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At least 1,531 records · Page 85Linked to original sources

PubMed2004

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques have motivated the development of a large number of bioinformatics methods for the detection of regulatory motifs. The regulatory process is extremely complex and individual computational algorithms typically have very limited success in genome-scale studies. Here, we argue the importance of integrating multiple computational algorithms and present an infrastructure that integrates eight web services covering key areas of transcriptional regulation. We have adopted the client-side integration technology and built a consistent input and output environment with a versatile visualization tool named SeqVISTA. The infrastructure will allow for easy integration of gene regulation analysis software that is scattered over the Internet. It will also enable bench biologists to perform an arsenal of analysis using cutting-edge methods in a familiar environment and bioinformatics researchers to focus on developing new algorithms without the need to invest substantial effort on complex pre- or post-processors. SeqVISTA is freely available to academic users and can be launched online at http://zlab.bu.edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu.edu/SeqVISTA.

Algorithms↗

PubMed2005

SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites.

SEARCHGTr is a web-based software for the analysis of glycosyltransferases (GTrs) involved in the biosynthesis of a variety of pharmaceutically important compounds like adriamycin, erythromycin, vancomycin etc. This software has been developed based on a comprehensive analysis of sequence/structural features of 102 GTrs of known specificity from 52 natural product biosynthetic gene clusters. SEARCHGTr is a powerful tool that correlates sequences of GTrs to the chemical structures of their corresponding substrates. This software indicates the donor/acceptor specificity and also identifies putative substrate binding residues. In addition, it provides interfaces to other public databases like GENBANK, SWISS-PROT, CAZY, PDB, PDBSum and PUBMED for extracting various information on GTrs homologous to the query sequence. SEARCHGTr would provide new dimension to our previously developed bioinformatics tool NRPS-PKS. Together, these tools facilitate comprehensive computational analysis of proteins involved in biosynthesis of aglycone core and its downstream glycosylations. Apart from presenting opportunities for rational design of novel natural products, these tools would assist in the identification of biosynthetic products of secondary metabolite gene clusters found in newly sequenced genomes. SEARCHGTr can be accessed at http://www.nii.res.in/searchgtr.html.

Anti-Bacterial Agents↗

PubMed2026

RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.

MOTIVATION: Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this problem. In particular, run-length Burrows-Wheeler transform (RLBWT) based compressed full text indexes have seen wide development and adoption. However, the construction of these RLBWT-based compressed full text indexes is still computationally expensive, sometimes prohibitively so, even for current dataset sizes. RESULTS: Therefore, we present algorithms for the construction of RLBWT-based compressed full text indexes and their supporting data structures in compressed space. The algorithms have a space complexity of O(r) words and run in O(n) time for repetitive datasets, where r is the number of runs in the BWT, n is the length of the text, and repetitive datasets implies nr∈Ω(log n). We provide the first algorithm to compute LCP-related information for repetitive datasets in optimal time and O(r) space, greatly reducing memory requirements. The key idea behind this algorithm is the utilization of r samples of the inverse suffix array at regular intervals. For example, on the Human Pangenome Reference Consortium Release 2 dataset, this reduces peak memory from 2135 GiB to 170 GiB (12.6x reduction) compared to the previous best method (pfp-thresholds). AVAILABILITY AND IMPLEMENTATION: The implementation is available at https://github.com/ucfcbb/TeraTools.

Algorithms↗

PubMedDate not supplied

An insight-based methodology for evaluating bioinformatics visualizations.

High-throughput experiments, such as gene expression microarrays in the life sciences, result in very large data sets. In response, a wide variety of visualization tools have been created to facilitate data analysis. A primary purpose of these tools is to provide biologically relevant insight into the data. Typically, visualizations are evaluated in controlled studies that measure user performance on predetermined tasks or using heuristics and expert reviews. To evaluate and rank bioinformatics visualizations based on real-world data analysis scenarios, we developed a more relevant evaluation method that focuses on data insight. This paper presents several characteristics of insight that enabled us to recognize and quantify it in open-ended user tests. Using these characteristics, we evaluated five microarray visualization tools on the amount and types of insight they provide and the time it takes to acquire it. The results of the study guide biologists in selecting a visualization tool based on the type of their microarray data, visualization designers on the key role of user interaction techniques, and evaluators on a new approach for evaluating the effectiveness of visualizations for providing insight. Though we used the method to analyze bioinformatics visualizations, it can be applied to other domains.

Algorithms↗

PubMed2001

Medical informatics and bioinformatics: European efforts to facilitate synergy.

Over the past decade there have been several attempts to rethink the basic strategies and scope of medical informatics. Meanwhile, bioinformatics has only recently experienced a similar debate about its scientific character. Both disciplines envision the development of novel diagnostic, therapeutic, and management tools, and products for patient care. A combination of the expertise of medical informatics in developing clinical applications and the focused principles that have guided bioinformatics could create a synergy between the two areas of application. Such interaction could have a great influence on future health research and the ultimate goal, namely continuity and individualization of health care. This article summarizes current activities related to facilitating synergy between medical informatics and bioinformatics, emphasizing activities in Europe while relating them to efforts in other parts of the world. The report provides examples of the analysis that European investigators are carrying out, aiming to propose new ideas for collaborations between medical informatics and bioinformatics researchers in a variety of areas.

Computational Biology↗

PubMed2027

Teratoma Formation and Genomic Profiling Using Multi-Omics Approaches.

Teratoma formation is the gold standard assay for evaluating the developmental pluripotency of human and mouse embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Following subcutaneous injection into immunodeficient mice, pluripotent stem cells spontaneously differentiate into derivatives representing all three embryonic germ layers-ectoderm, mesoderm, and endoderm. Beyond serving as a functional assay for pluripotency, teratomas provide a unique three-dimensional model system for studying early human development and lineage specification in vivo. This chapter describes comprehensive protocols for teratoma formation in immunodeficient mice, tissue processing for multiple downstream genomic applications, and multi-omics profiling approaches. We detail methods for embryonic stem cell culture, teratoma generation via subcutaneous injection, tissue dissection and processing for chromatin immunoprecipitation followed by sequencing (ChIP-Seq), RNA sequencing (RNA-Seq), single-cell multiome profiling combining chromatin accessibility (ATAC-Seq) and gene expression (scRNA-Seq), and histological analysis using hematoxylin and eosin (H&E) staining. Additionally, we provide bioinformatics workflows for analyzing the resulting genomic datasets to characterize the epigenetic and transcriptional landscapes of teratoma-derived tissues. These methods enable comprehensive molecular characterization of developmental processes and provide valuable resources for stem cell biologists studying pluripotency, differentiation, and early embryonic development.

Teratoma↗

PubMed2004

Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome.

In this study, we generated three SAGE libraries from melanoma tissues. Using bioinformatics tools usually applied to microarray data, we identified several genes, including novel transcripts, which are preferentially expressed in melanoma. SAGE results converged with previous microarray analysis on the importance of intracellular calcium and G-protein signaling, and the Wnt/Frizzled family. We also examined the expression of CD74, which was specifically, albeit not abundantly, expressed in the melanoma libraries using a melanoma progression tissue microarray, and demonstrate that this protein is expressed by melanoma cells but not by benign melanocytes. Many genes involved in intracellular calcium and G-protein signaling were highly expressed in melanoma, results we had observed earlier from microarray studies (Bittner et al., 2000). One of the genes most highly expressed in our melanoma SAGE libraries was a calcium-regulated gene, calpain 3 (p94). Immunohistochemical analysis demonstrated that calpain 3 moves from the nuclei of non-neoplastic cells to the cytoplasm of malignant cells, suggesting activation of this intracellular proteinase. Our SAGE results and the clinical validation data demonstrate how SAGE profiles can highlight specific links between signaling pathways as well as associations with tumor progression. This may provide insights into new genes that may be useful for the diagnosis and therapy of melanoma.

Aged↗

PubMed2006

Detection of conjugation related type four secretion machinery in Aeromonas culicicola.

BACKGROUND: Aeromonas sp. can now be considered relatively common enteropathogens due to the increase of diseases in humans. Aeromonas culicicola is a gram negative rod-shaped bacterium isolated for the first time from the mosquito mid-gut, but subsequently detected in other insects and waters also. Our previous study discovered that A. culicicola harbors three plasmids, which we designated as pAc3249A, pAc3249B and pAc3249C. We investigated and report here the existence and genetic organization of a Conjugal Type IV Secretion System (TFSS) in pAc3249A. METHODOLOGY/PRINCIPLE FINDING: The complete operon is 11,061 bp in length and has G+C content of 47.20% code for 12 ORFs. The gene order and orientation were similar to those found in other bacteria with some differences. We have designated this system as AcTra for Aeromonas culicicola transfer system. BLAST results of ORFs and phylogenetic analysis showed significant similarity towards the respective proteins of the IncI2 plasmid R721 of E. coli. Other bioinformatics studies have been performed to predict conserved motifs/domains, signal peptides, transmembrane helices, etc. of the ORFs. CONCLUSIONS/SIGNIFICANCE: BLAST results of ORFs and phylogenetic analysis showed significant similarity towards the respective proteins of the IncI2 plasmid R721 of E. coli.

Aeromonas↗

PubMed2000

Functional analysis of six novel ORFs on the left arm of chromosome XII in Saccharomyces cerevisiae reveals two essential genes, one of which is under cell-cycle control.

Six novel Open Reading Frames (ORFs) located on the left arm of chromosome XII (YLL044w, YLL042c, YLL040c, YLL038c, YLL035w and YLL034c) have been analysed using short-flanking homology (SFH) gene replacement. Sporulation and tetrad analysis showed that YLL035w and YLL034c are essential for cell growth; yll035w spores arrested after two or three cell divisions, while the majority of yll034c spores stopped growth within two cell cycles after germination. Complementation of the yll035w deletion with its cognate clone, and a promoter-substitution experiment, indicated that the promoter of YLL035w may lie within the adjacent ORF, YLL036c. Transcriptional analysis demonstrated that YLL035w is under cell-cycle regulation. Bioinformatic analyses produced significant matches between YLL034c and mammalian valosin and many other ATPases. The standard EUROFAN growth tests failed to reveal obvious phenotypes resulting from deletion of any of the four non-essential ORFs. Replacement cassettes, comprising the kanMX marker flanked by each ORF's promoter and terminator regions, were cloned into pUG7. All the cognate clones, except for YLL040c, were generated using direct PCR products amplified from genomic DNA or using gap-repair. All clones and strains produced have been deposited in the EUROFAN genetic stock centre (EUROSCARF, Frankfurt).

Cell Cycle↗

PubMed2005

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

In higher eukaryotes, transcriptional enhancers play critical roles in the integration of cellular signaling information, but apart from a few well-studied model enhancers, we lack a general picture of transcriptional information processing by most enhancers. Here we discuss recent studies that have provided fresh insights on information processing that occurs on enhancers, and propose that in addition to the highly cooperative and coordinate action of "enhanceosomes", a less integrative, but more flexible form of information processing is mediated by information display or "billboard" enhancers. Application of these models has important ramifications not only for the biochemical analysis of transcription, but also for the wider fields of bioinformatics and evolutionary biology.

Computational Biology↗

PubMed2006

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.

The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project. Standards and well-defined processing pipelines are important for these consortia. We show a way for choosing the right database model, through collecting data, processing these with a decoy database and end up with a quality controlled protein list merged from several search engines, including a known false-positive rate.

Algorithms↗

PubMed2006

The reactive oxygen species network pathways:an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants.

Availability of complete Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome sequences, together with molecular recourses of functional genomics and proteomics have revolutionized our understanding of reactive oxygen species (ROS) signalling network mediating disease resistance in plants. So far, ROS have been associated with aging, cellular and molecular alteration in animal and plant cells. Recently,concluding evidences suggest that ROS network is essential to induce disease resistance and even to mediate resistance to multiple stresses in plants. ROS are obligatory by-products emerging as a result of normal metabolic reactions. They have the potential to be both beneficial and harmful to cellular metabolism. Their dual effects on metabolic reactions are dosage specific. In this review we focus our attention on cellular ROS level to trigger beneficial effects on plant cells responding to pathogen attack. By exploring the research related contributions coupled with data of targeted gene disruption, and RNA interference approaches, we show here that ROS are ubiquitous molecules of redox-pathways that play a crucial role in plant defence mechanism. The molecular prerequisites of ROS network to activate plant defence system in response to pathogen infections are here underlined. Bioinformatic tools are now available to scientists for high throughput analysis of cellular metabolisms. These tools are used to illustrate crucial ROS-related genes that are involved in the defence mechanism of plants. The review describes also the emerging findings of ROS network pathways to modulate multiple stress resistance in plants.

Animals↗

PubMed2025

Unveiling the Genomic Landscape of Escherichia coli O1:K1:H7 ST59 in Non-complicated Urinary Infections from Colombia Through Whole-Genome Sequencing.

Escherichia coli (E. coli) is a Gram-negative bacterium known for causing both intestinal and extraintestinal infections in humans. Among extraintestinal infections, urinary tract infections (UTIs) are particularly prevalent and impactful. In Colombia, limited information is available regarding the molecular epidemiology of E. coli. This lack of data hinders the understanding of the local epidemiological landscape and the identification of pathogenic lineages that may contribute to public health concerns. This study aimed to characterize an E. coli strain isolated from a 24-year-old female patient with a community-acquired lower UTI, focusing on genotypic analysis through whole-genome shotgun sequencing (WGSS) and subsequent bioinformatics investigations. The identified strain belongs to phylogroup F, with serotype O1:H7 and sequence type (ST) 59. Several virulence factors, including traT and afimbrial adhesins (afaC), were identified, with afaC being notably uncommon in ST59 phylogroup F. In addition, an antibiotic susceptibility test was performed, and the isolate was found to be sensitive to all the antibiotics tested. This work contributes to the understanding of E. coli phylogroup F in Colombia and provides valuable genomic data, shedding light on the virulence profile of this strain in lower urinary tract infections.

Female↗

PubMed2026

Cryopreservation-induced proteomic alterations in Pêga donkey (Equus asinus) spermatozoa.

Semen cryopreservation is a key tool for assisted reproduction and genetic conservation, but its efficiency remains limited in donkeys, compromising post-thaw sperm quality. This study aimed to characterize the proteomic profile of Pêga donkey spermatozoa and to investigate molecular mechanisms associated with cryopreservation-induced impairment of sperm function. Semen samples were collected from Pêga jacks and evaluated for sperm motility and vigor before and after cryopreservation. Quantitative proteomic analysis was performed by LC-MS/MS, followed by bioinformatic characterization of differentially abundant proteins. Cryopreservation markedly reduced sperm motility in all animals, whereas sperm vigor showed only a non-significant tendency toward reduction, suggesting sublethal cryoinjury primarily affecting flagellar efficiency. Proteomic profiling identified 554 proteins, of which 98 were differentially abundant between in natura and cryopreserved spermatozoa. Functional enrichment analyses showed that these proteins were mainly associated with energy metabolism, mitochondrial oxidative phosphorylation, glycolysis, cytoskeletal organization, signal transduction, proteostasis, and oxidative stress response. Notably, proteins involved in ATP production, mitochondrial function, and axonemal organization were significantly altered, supporting a mechanistic link between metabolic dysfunction, flagellar structural disorganization, and reduced post-thaw motility. Overall, cryopreservation induced coordinated and compartment-specific remodeling of the donkey sperm proteome, particularly affecting pathways essential for motility and functional competence. These findings provide new molecular insights into the cryobiological vulnerability of donkey spermatozoa and establish a mechanistic basis for the development of more effective, biology-driven cryopreservation strategies for this species.

Animals↗

PubMed2000

Mining bacterial genomes for antimicrobial targets.

The elucidation of whole-genome sequences is expected to have a revolutionary impact on the discovery of novel medicines. With the availability of complete genome sequences of more than 30 different species, the field of antimicrobial drug discovery has the opportunity to access a remarkable diversity of genomic information. In this review, I summarize how microbial genomics has changed strategies of drug discovery by applying bioinformatics, novel genetic approaches and genomics-based technologies, including analysis of gene expression using DNA microarrays.

Anti-Bacterial Agents↗

PubMed2001

Bacterial fatty-acid biosynthesis: a genomics-driven target for antibacterial drug discovery.

In this review we demonstrate how the interplay of genomics, bioinformatics and genomic technologies has enabled an in-depth analysis of the component enzymes of the bacterial fatty-acid biosynthesis pathway as a source of novel antibacterial targets. This evaluation has revealed that many of the enzymes are potentially selective, broad-spectrum antibacterial targets. We also illustrate the suitability of some of these targets for HTS. Furthermore, we discuss how the availability of a robust selectivity assay, mode-of-action assays and numerous crystal structures provide an excellent set of tools with which to initiate integrated programs of research to identify novel antibiotics targeted at these enzymes.

Journal Article↗

PubMed2005

Computing chemistry on the web.

The development of on-line software tools is changing the way we traditionally perform our analysis in drug design, but will chemoinformatics be forever behind bioinformatics in this development?

Computer Simulation↗

PubMed2005

Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration.

The steroidal moulting hormones (ecdysteroids) mediate developmental transitions in insects, and their regulation is mainly controlled by the production and inactivation of these steroid hormones at the appropriate developmental times. One route of metabolism of ecdysteroids in insects involves EO (ecdysone oxidase)-catalysed conversion into 3-dehydroecdysteroid, which undergoes reduction to the corresponding 3-epiecdysteroid. By a twin-stranded bioinformatics approach, employing both phylogenomics and model structure-based analysis, we first predicted that DmEO (the EO of Drosophila melanogaster) corresponds to the protein product of gene CG9504. When CG9504 was expressed in COS7 cells, significant conversion of ecdysone into 3-dehydroecdysone was observed. Quantitative PCR and enzyme assay showed that DmEO was mainly expressed in the midgut during the late instars at a time corresponding to a hormone titre peak. DmEO shares only 27% amino acid sequence identity with Spodoptera littoralis (Lepidoptera) EO, yet key substrate-binding residues are well conserved. A model of DmEO is consistent with an inability to catalyse reaction of cholesterol derivatives. The significance of DmEO in ligand activation is discussed in relation to new evidence suggesting that 3-dehydro- and 3-epiecdysteroids may be functionally active as ligands in a novel, atypical ecdysteroid signalling pathway involving the Drosophila orphan nuclear receptor, DHR38, rather than being merely hormone inactivation products.

3-Hydroxysteroid Dehydrogenases↗