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PubMed2006

Beyond Mfold: recent advances in RNA bioinformatics.

Computational analysis of RNA secondary structure is a classical field of biosequence analysis, which has recently gained momentum due to the manyfold regulatory functions of RNA that have become apparent. We present five recent computational approaches that address the problems of synoptic folding space analysis, pseudoknot prediction, structure alignment, comparative structure prediction, and miRNA target prediction. All these programs are in current use and are available via the Bielefeld Bioinformatics Server at .

Animals↗

PubMed2004

Bioinformatics in reproductive biology--functional annotation based on comparative sequence analysis.

Recent studies of the genomes of a variety of model organisms have provided an unprecedented opportunity to identify and characterize all signaling molecules in the human genome. Regardless of the approaches used to decipher gene characteristics and their role in physiology, pairwise sequence comparison represents the fundamental bioinformatic tool for initial functional annotation of newly identified genes. Because genes evolved from duplication and adapted to different evolutionary niches for each organism during speciation, detailed sequence analysis could provide additional information on the biochemical and biological characteristics of novel genes. In addition, the integration of sequence-based gene discovery with phylogeny-based function prediction leads to a more complete understanding of the signaling pathways. For example, detailed pairwise sequence analysis has led to the identification of (1) stresscopin (SCP) and stresscopin-related peptides (SRP) as the CRH-related genes, (2) multiple relaxin-like factor genes, and (3) the novel glycoprotein hormone subunit family genes, alpha2 and beta5. Furthermore, based on the understanding that ligands and receptors coevolved during evolution, we have identified a variety of novel extracellular signaling polypeptides including (1) stresscopin and stresscopin-related peptides as selective ligands for the type 2 CRH receptor, (2) the pregnancy hormone, relaxin, and related peptides that activate two orphan G protein-coupled receptors (GPCRs), LGR7 and LGR8, and (3) alpha2 and beta5 that form a heterodimer capable of activating the TSH receptor. Thus, detailed studies on the characteristics and evolution of gene sequences have provided an inroad to the elucidation of novel signaling polypeptides and the associated signal transduction pathways.

Animals↗

PubMed2005

From worm to human: bioinformatics approaches to identify FOXO target genes.

Longevity regulatory genes include the Forkhead transcription factor FOXO, in addition to NAD-dependent histone deacetylase silent information regulator 2 (Sir2). The FOXO/DAF-16 family of transcription factors constitute an evolutionarily conserved subgroup within a larger family known as winged helix or Forkhead transcriptional regulators. Here we demonstrate how to identify FOXO target genes and their potential cis-regulatory binding sites in the promoters via bioinformatics approaches. These results provide new testable hypotheses for further experimental verifications.

Animals↗

PubMed2006

Bioinformatic identification and characterization of new members of short-chain dehydrogenase/reductase superfamily.

With about 60 genes known in the human genome, short-chain dehydrogenases/reductases (SDRs) form a large gene family with important implications for medicine. They are known to be involved in carcinogenesis (e.g. breast and prostate cancer) as well as in metabolic and degenerative defects such as the pathogenesis of Alzheimer's disease, osteoporosis and diabetes. Uncharacterized SDRs are thus potential candidates for many monogenic and multifactorial human diseases. The identification and functional analysis of such SDR enzymes is therefore the primary goal of the study leading to new targets for drug development. In all taxa (bacteria, plants, insects, vertebrates), members of SDR superfamily are known. Up to now, there are several thousand members annotated many of which have not been characterized biochemically with regard to enzymatic activity, substrate specificity, or subcellular localization. We bioinformatically identified 250 vertebrate candidate genes belonging to the SDR superfamily using the BioNetWorks software SDR finder. The number was reduced to 95 after continuative analysis, including manual SDR motif verification and focus on human, rat and murine enzymes. Here, we present several new mammalian SDRs that were clustered into several enzymatically different groups by detailed phylogenetic analyses. Furthermore, characteristic mRNA expression patterns were identified for some of these genes by a recently developed in silico Northern blot method supporting their putative functions in retinoid, steroid, sugar and other metabolic pathways.

Amino Acid Sequence↗

PubMed2026

Integrated molecular, epidemiological, and bioinformatics perspectives on the Mpox virus: Implications for surveillance and Global Health preparedness.

Mpox has re-emerged as a significant global zoonotic threat, driven mainly by two large waves the 2022 worldwide Clade IIb outbreak and the 2024 Clade Ib epidemic in Central Africa. This review examines the challenges of interpreting this evolving virus from molecular, epidemiological, and bioinformatics perspectives, with a focus on global health workforce preparedness. Clade IIb largely moved through sexual transmission across countries, but Clade Ib has appeared in a wider population-women, children, and individuals infected through household spread without any sexual contact. Early case series suggest that Clade Ib may cause a more severe disease burden, but more research is needed to directly compare severity and fatality rates with Clade IIb due to the limited number of current studies. The review examines the virus's strategies for evading the host's immune defenses throughout its ∼197 kbp genome, including how it disrupts interferon signaling and creates decoy receptors. This review summarizes the clinical findings of PALM007 and STOMP, noting that neither trial achieved its main efficacy endpoint making routine tecovirimat use less compelling-while leaving open whether it helps particular high-risk groups. A further point is that immunity from the MVA-BN vaccine wanes with time, leading to the growing adoption of booster vaccinations. In conclusion, the review calls for a One Health approach pairing genomic tracking with ecological intelligence and including wastewater surveillance to fill existing gaps in knowledge and enhance the global handling of new orthopoxvirus threats.

Animals↗

PubMed2005

Bioinformatics in otolaryngology.

This article reviews the recent literature on microarray analysis, bioinformatics techniques, and genomics in relation to the study of carcinogenesis of head and neck cancers.

Algorithms↗

PubMed2005

Bioinformatic analysis of neuropeptide and receptor expression profiles during midgut metamorphosis in Drosophila melanogaster.

Neuropeptides are important messenger molecules in invertebrates, serving as neuromodulators in the nervous system and as regulatory hormones released into the circulation. Understanding the function of neuropeptides will require the integration of genetic, biochemical, physiological and behavioral information. The advent of DNA microarrays and bioinformatic databases provides a wealth of data describing the expression profiles of thousands of genes during biological processes. One such array catalogs the developmental patterns of gene expression during the metamorphic transformation of the Drosophila midgut. We have mined the data from this experiment to explore changes of expression in genes coding for known neuropeptides, peptide hormones, and their receptors during the metamorphosis of the midgut. We found small but significant changes in the expression of the peptides diuretic hormone, FGLa-type allatostatins, myoinhibiting peptide, ecdysis-triggering hormone, drosokinin and the burs subunit of bursicon, as well as the receptors DAR-2, NPFR1, ALCR-2, Lkr and DH-R. Just as advances have been made in understanding the molecular basis of invertebrate neuropeptide action by analysis of genome projects, data mining of gene expression databases can help to integrate molecular, biochemical and physiological knowledge of biological processes.

Animals↗

PubMed2004

Bioinformatics in proteomics: application, terminology, and pitfalls.

Bioinformatics applies data mining, i.e., modern computer-based statistics, to biomedical data. It leverages on machine learning approaches, such as artificial neural networks, decision trees and clustering algorithms, and is ideally suited for handling huge data amounts. In this article, we review the analysis of mass spectrometry data in proteomics, starting with common pre-processing steps and using single decision trees and decision tree ensembles for classification. Special emphasis is put on the pitfall of overfitting, i.e., of generating too complex single decision trees. Finally, we discuss the pros and cons of the two different decision tree usages.

Computational Biology↗

PubMed2004

Comparative analysis of the catalytic domain of hemorrhagic and non-hemorrhagic snake venom metallopeptidases using bioinformatic tools.

Snake venom metalloproteases (SVMPs) are a set of interesting enzymes that are one of the major components of venom affecting hemostasis. A great challenge since their discovery has been to find molecular features responsible for their hemorrhagic potency and many attempts have been made without any consistent result. Here we describe a series of comparisons between the catalytic domains of hemorrhagic and non-hemorrhagic SVMPs made with the help of bioinformatics. These involved sequence and structure-based multiple alignments, phylogenetic reconstruction, predicted physical and chemical properties, motif scanning and structural analyses. Although hemorrhagic activity seems to be complex, involving multiple factors, we found some molecular characteristics that may influence the toxic effects. Among these findings, it was possible to use a molecular surface feature to subdivide the P-I class in hemorrhagic and non-hemorrhagic SVMPs. It was also possible to suggest a role for the conserved Asp148 and Ser176 residues in the stabilization of the active site.

Animals↗

PubMed2005

Toxic polypeptides of the hydra--a bioinformatic approach to cnidarian allomones.

Cnidarians such as hydrae and sea anemones are sessile, predatory, soft bodied animals which depend on offensive and defensive allomones for prey capture and survival. These allomones are distributed throughout the entire organism both in specialized stinging cells (nematocytes) and in the body tissues. The cnidarian allomonal system is composed of neurotoxins, cytolysins and toxic phospholipapses. The present bioinformatic survey was motivated by the fact that while hydrae are the most studied model cnidarian, little is known about their allomones. A large-scale EST database from Hydra magnipapillata was searched for orthologs of known cnidarian allomones, as well as for allomones found in other venomous organisms. We show that the hydrae express orthologs of cnidarian phospholipase A2 toxins and cytolysins belonging to the actinoporin family, but could not find orthologs of the 'classic' short chain neurotoxins affecting sodium and potassium conductance. Hydrae also express proteins similar to elapid-like phospholipases, CRISP proteins, Prokineticin-like polypeptides and toxic deoxyribonucleases. Our results illustrate a high level of complexity in the hydra allomonal system, suggest that several toxins represent a basal component of all cnidarian allomones, and raise the intriguing possibility that similar proteins may fulfill both endogenous and allomonal roles in cnidaria.

Amino Acid Sequence↗

PubMed2005

Genomic and bioinformatics analysis of HAdV-7, a human adenovirus of species B1 that causes acute respiratory disease: implications for vector development in human gene therapy.

Human adenovirus serotype 7 (HAdV-7) is a reemerging pathogen identified in acute respiratory disease (ARD), particularly in epidemics affecting basic military trainee populations of otherwise healthy young adults. The genome has been sequenced and annotated (GenBank accession no. ). Comparative genomics and bioinformatics analyses of the HAdV-7 genome sequence provide insight into its natural history and phylogenetic relationships. A putative origin of HAdV-7 from a chimpanzee host is observed. This has implications within the current biotechnological interest of using chimpanzee adenoviruses as vectors for human gene therapy and DNA vaccine delivery. Rapid genome sequencing and analyses of this species B1 member provide an example of exploiting accurate low-pass DNA sequencing technology in pathogen characterization and epidemic outbreak surveillance through the identification, validation, and application of unique pathogen genome signatures.

Adenovirus Infections, Human↗

PubMed2005

Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources.

The exponential growth of sequence data has become a challenge to database curators and end-users alike and biologists seeking to utilize the data effectively are faced with numerous analysis methods. Here, with practical examples from our bioinformatics analysis of the protein tyrosine phosphatases (PTPs), we show how computational analysis can be exploited to fuel hypothesis-driven experimental research through the exploration of online databases. We cover the following elements: (i) similarity searches and strategies to collect a non-redundant database of tyrosine-specific PTP domains; (ii) utilization of this database to classify human, fly, and worm PTPs (based on alignments and phylogenetic analysis); (iii) three-dimensional structural analysis to identify conserved regions (structure-function) and non-conserved selectivity-determining regions (substrate specificity); and (iv) genomic analysis, including mapping of exon structure, identification of pseudogenes, and exploration of disease databases. We discuss the importance of manual curation, illustrating examples in which pseudogenes give rise to predicted proteins in GenBank and note that domain servers, such as PFAM and SMART, erroneously include dual-specificity and lipid phosphatases in their collection of tyrosine-specific PTPs. To capitalize on our annotated set of 402 PTP domains (from 47 species and five phyla), we identify sequence conservation across taxonomic categories and explore structure-function relationships among tandem domain receptor-like PTPs. We define three Src homology 2 domain-containing PTP genes in stingray, zebrafish, and fugu and speculate on their evolutionary relationship with human pseudogenes. Our annotated sequences, along with a web service for phylogenetic classification of PTP domains, are available online (http://ptp.cshl.edu and http://science.novonordisk.com/ptp).

Amino Acid Sequence↗

PubMed2005

Bacteriophage P100 for control of Listeria monocytogenes in foods: genome sequence, bioinformatic analyses, oral toxicity study, and application.

Listeria monocytogenes is an opportunistic foodborne pathogen responsible for Listeriosis, a frequently fatal infection. This investigation represents a comprehensive approach to characterize and evaluate the broad host range, strictly virulent phage P100, which can infect and kill a majority of Listeria monocytogenes strains. First, the complete nucleotide sequence (131,384 basepairs) of the genome of P100 was determined, predicted to encode 174 gene products and 18 tRNAs. Bioinformatic analyses revealed that none of the putative phage proteins has any homologies to genes or proteins of Listeria or any other bacteria which are known or suspected to be toxins, pathogenicity factors, antibiotic resistance determinants, or any known allergens. Next, a repeated dose oral toxicity study in rats was conducted, which did not produce any abnormal histological changes, morbidity or mortality. Therefore, no indications for any potential risk associated with using P100 as a food additive were found. As proof of concept, and to determine the parameters for application of P100 to foods sensitive to Listeria contamination, surface-ripened red-smear soft cheese was produced. Cheeses were contaminated with low concentrations of L. monocytogenes at the beginning of the ripening period, and P100 was applied to the surface during the rind washings. Depending on the time points, frequency and dose of phage applications, we were able to obtain a significant reduction (at least 3.5 logs) or a complete eradication of Listeria viable counts, respectively. We found no evidence for phage resistance in the Listeria isolates recovered from samples. Taken together, our results indicate that P100 can provide an effective and safe measure for the control of Listeria contamination in foods and production equipment.

Animals↗

PubMed2005

Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources.

Harvester is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. The Harvester search engine works similar to Google, offering genome-wide ranked results at very high speed. Here we describe how to use this bioinformatic tool along with selected examples.

Animals↗

PubMed2001

Which craft is best in bioinformatics?

'Silicon-based' biology has gathered momentum as the world-wide sequencing projects have made possible the investigation and comparative analysis of complete genomes. Central to the quest to elucidate and characterise the genes and gene products encoded within genomes are pivotal concepts concerning the processes of evolution, the mechanisms of protein folding, and, crucially, the manifestation of protein function. Our use of computers to model such concepts is limited by, and must be placed in the context of, the current limits of our understanding of these biological processes. It is important to recognise that we do not have a common understanding of what constitutes a gene; we cannot invariably say that a particular sequence or fold has arisen via divergence or convergence; we do not fully understand the rules of protein folding, so we cannot predict protein structure; and we cannot invariably diagnose protein function, given knowledge only of its sequence or structure in isolation. Accepting what we cannot do with computers plays an essential role in forming an appreciation of what we can do. Without this understanding, it is easy to be misled, as spurious arguments are often used to promote over-enthusiastic notions of what particular programs can achieve. There are valuable lessons to be learned here from the field of artificial intelligence, principal among which is the realisation that capturing and representing complex knowledge is time consuming, expensive and hard. If bioinformatics is to tackle biological complexity meaningfully, the road ahead must therefore be paved with caution, rigour and pragmatism.

Amino Acid Sequence↗

PubMed1999

The complement regulator C4b-binding protein analyzed by molecular modeling, bioinformatics and computer-aided experimental design.

Molecular modeling and bioinformatics have gained recognition as scientific disciplines of importance in the field of biomedical research. Molecular modeling not only allows to predict the three-dimensional structure of a protein but also helps to define its function. Careful incorporation of the experimental findings in the structural/theoretical data provides means to understand molecular mechanisms for highly complex biological systems. C4b-binding protein (C4BP) is composed of one beta-chain and seven alpha-chains essentially built from three- and eight-complement control protein (CCP) modules, respectively, followed by a non-repeat carboxy-terminal region involved in polymerization of the chains. C4BP is involved in the regulation of the complement system and interacts with many molecules such as C4b, Arp, protein S and heparin. Here, we report experimental and computer data obtained for C4BP. Protein modeling together with site directed mutagenesis indicate that R39, R64 and R66 from the C4BP alpha-chain form a key binding site for heparin, suggesting that this region could be of major importance for interaction with C4b. We also propose that the first CCP of the C4BP beta-chain displays a key hydrophobic surface of major importance for the interaction with the coagulation cofactor protein S.

Complement C4b↗

PubMed2002

Bioinformatics and high throughput approach to create genomic resources for the study of bovine immunobiology.

The advent of technologies such as real-time reverse transcriptase polymerase chain reaction (RT-PCR) and cDNA microarrays herald a new era in the study of biological systems. In immunobiology, these advances have begun to impact studies of infectious diseases, inflammatory processes, and immune cell function. However, a lack of genetic reagents for domestic and companion animals has precluded widespread application of new technologies to studies in these systems. We have recently described development of cDNA microarrays for studying bovine immunobiology. Although powerful in revealing genes involved in immunological phenomena in cattle, these resources were limited by a lack of genes known to function in immune responses from other species, such as mouse and human. To address this shortcoming, we used a combination of bioinformatics and high throughput RT-PCR to create amplicons representing over 270 bovine genes whose orthologs in other species were known to function in immune responses. Amplified gene segments were prepared from cDNA representing RNA isolated from either unstimulated or concanavalin A (ConA) stimulated peripheral blood mononuclear cells (PBMCs). In total, 276 genes were amplified from cDNA representing unstimulated bovine PBMC RNA or from cDNA representing ConA stimulated bovine PBMC RNA. A web-accessible resource (http://gowhite.ans.msu.edu/public_php/gd-bovine-immunology.php) has been created to assist in dissemination of this novel resource. The web-accessible resource contains information on gene name, the forward and reverse primers used to amplify each segment, expected product size, and if the gene was found in unstimulated PBMCs or only in ConA stimulated PBMCs. Gene names appear as hyperlinks to the Genbank pages representing the bovine gene or expressed sequence tag (EST) used to generate each primer pair.

Animals↗

PubMed2001

Bioinformatics and the malaria genome: facilitating access and exploitation of sequence information.

The torrent of sequence information unleashed by the various genome sequencing projects, including that of Plasmodium falciparum, will lead to an unprecedented increase in the data available for research purposes. The scientific community is struggling to develop ways to assimilate this information and ensure that it is fully analysed in a way that enables rapid development of new therapeutic and diagnostic advances. This is particularly so for the field of tropical medicine where many of the scientists have had limited training in the area of Bioinformatics and may be further hampered by poor access to the sequence data. A number of collections of malaria genome sequence are available, each with their own advantages and disadvantages, however further improvements in these information resources are needed. In particular, there would be great benefit in integrating genomic sequence and functional genomics results with the large amount of pre-existing knowledge related to parasite biology and immunological interactions with the host. Attempts to achieve this include the PlasmoDB database, and the lessons learned in this effort could be of great utility to other organism-specific databases.

Animals↗