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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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bioinformatics analysis reveals shared molecular pathways for relationship between ulcerative colitis and primary sclerosing cholangitis

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Genomics & Informatics 2025年第1期23卷 1-16页

作者： Jalali, Pooya Rezaee, Malihe Yaghoobi, Alireza Piroozkhah, Moein Zabihi, Mohammad Reza Aliyari, Shahram Salehi, Zahra Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center Research Institute for Gastroenterology and Liver Diseases Shahid Beheshti University of Medical Sciences Tehran Iran Department of Pharmacology School of Medicine Shahid Beheshti University of Medical Sciences Tehran Iran Department of Immunology School of Medicine Tehran University of Medical Sciences Tehran Iran Division of Applied Bioinformatics German Cancer Research Center DKFZ Heidelberg Heidelberg Germany Hematology Oncology and Stem Cell Transplantation Research Center Research Institute for Oncology Hematology and Cell Therapy Tehran University of Medical Sciences Tehran Iran

Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders, including ulcerative colitis (UC) and Crohn’s disease, affecting the gastrointestinal tract and is associated with high morbidity and mortality. Accumulating evidence indicates that IBD not only impacts the gastrointestinal tract but also affects multiple extraintestinal organs, which may manifest prior to the diagnosis of IBD. Among these extraintestinal manifestations associated with IBD, primary sclerosing cholangitis (PSC) stands out as a prominent example. PSC is recognized as a progressive cholestatic disorder, characterized by the narrowing of bile ducts, eventual development of liver cirrhosis, end-stage liver disease, and the potential emergence of cholangiocarcinoma. This study aimed to identify the molecular contributors in UC-induced PSC by detecting the essential regulatory genes that are differentially expressed in both diseases. The common single-nucleotide polymorphisms (SNPs) and differentially expressed genes (DEGs) were detected using DisGeNET and GEO databases, respectively. Then, the top module and hub genes within the protein–protein interaction network were identified. Furthermore, the co-expression network of the top module was constructed using the HIPPIE database. Additionally, the gene regulatory network was constructed based on miRNAs and circRNAs. Finally, we searched the DGIdb database for possible interacting drugs with UC-PSC top module genes. A total of 132 SNPs and their associated genes were found to be shared between UC and PSC. Gene expression analysis identified 56 common DEGs between the two diseases. Following functional enrichment analysis, 207 significant biological processes (BP), 48 molecular functions (MF), and 8 KEGG pathways, with notable enrichment in mRNA-related processes such as mRNA splicing and RNA binding, were defined. Particularly, the PTPN2 gene was the only gene common between UC and PSC at both the SNP level and the expression lev

关键词： bioinformatics Inflammatory bowel disease Primary sclerosing cholangitis Ulcerative colitis

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Molecular docking and molecular dynamics simulation studies of inhibitor candidates against Anopheles gambiae 3-hydroxykynurenine transaminase and implications on vector control

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Heliyon 2025年第1期11卷 e41633页

作者： Adedeji, Eunice O. Ogunlana, Olubanke O. Oduselu, Gbolahan O. Koenig, Rainer Adebiyi, Ezekiel Soremekun, Opeyemi S. Fatumo, Segun Covenant University Bioinformatics Research (CUBRe) Covenant University Ogun State Ota Nigeria Department of Biochemistry Covenant University Ogun State Ota Nigeria Department of Biology University of York York United Kingdom Covenant Applied Informatics and Communication Africa Centre of Excellence Covenant University Ota Nigeria Institute for Infectious Diseases and Infection Control (IIMK RG Systems Biology) Jena University Hospital Am Klinikum 1 Jena 07747 Germany African Center of Excellence in Bioinformatics & Data Intensive Science Makerere University Kampala 10218 Uganda Division of Applied Bioinformatics German Cancer Research Center (DKFZ) G200 Im Neuenheimer Feld 280 Heidelberg 69120 Germany The African Computational Genomics (TACG) Research Group MRC/UVRI and LSHTM Entebbe Uganda Precision Healthcare University Research Institute Queen Mary University of London United Kingdom Department of Non-Communicable Disease Epidemiology London School of Hygiene & Tropical Medicine United Kingdom

Isoxazole and oxadiazole derivatives inhibiting 3-hydroxykynurenine transaminase (3HKT) are potential larvicidal candidates. This study aims to identify more suited potential inhibitors of Anopheles gambiae 3HKT (Ag3HKT) through molecular docking and molecular dynamics simulation. A total of 958 compounds were docked against Anopheles gambiae 3HKT (PDB ID: 2CH2) using Autodock vina and Autodock4. The top three identified hits were subjected to 300 ns molecular dynamics simulation using AMBER 18 and ADMET analysis using SWISSADME predictor and ADMETSAR. Replacement of alkyl attachment on C5 of isoxazole or oxadiazole derivative with a cycloalkyl group yielded compounds with lower binding energy than their straight chain counterparts. The top three compounds were brominated compounds, 2‐[3‐(4‐bromophenyl)‐1,2‐oxazol‐5‐yl]cyclopentane‐1‐carboxylic acid, 2-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]cyclopentane-1-carboxylic acid, 3-[3-(4-bromo-2-methylphenyl)-1,2,4-oxadiazol-5-yl]cyclopentane-1-carboxylic acid, and they had binding energies of −8.58, −8.25, and −8.18 kcal/mol in virtual screening against 2CH2 protein target, respectively. These compounds were predicted to be less toxic than temephos, a standard larvicide and more biodegradable than previously reported inhibitors. The three compounds exhibited a greater stabilizing effect on 2CH2 protein target than 4-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid, a previously reported inhibitor candidate with good larvicidal activity on Aedes aegypti. Further thermodynamic calculations revealed that the top three compounds possessed total binding energies (ΔG_bind) of −26.64 kcal/mol, −24.26 kcal/mol and −14.11 kcal/mol, respectively, as compared to −12.02 kcal/mol for 4-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid. These compounds could be better larvicides than previously reported isoxazole or oxadiazole derivatives and safer than temephos. © 2025 The Authors

关键词： 1,2,4-Oxadiazole 3HKT Isoxazoles Larvicide Mosquito Vector control

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Quantification of Oxygen Tension Variation in an in Vitro Tumor Microenvironment Model Based on Co-Culture of Tumor Spheroid and Endothelial Cells in a Microfluidic Device

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SSRN 2025年

作者： Chiang, Kuang-Hsing Chang, Wei-Jen Lin, Chih-Ting Wu, Hsiao-Mei Tung, Yi-Chung Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei10617 Taiwan Division of Cardiology Cardiovascular Research Center Department of Internal Medicine Taipei Medical University Hospital Taipei11031 Taiwan Taipei Heart Institute Taipei Medical University Taipei11031 Taiwan Division of Cardiology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Research Center for Applied Sciences Academia Sinica Taipei11529 Taiwan Institute of Biophotonics National Yang Ming Chiao Tung University Taipei11221 Taiwan Department of Biomechatronics Engineering National Taiwan University Taipei10617 Taiwan

In this study, we developed an innovative in vitro tumor microenvironment model that integrates a tumor spheroid and a monolayer of endothelial cells within a microfluidic device, aiming to replicate the complex conditions of an avascular solid tumor with limited oxygen supply. The tumor spheroid is cultured in a gas-impermeable plastic chamber, which effectively simulates the hypoxic environment characteristic of solid tumors, thereby providing a realistic platform for studying tumor behavior and interactions with surrounding cells. To characterize the three-dimensional spatial oxygen tension profiles, we utilized oxygen-sensitive microbeads with widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM). This approach allowed us to obtain detailed insights into the oxygen levels within the tumor microenvironment, which are critical for tumor growth and survival. Our findings highlight the significant interactions between the tumor spheroid and endothelial cells, emphasizing the crucial role of the endothelium in regulating oxygen microenvironments and influencing angiogenesis. Furthermore, the model provides a valuable tool for exploring the dynamics of tumor biology, enabling researchers to modulate environmental factors and create specific conditions for various research topics. This capability is particularly beneficial for drug development and clinical verification, as it allows for the observation of interactions among different cell types and the assessment of spatial stress or environmental factors. This work establishes a versatile platform for advancing our understanding of tumor biology and optimizing therapeutic strategies, paving the way for future researches in cancer treatment and drug discovery. © 2025, The Authors. All rights reserved.

关键词： Endothelial cells

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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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Sexual reproduction in land plants: an evolutionary perspective

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Plant reproduction 2025年第2期38卷 12页

作者： Annette Becker Xia Chen Thomas Dresselhaus Nora Gutsche Stefanie J Müller-Schüssele Stefanie Sprunck Günter Theißen Sophie de Vries Sabine Zachgo Institute of Botany Justus Liebig University Heinrich-Buff-Ring 38 35392 Giessen Germany. Annette.Becker@bot1.bio.uni-giessen.de. Institute of Plant Sciences Cell Biology and Plant Biochemistry Universitätsstraße 31 93053 Regensburg Germany. Division of Botany Osnabrück University Barbarastr. 11 49076 Osnabrück Germany. Molecular Botany Department of Biology RPTU Kaiserslautern-Landau 67663 Kaiserslautern Germany. Matthias Schleiden Institute/Genetics I Friedrich Schiller University Jena Philosophenweg 12 07743 Jena Germany. Department of Applied Bioinformatics Institute of Microbiology and Genetics University of Göttingen Goldschmidtstraße 1 37077 Göttingen Germany.

We link key aspects of land plant reproductive evolution and detail how successive molecular changes leading to novel tissues and organs require co-evolution of communication systems between tissues. The transition of water-dependent reproduction of algae to mechanisms with very limited water dependence in many land plant lineages allowed plants to colonize diverse terrestrial environments, leading to the vast variety of extant plant species. The emergence of modified cell types, novel tissues, and organs enabled this transition; their origin is associated with the co-evolution of novel or adapted molecular communication systems and gene regulatory networks. In the light of an increasing number of genome sequences in combination with the establishment of novel genetic model organisms from diverse green plant lineages, our knowledge and understanding about the origin and evolution of individual traits that arose in a concerted way increases steadily. For example, novel members of gene families in signaling pathways emerged for communication between gametes and gametophytes with additional tissues surrounding the gametes. Here, we provide a comprehensive overview on the origin and evolution of reproductive novelties such as pollen grains, immobile sperms, ovules and seeds, carpels, gamete/gametophytic communication systems, double fertilization, and the molecular mechanisms that have arisen anew or have been co-opted during evolution, including but not limited to the incorporation of phytohormones, reactive oxygen species and redox signaling as well as small RNAs in regulatory modules that contributed to the evolution of land plant sexual reproduction.

关键词： Carpel Co-evolution Double fertilization HAP2 MicroRNA evolution Ovule RALF ROS Redox signaling Sexual reproduction Sperm

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Mathematical modeling of malaria transmission dynamics in humans with mobility and control states

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Infectious Disease Modelling 2023年第4期8卷 1015-1031页

作者： Gbenga Adegbite Sunday Edeki Itunuoluwa Isewon Jerry Emmanuel Titilope Dokunmu Solomon Rotimi Jelili Oyelade Ezekiel Adebiyi Covenant University Bioinformatics Research Covenant UniversityOtaNigeria Department of Computer and Information Sciences Covenant UniversityOtaNigeria Department of Mathematics Covenant UniversityOtaNigeria Department of Biochemistry Covenant UniversityOtaNigeria Covenant Applied Informatics and Communications-African Centre of Excellence Covenant UniversityOtaOgun StateNigeria Division of Applied Bioinformatics German Cancer Research Center(DKFZ)HeidelbergGermany

Malaria importation is one of the hypothetical drivers of malaria transmission dynamics across the *** studies on malaria importation focused on the effect of the use of conventional malaria control strategies as approved by the World Health Organization(WHO)on malaria transmission dynamics but did not capture the effect of the use of traditional malaria control strategies by vigilant *** order to handle the aforementioned situation,a novel system of Ordinary Differential Equations(ODEs)was developed comprising the human and the malaria vector *** of the system was carried out to assess its quantitative *** novel computational algorithm used to solve the developed system of ODEs was implemented and benchmarked with the existing Runge-Kutta numerical solution ***,simulations of different vigilant conditions useful to control malaria were carried *** novel system of malaria models was well-posed and epidemiologically meaningful based on its quantitative *** novel algorithm performed relatively better in terms of model simulation accuracy than *** the best model-fit condition of 98%vigilance to the use of conventional and traditional malaria control strategies,this study revealed that malaria importation has a persistent impact on malaria transmission *** lieu of this,this study opined that total vigilance to the use of the WHO-approved and traditional malaria management tools would be the most effective control strategy against malaria importation.

关键词： Malaria importation Traditional malaria control Ordinary differential equation Quantitative properties Novel algorithm Runge-Kutta

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Anti-hypercholesterolemia properties of exopolysaccharide from Lactiplantibacillus plantarum MI01: Computational and in vivo approaches

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Case Studies in Chemical and Environmental Engineering 2025年 11卷

作者： Kusmiati, Kusmiati Nurkanto, Arif Fanani, Asrul Nurcahyanto, Dian Alfian Mamangkey, Jendri Marissa, Sarah Pasaribu, Khatarina Meldawati Afiati, Fifi Agustini, Ni Wayan Sri Ahmad, Riza Zainuddin Masrukhin Taufik, Muhammad Irawan, Herman Adalina, Yelin Kusmiati, Mia Gangga, Erlindha Research Center for Biosystematics and Evolution- Research Organization for Life Sciences and Environment National Research and Innovation Agency (BRIN) Indonesia Department of Biochemistry Faculty Mathematics and Natural Sciences IPB University Bogor Indonesia Research and Education Center for Bioinformatics Indonesia Institute of Bioinformatics Malang Indonesia Department of Biology Education Faculty of Education and Teacher Training Universitas Kristen Indonesia Jakarta Indonesia Faculty of Pharmacy University of Pancasila Srengseng Sawah Jagakarsa Jakarta Indonesia Research Center for Biomass and Bioproducts National Research and Innovation Agency of Indonesia (BRIN) Indonesia Research Center for Applied Microbiology-Research Organization for Life Sciences and Environment National Research and Innovation Agency (BRIN) Indonesia Research Center for Veterinary Science Research Organization for Health National Research and Innovation Agency (BRIN) Indonesia Organic Chemistry Division Faculty of Mathematics and Natural Sciences Bandung Institute of Technology West Java Bandung Indonesia Research Center for Genetic Engineering Research Organization for Life Sciences and Environment National Research and Innovation Agency (BRIN) Indonesia Research Centre for Applied Botany Research Organization for Life Science and Environment National Research and Innovation Agency Indonesia

Exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) are extensively studied for their health benefits, particularly in lowering cholesterol levels. This research utilized Lactiplantibacillus plantarum MI01, isolated from ripe mangoes, to produce EPS. The study aimed to investigate EPS as an anti-hypercholesterolemic agent through in silico and in vivo methods. Molecular docking revealed strong interactions between EPS monomers (glucose, galactose, rhamnose, and guluronic acid) and the HMG-CoA reductase enzyme, confirming EPS as a competitive inhibitor. In vivo tests on male Sprague Dawley mice involved administering varying doses of crude EPS. The experiment, using a completely randomized design with four replications, divided the mice into six groups: standard control, negative control, positive control (atorvastatin 20 mg/kg BW), and three EPS groups (20, 40, and 60 mg/kg BW per day). Measurements included total cholesterol, triglycerides, HDL, and LDL levels in blood serum. Administering 60 mg/kg BW/day of crude EPS to hypercholesterolemic mice reduced total cholesterol, triglycerides, and LDL by 21.66 %, 16.86 %, and 42.46 %, respectively, and increased HDL by 10.89 %. © 2025 The Authors

关键词： Exopolysaccharides Hypercholesterolemic In silico In vivo Lactiplantibacillus plantarum

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Employing Hexahydroquinolines as PfCDPK4 Inhibitors to Combat Malaria Transmission: An Advanced Computational Approach

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Advances and Applications in bioinformatics and Chemistry 2024年 17卷 83-105页

作者： Oduselu, Gbolahan O Elebiju, Oluwadunni F. Ogunnupebi, Temitope A. Akash, Shopnil Ajani, Olayinka O. Adebiyi, Ezekiel Covenant University Bioinformatics Research (CUBRe) Covenant University OG Ota Nigeria Department of Chemistry Covenant University OG Ota Nigeria Department of Pharmacy Daffodil International University Dhaka Bangladesh African Center of Excellence in Bioinformatics & Data Intensive Science Makerere University Kampala Uganda Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany

Background: Existing antimalarial drugs primarily target blood-stage parasites, but there is a need for transmission-blocking drugs to combat malaria effectively. Plasmodium falciparum Calcium-dependent Protein Kinase 4 (CDPK4) is a promising target for such drugs. This study employed advanced in silico analyses of hexahydroquinolines (HHQ) derivatives to identify PfCDPK4 inhibitors capable of disrupting malaria transmission. Structure-based virtual screening (SBVS) was employed to discover HHQ derivatives with the highest binding affinities against the 3D structure of PfCDPK4 (PDB 1D: 4QOX). Methods: Interaction analysis of protein-ligand complexes utilized Discovery Studio Client, while druglikeness and ADMET properties were assessed using SwissADME and pkCSM web servers, respectively. Quantum mechanical calculations of the top hits were conducted using density functional theory (DFT), and GROMACS was employed to perform the molecular dynamics (MD) simulations. Binding free energy was predicted using the *** tool from the AMBER package. Results: SBVS identified ten best hits possessing docking scores within the range of −11.2 kcal/mol and −10.6 kcal/mol, surpassing the known inhibitor, BKI-1294 (−9.9 kcal/mol). Among these, 4-[4-(Furan-2-carbonyl)piperazin-1-yl]-1-(naphthalen-2-ylmethyl)- 2-oxo-4a,5,6,7,8,8a-hexahydroquinoline-3-carbonitrile (PubChem ID: 145784778) exhibited the highest binding affinity (−11.2 kcal/ mol) against PfCDPK4. Conclusion: Comparative analysis of this compound with BKI-1294 using advanced computational approaches demonstrated competitive potential. These findings suggest the potential of 4-[4-(Furan-2-carbonyl)piperazin-1-yl]-1-(naphthalen-2-ylmethyl)- 2-oxo-4a,5,6,7,8,8a-hexahydroquinoline-3-carbonitrile as a promising PfCDPK4 inhibitor for disrupting malaria transmission. However, further experimental studies are warranted to validate its efficacy and safety profile. © 2024 Oduselu et al.

关键词： antimalarial drugs drug design gametocidal activity malaria molecular dynamics

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Sepsis prediction on ICU admission: Limits and opportunities for machine learning

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Journal of Critical Care 2025年 86卷 154973-154973页

作者： Albu, Alexandra Holke, Franziska Cao, Han Hahn, Bianka Lindner, Holger A. Feuerbach, Lars Schneider-Lindner, Verena Department of Anesthesiology and Surgical Intensive Care Medicine Mannheim Institute of Innate Immunoscience (MI3) Medical Faculty Mannheim Heidelberg University Mannheim Germany Department of Theoretical Neuroscience Central Institute of Mental Health Medical Faculty Heidelberg University Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany

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