Mining co-regulated gene profiles for the detection of functional associations in gene expression data

MOTIVATION: Association pattern discovery (APD) methods have been successfully applied to gene expression data. They find groups of co-regulated genes in which the genes are either up- or down-regulated throughout the identified conditions. These methods, however, fail to identify similarly expressed genes whose expressions change between up- and down-regulation from one condition to another. In order to discover these hidden patterns, we propose the concept of mining co-regulated gene profiles. Co-regulated gene profiles contain two gene sets such that genes within the same set behave identically (up or down) while genes from different sets display contrary behavior. To reduce and group the large number of similar resulting patterns, we propose a new similarity measure that can be applied together with hierarchical clustering methods. RESULTS: We tested our proposed method on two well-known yeast microarray data sets. Our implementation mined the data effectively and discovered patterns of co-regulated genes that are hidden to traditional APD methods. The high content of biologically relevant information in these patterns is demonstrated by the significant enrichment of co-regulated genes with similar functions. Our experimental results show that the Mining Attribute Profile (MAP) method is an efficient tool for the analysis of gene expression data and competitive with bi-clustering techniques.     

KUJIRA,a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure.     

YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information

The BioKnowledge Library is a relational database and web site (http://www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharomyces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease.     

FED: a web tool for foreign element detection of genome-edited organism

正Dear Editor,Genome editing, especially the newly developed CRISPR technology, is now widely implemented for diverse medical and agricultural applications (Puchta, 2018). However, for genome editing, the DNA cassettes encoding the editing components are usually assembled and delivered into the cells of organisms (Cong et al., 2013).     

GenCompass: a universal system for analysing gene expression for any genome

Microarrays have become indispensable tools for studying the gene expression of particular organisms on a genomic scale. However, despite its widespread use, there are several draw-backs to the current technology. First, it requires prior knowledge of the DNA sequence encoded in the organism of interest, and second, chips must be designed specifically for each genome, greatly increasing the initial cost incurred in manufacturing the arrays.     

Automated, PCR-RFLP genotyping of the urokinase gene

The urokinase-type plasminogen activator (u-PA) has been suggested to play a role in the early initiation and progression of atherosclerosis and coronary artery disease (CAD) (Grenett et aL, 1998). Recently, a common genetic polymorphism in the untranslated region of the u-PA gene was shown to be associated with syptomatic CAD. To study the possible role of this common genetic polymorphism in the u-PA gene, we have developed an automated, PCR-based assay. Automation of the PCR-RFLP genotyping of the BamHI polymorphism of the urokinase gene will support the screening of the large sample sizes required to do the population-based studies necessary to uncover disease susceptibility associations.     

Snf2-family proteins: chromatin remodellers for any occasion

Chromatin facilitates the housing of eukaryotic DNA within the nucleus and restricts access to the underlying sequences. Thus, the regulation of chromatin structure provides an excellent platform for regulating processes that require information stored within genomic DNA. Snf2 proteins are a family of helicase-like proteins that direct energy derived from ATP hydrolysis into the mechanical remodelling of chromatin structure. Here, we highlight some of the recent discoveries regarding this family of proteins and show Snf2 proteins have roles in many aspects of genetic metabolism. Recent developments include new insights into the mechanism for nucleosome spacing and histone dimer exchange; together with growing evidence for the involvement of Snf2 proteins in DNA repair.     

Common harms from amoxicillin: a systematic review and meta-analysis of randomized placebo-controlled trials for any indication

Background:When prescribing antibiotics for common indications, clinicians need information about both harms and benefits, information that is currently available only from observational studies. We quantified the common harms of the most frequently prescribed antibiotic, amoxicillin, from randomized placebo-controlled trials.Methods:For this systematic review, we searched MEDLINE, Embase and the Cochrane Central Register of Controlled Trials, without language restriction, for any randomized, participant-blinded, placebo-controlled trials of amoxicillin or amoxicillin–clavulanic acid for any indication, in any setting. Our main outcome was any reported adverse event.Results:Of 730 studies identified, we included 45 trials: 27 involving amoxicillin, 17 involving amoxicillin–clavulanic acid and 1 involving both. The indications for antibiotic therapy were variable. The risk of bias was low, although only 25 trials provided data suitable for assessment of harms, which suggested under-reporting. Diarrhea was attributed to amoxicillin only in the form of amoxicillin–clavulanic acid (Peto odds ratio [OR] 3.30, 95% confidence interval [CI] 2.23–4.87). The OR for candidiasis (3 trials) was significantly higher (OR 7.77, 95% CI 2.23–27.11). Rashes, nausea, itching, vomiting and abnormal results on liver function tests were not significantly increased. The results were not altered by sensitivity analyses, nor did funnel plots suggest publication bias. The number of courses of antibiotics needed to harm was 10 (95% CI 6–17) for diarrhea with amoxicillin–clavulanic acid and 27 (95% CI 24–42) for candidiasis with amoxicillin (with or without clavulanic acid).Interpretation:Diarrhea was caused by use of amoxicillin–clavulanic acid, and candidiasis was caused by both amoxicillin and amoxicillin–clavulanic acid. Harms were poorly reported in most trials, and their true incidence may have been higher than reported. Nevertheless, these rates of common harms associated with amoxicillin therapy may inform decisions by helping clinicians to balance harms against benefits.Most antibiotics are prescribed by primary care clinicians for common infections, particularly acute respiratory infections.¹ However, for most acute respiratory infections, antibiotics provide only marginal benefits, and an inevitable consequence of this injudicious use is the prospect of antibiotic resistance. One way to reduce antibiotic prescribing in primary care is to explain to patients how little these drugs help for many common infections and to apply a process of shared decision-making during the consultation.²The practice of shared decision-making requires not just an explanation of the paucity of benefits of antibiotics in most primary care situations, but also an explanation of the potential harms. Serious harms are probably sufficiently rare to be discounted by most clinicians and their patients.³ Yet when the decision to use or not use antibiotics relates to a self-remitting illness, for which the benefits are likely to be modest at best, the more common, mild harms of antibiotics become important. Unfortunately, common harms from antibiotics are poorly quantified, and clinicians cannot talk to patients with confidence about their likelihood.Current understanding of the common harms of antibiotics is derived largely from observational studies. However, estimates of common harms from such studies may be biased, principally because it is difficult to distinguish adverse drug reactions from disease-related symptoms. One approach to addressing this problem is to investigate common harms encountered in randomized controlled trials of antibiotic against placebo. This study design controls for disease-related symptoms, allowing for better quantification of antibiotic-related adverse effects.The most common antibiotic used in primary care is amoxicillin, either alone or in combination with clavulanic acid. “Common harms” can be defined as those frequent enough to be observable in the patient samples of most randomized trials and occurring during the recording of primary outcomes in such studies (with recognition that some of the adverse effects will occur later).Accordingly, we systematically reviewed all published placebo-controlled randomized trials of amoxicillin or amoxicillin–clavulanic acid for any indication, with the rationale that the risks of drug-induced harms are independent of the condition being treated.⁴     

Multiple forms of inducible drug-metabolizing enzymes: A reasonable mechanism by which any organism can cope with adversity

Summary All organisms possess a number of genetically regulated mechanisms in order to cope with rapid adverse changes in the environment. The two systems which appear to respond to a seemingly endless array of chemical specificities are the immune response and the induction of drug-metabolizing enzymes. Similarities and differences between the immunoglobulin and the cytochrome P-450-mediated monooxygenase systems are described. DNA insertion sequences, plasmid transposons, maize controlling elements, gene duplication, intervening sequences, and high-frequency intergenic recombination are all discussed as possible methods by which organisms can adapt quickly to a new selective pressure. If the regulation of P-450 induction resembles in any way the other methods by which pro- and eukaryotes cope genetically with numerous forms of environmental adversity, therefore, it is very likely that mammalian tissues contain hundreds, if not thousands, of inducible forms of P-450.Portions of this overview were presented at the Symposium on The Effects of Drugs on Enzyme Induction Related to the Metabolism of Drugs and Carcinogenic Compounds, 14th Symposium Medicum Hoechst, County Mayo, Ireland, May, 1978 (1), and the Symposium on Isolated Drug-Metabolizing Enzymes, Mainz, Germany, July, 1978 (2). The author is Chief of the Developmental Pharmacology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20205.     

Automated system for capture and detection of nucleic acids.

A fully automated nucleic acid analysis system is described, which offers positive sample identification, improved sensitivity and reduced user interaction compared to conventional techniques. The system relies on the sequence-specific capture of DNA onto solid-phase particles, confirming product identity without the problems of interpretation and lack of sequence information inherent in gel-based analyses. The system can be used for sequence confirmation, mutation analysis and semiquantitative detection of PCR products.     

Identification of susceptibility modules for coronary artery disease using a genome wide integrated network analysis

Although recent genome-wide association studies (GWAS) have identified a handful of variants with best significance for coronary artery disease (CAD), it remains a challenge to summarize the underlying biological information from the abundant genotyping data. Here, we propose an integrated network analysis that effectively combines GWAS genotyping dataset, protein–protein interaction (PPI) database, literature and pathway annotation information. This three-step approach was illustrated for a comprehensive network analysis of CAD as the following. First, a network was constructed from PPI database and CAD seed genes mined from the available literatures. Then, susceptibility network modules were captured from the results of gene-based association tests. Finally, susceptibility modules were annotated with potential mechanisms for CAD via the KEGG pathway database. Our network analysis identified four susceptibility modules for CAD including a complex module that consisted of 15 functional inter-connected sub-modules, AGPAT3–AGPAT4–PPAP2B module, ITGA11–ITGB1 module and EMCN–SELL module. MAPK10 and COL4A2 among the top-scored focal adhesion pathway related module were the most significant genes (MAPK10: OR = 32.5, P = 3.5 × 10^− 11; COL4A2: OR = 2.7, P = 2.8 × 10^− 10). The significance of the two genes were further validated by other two gene-based association tests (MAPK10: P = 0.009 and 0.007; COL4A2: P = 0.001 and 0.023) and another independent GWAS dataset (MAPK10: P = 0.001; COL4A2: P = 0.0004). Furthermore, 34 out of 44 previously reported CAD susceptibility genes were captured by our CAD PPI network and 17 of them were also significant genes. The susceptibility modules identified in our study might provide novel clues for the clarification of CAD pathogenesis in the future.     

PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type

Visualizing RNA pseudoknot structures is computationally more difficult than depicting RNA secondary structures, because a drawing of a pseudoknot structure is a graph (and possibly a nonplanar graph) with inner cycles within the pseudoknot, and possibly outer cycles formed between the pseudoknot and other structural elements. We previously developed PSEUDOVIEWER for visualizing H-type pseudoknots. PSEUDOVIEWER2 improves on the first version in many ways: (i) PSEUDOVIEWER2 is more general because it can visualize a pseudoknot of any type, including H-type pseudoknots, as a planar graph; (ii) PSEUDOVIEWER2 computes a drawing of RNA structures much more efficiently and is an order of magnitude faster in actual running time; and (iii) PSEUDOVIEWER2 is a web-based application program. Experimental results demonstrate that PSEUDOVIEWER2 generates an aesthetically pleasing drawing of pseudoknots of any type and that the new representation offered by PSEUDOVIEWER2 ensures uniform and clear drawings, with no edge crossing, for all types of pseudoknots. The PSEUDOVIEWER2 algorithm is the first developed for the automatic drawing of RNA secondary structures, including pseudoknots of any type. PSEUDOVIEWER2 is accessible at http://wilab.inha.ac.kr/pseudoviewer2/.     

Automated feature detection and imaging for high-resolution screening of zebrafish embryos

The development of automated microscopy platforms has enabled large-scale observation of biological processes, thereby complementing genome scale biochemical techniques. However, commercially available systems are restricted either by fixed-field-of-views, leading to potential omission of features of interest, or by low-resolution data of whole objects lacking cellular detail. This limits the efficiency of high-content screening assays, especially when large complex objects are used as in whole-organism screening. Here we demonstrate a toolset for automated intelligent high-content screening of whole zebrafish embryos at cellular resolution on a standard wide-field screening microscope. Using custom-developed algorithms, predefined regions of interest-such as the brain-are automatically detected. The regions of interest are subsequently imaged automatically at high magnification, enabling rapid capture of cellular resolution data. We utilize this approach for acquiring 3-D datasets of embryonic brains of transgenic zebrafish. Moreover, we report the development of a mold design for accurate orientation of zebrafish embryos for dorsal imaging, thereby facilitating standardized imaging of internal organs and cellular structures. The toolset is flexible and can be readily applied for the imaging of different specimens in various applications.     

Automated fluorescent detection of a 10 loci multiplex for paternity testing

The discovery of new highly efficient tetra repeat STR loci, development of fluorescence multicolour dye technology and capillary electrophoresis have made it possible to amplify ten loci in a single reaction. This combination provides an extraordinary effectiveness of simultaneous amplification and detection. With this method it became possible to determine individual identity and paternity at an enhanced level of precision and accuracy in 1 to 2 days with a high biostatistical probability. This review demonstrates the role of automated fluorescent multicolour dye genotyping technology in forensic paternity testing.     

An integrated, stacked microlaboratory for biological agent detection with DNA and immunoassays

An integrated, stacked microlaboratory for performing automated electric-field-driven immunoassays and DNA hybridization assays was developed. The stacked microlaboratory was fabricated by orderly laminating several different functional layers (all 76 x 76 mm(2)) including a patterned polyimide layer with a flip-chip bonded CMOS chip, a pressure sensitive acrylic adhesive (PSA) layer with a fluidic cutout, an optically transparent polymethyl methacrylate (PMMA) film, a PSA layer with a via, a patterned polyimide layer with a flip-chip bonded silicon chip, a PSA layer with a fluidic cutout, and a glass cover plate layer. Versatility of the stacked microlaboratory was demonstrated by various automated assays. Escherichia coli bacteria and Alexa-labeled protein toxin staphylococcal enterotoxin B (SEB) were detected by electric-field-driven immunoassays on a single chip with a specific-to-nonspecific signal ratios of 4.2:1 and 3.0:1, respectively. Furthermore, by integrating the microlaboratory with a module for strand displacement amplification (SDA), the identification of the Shiga-like toxin gene (SLT1) from E. coli was accomplished within 2.5 h starting from a dielectrophoretic concentration of intact E. coli bacteria and finishing with an electric-field-driven DNA hybridization assay, detected by fluorescently labeled DNA reporter probes. The integrated microlaboratory can be potentially used in a wide range of applications including detection of bacteria and biowarfare agents, and genetic identification.