白藜芦醇对松辽黑猪精液冷冻的影响

试验旨在评价白藜芦醇(resveratrol,Res)对松辽黑猪公猪精液冷冻的影响。试验分为5组,分别为对照组(不添加Res)和Res处理组(在冷冻基础液中分别加入25μM、50μM、100μM、200μM浓度的Res)。采用手握法采集松辽黑猪精液,用5种冷冻基础液稀释,在25℃平衡1 h,17℃平衡2 h,4℃平衡3 h后灌装于0.5 mL细管中,在液氮上方3 cm处熏蒸10 min,保存在液氮罐中30 d后进行检测。样本解冻后分别检测精子活力、谷胱甘肽过氧化物酶(GSH-Px)活性、质膜完整性、过氧化氢酶(CAT)活性、顶体完整性、线粒体活性、活性氧簇(ROS)水平、DNA完整性、超氧化物歧化酶(SOD)活性以及丙二醛(MDA)水平。结果显示:与对照组相比,冷冻基础液中添加50μM Res可以显著提高冻融后精子的活力、SOD活性、质膜完整性、CAT活性、线粒体活性、GSH-Px活性、顶体完整性(P<0.05);可以显著降低精子ROS水平和MDA水平(P<0.05);添加Res对DNA完整性未表现出具有显著影响(P>0.05)。结论:猪精液冷冻前添加Res可改善冻融后精子质量,添加量50μM效果最佳,但Res是否可以改善公猪冷冻精液的体外受精及人工授精能力,有待于进一步的研究。

BioTreasury:a community-based repository enabling indexing and rating of bioinformatics tools

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis assignments.Therefore,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently needed.In this study,we introduce Bio Treasury(http://biotreasury.rjmart.cn),an integrated communitybased repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics tools.Bio Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 entries.In the past two years,we have continuously improved and maintained Bio Treasury,adding several exciting features,including creating structured homepages for every tool and user,a hierarchical category of bioinformatics tools and classifying tools using large language model(LLM).Bio Treasury streamlines the tool submission process with intelligent auto-completion.Additionally,Bio Treasury provides a wide range of social features,for example,enabling users to participate in interactive discussions,rate tools,build and share tool collections for the public.We believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical community.It empowers researchers to effectively discover and evaluate bioinformatics tools,fostering collaboration and advancing bioinformatics research.

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning

Protein nitration and nitrosylation are essential post-translational modifications （PTMs）involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases.Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specific scoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively,demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%à42%improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http：//deepnitro.renlab.org.

Rottlerin plays an antiviral role at early and late steps of Zika virus infection

Infection of Zika virus(ZIKV)may cause microcephaly and other neurological disorders,while no vaccines and drugs are available.Our study revealed that rottlerin confers a broad antiviral activity against several enveloped viruses,including ZIKV,vesicular stomatitis virus,and herpes simplex virus,but not against two naked viruses(enterovirus 71 and encephalomyocarditis virus).Rottlerin does not have a direct virucidal effect on the virions,and its antiviral effect is independent of its regulation on PKCδor ATP.Both pretreatment and post-treatment of rottlerin effectively reduce the viral replication of ZIKV.The pretreatment of rottlerin disturbs the endocytosis of enveloped viruses,while the post-treatment of rottlerin acts at a late stage through disturbing the maturation of ZIKV.Importantly,administration of rottlerin in neonatal mice significantly decreased the ZIKV replication in vivo,and alleviated the neurological symptoms caused by ZIKV.Our work suggests that rottlerin exerts an antiviral activity at two distinct steps of viral infection,and can be potentially developed as a prophylactic and therapeutic agent.

VirusMap:A visualization database for the influenza A virus

Influenza A virus,a highly virulent pathogen that has caused several pandemic events over the course of human history,still remains a major threat to human health at present.The most serious influenza pandemic in recorded history was the 1918 Spanish flu outbreak,which killed about 20-100 million people worldwide（Murray et al.,2006）.Also,