MicroPhenoDB Associates Metagenomic Datawith Pathogenic Microbes,Microbial Core Genes,and Human Disease Phenotypes

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.     

慢性乙型肝炎患者血清IL-17A、GP73水平与肝功能指标及病情严重程度的关系分析

摘要 目的：探讨慢性乙型肝炎(CHB)患者血清白细胞介素-17A (IL-17A)、高尔基体蛋白73(GP73)水平与肝功能指标及病情严重程度的关系。方法：选取2018年10月至2019年10月于青海大学附属医院就诊的CHB患者93例作为研究对象（CHB组）,另选取同时期于我院体检的健康志愿者33例作为对照组。比较不同病情严重程度、不同乙型肝炎e抗原（HbeAg）表达的CHB患者IL-17A、GP73水平及肝功能相关指标[丙氨酸氨基转移酶（ALT）、门冬氨酸氨基转移酶（AST）、白蛋白、总胆红素（TBiL）]的差异,并分析IL-17A、GP73水平与患者病情严重程度及肝功能相关指标的相关性。结果：CHB组中轻度、中度、重度患者血清IL-17A、GP73、ALT、AST及TBiL水平均高于对照组,白蛋白水平低于对照组（P<0.05）,并且随着CHB患者病情严重程度的加重其血清中IL-17A、GP73、ALT、AST及TBiL水平逐渐升高,白蛋白水平逐渐降低（P<0.05）。CHB组HbeAg阴性患者血清中的IL-17A、GP73、ALT及AST水平均明显高于HbeAg阳性患者（P<0.05）,而白蛋白和TBiL水平无明显差异（P>0.05）。CHB患者血清IL-17A、GP73均与ALT、AST及TBiL呈正相关,与白蛋白呈负相关,与患者病情严重程度呈正相关（P<0.05）。结论：CHB患者血清中IL-17A、GP73水平明显升高,且与患者病情严重程度及肝功能相关指标呈明显相关性,临床中可联合检测用于患者病情评估及预后监测。     

Effect of Peroxisome Proliferator-Activated Receptor-γ Coactivator-1 Alpha Variants on Spontaneous Clearance and Fibrosis Progression during Hepatitis C Virus Infection in Moroccan Patients

Virologica Sinica - Hepatitis C virus (HCV) is still one of the main causes of liver disease worldwide. Metabolic disorders, including non-alcoholic fatty liver disease (NAFLD), induced by HCV have...     

IGF-1 concentration patterns and their relationship with follicle development after weaning in young sows fed different pre-mating diets

Piglet birth weight and within-litter birth weight variation are important for piglet survival and growth. Pre-mating diets may improve IGF-1 and follicle development during the weaning-to-oestrus interval (WEI) and subsequent piglet birth weight. The objective of this study was to modulate IGF-1 concentration during late lactation and the WEI of young sows by using specific pre-mating diets supplemented with microfibrillated cellulose (MF), l-carnitine (LC) or l-arginine (AR). A further objective was to investigate the relationship between IGF-1 and subsequent follicle development and oestrus and ovulation characteristics. In total, 56 first-parity and 20 second-parity sows in three consecutive batches were used for this experiment. Sows received daily either wheat (CON) or wheat plus MF, LC or AR at one of two supplementation levels (low and high) during last week of lactation and WEI. From weaning onwards, follicle and corpus luteum (CL) diameters were repeatedly measured with ultrasound. Blood samples were collected during the WEI for IGF-1 and on day 21 of pregnancy for progesterone analyses, respectively. Insulin-like growth factor-1 concentration, follicle diameter, oestrus and ovulation characteristics and CL diameter were not affected by pre-mating diets. Low IGF-1 class (≤156 ng/ml, N = 22) sows had smaller follicles at weaning (3.5 v. 3.8 mm, P < 0.05) and a longer weaning-to-ovulation interval (147.2 v. 129.8 h, P < 0.05) than high IGF-1 class sows. In first-parity sows, high loin muscle depth (LM) loss sows (≥8%, N = 28) had lower IGF-1 concentrations at weaning (167 v. 214 ng/ml, P < 0.05) compared to low LM loss sows (<8%, N = 28). However, after weaning, IGF-1 concentrations increased and did not differ between high LM loss and low LM loss sows. In conclusion, the different supplemented compounds in pre-mating diets did not improve IGF-1 concentrations around weaning in young sows. Furthermore, high body condition loss caused lower IGF-1 concentrations at weaning, but these levels rapidly recovered after weaning and were related to follicle development and the interval from weaning to ovulation.     

The ecology of chronic wasting disease in wildlife

Prions are misfolded infectious proteins responsible for a group of fatal neurodegenerative diseases termed transmissible spongiform encephalopathy or prion diseases. Chronic Wasting Disease (CWD) is the prion disease with the highest spillover potential, affecting at least seven Cervidae (deer) species. The zoonotic potential of CWD is inconclusive and cannot be ruled out. A risk of infection for other domestic and wildlife species is also plausible. Here, we review the current status of the knowledge with respect to CWD ecology in wildlife. Our current understanding of the geographic distribution of CWD lacks spatial and temporal detail, does not consider the biogeography of infectious diseases, and is largely biased by sampling based on hunters' cooperation and funding available for each region. Limitations of the methods used for data collection suggest that the extent and prevalence of CWD in wildlife is underestimated. If the zoonotic potential of CWD is confirmed in the short term, as suggested by recent results obtained in experimental animal models, there will be limited accurate epidemiological data to inform public health. Research gaps in CWD prion ecology include the need to identify specific biological characteristics of potential CWD reservoir species that better explain susceptibility to spillover, landscape and climate configurations that are suitable for CWD transmission, and the magnitude of sampling bias in our current understanding of CWD distribution and risk. Addressing these research gaps will help anticipate novel areas and species where CWD spillover is expected, which will inform control strategies. From an ecological perspective, control strategies could include assessing restoration of natural predators of CWD reservoirs, ultrasensitive CWD detection in biotic and abiotic reservoirs, and deer density and landscape modification to reduce CWD spread and prevalence.     

Does operational sex ratio influence relative strength of purging selection in males versus females?

According to theory, sexual selection in males may efficiently purge mutation load of sexual populations, reducing or fully compensating ‘the cost of males’. For this to occur, mutations not only need to be deleterious to both sexes, they also must affect males more than females. A frequently overlooked problem is that relative strength of selection on males versus females may vary between environments, with social conditions being particularly likely to affect selection in males and females differently. Here, we induced mutations in red flour beetles (Tribolium castaneum) and tested their effect in both sexes under three different operational sex ratios (1:2, 1:1 and 2:1). Induced mutations decreased fitness of both males and females, but their effect was not stronger in males. Surprisingly, operational sex ratio did not affect selection against deleterious mutations nor its relative strength in the sexes. Thus, our results show no support for the role of sexual selection in the evolutionary maintenance of sex.     

谷氨酸棒杆菌碱基编辑的条件优化

近年来,基于CRISPR/Cas9的碱基编辑技术因其具有不产生DNA双链断裂、无需外源DNA模板、不依赖宿主同源重组修复的优势,已经逐渐发展成为一种强大的基因组编辑工具,在动物、植物、酵母和细菌中得到了开发和应用。研究团队前期已在重要的工业模式菌株谷氨酸棒杆菌中开发了一种多元自动化的碱基编辑技术MACBETH,为进一步优化该方法,提高碱基编辑技术在谷氨酸棒杆菌中的应用效率,本研究首先在谷氨酸棒杆菌中构建了基于绿色荧光蛋白(GFP)的检测系统:将GFP基因的起始密码子ATG人工突变为ACG,GFP无法正常表达,当该密码子的C经编辑后恢复为T,即实现GFP蛋白的复活,结合流式细胞仪分析技术,可快速衡量编辑效率。然后,构建针对靶标位点的碱基编辑工具,经测试,该位点可成功被编辑,在初始编辑条件下碱基编辑效率为(13.11±0.21)%。在此基础上,通过对不同培养基类型、诱导初始OD600、诱导时间、诱导物浓度进行优化,确定最优编辑条件是:培养基为CGXII,初始OD600为0.05,诱导时间为20 h,IPTG浓度为0.01 mmol/L。经过优化,编辑效率达到(30.35±0.75)%,较初始条件提高了1.3倍。最后,选取原编辑条件下编辑效率较低的位点,进行了优化后编辑条件下的编辑效率评估,结果显示,不同的位点在最优编辑条件下的编辑效率提高了1.7–2.5倍,进一步证实该优化条件的有效性及通用性。研究结果为碱基编辑技术在谷氨酸棒杆菌中更好的应用提供了重要的参考价值。     

城市群新冠疫情时空分布格局与分异机制的地理探测

自从2019年12月湖北武汉爆发新型冠状病毒（COVID-19）以来,疫情在全国范围内迅速传播并蔓延。城市群既是我国新型城镇化主体特定的空间组织形态,也是相互连接的城市网,集合了相当数量不同性质、类型和等级规模的城市,城市群经济发展程度较高、人口密度大,交通发达,是疫情传染扩散-关联的重点区域,因而跨区域感染风险高,联防联控难度大。以疫情集中地区城市群为研究对象,通过核密度分析聚焦重点研究的城市群,从多层空间尺度对疫情在数量、人口迁移和空间分布上进行测度,利用空间自相关分析疫情分布特征,运用地理探测器方法客观地测度城市群疫情发展的差异性主导因素,从景观格局中挖掘相关主导因子,为生态、安全的空间规划和治理提供科学依据和思路。结果显示：①全国范围感染人数核密度高值区的空间分布与长江中游城市群和三大沿海城市群范围耦合,首位核心城市确诊感染数在城市群中占比均较高,城市群疫情扩散分布呈现典型的由核心城市向外辐射的特征,湖北地区迁出的人数对迁往地区的疫情形势构成一定程度的影响;②全国范围的COVID-19感染人数和感染增长率分布存在显著空间集聚特征,城市群范围感染人数的空间聚集性从长江中游城市群向其他城市群依次减弱;③地理探测器识别出人口密度、城乡建设、交通、卫生、科技、生态绿地为疫情的主导因素,并且交互后所产生的共同作用增加了对疫情的解释力;④生态与建设用地景观格局对疫情的解释能力较强,其中建设用地的聚集性和生态用地的蔓延性为主要因子。     

虎掌菌菌丝富硒培养的研究

为生产合适的硒源提供一种思路,以菌丝体生物量、含硒量、还原糖、氨态氮和蛋白质为指标,采用四因素三水平正交设计法优化虎掌菌的富硒发酵条件,探讨不同浓度的硒对虎掌菌固体培养菌丝生长和液体培养产生的生物组分的影响。结果表明,高浓度的硒抑制虎掌菌菌丝体生长;正交试验选择不同的衡量指标,由极差分析得出各因素的影响程度大小,结合证实试验得到以还原糖为指标的最优组合为葡萄糖6%(质量分数)、酵母浸膏3%(质量分数)、KH_2PO_4 0.1%(质量分数)、Na_2SeO_3 0.6 mmol/L,其菌丝体生物量和氨态氮含量较高。与对照相比,加硒后虎掌菌发酵液中氨态氮、还原糖和总糖含量显著增加(P0.05);当硒浓度为0.5 mmol/L时,氨态氮、还原糖和总糖含量均达到最高值。菌丝体生物量和可溶性蛋白质分别在硒浓度为0.2 mmol/L和0.4 mmol/L时达到最大值。虎掌菌富硒培养后,发酵液的营养成分含量会发生变化。     

A penalized structural equation modeling method accounting for secondary phenotypes for variable selection on genetically regulated expression from PrediXcan for Alzheimer's disease

As the global burden of mental illness is estimated to become a severe issue in the near future, it demands the development of more effective treatments. Most psychiatric diseases are moderately to highly heritable and believed to involve many genes. Development of new treatment options demands more knowledge on the molecular basis of psychiatric diseases. Toward this end, we propose to develop new statistical methods with improved sensitivity and accuracy to identify disease‐related genes specialized for psychiatric diseases. The qualitative psychiatric diagnoses such as case control often suffer from high rates of misdiagnosis and oversimplify the disease phenotypes. Our proposed method utilizes endophenotypes, the quantitative traits hypothesized to underlie disease syndromes, to better characterize the heterogeneous phenotypes of psychiatric diseases. We employ the structural equation modeling using the liability‐index model to link multiple genetically regulated expressions from PrediXcan and the manifest variables including endophenotypes and case‐control status. The proposed method can be considered as a general method for multivariate regression, which is particularly helpful for psychiatric diseases. We derive penalized retrospective likelihood estimators to deal with the typical small sample size issue. Simulation results demonstrate the advantages of the proposed method and the real data analysis of Alzheimer's disease illustrates the practical utility of the techniques. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative database.