库木塔格沙漠土壤细菌多样性及具有群体感应抑制活性放线菌筛选

【背景】群体感应抑制剂(quorum sensing inhibitor,QSI)作为抗生素潜在替代品,可有效降低致病菌传染性和毒性。沙漠土壤蕴藏着丰富的放线菌资源,是挖掘群体感应抑制剂的重要来源。【目的】解析库木塔格沙漠土壤细菌群落多样性,筛选并挖掘群体感应抑制活性放线菌资源。【方法】采用Illumina Nova Seq高通量测序技术揭示库木塔格沙漠土壤细菌群落组成,利用可培养方法进行土壤放线菌分离和鉴定;选用紫色杆菌CV026模型筛选群体感应抑制活性放线菌,并对其功能特性进行初步评价。【结果】Illumina Nova Seq高通量测序结果显示,样品土壤细菌涉及23门96目150属,优势菌门为变形菌门(Proteobacteria,61%)、放线菌门(Actinobacteria,28%),其中分枝杆菌属(Mycobacterium)为放线菌门最优势菌属(87.3%),其次为红球菌属(Rhodococcus,6.8%)和丙酸杆菌属(Cutibacterium,0.9%)。可培养方法共分离到108株放线菌,归属9科10属,其中优势菌属为链霉菌属(Streptomyces),占65....     

气候变化和经济发展对肾综合征出血热发生的影响

肾综合征出血热(hemorrhagic fever with renal syndrome, HFRS)是一种啮齿动物传播的自然疫源性疾病, 危害严重, 已成为全球重要的公共卫生问题。本研究采用数理统计模型及小波分析方法, 对陕西省西安市鄠邑区1984-2016年HFRS的发生与鼠类、气候和经济因素的关系进行分析, 探讨气候和经济因素对HFRS发生的影响。小波分析结果表明, 该地区的HFRS暴发史可能分为两个时期, 推测每个时期具有不同的主要宿主, 在2002年褐家鼠(Rattus norvegicus)可能取代黑线姬鼠(Apodemus agrarius)成为HFRS疫源地的主要宿主。广义可加模型模拟结果表明, HFRS的发生与1984-2001年黑线姬鼠密度间存在极显著非线性效应(F_2.06,9.02 = 102.415, P < 0.01), 两者间显现为正相关; 与2002-2016年的褐家鼠密度间呈正相关(F_1.67,9.02 = 73.929, P < 0.01); HFRS主要宿主的这种变化可能与当地气候变化和经济发展有关: HFRS的发生与年平均温度存在极显著的非线性效应(F_2.93,9.02 = 12.164, P < 0.01), 两者间呈负相关; 同样, HFRS的发生与上一年的国内生产总值(GDP)也存在显著非线性效应(F_1.70,9.02 = 2.917, P < 0.05), 两者间也呈负相关。结构方程模型通过直接和间接的影响途径证明了这种转移机制, 发现温度对HFRS发生有显著的直接负向影响以及通过褐家鼠的间接正向影响; GDP对HFRS发生有直接的负向影响。本研究表明HFRS的发生与气候变化和经济发展相关, 两者均能影响HFRS的暴发, 该结论有助于今后更好地对HFRS疾病进行预防和控制。     

Identifying Neural Patterns of Functional Dyspepsia Using Multivariate Pattern Analysis: A Resting-State fMRI Study

Background

Previous imaging studies on functional dyspepsia (FD) have focused on abnormal brain functions during special tasks, while few studies concentrated on the resting-state abnormalities of FD patients, which might be potentially valuable to provide us with direct information about the neural basis of FD. The main purpose of the current study was thereby to characterize the distinct patterns of resting-state function between FD patients and healthy controls (HCs).

Methodology/Principal Findings

Thirty FD patients and thirty HCs were enrolled and experienced 5-mintue resting-state scanning. Based on the support vector machine (SVM), we applied multivariate pattern analysis (MVPA) to investigate the differences of resting-state function mapped by regional homogeneity (ReHo). A classifier was designed by using the principal component analysis and the linear SVM. Permutation test was then employed to identify the significant contribution to the final discrimination. The results displayed that the mean classifier accuracy was 86.67%, and highly discriminative brain regions mainly included the prefrontal cortex (PFC), orbitofrontal cortex (OFC), supplementary motor area (SMA), temporal pole (TP), insula, anterior/middle cingulate cortex (ACC/MCC), thalamus, hippocampus (HIPP)/parahippocamus (ParaHIPP) and cerebellum. Correlation analysis revealed significant correlations between ReHo values in certain regions of interest (ROI) and the FD symptom severity and/or duration, including the positive correlations between the dmPFC, pACC and the symptom severity; whereas, the positive correlations between the MCC, OFC, insula, TP and FD duration.

Conclusions

These findings indicated that significantly distinct patterns existed between FD patients and HCs during the resting-state, which could expand our understanding of the neural basis of FD. Meanwhile, our results possibly showed potential feasibility of functional magnetic resonance imaging diagnostic assay for FD.     

Whole-Brain Functional Connectivity Identification of Functional Dyspepsia

Recent neuroimaging studies have shown local brain aberrations in functional dyspepsia (FD) patients, yet little attention has been paid to the whole-brain resting-state functional network abnormalities. The purpose of this study was to investigate whether FD disrupts the patterns of whole-brain networks and the abnormal functional connectivity could reflect the severity of the disease. The dysfunctional interactions between brain regions at rest were investigated in FD patients as compared with 40 age- and gender- matched healthy controls. Multivariate pattern analysis was used to evaluate the discriminative power of our results for classifying patients from controls. In our findings, the abnormal brain functional connections were mainly situated within or across the limbic/paralimbic system, the prefrontal cortex, the tempo-parietal areas and the visual cortex. About 96% of the subjects among the original dataset were correctly classified by a leave one-out cross-validation approach, and 88% accuracy was also validated in a replication dataset. The classification features were significantly associated with the patients’ dyspepsia symptoms, the self-rating depression scale and self-rating anxiety scale, but it was not correlated with duration of FD patients (p>0.05). Our results may indicate the effectiveness of the altered brain functional connections reflecting the disease pathophysiology underling FD. These dysfunctional connections may be the epiphenomena or causative agents of FD, which may be affected by clinical severity and its related emotional dimension of the disease rather than the clinical course.     

Regional Brain Structural Abnormality in Meal-Related Functional Dyspepsia Patients: A Voxel-Based Morphometry Study

Background and Aims

Brain dysfunction in functional dyspepsia (FD) has been identified by multiple neuroimaging studies. This study aims to investigate the regional gray matter density (GMD) changes in meal-related FD patients and their correlations with clinical variables, and to explore the possible influence of the emotional state on FD patients’s brain structures.

Methods

Fifty meal-related FD patients and forty healthy subjects (HS) were included and underwent a structural magnetic resonance imaging scan. Voxel-based morphometry analysis was employed to identify the cerebral structure alterations in meal-related FD patients. Regional GMD changes'' correlations with the symptoms and their durations, respectively, have been analyzed.

Results

Compared to the HS, the meal-related FD patients showed a decreased GMD in the bilateral precentral gyrus, medial prefrontal cortex (MPFC), anterior cingulate cortex (ACC) and midcingulate cortex (MCC), left orbitofrontal cortex (OFC) and right insula (p<0.05, FWE Corrected, Cluster size>50). After controlling for anxiety and depression, the meal-related FD patients showed a decreased GMD in the bilateral middle frontal gyrus, left MCC, right precentral gyrus and insula (p<0.05, FWE Corrected, Cluster size>50). Before controlling psychological factors, the GMD decreases in the ACC were negatively associated with the symptom scores of the Nepean Dyspepsia Index (NDI) (r = −0.354, p = 0.048, Bonferroni correction) and the duration of FD (r = −0.398, p = 0.02, Bonferroni correction) respectively.

Conclusions

The regional GMD of meal-related FD patients, especially in the regions of the homeostatic afferent processing network significantly differed from that of the HS, and the psychological factors might be one of the essential factors significantly affecting the regional brain structure of meal-related FD patients.     

黑果枸杞不同组织内生细菌群落多样性

【目的】黑果枸杞是我国荒漠区特有的药用盐生植物,本研究分析了黑果枸杞不同组织中内生细菌群落多样性特征及分布规律。【方法】应用Illumina MiSeq高通量测序技术对黑果枸杞内生细菌的16S rRNAV5-V7区域序列进行测定,并分析群落组成、多样性及功能等生物学信息。【结果】黑果枸杞不同组织内生细菌群落多样性及功能均有较大的差异。花、叶、果、茎和根产生的OTUs分别是182、173、119、187和254,群落多样性表现为根花果、茎叶。从门水平上看,变形菌门是优势菌门,在不同组织中均有分布,花、叶、果、茎和根中的相对丰度分别为87.66%、41.51%、81.76%、97.67%和61.85%。在属水平上显示内生细菌的分布表现出器官差异性。花部能够准确分类的优势菌属为沙雷氏菌属和不动杆菌属,相对丰度分别为11.57%和8.55%。叶部为红球菌属和慢生根瘤菌属,相对丰度分别为29.68%和5.53%。果实中为泛菌属、红球菌属和沙雷氏菌属,相对丰度分别为23.12%、5.52%和4.29%。茎部为沙雷氏菌属和假单胞菌属,相对丰度分别为12.03%和17.71%。根部为盐单胞菌属、Fodinicurvata和Lipingzhangella,相对丰度分别为24.18%、5.16%和4.86%。在不同组织中分布较广的盐单胞菌、沙雷氏菌、不动杆菌、红球菌、泛菌等菌属均具有较高耐盐性和促生、生防、降解有机污染物及抗氧化等功能。PICRUSt功能预测分析显示,黑果枸杞组织中内生细菌功能中涉及丰富的多糖、萜类和酮类、酶及维他命等次生代谢产物的生物合成。【结论】黑果枸杞内生细菌具有丰富的群落和功能多样性,拥有多种益生功能性状,也含有多个与人和植物体代谢相关的功能信息。不同组织优势菌属和功能信息各有不同,其中根部的内生细菌物种最丰富,花部和茎部参与各种代谢调控的细菌丰度最高。此外,不同组织中还含有大量未知种属的微生物类群,这些都为内生细菌功能利用和挖掘新的有益微生物资源提供广阔的发展空间。     

TaqMan-MGB探针检测文森巴尔通体博格霍夫亚种实时荧光定量PCR方法的建立及应用

【目的】应用TaqMan-MGB探针技术,建立具有种水平特异性、高敏感性的荧光定量PCR方法,用于快速检测文森巴尔通体博格霍夫亚种。【方法】在序列特异性扩增区标记(Sequence characterized amplifiedregion,SCAR)技术基础上,依据文森巴尔通体博格霍夫亚种一段特有的基因序列设计探针和引物,分别优化扩增反应的退火温度、探针和引物的反应浓度;分析此方法的特异性、敏感性及重复性;绘制标准曲线,评估PCR反应的扩增效率和稳定性。【结果】本研究设计的TaqMan-MGB探针具有种水平特异性;最低检出限为每个PCR反应11个拷贝;组内和组间的变异系数CV值分别为0.12%-0.70%和0.14%-0.55%,在允许范围内;标准曲线线性关系良好(R2=1),扩增效率高(E=104.7%)。【结论】本研究建立的基于TaqMan-MGB探针技术的荧光定量PCR方法能够在种水平特异性、高灵敏度检出文森巴尔通体博格霍夫亚种,为这种巴尔通体所引起的一系列疾病的早期快速诊断、监测和流行病学调查等研究提供有效手段。     

Quantitative Analysis of Burden of Infectious Diarrhea Associated with Floods in Northwest of Anhui Province,China: A Mixed Method Evaluation

Background

Persistent and heavy rainfall in the upper and middle Huaihe River of China brought about severe floods during the end of June and July 2007. However, there has been no assessment on the association between the floods and infectious diarrhea. This study aimed to quantify the impact of the floods in 2007 on the burden of disease due to infectious diarrhea in northwest of Anhui Province.

Methods

A time-stratified case-crossover analysis was firstly conducted to examine the relationship between daily cases of infectious diarrhea and the 2007 floods in Fuyang and Bozhou of Anhui Province. Odds ratios (ORs) of the flood risk were quantified by conditional logistic regression. The years lived with disability (YLDs) of infectious diarrhea attributable to floods were then estimated based on the WHO framework of the calculating potential impact fraction in the Burden of Disease study.

Results

A total of 197 infectious diarrheas were notified during the exposure and control periods in the two study areas. The strongest effect was shown with a 2-day lag in Fuyang and a 5-day lag in Bozhou. Multivariable analysis showed that floods were significantly associated with an increased risk of the number cases of infectious diarrhea (OR = 3.175, 95%CI: 1.126–8.954 in Fuyang; OR = 6.754, 95%CI: 1.954–23.344 in Bozhou). Attributable YLD per 1000 of infectious diarrhea resulting from the floods was 0.0081 in Fuyang and 0.0209 in Bozhou.

Conclusions

Our findings confirm that floods have significantly increased the risks of infectious diarrhea in the study areas. In addition, prolonged moderate flood may cause more burdens of infectious diarrheas than severe flood with a shorter duration. More attention should be paid to particular vulnerable groups, including younger children and elderly, in developing public health preparation and intervention programs. Findings have significant implications for developing strategies to prevent and reduce health impact of floods.     

Genetic differentiation of Arthrobacter population from heavy metal-contaminated environment

Six samples containing extremely high concentration of Pb, Zn, and Cd were obtained from the layers of 5–10 cm and 25–30 cm three tailing piles, with ages of about 10, 20 and more than 80 years, respectively. Then, 48 bacterial strains were obtained from these samples, and subsequently their phylogenetic positions were determined by analysis on the partial sequence of 16S rRNA gene (fragment length ranging from 474 to 708 bp). These isolates were members of the Arthrobacter genus, phylogenetically close to A. keyseri and A. ureafaciens, with sequence ranging from 99.1% to 100%. Furthermore, genetic variation between subpopulations from different samples was revealed by analysis on their randomly amplified polymorphic DNA profile. Nei genetic distance showed that the greatest differentiation occurred between subpopulation A and C. Notably, either genetic distance between subpopulations from the layers of 5–10 cm and 25–30 cm of each tailing pile or between same layers of different tailing pile increased with the history of tailings. Moreover, correlation analysis showed that soluble Pb has a significantly negative relationship with Nei’ gene diversity of subpopulation. It was assumed that soluble Pb may be responsible for the reduced genetic diversity of the Arthrobacter population. Our data provided evidence that genetic differentiation of microbial populations was consistent with the changes of environmental factors, particularly heavy metals. Translated from Acta Ecologica Sinica, 2005, 25(10): 2569–2573 [译自: 生态学报]     

黑果枸杞不同组织内生真菌群落组成及生态功能分析

探究了新疆盐生植物黑果枸杞不同组织中内生真菌群落的组成及多样性,为深入研究盐碱、干旱等环境下内生真菌与宿主的互作机制,筛选和开发促生、防病和抗逆等功能的有益内生真菌资源提供科学依据。利用ITS高通量测序技术比较黑果枸杞不同组织真菌群落组成及差异,并采用FUNGuild数据库预测真菌群落生态功能。测序共获得高质量内生真菌序列354 058条,涉及291个OTUs,分属于9门、19纲、34目、50科、60属。α多样性指数分析表明,根、果中真菌群落多样性和丰富度程度较高,叶居中,花的多样性最低,茎的丰富度最低。对黑果枸杞内生真菌群落组成和优势菌群的分析表明,子囊菌门为优势菌门,花、叶、果、茎和根中相对丰度分别为86.85%、72.36%、75.97%、84.44%和85.02%。链格孢属为黑果枸杞植株中的核心属,不同组织中均有分布,在花、叶、果、茎和根中占比分别为85.41%、69.79%、47.07%、79.94%和36.97%。较优势的菌尚有枝孢属、枝顶孢属、新凸轮孢菌属、茎点霉属和楔孢黑粉菌属等真菌。这些菌多具有促生、抗逆等特性,在宿主对盐碱、干旱等极端环境的适应性方面有着潜在功能。各组织独有属的相对丰度均未超过1%。共有菌和独有菌在不同组织中的组成和相对丰度差异较大。经FUNGuild软件平台解析显示,黑果枸杞中病理-腐生-共生营养型的相对丰度最高,在花、叶、果、茎和根中分别为85.41%、69.84%、47.24%、79.98%和37.09%。果和叶中含多种相对丰度≥1%的条件致病菌,而根中腐生真菌种类较多。黑果枸杞中蕴含着功能丰富的内生真菌菌群,在不同组织中的组成及其生态功能差异较大,同时还含有大量未鉴定出种属和未定义的功能菌群,这些可为黑果枸杞功能菌群发掘提供数据参考。