman J, Stahlschmidt M, Rattei T, Kraemer SM, Sawyer S, Pinhasi R. Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach. Sci Rep 2024; 14:19388. [PMID: 39169089 PMCID: PMC11339378 DOI: 10.1038/s41598-024-69741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
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Affiliation(s)
- Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Florian Brück
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Franz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Evelyn Zelger
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Sophie Szedlacsek
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | | | - Florian Exler
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Ivor Karavanić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Marko Banda
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, USA
- EvoAdapta Group Universidad de Cantabria, Santander, Spain
| | - Manuel R Gonzalez Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Gobierno de Cantabria, Banco Santander, Spain
| | - John Kappelman
- Department of Anthropology and Department of Earth and Planetary Sciences, The University of Texas, Austin, TX, USA
| | - Mareike Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan M Kraemer
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institut für Analytische Chemie, University of Vienna, Vienna, Austria
- Forschungsverbund Umwelt und Klima, University of Vienna, Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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Sarekoski A, Lipponen A, Hokajärvi AM, Räisänen K, Tiwari A, Paspaliari D, Lehto KM, Oikarinen S, Heikinheimo A, Pitkänen T. Simultaneous biomass concentration and subsequent quantitation of multiple infectious disease agents and antimicrobial resistance genes from community wastewater. ENVIRONMENT INTERNATIONAL 2024; 191:108973. [PMID: 39182255 DOI: 10.1016/j.envint.2024.108973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/01/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Wastewater-based surveillance (WBS) of infectious disease agents is increasingly seen as a reliable source of population health data. To date, wastewater-based surveillance efforts have largely focused on individual pathogens. However, given that wastewater contains a broad range of pathogens circulating in the population, a more comprehensive approach could enhance its usability. We focused on the simultaneous detection of SARS-CoV-2, sapovirus, Campylobacter jejuni, Campylobacter coli, Salmonella spp., pathogenic Escherichia coli, Cryptosporidium spp., Giardia spp. and antimicrobial resistance genes (ARGs) of clinical relevance. To achieve this goal, biomass concentration and nucleic acid extraction methods were optimized, and samples were analyzed by using a set of (RT)-qPCR and (HT)-qPCR methods. We determined the prevalence and the spatial and temporal trends of the targeted pathogens and collected novel information on ARGs in Finnish wastewater. In addition, the use of different wastewater concentrates, namely the ultrafiltered concentrate of the supernatant and the centrifuged pellet, and the effect of freezing and thawing wastewater prior to sample processing were investigated with the indicator microbe crAssphage. Freeze-thawing of wastewater decreased the gene copy count of crAssphage in comparison to analyzing fresh samples (p < 0.001). Campylobacters were most abundant in two of the four studied summer months (30 % detection rate) and in wastewaters from regions with intensive animal farming. Salmonella, however, was detected in 40 % of the samples without any clear seasonal trends, and the highest gene copy numbers were recorded from the largest wastewater treatment plants. Beta-lactamase resistance genes that have commonly been detected in bacteria isolated from humans in Finland, namely blaCTX-M, blaOXA48, blaNDM, and blaKPC, were also frequently detected in wastewaters (100, 98, 98, and 70 % detection rates, respectively). These results confirm the reliability of using wastewater in public health surveillance and demonstrate the possibility to simultaneously perform WBS of multiple pathogens.
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Affiliation(s)
- Anniina Sarekoski
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland.
| | - Anssi Lipponen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Kati Räisänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Mannerheimintie 166, Helsinki FI-00271, Finland.
| | - Ananda Tiwari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Dafni Paspaliari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Mannerheimintie 166, Helsinki FI-00271, Finland.
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland.
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland.
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland; Finnish Food Authority, Alvar Aallon katu 5, FI-60100 Seinäjoki, Finland.
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland.
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67
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Cai H, Zhu Y, Liu Y, Yan Z, Shen H, Fang S, Wang D, Liao S, Li J, Lv M, Lin X, Hu J, Song Y, Chen X, Yin L, Zhang J, Qi N, Sun M. Selection of a suitable reference gene for gene-expression studies in Trichomonas gallinae under various biotic and abiotic stress conditions. Gene 2024; 920:148522. [PMID: 38703865 DOI: 10.1016/j.gene.2024.148522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Trichomonas gallinae, a globally distributed protozoan parasite, significantly affects the pigeon-breeding industry. T. gallinae infection mainly causes yellow ulcerative nodules on the upper respiratory tract and crop mucosa of pigeons, impeding normal breathing and feeding and ultimately causing death. Real-time quantitative PCR (qPCR) is a crucial technique for gene-expression analysis in molecular biology. Reference-gene selection for normalization is critical for ensuring this technique's accuracy. However, no systematic screening or validation of T. gallinae reference genes has been reported. This study quantified the transcript levels of ten candidate reference genes in T. gallinae isolates with different genotypes and culture conditions using qPCR. Using the geNorm, NormFinder, and BestKeeper algorithms, we assessed these reference genes' stabilities and ranked them using RankAggreg analysis. The most stable reference gene was tubulin beta chain (TUBB), while the widely used reference genes TUBG and GAPDH demonstrated poor stability. Additionally, we evaluated these candidate reference genes' stabilities using the T. gallinae TgaAtg8 gene. On using TUBB as a reference gene, TgaAtg8's expression profiles in T. gallinae isolates with different genotypes remained relatively consistent under various culture conditions. Conversely, using ACTB as a reference gene distorted the data. These findings provide valuable reference-gene-selection guidance for functional gene research and gene-expression analysis in T. gallinae.
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Affiliation(s)
- Haiming Cai
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yibin Zhu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yu Liu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhuanqiang Yan
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, Guangdong 527400, China
| | - Hanqin Shen
- Guangdong Jingjie Inspection and Testing Co., Ltd., Xinxing, Guangdong 527400, China
| | - Siyun Fang
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, Guangdong 527400, China
| | - Dingai Wang
- Wen's Group Academy, Wen's Foodstuffs Group Co., Ltd., Xinxing, Guangdong 527400, China
| | - Shenquan Liao
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Juan Li
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Minna Lv
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xuhui Lin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Junjing Hu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yongle Song
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiangjie Chen
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Lijun Yin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianfei Zhang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Nanshan Qi
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Mingfei Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
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Länsivaara A, Lehto KM, Hyder R, Janhonen ES, Lipponen A, Heikinheimo A, Pitkänen T, Oikarinen S. Comparison of Different Reverse Transcriptase-Polymerase Chain Reaction-Based Methods for Wastewater Surveillance of SARS-CoV-2: Exploratory Study. JMIR Public Health Surveill 2024; 10:e53175. [PMID: 39158943 PMCID: PMC11369532 DOI: 10.2196/53175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/09/2024] [Accepted: 05/30/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND Many countries have applied the wastewater surveillance of the COVID-19 pandemic to their national public health monitoring measures. The most used methods for detecting SARS-CoV-2 in wastewater are quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) and reverse transcriptase-droplet digital polymerase chain reaction (RT-ddPCR). Previous comparison studies have produced conflicting results, thus more research on the subject is required. OBJECTIVE This study aims to compare RT-qPCR and RT-ddPCR for detecting SARS-CoV-2 in wastewater. It also aimed to investigate the effect of changes in the analytical pipeline, including the RNA extraction kit, RT-PCR kit, and target gene assay, on the results. Another aim was to find a detection method for low-resource settings. METHODS We compared 2 RT-qPCR kits, TaqMan RT-qPCR and QuantiTect RT-qPCR, and RT-ddPCR based on sensitivity, positivity rates, variability, and correlation of SARS-CoV-2 gene copy numbers in wastewater to the incidence of COVID-19. Furthermore, we compared 2 RNA extraction methods, column- and magnetic-bead-based. In addition, we assessed 2 target gene assays for RT-qPCR, N1 and N2, and 2 target gene assays for ddPCR N1 and E. Reverse transcription strand invasion-based amplification (RT-SIBA) was used to detect SARS-CoV-2 from wastewater qualitatively. RESULTS Our results indicated that the most sensitive method to detect SARS-CoV-2 in wastewater was RT-ddPCR. It had the highest positivity rate (26/30), and its limit of detection was the lowest (0.06 gene copies/µL). However, we obtained the best correlation between COVID-19 incidence and SARS-CoV-2 gene copy number in wastewater using TaqMan RT-qPCR (correlation coefficient [CC]=0.697, P<.001). We found a significant difference in sensitivity between the TaqMan RT-qPCR kit and the QuantiTect RT-qPCR kit, the first having a significantly lower limit of detection and a higher positivity rate than the latter. Furthermore, the N1 target gene assay was the most sensitive for both RT-qPCR kits, while no significant difference was found between the gene targets using RT-ddPCR. In addition, the use of different RNA extraction kits affected the result when the TaqMan RT-qPCR kit was used. RT-SIBA was able to detect SARS-CoV-2 RNA in wastewater. CONCLUSIONS As our study, as well as most of the previous studies, has shown RT-ddPCR to be more sensitive than RT-qPCR, its use in the wastewater surveillance of SARS-CoV-2 should be considered, especially if the amount of SARS-CoV-2 circulating in the population was low. All the analysis steps must be optimized for wastewater surveillance as our study showed that all the analysis steps including the compatibility of the RNA extraction, the RT-PCR kit, and the target gene assay influence the results. In addition, our study showed that RT-SIBA could be used to detect SARS-CoV-2 in wastewater if a qualitative result is sufficient.
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Affiliation(s)
- Annika Länsivaara
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rafiqul Hyder
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Anssi Lipponen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority - Ruokavirasto, Seinäjoki, Finland
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Zeng MZ, Zhou W, Wen SS, Wu H, Zhang Q, Fu KY, Guo WC, Shi JF. Identification and Functional Insights of Knickkopf Genes in the Larval Cuticle of Leptinotarsa decemlineata. INSECTS 2024; 15:623. [PMID: 39194827 DOI: 10.3390/insects15080623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/29/2024]
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata) is a major pest of potato crops. While Knickkopf (Knk) genes are essential for insect cuticle formation, their roles in pests like L. decemlineata remain unclear. This study aims to identify and characterize Knk genes in L. decemlineata and explore their functions in larval development and cuticle integrity. We used genomic and transcriptomic databases to identify LdKnk-family genes, validated through RT-PCR and RACE. Gene expression was analyzed at various developmental stages and tissues using qRT-PCR. RNA interference (RNAi) and Transmission electron microscopy (TEM) were applied to determine the functional roles of these genes. Four LdKnk-family genes were identified. Spatio-temporal expression analysis indicated significant gene expression during larval molting and pupal stages, especially in the epidermis. RNAi experiments showed that silencing LdKnk and LdKnk3-5' led to reduced larval weight, cuticle thinning, and increased mortality, while LdKnk3-FL knockdown caused abnormal cuticle thickening and molting disruptions. LdKnk2 knockdown increased epicuticle and endocuticle thickness without visible phenotypic changes. The study highlights the essential roles of LdKnk-family genes in maintaining cuticle structure and integrity, suggesting their potential as targets for RNAi-based pest control.
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Affiliation(s)
- Mu-Zi Zeng
- State Key Laboratory of Resource Insects, College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Wei Zhou
- State Key Laboratory of Resource Insects, College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Shan-Shan Wen
- State Key Laboratory of Resource Insects, College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Hao Wu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Qing Zhang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Kai-Yun Fu
- Institute of Plant Protection Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture/Xinjiang Key Laboratory of Agricultural Biosafety, Urumqi 830091, China
| | - Wen-Chao Guo
- Institute of Plant Protection Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture/Xinjiang Key Laboratory of Agricultural Biosafety, Urumqi 830091, China
| | - Ji-Feng Shi
- State Key Laboratory of Resource Insects, College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
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70
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Paulucio D, Ramirez-Sanchez C, Velasque R, Xavier R, Monnerat G, Dill A, Silveira J, Andrade GM, Meirelles F, Dornelas-Ribeiro M, Kirchner B, Pfaffl MW, Pompeu F, Santos CGM. Circulating miRNA Signaling for Fatty Acid Metabolism in Response to a Maximum Endurance Test in Elite Long-Distance Runners. Genes (Basel) 2024; 15:1088. [PMID: 39202447 PMCID: PMC11353293 DOI: 10.3390/genes15081088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Maximal oxygen uptake (VO2max) is a determining indicator for cardiorespiratory capacity in endurance athletes, and epigenetics is crucial in its levels and variability. This initial study examined a broad plasma miRNA profile of twenty-three trained elite endurance athletes with similar training volumes but different VO2max in response to an acute maximal graded endurance test. Six were clustered as higher/lower levels based on their VO2max (75.4 ± 0.9 and 60.1 ± 5.0 mL.kg-1.min-1). Plasma was obtained from athletes before and after the test and 15 ng of total RNA was extracted and detected using an SYBR-based 1113 miRNA RT-qPCR panel. A total of 51 miRNAs were differentially expressed among group comparisons. Relative amounts of miRNA showed a clustering behavior among groups regarding distinct performance/time points. Significantly expressed miRNAs were used to perform functional bioinformatic analysis (DIANA tools). Fatty acid metabolism pathways were strongly targeted for the significantly different miRNAs in all performance groups and time points (p < 0.001). Although this pathway does not solely determine endurance performance, their significant contribution is certainly achieved through the involvement of miRNAs. A highly genetically dependent gold standard variable for performance evaluation in a homogeneous group of elite athletes allowed genetic/epigenetic aspects related to fatty acid pathways to emerge.
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Affiliation(s)
- Dailson Paulucio
- Biometrics Laboratory (LADEBIO), Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil; (D.P.)
| | - Carlos Ramirez-Sanchez
- Biometrics Laboratory (LADEBIO), Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil; (D.P.)
| | - Rodolfo Velasque
- Biometrics Laboratory (LADEBIO), Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil; (D.P.)
| | - Raphael Xavier
- Biometrics Laboratory (LADEBIO), Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil; (D.P.)
| | - Gustavo Monnerat
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | - Adrieli Dill
- Brazilian Army Institute of Biology, Research, Teaching and Research Division, Rio de Janeiro 20911-270, Brazil
| | - Juliano Silveira
- Faculty of Animal Sciences and Food Engineering, Universidade de São Paulo, Pirassununga 13635-900, Brazil
| | - Gabriella M. Andrade
- Faculty of Animal Sciences and Food Engineering, Universidade de São Paulo, Pirassununga 13635-900, Brazil
| | - Flavio Meirelles
- Faculty of Animal Sciences and Food Engineering, Universidade de São Paulo, Pirassununga 13635-900, Brazil
| | - Marcos Dornelas-Ribeiro
- Brazilian Army Institute of Biology, Research, Teaching and Research Division, Rio de Janeiro 20911-270, Brazil
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 1, 85354 Freising, Germany
| | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 1, 85354 Freising, Germany
| | - Fernando Pompeu
- Biometrics Laboratory (LADEBIO), Federal University of Rio de Janeiro, Rio de Janeiro 21941-599, Brazil; (D.P.)
| | - Caleb G. M. Santos
- Brazilian Army Institute of Biology, Research, Teaching and Research Division, Rio de Janeiro 20911-270, Brazil
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 1, 85354 Freising, Germany
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Emam SM, Mohammadian B, Mohammadian T, Tabande MR. Autochthonous probiotic bacteria improve intestinal pathology and histomorphology, expression of immune and growth-related genes and resistance against Vibrio alginolyticus in Asian seabass (Lates calcarifer). Vet Res Commun 2024:10.1007/s11259-024-10502-0. [PMID: 39150648 DOI: 10.1007/s11259-024-10502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
The study isolated two strains of intestinal autochthonous bacteria Lactiplantibacillus plantarum1 (MH155966.1) (L1) and Lactiplantibacillus plantarum2 (MH105076.1) (L2) from the Choobdeh Abadan region. The aim of this study was to investigate the effects of different strains of probiotic bacteria on the growth performance, digestive enzyme activity, histopathologic and histomorphometric characterization of the intestine, expression of immune and growth related genes, and evaluate Lates calcarifer resistance against Vibrio alginolyticus. To achieve this, for each treatment 60 L. calcarifer juveniles (75 ± 12 g) were randomly distributed in three fiberglass tanks (300 L) and fed for 45 days. The treatments were established as Diet 1 (control diet); L1 (diet with Lb. plantarum isolated 1); L2 (diet with Lb. plantarum isolated 2) with a bacterial concentration of 1 × 109 CFU/g. Nine fish from each treatment were sampled and examined, after euthanasia. The fish were placed 2 cm from the beginning of the intestine for microscopic sampling of villi height, villi width and thickness of the epithelium, with 3 treatments: The result showed differences in the mean values of total weight were found at the end of the experiment. After 45 days of culture, the fish fed with L1 had higher (P < 0.05) growth performance than the other treatment groups. But at the end of the trial, in L2, the digestive enzyme activities were higher (P < 0.05) than the other treatment groups. The fishes fed diets supplemented with the L2 group, like the digestive enzyme activities test, presented an increase in the thickness of the epithelium of the intestine, and villus height, and villus width were greatest in L2. Fish feeding with L1 and L2 probiotics induced higher transcription levels of interleukin-10 (IL-10), granulocyte-macrophage colony-forming cells (GMCFC), epidermal growth factor (EGF), and Transforming Growth Factor Beta (TGF-β) genes in the gut, which may correlate with better immune and hematological parameters in these groups. The results of the challenge test revealed that the percentage of survival was significantly higher in L1 (76.2%) and L2 (80.95%) treatments than in the control (P < 0.05). These results indicate that host-derived probiotics (Lb. plantarum) have significant potential as important probiotics to enhance nutrient utilization, Digestive enzymes, and metabolism by increasing the gut surface area of Lates calcarifer juveniles at 45 days of culture.
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Affiliation(s)
- Seyyad Mojtaba Emam
- DVM Graduated from the Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Babak Mohammadian
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, 61357-831351, Iran.
| | - Takavar Mohammadian
- Department of Livestock, Poultry and Aquatic animal Health, Shahid Chamran University of Ahvaz, Ahvaz, 61357-831351, Iran.
- Member of Excellence Center of Warm Water Fish Health, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Mohammad Reza Tabande
- Department of Basic Science, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, 61357-831351, Iran
- Member of Excellence Center of Warm Water Fish Health, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Okpara MO, Weaver F, Whitehouse A, Veale CGL, Edkins AL. Discovery of a small-molecule inhibitor of KSHV lytic replication from the MMV pandemic response box. Antiviral Res 2024; 230:105990. [PMID: 39154751 DOI: 10.1016/j.antiviral.2024.105990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/02/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent for primary effusion lymphoma (PEL), multicentric Castleman's disease (MCD) and Kaposi's sarcoma (KS). KSHV is one of the oncoviruses that contribute to 1.5 million new infection-related cancer cases annually. Currently, there are no targeted therapies for KSHV-associated diseases. Through the development of a medium-throughput phenotype-based ELISA screening platform based on KSHV ORF57 protein detection, we screened the Medicines for Malaria Venture (MMV) Pandemic Response Box for non-cytotoxic inhibitors of KSHV lytic replication. MMV1645152 was identified as a promising inhibitor of KSHV lytic replication, suppressing KSHV immediate-early and late lytic gene expression and blocking the production of infectious KSHV virion particles at non-cytotoxic concentrations in cell line models of KSHV infection with or without EBV coinfection. MMV1645152 is a promising hit compound for the development of future therapeutic agents against KSHV-associated malignancies.
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Affiliation(s)
- Michael O Okpara
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Frederick Weaver
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Adrian Whitehouse
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK
| | - Clinton G L Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa; Centre for Chemico- and Biomedicinal Research (CCBR), Rhodes University, Grahamstown, South Africa.
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73
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Sivalingam P, Sabatino R, Sbaffi T, Corno G, Fontaneto D, Borgomaneiro G, Rogora M, Crotti E, Mapelli F, Borin S, Pilar AL, Eckert EM, Di Cesare A. Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134885. [PMID: 38876022 DOI: 10.1016/j.jhazmat.2024.134885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.
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Affiliation(s)
- Periyasamy Sivalingam
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Tomasa Sbaffi
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Gianluca Corno
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Diego Fontaneto
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Giulia Borgomaneiro
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy
| | - Michela Rogora
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy
| | - Elena Crotti
- Department of Food Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Sara Borin
- Department of Food Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Andrea Lopez Pilar
- Biological Science Faculty, Complutense University of Madrid, Jose Antonio Novais 12, 28040 Madrid, Spain
| | - Ester M Eckert
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Andrea Di Cesare
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy.
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74
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Tuo J, Shen Y, Jia S, Liu S, Zhang Q, Wang D, He X, Liu P, Zhang XX. HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment. WATER RESEARCH 2024; 260:121927. [PMID: 38941866 DOI: 10.1016/j.watres.2024.121927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/30/2024]
Abstract
Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.
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Affiliation(s)
- Jinhua Tuo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qifeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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75
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Emam M, Kumar S, Eslamloo K, Caballero-Solares A, Hall JR, Xue X, Paradis H, Gendron RL, Santander J, Rise ML. Transcriptomic response of lumpfish ( Cyclopterus lumpus) head kidney to viral mimic, with a focus on the interferon regulatory factor family. Front Immunol 2024; 15:1439465. [PMID: 39211041 PMCID: PMC11357929 DOI: 10.3389/fimmu.2024.1439465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/08/2024] [Indexed: 09/04/2024] Open
Abstract
The economic importance of lumpfish (Cyclopterus lumpus) is increasing, but several aspects of its immune responses are not well understood. To discover genes and mechanisms involved in the lumpfish antiviral response, fish were intraperitoneally injected with either the viral mimic polyinosinic:polycytidylic acid [poly(I:C)] or phosphate-buffered saline (PBS; vehicle control), and head kidneys were sampled 24 hours post-injection (hpi) for transcriptomic analyses. RNA sequencing (RNA-Seq) (adjusted p-value <0.05) identified 4,499 upregulated and 3,952 downregulated transcripts in the poly(I:C)-injected fish compared to the PBS-injected fish. Eighteen genes identified as differentially expressed by RNA-Seq were included in a qPCR study that confirmed the upregulation of genes encoding proteins with antiviral immune response functions (e.g., rsad2) and the downregulation of genes (e.g., jarid2b) with potential cellular process functions. In addition, transcript expression levels of 12 members of the interferon regulatory factor (IRF) family [seven of which were identified as poly(I:C)-responsive in this RNA-Seq study] were analyzed using qPCR. Levels of irf1a, irf1b, irf2, irf3, irf4b, irf7, irf8, irf9, and irf10 were significantly higher and levels of irf4a and irf5 were significantly lower in the poly(I:C)-injected fish compared to the PBS-injected fish. This research and associated new genomic resources enhance our understanding of the genes and molecular mechanisms underlying the lumpfish response to viral mimic stimulation and help identify possible therapeutic targets and biomarkers for viral infections in this species.
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Affiliation(s)
- Mohamed Emam
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
- Centre for Marine Applied Research, Dartmouth, NS, Canada
| | | | - Jennifer R. Hall
- Aquatic Research Cluster, Core Research Equipment and Instrument Training (CREAIT) Network, Ocean Sciences Centre, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Hélène Paradis
- Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Robert L. Gendron
- Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
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76
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Patyal P, Ameer FS, Verma A, Zhang X, Azhar G, Shrivastava J, Sharma S, Zhang R, Wei JY. The Role of Sirtuin-1 Isoforms in Regulating Mitochondrial Function. Curr Issues Mol Biol 2024; 46:8835-8851. [PMID: 39194739 DOI: 10.3390/cimb46080522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/05/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
The sirtuin-1 (SIRT1) gene contains multiple exons that usually undergo alternative splicing. The exclusion of one or more exons causes domain loss in the alternatively spliced isoforms and may change their functions. However, it is not completely established to what extent the loss of a non-catalytic domain could affect its regulatory function. Using muscle cells and SIRT1-knockout cells, we examined the function of the constitutively spliced isoform (SIRT1-v1) versus the alternatively spliced isoforms SIRT1-v2 and SIRT1-v3 that had lost part of the N-terminal region. Our data indicate that partial loss of the N-terminal domains in SIRT1-v2 and SIRT1-v3 attenuated their function. The full-length SIRT1-v1 significantly increased the oxidative phosphorylation and ATP production rate. Furthermore, SIRT1-v1 specifically upregulated the mitochondrial respiratory complex I without affecting the activity of complexes II, III, and IV. Additionally, domain loss affected the regulation of site-specific lysine acetylation in the histone H4 protein, the gene expression of respiratory complex I subunits, and the metabolic balance of oxidative phosphorylation versus glycolysis. Since alternatively spliced isoforms tend to increase with advancing age, the impact of SIRT1 isoforms on mitochondrial respiratory complexes warrants further investigation.
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Affiliation(s)
- Pankaj Patyal
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Fathima S Ameer
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ambika Verma
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Zhang
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Gohar Azhar
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jyotsna Shrivastava
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Shakshi Sharma
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Rachel Zhang
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jeanne Y Wei
- Donald W. Reynolds Department of Geriatrics and Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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77
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Guelfi G, Venanzi N, Capaccia C, Stefanetti V, Brachelente C, Sforna M, Porciello F, Lepri E. Feline hypertrophic cardiomyopathy: Does the microRNA-mRNA regulatory network contribute to heart sarcomeric protein remodelling? Int J Exp Pathol 2024. [PMID: 39138588 DOI: 10.1111/iep.12514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Feline primary hypertrophic cardiomyopathy (HCM) is an intrinsic myocardial disease characterized by concentric hypertrophy of the left ventricle. In the present study, we investigated the microRNA-mRNA regulatory network in feline myocardial tissue affected by primary (HCMI) and secondary HCM (HCMII). MRNA expression levels of sarcomeric genes, including, TNNT2, TNNI3, MYH7, MYBPC3, TPM1 and ACTC1 were assessed in the FFPE myocardial tissues. FFPE tissues from healthy cats were sequenced by the NGS, to explore, in the entire non-deposited miRNome, the expression level of microRNAs targeting the complementary sequences of selected sarcomeric mRNAs. The sarcomeric genes TNNT2, MYH7, MYBPC3 and TPM1 showed a statistically significant upregulation in HCMI compared to HCMII (p < .01), except ACTC1 which was downregulated (p < .01); TNNI3 showed no statistically significant difference. In HCMII miR-122-5p, miR-338-3p, miR-484, miR-370-3p, miR-92b-3p, miR-375 and miR-370-3p showed a significant upregulation (p < .01) compared to control. The exception was miR-30a-5p which showed downregulation. Worthy of note is the 4-fold higher expression of miR-370-3p, a key regulator of MYBPC3, in HMCI compared to HMCII. This research does not solve the aetiological mystery of HCM, but it may help to find a way to help diagnose and define the prognosis of HCM in cats.
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Affiliation(s)
- Gabriella Guelfi
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Noemi Venanzi
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Camilla Capaccia
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Valentina Stefanetti
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Chiara Brachelente
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Monica Sforna
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Francesco Porciello
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
| | - Elvio Lepri
- Department of Veterinary Medicine, Università Degli Studi di Perugia, Perugia, Italy
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78
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Singh V, Kumar P, Pandey A, Hallan V, Pati PK. Functional characterization of WsPR-1 reveals its interplay with cytokinin and gibberellin signaling pathways. Int J Biol Macromol 2024; 278:134691. [PMID: 39142483 DOI: 10.1016/j.ijbiomac.2024.134691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 05/30/2024] [Accepted: 08/10/2024] [Indexed: 08/16/2024]
Abstract
Pathogenesis-related protein 1 (PR-1) is an antimicrobial protein involved in systemic acquired resistance (SAR) in plants, but its regulatory role and interactions with other pathways remain unclear. In this study, we functionally characterize WsPR-1 gene of Withania somnifera in Nicotiana tabacum to elucidate its role in plant defense, growth, and development. Interestingly, transgenic tobacco plants with increased levels of cytokinin (CK) and decreased gibberellins (GAs) exhibited stunted shoot growth, an underdeveloped root system, modified leaf morphology, reduced seed pod production, and delayed leaf senescence. Transcriptional analysis revealed that WsPR-1 overexpression downregulated the GA 20-oxidase (GA20ox) gene involved in GA biosynthesis while upregulating GA 2-oxidase (GA2ox), a GA catabolic enzyme. Moreover, transcript levels of FRUITFULL (FUL) and LEAFY (NFL2) flowering genes exhibited a decrease in WsPR-1 plants, which could explain the delayed flowering and reduced seed pod development in transgenic plants. Confocal microscopy confirmed increased lignin deposition in stem cross-sections of WsPR-1 transgenic plants, supported by gene expression analysis and lignin content quantification. Additionally, our findings also suggest the involvement of Knotted1-like homeobox (KNOX) gene in enhancing cytokinin levels. This study highlights PR-1's regulatory role in plant growth and development, with potential to boost crop yields and enhance resilience.
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Affiliation(s)
- Varinder Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Paramdeep Kumar
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Vipin Hallan
- Plant Protection Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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79
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Banerjee S, Nagasawa C, Widen S, Garcia-Blanco M. Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing. Nucleic Acids Res 2024; 52:8534-8551. [PMID: 38801080 PMCID: PMC11317157 DOI: 10.1093/nar/gkae431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/01/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024] Open
Abstract
DExD-box RNA proteins DDX39A and DDX39B are highly homologous paralogs that are conserved in vertebrates. They are required for energy-driven reactions involved in RNA processing. Although we have some understanding of how their functions overlap in RNA nuclear export, our knowledge of whether or not these proteins have specific or redundant functions in RNA splicing is limited. Our previous work has shown that DDX39B is responsible for regulating the splicing of important immune transcripts IL7R and FOXP3. In this study, we aimed to investigate whether DDX39A, a highly homologous paralog of DDX39B, plays a similar role in regulating alternative RNA splicing. We find that DDX39A and DDX39B have significant redundancy in their gene targets, but there are targets that uniquely require one or the other paralog. For instance, DDX39A is incapable of complementing defective splicing of IL7R exon 6 when DDX39B is depleted. This exon and other cassette exons that specifically depend on DDX39B have U-poor/C-rich polypyrimidine tracts in the upstream intron and this variant polypyrimidine tract is required for DDX39B dependency. This study provides evidence that despite a high degree of functional redundancy, DDX39A and DDX39B are selectively required for the splicing of specific pre-mRNAs.
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Affiliation(s)
- Shefali Banerjee
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Chloe K Nagasawa
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Human Pathophysiology and Translational Medicine Program, Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555-5302, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Mariano A Garcia-Blanco
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
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80
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Chen W, Zhang K, Huang F, Zhao L, Waldren GC, Jiang Q, Chen SX, Wang B, Guo W, Zhang DY, Zhang JX. Advancing quantitative PCR with color cycle multiplex amplification. Nucleic Acids Res 2024:gkae683. [PMID: 39119904 DOI: 10.1093/nar/gkae683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.
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Affiliation(s)
- Wei Chen
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Kerou Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, Shanghai 200032, China
| | - Lan Zhao
- Department of Respiratory Diseases, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, Shanghai 200433, China
| | | | - Qi Jiang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Sherry X Chen
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Bonnie Wang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, Shanghai 200032, China
| | - David Y Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Jinny X Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
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81
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Kamiński K, Blatkiewicz M, Szyszka M, Olechnowicz A, Komarowska H, Klimont A, Wierzbicki T, Karczewski M, Ruchała M, Rucinski M. Expression Patterns of MOTS-c in Adrenal Tumors: Results from a Preliminary Study. Int J Mol Sci 2024; 25:8721. [PMID: 39201408 PMCID: PMC11354279 DOI: 10.3390/ijms25168721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
Adrenal tumors, such as adrenocortical carcinoma (ACC), adrenocortical adenoma (ACA), and pheochromocytoma (PCC) are complex diseases with unclear causes and treatments. Mitochondria and mitochondrial-derived peptides (MDPs) are crucial for cancer cell survival. The primary aim of this study was to analyze samples from different adrenal diseases, adrenocortical carcinoma, adrenocortical adenoma, and pheochromocytoma, and compare them with normal adrenal tissue to determine whether the expression levels of the mitochondrial open reading frame of the 12S rRNA type-c (MOTS-c) gene and protein vary between different types of adrenal tumors compared to healthy controls using qPCR, ELISA, and IHC methods. Results showed decreased MOTS-c mRNA expression in all adrenal tumors compared to controls, while serum MOTS-c protein levels increased in ACA and PCC but not in ACC. The local distribution of MOTS-c protein in adrenal tissue was reduced in all tumors. Notably, MOTS-c protein expression declined with ACC progression (stages III and IV) but was unrelated to patient age or sex. Tumor size and testosterone levels positively correlated with MOTS-c mRNA but negatively with serum MOTS-c protein. Additionally, serum MOTS-c protein correlated positively with glucose, total cholesterol, HDL, LDL, and SHGB levels. These findings suggest disrupted expression of MOTS-c in the spectrum of adrenal diseases, which might be caused by mechanisms involving increased mitochondrial dysfunction and structural changes in the tissue associated with disease progression. This study provides a detailed examination of MOTS-c mRNA and protein in adrenal tumors, indicating the potential role of MDPs in tumor biology and progression.
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Affiliation(s)
- Kacper Kamiński
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (K.K.); (M.B.); (M.S.); (A.O.)
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Małgorzata Blatkiewicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (K.K.); (M.B.); (M.S.); (A.O.)
| | - Marta Szyszka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (K.K.); (M.B.); (M.S.); (A.O.)
| | - Anna Olechnowicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (K.K.); (M.B.); (M.S.); (A.O.)
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Hanna Komarowska
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-356 Poznan, Poland; (H.K.); (A.K.); (M.R.)
| | - Anna Klimont
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-356 Poznan, Poland; (H.K.); (A.K.); (M.R.)
| | - Tomasz Wierzbicki
- Department of General, Endocrinological and Gastroenterological Surgery, Poznan University of Medical Sciences, 60-355 Poznan, Poland;
| | - Marek Karczewski
- Department of General and Transplantation Surgery, Poznan University of Medical Sciences, 60-356 Poznan, Poland;
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, 60-356 Poznan, Poland; (H.K.); (A.K.); (M.R.)
| | - Marcin Rucinski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (K.K.); (M.B.); (M.S.); (A.O.)
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82
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Reid RM, Turkmen S, Cleveland BM, Biga PR. Direct actions of growth hormone in rainbow trout, Oncorhynchus mykiss, skeletal muscle cells in vitro. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111725. [PMID: 39122107 DOI: 10.1016/j.cbpa.2024.111725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
The growth hormone (GH)-insulin-like growth factor-1 (IGF-1) system regulates skeletal muscle growth and function. GH has a major function of targeting the liver to regulate IGF-1 production and release, and IGF-1 mediates the primary anabolic action of GH on growth. However, skeletal muscle is a target tissue of GH as evidenced by dynamic GH receptor expression, but it is unclear if GH elicits any direct actions on extrahepatic tissues as it is difficult to distinguish the effects of IGF-1 from GH. Fish growth regulation is complex compared to mammals, as genome duplication events have resulted in multiple isoforms of GHs, GHRs, IGFs, and IGFRs expressed in most fish tissues. This study investigated the potential for GH direct actions on fish skeletal muscle using an in vitro system, where rainbow trout myogenic precursor cells (MPCs) were cultured in normal and serum-deprived media, to mimic in vivo fasting conditions. Fasting reduces IGF-1 signaling in the muscle, which is critical for disentangling the roles of GH from IGF-1. The direct effects of GH were analyzed by measuring changes in myogenic proliferation and differentiation genes, as well as genes regulating muscle growth and proteolysis. This study provides the first in-depth analysis of the direct actions of GH on serum-deprived fish muscle cells in vitro. Data suggest that GH induces the expression of markers for proliferation and muscle growth in the presence of serum, but all observed GH action was blocked in serum-deprived conditions. Additionally, serum deprivation alone reduced the expression of several proliferation and differentiation markers, while increasing growth and proteolysis markers. Results also demonstrate dynamic gene expression response in the presence of GH and a JAK inhibitor in serum-provided but not serum-deprived conditions. These data provide a better understanding of GH signaling in relation to serum in trout muscle cells in vitro.
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Affiliation(s)
- Ross M Reid
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Serhat Turkmen
- Department of Cell Development and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Beth M Cleveland
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service (ARS-USDA), Kearneysville, WV 25430, USA
| | - Peggy R Biga
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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83
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Li L, Bae S. Quantitative detection and survival analysis of VBNC Salmonella Typhimurium in flour using droplet digital PCR and DNA-intercalating dyes. Microbiol Spectr 2024; 12:e0024924. [PMID: 38975767 PMCID: PMC11302299 DOI: 10.1128/spectrum.00249-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/13/2024] [Indexed: 07/09/2024] Open
Abstract
The difficulty in detecting viable but non-culturable (VBNC) Salmonella by culture-dependent methods poses a risk to food safety. In our study, we applied a viability test to Salmonella following a lethal treatment and to flour samples inoculated with Salmonella to evaluate the effectiveness of viability polymerase chain reaction (PCR). Our findings revealed that the combination of both ddPCR and qPCR with those DNA-intercalating dyes could quantify viable cells at low concentrations when the plate counting method failed to detect them post-inactivation. Prolonged UV exposure did not induce cell membrane disruption, as confirmed with PMA-ddPCR, with insignificant differences in gene copies. However, samples exposed to DyeTox13 and DyeTox13 + EMA showed lower gene copy numbers, implying that enzymatic activity was decreased by UV exposure duration. In addition, temperature-dependent survival in flour revealed uniform decay rates and D values (time required for a 1 log reduction) of DNA in untreated samples across various temperatures. By contrast, different decay rates were observed with DNA-intercalating dyes (DyeTox13 and DyeTox13 + EMA), showing faster metabolic activity loss at higher temperatures in flour. The decay rates and D values, determined through plate counting and those DNA-intercalating dyes, indicated the potential presence of VBNC Salmonella. A strong correlation between DyeTox13 dyes and the plate counting method suggested DyeTox13 as a rapid alternative for detecting Salmonella in flour. The ddPCR with DNA-intercalating dyes could effectively evaluate Salmonella viability, facilitating more precise monitoring of VBNC in food. IMPORTANCE Salmonella, a major foodborne pathogen, poses significant risks, particularly to vulnerable groups like infants, older people, and the immunocompromised. Accurate detection is vital for public health and food safety, given its potential to cause severe and life-threatening symptoms. Our study demonstrated digital polymerase chain reaction (ddPCR) with DNA-intercalating dyes for identifying the different physiological statuses of Salmonella. Also, the application of ddPCR with DNA-intercalating dyes offers quantification of viable cells post-disinfection as an alternative method in food. Utilizing ddPCR and DNA-intercalating dyes, we enhanced the detection of VBNC Salmonella, a form often undetectable by conventional methods. This innovative approach could significantly improve the precision and efficiency of detection for viable Salmonella. By providing deeper insights into its transmission potential, our method is a critical tool in preventing outbreaks and ensuring the safety of food products. This research contributes substantially to global efforts in controlling foodborne illnesses and safeguarding public health.
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Affiliation(s)
- Liyan Li
- Department of Civil and Environmental Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
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84
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Guo Y, Wei Z, Zhang Y, Cao J. The Effects of trans-10, cis-12 Conjugated Linoleic Acid on the Production Performance of Dairy Cows and the Expression and Transcription Regulation of Lipid Metabolism-Related Genes in Bovine Mammary Epithelial Cells. ACS OMEGA 2024; 9:34161-34174. [PMID: 39130591 PMCID: PMC11308042 DOI: 10.1021/acsomega.4c05532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/13/2024]
Abstract
Dietary fatty acids (FAs) determine the quality of dairy products. The trans-10, cis-12 conjugated linoleic acid (t10c12-CLA) is commonly considered an FA factor leading to milk fat depression syndrome (MFDs) in dairy cow. However, its effect on dairy cow performance and involvement in milk fat metabolism have been insufficiently explored. This study administered 136.17 g/day of rumen-protected CLA (RP-CLA) to dairy cows and found a diminution in milk fat percentage and a trend of increasing milk protein percentage on day 21 postpartum. Lactose content, milk yield, and net energy for lactation were unaffected. In the cell experiments, Oil Red O staining showed a notable increase in lipid droplets. Gene and protein expression analysis showed that 300 μM t10c12-CLA upregulated the expression of CD36, DGAT2, and ADRP, while downregulating the expression of ACACA, FASN, SREBP1, FABP3, FATP3, ACSL4, LPIN1, DGAT1, BTN1A1, XDH, SNAP23, and VAMP4. This provides a possible mechanistic pathway for the contradictory phenomenon of t10c12-CLA reducing milk fat while increasing lipid droplets. Overall, t10c12-CLA, as a long-chain fatty acid, can promote lipid droplet synthesis but may reduce milk fat by inhibiting lipid droplet fusion and secretion, FAs de novo synthesis, and triglyceride biosynthesis.
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Affiliation(s)
- Yuanyin Guo
- College
of Veterinary Medicine, China Agricultural
University, Beijing 100193, China
| | - Ziang Wei
- College
of Veterinary Medicine, China Agricultural
University, Beijing 100193, China
| | - Yi Zhang
- College
of Animal Science and Technology, China
Agricultural University, Beijing 100193, China
| | - Jie Cao
- College
of Veterinary Medicine, China Agricultural
University, Beijing 100193, China
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85
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Moro A, Softić A, Travar M, Goletić Š, Omeragić J, Koro-Spahić A, Kapo N, Mrdjen V, Terzić I, Ostojic M, Cerkez G, Goletic T. Trends in SARS-CoV-2 Cycle Threshold Values in Bosnia and Herzegovina-A Retrospective Study. Microorganisms 2024; 12:1585. [PMID: 39203427 PMCID: PMC11356242 DOI: 10.3390/microorganisms12081585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to the COVID-19 pandemic, has significantly impacted global public health. The proper diagnosis of SARS-CoV-2 infection is essential for the effective control and management of the disease. This study investigated the SARS-CoV-2 infection using RT-qPCR tests from laboratories in Bosnia and Herzegovina. We performed a retrospective study of demographic data and Ct values from 170,828 RT-qPCR tests from April 2020 to April 2023, representing 9.3% of total national testing. Samples were collected from 83,413 individuals across different age groups. Of all tests, 33.4% were positive for SARS-CoV-2, with Ct values and positivity rates varying across demographics and epidemic waves. The distribution was skewed towards older age groups, although lower positivity rates were observed in younger age groups. Ct values, indicative of viral load, ranged from 12.5 to 38. Lower Ct values correlated with higher positive case numbers, while higher Ct values signaled outbreak resolution. Additionally, Ct values decreased during epidemic waves but increased with the dominance of certain variants. Ct value-distribution has changed over time, particularly after the introduction of SARS-CoV-2 variants of interest/concern. Established Ct value trends might, therefore, be used as an early indicator and additional tool for informed decisions by public health authorities in SARS-CoV-2 and future prospective pandemics. Moreover, they should not be overlooked in future epidemiological events.
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Affiliation(s)
- Almedina Moro
- Clinical Center of University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Adis Softić
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
| | - Maja Travar
- Department of Microbiology and Immunology, University Clinical Centre of the Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina; (M.T.); (V.M.)
- Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Bosnia and Herzegovina
| | - Šejla Goletić
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
| | - Jasmin Omeragić
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
| | - Amira Koro-Spahić
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
| | - Naida Kapo
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
| | - Visnja Mrdjen
- Department of Microbiology and Immunology, University Clinical Centre of the Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina; (M.T.); (V.M.)
- Faculty of Medicine, University of Banja Luka, 78000 Banja Luka, Bosnia and Herzegovina
| | - Ilma Terzić
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
| | - Maja Ostojic
- Institute for Public Health FB&H, 88000 Mostar, Bosnia and Herzegovina;
| | - Goran Cerkez
- Ministry of Health of the Federation of Bosnia and Herzegovina, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Teufik Goletic
- Veterinary Faculty, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; (A.S.); (Š.G.); (J.O.); (A.K.-S.); (N.K.); (I.T.)
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86
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Vasilyeva AA, Evseev PV, Ignatov AN, Dzhalilov FSU. Pectobacterium punjabense Causing Blackleg and Soft Rot of Potato: The First Report in the Russian Federation. PLANTS (BASEL, SWITZERLAND) 2024; 13:2144. [PMID: 39124263 PMCID: PMC11313954 DOI: 10.3390/plants13152144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024]
Abstract
Phytopathogenic bacteria of the genus Pectobacterium are responsible for several diseases that affect potato (Solanum tuberosum L.) production worldwide, including blackleg and tuber soft rot. These bacteria are highly diverse, with over 17 different species currently identified. However, some of the recently described species, such as Pectobacterium punjabense, are still poorly understood. In this study, we focused on P. punjabense isolates collected from diseased potato tubers in Russia in 2021. Whole-genome sequencing was used to characterise the genomic diversity of the pathogen and determine the biochemical profiles of the isolated bacteria. The ability of these isolates to cause soft rot symptoms was tested. A comparative assessment of the potential pathogenicity of the Pectobacterium isolates was conducted by infecting potato tubers and measuring the accumulation of biomass in a liquid medium during cultivation at different temperatures. A TaqMan qPCR assay was developed for the highly sensitive and specific characterisation of P. punjabense strains, which can be used in diagnostic systems. This is the first report on P. punjabense causing potato disease in the Russian Federation.
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Affiliation(s)
- Anna A. Vasilyeva
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
| | - Peter V. Evseev
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexandr N. Ignatov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
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87
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Ullrich N, Ramadani A, Paddenberg-Schubert E, Proff P, Jantsch J, Kirschneck C, Schröder A. Validation of reliable reference genes for qPCR of CD4+ T cells exposed to compressive strain. J Orofac Orthop 2024:10.1007/s00056-024-00543-0. [PMID: 39093346 DOI: 10.1007/s00056-024-00543-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/26/2024] [Indexed: 08/04/2024]
Abstract
For accurate interpretation of quantitative real-time PCR (qPCR) data, stable reference genes are essential for normalization of target genes. To date, there is no information on reliable housekeeping genes in CD4+ T cells in a three-dimensional (3D) matrix under pressure stimulation. This in vitro study describes for the first time a method for pressure stimulation of CD4+ T cells in a 3D matrix in the context of orthodontic tooth movement (OTM) and identifies a set of reliable reference genes. CD4+ T cells were isolated from murine spleen and activated with anti-CD3/-CD28 Dynabeads (Thermo Fisher, Langenselbold, Germany) on standard cell culture plates or in 3D scaffolds with or without compressive strain. Expression stability of nine potential reference genes was examined using four mathematical algorithms. Gene expression of Il2 was normalized to all potential reference genes to highlight the importance of correct normalization. Cell proliferation and the expression of the surface markers CD25 and CD69 were also determined. The 3D matrix did not inhibit proliferation after immunological activation of T cells and embedded the cells sufficiently to expose them to pressure load. Expression of ubiquitin C (Ubc) and hypoxanthine phosphoribosyltransferase (Hprt) was the most stable under all conditions tested. A combination of these two genes was suitable for normalization of qPCR data. Normalization of Il2 gene expression showed highly variable results depending on the reference gene used. Pressure reduced cell proliferation and the number of CD69-positive T cells. This study provides a basis for performing valid and reliable qPCR experiments with CD4+ T cells cultured in 3D scaffolds and exposed to compressive forces simulating OTM.
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Affiliation(s)
- Niklas Ullrich
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany.
| | - Ardita Ramadani
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany
| | | | - Peter Proff
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany
| | - Jonathan Jantsch
- Institute for Microbiology and Hygiene, University Medical Centre Regensburg, Regensburg, Germany
- Institute for Microbiology, Immunology and Hygiene, University Medical Center Cologne, Cologne, Germany
| | | | - Agnes Schröder
- Department of Orthodontics, University Medical Center Regensburg, Regensburg, Germany
- Institute for Microbiology and Hygiene, University Medical Centre Regensburg, Regensburg, Germany
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88
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Romero A, Sanchez A, Jones JD, Ledesma K, El-Halawany MS, Hamouda AK, Bill BR. Optimization of Zebrafish Larvae 6-OHDA Exposure for Neurotoxin Induced Dopaminergic Marker Reduction. Zebrafish 2024; 21:287-293. [PMID: 38608227 DOI: 10.1089/zeb.2023.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that is clinically assessed by motor symptoms associated with the loss of midbrain dopaminergic neurons affecting the quality of life for over 8.5 million people worldwide. The neurotoxin 6-hydroxydopamine (6-OHDA) has been used to chemically induce a PD-like state in zebrafish larvae by several laboratories; however, highly variable concentration, methodology, and reagents have resulted in conflicting results suggesting a need to investigate these issues of reproducibility. We propose a protocol that addresses the differences in methodology and induces changes in 6 days postfertilization (dpf) larvae utilizing a 24-h exposure at 3 dpf with 30 μM 6-OHDA. Despite ∼50% lethality, no morphological or development differences in surviving fish are observed. Definition of our model is defined by downregulation of the expression of th1 by reverse transcriptase-quantitative polymerase chain reaction, a marker for dopaminergic neurons and a reduction in movement. Additionally, we observed a downregulation of pink1 and an upregulation of sod1 and sod2, indicators of mitochondrial dysfunction and response to reactive oxygen species, respectively.
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Affiliation(s)
- Adrian Romero
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Armando Sanchez
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Jocelyn D Jones
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Kristel Ledesma
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Medhat S El-Halawany
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Ayman K Hamouda
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Brent R Bill
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
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89
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Lai YYL, Downs J, Leishman S, Leonard HM, Walsh LJ, Zafar S. qPCR assay optimisation for a clinical study comparing oral health risk in Rett syndrome. Eur Arch Paediatr Dent 2024; 25:547-560. [PMID: 38926242 PMCID: PMC11341660 DOI: 10.1007/s40368-024-00912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024]
Abstract
PURPOSE This study aimed to validate qPCR assays for specific microbiota, for use on dental plaque samples stored on Whatman FTA cards to compare relative oral health risk in Rett syndrome. METHODS Supragingival dental plaque samples were collected, using a sterile swab, (COPAN FLOQswab™) swabbed onto Whatman FTA™ cards. DNA extraction was performed using a modified Powersoil™ protocol. Where published assays were unsuitable, species-specific qPCR assays for caries-associated, gingivitis-associated and oral-health-associated bacteria were designed using multiple sequence alignment, Primer3Plus and PrimerQuest. Assays were run using absolute quantification. Limit of detection (LOD) and limit of quantification (LOQ) were calculated, and PCR products verified by Sanger sequencing. RESULTS Most assays allowed detection using real-time qPCR with high specificity on samples collected on FTA cards. Several assays showed low or even single gene copy numbers on the test samples. CONCLUSION Assays were optimised for detection and evaluation of oral health risk in dental plaque samples stored on FTA cards when cold storage is not feasible, except for F. nucleatum. Several assays showed gene copy numbers less than the LOQ or outside the range of the standard curve, so there is merit in optimising these assays using digital droplet PCR.
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Affiliation(s)
- Y Y L Lai
- UQ Oral Health Centre, The University of Queensland School of Dentistry, 288 Herston Rd, Herston, QLD, 4006, Australia.
- Child Disability, Telethon Kids Institute, PO Box 855, West Perth, WA, 6872, Australia.
| | - J Downs
- Child Disability, Telethon Kids Institute, PO Box 855, West Perth, WA, 6872, Australia
- Curtin School of Allied Health, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - S Leishman
- UQ Oral Health Centre, The University of Queensland School of Dentistry, 288 Herston Rd, Herston, QLD, 4006, Australia
| | - H M Leonard
- Child Disability, Telethon Kids Institute, PO Box 855, West Perth, WA, 6872, Australia
| | - L J Walsh
- UQ Oral Health Centre, The University of Queensland School of Dentistry, 288 Herston Rd, Herston, QLD, 4006, Australia
| | - S Zafar
- UQ Oral Health Centre, The University of Queensland School of Dentistry, 288 Herston Rd, Herston, QLD, 4006, Australia
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90
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Waldron R, Rodriguez MDLAB, Williams JM, Ning Z, Ahmed A, Lindsay A, Moore T. JRK binds satellite III DNA and is necessary for the heat shock response. Cell Biol Int 2024; 48:1212-1222. [PMID: 38946594 DOI: 10.1002/cbin.12216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/19/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
JRK is a DNA-binding protein of the pogo superfamily of transposons, which includes the well-known centromere binding protein B (CENP-B). Jrk null mice exhibit epilepsy, and growth and reproductive disorders, consistent with its relatively high expression in the brain and reproductive tissues. Human JRK DNA variants and gene expression levels are implicated in cancers and neuropsychiatric disorders. JRK protein modulates β-catenin-TCF activity but little is known of its cellular functions. Based on its homology to CENP-B, we determined whether JRK binds centromeric or other satellite DNAs. We show that human JRK binds satellite III DNA, which is abundant at the chromosome 9q12 juxtacentromeric region and on Yq12, both sites of nuclear stress body assembly. Human JRK-GFP overexpressed in HeLa cells strongly localises to 9q12. Using an anti-JRK antiserum we show that endogenous JRK co-localises with a subset of centromeres in non-stressed cells, and with heat shock factor 1 following heat shock. Knockdown of JRK in HeLa cells proportionately reduces heat shock protein gene expression in heat-shocked cells. A role for JRK in regulating the heat shock response is consistent with the mouse Jrk null phenotype and suggests that human JRK may act as a modifier of diseases with a cellular stress component.
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Affiliation(s)
- Rosalie Waldron
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | | | - John M Williams
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Zhenfei Ning
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Abrar Ahmed
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew Lindsay
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Tom Moore
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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91
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Shanks OC, Diedrich A, Sivaganesan M, Willis JR, Sharifi A. Quantitative fecal source characterization of urban municipal storm sewer system outfall 'wet' and 'dry' weather discharges. WATER RESEARCH 2024; 259:121857. [PMID: 38851116 DOI: 10.1016/j.watres.2024.121857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
Urban areas are built environments containing substantial amounts of impervious surfaces (e.g., streets, sidewalks, roof tops). These areas often include elaborately engineered drainage networks designed to collect, transport, and discharge untreated stormwater into local surface waters. When left uncontrolled, these discharges may contain unsafe levels of fecal waste from sources such as sanitary sewage and wildlife even under dry weather conditions. This study evaluates paired measurements of host-associated genetic markers (log10 copies per reaction) indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), canine (DG3), and avian (GFD) fecal sources, 12-hour cumulative precipitation (mm), four catchment land use metrics determined by global information system (GIS) mapping, and Escherichia coli (MPN/100 ml) from seven municipal separate storm sewer system outfall locations situated at the southern portion of the Anacostia River Watershed (District of Columbia, U.S.A.). A total of 231 discharge samples were collected twice per month (n = 24 sampling days) and after rain events (n = 9) over a 13-month period. Approximately 50 % of samples (n = 116) were impaired, exceeding the local E. coli single sample maximum of 2.613 log10 MPN/100 ml. Genetic quality controls indicated the absence of amplification inhibition in 97.8 % of samples, however 14.7 % (n = 34) samples showed bias in DNA recovery. Of eligible samples, quantifiable levels were observed for avian (84.1 %), human (57.4 % for HF183/BacR287 and 40 % for HumM2), canine (46.7 %), and ruminant (15.9 %) host-associated genetic markers. Potential links between paired measurements are explored with a recently developed Bayesian qPCR censored data analysis approach. Findings indicate that human, pet, and urban wildlife all contribute to storm outfall discharge water quality in the District of Columbia, but pollutant source contributions vary based on 'wet' and 'dry' conditions and catchment land use, demonstrating that genetic-based fecal source identification methods combined with GIS land use mapping can complement routine E. coli monitoring to improve stormwater management in urban areas.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
| | - Adam Diedrich
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Amirreza Sharifi
- Department of Energy and Environment, 1200 First St NE, Washington, D.C., USA
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92
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Soto-Dávila M, Rodríguez-Cornejo T, Benito VW, Rodríguez-Ramos T, Mahoney G, Supinski R, Heath G, Dang X, Valle FM, Hurtado C, Llanco LA, Serrano-Martinez E, Dixon B. Innate and adaptive immune response of Rainbow trout (Oncorhynchus mykiss) naturally infected with Yersinia ruckeri. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109742. [PMID: 38960109 DOI: 10.1016/j.fsi.2024.109742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024]
Abstract
Rainbow trout is an important fish species for Peruvian artisanal aquaculture, comprising over 60 % of the total aquaculture production. However, their industry has been highly affected by several bacterial agents such as Yersinia ruckeri. This pathogen is the causative agent of Enteric Redmouth Disease, and causes high mortality in fingerlings and chronic infection in adult rainbow trout. To date, the immune response of rainbow trout against Y. ruckeri has been well studied in laboratory-controlled infection studies (i.e. intraperitoneal infection, bath immersion), however, the immune response during natural infection has not been explored. To address this, in this study, 35 clinically healthy O. mykiss without evidence of lesions or changes in behavior and 32 rainbow trout naturally infected by Y. ruckeri, were collected from semi-intensive fish farms located in the Central Highlands of Peru. To evaluate the effect on the immune response, RT-qPCR, western blotting, and ELISA were conducted using head kidney, spleen, and skin tissues to evaluate the relative gene expression and protein levels. Our results show a significant increase in the expression of the pro-inflammatory cytokines il1b, tnfa, and il6, as well as ifng in all three tissues, as well as increases in IL-1β and IFN-γ protein levels. The endogenous pathway of antigen presentation showed to play a key role in defense against Y. ruckeri, due to the upregulation of mhc-I, tapasin, and b2m transcripts, and the significant increase of Tapasin protein levels in infected rainbow trout. None of the genes associated with the exogenous pathway of antigen presentation showed a significant increase in infected fish, suggesting that this pathway is not involved in the response against this intracellular pathogen. Finally, the transcripts of immunoglobulins IgM and IgT did not show a modulation, nor were the protein levels evaluated in this study.
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Affiliation(s)
- Manuel Soto-Dávila
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada; Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada
| | - Tania Rodríguez-Cornejo
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada; Faculty of Veterinary Medicine and Zootechnics, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Gracen Mahoney
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Rochelle Supinski
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - George Heath
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Xiaoqing Dang
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Fernando Mesías Valle
- CITEacuícola Pesquero Ahuashiyacu, Instituto Tecnológico de la Producción, La Banda de Shilcayo CP, 22200, San Martín, Peru
| | - Carmen Hurtado
- Faculty of Veterinary Medicine and Zootechnics, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis A Llanco
- School of Human Medicine, Universidad Privada San Juan Bautista, Apartado, Chincha, 15067, Peru
| | - Enrique Serrano-Martinez
- Faculty of Veterinary Medicine and Zootechnics, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Brian Dixon
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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93
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Palmier M, Maître M, Doat H, Lesté-Lasserre T, Maurel DB, Boiziau C. Osteocyte gene expression analysis in mouse bone: optimization of a laser-assisted microdissection protocol. JBMR Plus 2024; 8:ziae078. [PMID: 39045129 PMCID: PMC11264292 DOI: 10.1093/jbmrpl/ziae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/29/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024] Open
Abstract
Among bone cells, osteocytes are the most abundant, but also the most challenging to study because they are located inside a dense mineralized matrix. Due to their involvement in bone homeostasis, diverse tools are needed to understand their roles in bone physiology and pathology. This work was aimed at establishing a laser-assisted microdissection protocol to isolate osteocytes and analyze their gene expressions. The goal was to overcome the limitations of the technique currently most used: RNA extraction from the whole bone. To perform laser microdissection and subsequent gene expression analysis, the five main steps of the protocol have been adapted for the bone tissue. After testing many parameters, we found that the best options were (1) take unfixed snap-frozen tissue, (2) cryosection with a supported tape system to improve the tissue morphology if necessary, (3) microdissect regions of interest, and (4) recover the bone pieces by catapulting, if feasible, or by gravity. Finally, RNA extraction (5) was the most efficient with a precipitation method and allowed quantifying the expression of well described osteocyte genes (Gja1/Cx43, Phex, Pdpn, Dmp1, Sost). This work describes two protocols optimized for femur and calvaria and gives an overview of the many optimization options that one could try when facing difficulties with laser microdissection.
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Affiliation(s)
- Mathilde Palmier
- Inserm, University of Bordeaux, BioTis Laboratory UMR 1026, Bordeaux, France
| | - Marlène Maître
- Inserm, University of Bordeaux, Neurocentre Magendie UMR 1215, Bordeaux, France
| | - Hélène Doat
- Inserm, University of Bordeaux, Neurocentre Magendie UMR 1215, Bordeaux, France
| | | | - Delphine B Maurel
- Inserm, University of Bordeaux, BioTis Laboratory UMR 1026, Bordeaux, France
| | - Claudine Boiziau
- Inserm, University of Bordeaux, BioTis Laboratory UMR 1026, Bordeaux, France
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94
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Marolt N, Pavlič R, Kreft T, Gjogorska M, Rižner TL. Targeting estrogen metabolism in high-grade serous ovarian cancer shows promise to overcome platinum resistance. Biomed Pharmacother 2024; 177:117069. [PMID: 38968802 DOI: 10.1016/j.biopha.2024.117069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
The high mortality rate due to chemoresistance in patients with high-grade ovarian cancer (HGSOC) emphasizes the urgent need to determine optimal treatment strategies for advanced and recurrent cases. Our study investigates the interplay between estrogens and chemoresistance in HGSOC and shows clear differences between platinum-sensitive and -resistant tumors. Through comprehensive transcriptome analyzes, we uncover differences in the expression of genes of estrogen biosynthesis, metabolism, transport and action underlying platinum resistance in different tissues of HGSOC subtypes and in six HGSOC cell lines. Furthermore, we identify genes involved in estrogen biosynthesis and metabolism as prognostic biomarkers for HGSOC. Additionally, our study elucidates different patterns of estrogen formation/metabolism and their effects on cell proliferation between six HGSOC cell lines with different platinum sensitivity. These results emphasize the dynamic interplay between estrogens and HGSOC chemoresistance. In particular, targeting the activity of steroid sulfatase (STS) proves to be a promising therapeutic approach with potential efficacy in limiting estrogen-driven cell proliferation. Our study reveals potential prognostic markers as well as identifies novel therapeutic targets that show promise for overcoming resistance and improving treatment outcomes in HGSOC.
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Affiliation(s)
- Nika Marolt
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Renata Pavlič
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Tinkara Kreft
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Marija Gjogorska
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Tea Lanišnik Rižner
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia.
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95
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Luo L, Zheng Y, Li X, Chen Q, Yang D, Gu Z, Yang Y, Yang Y, Kong X, Yang Y. ICE1 interacts with IDD14 to transcriptionally activate QQS to increase pollen germination and viability. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1801-1819. [PMID: 38940322 DOI: 10.1111/jipb.13725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024]
Abstract
In flowering plants, sexual reproductive success depends on the production of viable pollen grains. However, the mechanisms by which QUA QUINE STARCH (QQS) regulates pollen development and how transcriptional activators facilitate the transcription of QQS in this process remain poorly understood. Here, we demonstrate that INDUCER OF CBF EXPRESSION 1 (ICE1), a basic helix-loop-helix (bHLH) transcription factor, acts as a key transcriptional activator and positively regulates QQS expression to increase pollen germination and viability in Arabidopsis thaliana by interacting with INDETERMINATE DOMAIN14 (IDD14). In our genetic and biochemical experiments, overexpression of ICE1 greatly promoted both the activation of QQS and high pollen viability mediated by QQS. IDD14 additively enhanced ICE1 function by promoting the binding of ICE1 to the QQS promoter. In addition, mutation of ICE1 significantly repressed QQS expression; the impaired function of QQS and the abnormal anther dehiscence jointly affected pollen development of the ice1-2 mutant. Our results also showed that the enhancement of pollen activity by ICE1 depends on QQS. Furthermore, QQS interacted with CUT1, the key enzyme for long-chain lipid biosynthesis. This interaction both promoted CUT1 activity and regulated pollen lipid metabolism, ultimately determining pollen hydration and fertility. Our results not only provide new insights into the key function of QQS in promoting pollen development by regulating pollen lipid metabolism, but also elucidate the mechanism that facilitates the transcription of QQS in this vital developmental process.
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Affiliation(s)
- Landi Luo
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Xishuangbanna, 666303, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Yan Zheng
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Xishuangbanna, 666303, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Xieshengyang Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Qian Chen
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Danni Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Xishuangbanna, 666303, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhijia Gu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Ya Yang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunqiang Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Xishuangbanna, 666303, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiangxiang Kong
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Xishuangbanna, 666303, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Yongping Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Xishuangbanna, 666303, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
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96
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Mollet KA, Tembrock LR, Zink FA, Timm AE, Gilligan TM. An Improved Bulk DNA Extraction Method for Detection of Helicoverpa armigera (Lepidoptera: Noctuidae) Using Real-Time PCR. INSECTS 2024; 15:585. [PMID: 39194790 DOI: 10.3390/insects15080585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/29/2024]
Abstract
Helicoverpa armigera is among the most problematic agricultural pests worldwide due to its polyphagy and ability to evolve pesticide resistance. Molecular detection methods for H. armigera have been developed to track its spread, as such methods allow for rapid and accurate differentiation from the native sibling species H. zea. Droplet digital PCR (ddPCR) is a preferred method for bulk screening due to its accuracy and tolerance to PCR inhibitors; however, real-time PCR is less expensive and more widely available in molecular labs. Improvements to DNA extraction yield, purity, and throughput are crucial for real-time PCR assay optimization. Bulk DNA extractions have recently been improved to where real-time PCR sensitivity can equal that of ddPCR, but these new methods require significant time and specialized equipment. In this study, we improve upon previously published bulk DNA extraction methods by reducing bench time and materials. Our results indicate that the addition of caffeine and RNase A improves DNA extraction, resulting in lower Cq values during real-time PCR while reducing the processing time and cost per specimen. Such improvements will enable the use of high throughput screening methods across multiple platforms to improve the probability of detection of H. armigera.
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Affiliation(s)
- Kayla A Mollet
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Frida A Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Alicia E Timm
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Todd M Gilligan
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523-1177, USA
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97
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Osman AM, Hassan-Kadle AA, Dias CM, Ibrahim AM, Collere FCM, Shair MA, Montiani-Ferreira F, André MR, Yusuf AA, Vieira TSWJ, Machado RZ, Vieira RFC. Bartonella species in dromedaries and ruminants from Lower Shabelle and Benadir regions, Somalia. Zoonoses Public Health 2024; 71:568-577. [PMID: 38816921 DOI: 10.1111/zph.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Bartonellosis, caused by bacteria of the genus Bartonella, is a zoonotic disease with several mammalian reservoir hosts. In Somalia, a country heavily reliant on livestock, zoonotic diseases pose significant public health and economic challenges. To the best of our knowledge, no study has been performed aiming to verify the occurrence of Bartonella spp. in Somalia. This study investigated the occurrence and molecular characterization of Bartonella in dromedary (Camelus dromedarius, Linnaeus, 1758), cattle, sheep, and goats from Somalia. MATERIALS AND METHODS 530 blood samples were collected from various animals (155 dromedary, 199 goat, 131 cattle, and 45 sheep) in Benadir and Lower Shabelle regions. DNA was extracted for molecular analysis, and a qPCR assay targeting the NADH dehydrogenase gamma subunit (nuoG) gene was used for Bartonella screening. Positive samples were also subjected to PCR assays targeting seven molecular markers including: nuoG, citrate synthase gene (gltA), RNA polymerase beta-subunit gene (rpoB), riboflavin synthase gene (ribC), 60 kDa heat-shock protein gene (groEL), cell division protein gene (ftsZ), and pap31 and qPCR targeting the 16-23S rRNA internal transcribed spacer (ITS) followed by Sanger sequencing, BLASTn and phylogenetic analysis. RESULTS Out of 530 tested animals, 5.1% were positive for Bartonella spp. by the nuoG qPCR assay. Goats showed the highest Bartonella occurrence (17/199, 8.5%), followed by sheep (6/44, 6.8%), cattle (4/131, 3.1%), and dromedary (1/155, 1.9%). Goats, sheep, and cattle had higher odds of infection compared to dromedary. Among nuoG qPCR-positive samples, 11.1%, 14.8%, 11.1%, and 25.9% were positive in PCR assays based on nuoG, gltA, and pap31 genes, and in the qPCR based on the ITS region, respectively. On the other hand, nuoG qPCR-positive samples were negative in the PCR assays targeting the ribC, rpoB, ftsZ, and groEL genes. While Bartonella bovis sequences were detected in cattle (nuoG and ITS) and goats (gltA), Bartonella henselae ITS sequences were detected in dromedary, goat, and sheep. Phylogenetic analysis placed gltA Bartonella sequence from a goat in the same clade of B. bovis. CONCLUSION The present study showed, for the first time, molecular evidence of Bartonella spp. in dromedary and ruminants from Somalia and B. henselae in sheep and goats globally. These findings contribute valuable insights into Bartonella spp. occurrence in Somali livestock, highlighting the need for comprehensive surveillance and control measures under the One Health approach.
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Affiliation(s)
- Aamir M Osman
- Graduate Program on Veterinary Sciences, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Somali One Health Centre, Abrar University, Mogadishu, Somalia
- Department of Animal Health and Veterinary Services, Ministry of Livestock, Forestry, and Range, Mogadishu, Somalia
| | - Ahmed A Hassan-Kadle
- Somali One Health Centre, Abrar University, Mogadishu, Somalia
- Abrar Research and Training Centre, Abrar University, Mogadishu, Somalia
| | - Clara Morato Dias
- Vector-Borne Bioagents Laboratory (VBBL), Department of Pathology, Reproduction and One Health, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (FCAV/UNESP), Jaboticabal, Brazil
| | - Abdalla M Ibrahim
- Graduate Program on Veterinary Sciences, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Somali One Health Centre, Abrar University, Mogadishu, Somalia
- Abrar Research and Training Centre, Abrar University, Mogadishu, Somalia
| | - Flávia C M Collere
- Graduate Program on Veterinary Sciences, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Mohamed A Shair
- Abrar Research and Training Centre, Abrar University, Mogadishu, Somalia
| | - Fabiano Montiani-Ferreira
- Graduate Program on Veterinary Sciences, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Department of Veterinary Medicine, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Marcos R André
- Vector-Borne Bioagents Laboratory (VBBL), Department of Pathology, Reproduction and One Health, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (FCAV/UNESP), Jaboticabal, Brazil
| | - Abdulkarim A Yusuf
- Abrar Research and Training Centre, Abrar University, Mogadishu, Somalia
- Department of Slaughterhouses, Somali Meat Company, Mogadishu, Somalia
| | - Thállitha S W J Vieira
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), The University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Rosangela Z Machado
- Vector-Borne Bioagents Laboratory (VBBL), Department of Pathology, Reproduction and One Health, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (FCAV/UNESP), Jaboticabal, Brazil
| | - Rafael F C Vieira
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), The University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- Department of Epidemiology and Community Health, The University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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98
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das Chagas MEM, de Mello-Oliveira VS, Guerro-de-Souza M, Calchi AC, Castro-Santiago AC, de Mello ÉM, de Suguiura IMS, Lourenço EC, Famadas KM, Dowling APG, André MR, Barros-Battesti DM, Jacinavicius FDC, Bassini-Silva R. Molecular detection of Bartonella spp. in bat-associated macronyssid mites (Acari: Macronyssidae) from Southern and Southeastern Brazil. Vet Res Commun 2024; 48:2743-2751. [PMID: 38662316 DOI: 10.1007/s11259-024-10393-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Despite the worldwide occurrence and high genetic diversity of Bartonella spp. in bats, few studies investigate their occurrence in bat-associated mites. To date, 26 species of Macronyssidae mite species have been reported from Brazil, and 15 of which were found parasitizing bats. The present study aimed to investigate the presence of Bartonella DNA in bat-associated macronyssid mites from Brazil. For this purpose, 393 macronyssid specimens were selected by convenience from the tissue bank of the Acari Collection of the Instituto Butantan (IBSP). These mites were collected from 14 different bat species in three different Brazilian States (Minas Gerais, Paraná, and Rio de Janeiro). Out of 165 mites positive in the PCR for the endogenous 18S rRNA gene, only eight were positive in the qPCR for Bartonella spp. based on the nuoG gene, and we were able to obtain two sequences base in this same gene, and one sequence based on the 16S rRNA gene. The phylogenetic inference based on the nuoG gene grouped the obtained sequences with Bartonella genotypes previously detected in bats and associated bat flies, while the phylogeny based on the 16S rRNA grouped the obtained sequence in the same clade of Bartonella genotypes previously detected in Dermanyssus gallinae. These findings suggest that macronyssid mites might be associated with the maintenance of bartonellae among bats.
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Affiliation(s)
- Maria Eduarda Moraes das Chagas
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil
| | - Victor Souza de Mello-Oliveira
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil
| | - Mariane Guerro-de-Souza
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil
| | - Ana Cláudia Calchi
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil
| | | | - Érica Munhoz de Mello
- Laboratório de Morcegos Urbanos, Centro de Controle de Zoonoses de Belo Horizonte, Belo Horizonte, MG, Brazil
| | | | - Elizabete Captivo Lourenço
- Laboratório de Ecologia de Mamíferos, Departamento de Ecologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Katia Maria Famadas
- Laboratório de Artrópodes Parasitos, Departamento de Parasitologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Ashley P G Dowling
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - Marcos Rogério André
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil
| | - Darci Moraes Barros-Battesti
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil
| | | | - Ricardo Bassini-Silva
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias-UNESP, Jaboticabal, SP, Brazil.
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Mongruel ACB, Medici EP, da Costa Canena A, Machado RZ, Clay K, Labruna MB, André MR. First molecular detection of Borrelia sp. in tapirs (Tapirus terrestris). Vet Res Commun 2024; 48:2767-2774. [PMID: 38713407 DOI: 10.1007/s11259-024-10406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Borrelia theileri is a tick-borne spirochete causative agent of fever, apathy and reduced food consumption in cattle. Molecular diagnosis has expanded the understanding of Borrelia theileri with new hosts and geographical locations being described. The present study aimed to describe the first molecular detection of B. theileri in wild tapirs (Tapirus terrestris) from South America. Blood DNA samples obtained from 99 tapirs sampled in Pantanal (n = 61) and Cerrado (n = 38) biomes were screened using a qPCR assay based on the 16 S rRNA gene of Borrelia sp. Positive samples in the qPCR assay were subjected to PCR assays to allow characterization of fragments from 16 S rRNA and flaB genes. Two (2/99; 2.0%) animals from Pantanal biome were positive in the qPCR and one sample presented bands of expected size for the flaB protocol. Amplicons from this sample were successfully cloned and sequenced. In the phylogenetic analysis, Borrelia sp. from T. terrestris grouped together with B. theileri sequences previously detected in Rhipicephalus microplus ticks and cattle from Minas Gerais State in Brazil, Rhipicephalus geigyi from Mali, and R. microplus and Haemaphysalis sulcata from Pakistan. This finding contributes to our knowledge regarding susceptible hosts species for B. theileri. More studies are necessary to understand the potential effects of B. theileri on tapir's health.
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Affiliation(s)
- Anna Claudia Baumel Mongruel
- Vector-Borne Bioagents Laboratory (VBBL), Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Jaboticabal, São Paulo, Brazil
| | - Emília Patrícia Medici
- Iniciativa Nacional para Conservação da Anta Brasileira (INCAB), Instituto de Pesquisas Ecológicas (IPÊ) , Campo Grande, Mato Grosso do Sul, Brazil
- Escola Superior de Conservação Ambiental e Sustentabilidade (ESCAS/IPÊ) - Nazaré Paulista, São Paulo, Brazil
- Tapir Specialist Group (TSG), International Union for Conservation of Nature (IUCN SSC), Campo Grande, Mato Grosso do Sul, Brazil
| | - Ariel da Costa Canena
- Iniciativa Nacional para Conservação da Anta Brasileira (INCAB), Instituto de Pesquisas Ecológicas (IPÊ) , Campo Grande, Mato Grosso do Sul, Brazil
| | - Rosangela Zacarias Machado
- Vector-Borne Bioagents Laboratory (VBBL), Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Jaboticabal, São Paulo, Brazil
| | - Keith Clay
- Department of Ecology and Evolutionary Biology, School of Sciences and Engineering, Tulane University, New Orleans, LA, USA
| | - Marcelo Bahia Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal (VPS), Faculdade de Ciências Veterinárias e Zootecnia, Universidade de São Paulo (USP), São Paulo, São Paulo, Brazil
| | - Marcos Rogério André
- Vector-Borne Bioagents Laboratory (VBBL), Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) - Jaboticabal, São Paulo, Brazil.
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100
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Ogihara A, Abe T, Shimoda K, Sasaki T, Kudo H. Messenger RNA transcription levels of neuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex components in the olfactory nerve system of the anadromous Pacific salmon, masu salmon Oncorhynchus masou. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1635-1650. [PMID: 38775866 DOI: 10.1007/s10695-024-01360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/14/2024] [Indexed: 07/30/2024]
Abstract
Anadromous Pacific salmon (genus Oncorhynchus) are known for homing behavior to their natal rivers based on olfactory imprinted memories during seaward migration. The SNARE complex is a regulator of vesicle exocytosis from the presynaptic membrane. Our previous study suggested that its component genes (Snap25, Stx1, and Vamp2) are more highly expressed in the olfactory nervous system (ONS) during the migration stages associated with olfactory imprinting in the evolutionary species of Pacific salmon, such as chum (O. keta) and pink (O. gorbuscha) salmon. Masu salmon (O. masou) has a significantly different life history from these species, living longer in rivers and being a more primitive Pacific salmon species. In this study, the transcription of snare mRNAs in the ONS was analyzed using mainly male wild masu salmon. Five cDNAs encoding masu salmon SNAREs, which are well conserved among vertebrates, were isolated and sequenced. Each snare mRNA was highly expressed in age 1+ (yearling) parr prior to smoltification, particularly in the olfactory bulb. Their transcription status was significantly different from that of chum and pink salmon, which showed high expression in earlier under-yearling juveniles. The present results and our previous studies indicate that snare mRNAs are highly transcripted until the seaward migration, reflecting neural development and neuroplasticity of the ONS for olfactory imprinting.
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Affiliation(s)
- Atsushi Ogihara
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate, Hokkaido, 041-8611, Japan
| | - Takashi Abe
- Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazutaka Shimoda
- Salmon and Freshwater Fisheries Research Institute, Hokkaido Research Organization, Eniwa, Hokkaido, Japan
| | - Takafumi Sasaki
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate, Hokkaido, 041-8611, Japan
| | - Hideaki Kudo
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate, Hokkaido, 041-8611, Japan.
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