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Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods

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Quantitative Biology 2020年第4期8卷 312-324页

作者： Xianyi Lian Xiaodi Yang jiqi shao Fujun Hou Shiping Yang Dongli Pan Ziding Zhang State Key Laboratory of Agrobiotechnology College of Biological SciencesChina Agricultural UniversityBeijing 100193China National Demonstration Center for Experimental Biological Sciences Education College of Biological SciencesChina Agricultural UniversityBeijing 100193China Department of Medical Microbiology and Parasitology and Department of Infectious Diseases of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou 310058China State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China

Background:Herpes simplex virus type 1(HSV-1)is a ubiquitous infectious pathogen that widely affects human health.To decipher the complicated human-HSV-1 interactions,a comprehensive protein-protein interaction(PPI)network between human and HSV-1 is highly demanded.Methods:To complement the experimental identification of human-HSV-1 PPIs,an integrative strategy to predict proteome-wide PPIs between human and HSV-1 was developed.For each human-HSV-1 protein pair,four popular PPI inference methods,including interolog mapping,the domain-domain interaction-based method,the domain-motif interaction-based method,and the machine learning-based method,were optimally implemented to generate four interaction probability scores,which were further integrated into a final probability score.Results:As a result,a comprehensive high-confidence PPI network between human and HSV-1 was established,covering 10,432 interactions between 4,546 human proteins and 72 HSV-1 proteins.Functional and network analyses of the HSV-1 targeting proteins in the context of human interactome can recapitulate the known knowledge regarding the HSV-1 replication cycle,supporting the overall reliability of the predicted PPI network.Considering that HSV-1 infections are implicated in encephalitis and neurodegenerative diseases,we focused on exploring the biological significance of the brain-specific human-HSV-1 PPIs.In particular,the predicted interactions between HSV-1 proteins and Alzheimer's-disease-related proteins were intensively investigated.Conclusion:The current work can provide testable hypotheses to assist in the mechanistic understanding of the human-HSV-1 relationship and the anti-HSV-1 pharmaceutical target discovery.To make the predicted PPI network and the datasets freely accessible to the scientific community,a user-friendly database browser was released at http://***/HintHSV/index.php.

关键词： human-virus interaction protein-protein interaction prediction herpes simplex virus type 1 Alzheimer's disease

Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items

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Integrative Zoology 2022年第6期17卷 1147-1161页

作者： Zhenwei CUI Andrew JHOLMES Wenjuan ZHANG Dalong HU Qi shao Zhenlong WANG jiqi LU David RAUBENHEIMER Centre for Nutritional Ecology Centre for Sport Nutrition and HealthZhengzhou UniversityZhengzhouChina School of Life Sciences Institute of Biodiversity and EcologyZhengzhou UniversityZhengzhouChina School of Basic Medical Sciences Zhengzhou UniversityZhengzhouChina Charles Perkins Centre School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia School of Life Sciences Henan Agricultural UniversityZhengzhouChina

Food supply is one of the major drivers of animal behavior,and the gut microbiome is an important mediator be-tween food supply and its effects on physiology.However,predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging.We propose this reﬂects processes occurring at different scales.Inadequate accounting for the multi-level complexity of nutrition(nutrients,foods,diets)obscures the diet inﬂuence on microbiome and subsequently animal.Here,we present a detailed year-round,multi-level analysis of diet and microbiome changes in a wild population of a temperate primate,the rhesus macaque(Macaca mulatta).Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 sea-sons(total 120 days observations).For each individual,we found signiﬁcant variation in the microbiome between all 4 seasons.This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds—sets of taxa sharing similar responses to nutrient intake.We conclude that study of diet,microbiome,and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake.Although microbiome response to diet does show variation in species-level taxa in response to food items,there is greater commonality in response at the level of guilds.A goal for microbiome researchers should be to identify genes encoding microbial attributes that can deﬁne such guilds.

关键词： gut microbiome macaque nutrition nutritional ecology seasonality

What does it mean to be a macronutritional generalist? A case study using wild rhesus macaques(Macaca mulatta)

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What does it mean to be a macronutritional generalist? A cas...

第十六届全国野生动物生态与资源保护学术研讨会

作者： Zhenwei Cui Ying Zhang Jiabao Yan Yifeng Zhang Yunlong,Dong Cuiru,Ren Hongjie Song Qi shao David Raubenheimer jiqi Lu Centre for Nutritional Ecology Zhengzhou University

Dietary generalism is widely associated with ecological flexibility, but the mechanisms of this relationship remain poorly understood. A recent body of theory concerning the relationship between generalism/specialism at the levels of foods selected vs. nutrients ingested, termed multi-level dietary niche theory, offers powerful opportunities for furthering the understanding of the dietary generalist-specialist spectrum. We applied this framework in an intensive and extensive study of food selection and nutrient regulation responses to natural resource variation by the most ecologically generalist non-human primate, the rhesus macaque(Macaca mulatta), which is also the only species thus far identified in the wild to show a pattern of macronutrient regulation predicted on theoretical grounds to be associated with ecological generalism. We used full-day individual animal follows over 17 successive seasons to examine the patterns of resource variation and the macaques’ responses to these at the levels of food selection and patterns of macronutrient intake. We additionally analysed seasonal availability over 10 years of the keystone resource, fat-and carbohydrate-rich acorns. Our results showed that the generalist mode of macronutrient regulation is not associated with exploitation of many different foods, as previously predicted, but with few foods that vary widely in their macronutrient composition and fluctuate predictably in their relative availability across seasons and across alternate years. We integrate these results with energy budgets and literature data to build a verbal model of how the generalist pattern of macronutrient regulation interfaces between nutritional physiology and resource variability to buffer rhesus macaques from broad climatic fluctuations.

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西藏苔藓植物新记录科——苞片苔科

植物资源与环境学报 2023年第5期32卷 95-97页

作者：洪嘉康宋晓彤谷际岐李微董营卓嘎巴永邵小明中国农业大学生物学院北京100193 中国农业大学资源与环境学院生物多样性与有机农业北京市重点实验室北京100193 中国科学院沈阳应用生态研究所森林生态与管理重点实验室辽宁沈阳110016 西藏农牧学院西藏高原生态研究所西藏林芝860000

经过野外调查和标本鉴定,报道了西藏苔藓植物新记录1种,即苞片苔(Calycularia crispula Mitt.),且苞片苔属(Calycularia Mitt.)和苞片苔科(Calyculariaceae)也是西藏新记录属和新记录科。凭证标本存放于中国农业大学生物学院植物标本室(... 详细信息

经过野外调查和标本鉴定,报道了西藏苔藓植物新记录1种,即苞片苔(Calycularia crispula Mitt.),且苞片苔属(Calycularia Mitt.)和苞片苔科(Calyculariaceae)也是西藏新记录属和新记录科。凭证标本存放于中国农业大学生物学院植物标本室(BAU)。

关键词：西藏苞片苔科新记录

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赣杭构造带中段岩石圈电性结构研究

高校地质学报 2022年第3期28卷 440-450页

作者：方吉琦邓居智陈辉余辉严加永东华理工大学地球物理与测控技术学院南昌330199 中国地质科学院地球深部探测中心北京100037

赣杭构造带(简称赣杭带)位于扬子板块和华夏板块的结合部,是中国重要的铀多金属矿成矿带,发育一系列中酸性火山—侵入杂岩;前人对岩浆喷发和侵入的地球动力学背景仍然存在诸多争议。文章对赣杭带中段(盛源盆地)及邻区收集的大地电磁测深... 详细信息

赣杭构造带(简称赣杭带)位于扬子板块和华夏板块的结合部,是中国重要的铀多金属矿成矿带,发育一系列中酸性火山—侵入杂岩;前人对岩浆喷发和侵入的地球动力学背景仍然存在诸多争议。文章对赣杭带中段(盛源盆地)及邻区收集的大地电磁测深(MT)数据,利用MT相位张量分解技术、二维非线性共轭梯度法(NLCG)等技术手段进行处理和反演获得到了研究区可靠的岩石圈电性结构。结合已有资料分析表明:赣杭带中段浅部火山—侵入杂岩带存在东南方向下倾的高导带和深部软流圈高导区且相连,揭示了该地区中酸性岩浆活动受区域江绍深断裂控制,在晚中生代岩石圈伸展作用下沿着区域深断裂上升侵入和喷发形成火山—侵入杂岩;该岩浆活动处在伸展构造环境与同期Izanagi板块俯冲后撤有关。

关键词：大地电磁测深法赣杭构造带二维反演电性结构岩石圈

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太行山猕猴下颌的生物力学研究

兽类学报 2001年第2期21卷 88-93页

作者：路纪琪吕九全薛德明瞿文元河南师范大学生命科学学院新乡453002

采用定点方法 ,对太行山猕猴下颌骨有关变量作了测量、统计和分析。通过对太行山猕猴下颌生物力学、异速生长的研究表明 ,雄性下颌相对较长 ,与此有关的生物力学特点是下颌髁后缘至M1近中侧长、下颌髁后缘至M3 下次小尖长和下颌支高等... 详细信息

采用定点方法 ,对太行山猕猴下颌骨有关变量作了测量、统计和分析。通过对太行山猕猴下颌生物力学、异速生长的研究表明 ,雄性下颌相对较长 ,与此有关的生物力学特点是下颌髁后缘至M1近中侧长、下颌髁后缘至M3 下次小尖长和下颌支高等阻力臂减小 ,而下颌髁长、下颌髁宽、下颌体高Ⅱ、下颌体宽Ⅱ、下颌联合长等变量则增强 ,使咀嚼力增加。这些特点均与其生态对策密切相关。研究结果还与有关材料进行了比较 ,表明太行山猕猴与国内其他地区的猕猴存在着明显差异。

关键词：太行山猕猴下颌生物力学异速生长食性

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太行山猕猴颅骨的形态学及多变量研究

兽类学报 2000年第4期20卷 263-269页

作者：吕九全路纪琪张建军薛德明瞿文元河南师范大学生命科学学院新乡453002

对 1 2例成年太行山猕猴颅骨的主要形态特征进行了描述和测量 ,并进行了初步的统计学分析。结果表明 ,成年太行山猕猴颅骨在耳点间宽 (X1 3)、上面宽 (X1 9)、左眶宽(X2 7)、右眶宽 (X2 8)、两眶宽 (X31 )、上颌齿槽弓长 (X37)等变量间... 详细信息

对 1 2例成年太行山猕猴颅骨的主要形态特征进行了描述和测量 ,并进行了初步的统计学分析。结果表明 ,成年太行山猕猴颅骨在耳点间宽 (X1 3)、上面宽 (X1 9)、左眶宽(X2 7)、右眶宽 (X2 8)、两眶宽 (X31 )、上颌齿槽弓长 (X37)等变量间存在显著的性别差异。与湘鄂、闽粤猕猴颅骨有关变量相比 ,有显著的不同。 3个猕猴种群的聚类分析结果显示 ,湘鄂、闽粤猕猴种群间的生物学距离相对较近 ,而太行山猕猴与前二种种群间的距离均较远。太行山猕猴长期适应于暖温带的气候与植被条件。

关键词：太行山猕猴颅骨形态学多变量