Proteasome modulators: essential chemical genetic tools for understanding human diseases

Primarily used for medicinal purposes in the past, biologically active small molecules have been increasingly employed to explore complex biological processes in the era of "chemical genetics". Since the contributions of this small molecule approach to biology have been extensive, we limit the focus of our review to the use of small-molecule modulators in the exciting field of proteasomal biology, one that has benefited significantly from a chemical genetics approach. Specifically, as the contributions of general inhibitors of proteasomal activity to the fields of cell biology and clinical oncology have been extensively discussed in several excellent reviews, we instead outline recent progress towards the development of novel, specific classes of proteasome modulators for studies of proteasomal biology and the types of proteasome inhibitors emerging as important new treatment options for cancer therapeutics.     

TB tools to tell the tale-molecular genetic methods for mycobacterial research

In spite of the availability of drugs and a vaccine, tuberculosis--one of man's medical nemeses--remains a formidable public health problem, particularly in the developing world. The persistent nature of the tubercle bacillus, with one third of the world's population is estimated to be infected, combined with the emergence of multi drug-resistant strains and the exquisite susceptibility of HIV-positive individuals, has underscored the urgent need for in-depth study of the biology of Mycobacterium tuberculosis address the resurgence of TB. In aiming to understand the mechanisms by which mycobacteria react to their immediate environments, molecular genetic tools have been developed from naturally occurring genetic elements. These include protein expressing genes, and episomal and integrating elements, which have been derived mainly from prokaryotic but also from eukaryotic organisms. Molecular genetic tools that had been established as routine procedures in other prokaryotic genera were thus mimicked. Knowledge of the underlying mechanisms greatly expedited the harnessing of these elements for mycobacteriological research and has brought us to a point where these molecular genetic tools are now employed routinely in laboratories worldwide.     

人类疾病遗传易感性研究方法进展

遗传易感性是指基于个人遗传背景的多基因遗传病发病风险,即来源于父母一方或双方的特定遗传变异在某些情况下会诱发疾病。在特定疾病的发病机制中某些高外显率的遗传变异发挥重要作用,此类疾病通过患病家系分析即可定位疾病相关遗传变异;但另一些低外显率变异的作用则不明显,需要大规模患病人群分析来解析遗传机制。近年来,随着二代测序和多组学分析技术的发展和基因组数据的大量积累,癌症、代谢性疾病、心脑血管疾病和精神疾病等疾病遗传易感性研究中取得了显著进展,为疾病的早期筛查和诊断治疗提供了参考。     

Database and tools for metabolic network analysis

Metabolic network analysis has attracted much attention in the area of systems biology. It has a profound role in understanding the key features of organism metabolic networks and has been successfully applied in several fields of systems biology, including in silico gene knockouts, production yield improvement using engineered microbial strains, drug target identification, and phenotype prediction. A variety of metabolic network databases and tools have been developed in order to assist research in these fields. Databases that comprise biochemical data are normally integrated with the use of metabolic network analysis tools in order to give a more comprehensive result. This paper reviews and compares eight databases as well as twenty one recent tools. The aim of this review is to study the different types of tools in terms of the features and usability, as well as the databases in terms of the scope and data provided. These tools can be categorised into three main types: standalone tools; toolbox-based tools; and web-based tools. Furthermore, comparisons of the databases as well as the tools are also provided to help software developers and users gain a clearer insight and a better understanding of metabolic network analysis. Additionally, this review also helps to provide useful information that can be used as guidance in choosing tools and databases for a particular research interest.     

分枝杆菌中基因敲除操作工具研究进展

致病性分枝杆菌仍然是人类健康的重要威胁。相对于传统模式原核生物,在分枝杆菌中进行基因敲除一直是一个难题。文章介绍了分枝杆菌中用于基因敲除的转运载体和序列特异性重组系统的研究进展,并进一步介绍了新近发展的分枝杆菌重组工程在基因敲除中的应用。最后,对分枝杆菌基因敲除系统的发展历程进行了回顾,并对未来的发展方向进行了展望。     

全基因组测序及其在遗传性疾病研究及诊断中的应用

最近,随着测序成本的不断降低,数据分析策略的不断提升,全基因组测序（whole-genome sequencing,WGS）已经在癌症、孟德尔遗传病、复杂疾病的致病基因检测中得到了一定运用,并逐步走向了临床诊断。全基因组测序不但可以检测编码区和非编码区的点突变（SNVs）和插入缺失（InDels）,还可以在全基因组范围内检测拷贝数变异（copy number variation,CNV）以及结构变异（structure variation,SV）。本文详细地介绍了全基因组测序的标准生物信息分析流程与方法,及其在疾病研究、临床诊断中的应用,并对全基因组测序在医学遗传学中的应用与研究进展,以及数据分析方面面临的挑战进行了概述。     

Survival analysis tools in genomics research

There is an increasing demand to determine the clinical implication of experimental findings in molecular biomedical research. Survival (or failure time) analysis methodologies have been adapted to the analysis of genomics data to link molecular information with clinical outcomes of interest. Genome-wide molecular profiles have served as sources for discovery of predictive/prognostic biomarkers as well as therapeutic targets in the past decade. In this review, we overview currently available software, web applications, and databases specifically developed for survival analysis in genomics research and discuss issues in assessing clinical utility of molecular features derived from genomic profiling.     

Lectins as tools in glycoconjugate research

Lectins are ubiquitous proteins of nonimmune origin, present in plants, microorganisms, animals and humans which specifically bind defined monosugars or oligosaccharide structures. Great progress has been made in recent years in understanding crucial roles played by lectins in many biological processes. Elucidation of carbohydrate specificity of human and animal lectins is of great importance for better understanding of these processes. Long before the role of carbohydrate–protein interactions had been explored, many lectins, mostly of plant origin, were identified, characterized and applied as useful tools in studying glycoconjugates. This review focuses on the specificity-based lectin classification and the methods of measuring lectin–carbohydrate interactions, which are used for determination of lectin specificity or for identification and characterization of glycoconjugates with lectins of known specificity. The most frequently used quantitative methods are shortly reviewed and the methods elaborated and used in our laboratories, based on biotinylated lectins, are described. These include the microtiter plate enzyme-linked lectinosorbent assay, lectinoblotting and lectin–glycosphingolipid interaction on thin-layer plates. Some chemical modifications of lectin ligands on the microtiter plates and blots (desialylation, Smith degradation, β-elimination), which extend the applicability of these methods, are also described.     

Metagenomic tools in microbial ecology research

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Novel genetic tools for Hansenula polymorpha

Hansenula polymorpha is an important yeast in industrial biotechnology. In addition, it is extensively used in fundamental research devoted to unravel the principles of peroxisome biology and nitrate assimilation. Here we present an overview of key components of the genetic toolbox for H.?polymorpha. In addition, we present new selection markers that we recently implemented in H. polymorpha. We describe novel strategies for the efficient creation of targeted gene deletions and integrations in H.?polymorpha. For this, we generated a yku80 mutant, deficient in non-homologous end joining, resulting in strongly enhanced efficiency of gene targeting relative to the parental strain. Finally, we show the implementation of Gateway technology and a single-step PCR strategy to create deletions in H.?polymorpha.     

Applications of retrotransposons as genetic tools in plant biology

Retrotransposons are mobile genetic elements that accomplish transposition via an RNA intermediate that is reverse transcribed before integration into a new location within the host genome. They are ubiquitous in eukaryotic organisms and constitute a major portion of the nuclear genome (often more than half of the total DNA) in plants. Furthermore, they are dispersed as interspersed repetitive sequences throughout most of the length of all host chromosomes. These unique properties of retrotransposons have been exploited as genetic tools for plant genome analysis. Major applications are in determining phylogeny and genetic diversity and in the functional analyses of genes in plants. Here, recent advances in molecular markers, gene tagging and functional genomics technologies using plant retrotransposons are described.     

Advantages and limitations of nonhuman primates as animal models in genetic research on complex diseases

Abstract: The genetic similarity between humans and nonhuman primates makes nonhuman primates uniquely suited as models for genetic research on complex physiological and behavioral phenotypes. By comparison with human subjects, nonhuman primates, like other animal models, have several advantages for these types of studies: 1) constant environmental conditions can be maintained over long periods of time, greatly increasing the power to detect genetic effects; 2) different environmental conditions can be imposed sequentially on individuals to characterize genotype-environment interactions; 3) complex pedigrees that are much more powerful for genetic analysis than typically available human pedigrees can be generated; 4) genetic hypotheses can be tested prospectively by selective matings; and 5) essential invasive and terminal experiments can be conducted. Limitations of genetic research with nonhuman primates include cost and availability. However, the ability to manipulate both genetic and environmental factors in captive primate populations indicates the promise of genetic research with these important animal models for illuminating complex disease processes. The utility of nonhuman primates for biomedical research on human health problems is illustrated by examples concerning the use of baboons in studies of osteoporosis, alcohol metabolism, and lipoproteins.     

Voltage-gated calcium channels in genetic diseases

Voltage-gated calcium channels (VGCCs) mediate calcium entry into excitable cells in response to membrane depolarization. During the past decade, our understanding of the gating and functions of VGCCs has been illuminated by the analysis of mutations linked to a heterogeneous group of genetic diseases called "calcium channelopathies". Calcium channelopathies include muscular, neurological, cardiac and vision syndromes. Recent data suggest that calcium channelopathies result not only from electrophysiological defects but also from altered alpha(1)/Ca(V) subunit protein processing, including folding, posttranslational modifications, quality control and trafficking abnormalities. Overall, functional analyses of VGCC mutations provide a more comprehensive view of the corresponding human disorders and offer important new insights into VGCC function. Ultimately, the understanding of these pathogenic channel mutations should lead to improved treatments of such hereditary diseases in humans.     

Protein interactions in human genetic diseases

We present a novel method that combines protein structure information with protein interaction data to identify residues that form part of an interaction interface. Our prediction method can retrieve interaction hotspots with an accuracy of 60% (at a 20% false positive rate). The method was applied to all mutations in the Online Mendelian Inheritance in Man (OMIM) database, predicting 1,428 mutations to be related to an interaction defect. Combining predicted and hand-curated sets, we discuss how mutations affect protein interactions in general.