微生物单细胞基因组技术及其在环境微生物研究中的应用

单细胞及单细胞基因组学研究是近年生命科学研究的热点之一,微生物单细胞基因组学研究是继微生物元基因组学(又称宏基因组学,Metagenomics)之后新发展起来的,可有效获取环境中大量无法培养的微生物遗传信息的技术。微生物单细胞基因组技术包括单细胞获取、全基因组扩增、全基因组测序以及数据分析等步骤,目前该技术在环境微生物研究中的应用主要集中于探索未被元基因组技术或其它常规技术探测到的新型功能基因,或是对环境中物种丰度极小的未培养微生物的发现,以及对微生物细胞生命进化过程的研究等。本文对微生物单细胞基因组技术中单细胞获取和全基因组扩增所涉及到的不同方法以及应用此技术对环境微生物取得的主要研究进展进行综述。     

病原微生物致病岛的研究

致病岛是病原微生物通过基因水平转移获得的外源DNA,它是在研究致病性肠道菌的基因组结构和致病性的基础上发展起来的,并在其他革兰氏阴性和阳性致病菌中得到证实。本就各类病原菌致病岛的研究近况作一综述,同时介绍了致病岛的特征,讨论了致病岛在微生物进化中的意义及与tRNA基因的关系。     

乳及乳制品中病原微生物溯源技术研究进展

牛奶营养丰富,素有"白色血液"之称,随着公众对食源性疾病原因和来源问责制的需求增加,准确追踪特定食源性病原微生物在暴发过程中所经过的途径变得越来越重要。微生物溯源研究有助于人们更深入地了解病原微生物种群结构及其多样性的起源和进化,为病原微生物的检验、流行监测、综合防治等研究提供重要的信息资料和科学依据。在牛奶中病原微生物溯源技术研究中,光谱技术、质谱技术、分子方法、全基因组测序等方法均发挥了重要作用。本文根据近年国内外相关文献资料,对检测奶及奶制品中病原微生物常用溯源技术的原理和应用进行了概述。     

宏基因组学与动物病原微生物检测

宏基因组学（ metagenome）是直接从土壤、海水、人及动物胃肠道、口腔、呼吸道、皮肤等环境中获取样品DNA,利用载体将其克隆到替代宿主细胞中构建宏基因文库,以高通量检测为主要技术来研究特定环境中全部微生物的基因组及筛选活性物质和基因的新兴学科。利用宏基因组学技术不仅能够有效地检测特定环境的微生物群落结构,扩展了微生物资源的利用空间,发展了新兴的高通量检测技术,丰富了生物信息学内容。基于宏基因组学研究方法在环境微生物研究中的优势,对近年来相关领域、方法及其在人及动物病原微生物研究中的应用进行综述,以期将此方法用于实验动物病原微生物的调查分析及动物疫情、生物安全的监测。     

基因组大数据在生物安全中的应用

基因组大数据时代的来临,为生物安全领域带来了前所未有的机遇。我们主要介绍基因组大数据在生物安全中的应用,重点在病原进化溯源分析、微生物基因组科学研究、精准医学发展等方面的应用,并对其未来的发展进行了讨论和展望。     

DNA微阵列技术在细菌感染后宿主反应研究中的应用

感染性疾病是病原微生物和宿主紧密相互作用的结果。深入理解宿主对病原微生物感染发生反应的分子基础是预防感染性疾病发生和组织损伤的必要条件。本文通过介绍体内、体外2种感染模型中宿主对细胞内和细胞外致病菌感染后的基因表达谱变化,简述了DNA微阵列技术在病原菌一宿主相互作用中宿主反应研究中的应用。     

病原微生物毒力因子与宿主细胞信号通路相互作用研究进展

病原微生物与宿主的相互作用是感染性疾病发生的基础,涉及病原微生物在宿主体内的生存、复制、传播及致病等多个过程。病原菌在进化过程中发展了多种策略以攻击宿主,其中最重要的一种方式就是通过毒力蛋白影响宿主细胞信号通路,病原菌可以通过多种方式阻断宿主信号通路的激活,如乙酰化、β消除等。研究病原体与宿主细胞相互作用的规律,有望发现具有广谱作用的传染病防治药物。我们就病原体通过信号转导影响细胞功能的研究进展做简要综述。     

细菌铁载体拮抗植物病原真菌及促生作用研究进展

铁载体是微生物在缺铁条件下分泌的小分子有机化合物,以获取铁元素维持其生长。细菌分泌的铁载体在拮抗植物病原菌和促进植物生长方面具有重要作用。本文总结了细菌铁载体拮抗植物病原真菌的营养和生态位竞争、诱导植物诱导性系统抗性、扰乱病原菌铁稳态的机制,以及促进植物生长的作用,以解释细菌分泌的铁载体在多功能微生物菌剂研制中的重要作用。     

病原微生物蛋白质组研究

随着蛋白质组研究技术的发展,微生物蛋白质组学研究进展很快。本文从病原菌遗传变异、致病机理、潜在疫苗和对药物抗性的研究四个方面对病原微生物蛋白质组研究进展作一综述。     

病原菌毒力岛研究进展

毒力岛作为基因组岛的一种亚类,是细菌染色体上具有特定结构和功能特征的可移动基因大片段,经基因水平转移（转导、接合或转化）获得,可使细菌基因组进化在短期内发生“量的飞跃”,直接或间接增强细菌的生态适应性,与病原菌的致病性密切相关。毒力岛存在于多种动植物病原细菌中,对于细菌的毒力变异、遗传进化甚至新病原亚种形成有重要意义。简要综述了病原菌毒力岛的研究进展,介绍了毒力岛的结构、功能特征及其在病原菌进化中作用。     

靶向宿主致病菌sRNA的发现及其靶标确定的实验技术进展

人类时常暴露于充满各种致病菌的环境中,这些致病菌与人体细胞或组织之间存在多种相互作用。在相互作用的过程中,细菌通过调节自身毒性、侵袭性等致病性,以适应宿主环境并生存下来,同样,宿主细胞也会通过调动自身的免疫系统来抵抗致病菌的入侵。然而,大多数研究者主要聚焦于致病菌sRNA (small RNA, sRNA)自身生理功能的研究,致病菌与宿主相互作用的认识仍然处于起步阶段。因此,如何使用高灵敏性、高分辨率的方法研究致病菌与宿主之间的相互作用成为当前研究面临的一大难题。本文综合国内外相关研究,概述了目前研究致病菌与宿主相互作用常用的技术方法及实验流程,提高对其机制原理的理解,为致病菌sRNA-宿主靶标的相关研究提供技术参考。     

Exposure of Primate Reservoir Hosts to Mosquito Vectors in Malaysian Borneo

EcoHealth - Several vector-borne pathogens of primates have potential for human spillover. An example is the simian malaria Plasmodium knowlesi which is now a major public health problem in...     

Epidemiological study of zoonoses derived from humans in captive chimpanzees

Emerging infectious diseases (EIDs) in wildlife are major threats both to human health and to biodiversity conservation. An estimated 71.8 % of zoonotic EID events are caused by pathogens in wildlife and the incidence of such diseases is increasing significantly in humans. In addition, human diseases are starting to infect wildlife, especially non-human primates. The chimpanzee is an endangered species that is threatened by human activity such as deforestation, poaching, and human disease transmission. Recently, several respiratory disease outbreaks that are suspected of having been transmitted by humans have been reported in wild chimpanzees. Therefore, we need to study zoonotic pathogens that can threaten captive chimpanzees in primate research institutes. Serological surveillance is one of several methods used to reveal infection history. We examined serum from 14 captive chimpanzees in Japanese primate research institutes for antibodies against 62 human pathogens and 1 chimpanzee-borne infectious disease. Antibodies tested positive against 29 pathogens at high or low prevalence in the chimpanzees. These results suggest that the proportions of human-borne infections may reflect the chimpanzee’s history, management system in the institute, or regional epidemics. Furthermore, captive chimpanzees are highly susceptible to human pathogens, and their induced antibodies reveal not only their history of infection, but also the possibility of protection against human pathogens.     

Genetic control of susceptibility to bacterial infections in mouse models

Historically, the laboratory mouse (Mus musculus) has been the experimental model of choice to study pathophysiology of infection with bacterial pathogens, including natural and acquired host defence mechanisms. Inbred mouse strains differ significantly in their degree of susceptibility to infection with various human pathogens such as Mycobacterium, Salmonella, Legionella and many others. Segregation analyses and linkage studies have indicated that some of these differences are under simple genetic control whereas others behave as complex traits. Major advances in genome technologies have greatly facilitated positional cloning of single gene effects. Thus, a number of genes playing a key role in initial susceptibility, progression and outcome of infection have been uncovered and the functional characterization of the encoded proteins has provided new insight into the molecular basis of antimicrobial defences of polymorphonuclear leukocytes, macrophages, as well as T and B lymphocytes. The multigenic control of susceptibility to infection with certain human pathogens is beginning to be characterized by quantitative trait locus mapping in genome wide scans. This review summarizes recent progress on the mapping, cloning and characterization of genes and proteins that affect susceptibility to infection with major intracellular bacterial pathogens.     

DNA microarrays in the clinic: infectious diseases

We argue that the most-promising area of clinical application of microarrays in the foreseeable future is the diagnostics and monitoring of infectious diseases. Microarrays for the detection and characterization of human pathogens have already found their way into clinical practice in some countries. After discussing the persistent, yet often underestimated, importance of infectious diseases for public health, we consider the technologies that are best suited for the detection and clinical investigation of pathogens. Clinical application of microarray technologies for the detection of mycobacteria, Bacillus anthracis, HIV, hepatitis and influenza viruses, and other major pathogens, as well as the analysis of their drug-resistance patterns, illustrate our main thesis.     

益生菌抑制致病菌作用的机制研究进展

致病菌引起的各种胃肠道疾病对人类健康造成危害,应用益生菌制剂防治致病菌感染,具有安全和减少耐药性等优点,为控制致病菌感染性疾病提供了新的途径。主要从益生菌与致病菌竞争黏附位点、与致病菌的共聚作用及其产生的抗菌物质三个方面综述益生菌抑制致病菌的作用机制。     

Plant‐based oral vaccines against zoonotic and non‐zoonotic diseases

The shared diseases between animals and humans are known as zoonotic diseases and spread infectious diseases among humans. Zoonotic diseases are not only a major burden to livestock industry but also threaten humans accounting for >60% cases of human illness. About 75% of emerging infectious diseases in humans have been reported to originate from zoonotic pathogens. Because antibiotics are frequently used to protect livestock from bacterial diseases, the development of antibiotic‐resistant strains of epidemic and zoonotic pathogens is now a major concern. Live attenuated and killed vaccines are the only option to control these infectious diseases and this approach has been used since 1890. However, major problems with this approach include high cost and injectable vaccines is impractical for >20 billion poultry animals or fish in aquaculture. Plants offer an attractive and affordable platform for vaccines against animal diseases because of their low cost, and they are free of attenuated pathogens and cold chain requirement. Therefore, several plant‐based vaccines against human and animals diseases have been developed recently that undergo clinical and regulatory approval. Plant‐based vaccines serve as ideal booster vaccines that could eliminate multiple boosters of attenuated bacteria or viruses, but requirement of injectable priming with adjuvant is a current limitation. So, new approaches like oral vaccines are needed to overcome this challenge. In this review, we discuss the progress made in plant‐based vaccines against zoonotic or other animal diseases and future challenges in advancing this field.     

Fungal factors involved in host immune evasion,modulation and exploitation during infection

Human and plant pathogenic fungi have a major impact on public health and agriculture. Although these fungi infect very diverse hosts and are often highly adapted to specific host niches, they share surprisingly similar mechanisms that mediate immune evasion, modulation of distinct host targets and exploitation of host nutrients, highlighting that successful strategies have evolved independently among diverse fungal pathogens. These attributes are facilitated by an arsenal of fungal factors. However, not a single molecule, but rather the combined effects of several factors enable these pathogens to establish infection. In this review, we discuss the principles of human and plant fungal pathogenicity mechanisms and discuss recent discoveries made in this field.     

TRIPATH: A Biological Genetic and Genomic Database of Three Economically Important Fungal Pathogen of Wheat – Rust: Smut: Bunt

Wheat, the major source of vegetable protein in human diet, provides staple food globally for a large proportion of the human population. With higher protein content than other major cereals, wheat has great socio- economic importance. Nonetheless for wheat, three important fungal pathogens i.e. rust, smut and bunt are major cause of significant yield losses throughout the world. Researchers are putting up a strong fight against devastating wheat pathogens, and have made progress in tracking and controlling disease outbreaks from East Africa to South Asia. The aim of the present work hence was to develop a fungal pathogens database dedicated to wheat, gathering information about different pathogen species and linking them to their biological classification, distribution and control. Towards this end, we developed an open access database Tripath: A biological, genetic and genomic database of economically important wheat fungal pathogens – rust: smut: bunt. Data collected from peer-reviewed publications and fungal pathogens were added to the customizable database through an extended relational design. The strength of this resource is in providing rapid retrieval of information from large volumes of text at a high degree of accuracy. Database TRIPATH is freely accessible.

Availability

http://www.gbpuat-cbsh.ac.in/departments/bi/database/tripath/     

A multiplexed protein microarray for the simultaneous serodiagnosis of human immunodeficiency virus/hepatitis C virus infection and typing of whole blood

All donor blood samples must be tested pretransfusion to determine the donor blood type. Standard testing protocols require that assays be performed for important bloodborne pathogens such as hepatitis C, syphilis, hepatitis B, and human immunodeficiency virus. We have demonstrated proof of the concept that a protein microarray can type whole blood and detect antibody to significant pathogens simultaneously from the same donor blood sample. The data collected demonstrate the ability of the array to accurately type blood samples while also detecting the presence of antibodies against both human immunodeficiency virus and hepatitis C virus. In conclusion, we have successfully developed a platform capable of typing human whole blood samples, while at the same time testing for the presence of antibodies specific for human immunodeficiency virus/hepatitis C virus. The major benefits of this system are its amenability to expansion with additional assays, for example, rhesus typing and syphilis and/or hepatitis B virus detection, and also the adaptability of the assay to higher-throughput analysis, currently 16 individual samples per slide, but readily expandable to a 96-well format.