The Human Genome Project--an overview

The Role of Epigenomics in Mapping Potential Precursors for Foot and Ankle Tendinopathy: A Systematic Review

Tendinopathy of the foot and ankle is a common clinical problem for which the exact etiology is poorly understood. The field of epigenetics has been a recent focus of this investigation. The purpose of this article was to review the genomic advances in foot and ankle tendinopathy that could potentially be used to stratify disease risk and create preventative or therapeutic agents. A multi-database search of PubMed, Cochrane, Google Scholar, and clinicaltrials.gov from January 1, 2000 to July 1, 2022 was performed. A total of 18 articles met inclusion and exclusion criteria for this review. The majority of such research utilized case-control candidate gene association to identify different genetic risk factors associated with chronic tendinopathy. Polymorphisms in collagen genes COL5A1, COL27A1, and COL1A1 were noted at a significantly higher frequency in Achilles tendinopathy versus control groups. Other allelic variations that were observed at an increased incidence in Achilles tendinopathy were TNC and CASP8. The extracellular matrix (ECM) demonstrated macroscopic changes in Achilles tendinopathy, including an increase in aggrecan and biglycan mRNA expression, and increased expression of multiple matrix metalloproteinases. Cytokine expression was also influenced in pathology and aberrantly demonstrated dynamic response to mechanical load. The pathologic accumulation of ECM proteins and cytokine expression alters the adaptive response normal tendon has to physiologic stress, further propagating the risk for tendinopathy. By identifying and understanding the epigenetic mediators that lead to tendinopathy, therapeutic agents can be developed to target the exact underlying etiology and minimize side effects.Level of Evidence: Level IV: Systematic Review of Level II-IV Studies.

Heuristic Pairwise Alignment in Database Environments

Biological data have gained wider recognition during the last few years, although managing and processing these data in an efficient way remains a challenge in many areas. Increasingly, more DNA sequence databases can be accessed; however, most algorithms on these sequences are performed outside of the database with different bioinformatics software. In this article, we propose a novel approach for the comparative analysis of sequences, thereby defining heuristic pairwise alignment inside the database environment. This method takes advantage of the benefits provided by the database management system and presents a way to exploit similarities in data sets to quicken the alignment algorithm. We work with the column-oriented MonetDB, and we further discuss the key benefits of this database system in relation to our proposed heuristic approach.

Integration of Omics Approaches Enhances the Impact of Scientific Research in Environmental Applications

In the original article [...]

Advances in RNA 3D Structure Modeling Using Experimental Data

RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.

[New developments in molecularbiological diagnostic]

Today, we have access to excellent and advanced molecular methods that are already widely used. This requires rules to control the quality of the methods as well as the laboratory. Both aspects will be discussed in the article. Following the isolation of nucleic acids they are used for genotyping which allows to address several questions: diagnosis of inherited diseases, inherited predispositions, forensic analyses, identification and typing of bacteria or viruses, elucidation of evolutionary aspects. Importantly, it has to be realized that the type and heterogeneity of phenotypically relevant mutations determines the method used for testing. Today, most laboratories use either PCR analyses or Sanger sequencing for diagnostic applications. However, increasingly next generation sequencing (NGS) is applied. The clinical use of NGS is still very challenging, but we can expect that the switch to regular application of this method will be coming in the very near future. The price for NGS has gone down to approx. USD 1000,- which makes the routine diagnostic use feasible. Nevertheless, several challenges have yet to be solved, such as the processing of the large data volume as well as storage of the data. Supporting data bases exist already and some will be discussed in the article. The understanding of the clinical relevance of many polymorphisms is another issue that has yet to be solved, particularly as in the context of personalized medicine polymorphisms have become increasingly important.

Development and validation of a novel single nucleotide polymorphism (SNP) panel for genetic analysis of Blastomyces spp. and association analysis

BACKGROUND

Single nucleotide polymorphism (SNP) genotyping is increasingly being utilized for molecular typing of pathogens and is cost-effective, especially for large numbers of isolates. The goals of this study were 1) to develop and validate a SNP assay panel for genetic analysis of Blastomyces spp., 2) ascertain whether microsatellite genotyping and the SNP genotyping with the developed panel resolve identical genetic groups, and 3) explore the utility of SNPs for examining phylogenetic and virulence questions in humans.

METHODS

Three hundred sixty unique Blastomyces spp. isolates previously genotyped with microsatellite markers were genotyped with the MassARRAY® SNP genotyping system (Agena Bioscience™, San Diego, CA), for a custom panel of 28 SNPs. Clinical presentation data was analyzed for association with SNP variants.

RESULTS

Three hundred twenty-three Blastomyces spp. isolates (90 %) were successfully genotyped by SNP analysis, with results obtained for at least 27 of 28 assays. For 99.7 % of isolates tested by both genotyping methods, microsatellite genetic group assignment correlated with species assignment based on internal transcribed spacer 2 (ITS2) genotyping, with Group 1 (Gr 1) being equivalent to B. gilchristii and Group 2 (Gr 2) being equivalent to B. dermatitidis. Thirteen isolates were genetic hybrids by one or both methods of genotyping and were difficult to assign to a particular genetic group or species. Fifteen SNP loci showed significantly different alleles in cases of pulmonary vs disseminated disease, at a p-value of <0.01 or less.

CONCLUSIONS

This study is the largest genotyping study of Blastomyces spp. isolates and presents a new method for genetic analysis with which to further explore the relationship between the genetic diversity in Blastomyces spp. and clinical disease presentation. We demonstrated that microsatellite Gr 1 is equivalent to B. gilchristii and Gr 2 is equivalent to B. dermatitidis. We also discovered potential evidence of infrequent recombination between the two Blastomyces spp. Several Blastomyces spp. SNPs were identified as associated with dissemination or pulmonary disease presentation, but additional work is needed to examine virulence SNPs separately within B. dermatitidis and B. gilchristii.

Identification of Genomic Somatic Variants in Cancer: From Discovery to Actionability

The perfect method to discover and validate actionable somatic variants in cancer has not yet been developed, yet significant progress has been made toward this goal. There have been huge increases in the throughput and cost of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) sequencing technologies that have led to the burgeoning possibility of using sequencing data in clinical settings. Discovery of somatic mutations is relatively simple and has been improved recently due to laboratory methods optimization, bioinformatics algorithms development, and the expansion of various databases of population genomic information. Tiered systems of evidence evaluation are currently being used to classify genomic variants for clinicians to more rapidly and accurately determine actionability of these aberrations. These efforts are complicated by the intricacies of communicating sequencing results to physicians and supporting its biological relevance, emphasizing the need for increasing education of clinicians and administrators, and the ongoing development of ethical standards for dealing with incidental results. This chapter will focus on general aspects of DNA and RNA tumor sequencing technologies, data analysis and interpretation, assessment of biological and clinical relevance of genomic aberrations, ethical aspects of germline sequencing, and how these factors impact cancer personalized care.

Lifestyle Behaviours Add to the Armoury of Treatment Options for Panic Disorder: An Evidence-Based Reasoning

This article presents an evidence-based reasoning, focusing on evidence of an Occupational Therapy input to lifestyle behaviour influences on panic disorder that also provides potentially broader application across other mental health problems (MHP). The article begins from the premise that we are all different. It then follows through a sequence of questions, examining incrementally how MHPs are experienced and classified. It analyses the impact of individual sensitivity at different levels of analysis, from genetic and epigenetic individuality, through neurotransmitter and body system sensitivity. Examples are given demonstrating the evidence base behind the logical sequence of investigation. The paper considers the evidence of how everyday routine lifestyle behaviour impacts on occupational function at all levels, and how these behaviours link to individual sensitivity to influence the level of exposure required to elicit symptomatic responses. Occupational Therapists can help patients by adequately assessing individual sensitivity, and through promoting understanding and a sense of control over their own symptoms. It concludes that present clinical guidelines should be expanded to incorporate knowledge of individual sensitivities to environmental exposures and lifestyle behaviours at an early stage.

Identifying disease genes by integrating multiple data sources

BACKGROUND

Now multiple types of data are available for identifying disease genes. Those data include gene-disease associations, disease phenotype similarities, protein-protein interactions, pathways, gene expression profiles, etc.. It is believed that integrating different kinds of biological data is an effective method to identify disease genes.

RESULTS

In this paper, we propose a multiple data integration method based on the theory of Markov random field (MRF) and the method of Bayesian analysis for identifying human disease genes. The proposed method is not only flexible in easily incorporating different kinds of data, but also reliable in predicting candidate disease genes.

CONCLUSIONS

Numerical experiments are carried out by integrating known gene-disease associations, protein complexes, protein-protein interactions, pathways and gene expression profiles. Predictions are evaluated by the leave-one-out method. The proposed method achieves an AUC score of 0.743 when integrating all those biological data in our experiments.

Efficient feature selection and classification of protein sequence data in bioinformatics

Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth.

CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis

INTRODUCTION

The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes.

IMPLEMENTATION

We developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytargetlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released CyTargetLinker as one of the first apps for Cytoscape 3. It provides a user-friendly and flexible interface to extend biological networks with regulatory interactions, such as microRNA-target, transcription factor-target and/or drug-target. Importantly, CyTargetLinker employs identifier mapping to combine various interaction data resources that use different types of identifiers.

RESULTS

Three case studies demonstrate the strength and broad applicability of CyTargetLinker, (i) extending a mouse molecular interaction network, containing genes linked to diabetes mellitus, with validated and predicted microRNAs, (ii) enriching a molecular interaction network, containing DNA repair genes, with ENCODE transcription factor and (iii) building a regulatory meta-network in which a biological process is extended with information on transcription factor, microRNA and drug regulation.

CONCLUSIONS

CyTargetLinker provides a simple and extensible framework for biologists and bioinformaticians to integrate different regulatory interactions into their network analysis approaches. Visualization options enable biological interpretation of complex regulatory networks in a graphical way. Importantly the incorporation of our tool into the Cytoscape framework allows the application of CyTargetLinker in combination with a wide variety of other apps for state-of-the-art network analysis.

When Medicine Meets Engineering-Paradigm Shifts in Diagnostics and Therapeutics

During the last two decades, the manufacturing techniques of microfluidics-based devices have been phenomenally advanced, offering unlimited potential for bio-medical technologies. However, the direct applications of these technologies toward diagnostics and therapeutics are still far from maturity. The present challenges lay at the interfaces between the engineering systems and the biocomplex systems. A precisely designed engineering system with narrow dynamic range is hard to seamlessly integrate with the adaptive biological system in order to achieve the design goals. These differences remain as the roadblock between two fundamentally non-compatible systems. This paper will not extensively review the existing microfluidic sensors and actuators; rather, we will discuss the sources of the gaps for integration. We will also introduce system interface technologies for bridging the differences to lead toward paradigm shifts in diagnostics and therapeutics.

Functional identification of an 8-oxoguanine specific endonuclease from Thermotoga maritima

To date, no 8-oxoguanine-specific endonuclease-coding gene has been identified in Thermotoga maritima of the order Thermotogales, although its entire genome has been deciphered. However, the hypothetical protein Tm1821 from T. maritima, has a helix-hairpin-helix motif that is considered to be important for DNA binding and catalytic activity. Here, Tm1821 was overexpressed in Escherichia coli and purified using Ni-NTA affinity chromatography, protease digestion, and gel filtration. Tm1821 protein was found to efficiently cleave an oligonucleotide duplex containing 8-oxoguanine, but Tm1821 had little effect on other substrates containing modified bases. Moreover, Tm1821 strongly preferred DNA duplexes containing an 8-oxoguanine:C pair among oligonucleotide duplexes containing 8-oxoguanine paired with four different bases (A, C, G, or T). Furthermore, Tm1821 showed AP lyase activity and Schiff base formation with 8-oxoguanine in the presence of NaBH4, which suggests that it is a bifunctional DNA glycosylase. Tm1821 protein shares unique conserved amino acids and substrate specificity with an 8-oxoguanine DNA glycosylase from the hyperthermophilic archaeon. Thus, the DNA recognition and catalytic mechanisms of Tm1821 protein are likely to be similar to archaeal repair protein, although T. maritima is an eubacterium.

Linkage disequilibrium analyses of natriuretic peptide precursor B locus reveal risk haplotype conferring high plasma BNP levels

BACKGROUND

Brain natriuretic peptide (BNP) has been widely used for the diagnosis and prognostic evaluation of chronic heart failure (CHF). In the present study, we performed association study of single nucleotide polymorphisms (SNPs) surrounding the natriuretic peptide precursor B (NPPB) gene with plasma BNP levels in 2970 adult Japanese.

METHODS AND RESULTS

Association analysis between SNPs of the NPPB gene and plasma BNP revealed significant associations of the 8 SNPs surrounding the entire NPPB gene with plasma BNP levels. For instance, as to SNP rs198389 (T-381C), plasma BNP levels among the three genotypic categories, i.e., 2189 homozygous T-allele carriers (BNP 26.4+/-0.6pg/ml), 697 heterozygous carriers (35.0+/-1.1pg/ml), and 52 homozygous C-allele carriers (46.0+/-4.1pg/ml) indicated a co-dominant effect of the minor C-allele on elevating plasma BNP levels (P<0.0001). Linkage disequilibrium (LD) analysis among the 8 SNPs revealed that the region consisted of two, 5' major and 3' minor, LD blocks. Haplotype-based association analysis demonstrated that plasma BNP levels were associated closely with the haplotypes-1 and -2 of the major LD block.

CONCLUSION

These results suggest that genetic variation at the primary locus NPPB gene, represented by definition of risk haplotypes, may be an important determinant of plasma BNP levels.

Discovering drug targets through the web

Traditionally, drug-target discovery is a "wet-bench" experimental process, depending on carefully designed genetic screens, biochemical tests and cellular assays to identify proteins and genes that are associated with a particular disease or condition. However, recent advances in DNA sequencing, transcript profiling, protein identification and protein quantification are leading to a flood of genomic and proteomic data that is, or potentially could be, linked to disease data. The quantity of data generated by these high throughput methods is forcing scientists to re-think the way they do traditional drug-target discovery. In particular it is leading them more and more towards identifying potential drug targets using computers. In fact, drug-target identification is now being done as much on the desk-top as on the bench-top. This review focuses on describing how drug-target discovery can be done in silico (i.e. via computer) using a variety of bioinformatic resources that are freely available on the web. Specifically, it highlights a number of web-accessible sequence databases, automated genome annotation tools, text mining tools; and integrated drug/sequence databases that can be used to identify drug targets for both endogenous (genetic and epigenetic) diseases as well as exogenous (infectious) diseases.

Detecting functional modules in the yeast protein–protein interaction network

MOTIVATION

Identification of functional modules in protein interaction networks is a first step in understanding the organization and dynamics of cell functions. To ensure that the identified modules are biologically meaningful, network-partitioning algorithms should take into account not only topological features but also functional relationships, and identified modules should be rigorously validated.

RESULTS

In this study we first integrate proteomics and microarray datasets and represent the yeast protein-protein interaction network as a weighted graph. We then extend a betweenness-based partition algorithm, and use it to identify 266 functional modules in the yeast proteome network. For validation we show that the functional modules are indeed densely connected subgraphs. In addition, genes in the same functional module confer a similar phenotype. Furthermore, known protein complexes are largely contained in the functional modules in their entirety. We also analyze an example of a functional module and show that functional modules can be useful for gene annotation.

CONTACT

yuan.33@osu.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Host genetics and the outcome of hepatitis B viral infection

Hepatitis B Virus (HBV) infection can result in numerous different clinical outcomes. A complex combination of environment, and viral and host genetic factors play a critical role in determining both susceptibility to HBV persistence and the course of infection. Evidence is presented that suggests that host genetic factors play an important role in determining the outcome of HBV infection. This data from various groups demonstrates that multiple genes play a role in determining hepatitis B viral clearance or persistence. However, to identify all the relevant variants that affect the outcome of infection, alternative strategies such as genome-wide association studies with large sample sizes will be required to define the majority of the relevant polygenes.

Systems biology: new approaches to old environmental health problems

The environment plays a pivotal role as a human health determinant and presence of hazardous pollutants in the environment is often implicated in human disease. That pollutants cause human diseases however is often controversial because data connecting exposure to environmental hazards and human diseases are not well defined, except for some cancers and syndromes such as asthma. Understanding the complex nature of human-environment interactions and the role they play in determining the state of human health is one of the more compelling problems in public health. We are becoming more aware that the reductionist approach promulgated by current methods has not, and will not yield answers to the broad questions of population health risk analysis. If substantive applications of environment-gene interactions are to be made, it is important to move to a systems level approach, to take advantage of epidemiology and molecular genomic advances. Systems biology is the integration of genomics, transcriptomics, proteomics, and metabolomics together with computer technology approaches to elucidate environmentally caused disease in humans. We discuss the applications of environmental systems biology as a route to solution of environmental health problems.

Tissue microarray for high-throughput analysis of gene expression profiles in hepatocellular carcinoma

AIM: To study the expression profiles of HBsAg, HBcAg, p21^WAF1/CIP1 (p21), Rb genes in hepatocellular carcinoma (HCC) and to investigate their roles in the hepatocar-cinogenesis.

METHODS: HCC tissue microarray containing 120-min tissues of 40 HCC cases was constructed. HBsAg, HBcAg, p21 and Rb proteins were immunohistochemically stained by streptavidin-peroxidase conjugated method (S-P). The expression loss of these genes in cancerous, para-cancerous tissues and adjacent normal liver tissues of 40 HCCs were comparatively examined.

RESULTS: The positive rate of HBsAg expression in cancerous tissues of 40 HCCs was 7.5%, which was lower than that in para-cancerous and adjacent normal liver tissues (χ² =12.774, P<0.01; χ² = 18.442, P<0.01). The positive rate of HBcAg expression in cancerous tissues of 40 HCCs was 20.0%, which was also lower than that in para-cancerous and adjacent normal liver tissues (χ² = 9.482, P<0.01; χ² = 14.645, P<0.01). p21 protein deletion rate in cancerous tissues of 40 HCCs was 27.5%, which was higher than that in para-cancerous and adjacent normal liver tissues (χ² = 7.439, P<0.01; χ² = 11.174, P<0.01). p21 protein deletion correlated remarkably with the pathological grade of HCC (χ² = 0.072, P<0.05). Rb protein deletion rate in cancerous tissues of 40 HCCs was 42.5%, which was also higher than that in para-cancerous and adjacent normal liver tissues (χ² = 10.551, P<0.01; χ² = 18.353, P<0.01). Rb protein deletion rate did not correlate remarkably with tumor size or pathological grade of HCC (χ² = 0.014, P>0.05; χ² = 0.017, P>0.05).

CONCLUSION: Expression deletion of HBsAg, HBcAg, p21 and Rb proteins in HCCs may play important roles in the carcinogenesis of HCC. Tissue microarray is an effective high-throughput technique platform for cancer research.

Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors

We report here a cancer drug therapy use of a gene involved in Down's syndrome. Using bioinformatics approaches, we recently predicted Single Minded 2 gene (SIM2) from Down's syndrome critical region to be specific to certain solid tumors. Involvement of SIM2 in solid tumors has not previously been reported. Intrigued by a possible association between a Down's syndrome gene and solid tumors, we monitored SIM2 expression in solid tumors. Isoform-specific expression of SIM2 short-form (SIM2-s) was seen selectively in colon, prostate, and pancreatic carcinomas but not in breast, lung, or ovarian carcinomas nor in most normal tissues. In colon tumors, SIM2-s expression was seen in early stages. Antisense inhibition of SIM2-s expression in a colon cancer cell line caused inhibition of gene expression, growth inhibition, and apoptosis. The administration of the antisense, but not the control, oligonucleotides caused a pronounced inhibition of tumor growth in nude mice with no major toxicity. Our findings provide a strong rationale for the genes-to-drugs paradigm, establish SIM2-s as a molecular target for cancer therapeutics, and may further understanding of the cancer risk of Down's syndrome patients.

Congenic mice: cutting tools for complex immune disorders

Autoimmune diseases are, in general, under complex genetic control and subject to strong interactions between genetics and the environment. Greater knowledge of the underlying genetics will provide immunologists with a framework for study of the immune dysregulation that occurs in such diseases. Ascertaining the number of genes that are involved and their characterization have, however, proven to be difficult. Improved methods of genetic analysis and the availability of a draft sequence of the complete mouse genome have markedly improved the outlook for such research, and they have emphasized the advantages of mice as a model system. In this review, we provide an overview of the genetic analysis of autoimmune diseases and of the crucial role of congenic and consomic mouse strains in such research.

Endovascular restorative neurosurgery: a novel concept for molecular and cellular therapy of the nervous system

The amalgam of molecular biology and neurosurgery offers immense promise for neurorestoration and the management of neurodegenerative deficiencies, developmental disorders, neoplasms, stroke, and trauma. This article summarizes present strategies for and impediments to gene therapy and stem cell therapy of the central nervous system and advances the concept of a potential new approach, namely endovascular restorative neurosurgery. The objectives of gene transfer to the central nervous system are efficient transfection of host cells, selective sustained expression of the transgene, and lack of toxicity or immune excitation. The requisite elements of this process are the identification of candidate diseases, the construction of vehicles for gene transfer, regulated expression, and physical delivery. In the selection of target disorders, the underlying genetic events to be overcome, as well as their spatial and temporal distributions, must be considered. These factors determine the requirements for the physical dispersal of the transgene, the duration of transgene expression, and the quantity of transgene product needed to abrogate the disease phenotype. Vehicles for conveying the transgene to the central nervous system include viral vectors (retroviruses, lentiviruses, adenoviruses, adeno-associated viruses, and herpes simplex virus), liposomes, and genetically engineered cells, including neural stem cells. Delivery of the transgene into the brain presents several challenges, including limited and potentially risky access through the cranium, sensitivity to volumetric changes, restricted diffusion, and the blood-brain barrier. Genetic or cellular therapeutic agents may be injected directly into the brain parenchyma (via stereotaxy or craniotomy), into the cerebrospinal fluid (in the ventricles or cisterns), or into the bloodstream (intravenously or intra-arterially). The advantages of the endovascular route include the potential for widespread distribution, the ability to deliver large volumes, limited perturbation of neural tissue, and the feasibility of repeated administration.

Helicobacter pylori expresses an autolytic enzyme: gene identification, cloning, and theoretical protein structure

Helicobacter pylori is an important pathogen of the gastric system. The clinical outcome of infection is thought to be correlated with some genetic features of the bacterium. However, due to the extreme genetic variability of this organism, it is hard to draw definitive conclusions concerning its virulence factors. Here we describe a novel H. pylori gene which expresses an autolytic enzyme that is also capable of degrading the cell walls of both gram-positive and gram-negative bacteria. We designated this gene lys. We found this gene and observed its expression in a number of unrelated clinical strains, a fact that suggests that it is well conserved in the species. A comparison of the nucleotide sequences of lys and the hypothetical gene HP0339 from H. pylori strain ATCC 26695 revealed almost total identity, except for the presence of an insertion consisting of 24 nucleotides in the lys sequence. The coding sequences of lys and HP0339 show a high degree of homology with the coding sequence of bacteriophage T4 lysozyme. Because of this similarity, it was possible to model the three-dimensional structures of both the lys and HP0339 products.

A new ultrasound instrument for in vivo microimaging of mice

We report here on the design and evaluation of the first high-frequency ultrasound (US) imaging system specifically designed for microimaging of the mouse. High-frequency US or US biomicroscopy (UBM) has the advantage of low cost, rapid imaging speed, portability and high resolution. In combination with the ability to provide functional information on blood flow, UBM provides a powerful method for the investigation of development and disease models. The new UBM imaging system is demonstrated for mouse development from day 5.5 of embryogenesis through to the adult mouse. At a frequency of 40 MHz, the resolution voxel of the new mouse scanner measures 57 microm x 57 microm x 40 microm. Duplex Doppler provides blood velocity sensitivity to the mm per s range, consistent with flow in the microcirculation, and can readily detect blood flow in the embryonic mouse heart, aorta, liver and placenta. Noninvasive UBM assessment of development shows striking similarity to invasive atlases of mouse anatomy. The most detailed noninvasive in vivo images of mouse embryonic development achieved using any imaging method are presented.

Association between SAH, an acyl-CoA synthetase gene, and hypertriglyceridemia, obesity, and hypertension

BACKGROUND

The SA gene (SAH) has been isolated by differential screening from a genetically hypertensive rat strain as a candidate gene that may contribute to hypertension. Recently, the SA protein has been reported to be highly homologous to bovine xenobiotic-metabolizing medium-chain fatty acid:CoA ligase.

METHODS AND RESULTS

To clarify the pathophysiological significance of SAH, we searched for polymorphisms of human SAH and performed association studies using a large cohort (4000 subjects) representing the general population in Japan. We found 2 polymorphisms in the promoter region and single-nucleotide polymorphisms in introns 5, 7, and 12 and exon 8. One of the variants, an A/G polymorphism in intron 12, just 7 bp upstream from exon 13, strongly affected plasma triglyceride, plasma cholesterol, body mass index (BMI), waist-to-hip ratio (W/H), and blood pressure status. The effect of this genotype on blood pressure seems to be conveyed through its effects on BMI and W/H. Transient expression of the SA protein in mammalian cells confirmed that it is expressed in mitochondria and has medium-chain fatty acid:CoA ligase activity. The A/G polymorphism was found to be associated with the expression level of SA mRNA in peripheral mononuclear cells in vivo.

CONCLUSIONS

The G allele of SAH was found to be associated with multiple risk factors, including hypertriglyceridemia, hypercholesterolemia, obesity, and hypertension. This observation should open a new area for future research in multiple-risk-factor syndromes.

Ferramentas de análise molecular e os agentes das grandes endemias

Os desenvolvimentos recentes no campo da biologia molecular abrem novas perspectivas para o estudo, diagnóstico e terapêutica das grandes endemias que afetam sobretudo as nações em desenvolvimento. As técnicas de manipulação de genes permitem a expressão de antígenos de patógenos em larga escala, com a potencial utilização como reagentes para diagnóstico ou imunógenos. Adicionalmente, essas técnicas poderão levar à obtenção de novas vacinas vivas atenuadas. Por outro lado, a determinação da seqüência dos genomas de patógenos poderá levar a novos alvos para o desenho racional de drogas com potencial quimioterápico. Entretanto, esses avanços só estarão à disposição dos países em desenvolvimento se houver um programa contínuo de investimento e de formação e valorização de recursos humanos competentes nessas novas tecnologias.

Genetic approaches to understanding human adaptation to altitude in the Andes

Despite the initial discomfort often experienced by visitors to high altitude, humans have occupied the Andean altiplano for more than 10000 years, and millions of people, indigenous and otherwise, currently live on these plains, high in the mountains of South America, at altitudes exceeding 3000m. While, to some extent, acclimatisation can accommodate the one-third decrease in oxygen availability, having been born and raised at altitude appears to confer a substantial advantage in high-altitude performance compared with having been born and raised at sea level. A number of characteristics have been postulated to contribute to a high-altitude Andean phenotype; however, the relative contributions of developmental adaptation (within the individual) and genetic adaptation (within the population of which the individual is part) to the acquisition of this phenotype have yet to be resolved.

A complex trait is influenced by multiple genetic and environmental factors and, in humans, it is inherently very difficult to determine what proportion of the trait is dictated by an individual’s genetic heritage and what proportion develops in response to the environment in which the person is born and raised. Looking for changes in putative adaptations in vertically migrant populations, determining the heritability of putative adaptive traits and genetic association analyses have all been used to evaluate the relative contributions of nurture and nature to the Andean phenotype. As the evidence for a genetic contribution to high-altitude adaptation in humans has been the subject of several recent reviews, this article instead focuses on the methodology that has been employed to isolate the effects of ‘nature’ from those of ‘nurture’ on the acquisition of the high-altitude phenotype in Andean natives (Quechua and Aymara). The principles and assumptions underlying the various approaches, as well as some of the inherent strengths and weaknesses of each, are briefly discussed.

Cancer therapy. New strategies and treatment modalities for optimizing patient outcomes

In the postgenome era, development of novel targeted therapeutics is anticipated to accelerate, with the promise of specifically tailored strategies to treat specific molecularly characterized disease entities. Greater understanding of disease pathophysiology and pharmacologic actions at the molecular, cellular, and tissue levels have provided the basis for expanding the clinical application of available therapies such as recombinant human erythropoietin (r-HuEPO, epoetin alfa). The role of epoetin alfa in anemic cancer patients receiving chemotherapy has grown as our understanding of the relationship between anemia and quality of life in this patient population has evolved. With anemia and tumor hypoxia associated with poorer outcomes in various solid tumors, the potential impact of epoetin alfa on outcomes, as well as quality of life, in patients undergoing radiation or chemoradiation is of considerable interest. Anemia occurs almost universally in critically ill patients, resulting in substantial transfusion requirements. In this setting, the anemia appears to be consistent with anemia of chronic inflammatory disease and is potentially treatable by epoetin alfa. Recent preclinical studies indicate that erythropoietin exhibits neuroprotective effects in models of central nervous system injury, suggesting additional potential novel clinical applications for epoetin alfa worthy of careful investigation. Advances in the understanding of the ras genes and their functional proteins in signaling pathways involved in the development of cancer, particularly hematologic malignancies, over the last decade have prompted development of a new class of agents, farnesyl protein transferase inhibitors (FTIs), designed specifically to inhibit the initial step in Ras protein activation. Initial clinical evaluation of FTIs is ongoing, and preliminary results demonstrate antitumor activity in hematologic malignancies. Further identification and understanding of the function and complex interactions of proteins involved in diseases holds the promise of targeted therapies and improved patient outcomes.

Applying genomic technologies in environmental health research: challenges and opportunities

Recent discoveries in molecular biology and genetics have made it possible for environmental health researchers to examine how genetic characteristics affect response to environmental exposures. Understanding such gene-environment interactions offers exciting possibilities for the prevention and control of environmentally induced diseases. Despite these potential benefits, the collection and analysis of genetic information in environmental health research presents many of the same ethical, legal, and social (ELSI) challenges found in other types of genetic research. In this article, we describe a number of ELSI challenges in environmental genomic research and the opportunities and responsibilities that accompany this research.

Nucleotide sequence, transcription map, and mutation analysis of the 13q14 chromosomal region deleted in B-cell chronic lymphocytic leukemia

Deletions of the 13q14 chromosome region are associated with B-cell chronic lymphocytic leukemia (B-CLL) and several other types of cancer, suggesting the presence of a tumor suppressor gene. In previous studies the minimal region of deletion (MDR) was mapped to a less than 300-kilobase (kb) interval bordered by the markers 173a12-82 and 138G4/1.3R. For the identification of the putative tumor suppressor gene, the entire MDR (approximately 347 kb) has been sequenced, and transcribed regions have been identified by exon trapping, EST-based full-length complementary DNA cloning, database homology searches, and computer-assisted gene prediction analyses. The MDR contains 2 pseudogenes and 3 transcribed genes: CAR, encoding a putative RING-finger containing protein; 1B4/Leu2, generating noncoding transcripts; and EST70/Leu1, probably representing another noncoding gene (longest open reading frame of 78 codons). These genes have been sequenced in 20 B-CLL cases with 13q14 hemizygous deletion, and no mutations were found. Moreover, no somatic variants were found in the entire MDR analyzed for nucleotide substitutions by a combination of direct sequencing and fluorescence-assisted mismatch analysis in 5 B-CLL cases displaying 13q14-monoallelic deletion. The nondeleted allele of the CAR and EST70/Leu1 genes was expressed in B-CLL specimens, including those with monoallelic loss, whereas no expression of 1B4/Leu2 was detectable in B-CLL, regardless of the 13q14 status. These results indicate that allelic loss and mutation of a gene within the MDR is an unlikely pathogenetic mechanism for B-CLL. However, haplo-insufficiency of one of the identified genes may contribute to tumorigenesis. (Blood. 2001;97:2098-2104)

What parents are told after prenatal diagnosis of a sex chromosome abnormality: interview and questionnaire study

OBJECTIVE

To investigate how the prenatal diagnosis of a sex chromosome anomaly is first communicated to parents.

DESIGN

Health professionals were interviewed by telephone and the conversation was taped; parents were sent questionnaires at 1 month after diagnosis and those who responded were sent another at 6 months.

PARTICIPANTS

29 health professionals who had recently informed parents that a sex chromosome anomaly had been identified in an apparently anatomically normal, viable fetus. 23 mothers and partners who had been informed of such a diagnosis.

MAIN OUTCOME MEASURES

Health professionals' knowledge about sex chromosome anomalies and parents' responses to information provided by health professionals.

RESULTS

Analysis of the telephone interviews identified great variation in what different healthcare professionals know, think, and say about the same sex chromosome anomaly. The small numbers and the low response rate for the questionnaire (39% for women and 30% for men) meant that statistical analysis was not appropriate.

CONCLUSIONS

It is essential for obstetric units to have an established protocol for giving results and for all staff who communicate results to parents to have accurate, up to date information about the condition identified.

Exploiting human genetic variation in drug discovery and development

'The right drug for the right patient at the right time'Is this a realistic goal for today's pharmaceutical industry and tomorrow's medical practitioner? Or merely an over-simplistic refrain that can only ever be an unfulfilled dream? Here we discuss the reality behind the dream and illustrate how the analysis of genetic variation is a complex science that has the capacity to make significant contributions to drug discovery and development strategies. An understanding of the impact of human variation must be a central consideration in the future practice of pharmaceutical R&D.

Chromosome painting in farm, pet and wild animal species

Among the advanced karyotype analysis approaches embraced by animal cytogenetics during the past decade, chromosome painting has had the greatest impact. Generation of chromosome specific paints is considered pivotal to his development. Additionally, ability to use these paints across species (referred to as Zoo-FISH or comparative painting) is undisputedly the most important breakthrough that has contributed to our ability to compare karyotypes of a wide range of evolutionarily highly diverged chromosome painting, and makes them aware of the tools/resources available to carry out this research in a variety of animal species. An overview of the current status of comparative chromosome painting results across closely as well as distantly related species is presented. Findings from different studies show how some segmental syntenies are more conserved as compared to others. The comparisons provide insight into the likely constitution of a vertebrate/mammalian ancestral karyotype and help understand some of the intricacies about karyotype evolution. Importance of comparative painting in setting the stage for rapid development of gene maps in a number of economically important species is elaborated.

Using single nucleotide polymorphisms as a means to understanding the pathophysiology of asthma

Asthma is the most common chronic childhood disease in the developed nations, and is a complex disease that has high social and economic costs. Studies of the genetic etiology of asthma offer a way of improving our understanding of its pathogenesis, with the goal of improving preventive strategies, diagnostic tools, and therapies. Considerable effort and expense have been expended in attempts to detect specific polymorphisms in genetic loci contributing to asthma susceptibility. Concomitantly, the technology for detecting single nucleotide polymorphisms (SNPs) has undergone rapid development, extensive catalogues of SNPs across the genome have been constructed, and SNPs have been increasingly used as a method of investigating the genetic etiology of complex human diseases. This paper reviews both current and potential future contributions of SNPs to our understanding of asthma pathophysiology.