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Histological demonstration of gonad development in the banana shrimp,Fenneropenaeus merguiensis

Aquaculture and Fisheries 2025年第1期10卷 94-104页

作者： Jirakanit Chimnual Jirawat Saetan Wilaiwan Chotigeat Division of Biological Science Molecular Biotechnology and Bioinformatics ProgramFaculty of SciencePrince of Songkla UniversitySongkhla90110Thailand Division of Health and Applied Sciences Faculty of SciencePrince of Songkla UniversitySongkhla90110Thailand Center for Genomics and Bioinformatics Research Faculty of SciencePrince of Songkla UniversitySongkhla90110Thailand

The genetic diversity of the banana shrimp Fenneropenaeus merguiensis is at risk because of over-harvesting,which consequently reduces food *** endangerment is exacerbated because this species is not commonly cultivated by ***,these factors necessitate conservation of this shrimp species across its natural *** on the migration of primordial germ cells(PGCs)to form a gonad is essential for shrimp preservation techniques such as broodstock preparation,sex differentiation,and germ cell *** this study,histological analysis and in situ hybridization of vasa expression(from embryo to testis development)were used to demonstrate the movement of *** and Eosin staining and in situ hybridization with the VASA probe revealed that the PGCs migrated retrogradely along the midgut,colonizing the area between the hepatopancreas and heart,a region that becomes the genital ridge in the postlarval *** sexual organs appeared at approximately 4 months of *** real-time PCR,the expression of the vasa gene was detected early on postlarval day 7,whereas its abundant expression was detected in the ovaries and testes of adult *** study could help with the identification and monitoring of PGCs or spermatogonia in banana shrimp and facilitate the implementation of other germ cell-relevant techniques in the future.

关键词： Fenneropenaeus merguiensis Primordial germ cell Spermatogonia vasa

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Exploring the genomic and transcriptomic profiles of glycemic traits and drug repurposing

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Journal of Biomedical Science 2025年第1期32卷 1-14页

作者： Lin, Min-Rou Tsai, Cheng-Lin Liao, Cai-Sian Wei, Chun-Yu Chou, Wan-Hsuan Hsiao, Tzu-Hung Chang, Wei-Chiao Department of Clinical Pharmacy School of Pharmacy Taipei Medical University Taipei Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei Taiwan Bioinformatics Program Taiwan International Graduate Program National Taiwan University Taipei Taiwan Core Laboratory of Neoantigen Analysis for Personalized Cancer Vaccine Office of R&D Taipei Medical University Taipei Taiwan Department of Medical Research Taichung Veterans General Hospital Taichung Taiwan Department of Public Health Fu Jen Catholic University New Taipei City Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung Taiwan Master Program in Clinical Genomics and Proteomics School of Pharmacy Taipei Medical University Taipei Taiwan Integrative Research Center in Critical Care Wan Fang Hospital Taipei Medical University Taipei Taiwan

Type 2 diabetes is an increasingly prevalent metabolic disorder with moderate to high heritability. Glycemic indices are crucial for diagnosing and monitoring the disease. Previous genome-wide association study (GWAS) have identified several risk loci associated with type 2 diabetes, but data from the Taiwanese population remain relatively sparse and primarily focus on type 2 diabetes status rather than glycemic trait levels. We conducted a comprehensive genome-wide meta-analysis to explore the genetics of glycemic traits. The study incorporated a community-based cohort of 145,468 individuals and a hospital-based cohort of 35,395 individuals. The study integrated genetics, transcriptomics, biological pathway analyses, polygenic risk score calculation, and drug repurposing for type 2 diabetes. This study assessed hemoglobin A1c and fasting glucose levels, validating known loci (FN3K, SPC25, MTNR1B, and FOXA2) and discovering new genes, including MAEA and PRC1. Additionally, we found that diabetes, blood lipids, and liver- and kidney-related traits share genetic foundations with glycemic traits. A higher PRS was associated with an increased risk of type 2 diabetes. Finally, eight repurposed drugs were identified with evidence to regulate blood glucose levels, offering new avenues for the management and treatment of type 2 diabetes. This research illuminates the unique genetic landscape of glucose regulation in Taiwanese Han population, providing valuable insights to guide future treatment strategies for type 2 diabetes.

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Correction: Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake

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BMC microbiology 2025年第1期25卷 225页

作者： Linton Freund Caroline Hung Talyssa M Topacio Charles Diamond Alyson Fresquez Timothy W Lyons Emma L Aronson Genetics Genomics and Bioinformatics Program University of California Riverside 900 University Ave Riverside CA 92521 USA. lintonfreund@***. Department of Microbiology and Plant Pathology University of California Riverside 900 University Ave Riverside CA 92521 USA. Department of Earth and Planetary Sciences University of California Riverside 900 University Ave Riverside CA 92521 USA.

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Characterization and comparative profiling of piRNAs in serum biopsies of pediatric Wilms tumor patients

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Cancer Cell International 2025年第1期25卷 1-15页

作者： Mohamed, Fatma S. Jalal, Deena Fadel, Youssef M. El-Mashtoly, Samir F. Khaled, Wael Z. Sayed, Ahmed A. Ghazy, Mohamed A. Biotechnology Program Institute of Basic and Applied Science Egypt-Japan University of Science and Technology Alexandria New Borg El-Arab City Egypt Biochemistry ProgramFaculty of Science Minia University El-Minia Egypt Genomics and Metagenomics Program Department of Basic Research Children’s Cancer Hospital Egypt Cairo 57357 Egypt Bioinformatics Group Center for Informatics Science School of Information Technology and Computer Science Nile University Giza Egypt Leibniz Institute of Photonic Technology Albert Einstein-Straße 9 Jena 07745 Germany Department of Pediatric Oncology National Cancer Institute Cairo Egypt Department of Pediatric Oncology Children’s Cancer Hospital Egypt Cairo 57357 Egypt Consultant Pediatric Oncology Mouwasat Hospital Dammam Saudi Arabia Department of Biochemistry Faculty of Science Ain Shams University Cairo Egypt

Piwi-interacting RNAs (piRNAs) are small non-coding RNAs involved in transposon silencing and linked to cancer progression. However, their role in Wilms tumors (WT) remains unexplored. We conducted a thorough analysis and characterization of piRNAs in serum liquid biopsies of WT patients. Our study examined their expression patterns and functional annotations related to WT pathogenesis, as well as their clinical potential for diagnosis and monitoring. We identified 307 piRNAs expressed in WT serum samples, with 4% classified as repeat-related and 96% as non-repeat-related. The most abundant repeat-related piRNAs originated from LINEs retrotransposon, while tRNA-derived piRNAs were the most prevalent among non-repeat-related piRNAs. Furthermore, a distinct profile of 34 piRNAs showed significant differential expression in WT patients compared to healthy controls—22 downregulated and 12 upregulated. The target genes of differentially expressed piRNAs exhibited significant enrichment in biological pathways related to cytokine activity, inflammatory responses, TGF-beta signaling, p38 MAPK, and ErbB signaling. These genes are also involved in DNA damage response, DNA methylation, cell cycle regulation, as well as kidney development and function. Low expression levels of several piRNAs, especially piR-hsa-1,913,711, piR-hsa-28,190, piR-hsa-28,849, piR-hsa-28,848, and piR-hsa-28,318, showed significant diagnostic potential as non-invasive biomarkers for WT (AUC > 0.8, p < 0.05). Their expression levels also significantly correlated with adverse pathological features, including metastasis, anaplasia, and bilateral WT development. In conclusion, non-transposon-related piRNAs may serve as reliable biomarkers for WT and possess potential non-germline functions, particularly in regulating DNA methylation, cell growth, immune responses, and immune responses. Further studies are warranted to elucidate their functional significance. © The Author(s) 2025.

关键词： Blood-based biomarkers Diagnostic potential Non-germline functions Non-transposon-related PiRNAs PiRNAome profiling Wilms tumor

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Genomic data processing with GenomeFlow

arXiv

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arXiv 2025年

作者： Park, Junseok Maury, Eduardo A. Oh, Changhoon Shin, Donghoon Denisko, Danielle Lee, Eunjung Alice Division of Genetics and Genomics Boston Children’s Hospital 3 Blackfan Circle BostonMA United States Department of Pediatrics Harvard Medical School 25 Shattuck St BostonMA United States Bioinformatics Integrative Genomics Program Harvard/MIT MD-PHD Program Harvard Medical School BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Graduate School of Information Yonsei University 50 Yonsei-ro Seodaemun-gu Seoul Korea Republic of Department of Human Centered Design and Engineering University of Washington SeattleWA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States

Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing of such large-scale genomic sequence data in distributed processing environments with a significant reduction in analysis time. However, parallel processing on cloud computing platforms presents many challenges to researchers, even skillful bioinformaticians. In particular, it is difficult to design a computing architecture optimized to reduce the cost of computing and disk storage as genomic data analysis pipelines often employ many heterogeneous tools with different resource requirements. To address these issues, we developed GenomeFlow, a tool for automated development of computing architecture and resource optimization on Google Cloud Platform, which allows users to process a large number of samples at minimal cost. We outline multiple use cases of GenomeFlow demonstrating its utility to significantly reduce computing time and cost associated with analyzing genomic and transcriptomic data from hundreds to tens of thousands of samples from several consortia. Here, we describe a step-by-step protocol on how to use GenomeFlow for a common genomic data processing task. We introduce this example protocol geared toward a bioinformatician with little experience in cloud computing. © 2025, CC BY.

关键词： Cloud platforms

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Polygalacturonase-inhibiting proteins as an exogenously applied natural solution for prevention of postharvest fungal infections

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Synthetic and Systems Biotechnology 2024年第3期9卷 481-493页

作者： Tiffany Chiu Yanran Li Graduate Program in Genetics Genomicsand Bioinformatics1140 Batchelor HallUniversity of California RiversideCalifornia92521USA Program of Chemical Engineering Department of NanoengineeringUniversity of CaliforniaSan DiegoCA92521USA

Polygalacturonase inhibiting proteins(PGIPs)are plant proteins involved in the inhibition of polygalacturonases(PGs),cell-wall degrading enzymes often secreted by phytopathogenic ***,we confirmed that PGIP2 from Phaseolus vulgaris(PvPGIP2)can inhibit the growth of Aspergillus niger and Botrytis cinerea on agar *** this study,we further validated the feasibility of using PGIP as an environmental and ecological friendly agent to prevent fungal infection *** found that application of either purified PGIP(full length PvPGIP2 or truncated tPvPGIP2_5-8),or PGIP-secreting Saccharomyces cerevisiae strains can effectively inhibit fungal growth and necrotic lesions on tobacco *** also examined the effective amount and thermostability of PGIP when applied on plants.A concentration of 0.75 mg/mL or higher can significantly reduce the area of *** *** activity of full-length PvPGIPs is not affected after incubation at various temperatures ranging from􀀀20 to 42◦C for 24 h,while truncated tPvPGIP2_5-8 lost some efficacy after incubation at 42◦***,we have also examined the efficacy of PGIP on tomato *** the purified PvPGIP2 proteins were applied to tomato fruit inoculated with *** at a concentration of roughly 1.0 mg/mL,disease inci-dence and area of disease had reduced by more than half compared to the controls without PGIP *** study explores the potential of PGIPs as exogenously applied,eco-friendly fungal control agents on fruit and vegetables post-harvest.

关键词： PGIP Antifungal agent Pest control Postharvest treatment

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Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture

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Journal of Molecular Diagnostics 2025年第5期27卷 346-359页

作者： Galbraith, Kristyn Wu, Jamin Sikkink, Kristin Mohamed, Hussein Reid, Derek Perez-Arreola, Michelle Belton, Jon-Matthew Nomikou, Sofia Melnyk, Shadi Yang, Yiying Liechty, Benjamin L. Jour, George Tsirigos, Aristotelis Hermel, David J. Beck, Alyssa Sigal, Darren Dahl, Nathan A. Vibhakar, Rajeev Schmitt, Anthony Snuderl, Matija Department of Pathology NYU Langone Health and NYU Grossman School of Medicine New York New York United States Arima Genomics Inc. Carlsbad California United States Department of Pathology Weill Cornell School of Medicine New York New York United States Division of Precision Medicine Department of Medicine NYU School of Medicine New York New York United States Applied Bioinformatics Laboratories NYU School of Medicine New York New York United States Scripps Clinic/Scripps Cancer Center La Jolla California United States Moores Cancer Center University of California San Diego San Diego California United States Morgan Adams Foundation Pediatric Brain Tumor Research Program Department of Pediatrics University of Colorado School of Medicine Aurora Colorado United States Brain and Spine Tumor Center Laura and Isaac Perlmutter Cancer Center NYU Langone Health New York New York United States

Chromosomal structural variants (SVs) are major contributors to cancer development. Although multiple methods exist for detecting SVs, they are limited in throughput, such as fluorescent in situ hybridization and targeted panels, and use RNA, which degrades in formalin-fixed, paraffin-embedded (FFPE) blocks and is unable to detect SVs that do not produce a fusion transcript. High-throughput chromosome conformation capture (Hi-C) is a DNA-based next-generation sequencing (NGS) method that preserves the spatial conformation of the genome, capturing long-range genetic interactions and SVs. Herein, a retrospective study analyzing 71 FFPE specimens from 10 different solid tumors was performed. Results showed high concordance (98%) with clinical fluorescent in situ hybridization and RNA NGS in detecting known SVs. Furthermore, Hi-C provided insight into the mechanism of SV formation, including chromothripsis and extrachromosomal DNA, and detected rearrangements between genes and regulatory regions, all of which are undetectable by RNA NGS. Lastly, SVs were detected in 71% of cases in which previous clinical methods failed to identify a driver. Of these, 14% were clinically actionable based on current medical guidelines, and an additional 14% were not in medical guidelines but involve targetable biomarkers. Current data suggest that Hi-C is a robust and accurate method for genome-wide SV analyses from FFPE tissue and can be incorporated into current clinical NGS workflows. © 2025 Association for Molecular Pathology and American Society for Investigative Pathology

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Impact of substance use disorders on critical care management and health outcomes in septic adolescents

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Annals of Intensive Care 2025年第1期15卷 1-9页

作者： Markus, Havell Ceneviva, Gary D. Thomas, Neal J. Krawiec, Conrad Pennsylvania State University College of Medicine P.O. Box 850 500 University Drive Hershey 17033-0850 PA United States Program in Bioinformatics and Genomics Pennsylvania State University Huck Life Sciences Building University Park 16802 PA United States Medical Scientist Training Program Pennsylvania State University College of Medicine 500 University Drive Hershey 17033 PA United States Pediatric Critical Care Medicine Department of Pediatrics Penn State Hershey Children’s Hospital P.O. Box 850 500 University Drive Hershey 17033-0850 PA United States Department of Public Health Sciences Pennsylvania State University College of Medicine 500 University Drive Hershey 17033-0850 PA United States

Background: Adult septic patients with substance abuse disorder (SUD) are at increased risk of poor outcomes, but the impact on adolescents is unknown. We aimed to determine if pre-existing SUD is associated with increased adverse outcomes and critical care resources in critically ill adolescents hospitalized with sepsis. We hypothesize that SUD is associated with increased risk of adverse outcomes and usage of critical care resources in this adolescent patient population. Methods: This was a retrospective cohort study utilizing the TriNetX© electronic health record (EHR) database, which consists of EHR from participating healthcare organizations predominantly in the United States. Critically ill adolescents with sepsis aged 12–21 years were divided into two groups (SUD history and no-SUD history). Data related to demographics, diagnostic, procedural, and medication codes were analyzed. The primary outcomes were organ dysfunction, critical care therapies, and all-cause 1-year mortality. Results: We included 5,436 critically ill adolescents with sepsis [730 (13.43%) SUD history and 4706 (86.57%) no-SUD history]. SUD history was associated with increased odds of organ dysfunction (adjusted odds ratio [aOR] 1.84;95% confidence interval [CI] 1.56–2.16;p < 0.001), vasoactive/inotropic drug usage (aOR 1.29;95% CI 1.10–1.52;p = 0.002), mechanical ventilation (aOR 2.19;95% CI 1.85–2.59;p < 0.001), but not mortality (aOR 1.03;95% CI 0.76–1.41;p = 0.83). Conclusions: Our retrospective analysis suggests history of SUD in critically ill septic adolescent patients is associated with increased utilization of critical care resources and organ dysfunction. Further study is needed to determine if substance abuse represents a potentially modifiable risk factor for critical illness in adolescent patients. © The Author(s) 2025.

关键词： Adolescent Critical care Electronic health records Substance use disorders Young adult

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Plant biotic interactions

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Journal of Integrative Plant Biology 2016年第4期58卷 282-283页

作者： Hailing Jin Special Issue EditorUC President's Chair Director of Genetics Genomics and Bioinformatics Graduate ProgramCenter for Plant Cell BiologyInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideUSA

Plants are constantly under attack by pathogens,pests,and parasites,resulting in severe consequences on global food production and human *** pathogens and pests find their ways to invade and communicate with their hos... 详细信息

关键词： communicate constantly sophisticated consequences microbial fight biotic evolved pathogen volatile

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The potential of plant proteins as antifungal agents for agricultural applications

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Synthetic and Systems Biotechnology 2022年第4期7卷 1075-1083页

作者： Tiffany Chiu Theo Poucet Yanran Li Graduate Program in Genetics GenomicsAnd Bioinformatics1140 Batchelor HallUniversity of California RiversideCalifornia92521USA Department of Chemical and Environmental Engineering University of CaliforniaRiversideCA92521USA

Fungal pathogens induce a variety of diseases in both plants and post-harvest food crops,resulting in significant crop losses for the agricultural *** the usage of chemical-based fungicides is the most common way to control these diseases,they damage the environment,have the potential to harm human and animal life,and may lead to resistant fungal ***,there is an urgent need for diverse and effective agricultural fungicides that are environmentally-and *** have evolved various mechanisms in their innate immune system to defend against fungal pathogens,including soluble proteins secreted from plants with antifungal *** proteins can inhibit fungal growth and infection through a variety of mechanisms while exhibiting diverse functionality in addition to antifungal *** this mini review,we summarize and discuss the potential of using plant antifungal proteins for future agricultural applications from the perspective of bioengineering and biotechnology.

关键词： antifungal potential crops

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