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Kim M, Park W, Lim W, Song G, Park S. Impacts of tolylfluanid on implantation and placental development: Disruption of mitochondrial function and implantation-related gene expression in vitro and in vivo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175549. [PMID: 39151622 DOI: 10.1016/j.scitotenv.2024.175549] [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: 06/24/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Tolylfluanid is a widely used pesticide and antifouling agent in agricultural and marine industries and is recognized as a potential endocrine disruptor. However, the toxicological effects of tolylfluanid on the placenta development was not elucidated. This study used trophoblastic cell (HTR-8/SVneo cell) and endometrial cell (T HESCs) lines as in vitro model and mouse models as in vivo model to investigate the toxic effects of tolylfluanid on implantation-associated cell and placenta development during early pregnancy. Experimental results indicated that both cell lines exhibited reduced viability upon tolylfluanid exposure. Various in vitro experiments were conducted at <1 mg/L concentration. The results indicate that tolylfluanid can arrest cell cycle and induce apoptosis in endometrial and trophoblastic cells, abnormally regulate Ca2+ homeostasis and MAPK signaling pathways, and disrupt mitochondrial function. In vivo experiments, subchronic tolylfluanid exposure to mouse during puberty and pregnancy period impaired placenta development, resulting in reduced fetal and placental weight, abnormal placental structures, and altered gene expression. Specifically, a decrease in the ratio of labyrinth/junctional zones and changes in placenta gene expression patterns after tolylfluanid exposure were similar to characters of adverse pregnancy outcomes such as preeclampsia and fetal growth restriction (FGR). This study suggests that tolylfluanid exposure may have negative outcomes on female reproduction, and highlights the need for stricter regulation and monitoring of tolylfluanid use to protect women's reproductive health. This is the first study indicating the adverse effects of tolylfluanid on implantation and placental development during pregnancy.
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Affiliation(s)
- Miji Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Wonhyoung Park
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Whasun Lim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gwonhwa Song
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Sunwoo Park
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Republic of Korea.
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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Iosa I, Agrimonti C, Marmiroli N. Real-Time PCR (qtPCR) to Discover the Fate of Plant Growth-Promoting Rhizobacteria (PGPR) in Agricultural Soils. Microorganisms 2024; 12:1002. [PMID: 38792831 PMCID: PMC11124357 DOI: 10.3390/microorganisms12051002] [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: 04/10/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: Burkholderia ambifaria, Bacillus amyloliquefaciens, Azotobacter chroococcum, Pseudomonas fluorescens, and Rahnella aquatilis. Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (B. ambifaria, B. amyloliquefaciens and R. aquatilis) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus Rhizophagus intraradices. The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery.
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Perez-Bou L, Gonzalez-Martinez A, Cabrera JJ, Juarez-Jimenez B, Rodelas B, Gonzalez-Lopez J, Correa-Galeote D. Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR. MICROBIAL ECOLOGY 2024; 87:71. [PMID: 38748252 PMCID: PMC11096201 DOI: 10.1007/s00248-024-02385-0] [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: 10/25/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.
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Affiliation(s)
- Lizandra Perez-Bou
- Environmental Microbiology Group, Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Juan J Cabrera
- Nitrogen Metabolism Group, Zaidín Experimental Station, Spanish National Research Council, EEZ-CSIC, Granada, Spain
| | - Belen Juarez-Jimenez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Belen Rodelas
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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Yamashita E, Negishi S, Kikuta J, Shimizu M, Senpuku H. Effects of Improper Mechanical Force on the Production of Sonic Hedgehog, RANKL, and IL-6 in Human Periodontal Ligament Cells In Vitro. Dent J (Basel) 2024; 12:108. [PMID: 38668020 PMCID: PMC11049549 DOI: 10.3390/dj12040108] [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: 12/28/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Improper mechanical stress may induce side effects during orthodontic treatment. If the roots and alveolar bones are extensively resorbed following excess mechanical stress, unplanned tooth mobility and inflammation can occur. Although multiple factors are believed to contribute to the development of side effects, the cause is still unknown. Sonic hedgehog (Shh), one of the hedgehog signals significantly associated with cell growth and cancer development, promotes osteoclast formation in the jawbone. Shh may be associated with root and bone resorptions during orthodontic treatment. In this study, we investigated the relationships between Shh, RANKL, and IL-6 in human periodontal ligament (hPDL) cells exposed to improper mechanical force. Weights were placed on hPDL cells and human gingival fibroblasts (HGFs) for an optimal orthodontic force group (1.0 g/cm2) and a heavy orthodontic force group (4.0 g/cm2). A group with no orthodontic force was used as a control group. Real-time PCR, SDS-PAGE, and Western blotting were performed to examine the effects of orthodontic forces on the expression of Shh, RANKL, and IL-6 at 2, 4, 6, 8, 12, and 24 h after the addition of pressure. The protein expression of Shh was not clearly induced by orthodontic forces of 1.0 and 4.0 g/cm2 compared with the control in HGFs and hPDL cells. In contrast, RANKL and IL-6 gene and protein expression was significantly induced by 1.0 and 4.0 g/cm2 in hPDL cells for forces lasting 6~24 h. However, neither protein was expressed in HGFs. RANKL and IL-6 expressions in response to orthodontic forces and in the control were clearly inhibited by Shh inhibitor RU-SKI 43. Shh did not directly link to RANKL and IL-6 for root and bone resorptions by orthodontic force but was associated with cell activities to be finally guided by the production of cytokines in hPDL cells.
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Affiliation(s)
- Erika Yamashita
- Department of Orthodontics, Nihon University of School at Matsudo, Matsudo 271-8587, Japan; (E.Y.); (S.N.); (J.K.)
| | - Shinichi Negishi
- Department of Orthodontics, Nihon University of School at Matsudo, Matsudo 271-8587, Japan; (E.Y.); (S.N.); (J.K.)
| | - Jun Kikuta
- Department of Orthodontics, Nihon University of School at Matsudo, Matsudo 271-8587, Japan; (E.Y.); (S.N.); (J.K.)
| | - Mami Shimizu
- Department of Orthodontics, Nihon University of School at Matsudo, Matsudo 271-8587, Japan; (E.Y.); (S.N.); (J.K.)
| | - Hidenobu Senpuku
- Department of Microbiology and Immunology, Nihon University of School at Matsudo, Matsudo 271-8587, Japan
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Wu W, Jin Q, Östlund C, Tanji K, Shin JY, Han J, Leu CS, Kushner J, Worman HJ. mTOR Inhibition Prolongs Survival and Has Beneficial Effects on Heart Function After Onset of Lamin A/C Gene Mutation Cardiomyopathy in Mice. Circ Heart Fail 2024; 17:e011110. [PMID: 38567527 PMCID: PMC11008450 DOI: 10.1161/circheartfailure.123.011110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Mutations in LMNA encoding nuclear envelope proteins lamin A/C cause dilated cardiomyopathy. Activation of the AKT/mTOR (RAC-α serine/threonine-protein kinase/mammalian target of rapamycin) pathway is implicated as a potential pathophysiologic mechanism. The aim of this study was to assess whether pharmacological inhibition of mTOR signaling has beneficial effects on heart function and prolongs survival in a mouse model of the disease, after onset of heart failure. METHODS We treated male LmnaH222P/H222P mice, after the onset of heart failure, with placebo or either of 2 orally bioavailable mTOR inhibitors: everolimus or NV-20494, a rapamycin analog highly selective against mTORC1. We examined left ventricular remodeling, and the cell biological, biochemical, and histopathologic features of cardiomyopathy, potential drug toxicity, and survival. RESULTS Everolimus treatment (n=17) significantly reduced left ventricular dilatation and increased contractility on echocardiography, with a 7% (P=0.018) reduction in left ventricular end-diastolic diameter and a 39% (P=0.0159) increase fractional shortening compared with placebo (n=17) after 6 weeks of treatment. NV-20494 treatment (n=15) yielded similar but more modest and nonsignificant changes. Neither drug prevented the development of cardiac fibrosis. Drug treatment reactivated suppressed autophagy and inhibited mTORC1 signaling in the heart, although everolimus was more potent. With regards to drug toxicity, everolimus alone led to a modest degree of glucose intolerance during glucose challenge. Everolimus (n=20) and NV-20494 (n=20) significantly prolonged median survival in LmnaH222P/H222P mice, by 9% (P=0.0348) and 11% (P=0.0206), respectively, compared with placebo (n=20). CONCLUSIONS These results suggest that mTOR inhibitors may be beneficial in patients with cardiomyopathy caused by LMNA mutations and that further study is warranted.
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Affiliation(s)
- Wei Wu
- Department of Medicine, Vagelos College of Physicians and Surgeons, (W.W., Q.J., C.Ö., J.-Y.S., J.K., H.J.W.), Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons (W.W., Q.J., C.Ö., K.T., H.J.W.), Columbia University, New York, NY
| | - Qi Jin
- Department of Medicine, Vagelos College of Physicians and Surgeons, (W.W., Q.J., C.Ö., J.-Y.S., J.K., H.J.W.), Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons (W.W., Q.J., C.Ö., K.T., H.J.W.), Columbia University, New York, NY
| | - Cecilia Östlund
- Department of Medicine, Vagelos College of Physicians and Surgeons, (W.W., Q.J., C.Ö., J.-Y.S., J.K., H.J.W.), Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons (W.W., Q.J., C.Ö., K.T., H.J.W.), Columbia University, New York, NY
| | - Kurenai Tanji
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons (W.W., Q.J., C.Ö., K.T., H.J.W.), Columbia University, New York, NY
| | - Ji-Yeon Shin
- Department of Medicine, Vagelos College of Physicians and Surgeons, (W.W., Q.J., C.Ö., J.-Y.S., J.K., H.J.W.), Columbia University, New York, NY
| | - Jiying Han
- Department of Biostatistics, Mailman School of Public Health (J.H., C.-S.L.), Columbia University, New York, NY
| | - Cheng-Shiun Leu
- Department of Biostatistics, Mailman School of Public Health (J.H., C.-S.L.), Columbia University, New York, NY
| | - Jared Kushner
- Department of Medicine, Vagelos College of Physicians and Surgeons, (W.W., Q.J., C.Ö., J.-Y.S., J.K., H.J.W.), Columbia University, New York, NY
| | - Howard J. Worman
- Department of Medicine, Vagelos College of Physicians and Surgeons, (W.W., Q.J., C.Ö., J.-Y.S., J.K., H.J.W.), Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons (W.W., Q.J., C.Ö., K.T., H.J.W.), Columbia University, New York, NY
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Grinstein-Koren O, Lusthaus M, Tabibian-Keissar H, Kaplan I, Buchner A, Ilatov R, Vered M, Zlotogorski-Hurvitz A. Pathological changes in oral epithelium and the expression of SARS-CoV-2 entry receptors, ACE2 and furin. PLoS One 2024; 19:e0300269. [PMID: 38489333 PMCID: PMC10942036 DOI: 10.1371/journal.pone.0300269] [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: 09/29/2023] [Accepted: 02/24/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Expression of angiotensin-converting enzyme (ACE)-2 and co-factors like furin, play key-roles in entry of SARS-CoV-2 into host cells. Furin is also involved in oral carcinogenesis. We investigated their expression in oral pre-malignant/malignant epithelial pathologies to evaluate whether ACE2 and furin expression might increase susceptibility of patients with these lesions for SARS-CoV-2 infection. METHODS Study included normal oral mucosa (N = 14), epithelial hyperplasia-mild dysplasia (N = 27), moderate-to-severe dysplasia (N = 24), squamous cell carcinoma (SCC, N = 34) and oral lichen planus (N = 51). Evaluation of ACE2/furin membranous/membranous-cytoplasmic immunohistochemical expression was divided by epithelial thirds (basal/middle/upper), on a 5-tier scale (0, 1-weak, 1.5 -weak-to-moderate, 2-moderate, 3-strong). Total score per case was the sum of all epithelial thirds, and the mean staining score per group was calculated. Real time-polymerase chain reaction was performed for ACE2-RNA. Statistical differences were analyzed by One-way ANOVA, significance at p<0.05. RESULTS All oral mucosa samples were negative for ACE2 immuno-expression and its transcripts. Overall, furin expression was weakly present with total mean expression being higher in moderate-to-severe dysplasia and hyperplasia-mild dysplasia than in normal epithelium (p = 0.01, each) and SCC (p = 0.008, p = 0.009, respectively). CONCLUSIONS Oral mucosa, normal or with epithelial pathologies lacked ACE2 expression. Furin was weak and mainly expressed in dysplastic lesions. Thus, patients with epithelial pathologies do not seem to be at higher risk for SARS-CoV-2 infection. Overall, results show that oral mucosae do not seem to be a major site of SARS-CoV-2 entry and these were discussed vis-à-vis a comprehensive analysis of the literature.
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Affiliation(s)
- Osnat Grinstein-Koren
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Lusthaus
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Ilana Kaplan
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Pathology, Rabin Medical Center, Petach-Tikva, Israel
| | - Amos Buchner
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ron Ilatov
- Goldschleger School of Dental Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Marilena Vered
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Pathology, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Ayelet Zlotogorski-Hurvitz
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Oral and Maxillofacial Surgery, Rabin Medical Center, Petach-Tikva, Israel
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Vingan I, Phatarpekar S, Tung VSK, Hernández AI, Evgrafov OV, Alarcon JM. Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions and Arc-Expressing Ensembles in Active Place Avoidance Memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573225. [PMID: 38260257 PMCID: PMC10802250 DOI: 10.1101/2023.12.30.573225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The rodent hippocampus is a spatially organized neuronal network that supports the formation of spatial and episodic memories. We conducted bulk RNA sequencing and spatial transcriptomics experiments to measure gene expression changes in the dorsal hippocampus following the recall of active place avoidance (APA) memory. Through bulk RNA sequencing, we examined the gene expression changes following memory recall across the functionally distinct subregions of the dorsal hippocampus. We found that recall induced differentially expressed genes (DEGs) in the CA1 and CA3 hippocampal subregions were enriched with genes involved in synaptic transmission and synaptic plasticity, while DEGs in the dentate gyrus (DG) were enriched with genes involved in energy balance and ribosomal function. Through spatial transcriptomics, we examined gene expression changes following memory recall across an array of spots encompassing putative memory-associated neuronal ensembles marked by the expression of the IEGs Arc, Egr1, and c-Jun. Within samples from both trained and untrained mice, the subpopulations of spatial transcriptomic spots marked by these IEGs were transcriptomically and spatially distinct from one another. DEGs detected between Arc+ and Arc- spots exclusively in the trained mouse were enriched in several memory-related gene ontology terms, including "regulation of synaptic plasticity" and "memory." Our results suggest that APA memory recall is supported by regionalized transcriptomic profiles separating the CA1 and CA3 from the DG, transcriptionally and spatially distinct IEG expressing spatial transcriptomic spots, and biological processes related to synaptic plasticity as a defining the difference between Arc+ and Arc- spatial transcriptomic spots.
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Affiliation(s)
- Isaac Vingan
- School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - Shwetha Phatarpekar
- Institute of Genomics in Health, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - Victoria Sook Keng Tung
- School of Graduates Studies, Program in Molecular and Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - A Iván Hernández
- School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Pathology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- The Robert F. Furchgott Center for Neural & Behavioral Science, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - Oleg V Evgrafov
- Institute of Genomics in Health, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- School of Graduates Studies, Program in Molecular and Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Juan Marcos Alarcon
- School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Pathology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- The Robert F. Furchgott Center for Neural & Behavioral Science, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
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Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [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: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
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Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
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Bohn T, Balbuena E, Ulus H, Iddir M, Wang G, Crook N, Eroglu A. Carotenoids in Health as Studied by Omics-Related Endpoints. Adv Nutr 2023; 14:1538-1578. [PMID: 37678712 PMCID: PMC10721521 DOI: 10.1016/j.advnut.2023.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023] Open
Abstract
Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.
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Affiliation(s)
- Torsten Bohn
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg.
| | - Emilio Balbuena
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Hande Ulus
- Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States
| | - Mohammed Iddir
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Genan Wang
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, United States
| | - Abdulkerim Eroglu
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, United States.
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11
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Nishie T, Ohta Y, Shirai E, Higaki S, Shimozawa N, Narita K, Kawaguchi K, Tanaka H, Mori C, Tanaka T, Hirabayashi M, Suemori H, Kurisaki A, Tooyama I, Asano S, Takeda S, Takada T. Identification of TEKTIN1-expressing multiciliated cells during spontaneous differentiation of non-human primate embryonic stem cells. Genes Cells 2023. [PMID: 37186436 DOI: 10.1111/gtc.13031] [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: 10/12/2022] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Tektins are a group of microtubule-stabilizing proteins necessary for cilia and flagella assembly. TEKTIN1 (TEKT1) is used as a sperm marker for monitoring germ cell differentiation in embryonic stem (ES) and induced pluripotent stem (iPS) cells. Although upregulation of TEKT1 has been reported during spontaneous differentiation of ES and iPS cells, it is unclear which cells express TEKT1. To identify TEKT1-expressing cells, we established an ES cell line derived from cynomolgus monkeys (Macaca fascicularis), which expresses Venus controlled by the TEKT1 promoter. Venus expression was detected at 5 weeks of differentiation on the surface of the embryoid body (EB), and it gradually increased with the concomitant formation of a leash-like structure at the EB periphery. Motile cilia were observed on the surface of the Venus-positive leash-like structure after 8 weeks of differentiation. The expression of cilia markers as well as TEKT1-5 and 9 + 2 microtubule structures, which are characteristic of motile cilia, were detected in Venus-positive cells. These results demonstrated that TEKT1-expressing cells are multiciliated epithelial-like cells that form a leash-like structure during the spontaneous differentiation of ES and iPS cells. These findings will provide a new research strategy for studying cilia biology, including ciliogenesis and ciliopathies.
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Affiliation(s)
- Tomomi Nishie
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Yoshio Ohta
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Emi Shirai
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Shogo Higaki
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Nobuhiro Shimozawa
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba-shi, Ibaraki, Japan
| | - Keishi Narita
- Department of Anatomy and Cell Biology, Interdisciplinary Graduate School, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Kotoku Kawaguchi
- Department of Molecular Physiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Hideyuki Tanaka
- Department of Anatomy, Teikyo University School of Medicine, Itabashi, Tokyo, Japan
| | - Chika Mori
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Taiga Tanaka
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
| | - Hirofumi Suemori
- Center for Human ES Cell Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akira Kurisaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center and Medical Innovation Research Center, Shiga University of Medical Science, Shiga, Japan
| | - Shinji Asano
- Department of Molecular Physiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Sén Takeda
- Department of Anatomy and Cell Biology, Interdisciplinary Graduate School, University of Yamanashi, Chuo, Yamanashi, Japan
- Department of Anatomy, Teikyo University School of Medicine, Itabashi, Tokyo, Japan
| | - Tatsuyuki Takada
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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12
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Transcription of Autophagy Associated Gene Expression as Possible Predictors of a Colorectal Cancer Prognosis. Biomedicines 2023; 11:biomedicines11020418. [PMID: 36830954 PMCID: PMC9952998 DOI: 10.3390/biomedicines11020418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
(1) Background: Autophagy plays a dual role in oncogenesis-it contributes to the growth of the tumor and can inhibit its development. The aim of this study was to assess changes in the transcriptional activity of LAMP-2, BECN1, PINK1, and FOXO1 genes involved in the autophagy process in histopathologically confirmed adenocarcinoma sections of colorectal cancer: (2) Methods: A gene expression profile analysis was performed using HG-U133A and the RT-qPCR reaction. The transcriptional activity of genes was compared in sections of colorectal cancer in the four clinical stages (CSI-CSIV) concerning the control group; (3) Results: In CSI, the transcriptional activity of the PINK1 gene is highest; in CS II, the LAMP-2 gene is highest, while FOXO1 increases gradually from CSI reaching a maximum in CSIII. There is no BECN1 gene expression in colorectal cancer cells; (4) Conclusions: The observed differences in the mRNA concentration profile of autophagy-related genes in colon cancer specimens may indicate the role of autophagy in the pathogenesis of this cancer. Genes involved in autophagy may be diagnostic tools for colorectal cancer screening and personalized therapy in the future.
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Reich SJ, Goldbeck O, Lkhaasuren T, Weixler D, Weiß T, Eikmanns BJ. C-di-AMP Is a Second Messenger in Corynebacterium glutamicum That Regulates Expression of a Cell Wall-Related Peptidase via a Riboswitch. Microorganisms 2023; 11:296. [PMID: 36838266 PMCID: PMC9960051 DOI: 10.3390/microorganisms11020296] [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: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger discovered in Bacillus subtilis and involved in potassium homeostasis, cell wall maintenance and/or DNA stress response. As the role of c-di-AMP has been mostly studied in Firmicutes, we sought to increase the understanding of its role in Actinobacteria, namely in Corynebacterium glutamicum. This organism is a well-known industrial production host and a model organism for pathogens, such as C. diphtheriae or Mycobacterium tuberculosis. Here, we identify and analyze the minimal set of two C. glutamicum enzymes, the diadenylate cyclase DisA and the phosphodiesterase PdeA, responsible for c-di-AMP metabolism. DisA synthesizes c-di-AMP from two molecules of ATP, whereas PdeA degrades c-di-AMP, as well as the linear degradation intermediate phosphoadenylyl-(3'→5')-adenosine (pApA) to two molecules of AMP. Here, we show that a ydaO/kimA-type c-di-AMP-dependent riboswitch controls the expression of the strictly regulated cell wall peptidase gene nlpC in C. glutamicum. In contrast to previously described members of the ydaO/kimA-type riboswitches, our results suggest that the C. glutamicum nlpC riboswitch likely affects the translation instead of the transcription of its downstream gene. Although strongly regulated by different mechanisms, we show that the absence of nlpC, the first known regulatory target of c-di-AMP in C. glutamicum, is not detrimental for this organism under the tested conditions.
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Affiliation(s)
- Sebastian J. Reich
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | | | - Dominik Weixler
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Tamara Weiß
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
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14
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Chaudhary V, Jangra S, Mishra A, Yadav NR. MicroRNA Identification, Target Prediction, and Validation for Crop Improvement. Methods Mol Biol 2023; 2630:13-24. [PMID: 36689173 DOI: 10.1007/978-1-0716-2982-6_2] [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: 01/24/2023]
Abstract
Micro-RNAs (mi-RNAs) are regulatory elements that play a vital role in the growth, development, and metabolic regulation of plants. In current research, the isolation of miRNAs is a tedious and difficult task using in vitro methods. However, recent exploration into the remarkably highly conserved nature of nucleotide sequences of miRNAs assists in the identification of miRNAs in plant species through homologous approaches. Here, we describe the in silico-based method for identification of miRNAs from the EST database which is emerging as a faster and more reliable approach along with the development of miRNA-SSR markers. This approach has the potential to accelerate research into the regulation of gene expression in various plant species such as tea, potato, tomato, tobacco, and orphan crops like cluster bean.
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Affiliation(s)
- Vrantika Chaudhary
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
| | - Sumit Jangra
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Apurva Mishra
- Department of Molecular Biology and Genetics, Arsuaga-Vazquez Lab, University of California, Davis, CA, USA
| | - Neelam R Yadav
- Department of Molecular Biology, Biotechnology, and Bioinformatics, CCS Haryana Agricultural University, Hisar, India.
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15
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Manjunath M, Nirgude S, Mhatre A, Vemuri SG, Nataraj M, Thumsi J, Choudhary B. Transcriptomic profiling of Indian breast cancer patients revealed subtype-specific mRNA and lncRNA signatures. Front Genet 2022; 13:932060. [PMID: 36386805 PMCID: PMC9641000 DOI: 10.3389/fgene.2022.932060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022] Open
Abstract
Breast cancer (BC) is one of the leading causes of cancer-associated death in women. Despite the progress in therapeutic regimen, resistance and recurrence of breast cancer have affected the overall survival of patients. The present signatures, such as PAM50 and Oncotype DX, do not segregate the Indian breast samples based on molecular subtypes. This study aims at finding signatures of long noncoding RNA (lncRNA) and mRNA in Indian breast cancer patients using RNA-seq. We have analyzed the survival based on the menopausal and hormone status of 380 Indian breast cancer patients, and of these, we have sequenced and analyzed matched tumor–normal transcriptome of 17 (pre- and postmenopausal) Indian breast cancer patients representing six different subtypes, namely, four patients in triple-positive, three patients in estrogen receptor–positive (ER+ve), three patients in estrogen and progesterone receptors–positive (ER+ve, PR+ve), two patients in human epidermal growth factor receptor (Her2+ve), three patients in triple-negative, and one patient in ER+ve and Her2+ve subtypes. We have identified a 25 mRNA–27 lncRNA gene set, which segregated the subtypes in our data. A pathway analysis of the differentially expressed genes revealed downregulated ECM interaction and upregulated immune regulation, cell cycle, DNA damage response and repair, and telomere elongation in premenopausal women. Postmenopausal women showed downregulated metabolism, innate immune system, upregulated translation, sumoylation, and AKT2 activation. A Kaplan–Meier survival analysis revealed that menopausal status, grade of the tumor, and hormonal status displayed statistically significant effects (p < 0.05) on the risk of mortality due to breast cancer. Her2+ve patients showed low overall survival. One of the unique lncRNA-mRNA pairs specific to the EP-subtype, SNHG12 and EPB41, showed interaction, which correlates with their expression level; SNHG12 is downregulated and EPB41 is upregulated in EP samples.
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Affiliation(s)
- Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
- Manipal Academy of Higher Education, Manipal, India
| | - Snehal Nirgude
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
- Division of Human Genetics,Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Anisha Mhatre
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Sai G. Vemuri
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | | | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
- *Correspondence: Bibha Choudhary,
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16
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Genes, Structural, and Biochemical Characterization of Four Chlorophyllases from Solanum lycopersicum. Int J Mol Sci 2022; 23:ijms231911716. [PMID: 36233017 PMCID: PMC9570282 DOI: 10.3390/ijms231911716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Recent studies have confirmed that chlorophyllase (CLH), a long-found chlorophyll (Chl) dephytylation enzyme for initiating Chl catabolism, has no function in leaf senescence-related Chl breakdown. Yet, CLH is considered to be involved in fruit degreening and responds to external and hormonal stimuli. The purpose of this work was to elucidate in detail the biochemical, structural properties, and gene expression of four CLHs from the Solanum lycopersicum genome so as to understand the roles of Solanum lycopersicum chlorophyllases (SlCLHs). SlCLH1/4 were the predominantly expressed CLH genes during leaf and fruit development/ripening stages, and SlCLH1 in mature green fruit was modulated by light. SlCLH1/2/3/4 contained a highly conserved GHSXG lipase motif and a Ser-Asp-His catalytic triad. We identified Ser159, Asp226, and His258 as the essential catalytic triad by site-directed mutagenesis in recombinant SlCLH1. Kinetic analysis of the recombinant enzymes revealed that SlCLH1 had high hydrolysis activities against Chl a, Chl b, and pheophytin a (Phein a), but preferred Chl a and Chl b over Phein a; SlCLH2/3 only showed very low activity to Chl a and Chl b, while SlCLH4 showed no Chl dephytylation activity. The recombinant SlCLH1/2/3 had different pH stability and temperature optimum. Removal of the predicted N-terminal processing peptide caused a partial loss of activity in recombinant SlCLH1/2 but did not compromise SlCLH3 activity. These different characteristics among SlCLHs imply that they may have different physiological functions in tomato.
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17
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Jubair N, R. M, Fatima A, Mahdi YK, Abdullah NH. Evaluation of Catechin Synergistic and Antibacterial Efficacy on Biofilm Formation and acrA Gene Expression of Uropathogenic E. coli Clinical Isolates. Antibiotics (Basel) 2022; 11:1223. [PMID: 36140002 PMCID: PMC9495025 DOI: 10.3390/antibiotics11091223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Uropathogenic Escherichia coli has a propensity to build biofilms to resist host defense and antimicrobials. Recurrent urinary tract infection (UTI) caused by multidrug-resistant, biofilm-forming E. coli is a significant public health problem. Consequently, searching for alternative medications has become essential. This study was undertaken to investigate the antibacterial, synergistic, and antibiofilm activities of catechin isolated from Canarium patentinervium Miq. against three E. coli ATCC reference strains (ATCC 25922, ATCC 8739, and ATCC 43895) and fifteen clinical isolates collected from UTI patients in Baghdad, Iraq. In addition, the expression of the biofilm-related gene, acrA, was evaluated with and without catechin treatment. Molecular docking was performed to evaluate the binding mode between catechin and the target protein using Autodock Vina 1.2.0 software. Catechin demonstrated significant bactericidal activity with a minimum inhibitory concentration (MIC) range of 1-2 mg/mL and a minimum bactericidal concentration (MBC) range of 2-4 mg/mL and strong synergy when combined with tetracycline at the MBC value. In addition, catechin substantially reduced E. coli biofilm by downregulating the acrA gene with a reduction percent ≥ 60%. In silico analysis revealed that catechin bound with high affinity (∆G = -8.2 kcal/mol) to AcrB protein (PDB-ID: 5ENT), one of the key AcrAB-TolC efflux pump proteins suggesting that catechin might inhibit the acrA gene indirectly by docking at the active site of AcrB protein.
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Affiliation(s)
- Najwan Jubair
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Mogana R.
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
| | - Ayesha Fatima
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820 Istanbul, Turkey
| | - Yasir K. Mahdi
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia
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18
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Lawrence GW, McCarthy N, Walsh CJ, Kunyoshi TM, Lawton EM, O’Connor PM, Begley M, Cotter PD, Guinane CM. Effect of a bacteriocin-producing Streptococcus salivarius on the pathogen Fusobacterium nucleatum in a model of the human distal colon. Gut Microbes 2022; 14:2100203. [PMID: 35877697 PMCID: PMC9318236 DOI: 10.1080/19490976.2022.2100203] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome is a vast reservoir of microbes, some of which produce antimicrobial peptides called bacteriocins that may inhibit specific bacteria associated with disease. Fusobacterium nucleatum is an emerging human bacterial pathogen associated with gastrointestinal diseases including colorectal cancer (CRC). In this study, fecal samples of healthy donors were screened for potential bacteriocin-producing probiotics with antimicrobial activity against F. nucleatum. A novel isolate, designated as Streptococcus salivarius DPC6993 demonstrated a narrow-spectrum of antimicrobial activity against F. nucleatum in vitro. In silico analysis of the S. salivarius DPC6993 genome revealed the presence of genes involved in the production of the bacteriocins salivaricin A5 and salivaricin B. After 6 h in a colon fermentation model, there was a significant drop in the number of F. nucleatum in samples that had been simultaneously inoculated with S. salivarius DPC6993 + F. nucleatum DSM15643 compared to those inoculated with F. nucleatum DSM15643 alone (mean ± SD: 9243.3 ± 3408.4 vs 29688.9 ± 4993.9 copies/μl). Furthermore, 16S rRNA amplicon analysis revealed a significant difference in the mean relative abundances of Fusobacterium between samples inoculated with both S. salivarius DPC6993 and F. nucleatum DSM15643 (0.05%) and F. nucleatum DSM15643 only (0.32%). Diversity analysis indicated minimal impact exerted by S. salivarius DPC6993 on the surrounding microbiota. Overall, this study highlights the ability of a natural gut bacterium to target a bacterial pathogen associated with CRC. The specific targeting of CRC-associated pathogens by biotherapeutics may ultimately reduce the risk of CRC development and positively impact CRC outcomes.
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Affiliation(s)
- Garreth W. Lawrence
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Niamh McCarthy
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Calum J. Walsh
- Food Biosciences, Teagasc Food Research Centre Moorepark, Cork, Ireland,VistaMilk SFI Research Centre, Moorepark, Fermoy, Cork, Ireland
| | | | | | - Paula M. O’Connor
- Food Biosciences, Teagasc Food Research Centre Moorepark, Cork, Ireland,VistaMilk SFI Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Máire Begley
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences, Teagasc Food Research Centre Moorepark, Cork, Ireland,VistaMilk SFI Research Centre, Moorepark, Fermoy, Cork, Ireland,Paul D. Cotter Food Biosciences, Teagasc Food Research Centre Moorepark, APC Microbiome Ireland, Cork, Ireland
| | - Caitriona M. Guinane
- Department of Biological Sciences, Munster Technological University, Cork, Ireland,CONTACT Caitriona M. Guinane Department of Biological Sciences, Munster Technological University, Cork, Ireland
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Manjunath M, Swaroop S, Pradhan SS, Rao K R, Mahadeva R, Sivaramakrishnan V, Choudhary B. Integrated Transcriptome and Metabolomic Analysis Reveal Anti-Angiogenic Properties of Disarib, a Novel Bcl2-Specific Inhibitor. Genes (Basel) 2022; 13:genes13071208. [PMID: 35885991 PMCID: PMC9316176 DOI: 10.3390/genes13071208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022] Open
Abstract
Transcriptomic profiling of several drugs in cancer cell lines has been utilised to obtain drug-specific signatures and guided combination therapy to combat drug resistance and toxicity. Global metabolomics reflects changes due to altered activity of enzymes, environmental factors, etc. Integrating transcriptomics and metabolomics can provide genotype-phenotype correlation, providing meaningful insights into alterations in gene expression and its outcome to understand differential metabolism and guide therapy. This study uses a multi-omics approach to understand the global gene expression and metabolite changes induced by Disarib, a novel Bcl2-specific inhibitor in the Ehrlich adenocarcinoma (EAC) breast cancer mouse model. RNAseq analysis was performed on EAC mouse tumours treated with Disarib and compared to the controls. The expression of 6 oncogenes and 101 tumour suppressor genes interacting with Bcl2 and Bak were modulated upon Disarib treatment. Cancer hallmark pathways like DNA repair, Cell cycle, angiogenesis, and mitochondrial metabolism were downregulated, and programmed cell death platelet-related pathways were upregulated. Global metabolomic profiling using LC-MS revealed that Oncometabolites like carnitine, oleic acid, glycine, and arginine were elevated in tumour mice compared to normal and were downregulated upon Disarib treatment. Integrated transcriptomic and metabolomic profiles identified arginine metabolism, histidine, and purine metabolism to be altered upon Disarib treatment. Pro-angiogenic metabolites, arginine, palmitic acid, oleic acid, and myristoleic acid were downregulated in Disarib-treated mice. We further validated the effect of Disarib on angiogenesis by qRT-PCR analysis of genes in the VEGF pathway. Disarib treatment led to the downregulation of pro-angiogenic markers. Furthermore, the chorioallantoic membrane assay displayed a reduction in the formation of the number of secondary blood vessels upon Disarib treatment. Disarib reduces tumours by reducing oncometabolite and activating apoptosis and downregulating angiogenesis.
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Affiliation(s)
- Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India; (M.M.); (R.R.K.); (R.M.)
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sai Swaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur 515001, Andhra Pradesh, India; (S.S.); (S.S.P.); (V.S.)
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur 515001, Andhra Pradesh, India; (S.S.); (S.S.P.); (V.S.)
| | - Raksha Rao K
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India; (M.M.); (R.R.K.); (R.M.)
| | - Raghunandan Mahadeva
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India; (M.M.); (R.R.K.); (R.M.)
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur 515001, Andhra Pradesh, India; (S.S.); (S.S.P.); (V.S.)
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India; (M.M.); (R.R.K.); (R.M.)
- Correspondence:
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20
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Tseng H, Zeng Y, Lin YJ, Huang J, Lin C, Lee M, Yang F, Fang T, Mar A, Su J. A novel AMPK activator shows therapeutic potential in hepatocellular carcinoma by suppressing HIF1α-mediated aerobic glycolysis. Mol Oncol 2022; 16:2274-2294. [PMID: 35298869 PMCID: PMC9168760 DOI: 10.1002/1878-0261.13211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/15/2022] [Accepted: 03/15/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is characterized by rapid growth, early vascular invasion, and high metastasis. Currently available US Food and Drug Administration (FDA)-approved drugs show low therapeutic efficacy, limiting HCC treatment to chemotherapy. We designed and synthesized a novel small molecule, SCT-1015, that allosterically activated adenosine monophosphate-activated protein kinase (AMPK) to suppress the aerobic glycolysis in HCC. SCT-1015 was shown to bind the AMPK α and β-subunit interface, thereby exposing the kinase α domain to the upstream kinases, resulting in the increased AMPK activity. SCT-1015 dramatically reduced HCC cell growth in vitro and tumor growth in vivo. We further found that AMPK formed protein complexes with hypoxia-inducible factor 1-alpha (HIF1α) and that SCT-1015-activated AMPK promoted hydroxylation of HIF1α (402P and 564P), resulting in HIF1α degradation by the ubiquitin-proteasome system. With declined HIF1α abundance, many glycolysis-related enzymes were downregulated, suppressing aerobic glycolysis, and promoting oxidative phosphorylation. These results indicated that SCT-1015 channeled HCC cells into an unfavorable metabolic status. Overall, we reported SCT-1015 as a direct activator of AMPK signaling that held therapeutic potential in HCC.
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Affiliation(s)
- Hsing‐I Tseng
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Institute of Biopharmaceutical SciencesNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yi‐Siang Zeng
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Department & Institute of PhysiologyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ying‐Chung Jimmy Lin
- Department of Life Science and Institute of Plant BiologyNational Taiwan UniversityTaipeiTaiwan
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipeiTaiwan
| | - Jui‐Wen Huang
- Biomedical Technology and Device Research LabsIndustrial Technology Research InstituteHsinchuTaiwan
| | - Chih‐Lung Lin
- Biomedical Technology and Device Research LabsIndustrial Technology Research InstituteHsinchuTaiwan
| | - Meng‐Hsuan Lee
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Fan‐Wei Yang
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Te‐Ping Fang
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ai‐Chung Mar
- Taiwan International Graduate Program in Molecular MedicineNational Yang Ming Chiao Tung University and Academia SinicaTaipeiTaiwan
| | - Jung‐Chen Su
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
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21
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Fu H, Zhang C, Wang Y, Chen G. Advances in multiplex molecular detection technologies for harmful algae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:43745-43757. [PMID: 35449333 DOI: 10.1007/s11356-022-20269-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
As the eutrophication of natural water bodies becomes more and more serious, the frequency of outbreaks of harmful algal blooms (HABs) mainly formed by harmful algae also increases. HABs have become a global ecological problem that poses a serious threat to human health and food safety. Therefore, it is extremely important to establish methods that can rapidly detect harmful algal species for early warning of HABs. The traditional morphology-based identification method is inefficient and inaccurate. In recent years, the rapid development of molecular biology techniques has provided new ideas for the detection of harmful algae and has become a research hotspot. The current molecular detection methods for harmful algal species mainly include fluorescence in situ hybridization, sandwich hybridization, and quantitative PCR (qPCR), but all of these methods can only detect single harmful algal species at a time. The establishment of methods for the simultaneous detection of multiple harmful algal species has become a new trend in the development of molecular detection technology because various harmful algal species may coexist in the natural water environment. The established molecular techniques for multiple detections of harmful algae mainly include gene chip, multiplex PCR, multiplex qPCR, massively parallel sequencing, antibody chip, and multiple isothermal amplification. This review mainly focuses on the principles, advantages and disadvantages, application progress, and application prospects of these multiple detection technologies, aiming at providing effective references not only for the fisheries but also for economic activities, environment, and human health.
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Affiliation(s)
- Hanyu Fu
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Chunyun Zhang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Yuanyuan Wang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Guofu Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China.
- School of Environment, Harbin Institute of Technology, Harbin, 150009, People's Republic of China.
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22
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Identification and Validation of Reliable Reference Genes for Gene Expression Studies in Koelreuteria paniculata. Genes (Basel) 2022; 13:genes13050714. [PMID: 35627099 PMCID: PMC9141280 DOI: 10.3390/genes13050714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
RT-qPCR is considered a rapid and reliable technique for analyzing gene expression. This technique is commonly used to analyze the expression of various genes at diverse transcriptional levels in different samples. However, few studies have characterized ornamental Koelreuteria species for reliable reference genes. In this study, eight reference genes were evaluated as controls in RT-qPCR with SYBR green to quantify gene expression in different Koelreuteria paniculata samples. All selected reference genes showed a broad range of Ct values in all samples, which was supportive of their variable expression. Our results showed significant variation in the stable expression of K. paniculata genes. Sample data, analyzed using geNorm, NormFinder, and BestKeeper, showed that phospholipase (PLA2) and β-actin (ACT) were the most suitable and statistically reliable reference genes, whereas ribosomal protein L13 (RPL13) and elongation factor 1-α (EF1α) were less stable and unsuitable for use as internal controls. To compare gene expression levels, two or more reference genes should be used for data normalization. Thus, the stability and expression of both PLA2 and ACT were believed to provide better normalization and quantification of the transcript levels for gene expression studies in K. paniculata.
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23
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Ogundero A, Vignola M, Connelly S, Sloan WT. Validating Flow Cytometry as a Method for Quantifying Bdellovibrio Predatory Bacteria and Its Prey for Microbial Ecology. Microbiol Spectr 2022; 10:e0103321. [PMID: 35196816 PMCID: PMC8865432 DOI: 10.1128/spectrum.01033-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/31/2022] [Indexed: 12/19/2022] Open
Abstract
Bdellovibrio bacteriovorus is a predatory, Gram-negative bacteria that feeds on many pathogenic bacteria and has been investigated as a possible solution for mitigating biofilms in different fields. The application depends on more fundamental ecological studies into the dynamics between Bdellovibrio and their prey. To do so requires an accurate, reliable, and, preferably rapid, way of enumerating the cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated in the enumeration of Bdellovibrio. In this study, we developed a protocol to measure the number of Bdellovibrio in samples of various densities using FCM and compared the results with those of other methods: optical density (OD), PFU assay (PFU), and quantitative PCR (qPCR). We observed a strong correlation between values obtained using FCM and PFU (ρ = 0.923) and FCM and qPCR (ρ = 0.987). Compared to optical density there was a much weaker correlation (ρ = 0.784), which was to be expected given the well-documented uncertainty in converting optical density (OD) to cell numbers. The FCM protocol was further validated by demonstrating its ability to distinguish and count mixed populations of Bdellovibrio and the prey Pseudomonas. Thus, the accuracy of FCM as well as its speed and reproducibility make it a suitable alternative for measuring Bdellovibrio cell numbers, especially where many samples are required to capture the dynamics of predator-prey interactions. IMPORTANCE The rise of antibiotic resistance and the unwanted growth of bacteria is a universally growing problem. Predatory bacteria can be used as a biological alternative to antibiotics because they grow by feeding on other bacteria. To apply this effectively requires further study and a deeper understanding of the forces that drive a prey population to elimination. Initially, such studies require more reliable methods to count these cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated for predatory bacteria. This study develops a protocol to count the predatory bacteria Bdellovibrio bacteriovorus and its Pseudomonas prey using FCM and compare the results with those of other methods, demonstrating its ability for studies into B. bacteriovorus predation dynamics. This could lead to the use of B. bacteriovorus for killing bacterial biofilms in fields, such as drinking water and agriculture.
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Affiliation(s)
- Ayo Ogundero
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - Marta Vignola
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - Stephanie Connelly
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - William T. Sloan
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
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24
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Shaha M, Roy B, Islam MA. Detection of herpes simplex virus 2: a SYBR-Green-based real-time PCR assay. F1000Res 2021; 10:655. [PMID: 34900232 PMCID: PMC8634051 DOI: 10.12688/f1000research.53541.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 11/21/2022] Open
Abstract
The prevalence of Herpes simplex virus 2 (HSV2) is increasing at an alarming rate in the world. Most of the HSV2 cases are not diagnosed properly, although a range of molecular and serological diagnoses exist. Herein, we have reported a very rapid detection method specific for HSV2 using real-time PCR. The primers specific for HSV2 were designed using the Primer-BLAST tool and 120 base pairs of the polymerase gene were amplified using real-time PCR with SYBR Green dye. The designed primer pair was found highly efficient in detecting only HSV2 DNA, but not HSV1. The threshold cycle (Ct) value for HSV2 reactions by designed primers was found to be an average of 22.55 for a standard copy number of viral DNA that may denote the efficiency of the primers. The melting temperature (Tm) of the amplicon using designed primers (82.6
0C) was also higher than that using reference primers (about 78
0C), indicating the high GC content of the amplified template. The designed primer pair will help clinicians to detect the HSV2 DNA specifically and diagnose the associated disease rapidly.
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Affiliation(s)
- Modhusudon Shaha
- Microbial Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Bithi Roy
- Agronomy, Bangladesh Agricultural University, Mymensingh, Mymensingh, Bangladesh
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25
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Bridgeman S, Ellison G, Newsholme P, Mamotte C. The HDAC Inhibitor Butyrate Impairs β Cell Function and Activates the Disallowed Gene Hexokinase I. Int J Mol Sci 2021; 22:ijms222413330. [PMID: 34948127 PMCID: PMC8705743 DOI: 10.3390/ijms222413330] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/26/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors such as butyrate have been reported to reduce diabetes risk and protect insulin-secreting pancreatic β cells in animal models. However, studies on insulin-secreting cells in vitro have found that butyrate treatment resulted in impaired or inappropriate insulin secretion. Our study explores the effects of butyrate on insulin secretion by BRIN BD-11 rat pancreatic β cells and examined effects on the expression of genes implicated in β cell function. Robust HDAC inhibition with 5 mM butyrate or trichostatin A for 24 h in β cells decreased basal insulin secretion and content, as well as insulin secretion in response to acute stimulation. Treatment with butyrate also increased expression of the disallowed gene hexokinase I, possibly explaining the impairment to insulin secretion, and of TXNIP, which may increase oxidative stress and β cell apoptosis. In contrast to robust HDAC inhibition (>70% after 24 h), low-dose and acute high-dose treatment with butyrate enhanced nutrient-stimulated insulin secretion. In conclusion, although protective effects of HDAC inhibition have been observed in vivo, potent HDAC inhibition impairs β cell function in vitro. The chronic low dose and acute high dose butyrate treatments may be more reflective of in vivo effects.
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26
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Kim SS, Kim KI, Yoo HK, Han YS, Jegal ME, Byun SG, Lim HJ, Park JS, Kim YJ. Differential virulence of infectious hematopoietic necrosis virus (IHNV) isolated from salmonid fish in Gangwon Province, Korea. FISH & SHELLFISH IMMUNOLOGY 2021; 119:490-498. [PMID: 34715327 DOI: 10.1016/j.fsi.2021.10.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/01/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
The present study investigated the virulence and expression of innate immunity genes in isolates of infectious hematopoietic necrosis virus (IHNV) in Gangwon province, South Korea, by challenging rainbow trout, Atlantic salmon, and coho salmon. Eight IHNV isolates were used to infect RTG-2 cells for viral replication using plaque assays. Three isolates with the highest replication rates, the RtPc0314g and RtPc0314c isolates of the JRt-Shizuoka type and the RtPc0816g isolate of the JRt-Nagano type, were experimentally infected into the fish. In rainbow trout, both RtPc0314c and RtPc0314g isolates showed 100% cumulative mortality while the RtPc0816g isolate showed 60% cumulative mortality for 14 days. In contrast, all three isolates showed <60% cumulative mortality in Atlantic salmon and coho salmon. The expression of G genes in the kidney was higher than that in the spleen-infected fish, with the highest expression observed in the kidneys of rainbow trout. The relative expression levels of innate immunity genes were higher in rainbow trout than in Atlantic salmon and coho salmon. The expression level of immunoglobulin M increased until day 7, and the expression of type I interferon was higher in the spleen than in other tissues. The expression of Mx-1 was higher in the kidney and liver than other tissues. These results indicate that IHNV isolates from Gangwon province show host-specific virulence in rainbow trout and that their virulence and replication were higher in JRt-Shizuoka type than in JRt-Nagano type isolates.
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Affiliation(s)
- So-Sun Kim
- East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangneung-si, 25435, Republic of Korea; Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Kwang-Il Kim
- Department of Aquatic Life Medicine, Pukyoung National University, Busan, 48513, Republic of Korea
| | - Hae-Kyun Yoo
- East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangneung-si, 25435, Republic of Korea
| | - Yu-Seon Han
- Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Myeong-Eun Jegal
- Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Soon-Gyu Byun
- East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangneung-si, 25435, Republic of Korea
| | - Hyun-Jeong Lim
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong, Republic of Korea
| | - Jang-Su Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Yung-Jin Kim
- Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea.
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27
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Ashwood LM, Undheim EAB, Madio B, Hamilton BR, Daly M, Hurwood DA, King GF, Prentis PJ. Venoms for all occasions: The functional toxin profiles of different anatomical regions in sea anemones are related to their ecological function. Mol Ecol 2021; 31:866-883. [PMID: 34837433 DOI: 10.1111/mec.16286] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/22/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022]
Abstract
The phylum Cnidaria is the oldest extant venomous group and is defined by the presence of nematocysts, specialized organelles responsible for venom production and delivery. Although toxin peptides and the cells housing nematocysts are distributed across the entire animal, nematocyte and venom profiles have been shown to differ across morphological structures in actiniarians. In this study, we explore the relationship between patterns of toxin expression and the ecological roles of discrete anatomical structures in Telmatactis stephensoni. Specifically, using a combination of proteomic and transcriptomic approaches, we examined whether there is a direct correlation between the functional similarity of regions and the similarity of their associated toxin expression profiles. We report that the regionalization of toxin production is consistent with the partitioning of the ecological roles of venom across envenomating structures, and that three major functional regions are present in T. stephensoni: tentacles, epidermis and gastrodermis. Additionally, we find that most structures that serve similar functions not only have comparable putative toxin profiles but also similar nematocyst types. There was no overlap in the putative toxins identified using proteomics and transcriptomics, but the expression patterns of specific milked venom peptides were conserved across RNA-sequencing and mass spectrometry imaging data sets. Furthermore, based on our data, it appears that acontia of T. stephensoni may be transcriptionally inactive and only mature nematocysts are present in the distal portions of the threads. Overall, we find that the venom profile of different anatomical regions in sea anemones varies according to its ecological functions.
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Affiliation(s)
- Lauren M Ashwood
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St Lucia, Queensland, Australia.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Bruno Madio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Brett R Hamilton
- Centre for Advanced Imaging, University of Queensland, St Lucia, Queensland, Australia.,Centre for Microscopy and Microscopy and Microanalysis, University of Queensland, St Lucia, Queensland, Australia
| | - Marymegan Daly
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - David A Hurwood
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia.,Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia.,ARC Centre for Innovations in Peptide and Protein Science, The University of Queensland, St Lucia, Queensland, Australia
| | - Peter J Prentis
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia.,Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
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28
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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29
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Wang Y, Liu M, Wang X, Zhong L, Shi G, Xu Y, Li Y, Li R, Huang Y, Ye X, Li Z, Cui Z. A novel β-1,3-glucanase Gns6 from rice possesses antifungal activity against Magnaporthe oryzae. JOURNAL OF PLANT PHYSIOLOGY 2021; 265:153493. [PMID: 34403886 DOI: 10.1016/j.jplph.2021.153493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 05/21/2023]
Abstract
As members of the pathogenesis-related protein (PR)-2 family, β-1,3-glucanases play pivotal roles in plant defense. Previous study showed that the rice genome contains 16 genes encoding putative β-1,3-glucanases, and the β-1,3-glucanases in subfamily A were deduced to be involved in plant defense. However, there was limited direct evidence. In this study, the expression of rice β-1,3-glucanases Gns2-Gns6 belonging to subfamily A in rice plant infection with Magnaporthe oryzae was investigated, and the enhanced expression of Gns6 during infection confirmed its crucial role in the defense of rice seedlings. Enzymological characterization revealed that Gns6 preferentially hydrolyzed laminarin, pachymaran, and yeast glucan. The β-1,3; 1,6-glucanase Gns6 exhibited a specific activity of 1.2 U/mg with laminarin as the substrate. In addition, Gns6 could hydrolyze laminarin via an endo-type mechanism, yielding a series of oligosaccharides with various degrees of polymerization that are known immune elicitors in plants. Moreover, Gns6 exhibited a significant inhibitory effect against the formation of the germ tubes and appressoria, with potential applications in plant protection. Taken together, this study shows that Gns6 is an essential effector in the defensive response of rice against pathogenic fungi.
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Affiliation(s)
- Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Muxing Liu
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Chinese Ministry of Agriculture, College of Plant Protection, Nanjing Agriculture University, 210095, Nanjing, PR China
| | - Xiaowen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Lingli Zhong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Guolong Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Ye Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Yangqing Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Ruolin Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China.
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China; Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, PR China.
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30
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Fronik P, Poetsch I, Kastner A, Mendrina T, Hager S, Hohenwallner K, Schueffl H, Herndler-Brandstetter D, Koellensperger G, Rampler E, Kopecka J, Riganti C, Berger W, Keppler BK, Heffeter P, Kowol CR. Structure-Activity Relationships of Triple-Action Platinum(IV) Prodrugs with Albumin-Binding Properties and Immunomodulating Ligands. J Med Chem 2021; 64:12132-12151. [PMID: 34403254 PMCID: PMC8404199 DOI: 10.1021/acs.jmedchem.1c00770] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Indexed: 12/27/2022]
Abstract
Chemotherapy with platinum complexes is essential for clinical anticancer therapy. However, due to side effects and drug resistance, further drug improvement is urgently needed. Herein, we report on triple-action platinum(IV) prodrugs, which, in addition to tumor targeting via maleimide-mediated albumin binding, release the immunomodulatory ligand 1-methyl-d-tryptophan (1-MDT). Unexpectedly, structure-activity relationship analysis showed that the mode of 1-MDT conjugation distinctly impacts the reducibility and thus activation of the prodrugs. This in turn affected ligand release, pharmacokinetic properties, efficiency of immunomodulation, and the anticancer activity in vitro and in a mouse model in vivo. Moreover, we could demonstrate that the design of albumin-targeted multi-modal prodrugs using platinum(IV) is a promising strategy to enhance the cellular uptake of bioactive ligands with low cell permeability (1-MDT) and to improve their selective delivery into the malignant tissue. This will allow tumor-specific anticancer therapy supported by a favorably tuned immune microenvironment.
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Affiliation(s)
- Philipp Fronik
- Faculty
of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
| | - Isabella Poetsch
- Faculty
of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
- Research
Cluster “Translational Cancer Therapy Research”, 1090 Vienna, Austria
| | - Alexander Kastner
- Faculty
of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
| | - Theresa Mendrina
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
| | - Sonja Hager
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
| | - Katharina Hohenwallner
- Faculty
of Chemistry, Institute of Analytical Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Hemma Schueffl
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
| | - Dietmar Herndler-Brandstetter
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Faculty
of Chemistry, Institute of Analytical Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Evelyn Rampler
- Faculty
of Chemistry, Institute of Analytical Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Joanna Kopecka
- Department
of Oncology, University of Torino, via Santena 5/bis, 10126 Torino, Italy
| | - Chiara Riganti
- Department
of Oncology, University of Torino, via Santena 5/bis, 10126 Torino, Italy
| | - Walter Berger
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
- Research
Cluster “Translational Cancer Therapy Research”, 1090 Vienna, Austria
| | - Bernhard K. Keppler
- Faculty
of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
- Research
Cluster “Translational Cancer Therapy Research”, 1090 Vienna, Austria
| | - Petra Heffeter
- Institute
of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria
- Research
Cluster “Translational Cancer Therapy Research”, 1090 Vienna, Austria
| | - Christian R. Kowol
- Faculty
of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
- Research
Cluster “Translational Cancer Therapy Research”, 1090 Vienna, Austria
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31
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Wang Y, Zhao Y, Wang X, Zhong L, Fan Q, Lan Z, Ye X, Huang Y, Li Z, Cui Z. Functional Characterization of the Novel Laminaripentaose-Producing β-1,3-Glucanase MoGluB and Its Biocontrol of Magnaporthe oryzae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9571-9584. [PMID: 34378924 DOI: 10.1021/acs.jafc.1c03072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fungal cell wall synthesizing enzymes or remodeling enzymes represent key factors for the interaction of plant pathogen and antifungal agents, which are regarded as potential biocontrol agents. In this study, a novel endo-β-1,3-glucanase from Magnaporthe oryzae was expressed and characterized. The expression of MoGluB was significantly upregulated after 2 days of liquid culture and 48 h after infection, indicating that it may be involved in cell wall reconstitution. Purified MoGluB exhibited high activity on insoluble β-glucans, with a specific activity of 8.18 U/mg toward yeast glucan at pH 9.0 and 50 °C. MoGluB hydrolyzed pachymaran and yeast glucan into oligosaccharides dominated by laminaripentaose, suggesting that it is an endo-β-1,3-glucanase. Incubation of 8 μg of MoGluB with 106 spores/mL resulted in the inhibition of conidial germination and appressorium formation of M. oryzae, illustrating effective biocontrol activity. Hydrolysates of pachymaran induced the expression of defense genes restricting M. oryzae infection in rice plants, indicating an immunostimulatory effect of MoGluB hydrolysates.
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Affiliation(s)
- Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, P. R. China
| | - Xiaowen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Lingli Zhong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Qiwen Fan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zejun Lan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, P. R. China
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32
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Phytoplasma diseases of plants: molecular diagnostics and way forward. World J Microbiol Biotechnol 2021; 37:102. [PMID: 34009500 DOI: 10.1007/s11274-021-03061-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Phytoplasmas are obligate phytopathogenic bacteria associated with devastating diseases in hundreds of crops across the world. They have been responsible for huge economic losses in many crop plants for decades now. Isolation and establishment of axenic culture of phytoplasma in complex media is a recent progress in phytoplasma research. Earlier methods for phytoplasma disease detection included symptom profiling, microscopy, serology and dodder transmission studies. With advancement in the field of molecular biology, phytoplasma diagnostics and characterisation witnessed radical improvement. Starting from PCR amplification which often necessities a nested PCR on account of low titre of phytoplasmas, to the closed tube quantitative PCR assays and then the ddPCR, an array of diagnostics have been developed for phytoplasma. The isothermal diagnostic platforms are the latest addition to this and the Loop Mediated Isothermal Amplification (LAMP) assay has been applied for the detection of phytoplasma from several hosts. The futuristic approach in phytoplasma detection will be very likely provided by an integration of nanotechnology and molecular diagnostics. Phytoplasma disease management majorly relies on early detection, vector control, use of disease free planting materials and cultivation of resistant varieties. Hence understanding the molecular mechanism of phytoplasma-host interaction is as important as timely and accurate detection, in the management of phytoplasma diseases. Further, the changing climatic scenario and global warming may lead to an upsurge in the phytoplasma diseases spread and severity across the world, making disease management even more challenging.
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33
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Sazed SA, Kibria MG, Alam MS. An Optimized Real-Time qPCR Method for the Effective Detection of Human Malaria Infections. Diagnostics (Basel) 2021; 11:736. [PMID: 33919020 PMCID: PMC8142979 DOI: 10.3390/diagnostics11050736] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/24/2022] Open
Abstract
Polymerase chain reaction, although an expensive method for the detection of human Plasmodium spp., is still considered the finest for the diagnosis of malaria. The conventional diagnostic PCR is an inexpensive process but consumes a lot of time, reagents and lacks sensitivity. On the other hand, real-time PCR assays currently being used are mostly probe-based expensive methods and sometimes not feasible to detect all the species in a single amplification reaction condition. Here we have established a real-time PCR method that is time and cost effective with a single protocol to detect and distinguish five human Plasmodium species using the existing primers efficiently. The primers used here are being used in the conventional method and the sensitivity as well as specificity of this method has also been immensely improved (100%). The lower limit of detection for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae are 0.064 parasites/µL, 1.6 parasites/µL, and 0.32 parasites/µL respectively and no cross reactivity was observed. Besides, we have analyzed melt curves that can be used for further species confirmation and validation purposes using multiplex systems. This method, therefore, can be considered as an alternative to the existing lineup for molecular diagnosis of malaria in endemic countries.
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Affiliation(s)
| | | | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh Mohakhali, Dhaka 1212, Bangladesh; (S.A.S.); (M.G.K.)
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34
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Morphologic and genetic analysis for geographic populations of greenbug Schizaphis graminum (Hemiptera: Aphididae) in Egypt. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00501-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Anoshkin K, Vasilyev I, Karandasheva K, Shugay M, Kudryavtseva V, Egorov A, Gurevich L, Mironova A, Serikov A, Kutsev S, Strelnikov V. New Regions With Molecular Alterations in a Rare Case of Insulinomatosis: Case Report With Literature Review. Front Endocrinol (Lausanne) 2021; 12:760154. [PMID: 34737724 PMCID: PMC8563021 DOI: 10.3389/fendo.2021.760154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Insulinomatosis is characterized by monohormonality of multiple macro-tumors and micro-tumors that arise synchronously and metachronously in all regions of the pancreas, and often recurring hypoglycemia. One of the main characteristics of insulinomatosis is the presence of insulin-expressing monohormonal endocrine cell clusters that are exclusively composed of proliferating insulin-positive cells, are less than 1 mm in size, and show solid islet-like structure. It is presumed that insulinomatosis affects the entire population of β-cells. With regards to molecular genetics, this phenomenon is not related to mutation in MEN1 gene and is more similar to sporadic benign insulinomas, however, at the moment molecular genetics of this disease remains poorly investigated. NGS sequencing was performed with a panel of 409 cancer-related genes. Results of sequencing were analyzed by bioinformatic algorithms for detecting point mutations and copy number variations. DNA copy number variations were detected that harbor a large number of genes in insulinoma and fewer genes in micro-tumors. qPCR was used to confirm copy number variations at ATRX, FOXL2, IRS2 and CEBPA genes. Copy number alterations involving FOXL2, IRS2, CEBPA and ATRX genes were observed in insulinoma as well as in micro-tumors samples, suggesting that alterations of these genes may promote malignization in the β-cells population.
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Affiliation(s)
- Kirill Anoshkin
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ivan Vasilyev
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Valeriya Kudryavtseva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Egorov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Larisa Gurevich
- Morphological Department of Oncology, M.F. Vladimirsky Moscow Regional Research and Clinical Institute, Moscow, Russia
| | - Anna Mironova
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey Serikov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergei Kutsev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Vladimir Strelnikov
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
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36
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High Resolution Melting Analysis for Evaluation of mir-612 (Rs12803915) Genetic Variant with Susceptibility to Pediatric Acute Lymphoblastic Leukemia. Rep Biochem Mol Biol 2021; 9:385-393. [PMID: 33969131 DOI: 10.52547/rbmb.9.4.385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background Acute lymphoblastic leukemia (ALL) is a highly heterogeneous malignancy that accounts for nearly 75% of leukemias in children. While the exact mechanism of ALL is not fully understood, some genetic variants have been implicated as associated with ALL susceptibility. The association between some genetic variants in miRNA genes and ALL risk has been described previously. A previous study suggested that mir-612 rs12803915 G> A may be associated with pediatric ALL risk. High-resolution melting (HRM) analysis is a reliable method that can be applied for polymorphism detection. Methods This retrospective study was performed on 100 B-ALL patients (52 males and 48 females; age 4.6 ± 3.2 years) and 105 age- and sex-matched healthy controls (48 males and 57 females; age 5.1 ± 3 years). We used HRM to identify mir-612 rs12803915 genotypes. Sanger sequencing was applied to validate the HRM results. Results High resolution melting analysis was used to genotype the mir-612 rs12803915 polymorphism. We found no association between rs12803915 allele A and B-ALL risk in any inheritance models (p> 0.05). Conclusion HRM is a suitable method to detect SNP rs12803915 in the mir-612 gene; however, we found no significant association between the rs12803915 polymorphism and ALL risk.
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37
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Riolo G, Cantara S, Marzocchi C, Ricci C. miRNA Targets: From Prediction Tools to Experimental Validation. Methods Protoc 2020; 4:1. [PMID: 33374478 PMCID: PMC7839038 DOI: 10.3390/mps4010001] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in both animals and plants. By pairing to microRNA responsive elements (mREs) on target mRNAs, miRNAs play gene-regulatory roles, producing remarkable changes in several physiological and pathological processes. Thus, the identification of miRNA-mRNA target interactions is fundamental for discovering the regulatory network governed by miRNAs. The best way to achieve this goal is usually by computational prediction followed by experimental validation of these miRNA-mRNA interactions. This review summarizes the key strategies for miRNA target identification. Several tools for computational analysis exist, each with different approaches to predict miRNA targets, and their number is constantly increasing. The major algorithms available for this aim, including Machine Learning methods, are discussed, to provide practical tips for familiarizing with their assumptions and understanding how to interpret the results. Then, all the experimental procedures for verifying the authenticity of the identified miRNA-mRNA target pairs are described, including High-Throughput technologies, in order to find the best approach for miRNA validation. For each strategy, strengths and weaknesses are discussed, to enable users to evaluate and select the right approach for their interests.
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Affiliation(s)
| | | | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.); (C.M.)
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38
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Volpato M, Cummings M, Shaaban AM, Abderrahman B, Hull MA, Maximov PY, Broom BM, Hoppe R, Fan P, Brauch H, Jordan VC, Speirs V. Downregulation of 15-hydroxyprostaglandin dehydrogenase during acquired tamoxifen resistance and association with poor prognosis in ERα-positive breast cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:355-371. [PMID: 33210098 PMCID: PMC7116369 DOI: 10.37349/etat.2020.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: Tamoxifen (TAM) resistance remains a clinical issue in breast cancer. The authors previously reported that 15-hydroxyprostaglandin dehydrogenase (HPGD) was significantly downregulated in tamoxifen-resistant (TAMr) breast cancer cell lines. Here, the authors investigated the relationship between HPGD expression, TAM resistance and prediction of outcome in breast cancer. Methods: HPGD overexpression and silencing studies were performed in isogenic TAMr and parental human breast cancer cell lines to establish the impact of HPGD expression on TAM resistance. HPGD expression and clinical outcome relationships were explored using immunohistochemistry and in silico analysis. Results: Restoration of HPGD expression and activity sensitised TAMr MCF-7 cells to TAM and 17β-oestradiol, whilst HPGD silencing in parental MCF-7 cells reduced TAM sensitivity. TAMr cells released more prostaglandin E2 (PGE2) than controls, which was reduced in TAMr cells stably transfected with HPGD. Exogenous PGE2 signalled through the EP4 receptor to reduce breast cancer cell sensitivity to TAM. Decreased HPGD expression was associated with decreased overall survival in ERα-positive breast cancer patients. Conclusions: HPGD downregulation in breast cancer is associated with reduced response to TAM therapy via PGE2-EP4 signalling and decreases patient survival. The data offer a potential target to develop combination therapies that may overcome acquired tamoxifen resistance.
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Affiliation(s)
- Milene Volpato
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, LS9 7TF Leeds, UK
| | - Michele Cummings
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, LS9 7TF Leeds, UK
| | - Abeer M Shaaban
- Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Balkees Abderrahman
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, LS9 7TF Leeds, UK.,Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark A Hull
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, LS9 7TF Leeds, UK
| | - Philipp Y Maximov
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bradley M Broom
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Auerbachstr. 112, D-70376 Stuttgart, Germany.,Germany iFIT Cluster of Excellence, University of Tübingen, Auerbachstr. 112, D-70376 Stuttgart, Germany
| | - Ping Fan
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Auerbachstr. 112, D-70376 Stuttgart, Germany.,Germany iFIT Cluster of Excellence, University of Tübingen, Auerbachstr. 112, D-70376 Stuttgart, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - V Craig Jordan
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Valerie Speirs
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, LS9 7TF Leeds, UK.,Institute of Medical Sciences, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
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39
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Grabski DF, Broseus L, Kumari B, Rekosh D, Hammarskjold ML, Ritchie W. Intron retention and its impact on gene expression and protein diversity: A review and a practical guide. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1631. [PMID: 33073477 DOI: 10.1002/wrna.1631] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/16/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Intron retention (IR) occurs when a complete and unspliced intron remains in mature mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions, including several that impact human health and disease. Although experimental technologies used to study other forms of mRNA splicing can also be used to investigate IR, a specialized downstream computational analysis is optimal for IR discovery and analysis. Here we provide a review of IR and its biological implications, as well as a practical guide for how to detect and analyze it. Several methods, including long read third generation direct RNA sequencing, are described. We have developed an R package, FakIR, to facilitate the execution of the bioinformatic tasks recommended in this review and a tutorial on how to fit them to users aims. Additionally, we provide guidelines and experimental protocols to validate IR discovery and to evaluate the potential impact of IR on gene expression and protein output. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Regulation/Alternative Splicing RNA Methods > RNA Analyses in vitro and In Silico.
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Affiliation(s)
- David F Grabski
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Lucile Broseus
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Bandana Kumari
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - William Ritchie
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
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40
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Xu YL, Liu Y, Cai RP, He SR, Dai RX, Yang XH, Kong BH, Qin ZB, Su Q. Long non-coding RNA CASC7 is associated with the pathogenesis of heart failure via modulating the expression of miR-30c. J Cell Mol Med 2020; 24:11500-11511. [PMID: 32860492 PMCID: PMC7576250 DOI: 10.1111/jcmm.15764] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022] Open
Abstract
MiRNAs can be used as promising diagnostic biomarkers of heart failure, while lncRNAs act as competing endogenous RNAs of miRNAs. In this study, we collected peripheral blood monocytes from subjects with or without HF to explore the association between certain lncRNAs, miRNAs and HF. Heart failure patients with preserved or reduced ejection fraction were recruited for investigation. ROC analysis was carried out to evaluate the diagnostic values of certain miRNAs and lncRNAs in HF. Luciferase assays were used to study the regulatory relationship between above miRNAs and lncRNAs. LncRNA overexpression was used to explore the effect of certain miRNAs in H9C2 cells. Expression of miR‐30c was significantly decreased in the plasma and peripheral blood monocytes of patients suffering from heart failure, especially in these with reduced ejection fraction. On the contrary, the expression of lncRNA‐CASC7 was remarkably increased in the plasma and peripheral blood monocytes of patients suffering from heart failure. Both miR‐30c and lncRNA‐CASC7 expression showed a promising efficiency as diagnostic biomarkers of heart failure. Luciferase assays indicated that miR‐30c played an inhibitory role in lncRNA‐CASC7 and IL‐11 mRNA expression. Moreover, the overexpression of lncRNA‐CASC7 suppressed the expression of miR‐30c while evidently increasing the expression of IL‐11 mRNA and protein in H9C2 cells. This study clarified the relationship among miR‐30c, lncRNA‐CASC7 and IL‐11 expression and the risk of heart failure and showed that lncRNA‐CASC7 is potentially involved in the pathogenesis of HF via modulating the expression of miR‐30c.
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Affiliation(s)
- Yu-Li Xu
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yang Liu
- Department of Cardiology, The Second People's Hospital of Nanning City, The Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ru-Ping Cai
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Shi-Rong He
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Ri-Xin Dai
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xi-Heng Yang
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Bing-Hui Kong
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhen-Bai Qin
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiang Su
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
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41
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Sommer N, Noack S, Hecker A, Hackstein H, Bein G, Weissmann N, Seeger W, Mayer K, Hecker M. Decreased Thymic Output Contributes to Immune Defects in Septic Patients. J Clin Med 2020; 9:jcm9092695. [PMID: 32825352 PMCID: PMC7565146 DOI: 10.3390/jcm9092695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/02/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022] Open
Abstract
Background: Prolonged immunosuppression and hypoinflammation, termed compensatory anti-inflammatory response syndrome (CARS), contribute to high morbidity and mortality in the late phase of sepsis. Although apoptosis is a well-known cause of lymphopenia in sepsis, the contribution of thymic output to immune alterations in sepsis and potential compensatory mechanisms are largely unknown. Methods: We investigate the release of CD4+ T cells from the thymus and their peripheral proliferation by evaluating T-cell receptor excision circles (TREC) and the expression of CD31 as markers for recent thymic emigrants (RTE) and their proliferative offspring in septic patients with relevant lymphopenia in the CARS phase. Moreover, we determine the aging of T cells by measuring telomere characteristics. Results: In septic patients, we found decreased CD4+ T-helper cell numbers, while CD8+ T cell numbers were unchanged. As a possible cause, we detected increased apoptosis of CD4+ T-helper cells and decreased levels of IL-7, which promotes the maturation of T cells in the thymus. Accordingly, the relative number of mature CD4+ T cells, TREC-containing CD4+ T cells, and CD31+ RTEs (characteristic of thymic output) was decreased, while the relative number of CD31-T cells (peripherally expanded naïve T cells) was increased. Furthermore, the telomere length decreased, although telomerase activity and markers for the shelterin complex were increased specifically in CD4+ but not in CD8+ T cells. Conclusion: We thus conclude that, in addition to T-cell apoptosis, decreased thymic output and increased aging of CD4+ T cells may contribute to lymphopenia and immunosuppression in sepsis. Increased proliferation of peripheral T cells cannot compensate for these effects.
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Affiliation(s)
- Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University of Giessen, 35392 Giessen, Germany; (N.S.); (S.N.); (N.W.); (W.S.); (K.M.)
| | - Steffen Noack
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University of Giessen, 35392 Giessen, Germany; (N.S.); (S.N.); (N.W.); (W.S.); (K.M.)
| | - Andreas Hecker
- Department of General and Thoracic Surgery, Justus-Liebig-University of Giessen, 35392 Giessen, Germany;
| | - Holger Hackstein
- Department of Transfusion Medicine and Hemostaseology, University Hospital Erlangen, 91054 Erlangen, Germany;
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig-University, 35392 Giessen, Germany;
| | - Gregor Bein
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig-University, 35392 Giessen, Germany;
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University of Giessen, 35392 Giessen, Germany; (N.S.); (S.N.); (N.W.); (W.S.); (K.M.)
| | - Werner Seeger
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University of Giessen, 35392 Giessen, Germany; (N.S.); (S.N.); (N.W.); (W.S.); (K.M.)
| | - Konstantin Mayer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University of Giessen, 35392 Giessen, Germany; (N.S.); (S.N.); (N.W.); (W.S.); (K.M.)
- Department of Pulmonary and Sleep Medicine, ViDia hospitals, 76137 Karlsruhe, Germany
| | - Matthias Hecker
- Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University of Giessen, 35392 Giessen, Germany; (N.S.); (S.N.); (N.W.); (W.S.); (K.M.)
- Correspondence: ; Tel.: +49-641-985-56755; Fax: +49-641-985-51259
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The Role of Atypical Cannabinoid Ligands O-1602 and O-1918 on Skeletal Muscle Homeostasis with a Focus on Obesity. Int J Mol Sci 2020; 21:ijms21165922. [PMID: 32824681 PMCID: PMC7460607 DOI: 10.3390/ijms21165922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 11/17/2022] Open
Abstract
O-1602 and O-1918 are atypical cannabinoid ligands for GPR55 and GPR18, which may be novel pharmaceuticals for the treatment of obesity by targeting energy homeostasis regulation in skeletal muscle. This study aimed to determine the effect of O-1602 or O-1918 on markers of oxidative capacity and fatty acid metabolism in the skeletal muscle. Diet-induced obese (DIO) male Sprague Dawley rats were administered a daily intraperitoneal injection of O-1602, O-1918 or vehicle for 6 weeks. C2C12 myotubes were treated with O-1602 or O-1918 and human primary myotubes were treated with O-1918. GPR18 mRNA was expressed in the skeletal muscle of DIO rats and was up-regulated in red gastrocnemius when compared with white gastrocnemius. O-1602 had no effect on mRNA expression on selected markers for oxidative capacity, fatty acid metabolism or adiponectin signalling in gastrocnemius from DIO rats or in C2C12 myotubes, while APPL2 mRNA was up-regulated in white gastrocnemius in DIO rats treated with O-1918. In C2C12 myotubes treated with O-1918, PGC1α, NFATc1 and PDK4 mRNA were up-regulated. There were no effects of O-1918 on mRNA expression in human primary myotubes derived from obese and obese T2DM individuals. In conclusion, O-1602 does not alter mRNA expression of key pathways important for skeletal muscle energy homeostasis in obesity. In contrast, O-1918 appears to alter markers of oxidative capacity and fatty acid metabolism in C2C12 myotubes only. GPR18 is expressed in DIO rat skeletal muscle and future work could focus on selectively modulating GPR18 in a tissue-specific manner, which may be beneficial for obesity-targeted therapies.
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Somuncu S, Somuncu ÖS, Ballıca B, Tabandeh B. Deficiency of epithelial-mesenchymal transition causes child indirect inguinal hernia. J Pediatr Surg 2020; 55:665-671. [PMID: 31288923 DOI: 10.1016/j.jpedsurg.2019.06.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/11/2019] [Accepted: 06/21/2019] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Epithelial-mesenchymal transition (EMT) describes rapid changes in cellular phenotype. During EMT, epithelial cells down-modulate cell-cell adhesion, alter polarity, reorganize cytoskeleton, become isolated, motile, and resistant to anoikis. Epithelial breakdown and epithelial cell migration are the key processes involved in the obliteration of processus vaginalis. The great majority of abnormalities are because of nonobliteration or incomplete fusion of PV. We aimed to analyze the quantitative changes of epithelial genes in adult/child patients and their controls to examine differences of the genesis of these hernias. We also aimed to investigate the potential epigenetic causes of indirect inguinal hernia in adult patients. METHODS Ten adult, ten child indirect inguinal hernia sacs and ten adult, ten child parietal peritonea were used. Hernial sac samples were obtained from indirect inguinal hernia surgeries. Peritonea of adult patients who underwent open cholecystectomy for cholelithiasis via subcostal incision were included in the study as the healthy control groups. Ages of the children were selected to be between 0 and 5 whereas the age of adults was chosen as 35-55, respectively. Total RNA isolation and cDNA synthesis were made from hernia sacs and peritoneum samples. Relative Keratin 1, Keratin 15, Filaggrin2 and STAT3 expressions were analyzed via qPCR. Indirect inguinal hernia sac cells were seeded and grown in vitro. Child diseased cells were employed in immunocytochemistry (ICC) analysis for Cytokeratin 15, Filaggrin2 and Bcl-2. Adult indirect inguinal hernia cells were examined for H3 modifications through ICC. RESULTS In child indirect inguinal hernia, Keratin expressions were found higher than their controls. They were meaningfully lower than the healthy group in adult indirect inguinal hernia. Keratin 15, Keratin 1 and Filaggrin2 expressions were all correlating since they are members of related pathways. STAT3 expressions were opposite to Keratin and Filaggrin expressions suggesting that adult cells might have a switch to the mesenchymal state from the epithelial state. Adult indirect inguinal hernia samples have switched to the mesenchymal state whereas child indirect inguinal hernia samples have shown lack of transition. CONCLUSION Irregular changes of EMT associated genes act in the progression of indirect inguinal hernia. Hence, the information on the epigenetic regulation of EMT in patients with primary inguinal hernia can aid to comprehend the pathogenesis in adults and infers new therapeutic approaches for this disease. TYPE OF STUDY Prognosis study. LEVEL OF EVIDENCE Level 2.
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Affiliation(s)
- Salih Somuncu
- Bezmialem Vakıf University Hospital, Department of Pediatric Surgery, Turkey.
| | - Özge Sezin Somuncu
- Bahçeşehir University, Faculty of Medicine, Department of Basic Sciences, Turkey
| | | | - Babek Tabandeh
- Bahçeşehir University, Faculty of Medicine, Department of General Surgery, Turkey
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Tomás FJB, Turko P, Heilmann H, Trimbuch T, Yanagawa Y, Vida I, Münster-Wandowski A. BDNF Expression in Cortical GABAergic Interneurons. Int J Mol Sci 2020; 21:E1567. [PMID: 32106593 PMCID: PMC7084226 DOI: 10.3390/ijms21051567] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a major neuronal growth factor that is widely expressed in the central nervous system. It is synthesized as a glycosylated precursor protein, (pro)BDNF and post-translationally converted to the mature form, (m)BDNF. BDNF is known to be produced and secreted by cortical glutamatergic principal cells (PCs); however, it remains a question whether it can also be synthesized by other neuron types, in particular, GABAergic interneurons (INs). Therefore, we utilized immunocytochemical labeling and reverse transcription quantitative PCR (RT-qPCR) to investigate the cellular distribution of proBDNF and its RNA in glutamatergic and GABAergic neurons of the mouse cortex. Immunofluorescence labeling revealed that mBDNF, as well as proBDNF, localized to both the neuronal populations in the hippocampus. The precursor proBDNF protein showed a perinuclear distribution pattern, overlapping with the rough endoplasmic reticulum (ER), the site of protein synthesis. RT-qPCR of samples obtained using laser capture microdissection (LCM) or fluorescence-activated cell sorting (FACS) of hippocampal and cortical neurons further demonstrated the abundance of BDNF transcripts in both glutamatergic and GABAergic cells. Thus, our data provide compelling evidence that BDNF can be synthesized by both principal cells and INs of the cortex.
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Affiliation(s)
- Federico José Barreda Tomás
- Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117 Berlin, Germany; (F.J.B.T.); (P.T.); (H.H.); (I.V.)
- Bernstein Center for Computational Neuroscience (BCCN) Berlin, 10115 Berlin, Germany
| | - Paul Turko
- Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117 Berlin, Germany; (F.J.B.T.); (P.T.); (H.H.); (I.V.)
| | - Heike Heilmann
- Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117 Berlin, Germany; (F.J.B.T.); (P.T.); (H.H.); (I.V.)
| | - Thorsten Trimbuch
- Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Campus Mitte, 10117 Berlin, Germany;
| | - Yuchio Yanagawa
- Departments of Genetic and Behavioral Neuroscience, Graduate School of Medicine, Gunma University, Graduate School of Medicine, Maebashi City 371-8511, Japan;
| | - Imre Vida
- Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117 Berlin, Germany; (F.J.B.T.); (P.T.); (H.H.); (I.V.)
- Bernstein Center for Computational Neuroscience (BCCN) Berlin, 10115 Berlin, Germany
| | - Agnieszka Münster-Wandowski
- Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117 Berlin, Germany; (F.J.B.T.); (P.T.); (H.H.); (I.V.)
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Kiliç HB, Bulduk BK, Kocaefe YÇ. A single-tube multiplex qPCR assay for mitochondrial DNA (mtDNA) copy number assessment. TURKISH JOURNAL OF BIOCHEMISTRY 2019. [DOI: 10.1515/tjb-2018-0372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Objective
Detection of mtDNA copy number is required for diagnosis of mtDNA depletion. Multiplex quantification of mtDNA in blood samples was claimed via normalizing to a nuclear single copy gene using qPCR. This is not possible in high mtDNA samples due to template abundance. Multiplex qPCR assays cannot be normalized to single copy sequences of the nuclear genome.
Methods
mtDNA quantification was tested normalizing to a single copy nuclear gene via singleplex and multiplex reactions. Failure in normalization directed to design and test targeting multi-copy 18S rDNA gene with success. mtDNA quantification was standardized both in separate and multiplexed single-tube reactions based on molecular beacon technology.
Results
mtDNA copy number assessment cannot be normalized to a single copy sequence in high-copy-number tissues. However, normalizing mtDNA to the nuclear 18S rDNA multiple copy sequence is amenable to be standardized in single tube. When compared, multiplexing exhibited higher resolution power for quantification of mtDNA in various samples from the most abundant to the scant ones.
Conclusion
We describe a multiplex assay that can be translated as a standard technique for single-tube quantification of mtDNA copy number. Our findings show higher accuracy and reproducibility over canonical approach, reducing cost and error rate.
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Screening and Evaluation of Stable Reference Genes for Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Analysis in Chinese Fir Roots under Water, Phosphorus, and Nitrogen Stresses. FORESTS 2019. [DOI: 10.3390/f10121087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chinese fir (Cunninghamia lanceolata) is an economical important timber species widely planted in southeastern Asia. Decline in yield and productivity during successive rotation is believed to be linked with abiotic stress, such as drought stress and nitrogen (N) and phosphorus (P) starvation. Molecular breeding could be an option to develop tolerant genotypes. For gene expression studies using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR), stable reference genes are needed for normalization of gene expression under different experimental conditions. However, there is no internal reference genes identified for Chinese fir under abiotic stresses. Thus, nine internal reference genes based on transcriptome data were selected and analyzed in the root of Chinese fir under drought stress and N and P starvation. Data were analyzed using geNorm, NormFinder, and BestKeeper, to screen and identify the best reference genes. The results showed that the UBQ and GAPDH genes were the two most stable genes under drought stress and the Actin1 and GAPDH were the two most stable genes under P starvation. Further, it was discovered that the Actin1 and UBC were the two most stable genes under N starvation among nine candidate reference genes. The gene expression of drought stress induced expression protein 14-3-3-4, the P transporter gene ClPht1;3, and the nitrate transporter gene NRT1.1 were used to verify the stability of the selected reference genes under drought stress and P and N starvation, respectively, and the results revealed that the screened reference genes were sufficient to normalize expression of the target genes. In conclusion, the results demonstrate that the stability of reference genes was closely related to the external conditions and reference genes applied to the roots of Chinese fir under different abiotic stress treatments were different. Our data will facilitate further studies on stress ecology and gene function analysis in Chinese fir.
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Jeong H, Cha S, Jang KL. HBx natural variants containing Ser-101 instead of Pro-101 evade ubiquitin-dependent proteasomal degradation by activating proteasomal activator 28 gamma expression. J Gen Virol 2019; 100:1554-1566. [PMID: 31596196 DOI: 10.1099/jgv.0.001337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proteasomal activator 28 gamma (PA28γ) is frequently overexpressed in hepatocellular carcinoma; however, its underlying mechanism and role in hepatitis B virus (HBV) replication are largely unknown. Here, we found that HBV X protein (HBx) natural variants containing Ser-101 instead of Pro-101 increase reactive oxygen species levels in the mitochondria and activate the ataxia telangiectasia mutated/checkpoint kinase 2 pathway in the nucleus, resulting in the phosphorylation of p53 at Ser-15 and Ser-20 and the subsequent upregulation of its protein levels. Therefore, HBx variants containing Ser-101 induced p53-dependent activation of PA28γ expression in human hepatoma cells. The elevated PA28γ levels upregulated HBx levels through the inhibition of seven in absentia homologue 1-dependent proteasomal degradation. The self-amplifying ability of HBx variants containing Ser-101 via a positive feedback loop involving p53 and PA28γ was accurately reproduced in both a 1.2-mer HBV replicon and in vitro HBV infection systems, which also provided evidence for the stimulation of HBV replication by these HBx variants. In conclusion, the ability of HBx to upregulate PA28γ levels via p53 activation, in a Ser-101-dependent pathway, is critical for the stimulation of HBV replication.
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Affiliation(s)
- Hyerin Jeong
- Department of Microbiology, College of Natural Science, Pusan National University, Busan 46241, Republic of Korea
| | - Sungkyung Cha
- Department of Microbiology, College of Natural Science, Pusan National University, Busan 46241, Republic of Korea
| | - Kyung Lib Jang
- Department of Microbiology, College of Natural Science, Pusan National University, Busan 46241, Republic of Korea
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Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
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Park M, Sutherland JB, Rafii F. Effects of nano-hydroxyapatite on the formation of biofilms by Streptococcus mutans in two different media. Arch Oral Biol 2019; 107:104484. [PMID: 31382161 DOI: 10.1016/j.archoralbio.2019.104484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/20/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVES The aim of this study was to examine the effect of nano-hydroxyapatite (nHA) on biofilm formation by Streptococcus mutans, which is actively involved in the initiation of dental caries. DESIGN The effects of nHA on growth and biofilm formation by S. mutans were investigated in two media: a saliva analog medium, basal medium mucin (BMM); and a nutrient-rich medium, brain heart infusion (BHI); in the presence and absence of sucrose. RESULTS Sucrose enhanced the growth of S. mutans in both media. In the presence of sucrose, nHA enhanced bacterial growth and biofilm formation more in BMM medium than in BHI. nHA also affected the transcription of glucosyltransferase (gtf) genes and production of polysaccharide differently in the two media. In BHI medium, the transcription of all three gtf genes, coding for enzymes that synthesize soluble and insoluble glucans from sucrose, was increased more than 3-fold by nHA. However, in BMM medium, only the transcription of gtfB and gtfC, coding for insoluble glucans, was substantially enhanced by nHA. CONCLUSIONS nHA appeared to enhance biofilm formation by increasing glucosyltransferase transcription, which resulted in an increase in production of insoluble glucans. This effect was influenced by the growth conditions.
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Affiliation(s)
- Miseon Park
- Division of Microbiology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
| | - John B Sutherland
- Division of Microbiology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
| | - Fatemeh Rafii
- Division of Microbiology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA.
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