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Liu D, Tian Z, Tusong K, Mamat H, Luo Y. Expression, purification and characterization of CTP synthase PyrG in Staphylococcusaureus. Protein Expr Purif 2024; 221:106520. [PMID: 38833752 DOI: 10.1016/j.pep.2024.106520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/06/2024]
Abstract
Staphylococcus aureus (S. aureus) presents a significant challenge in both nosocomial and community settings due to its pathogenicity. The emergence of drug-resistant strains exacerbates S. aureus infections, leading to increased mortality rates. PyrG, a member of the cytidine triphosphate (CTP) synthase family, serves as a crucial therapeutic target against S. aureus due to the pivotal role of CTP in cellular metabolism. However, the structural and mechanistic details of S. aureus PyrG remains unknown. Here, we successfully expressed and purified monomeric PyrG. Mutational experiments were conducted based on the results of molecular docking. Based on the results of the molecular docking, we carried out mutation experiments and found that Q386A dramatically decreased the CTP synthase activity compared to the wild-type protein, while Y54A almost completely abolished the activity. Exposure of S. aureus to the kinase inhibitor crizotinib increased expression of gene pyrG. Our results identify the two key sites on PyrG for the CTP synthase activity, and present PyrG gene expression increased during the treatment of crizotinib, which may eventually provide valuable guidance for the development of new drugs against S. aureus infections.
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Affiliation(s)
- Dafeng Liu
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China; School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Zhu Tian
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
| | - Kuerban Tusong
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
| | - Hayrinsa Mamat
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
| | - Yihan Luo
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
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Shahbazi E, Moradi A, Mollasalehi H, Mohebbi SR. Unravelling the diagnostic methodologies for SARS-CoV-2; the Indispensable need for developing point-of-care testing. Talanta 2024; 275:126139. [PMID: 38696900 DOI: 10.1016/j.talanta.2024.126139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/13/2024] [Accepted: 04/20/2024] [Indexed: 05/04/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic that continues to be a global menace and since its emergence in the late 2019, SARS-CoV-2 has been vigorously spreading throughout the globe putting the whole world into a multidimensional calamity. The suitable diagnosis strategies are on the front line of the battle against preventing the spread of infections. Since the clinical manifestation of COVID-19 is shared between various diseases, detection of the unique impacts of the pathogen on the host along with the diagnosis of the virus itself should be addressed. Employing the most suitable approaches to specifically, sensitively and effectively recognize the infected cases may be a real game changer in controlling the outbreak and the crisis management. In that matter, point-of-care assays (POC) appears to be the potential option, due to sensitivity, specificity, affordable, and availability. Here we brief the most recent findings about the virus, its variants, and the conventional methods that have been used for its detection, along with the POC strategies that have been applied to the virus diagnosis and the developing technologies which can accelerate the diagnosis procedure yet maintain its efficiency.
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Affiliation(s)
- Erfan Shahbazi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Asma Moradi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Hamidreza Mollasalehi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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3
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Zakzak K, Semenescu AD, Moacă EA, Predescu I, Drăghici G, Vlaia L, Vlaia V, Borcan F, Dehelean CA. Comprehensive Biosafety Profile of Carbomer-Based Hydrogel Formulations Incorporating Phosphorus Derivatives. Gels 2024; 10:477. [PMID: 39057500 PMCID: PMC11276259 DOI: 10.3390/gels10070477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Determining the safety of a newly developed experimental product is a crucial condition for its medical use, especially for clinical trials. In this regard, four hydrogel-type formulations were manufactured, all of which were based on carbomer (Blank-CP940) and encapsulated with caffeine (CAF-CP940), phosphorus derivatives (phenyl phosphinic (CAF-S1-CP940) and 2-carboxyethyl phenyl phosphinic acids (CAF-S2-CP940)). The main aim of this research was to provide a comprehensive outline of the biosafety profile of the above-mentioned hydrogels. The complex in vitro screening (cell viability, cytotoxicity, morphological changes in response to exposure, and changes in nuclei morphology) on two types of healthy skin cell lines (HaCaT-human keratinocytes and JB6 Cl 41-5a-murine epidermal cells) exhibited a good biosafety profile when both cell lines were treated for 24 h with 150 μg/mL of each hydrogel. A comprehensive analysis of the hydrogel's impact on the genetic profile of HaCaT cells sustains the in vitro experiments. The biosafety profile was completed with the in vivo and in ovo assays. The outcome revealed that the developed hydrogels exerted good biocompatibility after topical application on BALB/c nude mice's skin. It also revealed a lack of toxicity after exposure to the hen's chicken embryo. Further investigations are needed, regarding the in vitro and in vivo therapeutic efficacy and safety for long-term use and potential clinical translatability.
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Affiliation(s)
- Khaled Zakzak
- Department of Pharmaceutical Technology, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (K.Z.); (L.V.)
| | - Alexandra-Denisa Semenescu
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (A.-D.S.); (I.P.); (G.D.); (C.-A.D.)
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Elena-Alina Moacă
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (A.-D.S.); (I.P.); (G.D.); (C.-A.D.)
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Iasmina Predescu
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (A.-D.S.); (I.P.); (G.D.); (C.-A.D.)
| | - George Drăghici
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (A.-D.S.); (I.P.); (G.D.); (C.-A.D.)
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Lavinia Vlaia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (K.Z.); (L.V.)
- Formulation and Technology of Drugs Research Center, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania;
| | - Vicenţiu Vlaia
- Formulation and Technology of Drugs Research Center, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania;
- Department of Organic Chemistry, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Florin Borcan
- Department of Analytical Chemistry, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania;
| | - Cristina-Adriana Dehelean
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania; (A.-D.S.); (I.P.); (G.D.); (C.-A.D.)
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babes” University of Medicine and Pharmacy Timisoara, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
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Lee SJ, Kim Y, Kang K, Yoon H, Kang J, Cho SH, Paek NC. Rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE interacts with OsCRY2 and promotes flowering by upregulating Early heading date 1. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39012205 DOI: 10.1111/pce.15046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024]
Abstract
Flowering time is a crucial adaptive response to seasonal variation in plants and is regulated by environmental cues such as photoperiod and temperature. In this study, we demonstrated the regulatory function of rice CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1-LIKE (OsCIBL1) in flowering time. Overexpression of OsCIB1L promoted flowering, whereas the oscib1l knockout mutation did not alter flowering time independent of photoperiodic conditions. Cryptochromes (CRYs) are blue light photoreceptors that enable plants to sense photoperiodic changes. OsCIBL1 interacted with OsCRY2, a member of the rice CRY family (OsCRY1a, OsCRY1b, and OsCRY2), and bound to the Early heading date 1 (Ehd1) promoter, activating the rice-specific Ehd1-Heading date 3a/RICE FLOWERING LOCUS T 1 pathway for flowering induction. Dual-luciferase reporter assays showed that the OsCIBL1-OsCRY2 complex required blue light to induce Ehd1 transcription. Natural alleles resulting from nonsynonymous single nucleotide polymorphisms in OsCIB1L and OsCRY2 may contribute to the adaptive expansion of rice cultivation areas. These results expand our understanding of the molecular mechanisms controlling rice flowering and highlight the importance of blue light-responsive genes in the geographic distribution of rice.
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Affiliation(s)
- Sang-Ji Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yunjeong Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kiyoon Kang
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Hyeryung Yoon
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jinku Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sung-Hwan Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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5
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Nanes BA, Bhatt K, Azarova E, Rajendran D, Munawar S, Isogai T, Dean KM, Danuser G. Shifts in keratin isoform expression activate motility signals during wound healing. Dev Cell 2024:S1534-5807(24)00389-7. [PMID: 39002537 DOI: 10.1016/j.devcel.2024.06.011] [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: 06/09/2023] [Revised: 04/15/2024] [Accepted: 06/17/2024] [Indexed: 07/15/2024]
Abstract
Keratin intermediate filaments confer structural stability to epithelial tissues, but the reason this simple mechanical function requires a protein family with 54 isoforms is not understood. During skin wound healing, a shift in keratin isoform expression alters the composition of keratin filaments. If and how this change modulates cellular functions that support epidermal remodeling remains unclear. We report an unexpected effect of keratin isoform variation on kinase signal transduction. Increased expression of wound-associated keratin 6A, but not of steady-state keratin 5, potentiated keratinocyte migration and wound closure without compromising mechanical stability by activating myosin motors to increase contractile force generation. These results substantially expand the functional repertoire of intermediate filaments from their canonical role as mechanical scaffolds to include roles as isoform-tuned signaling scaffolds that organize signal transduction cascades in space and time to influence epithelial cell state.
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Affiliation(s)
- Benjamin A Nanes
- Department of Dermatology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Kushal Bhatt
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Evgenia Azarova
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sabahat Munawar
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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6
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M AL, B R A, Manyam P, Javeedvali S, Khan AS, Palnam DW, Kandan A. Traditional to technological advancements in Ganoderma detection methods in oil palm. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01177-w. [PMID: 38976188 DOI: 10.1007/s12223-024-01177-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 05/19/2024] [Indexed: 07/09/2024]
Abstract
Ganoderma sp., the fungal agent causing basal stem rot (BSR), poses a severe threat to global oil palm production. Alarming increases in BSR occurrences within oil palm growing zones are attributed to varying effectiveness in its current management strategies. Asymptomatic progression of the disease and the continuous monoculture of oil palm pose challenges for prompt and effective management. Therefore, the development of precise, early, and timely detection techniques is crucial for successful BSR management. Conventional methods such as visual assessments, culture-based assays, and biochemical and physiological approaches prove time-consuming and lack specificity. Serological-based diagnostic methods, unsuitable for fungal diagnostics due to low sensitivity, assay affinity, cross-contamination which further underscores the need for improved techniques. Molecular PCR-based assays, utilizing universal, genus-specific, and species-specific primers, along with functional primers, can overcome the limitations of conventional and serological methods in fungal diagnostics. Recent advancements, including real-time PCR, biosensors, and isothermal amplification methods, facilitate accurate, specific, and sensitive Ganoderma detection. Comparative whole genomic analysis enables high-resolution discrimination of Ganoderma at the strain level. Additionally, omics tools such as transcriptomics, proteomics, and metabolomics can identify potential biomarkers for early detection of Ganoderma infection. Innovative on-field diagnostic techniques, including remote methods like volatile organic compounds profiling, tomography, hyperspectral and multispectral imaging, terrestrial laser scanning, and Red-Green-Blue cameras, contribute to a comprehensive diagnostic approach. Ultimately, the development of point-of-care, early, and cost-effective diagnostic techniques accessible to farmers is vital for the timely management of BSR in oil palm plantations.
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Affiliation(s)
- Amrutha Lakshmi M
- Plant Pathology, ICAR-Indian Institute of Oil Palm Research, India, Andhra Pradesh.
| | - Ajesh B R
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Pradeep Manyam
- Acharya N. G, Ranga Agricultural University, Guntur, Andhra Pradesh, India
| | - Shaik Javeedvali
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Amjada S Khan
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dauda Wadzani Palnam
- Crop Science Unit, Department of Agronomy, Federal University, Yobe State, Gashua, Nigeria
| | - A Kandan
- ICAR-National Bureau of Agricultural Insect Resources, Bangalore, India
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7
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Singh M, Young RG, Hellberg RS, Hanner RH, Corradini MG, Farber JM. Twenty-three years of PCR-based seafood authentication assay development: What have we learned? Compr Rev Food Sci Food Saf 2024; 23:e13401. [PMID: 39073284 DOI: 10.1111/1541-4337.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA-based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer-probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay-based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA-based method was real-time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species-specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA-based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.
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Affiliation(s)
- Maleeka Singh
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rosalee S Hellberg
- Schmid College of Science and Technology, Food Science Program, Chapman University, Orange, California, USA
| | - Robert H Hanner
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Maria G Corradini
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
- Arrell Food Institute, University of Guelph, Guelph, Ontario, Canada
| | - Jeffrey M Farber
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada
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Bzdok J, Czibere L, Burggraf S, Landt O, Maier EM, Röschinger W, Albert MH, Hegert S, Janzen N, Becker M, Durner J. Quality considerations and major pitfalls for high throughput DNA-based newborn screening for severe combined immunodeficiency and spinal muscular atrophy. PLoS One 2024; 19:e0306329. [PMID: 38941330 PMCID: PMC11213327 DOI: 10.1371/journal.pone.0306329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Many newborn screening programs worldwide have introduced screening for diseases using DNA extracted from dried blood spots (DBS). In Germany, DNA-based assays are currently used to screen for severe combined immunodeficiency (SCID), spinal muscular atrophy (SMA), and sickle cell disease (SCD). METHODS This study analysed the impact of pre-analytic DNA carry-over in sample preparation on the outcome of DNA-based newborn screening for SCID and SMA and compared the efficacy of rapid extraction versus automated protocols. Additionally, the distribution of T cell receptor excision circles (TREC) on DBS cards, commonly used for routine newborn screening, was determined. RESULTS Contaminations from the punching procedure were detected in the SCID and SMA assays in all experimental setups tested. However, a careful evaluation of a cut-off allowed for a clear separation of true positive polymerase chain reaction (PCR) amplifications. Our rapid in-house extraction protocol produced similar amounts compared to automated commercial systems. Therefore, it can be used for reliable DNA-based screening. Additionally, the amount of extracted DNA significantly differs depending on the location of punching within a DBS. CONCLUSIONS Newborn screening for SMA and SCID can be performed reliably. It is crucial to ensure that affected newborns are not overlooked. Therefore a carefully consideration of potential contaminating factors and the definition of appropriate cut-offs to minimise the risk of false results are of special concern. It is also important to note that the location of punching plays a pivotal role, and therefore an exact quantification of TREC numbers per μl may not be reliable and should therefore be avoided.
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Affiliation(s)
- Jessica Bzdok
- Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig-Maximilians-Universität München, Munich, Germany
- Laboratory Becker MVZ GbR, Munich, Germany
| | | | | | | | | | | | - Michael H. Albert
- Department of Paediatrics, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Nils Janzen
- Screening-Labor Hannover, Hanover, Germany
- Department of Clinical Chemistry, Hanover Medical School, Hanover, Germany
- Division of Laboratory Medicine, Centre for Children and Adolescents, Kinder- und Jugendkrankenhaus Auf der Bult, Hanover, Germany
| | - Marc Becker
- Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig-Maximilians-Universität München, Munich, Germany
- Laboratory Becker MVZ GbR, Munich, Germany
| | - Jürgen Durner
- Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig-Maximilians-Universität München, Munich, Germany
- Laboratory Becker MVZ GbR, Munich, Germany
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9
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Ramsey K, Britt M, Maramba J, Ushijima B, Moller E, Anishkin A, Häse C, Sukharev S. The dynamic hypoosmotic response of Vibrio cholerae relies on the mechanosensitive channel mechanosensitive channel of small conductance. iScience 2024; 27:110001. [PMID: 38868203 PMCID: PMC11167432 DOI: 10.1016/j.isci.2024.110001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Vibrio cholerae adapts to osmotic down-shifts by releasing metabolites through two mechanosensitive (MS) channels, low-threshold MscS and high-threshold MscL. To investigate each channel's contribution to the osmotic response, we generated ΔmscS, ΔmscL, and double ΔmscL ΔmscS mutants in V. cholerae O395. We characterized their tension-dependent activation in patch-clamp, and the millisecond-scale osmolyte release kinetics using a stopped-flow light scattering technique. We additionally generated numerical models describing osmolyte and water fluxes. We illustrate the sequence of events and define the parameters that characterize discrete phases of the osmotic response. Survival is correlated to the extent of cell swelling, the rate of osmolyte release, and the completeness of post-shock membrane resealing. Not only do the two channels interact functionally, but there is also an up-regulation of MscS in the ΔmscL strain, suggesting transcriptional crosstalk. The data reveal the role of MscS in the termination of the osmotic permeability response in V. cholerae.
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Affiliation(s)
- Kristen Ramsey
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Madolyn Britt
- Department of Biology, University of Maryland, College Park, MD, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD, USA
| | - Joseph Maramba
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Blake Ushijima
- Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Elissa Moller
- Department of Biology, University of Maryland, College Park, MD, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD, USA
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudia Häse
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Sergei Sukharev
- Department of Biology, University of Maryland, College Park, MD, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
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10
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Tomescu LC, Cosma AA, Fenesan MP, Melnic E, Petrovici V, Sarb S, Chis M, Sas I, Ribatti D, Cimpean AM, Dorobantu FR. Combining RNAscope, Immunohistochemistry (IHC) and Digital Image Analysis to Assess Podoplanin (PDPN) Protein and PDPN_mRNA Expression on Formalin-Fixed Paraffin-Embedded Normal Human Placenta Tissues. Curr Issues Mol Biol 2024; 46:5161-5177. [PMID: 38920982 PMCID: PMC11202497 DOI: 10.3390/cimb46060310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
The expression and function of podoplanin (PDPN) in the normal human placenta has been debated in placental evaluation. This study emphasizes the importance of a multimodal approach of PDPN expression in normal human placentas. A complete examination is performed using immunohistochemistry, RNAscope and automated Digital Image examination (DIA) interpretation. QuPath DIA-based analysis automatically generated the stromal and histological scores of PDPN expression for immunohistochemistry and RNAscope stains. The umbilical cord's isolated fibroblasts and luminal structures expressed PDPN protein and PDPN_mRNA. RNAscope detected PDPN_mRNA upregulation in syncytial placental knots trophoblastic cells, but immunohistochemistry did not certify this at the protein level. The study found a significant correlation between the IHC and RNAscope H-Score (p = 0.033) and Allred Score (p = 0.05). A successful multimodal strategy for PDPN assessment in human placentas confirmed PDPN expression heterogeneity in the full-term human normal placenta and umbilical cord at the protein and mRNA level. In placental syncytial knots trophoblastic cells, PDPN showed mRNA overexpression, suggesting a potential role in placenta maturation.
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Affiliation(s)
- Larisa Cristina Tomescu
- Doctoral School in Medicine, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (L.C.T.); (A.A.C.); (M.P.F.)
- Department of Obstetrics and Gynecology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Andrei Alexandru Cosma
- Doctoral School in Medicine, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (L.C.T.); (A.A.C.); (M.P.F.)
- Department of Microscopic Morphology/Histology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- OncoHelp Hospital, 300239 Timisoara, Romania
| | - Mihaela Pasca Fenesan
- Doctoral School in Medicine, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (L.C.T.); (A.A.C.); (M.P.F.)
- Department of Microscopic Morphology/Histology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- OncoHelp Hospital, 300239 Timisoara, Romania
| | - Eugen Melnic
- Department of Pathology, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova; (E.M.); (V.P.)
| | - Vergil Petrovici
- Department of Pathology, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova; (E.M.); (V.P.)
| | - Simona Sarb
- Department of Microscopic Morphology/Histology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Monica Chis
- Department ME2/Rheumatology, Rehabilitation, Physical Medicine and Balneology, Faculty of Medicine, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of TârguMureş (UMPhST), 540088 Targu Mures, Romania;
- Clinic of Rheumatology, Emergency County Hospital of Târgu Mureş, 540088 Targu Mures, Romania
| | - Ioan Sas
- Department of Obstetrics and Gynecology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Domenico Ribatti
- Department of Translational Biomedicine and Neuroscience, University of Bari Medical School, 70124 Bari, Italy;
| | - Anca Maria Cimpean
- Department of Microscopic Morphology/Histology, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Center of Expertise for Rare Vascular Disease in Children, Emergency Hospital for Children Louis Turcanu, 300011 Timisoara, Romania
| | - Florica Ramona Dorobantu
- Department of Neonatology, Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania;
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Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [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: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
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Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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12
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Rashid Z, Nabi A, Nabi N, Lateef I, Nisa Q, Fayaz T, Gulzar G, Bashir A, Shah MD, Zargar SM, Khan I, Nahvi AI, Itoo H, Shah RA, Padder BA. Selection of stable reference genes for qPCR expression of Colletotrichum lindemuthianum, the bean anthracnose pathogen. Fungal Biol 2024; 128:1771-1779. [PMID: 38796261 DOI: 10.1016/j.funbio.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/10/2024] [Accepted: 03/19/2024] [Indexed: 05/28/2024]
Abstract
Phaseolus vulgaris L., commonly known as the common bean, is a highly nutritious crop often called the "poor man's meat". However, it is susceptible to various diseases throughout the cropping season, with anthracnose caused by Colletotrichum lindemuthianum being a significant threat that leads to substantial losses. There is still a lack of understanding about the molecular basis of C. lindemuthianum pathogenicity. The first step in understanding this is to identify pathogenicity genes that express more during infection of common beans. A reverse transcription quantitative real-time PCR (qPCR) method can be used for virulence gene expression. However, this approach requires selecting appropriate reference genes to normalize relative gene expression data. Currently, there is no reference gene available for C. lindemuthianum. In this study, we selected eight candidate reference genes from the available genome of C. lindemuthianum to bridge the gap. These genes were ACT (Actin), β-tub (β-tubulin), EF (Elongation Factor), Cyt C (Cytochrome C), His H3 (Histone H3), CHS1 (Chitin synthetase), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) and abfA (Alpha-l-Arabinofuranosidase A). The primers for these candidate reference genes were able to amplify cDNA only from the pathogen, demonstrating their specificity. The qPCR efficiency of the primers ranged from 80% to 103%. We analyzed the stability of gene expression in C. lindemuthianum by exposing the mycelium to nine different stress conditions. We employed algorithms, such as GeNorm, NormFinder, BestKeeper, and RefFinder tools, to identify the most stable gene. The analysis using these tools revealed that EF, GAPDH, and β-tub most stable genes, while ACT and CHS1 showed relatively low expression stability. A large number of potential effector genes have been identified through bioinformatics analysis in C. lindemuthianum. The stable genes for qPCR (EF and GAPDH) discovered in this study will aid the scientific community in determining the relative expression of C. lindemuthianum effector genes.
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Affiliation(s)
- Zainab Rashid
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Naziya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Tabia Fayaz
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Gazala Gulzar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Adfar Bashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Research Center for Residue and Quality Control Analysis, SKUAST-Kashmir, 190025, India
| | - Sajad M Zargar
- Division of Plant Biotechnology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Imran Khan
- Division of Agricultural Statistics, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Afsah Iqbal Nahvi
- Extension Training Centre, Malangpora, Pulwama, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - H Itoo
- Ambri Apple Research Centre, Pahnoo, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rafiq A Shah
- Ambri Apple Research Centre, Pahnoo, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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Nanes BA, Bhatt K, Boujemaa-Paterski R, Azarova E, Munawar S, Rajendran D, Isogai T, Dean KM, Medalia O, Danuser G. Keratin isoform shifts modulate motility signals during wound healing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.04.538989. [PMID: 37205459 PMCID: PMC10187270 DOI: 10.1101/2023.05.04.538989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Keratin intermediate filaments form strong mechanical scaffolds that confer structural stability to epithelial tissues, but the reason this function requires a protein family with 54 isoforms is not understood. During skin wound healing, a shift in keratin isoform expression alters the composition of keratin filaments. How this change modulates cellular function to support epidermal remodeling remains unclear. We report an unexpected effect of keratin isoform variation on kinase signal transduction. Increased expression of wound-associated keratin 6A, but not of steady-state keratin 5, potentiated keratinocyte migration and wound closure without compromising epidermal stability by activating myosin motors. This pathway depended on isoform-specific interaction between intrinsically disordered keratin head domains and non-filamentous vimentin shuttling myosin-activating kinases. These results substantially expand the functional repertoire of intermediate filaments from their canonical role as mechanical scaffolds to include roles as isoform-tuned signaling scaffolds that organize signal transduction cascades in space and time to influence epithelial cell state.
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Affiliation(s)
- Benjamin A Nanes
- Department of Dermatology, UT Southwestern Medical Center; Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Kushal Bhatt
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | | | - Evgenia Azarova
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
- Present address: Department of Materials Science and Engineering, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Sabahat Munawar
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich; Zurich CH-8057, Switzerland
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
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Das S, Malik M, Dastidar DG, Roy R, Paul P, Sarkar S, Chakraborty P, Maity A, Dasgupta M, Gupta AD, Chatterjee S, Sarker RK, Maiti D, Tribedi P. Piperine, a phytochemical prevents the biofilm city of methicillin-resistant Staphylococcus aureus: A biochemical approach to understand the underlying mechanism. Microb Pathog 2024; 189:106601. [PMID: 38423404 DOI: 10.1016/j.micpath.2024.106601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant human pathogen causes several nosocomial as well as community-acquired infections involving biofilm machinery. Hence, it has gained a wide interest within the scientific community to impede biofilm-induced MRSA-associated health complications. The current study focuses on the utilization of a natural bioactive compound called piperine to control the biofilm development of MRSA. Quantitative assessments like crystal violet, total protein recovery, and fluorescein-di-acetate (FDA) hydrolysis assays, demonstrated that piperine (8 and 16 μg/mL) could effectively compromise the biofilm formation of MRSA. Light and scanning electron microscopic image analysis confirmed the same. Further investigation revealed that piperine could reduce extracellular polysaccharide production by down-regulating the expression of icaA gene. Besides, piperine could reduce the cell-surface hydrophobicity of MRSA, a crucial factor of biofilm formation. Moreover, the introduction of piperine could interfere with microbial motility indicating the interaction of piperine with the quorum-sensing components. A molecular dynamics study showed a stable binding between piperine and AgrA protein (regulator of quorum sensing) suggesting the possible meddling of piperine in quorum-sensing of MRSA. Additionally, the exposure to piperine led to the accumulation of intracellular reactive oxygen species (ROS) and potentially heightened cell membrane permeability in inhibiting microbial biofilm formation. Besides, piperine could reduce the secretion of diverse virulence factors from MRSA. Further exploration revealed that piperine interacted with extracellular DNA (e-DNA), causing disintegration by weakening the biofilm architecture. Conclusively, this study suggests that piperine could be a potential antibiofilm molecule against MRSA-associated biofilm infections.
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Affiliation(s)
- Sharmistha Das
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Moumita Malik
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Debabrata Ghosh Dastidar
- Guru Nanak Institute of Pharmaceutical Science and Technology, 157/F Nilgunj Road, Panihati, Kolkata, West Bengal, 700114, India.
| | - Ritwik Roy
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Payel Paul
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Sarita Sarkar
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Poulomi Chakraborty
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Alakesh Maity
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Monikankana Dasgupta
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Anirban Das Gupta
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Sudipta Chatterjee
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Ranojit Kumar Sarker
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| | - Debasish Maiti
- Department of Human Physiology, Tripura University, Suryamaninagar, Agartala, Tripura, 799022, India.
| | - Prosun Tribedi
- Microbial Ecology Research Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
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15
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Pugsley K, Namipashaki A, Bellgrove MA, Hawi Z. Evaluating the regulatory function of non-coding autism-associated single nucleotide polymorphisms on gene expression in human brain tissue. Autism Res 2024; 17:467-481. [PMID: 38323502 DOI: 10.1002/aur.3101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Common variants account for most of the estimated heritability associated with autism spectrum disorder (autism). Although several replicable single nucleotide polymorphisms (SNPs) for the condition have been detected using genome-wide association study (GWAS) methodologies, their pathophysiological relevance remains elusive. Examining this is complicated, however, as all detected loci are situated within non-coding regions of the genome. It is therefore likely that they possess roles of regulatory function as opposed to directly affecting gene coding sequences. To bridge the gap between SNP discovery and mechanistic insight, we applied a comprehensive bioinformatic pipeline to functionally annotate autism-associated polymorphisms and their non-coding linkage disequilibrium (i.e., non-randomly associated) partners. We identified 82 DNA variants of probable regulatory function that may contribute to autism pathogenesis. To validate these predictions, we measured the impact of 11 high-confidence candidates and their GWAS linkage disequilibrium partners on gene expression in human brain tissue from Autistic and non-Autistic donors. Although a small number of the surveyed variants exhibited measurable influence on gene expression as determined via quantitative polymerase chain reaction, these did not survive correction for multiple comparisons. Additionally, no significant genotype-by-diagnosis effects were observed for any of the SNP-gene associations. We contend that this may reflect an inability to effectively capture the modest, neurodevelopmental-specific impact of individual variants on biological dysregulation in available post-mortem tissue samples, as well as limitations in the existing autism GWAS data.
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Affiliation(s)
- Kealan Pugsley
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Atefeh Namipashaki
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
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16
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Zahid A, Eiza NU, Khalid M, Irshad HU, Shabbir MAB, Ali A, Chaudhry TH, Ahmed S, Maan MK, Huang L. Targeting inflammation for the treatment of endometritis in bovines. Microb Pathog 2024; 188:106536. [PMID: 38199446 DOI: 10.1016/j.micpath.2024.106536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
The uterine endometrial surface of bovines is in constant exposureconstantly exposed with to a multitude ofmany microbial populations that changes throughout the post-partum phase in terms of complexity and dynamics. These microbes contribute to the host pathology, leading to severe economic losses along withnd reproductive capabilities. The basic primary interface that occurs between the internal tissues of the body of the hostbetween the host body's internal tissues and the microbes is the endometrial surface of the uterus. As a result of the infinite pathogenic population, there is always a danger for the opportunistic organisms to attack. Therefore, it is paramount that any interactions, especially microbial microbes with the endometrial surface, are regulated by the host cells. However, the inflammatory response as the defense mechanism contributes a pivotal roleis pivotal in host immunity and pathology. The inflammatory cascade and pathways are important essential to eliminate this clinical problem. In this review, we will discuss and explain how the inflammation and the various components of the immune system play their role in host pathology and therapeutic strategies, taking into account the interface between the host and the microbes on the surface of the endometrium. This review is also instrumental in further explanation of inflammatory uterine disease by discussing the response of inflammation to external insult.
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Affiliation(s)
- Ayesha Zahid
- Department of Veterinary Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Noor Ul Eiza
- Department of Veterinary Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muntaha Khalid
- Department of Veterinary Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Hafiz Usman Irshad
- Department of Veterinary Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Abu Bakr Shabbir
- Department of Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ahsan Ali
- Department of Veterinary Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tamoor Hamid Chaudhry
- Public Health Laboratory Division, National Institute of Health, Islamabad, Pakistan
| | - Saeed Ahmed
- Department of Microbiology, National University of Medical Sciences, Islamabad, Pakistan
| | - Muhammad Kashif Maan
- Department of Veterinary Surgery, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues/ MAO Key Laboratory for the Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, PR China.
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17
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Yacca SS, Kanasaki H, Tumurbaatar T, Cairang Z, Oride A, Okada H, Kyo S. Changes in pituitary gonadotropin subunits and hypothalamic Kiss-1 gene expression by administration of sex steroids in ovary-intact female rats. Endocrine 2024; 83:733-746. [PMID: 37966704 DOI: 10.1007/s12020-023-03596-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023]
Abstract
OBJECTIVE We examined how the sex steroids influence the synthesis of gonadotropins. MATERIALS AND METHODS The effects of sex steroids estradiol (E2), progesterone (P4), and dihydrotestosterone (DHT) in pituitary gonadotroph cell model (LβT2 cells) in vitro and ovary-intact rats in vivo were examined. The effects of sex steroids on Kiss1 gene expression in the hypothalamus were also examined in ovary-intact rats. RESULTS In LβT2 cells, E2 increased common glycoprotein alpha (Cga) and luteinizing hormone beta (Lhb) subunit promoter activity as well as their mRNA expression. Although gonadotropin subunit promoter activity was not modulated by P4, Cga and Lhb mRNA expression was increased by P4. DHT inhibited Cga and Lhb mRNA expression with a concomitant decrease in their promoter activity. During the 2-week administration of exogenous E2 to ovary-intact rats, the estrous cycle determined by vaginal smears was disrupted. P4 or DHT administration completely eliminated the estrous cycle. Protein expression of all three gonadotropin subunits within the pituitary gland was inhibited by E2 or P4 treatment in vivo; however, DHT reduced Cga expression but did not modulate Lhb or follicle-stimulating hormone beta subunit expression. E2 administration significantly repressed Kiss1 mRNA expression in a posterior hypothalamic region that included the arcuate nucleus. P4 and DHT did not modulate Kiss1 mRNA expression in this region. In contrast, P4 administration significantly inhibited Kiss1 mRNA expression in the anterior region of the hypothalamus that included the anteroventral periventricular nucleus. The expression of gonadotropin-releasing hormone (Gnrh) mRNA in the anterior hypothalamic region, where the preoptic area is located, appeared to be decreased by treatment with E2 and P4. CONCLUSION Our findings suggest that sex steroids have different effects in the hypothalamus and pituitary gland.
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Affiliation(s)
- Susdiaman S Yacca
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan
| | - Haruhiko Kanasaki
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan.
| | - Tuvshintugs Tumurbaatar
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan
| | - Zhuoma Cairang
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan
| | - Aki Oride
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan
| | - Hiroe Okada
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, 693-8501, Japan
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Chau KM, Dominic A, Davis EL, Kotla S, Berrios ET, Fahim A, Arunesh A, Li S, Zhao D, Chen K, Davis AR, Nguyen MTH, Wang Y, Evans SE, Wang G, Cooke JP, Abe JI, Huston DP, Le NT. TNIK regulation of interferon signaling and endothelial cell response to virus infection. Front Cardiovasc Med 2024; 10:1213428. [PMID: 38264262 PMCID: PMC10803426 DOI: 10.3389/fcvm.2023.1213428] [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: 04/27/2023] [Accepted: 11/27/2023] [Indexed: 01/25/2024] Open
Abstract
Background Traf2 and Nck-interacting kinase (TNIK) is known for its regulatory role in various processes within cancer cells. However, its role within endothelial cells (ECs) has remained relatively unexplored. Methods Leveraging RNA-seq data and Ingenuity Pathway Analysis (IPA), we probed the potential impact of TNIK depletion on ECs. Results Examination of RNA-seq data uncovered more than 450 Differentially Expressed Genes (DEGs) in TNIK-depleted ECs, displaying a fold change exceeding 2 with a false discovery rate (FDR) below 0.05. IPA analysis unveiled that TNIK depletion leads to the inhibition of the interferon (IFN) pathway [-log (p-value) >11], downregulation of IFN-related genes, and inhibition of Hypercytokinemia/Hyperchemokinemia [-log (p-value) >8]. The validation process encompassed qRT-PCR to evaluate mRNA expression of crucial IFN-related genes, immunoblotting to gauge STAT1 and STAT2 protein levels, and ELISA for the quantification of IFN and cytokine secretion in siTNIK-depleted ECs. These assessments consistently revealed substantial reductions upon TNIK depletion. When transducing HUVECs with replication incompetent E1-E4 deleted adenovirus expressing green fluorescent protein (Ad-GFP), it was demonstrated that TNIK depletion did not affect the uptake of Ad-GFP. Nonetheless, TNIK depletion induced cytopathic effects (CPE) in ECs transduced with wild-type human adenovirus serotype 5 (Ad-WT). Summary Our findings suggest that TNIK plays a crucial role in regulating the EC response to virus infections through modulation of the IFN pathway.
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Affiliation(s)
- Khanh M. Chau
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - Abishai Dominic
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
- Department of Molecular and Cellular Medicine, College of Medicine Texas A&M University, College Station, TX, United States
| | - Eleanor L. Davis
- Center for Cell and Gene Therapy, Baylor College of Medicine, College Station, TX, United States
| | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Estefani Turcios Berrios
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - Arsany Fahim
- Center for Cell and Gene Therapy, Baylor College of Medicine, College Station, TX, United States
| | - Ashwin Arunesh
- Center for Cell and Gene Therapy, Baylor College of Medicine, College Station, TX, United States
| | - Shengyu Li
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - Dongyu Zhao
- Department of Molecular and Cellular Medicine, College of Medicine Texas A&M University, College Station, TX, United States
| | - Kaifu Chen
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - Alan R. Davis
- Center for Cell and Gene Therapy, Baylor College of Medicine, College Station, TX, United States
- Department of Cellular and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
- Department of Orthopedic Surgery, Baylor College of Medicine, Houston, TX, United States
| | - Minh T. H. Nguyen
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - Yongxing Wang
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Scott E. Evans
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Guangyu Wang
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - John P. Cooke
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
| | - Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - David P. Huston
- Department of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, College Station, Houston, TX, United States
| | - Nhat-Tu Le
- Department of Cardiovascular Sciences, Center for Cardiovascular Sciences, Academic Institute, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX, United States
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Jang WJ, Lee S, Jeong CH. Uncovering transcriptomic biomarkers for enhanced diagnosis of methamphetamine use disorder: a comprehensive review. Front Psychiatry 2024; 14:1302994. [PMID: 38260797 PMCID: PMC10800441 DOI: 10.3389/fpsyt.2023.1302994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Methamphetamine use disorder (MUD) is a chronic relapsing disorder characterized by compulsive Methamphetamine (MA) use despite its detrimental effects on physical, psychological, and social well-being. The development of MUD is a complex process that involves the interplay of genetic, epigenetic, and environmental factors. The treatment of MUD remains a significant challenge, with no FDA-approved pharmacotherapies currently available. Current diagnostic criteria for MUD rely primarily on self-reporting and behavioral assessments, which have inherent limitations owing to their subjective nature. This lack of objective biomarkers and unidimensional approaches may not fully capture the unique features and consequences of MA addiction. Methods We performed a literature search for this review using the Boolean search in the PubMed database. Results This review explores existing technologies for identifying transcriptomic biomarkers for MUD diagnosis. We examined non-invasive tissues and scrutinized transcriptomic biomarkers relevant to MUD. Additionally, we investigated transcriptomic biomarkers identified for diagnosing, predicting, and monitoring MUD in non-invasive tissues. Discussion Developing and validating non-invasive MUD biomarkers could address these limitations, foster more precise and reliable diagnostic approaches, and ultimately enhance the quality of care for individuals with MA addiction.
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Affiliation(s)
| | | | - Chul-Ho Jeong
- College of Pharmacy, Keimyung University, Daegu, Republic of Korea
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20
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Hammad G, Mamdouh S, Seoudi DM, Seleem MI, Safwat G, Mohamed RH. Elevated expression patterns of P-element Induced Wimpy Testis (PIWI) transcripts are potential candidate markers for Hepatocellular Carcinoma. Cancer Biomark 2024; 39:95-111. [PMID: 38043006 PMCID: PMC11002723 DOI: 10.3233/cbm-230134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/25/2023] [Indexed: 12/04/2023]
Abstract
BACKGROUND P-Element-induced wimpy testis (PIWI) proteins, when in combination with PIWI-interacting RNA (piRNA), are engaged in the epigenetic regulation of gene expression in germline cells. Different types of tumour cells have been found to exhibit abnormal expression of piRNA, PIWIL-mRNAs, and proteins. We aimed to determine the mRNA expression profiles of PIWIL1, PIWIL2, PIWIL3, & PIWIL4, in hepatocellular carcinoma patients, and to associate their expression patterns with clinicopathological features. METHODS The expression patterns of PIWIL1, PIWIL2, PIWIL3, PIWIL4 mRNA, was assessed via real-time quantitative polymerase chain reaction (RT-QPCR), on tissue and serum samples from HCC patients, their impact for diagnosis was evaluated by ROC curves, prognostic utility was determined, and In Silico analysis was conducted for predicted variant detection, association with HCC microRNAs and Network Analysis. RESULTS Expression levels were significantly higher in both HCC tissue and serum samples than in their respective controls (p< 0.001). Additionally, the diagnostic performance was assessed, Risk determination was found to be statistically significant. CONCLUSION PIWIL mRNAs are overexpressed in HCC tissue and serum samples, the expression patterns could be valuable molecular markers for HCC, due to their association with age, tumour grade and pattern. To the best of our knowledge, our study is the first to report the expression levels of all PIWIL mRNA and to suggest their remarkable values as diagnostic and prognostic biomarkers, in addition to their correlation to HCC development. Additionally, a therapeutic opportunity might be also suggested through in silico miRNA prediction for HCC and PIWIL genes through DDX4 and miR-124-3p.
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Affiliation(s)
- Gehan Hammad
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Samah Mamdouh
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Cairo, Egypt
| | - Dina Mohamed Seoudi
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed Ismail Seleem
- Department of Surgery, National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt
| | - Gehan Safwat
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt
| | - Rania Hassan Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
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21
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Meira FS, Ribeiro DG, de Campos SS, Falcão LL, Gomes ACMM, de Alencar Dusi DM, Marcellino LH, Mehta A, Scherwinski-Pereira JE. Differential expression of genes potentially related to the callogenesis and in situ hybridization of SERK gene in macaw palm (Acrocomia aculeata Jacq.) Lodd. ex Mart. PROTOPLASMA 2024; 261:89-101. [PMID: 37482557 DOI: 10.1007/s00709-023-01881-3] [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: 01/05/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
For the purpose of understanding the molecular processes triggered during callus formation in macaw palm, the expression of seven genes potentially involved in this process, identified in previous studies and from the literature, was investigated by RT-qPCR. In addition, in situ hybridization of the SERK gene was performed. Leaf tissues from adult plants from two macaw palm accession were inoculated in a medium combined with Picloram at a concentration of 450 μM to induce callus. The expression analysis was performed from leaf samples from two accessions of different origins (Municipalities of Tiros, MG, and Buriti Vermelho, DF, Brazil), which are characterized as non-responsive (NR) and responsive (R), respectively. The material was collected before callus induction (0 DAI, initial day) and 120 days after callus induction (120 DAI). Genes related to development (SERK, OASA, EF1, ANN1) and stress (LEA, CAT2, and MDAR5) were evaluated. The results obtained showed that all the genes involved with the development had their expressions downregulated at 0 DAI when the accession R was compared with the accession NR. On the other hand, it was possible to observe that these genes were upregulated at 120 DAI. The LEA stress gene showed a tendency to increase expression in the NR accession, while the R accession showed decreased expression and the CAT2 and MDAR5 genes showed upregulation in both accessions. In situ hybridization showed SERK transcripts in the vascular bundles, indicating the expression of SERK in this region, in addition to its expression in calluses. The results obtained in this study support our hypothesis that the regulation of genes involved in the control of oxidative stress and development is crucial for the formation of calluses in macaw palm.
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Affiliation(s)
- Filipe Sathler Meira
- Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Daiane Gonzaga Ribeiro
- Universidade de Brasília, Instituto de Ciências Biológicas, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Samanta Siqueira de Campos
- Universidade Federal do Rio Grande do Sul, Departamento de Horticultura e Silvicultura, Porto Alegre, RS, 91540-000, Brazil
| | - Loeni Ludke Falcão
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
| | | | | | - Lucilia Helena Marcellino
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Brasília, 70770-917, Brazil
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22
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Jiang X, Xie B, Li K, Zhou F. Prolonged Linear Amplification of qPCR for the Correction of Amplification Variation and the Absolute Quantification without Standard Curves. Anal Chem 2023; 95:18451-18459. [PMID: 38063082 DOI: 10.1021/acs.analchem.3c03637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The variable amplification efficiency of each thermal cycle of qPCR obeys the Poisson distribution, and the qPCR system dynamically changes, so there must be a detection error in its quantitative analysis. Here, more than 20 cycles of the linear amplification of qPCR can be produced as the BSA hydrogel is introduced to achieve the controlled release of Taq DNA polymerase. There is a significant negative correlation between the slope of linear amplification and Ct values (r = -0.9455), and it is well evident that the slope can reflect the amplification efficiency and a linear positive correlation exists between them. Through the change in the concentration of primers in the qPCR system, an exponential equation between Ct values and the slopes can be fitted (R2 = 0.9995). The slopes and Ct values of each qPCR system can be corrected by using this equation to guarantee that there will be significant consistency in their amplification efficiency because the degree of linear fitting (R2) between Ct values and the logarithm of their corresponding concentration of the DNA template increased significantly. By this time, the accurate amplification efficiency can be calculated in a known multiple of two initial concentrations of DNA templates. With the aid of the relationship between the known primer concentration and the fluorescence intensity at the end of PCR (End RFU), the initial concentrations of DNA templates can be reversely calculated in the absence of standard curves.
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Affiliation(s)
- Xinglu Jiang
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - BeiBei Xie
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Conservative Dentistry & Endodontics Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Kangjing Li
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Conservative Dentistry & Endodontics Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Fengyuan Zhou
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
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23
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Jang H, Song J, Kim S, Byun JH, Lee KG, Park KH, Woo E, Lim EK, Jung J, Kang T. ANCA: artificial nucleic acid circuit with argonaute protein for one-step isothermal detection of antibiotic-resistant bacteria. Nat Commun 2023; 14:8033. [PMID: 38052830 DOI: 10.1038/s41467-023-43899-4] [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: 06/15/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Endonucleases have recently widely used in molecular diagnostics. Here, we report a strategy to exploit the properties of Argonaute (Ago) proteins for molecular diagnostics by introducing an artificial nucleic acid circuit with Ago protein (ANCA) method. The ANCA is designed to perform a continuous autocatalytic reaction through cross-catalytic cleavage of the Ago protein, enabling one-step, amplification-free, and isothermal DNA detection. Using the ANCA method, carbapenemase-producing Klebsiella pneumoniae (CPKP) are successfully detected without DNA extraction and amplification steps. In addition, we demonstrate the detection of carbapenem-resistant bacteria in human urine and blood samples using the method. We also demonstrate the direct identification of CPKP swabbed from surfaces using the ANCA method in conjunction with a three-dimensional nanopillar structure. Finally, the ANCA method is applied to detect CPKP in rectal swab specimens from infected patients, achieving sensitivity and specificity of 100% and 100%, respectively. The developed method can contribute to simple, rapid and accurate diagnosis of CPKP, which can help prevent nosocomial infections.
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Affiliation(s)
- Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 175 Cambridge Street, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA, 02114, USA
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kwang-Hyun Park
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Euijeon Woo
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea.
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Hasterok S, Scott TG, Roller DG, Spencer A, Dutta AB, Sathyan KM, Frigo DE, Guertin MJ, Gioeli D. The Androgen Receptor Does Not Directly Regulate the Transcription of DNA Damage Response Genes. Mol Cancer Res 2023; 21:1329-1341. [PMID: 37698543 PMCID: PMC11022999 DOI: 10.1158/1541-7786.mcr-23-0358] [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: 05/14/2023] [Revised: 08/02/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
The clinical success of combined androgen deprivation therapy (ADT) and radiotherapy (RT) in prostate cancer created interest in understanding the mechanistic links between androgen receptor (AR) signaling and the DNA damage response (DDR). Convergent data have led to a model where AR both regulates, and is regulated by, the DDR. Integral to this model is that the AR regulates the transcription of DDR genes both at a steady state and in response to ionizing radiation (IR). In this study, we sought to determine which immediate transcriptional changes are induced by IR in an AR-dependent manner. Using PRO-seq to quantify changes in nascent RNA transcription in response to IR, the AR antagonist enzalutamide, or the combination of the two, we find that enzalutamide treatment significantly decreased expression of canonical AR target genes but had no effect on DDR gene sets in prostate cancer cells. Surprisingly, we also found that the AR is not a primary regulator of DDR genes either in response to IR or at a steady state in asynchronously growing prostate cancer cells. IMPLICATIONS Our data indicate that the clinical benefit of combining ADT with RT is not due to direct AR regulation of DDR gene transcription, and that the field needs to consider alternative mechanisms for this clinical benefit.
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Affiliation(s)
- Sylwia Hasterok
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Thomas G. Scott
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Devin G. Roller
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Adam Spencer
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Arun B. Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Kizhakke M Sathyan
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut 06030, USA
| | - Daniel E. Frigo
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Michael J. Guertin
- R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut, Farmington, Connecticut 06030, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut 06030, USA
| | - Daniel Gioeli
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
- Cancer Center Member, University of Virginia, Charlottesville, Virginia, USA
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Jongejan YK, Schrader Echeverri E, Dirven RJ, Paunovska K, Linthorst NA, de Jong A, Wellershoff JC, van der Gouw KD, van Vlijmen BJM, Dahlman JE, Eikenboom JCJ. Small interfering RNA-mediated allele-selective silencing of von Willebrand factor in vitro and in vivo. Blood Adv 2023; 7:6108-6119. [PMID: 37467023 PMCID: PMC10582391 DOI: 10.1182/bloodadvances.2023010643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
An imbalance in von Willebrand factor (VWF) may either lead to bleeding (von Willebrand disease, VWD) or thrombosis. Both disorders have shortcomings in the currently available treatments. VWF itself could be a potential therapeutic target because of its role in both bleeding and thrombosis. Inhibiting VWF gene expression through allele-selective silencing of VWF with small interfering RNAs (siRNAs) could be a personalized approach to specifically inhibit mutant VWF in VWD or to normalize increased VWF levels in thrombotic disorders without complete VWF knockdown. Therefore, we investigated a method to allele-selectively silence the VWF gene in mice as a therapeutic strategy. Fourteen candidate siRNAs targeting murine Vwf of either the C57BL/6J (B6) or the 129S1/SvImJ (129S) strain were tested in vitro in cells expressing B6- and 129S-Vwf for inhibitory effect and allele-selective potential. Together with a nonselective siVwf, 2 lead candidate siRNAs, siVwf.B6 and siVwf.129S, were further tested in vivo in B6 and 129S mice. Efficient endothelial siRNA delivery was achieved by siRNA encapsulation into 7C1 oligomeric lipid nanoparticles. Treatment with the nonselective siVwf resulted in dose-dependent inhibition of up to 80% of both lung messenger RNA and plasma VWF protein in both mouse strains. In contrast, the allele-selective siVwf.B6 and siVwf.129S were shown to be effective in and selective solely for their corresponding mouse strain. To conclude, we showed efficient endothelial delivery of siRNAs that are highly effective in allele-selective inhibition of Vwf in mice, which constitutes an in vivo proof of principle of allele-selective VWF silencing as a therapeutic approach.
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Affiliation(s)
- Yvonne K. Jongejan
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisa Schrader Echeverri
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA
| | - Richard J. Dirven
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Kalina Paunovska
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA
| | - Noa A. Linthorst
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Annika de Jong
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Johannes C. Wellershoff
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim D. van der Gouw
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Bart J. M. van Vlijmen
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - James E. Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA
| | - Jeroen C. J. Eikenboom
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
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Ye M, Liu C, Li N, Yuan C, Liu M, Xin Z, Lei S, Sun X. A constitutive serine protease inhibitor suppresses herbivore performance in tea ( Camellia sinensis). HORTICULTURE RESEARCH 2023; 10:uhad178. [PMID: 37868619 PMCID: PMC10585712 DOI: 10.1093/hr/uhad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/25/2023] [Indexed: 10/24/2023]
Abstract
Protease inhibitors promote herbivore resistance in diverse plant species. Although many inducible protease inhibitors have been identified, there are limited reports available on the biological relevance and molecular basis of constitutive protease inhibitors in herbivore resistance. Here, we identified a serine protease inhibitor, CsSERPIN1, from the tea plant (Camellia sinensis). Expression of CsSERPIN1 was not strongly affected by the assessed biotic and abiotic stresses. In vitro and in vivo experiments showed that CsSERPIN1 strongly inhibited the activities of digestive protease activities of trypsin and chymotrypsin. Transient or heterologous expression of CsSERPIN1 significantly reduced herbivory by two destructive herbivores, the tea geometrid and fall armyworm, in tea and Arabidopsis plants, respectively. The expression of CsSERPIN1 in Arabidopsis did not negatively influence the growth of the plants under the measured parameters. Our findings suggest that CsSERPIN1 can inactivate gut digestive proteases and suppress the growth and development of herbivores, making it a promising candidate for pest prevention in agriculture.
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Affiliation(s)
- Meng Ye
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Chuande Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Nana Li
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Chenhong Yuan
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Miaomiao Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Zhaojun Xin
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Shu Lei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Xiaoling Sun
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
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Tokamani M, Figgou E, Papamichail L, Sakka E, Toros A, Bouchorikou A, Giannakakis A, Matthaiou EI, Sandaltzopoulos R. A Multiplex PCR Melting-Curve-Analysis-Based Detection Method for the Discrimination of Five Aspergillus Species. J Fungi (Basel) 2023; 9:842. [PMID: 37623613 PMCID: PMC10455196 DOI: 10.3390/jof9080842] [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: 06/17/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Aspergillus mold is a ubiquitously found, airborne pathogen that can cause a variety of diseases from mild to life-threatening in severity. Limitations in diagnostic methods combined with anti-fungal resistance render Aspergillus a global emerging pathogen. In industry, Aspergilli produce toxins, such as aflatoxins, which can cause food spoilage and pose public health risk issues. Here, we report a multiplex qPCR method for the detection and identification of the five most common pathogenic Aspergillus species, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, and Aspergillus nidulans. Our approach exploits species-specific nucleotide polymorphisms within their ITS genomic regions. This novel assay combines multiplex single-color real time qPCR and melting curve analysis and provides a straight-forward, rapid, and cost-effective detection method that can identify five Aspergillus species simultaneously in a single reaction using only six unlabeled primers. Due to their unique fragment lengths, the resulting amplicons are directly linked to certain Aspergillus species like fingerprints, following either electrophoresis or melting curve analysis. Our method is characterized by high analytical sensitivity and specificity, so it may serve as a useful and inexpensive tool for Aspergillus diagnostic applications both in health care and the food industry.
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Affiliation(s)
- Maria Tokamani
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleftheria Figgou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Lito Papamichail
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleni Sakka
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Athanasios Toros
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Anastasia Bouchorikou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Efthymia Iliana Matthaiou
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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Mesalam NM, Ibrahim MA, Mousa MR, Said NM. Selenium and vitamin E ameliorate lead acetate-induced hepatotoxicity in rats via suppression of oxidative stress, mRNA of heat shock proteins, and NF-kB production. J Trace Elem Med Biol 2023; 79:127256. [PMID: 37442019 DOI: 10.1016/j.jtemb.2023.127256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/06/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND Lead exposure results in a terrible rise in heat shock protein levels. OBJECTIVE This research was conducted to look at the effects of lead poisoning on heat shock response, oxidative stress, and inflammatory markers in albino rats, as well as the power of selenium and vitamin E to resist lead toxic effects. METHODS Eight groups of albino rats are used. Each group contained six rats where the first group represented the negative control, and the other groups were treated with olive oil, vitamin E, selenium, lead, (vitamin E + lead), (selenium + lead), and (vitamin E + selenium + lead). All the treatments lasted for 28 days. Then, the mRNA expression of interested heat shock proteins (HSP90, HSP70, and HSP60) was assessed. For oxidative stress disruption, we investigated nitric oxide (NO) and malondialdehyde (MDA) content, and enzymatic and non-enzymatic antioxidants activity respectively in rat livers. RESULTS our results revealed the synergetic protective effect of the combination of two antioxidants (vitamin E and selenium) against lead poising. This was clear in regulating HSPs expression, inflammatory markers, glucose, lipid profile, liver functions, and antioxidant enzymes more than the treatment with one antioxidant. CONCLUSION Pb is a toxic material that can induce HSPs and inflammatory markers expression. Selenium and vitamin E can give excellent effects in ameliorating Pb toxicity when used together.
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Affiliation(s)
- Noura M Mesalam
- Biological Application Department, Nuclear Research Center, Egyptian Atomic Energy Authority, 13759 Cairo, Egypt
| | - Marwa A Ibrahim
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Mohamed R Mousa
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Noha Mohamed Said
- Biochemistry Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
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Abe JI, Imanishi M, Li S, Zhang A, Ae Ko K, Samanthapudi VSK, Lee LL, Bojorges AP, Gi YJ, Hobbs BP, Deswal A, Herrmann J, Lin SH, Chini EN, Shen YH, Schadler KL, Nguyen THM, Gupte AA, Reyes-Gibby C, Yeung SCJ, Abe RJ, Olmsted-Davis EA, Krishnan S, Dantzer R, Palaskas NL, Cooke JP, Pownall HJ, Yoshimoto M, Fujiwara K, Hamilton DJ, Burks JK, Wang G, Le NT, Kotla S. An ERK5-NRF2 Axis Mediates Senescence-Associated Stemness and Atherosclerosis. Circ Res 2023; 133:25-44. [PMID: 37264926 PMCID: PMC10357365 DOI: 10.1161/circresaha.122.322017] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND ERK5 (extracellular signal-regulated kinase 5) is a dual kinase transcription factor containing an N-terminal kinase domain and a C-terminal transcriptional activation domain. Many ERK5 kinase inhibitors have been developed and tested to treat cancer and inflammatory diseases. However, recent data have raised questions about the role of the catalytic activity of ERK5 in proliferation and inflammation. We aimed to investigate how ERK5 reprograms myeloid cells to the proinflammatory senescent phenotype, subsequently leading to atherosclerosis. METHODS A ERK5 S496A (dephosphorylation mimic) knock in (KI) mouse model was generated using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9), and atherosclerosis was characterized by hypercholesterolemia induction. The plaque phenotyping in homozygous ERK5 S496A KI and wild type (WT) mice was studied using imaging mass cytometry. Bone marrow-derived macrophages were isolated from hypercholesterolemic mice and characterized using RNA sequencing and functional in vitro approaches, including senescence, mitochondria reactive oxygen species, and inflammation assays, as well as by metabolic extracellular flux analysis. RESULTS We show that atherosclerosis was inhibited in ERK5 S496A KI mice. Furthermore, ERK5 S496 phosphorylation mediates both senescence-associated secretory phenotype and senescence-associated stemness by upregulating AHR (aryl hydrocarbon receptor) in plaque and bone marrow-derived macrophages isolated from hypercholesterolemic mice. We also discovered that ERK5 S496 phosphorylation could induce NRF2 (NFE2-related factor 2) SUMOylation at a novel K518 site to inhibit NRF2 transcriptional activity without altering ERK5 catalytic activity and mediates oxidized LDL (low-density lipoprotein)-induced senescence-associated secretory phenotype. Specific ERK5 kinase inhibitors (AX15836 and XMD8-92) also inhibited ERK5 S496 phosphorylation, suggesting the involvement of ERK5 S496 phosphorylation in the anti-inflammatory effects of these ERK5 kinase inhibitors. CONCLUSIONS We discovered a novel mechanism by which the macrophage ERK5-NRF2 axis develops a unique senescence-associated secretory phenotype/stemness phenotype by upregulating AHR to engender atherogenesis. The finding of senescence-associated stemness phenotype provides a molecular explanation to resolve the paradox of senescence in proliferative plaque by permitting myeloid cells to escape the senescence-induced cell cycle arrest during atherosclerosis formation.
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Affiliation(s)
- Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors contributed equally to this work and were designated as co-first authors
| | - Masaki Imanishi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors contributed equally to this work and were designated as co-first authors
| | - Shengyu Li
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- These authors contributed equally to this work and were designated as co-first authors
| | - Aijun Zhang
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Ling-Ling Lee
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Young Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brian P. Hobbs
- Department of Population Health, The University of Texas at Austin, Austin, Texas, USA
| | - Anita Deswal
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joerg Herrmann
- Cardio Oncology Clinic, Division of Preventive Cardiology, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Steven H. Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Eduardo N. Chini
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Ying H. Shen
- Division of Cardiothoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Keri L. Schadler
- Department of Pediatric Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Thi-Hong-Minh Nguyen
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Anisha A. Gupte
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
| | - Cielito Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sai-Ching J. Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rei J. Abe
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | | | - Sunil Krishnan
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Robert Dantzer
- Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicolas L. Palaskas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John P. Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Henry J. Pownall
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
| | - Momoko Yoshimoto
- Center for Stem Cell & Regenerative Medicine, Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Keigi Fujiwara
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dale J. Hamilton
- Center for Bioenergetics, Houston Methodist Research Institute, Texas, and Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, Texas, USA
- These authors contributed equally to this work
| | - Jared K. Burks
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors contributed equally to this work
| | - Guangyu Wang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- These authors were equivalent co-senior authors
| | - Nhat-Tu Le
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- These authors were equivalent co-senior authors
| | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- These authors were equivalent co-senior authors
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Liu D, Jiang L, Chen J, Chen Z, Yuan C, Lin D, Huang M. Monomer and Oligomer Transition of Zinc Phthalocyanine Is Key for Photobleaching in Photodynamic Therapy. Molecules 2023; 28:4639. [PMID: 37375194 PMCID: PMC10305241 DOI: 10.3390/molecules28124639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Photodynamic therapy (PDT) is recognized as a powerful method to inactivate cells. However, the photosensitizer (PS), a key component of PDT, has suffered from undesired photobleaching. Photobleaching reduces reactive oxygen species (ROS) yields, leading to the compromise of and even the loss of the photodynamic effect of the PS. Therefore, much effort has been devoted to minimizing photobleaching in order to ensure that there is no loss of photodynamic efficacy. Here, we report that a type of PS aggregate showed neither photobleaching nor photodynamic action. Upon direct contact with bacteria, the PS aggregate was found to fall apart into PS monomers and thus possessed photodynamic inactivation against bacteria. Interestingly, the disassembly of the bound PS aggregate in the presence of bacteria was intensified by illumination, generating more PS monomers and leading to an enhanced antibacterial photodynamic effect. This demonstrated that on a bacterial surface, the PS aggregate photo-inactivated bacteria via PS monomer during irradiation, where the photodynamic efficiency was retained without photobleaching. Further mechanistic studies showed that PS monomers disrupted bacterial membranes and affected the expression of genes related to cell wall synthesis, bacterial membrane integrity, and oxidative stress. The results obtained here are applicable to other types of PSs in PDT.
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Affiliation(s)
- Dafeng Liu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Jincan Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Cai Yuan
- College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou 350002, China
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Ellur V, Wei W, Ghogare R, Solanki S, Vandemark G, Brueggeman R, Chen W. Unraveling the genomic reorganization of polygalacturonase-inhibiting proteins in chickpea. Front Genet 2023; 14:1189329. [PMID: 37342773 PMCID: PMC10278945 DOI: 10.3389/fgene.2023.1189329] [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: 03/19/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Polygalacturonase-inhibiting proteins (PGIPs) are cell wall proteins that inhibit pathogen polygalacturonases (PGs). PGIPs, like other defense-related proteins, contain extracellular leucine-rich repeats (eLRRs), which are required for pathogen PG recognition. The importance of these PGIPs in plant defense has been well documented. This study focuses on chickpea (Cicer arietinum) PGIPs (CaPGIPs) owing to the limited information available on this important crop. This study identified two novel CaPGIPs (CaPGIP3 and CaPGIP4) and computationally characterized all four CaPGIPs in the gene family, including the previously reported CaPGIP1 and CaPGIP2. The findings suggest that CaPGIP1, CaPGIP3, and CaPGIP4 proteins possess N-terminal signal peptides, ten LRRs, theoretical molecular mass, and isoelectric points comparable to other legume PGIPs. Phylogenetic analysis and multiple sequence alignment revealed that the CaPGIP1, CaPGIP3, and CaPGIP4 amino acid sequences are similar to the other PGIPs reported in legumes. In addition, several cis-acting elements that are typical of pathogen response, tissue-specific activity, hormone response, and abiotic stress-related are present in the promoters of CaPGIP1, CaPGIP3, and CaPGIP4 genes. Localization experiments showed that CaPGIP1, CaPGIP3, and CaPGIP4 are located in the cell wall or membrane. Transcript levels of CaPGIP1, CaPGIP3, and CaPGIP4 genes analyzed at untreated conditions show varied expression patterns analogous to other defense-related gene families. Interestingly, CaPGIP2 lacked a signal peptide, more than half of the LRRs, and other characteristics of a typical PGIP and subcellular localization indicated it is not located in the cell wall or membrane. The study's findings demonstrate CaPGIP1, CaPGIP3, and CaPGIP4's similarity to other legume PGIPs and suggest they might possess the potential to combat chickpea pathogens.
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Affiliation(s)
- Vishnutej Ellur
- Molecular Plant Science, Washington State University, Pullman, WA, United States
| | - Wei Wei
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Rishikesh Ghogare
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Shyam Solanki
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - George Vandemark
- Grain Legume Genetics Physiology Research, Pullman, WA, United States
| | - Robert Brueggeman
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Weidong Chen
- Grain Legume Genetics Physiology Research, Pullman, WA, United States
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Martínez-Iglesias O, Naidoo V, Corzo L, Carrera I, Seoane S, Rodríguez S, Alcaraz M, Muñiz A, Cacabelos N, Cacabelos R. Proteomic and Global DNA Methylation Modulation in Lipid Metabolism Disorders with a Marine-Derived Bioproduct. BIOLOGY 2023; 12:806. [PMID: 37372091 DOI: 10.3390/biology12060806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
Dyslipidemia is a significant risk factor for cardiovascular disease and stroke. Our recent findings showed that RCI-1502, a bioproduct derived from the muscle of the European S. pilchardus, has lipid-lowering effects in the liver and heart in high-fat diet (HFD) fed mice. In the present follow-up study, we investigated the therapeutic potential of RCI-1502 on gene expression and DNA methylation in HFD-fed mice and in patients with dyslipidemia. Using LC-MS/MS, we identified 75 proteins in RCI-1502 that are primarily involved in binding and catalytic activity and which regulate pathways implicated in cardiovascular diseases. In HFD-fed mice, RCI-1502 treatment significantly reduced the expression of cardiovascular disease-related genes, including vascular cell adhesion molecule and angiotensin. RCI-1502 also decreased DNA methylation levels, which were elevated in HFD-fed mice, to levels similar to those in control animals. Furthermore, peripheral blood leukocyte DNA from dyslipidemic patients exhibited higher DNA methylation levels than healthy individuals, suggesting a potential association with cardiovascular risk. Serum analysis also revealed that RCI-1502 treatment regulated cholesterol and triglyceride levels in patients with dyslipidemia. Our findings appear to suggest that RCI-1502 is an epigenetic modulator for the treatment of cardiovascular diseases, specifically in individuals with dyslipidemia.
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Affiliation(s)
- Olaia Martínez-Iglesias
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Vinogran Naidoo
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Lola Corzo
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Iván Carrera
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Silvia Seoane
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Susana Rodríguez
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Margarita Alcaraz
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Adriana Muñiz
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Natalia Cacabelos
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
| | - Ramón Cacabelos
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
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Ko B, Van Raamsdonk JM. RNA Sequencing of Pooled Samples Effectively Identifies Differentially Expressed Genes. BIOLOGY 2023; 12:812. [PMID: 37372097 DOI: 10.3390/biology12060812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
Analysis of gene expression changes across the genome provides a powerful, unbiased tool for gaining insight into molecular mechanisms. We have effectively used RNA sequencing to identify differentially expressed genes in long-lived genetic mutants in C. elegans to advance our understanding of the genetic pathways that control longevity. Although RNA sequencing costs have come down, cost remains a barrier to examining multiple strains and time points with a sufficient number of biological replicates. To circumvent this, we have examined the efficacy of identifying differentially expressed genes by sequencing a pooled RNA sample from long-lived isp-1 mitochondrial mutant worms. We found that sequencing a pooled RNA sample could effectively identify genes that were found to be significantly upregulated in the two individually sequenced RNA-seq experiments. Finally, we compared the genes significantly upregulated in the two individually sequenced RNA-seq experiments to two previous microarray experiments to come up with a high-confidence list of modulated genes in long-lived isp-1 mutant worms. Overall, this work demonstrates that RNA sequencing of pooled RNA samples can be used to identify differentially expressed genes.
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Affiliation(s)
- Bokang Ko
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada
- Metabolic Disorders and Complications Program (MeDiC), Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Jeremy M Van Raamsdonk
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada
- Metabolic Disorders and Complications Program (MeDiC), Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Brain Repair and Integrative Neuroscience Program (BRaIN), Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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Yu B, Xu C, Huang S, Ni J, Zhou J, Zhang Y, Wu M, Zhang J, Fang L. Development of a universal real-time RT-PCR assay for detection of pan-SARS-coronaviruses with an RNA-based internal control. Front Microbiol 2023; 14:1181097. [PMID: 37275136 PMCID: PMC10232947 DOI: 10.3389/fmicb.2023.1181097] [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: 03/07/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
The current pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for rapid diagnostic assays to prompt intensified virological monitoring both in human and wild animal populations. To date, there are no clinical validated assays for pan-SARS-coronavirus (pan-SARS-CoV) detection. Here, we suggest an innovative primer design strategy for the diagnosis of pan-SARS-CoVs targeting the envelope (E) gene using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Furthermore, we developed a new primer-probe set targeting human β2-microglobulin (B2M) as an RNA-based internal control for process efficacy. The universal RT-qPCR assay demonstrated no false-positive amplifications with other human coronaviruses or 20 common respiratory viruses, and its limit of detection (LOD) was 159.16 copies/ml at 95% detection probability. In clinical validation, the assay delivered 100% sensitive results in the detection of SARS-CoV-2-positive oropharyngeal samples (n = 120), including three variants of concern (Wuhan, Delta, and Omicron). Taken together, this universal RT-qPCR assay provides a highly sensitive, robust, and rapid detection of SARS-CoV-1, SARS-CoV-2, and animal-derived SARS-related CoVs.
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Affiliation(s)
- Beibei Yu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Changping Xu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Shiwang Huang
- Shangcheng District Center for Disease Control and Prevention, Hangzhou, China
| | - Jun Ni
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yuting Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Maomao Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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Moller E, Britt M, Schams A, Cetuk H, Anishkin A, Sukharev S. Mechanosensitive channel MscS is critical for termination of the bacterial hypoosmotic permeability response. J Gen Physiol 2023; 155:e202213168. [PMID: 37022337 PMCID: PMC10082366 DOI: 10.1085/jgp.202213168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/06/2023] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
Free-living microorganisms are subjected to drastic changes in osmolarity. To avoid lysis under sudden osmotic down-shock, bacteria quickly expel small metabolites through the tension-activated channels MscL, MscS, and MscK. We examined five chromosomal knockout strains, ∆mscL, ∆mscS, a double knockout ∆mscS ∆mscK, and a triple knockout ∆mscL ∆mscS ∆mscK, in comparison to the wild-type parental strain. Stopped-flow experiments confirmed that both MscS and MscL mediate fast osmolyte release and curb cell swelling, but osmotic viability assays indicated that they are not equivalent. MscS alone was capable of rescuing the cell population, but in some strains, MscL did not rescue and additionally became toxic in the absence of both MscS and MscK. Furthermore, MscS was upregulated in the ∆mscL strain, suggesting either a crosstalk between the two genes/proteins or the influence of cell mechanics on mscS expression. The data shows that for the proper termination of the permeability response, the high-threshold (MscL) and the low-threshold (MscS/MscK) channels must act sequentially. In the absence of low-threshold channels, at the end of the release phase, MscL should stabilize membrane tension at around 10 mN/m. Patch-clamp protocols emulating the tension changes during the release phase indicated that the non-inactivating MscL, residing at its own tension threshold, flickers and produces a protracted leakage. The MscS/MscK population, when present, stays open at this stage to reduce tension below the MscL threshold and silence the large channel. When MscS reaches its own threshold, it inactivates and thus ensures proper termination of the hypoosmotic permeability response. This functional interplay between the high- and low-threshold channels is further supported by the compromised osmotic survival of bacteria expressing non-inactivating MscS mutants.
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Affiliation(s)
- Elissa Moller
- Department of Biology, University of Maryland, College Park, College Park, MD, USA
- Biophysics Graduate Program, University of Maryland, College Park, College Park, MD, USA
| | - Madolyn Britt
- Department of Biology, University of Maryland, College Park, College Park, MD, USA
- Biophysics Graduate Program, University of Maryland, College Park, College Park, MD, USA
| | - Anthony Schams
- Department of Biology, University of Maryland, College Park, College Park, MD, USA
| | - Hannah Cetuk
- Department of Biology, University of Maryland, College Park, College Park, MD, USA
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, College Park, MD, USA
| | - Sergei Sukharev
- Department of Biology, University of Maryland, College Park, College Park, MD, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, College Park, MD, USA
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Chauhan K, Kim DM, Cho E, Kim DE. Facilitation of Dye-Based Quantitative Real-Time Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1348. [PMID: 37110934 PMCID: PMC10144433 DOI: 10.3390/nano13081348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is an important and extensively utilized technique in medical and biotechnological applications. qPCR enables the real-time detection of nucleic acid during amplification, thus surpassing the necessity of post-amplification gel electrophoresis for amplicon detection. Despite being widely employed in molecular diagnostics, qPCR exhibits limitations attributed to nonspecific DNA amplification that compromises the efficiency and fidelity of qPCR. Herein, we demonstrate that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the efficiency and specificity of qPCR by adsorbing single-stranded DNA (ssDNA) without affecting the fluorescence of double-stranded DNA binding dye during DNA amplification. PEG-nGO adsorbs surplus ssDNA primers in the initial phase of PCR, having lower concentrations of DNA amplicons and thus minimizing the nonspecific annealing of ssDNA and false amplification due to primer dimerization and erroneous priming. As compared to conventional qPCR, the addition of PEG-nGO and the DNA binding dye, EvaGreen, in the qPCR setup (dubbed as PENGO-qPCR) significantly enhances the specificity and sensitivity of DNA amplification by preferential adsorption of ssDNA without inhibiting DNA polymerase activity. The PENGO-qPCR system for detection of influenza viral RNA exhibited a 67-fold higher sensitivity than the conventional qPCR setup. Thus, the performance of a qPCR can be greatly enhanced by adding PEG-nGO as a PCR enhancer as well as EvaGreen as a DNA binding dye to the qPCR mixture, which exhibits a significantly improved sensitivity of the qPCR.
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Fernandes-Braga W, Aguilar EC, Navia-Pelaez JM, Ávila DL, Rezende L, Andrade LDO, Miranda SEM, Barros ALBD, Capettini LDSA, Alvarez-Leite JI. The atheroprotective role of fucoidan involves the reduction of foam cell formation by altering cholesterol flux-associated factors in macrophages. Biochem Biophys Res Commun 2023; 650:21-29. [PMID: 36764209 DOI: 10.1016/j.bbrc.2023.01.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/02/2023]
Abstract
Atherosclerosis is characterized by the accumulation of lipid-laden cells in the arterial walls, resulting from dysregulation of cholesterol homeostasis in the macrophage, triggered by oxidized low-density lipoprotein (oxLDL). Previous studies have shown that fucoidan, a sulfated polysaccharide from brown seaweeds, has several atheroprotective activities, however, the mechanism of fucoidan protection is not fully understood. Thus, we investigated the effect of fucoidan on atherogenesis in apolipoprotein E-deficient (ApoE-/-) mice, on oxLDL uptake by macrophages, and on the expression of the flux-associated scavenger receptors by macrophages. Also, we examined the absorption and biodistribution of orally administered fucoidan. ApoE-/- mice fed on a cholesterol-rich diet supplemented with 1% fucoidan showed reduced dyslipidemia and atherosclerosis. Fucoidan was detected in blood and peripheral tissue after gavage, suggesting that it can exert direct systemic effects. In vitro, fucoidan reduced macrophage oxLDL uptake, which resulted in lower foam cell formation. This effect was associated with downregulation of the cholesterol influx-associated scavenger receptor (SR)-A expression, and upregulation of the cholesterol efflux-associated SR-B1 expression. In conclusion, fucoidan prevented oxLDL-mediated foam cell formation in macrophages by downregulating SR-A1/2 and by up-regulating SR-B1.
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Affiliation(s)
- Weslley Fernandes-Braga
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Edenil Costa Aguilar
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | | | - Danielle Lima Ávila
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Luisa Rezende
- Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | | | | | - Andre Luis Branco de Barros
- Department of Clinical and Toxicological Analysis, Federal University of Minas Gerais, Belo Horizonte, Brazil.
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Zhou L, Liu L, Chang MA, Ma C, Chen W, Chen P. Spatiotemporal dissection of tumor microenvironment via in situ sensing and monitoring in tumor-on-a-chip. Biosens Bioelectron 2023; 225:115064. [PMID: 36680970 PMCID: PMC9918721 DOI: 10.1016/j.bios.2023.115064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Real-time monitoring in the tumor microenvironment provides critical insights of cancer progression and mechanistic understanding of responses to cancer treatments. However, clinical challenges and significant questions remain regarding assessment of limited clinical tissue samples, establishment of validated, controllable pre-clinical cancer models, monitoring of static versus dynamic markers, and the translation of insights gained from in vitro tumor microenvironments to systematic investigation and understanding in clinical practice. State-of-art tumor-on-a-chip strategies will be reviewed herein, and emerging real-time sensing and monitoring platforms for on-chip analysis of tumor microenvironment will also be examined. The integration of the sensors with tumor-on-a-chip platforms to provide spatiotemporal information of the tumor microenvironment and the associated challenges will be further evaluated. Though optimal integrated systems for in situ monitoring are still in evolution, great promises lie ahead that will open new paradigm for rapid, comprehensive analysis of cancer development and assist clinicians with powerful tools to guide the diagnosis, prognosis and treatment course in cancer.
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Affiliation(s)
- Lang Zhou
- Materials Engineering, Department of Mechanical Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Lunan Liu
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY, 11201, USA; Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Muammar Ali Chang
- Materials Engineering, Department of Mechanical Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY, 11201, USA; Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, Brooklyn, NY, 11201, USA; Department of Biomedical Engineering, New York University, Brooklyn, NY, 11201, USA
| | - Pengyu Chen
- Materials Engineering, Department of Mechanical Engineering, Auburn University, Auburn, AL, 36849, USA.
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Bhat IA, Dubiel MM, Rodriguez E, Jónsson ZO. Insights into Early Ontogenesis of Salmo salar: RNA Extraction, Housekeeping Gene Validation and Transcriptional Expression of Important Primordial Germ Cell and Sex-Determination Genes. Animals (Basel) 2023; 13:ani13061094. [PMID: 36978635 PMCID: PMC10044239 DOI: 10.3390/ani13061094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The challenge in extracting high-quality RNA impedes the investigation of the transcriptome of developing salmonid embryos. Furthermore, the mRNA expression pattern of important PGC and SD genes during the initial embryonic development of Salmo salar is yet to be studied. So, in the present study, we aimed to isolate high-quality RNA from eggs and developing embryos to check vasa, dnd1, nanos3a, sdf1, gsdf, amh, cyp19a, dmrt1 and foxl2 expression by qPCR. Additionally, four HKGs (GAPDH, UB2L3, eEf1a and β-actin) were validated to select the best internal control for qPCR. High-quality RNA was extracted, which was confirmed by spectrophotometer, agarose gel electrophoresis and Agilent TapeStation analysis. UB2L3 was chosen as a reference gene because it exhibited lower intra- and inter-sample variation. vasa transcripts were expressed in all the developmental stages, while dnd1 was expressed only up to 40 d°C. Nanos3a was expressed in later stages and remained at its peak for a shorter period, while sdf1 showed an irregular pattern of mRNA expression. The mRNA expression levels of SD genes were observed to be upregulated during the later stages of development, prior to hatching. This study presents a straightforward methodology for isolating high-quality RNA from salmon eggs, and the resulting transcript profiles of significant PGC and SD genes in S. salar could aid in improving our comprehension of reproductive development in this commercially important species.
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Affiliation(s)
- Irfan Ahmad Bhat
- Institute of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavik, Iceland
| | - Milena Malgorzata Dubiel
- Institute of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavik, Iceland
| | | | - Zophonías Oddur Jónsson
- Institute of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavik, Iceland
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Kim S, Yoon J, Lee K, Kim Y. Analysis of mitochondrial double-stranded RNAs in human cells. STAR Protoc 2023; 4:102007. [PMID: 36853732 PMCID: PMC9850877 DOI: 10.1016/j.xpro.2022.102007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 02/08/2022] [Indexed: 01/20/2023] Open
Abstract
Human mitochondrial genome is transcribed bidirectionally, generating long complementary RNAs that can form double-stranded RNAs (mt-dsRNAs). When released to the cytosol, these mt-dsRNAs can activate antiviral signaling. Here, we present a detailed protocol for the analysis of mt-dsRNA expression. The protocol provides three approaches that can complement one another in examining mt-dsRNAs. While the described protocol is optimized for human cells, this approach can be adapted for use in other animal cell lines and tissue samples. For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).1.
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Affiliation(s)
- Sujin Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Jimin Yoon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Republic of Korea; KAIST Institute for BioCentury, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea.
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Tumurbaatar T, Kanasaki H, Yacca SS, Cairang Z, Tumurgan Z, Oride A, Okada H, Kyo S. Kisspeptin induces Kiss-1 and GnRH gene expression in mHypoA-55 hypothalamic cell models: Involvement of the ERK and PKA signaling pathways. Gen Comp Endocrinol 2023; 337:114260. [PMID: 36933747 DOI: 10.1016/j.ygcen.2023.114260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/06/2023] [Accepted: 03/05/2023] [Indexed: 03/18/2023]
Abstract
mHypoA-55 cells are kisspeptin-expressing neuronal cells originating from the arcuate nucleus of the mouse hypothalamus. These cells are called KNDy neurons because they co-express kisspeptin, neurokinin B, and dynorphin A. In addition, they express gonadotropin-releasing hormone (GnRH). Here, we found that kisspeptin 10 (KP10) increased Kiss-1 (encoding kisspeptin) and GnRH gene expression in kisspeptin receptor (Kiss-1R)-overexpressing mHypoA-55 cells. KP10 greatly increased serum response element (SRE) promoter activity, which is a target of extracellular signal-regulated kinase (ERK) (20.0 ± 2.54-fold). KP10 also increased cAMP-response element (CRE) promoter activity in these cells (2.32 ± 0.36-fold). KP10-increased SRE promoter activity was significantly prevented in the presence of PD098095, a MEK kinase (MEKK) inhibitor, and KP10-induced CRE promoter activity was also inhibited by PD098059. Similarly, H89, a protein kinase A (PKA) inhibitor, significantly inhibited the KP10 induction of SRE and CRE promoters. KP10-induced Kiss-1 and GnRH gene expressions were inhibited in the presence of PD098059. Likewise, H89 significantly inhibited the KP10-induced increase in Kiss-1 and GnRH. Transfection of mHypoA-55 cells with constitutively active MEKK (pFC-MEKK) increased SRE and CRE promoter activities by 9.75 ± 1.77- and 1.36 ± 0.12-fold, respectively. Induction of constitutively active PKA (pFC-PKA) also increased SRE and CRE promoter activities by 2.41 ± 0.42- and 40.71 ± 7.77-fold, respectively. Furthermore, pFC-MEKK and -PKA transfection of mHypoA-55 cells increased both Kiss-1 and GnRH gene expression. Our current observations suggest that KP10 increases both the ERK and PKA pathways and that both pathways mutually interact in mHypoA-55 hypothalamic cells. Activation of both ERK and PKA signaling might be necessary to induce Kiss-1 and GnRH gene expressions.
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Affiliation(s)
- Tuvshintugs Tumurbaatar
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Haruhiko Kanasaki
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan.
| | - Susdiaman Sudin Yacca
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Zhuoma Cairang
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Zolzaya Tumurgan
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Aki Oride
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Hiroe Okada
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
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Moller E, Britt M, Schams A, Cetuk H, Anishkin A, Sukharev S. Mechanosensitive channel MscS is critical for termination of the bacterial hypoosmotic permeability response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530336. [PMID: 36909569 PMCID: PMC10002685 DOI: 10.1101/2023.02.27.530336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Free-living microorganisms are subjected to drastic changes in osmolarity. To avoid lysis under sudden osmotic down-shock, bacteria quickly expel small metabolites through the tension-activated channels MscL, MscS, and MscK. We examined five chromosomal knockout strains, Δ mscL , Δ mscS , a double knockout Δ mscS Δ mscK , and a triple knockout Δ mscL Δ mscS Δ mscK in comparison to the wild-type parental strain. Stopped-flow experiments confirmed that both MscS and MscL mediate fast osmolyte release and curb cell swelling, but osmotic viability assays indicated that they are not equivalent. MscS alone was capable of rescuing the cell population, but in some strains MscL did not rescue and additionally became toxic in the absence of both MscS and MscK. Furthermore, MscS was upregulated in the Δ mscL strain, suggesting either a cross-talk between the two genes/proteins or the influence of cell mechanics on mscS expression. The data shows that for the proper termination of the permeability response, the high-threshold (MscL) and the low-threshold (MscS/MscK) channels must act sequentially. In the absence of low-threshold channels, at the end of the release phase, MscL should stabilize membrane tension at around 10 mN/m. Patch-clamp protocols emulating the tension changes during the release phase indicated that the non-inactivating MscL, residing at its own tension threshold, flickers and produces a protracted leakage. The MscS/MscK population, when present, stays open at this stage to reduce tension below the MscL threshold and silence the large channel. When MscS reaches its own threshold, it inactivates and thus ensures proper termination of the hypoosmotic permeability response. This functional interplay between the high- and low-threshold channels is further supported by the compromised osmotic survival of bacteria expressing non-inactivating MscS mutants. Summary for the table of contents The kinetics of hypotonic osmolyte release from E. coli is analyzed in conjunction with bacterial survival. It is shown that MscL, the high-threshold 'emergency release valve', rescues bacteria from down-shocks only in the presence of MscS, MscK or other low-threshold channels that are necessary to pacify MscL at the end of the release phase.
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Nomair AM, Mekky JF, El-Hamshary SA, Nomeir HM. Circulating miR-146a-5p and miR-132-3p as potential diagnostic biomarkers in epilepsy. Epilepsy Res 2023; 191:107089. [PMID: 36801489 DOI: 10.1016/j.eplepsyres.2023.107089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/11/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVE MiRNAs are important gene-regulating agents in epilepsy development, according to new research. The purpose of this study is to investigate the relationship between serum expression of miR-146a-5p and miR-132-3p and epilepsy in Egyptian patients as potential diagnostic and therapeutic biomarkers. METHODS MiR-146a-5p and miR-132-3p were measured in the serum of 40 adult epilepsy patients and 40 controls using real-time polymerase chain reaction. The comparative cycle threshold (CT) approach (2-ΔΔCT) was used to compute relative expression levels, which were normalized to cel-miR-39 expression and compared to healthy controls. The diagnostic performance of miR-146a-5p and miR-132-3p was assessed using receiver operating characteristic curve analysis. RESULTS The relative expression levels of miR-146a-5p and miR-132-3p in serum were considerably greater in epilepsy patients than in the control group. There was a significant difference in the miRNA-146a-5p relative expression in the focal group when the non-responders were compared with the responders' groups, and a significant difference when comparing the non-responders' focal and the non-responders' generalized groups, however, univariate logistic regression analysis revealed that increased seizure frequency is the only risk factor among all factors affecting the drug response There was a significant difference in epilepsy duration between miR-132-3p high and low expression. With an area under the curve of 0.714 (95% C. I 0.598-0.830; P = 0.001), the combined miR-146a-5p and miR-132-3p serum levels performed better than each separately as a diagnostic biomarker to distinguish epilepsy patients from controls. SIGNIFICANCE The findings imply that both miR-146a-5p and miR-132-3p may be involved in epileptogenesis regardless of epilepsy subtypes. Although the combined circulating miRNAs may be useful as a diagnostic biomarker, they are not a predictor of drug response. MiR-132-3p might be used to predict epilepsy's prognosis by demonstrating its chronicity.
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Affiliation(s)
- Azhar Mohamed Nomair
- Department of Chemical Pathology, Medical Research Institute, Alexandria University, Egypt.
| | - Jaidaa Farouk Mekky
- Department of Neuropsychiatry, Faculty of Medicine, Alexandria University, Egypt.
| | | | - Hanan Mohamed Nomeir
- Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Egypt.
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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Yousuf SD, Ganie MA, Urwat U, Andrabi SM, Zargar MA, Dar MA, Manzoor-ul-Rehman M, Mudassar S, Rashid F. Oral contraceptive pill (OCP) treatment alters the gene expression of intercellular adhesion molecule-1 (ICAM-1), tumor necrosis factor-α (TNF-α), monocyte chemoattractant protein-1 (MCP-1) and plasminogen activator inhibitor-1 (PAI-1) in polycystic ovary syndrome (PCOS) women compared to drug-naive PCOS women. BMC Womens Health 2023; 23:68. [PMID: 36793022 PMCID: PMC9933286 DOI: 10.1186/s12905-023-02187-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/20/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) presents clinical symptoms of menstrual abnormalities, excessive hair growth (hirsutism), scalp hair loss, acne and infertility. Metabolic abnormalities such as obesity, insulin resistance, glucose intolerance and cardiovascular problems constitute an essential part of PCOS, all of which can have significant long-term health consequences. Low-grade chronic inflammation demonstrated by persistent moderately elevated serum levels of inflammatory and coagulatory markers plays a critical role in the pathogenesis of PCOS. Oral contraceptive pills (OCPs) constitute the mainstay of pharmacologic therapy for women with PCOS to regularize cyclicity and ameliorate androgen excess. On the other hand, OCP use is associated with various venous thromboembolic and proinflammatory events in the general population. PCOS women always carriers the increased lifetime risk of these events. The studies on the effect of OCPs on inflammatory, coagulation and metabolic parameters in PCOS are less robust. Therefore in this study, we investigated and compared the messenger RNA (mRNA) expression profiles of genes implicated in inflammatory and coagulation pathways between drug-naive and OCP-treated PCOS women. The selected genes include intercellular adhesion molecule-1 (ICAM-1), tumor necrosis factor-α (TNF-α), monocyte chemoattractant protein-1 (MCP-1) and plasminogen activator inhibitor-1 (PAI-1). Furthermore, the correlation between the selected markers and various metabolic indices in the OCP group has also been explored. METHOD The relative amounts of ICAM-1, TNF-α, MCP-1 and PAI-1 mRNA in peripheral blood mononuclear cells from 25 drug-naive PCOS subjects (controls) and 25 PCOS subjects who received OCPs containing 0.03 mg-ethinyl-estradiol and 0.15 mg-levonorgestrel for at least six months (cases) were estimated using real-time qPCR. The statistical interpretation was conducted using SPSS version 20.0 (SPSS, Inc, Chicago, IL), Epi Info version 2002 (Disease Control and Prevention Centres, Atlanta, GA) and GraphPad Prism 5 (GraphPad Software, La Jolla, CA) software. RESULT Six months of OCP therapy enhanced the expression of inflammatory genes viz ICAM-1, TNF-α and MCP-1 mRNA in PCOS women by 2.54, 2.05 and 1.74 folds, respectively, in this study. However, PAI-1 mRNA in the OCP group showed no significant increase. Furthermore, in cases, ICAM-1 mRNA expression positively correlated with body mass index (BMI) (p = 0.01), fasting insulin (p = 0.01), insulin 2 h p = 0.02), glucose 2 h (p = 0.01) and triglycerides (p = 0.01). TNF-α mRNA expression positively correlated with fasting insulin (p = 0.0007). MCP-1 mRNA expression positively correlated with (BMI) (p = 0.002). CONCLUSION OCPs helped reduce clinical hyperandrogenism and regularise menstrual cycles in women with PCOS. However, OCP use was associated with increased fold expression of inflammatory markers which positively correlated with metabolic abnormalities.
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Affiliation(s)
- Syed Douhath Yousuf
- grid.414739.c0000 0001 0174 2901Department of Clinical Biochemistry, Sheri- Kashmir Institute of Medical Sciences, SKIMS, Srinagar, J&K India
| | - Mohammad Ashraf Ganie
- grid.414739.c0000 0001 0174 2901Department of Endocrinology and Metabolism, Sheri- Kashmir Institute of Medical Sciences, SKIMS, Srinagar, J&K India
| | - Uneeb Urwat
- Division of Animal Biotechnology, Sheri- Kashmir Institute of Agricultural Sciences, Shuhama, J&K India
| | - Syed Mudasir Andrabi
- Division of Animal Biotechnology, Sheri- Kashmir Institute of Agricultural Sciences, Shuhama, J&K India
| | | | - Mashooq Ahmad Dar
- Division of Animal Biotechnology, Sheri- Kashmir Institute of Agricultural Sciences, Shuhama, J&K India
| | - Mir Manzoor-ul-Rehman
- Division of Animal Biochemistry, Sheri- Kashmir Institute of Agricultural Sciences, Shuhama, J&K India
| | - Syed Mudassar
- grid.414739.c0000 0001 0174 2901Department of Clinical Biochemistry, Sheri- Kashmir Institute of Medical Sciences, SKIMS, Srinagar, J&K India
| | - Fouzia Rashid
- Clinical Biochemistry, University of Kashmir, Srinagar, J&K, India.
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Measuring Transposable Element Activity in Adult Drosophila Ovaries. Methods Mol Biol 2023; 2626:309-321. [PMID: 36715912 DOI: 10.1007/978-1-0716-2970-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Transposons are genetic elements that use various mechanisms of transposition to move around the genome, thus posing a risk to genomic integrity. Repression of transposable elements (TEs) involves the complex PIWI pathway and several proteins associated with heterochromatinization. All players of TE repression are indispensable for proper reproductive fitness, as loss-of-function mutations in these genes result primarily in sterility and impaired reproductive development. When investigating the function of novel genes with similar phenotypes, elevated transposon expression in reproductive tissues can be a marker for involvement in the aforementioned processes. Here, we present a protocol for investigating TE levels in adult Drosophila ovaries, from dissection to data analysis.
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Fujita M, Chiu CH, Nagano K. Transcriptional analysis of the mfa-cluster genes in Porphyromonas gingivalis strains with one and two mfa5 genes. Mol Oral Microbiol 2023; 38:41-47. [PMID: 36333926 DOI: 10.1111/omi.12399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/08/2022]
Abstract
The Porphyromonas gingivalis Mfa1 fimbria is composed of the Mfa1 to Mfa5 proteins, encoded by the mfa1 to mfa5 genes, respectively, which are tandemly arranged on chromosomes. A recent study discovered that many P. gingivalis strains possess two mfa5 genes (called herein mfa5-1 and mfa5-2), which are also in tandem. This study examined the transcriptional unit and activity of mfa-cluster genes in strains with one (the ATCC 33277 and TDC60 strains) and two (the HG66 and A7436 strains) mfa5 genes. Complementary DNA was prepared from the total RNA extracted from the bacterial cells in the logarithmic growth phase using a random primer. PCR analysis for the intergenic regions from mfa1 to mfa5 or mfa5-2 showed that mfa1 to mfa5 or mfa5-2 formed a polycistronic gene cluster. Quantitative real-time PCR showed that the mfa1 transcription was 5-10 times higher than that of mfa2 in all the strains. However, mfa2 to mfa5 mostly showed a comparable expression. Both mfa5 genes were comparably transcribed in HG66 and A7436 strains. The transcriptional levels were almost consistent with the respective protein expression levels. In silico analysis identified a transcriptional terminator structure in the intergenic region between mfa1 and mfa2 that was probably responsible for the decreased transcription rate of mfa2 and the downstream genes.
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Affiliation(s)
- Mari Fujita
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Chen-Hsuan Chiu
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Keiji Nagano
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu, Japan
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Rozance PJ, Boehmer BH, Chang EI, Wesolowski SR, Brown LD. Chronic Fetal Leucine Infusion Increases Rate of Leucine Oxidation but Not of Protein Synthesis in Late Gestation Fetal Sheep. J Nutr 2023; 153:493-504. [PMID: 36894241 PMCID: PMC10196590 DOI: 10.1016/j.tjnut.2022.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/19/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Leucine increases protein synthesis rates in postnatal animals and adults. Whether supplemental leucine has similar effects in the fetus has not been determined. OBJECTIVE To determine the effect of a chronic leucine infusion on whole-body leucine oxidation and protein metabolic rates, muscle mass, and regulators of muscle protein synthesis in late gestation fetal sheep. METHODS Catheterized fetal sheep at ∼126 d of gestation (term = 147 d) received infusions of saline (CON, n = 11) or leucine (LEU; n = 9) adjusted to increase fetal plasma leucine concentrations by 50%-100% for 9 d. Umbilical substrate net uptake rates and protein metabolic rates were determined using a 1-13C leucine tracer. Myofiber myosin heavy chain (MHC) type and area, expression of amino acid transporters, and abundance of protein synthesis regulators were measured in fetal skeletal muscle. Groups were compared using unpaired t tests. RESULTS Plasma leucine concentrations were 75% higher in LEU fetuses compared with CON by the end of the infusion period (P < 0.0001). Umbilical blood flow and uptake rates of most amino acids, lactate, and oxygen were similar between groups. Fetal whole-body leucine oxidation was 90% higher in LEU (P < 0.0005) but protein synthesis and breakdown rates were similar. Fetal and muscle weights and myofiber areas were similar between groups, however, there were fewer MHC type IIa fibers (P < 0.05), greater mRNA expression levels of amino acid transporters (P < 0.01), and a higher abundance of signaling proteins that regulate protein synthesis (P < 0.05) in muscle from LEU fetuses. CONCLUSIONS A direct leucine infusion for 9 d in late gestation fetal sheep does not increase protein synthesis rates but results in higher leucine oxidation rates and fewer glycolytic myofibers. Increasing leucine concentrations in the fetus stimulates its own oxidation but also increases amino acid transporter expression and primes protein synthetic pathways in skeletal muscle.
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Affiliation(s)
- Paul J Rozance
- Department of Pediatrics, University of Colorado School of Medicine, Perinatal Research Center, Aurora, Colorado, USA
| | - Brit H Boehmer
- Department of Pediatrics, University of Colorado School of Medicine, Perinatal Research Center, Aurora, Colorado, USA
| | - Eileen I Chang
- Department of Pediatrics, University of Colorado School of Medicine, Perinatal Research Center, Aurora, Colorado, USA
| | - Stephanie R Wesolowski
- Department of Pediatrics, University of Colorado School of Medicine, Perinatal Research Center, Aurora, Colorado, USA
| | - Laura D Brown
- Department of Pediatrics, University of Colorado School of Medicine, Perinatal Research Center, Aurora, Colorado, USA.
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Mo W, Wen J, Huang J, Yang Y, Zhou M, Ni S, Le W, Wei L, Qi D, Wang S, Su J, Wu Y, Zhou W, Du K, Wang X, Zhao Z. Classification of Coronavirus Spike Proteins by Deep-Learning-Based Raman Spectroscopy and its Interpretative Analysis. JOURNAL OF APPLIED SPECTROSCOPY 2023; 89:1203-1211. [PMID: 36718373 PMCID: PMC9876753 DOI: 10.1007/s10812-023-01487-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The outbreak of COVID-19 has spread worldwide, causing great damage to the global economy. Raman spectroscopy is expected to become a rapid and accurate method for the detection of coronavirus. A classification method of coronavirus spike proteins by Raman spectroscopy based on deep learning was implemented. A Raman spectra dataset of the spike proteins of five coronaviruses (including MERS-CoV, SARS-CoV, SARS-CoV-2, HCoVHKU1, and HCoV-OC43) was generated to establish the neural network model for classification. Even for rapidly acquired spectra with a low signal-to-noise ratio, the average accuracy exceeded 97%. An interpretive analysis of the classification results of the neural network was performed, which indicated that the differences in spectral characteristics captured by the neural network were consistent with the experimental analysis. The interpretative analysis method provided a valuable reference for identifying complex Raman spectra using deep-learning techniques. Our approach exhibited the potential to be applied in clinical practice to identify COVID-19 and other coronaviruses, and it can also be applied to other identification problems such as the identification of viruses or chemical agents, as well as in industrial areas such as oil and gas exploration.
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Affiliation(s)
- Wenbo Mo
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Jiaxing Wen
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Jinglin Huang
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Yue Yang
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Minjie Zhou
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Shuang Ni
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Wei Le
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Lai Wei
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Daojian Qi
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Shaoyi Wang
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Jingqin Su
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Yuchi Wu
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Weimin Zhou
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Kai Du
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Xuewu Wang
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Zongqing Zhao
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
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