PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Biological sequence analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,153 records · Page 64Linked to original sources

Regulatory networks: linking microarray data to systems biology.

Gene regulation and aging are intrinsically linked and these links often reach directly to transcription factors and their actions in gene regulation. However, it is very difficult to follow all the individual directions such factors can affect. Therefore, the opposite approach became more popular recently, i.e. observing the endpoints of all these actions. Microarrays are the preferred technology to monitor large-scale changes in transcripts across whole genomes. The trade-off for being able to survey whole genome transcriptomes is that the results are mere observations, which do not directly reveal the underlying mechanisms that represent the real link to transcription factors and their actions. Fortunately, a combination of knowledge mining (including but not restricted to literature mining) with genomics analyses can be harnessed to elucidate at least some of the regulatory networks orchestrating the transcriptional changes observed by microarray experiments. Thus, a considerable part of the functional system structure of cells and organisms can be revealed, which is a pivotal prerequisite for any meaningful systems biology approach towards aging related phenotypes.

Animals↗

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

An unusual pattern in a nucleic acid or protein sequence or a region of strong similarity shared by two or more sequences may have biological significance. It is therefore desirable to know whether such a pattern can have arisen simply by chance. To identify interesting sequence patterns, appropriate scoring values can be assigned to the individual residues of a single sequence or to sets of residues when several sequences are compared. For single sequences, such scores can reflect biophysical properties such as charge, volume, hydrophobicity, or secondary structure potential; for multiple sequences, they can reflect nucleotide or amino acid similarity measured in a wide variety of ways. Using an appropriate random model, we present a theory that provides precise numerical formulas for assessing the statistical significance of any region with high aggregate score. A second class of results describes the composition of high-scoring segments. In certain contexts, these permit the choice of scoring systems which are "optimal" for distinguishing biologically relevant patterns. Examples are given of applications of the theory to a variety of protein sequences, highlighting segments with unusual biological features. These include distinctive charge regions in transcription factors and protooncogene products, pronounced hydrophobic segments in various receptor and transport proteins, and statistically significant subalignments involving the recently characterized cystic fibrosis gene.

Amino Acid Sequence↗

Towards optimally multiplexed applications of universal arrays.

We study a design and optimization problem that occurs, for example, when single nucleotide polymorphisms (SNPs) are to be genotyped using a universal DNA tag array. The problem of optimizing the universal array to avoid disruptive cross-hybridization between universal components of the system was addressed in previous work. Cross-hybridization can, however, also occur assay specifically, due to unwanted complementarity involving assay-specific components. Here we examine the problem of identifying the most economic experimental configuration of the assay-specific components that avoids cross-hybridization. Our formalization translates this problem into the problem of covering the vertices of one side of a bipartite graph by a minimum number of balanced subgraphs of maximum degree 1. We show that the general problem is NP-complete. However, in the real biological setting, the vertices that need to be covered have degrees bounded by d. We exploit this restriction and develop an O(d)-approximation algorithm for the problem. We also give an O(d)-approximation for a variant of the problem in which the covering subgraphs are required to be vertex disjoint. In addition, we propose a stochastic model for the input data and use it to prove a lower bound on the cover size. We complement our theoretical analysis by implementing two heuristic approaches and testing their performance on synthetic data as well as on simulated SNP data.

Algorithms↗

A genomic analysis of rat proteases and protease inhibitors.

Proteases perform important roles in multiple biological and pathological processes. The availability of the rat genome sequence has facilitated the analysis of the complete protease repertoire or degradome of this model organism. The rat degradome consists of at least 626 proteases and homologs, which are distributed into 24 aspartic, 160 cysteine, 192 metallo, 221 serine, and 29 threonine proteases. This distribution is similar to that of the mouse degradome but is more complex than that of the human degradome composed of 561 proteases and homologs. This increased complexity of rat proteases mainly derives from the expansion of several families, including placental cathepsins, testases, kallikreins, and hematopoietic serine proteases, involved in reproductive or immunological functions. These protease families have also evolved differently in rat and mouse and may contribute to explain some functional differences between these closely related species. Likewise, genomic analysis of rat protease inhibitors has shown some differences with mouse protease inhibitors and the expansion of families of cysteine and serine protease inhibitors in rodents with respect to human. These comparative analyses may provide new views on the functional diversity of proteases and inhibitors and contribute to the development of innovative strategies for treating proteolysis diseases.

Animals↗

Ancient DNA analysis reveals woolly rhino evolutionary relationships.

With ancient DNA technology, DNA sequences have been added to the list of characters available to infer the phyletic position of extinct species in evolutionary trees. We have sequenced the entire 12S rRNA and partial cytochrome b (cyt b) genes of one 60-70,000-year-old sample, and partial 12S rRNA and cyt b sequences of two 40-45,000-year-old samples of the extinct woolly rhinoceros (Coelodonta antiquitatis). Based on these two mitochondrial markers, phylogenetic analyses show that C. antiquitatis is most closely related to one of the three extant Asian rhinoceros species, Dicerorhinus sumatrensis. Calculations based on a molecular clock suggest that the lineage leading to C. antiquitatis and D. sumatrensis diverged in the Oligocene, 21-26 MYA. Both results agree with morphological models deduced from palaeontological data. Nuclear inserts of mitochondrial DNA were identified in the ancient specimens. These data should encourage the use of nuclear DNA in future ancient DNA studies. It also further establishes that the degraded nature of ancient DNA does not completely protect ancient DNA studies based on mitochondrial data from the problems associated with nuclear inserts.

Animals↗

Gene expression and feeding ecology: evolution of piscivory in the venomous gastropod genus Conus.

Differential expression of gene-family members is typically associated with the specific development of certain tissues and organs, but its importance in the ecological adaptation of organisms has rarely been investigated. Several specialized feeding modes have evolved within the predatory marine gastropod genus Conus, including molluscivory and piscivory. Based on phylogenetic investigations of Conus species, it has been concluded that piscivory arose at least twice in this genus. Moreover, molecular analyses of conotoxin mRNA transcripts reveal that piscivores from independent evolutionary lineages express the same subset of four-loop conotoxins, contrary to phylogenetic expectations. These results demonstrate that differential expression of gene-family members can play a key role in adaptive evolution, particularly during shifts to new ecological niches.

Adaptation, Physiological↗

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↗

Simple consensus procedures are effective and sufficient in secondary structure prediction.

We have analyzed the performance of majority voting on minimal combination sets of three state-of-the-art secondary structure prediction methods in order to obtain a consensus prediction. Using three large benchmark sets from the EVA server, our results show a significant improvement in the average Q3 prediction accuracy of up to 1.5 percentage points by consensus formation. The application of an additional trivial filtering procedure for predicted secondary structure elements that are too short, does not significantly affect the prediction accuracy. Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure.

Computational Biology↗

The Class II cytokine receptor (CRF2) family: overview and patterns of receptor-ligand interactions.

Expanded genomic information has driven the discovery of new members of the human Class II family of cytokine receptors (CRF2), which now includes 12 proteins. The corresponding cytokines have been identified, paired with their receptors and initially characterized for function. These cytokines include: a new human Type I IFN, IFN-kappa; molecules related to IL-10 (IL-19, IL-20, IL-22, IL-24, IL-26); and IFN-lambdas (IL-28/29), which have antiviral and cell stimulatory activities reminiscent of Type I IFNs, but act through a distinct receptor. In response to ligand binding, the CRF2 proteins form heterodimers, leading to cytokine-specific cellular responses; these diverse physiological functions are just beginning to be explored. Progress in structural and mutational analysis of ligand-receptor interactions now presents a more reliable framework for understanding receptor-ligand interactions, and for predicting key regions in less well studied members of the CRF2 family. The relationships between the CRF2 proteins will be summarized, as will the progress in identifying patterns of receptor interactions with ligands.

Amino Acid Sequence↗

Biochemical and biological activities of the venom of the Chinese pitviper Zhaoermia mangshanensis, with the complete amino acid sequence and phylogenetic analysis of a novel Arg49 phospholipase A2 myotoxin.

Zhaoermia mangshanensis (formerly Trimeresurus mangshanensis, Ermia mangshanensis) represents a monotypic genus of pitviper known only from Mt Mang in China's Hunan Province, and is among the largest and most spectacular of Asian venomous snakes. The venom of Zhaoermia exhibits high coagulant activity on bovine and human fibrinogen and human plasma, high phosphodiesterase and arginine ester hydrolytic activity, and moderate to low l-amino acid oxidase, kallikrein, caseinolytic, phospholipase A(2) (PLA(2)), haemorrhagic and myotoxic activities. The approximate i.p. LD(50) of the venom in mice was estimated to be 4 mg/kg. We purified the major toxin of Zhaoermia venom by gel-filtration, cation-exchange chromatography and HPLC. The toxin, a homodimer with an experimental monomeric mass of 13,972 Da, induced edema and myonecrosis in mice, but was devoid of detectable PLA(2) catalytic activity. Its complete amino acid sequence is composed of 121 amino acid residues cross-linked by seven disulfide bridges, and shows more than 80% identity to two Lys49-PLA(2)s from distantly related Asian pitvipers, Protobothrops mucrosquamatus and Calloselasma rhodostoma. Phylogenetic analysis of the novel toxin, zhaoermiatoxin, confirmed that it is rooted within a comprehensive sample of Lys49-PLA(2)s despite having an arginine residue in position 49, suggesting a secondary Lys49-->Arg substitution which did not alter the catalytic inactivity of the molecule.

Amino Acid Sequence↗

Search algorithm for pattern match analysis of nucleic acid sequences.

A new type of search algorithm to find biological information inherited in nucleic acid sequences was developed. The algorithm is of pattern match type and is based on the fact that genetic information often is a function of a predictable statistical occurrence of the four bases within parts of the sequence. The search algorithm compares the known statistical pattern of bases in e.g. a promoter, with an unknown sequence and calculates the statistical significance of the match at all positions in the unknown sequence. The program was tested on 54 published prokaryotic promoters. 44 or 49 could be found with 1 or 4 false answers, respectively. The program was also used on plasmid pBR322. All promoters functioning in an in vitro transcription system were found (tet, anti-tet, p4, bla and ori) except the so called p5 promoter. A search for donor and acceptor sites was performed in a human HLA genomic sequence that contains six introns. Five of the possible six donor and acceptor sites were found.

Base Sequence↗

Gene Designer: a synthetic biology tool for constructing artificial DNA segments.

BACKGROUND: Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes. RESULTS: Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference. CONCLUSION: Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.

Base Sequence↗

[Molecular biological analysis of unclassified and uncultured bacteria].

With the advent of comparative rRNA sequence analysis and the introduction of molecular genetic methods, such as nucleic acid hybridization and amplification techniques, microbiology is gaining new grounds. Taxonomy based upon phylogenetic analysis leads to a reliable classification. Culture-independent identification procedures allow for the analysis of complex microbial ecosystems and the description of new, as-yet uncultivable infectious disease agents.

Bacteria↗

BioViews: Java-based tools for genomic data visualization.

Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a language designed for distributed programming over the Web, the technology now exists to build a genomic data visualization tool that meets these requirements. Using Java we have developed a prototype genome browser applet (BioViews) that incorporates a three-level graphical view of genomic data: a physical map, an annotated sequence map, and a DNA sequence display. Annotated biological features are displayed on the physical and sequence-based maps, and the different views are interconnected. The applet is linked to several databases and can retrieve features and display hyperlinked textual data on selected features. In addition to browsing genomic data, different types of analyses can be performed interactively and the results of these analyses visualized alongside prior annotations. Our genome browser is built on top of extensible, reusable graphic components specifically designed for bioinformatics. Other groups can (and do) reuse this work in various ways. Genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology laboratories can reuse components to publish results as dynamic Web documents.

Animals↗

Commensal and mutualistic relationships of reoviruses with their parasitoid wasp hosts.

During evolution, certain endoparasitoid wasps have developed mechanisms to suppress the defence systems of their hosts. For this purpose, these species, all of which belong to the families Ichneumonidae and Braconidae, inject various kinds of virus-like particles. The most studied of these particles are classified as polydnaviruses (family Polydnaviridae) which are symbiotic viruses. Over the past decade, it has also been shown that several wasp species harbour reoviruses (family Reoviridae), and that two of these suppress host defence, allowing the development of the parasitoid eggs. In this paper, we summarize the key features of these viruses and their relationships with their wasp hosts. Five reoviruses are known that appear to be non-pathogenic for the wasps. Three of these, McRVLP, HeRV, OpRVLP, use their wasp hosts as vectors, and do not appear to be involved in host defence suppression. The fourth, DpRV-1, is a commensal reovirus detected in most field populations of the wasp, Diadromus pulchellus. This reovirus is always found associated with an ascovirus, DpAV-4a, which is indispensable for host immune suppression. Although DpRV-1 has not been shown to directly increase D. pulchellus parasitic success, it may contribute to this success by retarding DpAV-4a replication in the wasp. The fifth reovirus, DpRV-2, occurs in a specific population of D. pulchellus in which DpRV-1 and DpAV-4 are absent. This virus has a mutualistic relationship with its wasp host, as its injection by females during oviposition is essential for host immunosuppression. Interestingly, these viruses belong to several different reovirus genera.

Amino Acid Sequence↗

Molecular basis of genetic disease and molecular methods.

Nucleic acid testing is possible because of the physical and biomechanical properties of DNA and RNA such as hybridization, which also form the basis for the physiologic role of nucleic acids. The entire framework of genetic analysis involves the nucleotide sequence of genes, intragenic structure, supragene organization, and mapping of genes onto chromosomes. Genetic diseases are the consequence of mutations affecting one to many nucleotides. Such genetic alterations are detectable by several special assays for examining nucleic acids that are now common in genetic laboratories.

Chromosome Mapping↗

Barriers to sympatry between avian sibling species (Paridae: Baeolophus) in local secondary contact.

Range limits and secondary contact zones often occur at ecotones between major associations of habitat and climate. Therefore, understanding processes that limit sympatry between species in such areas provides an important framework for testing biogeographic and evolutionary hypotheses. Theoretical and empirical work has shown that the evolution of species borders is influenced by a complexity of factors, including gene flow from central to peripheral populations and the ability of species to adapt locally to environmental conditions. However, few studies have used bioclimatic models, combined with molecular and morphological data, to predict geographic range limits in the context of gene flow across a secondary contact zone. In this study, I applied these methods to test specific hypotheses about barriers to sympatry between closely related species where they approach and contact each other. Specifically, I examined the importance of historical isolation, local adaptation, and symmetry of gene flow in limiting sympatry and range expansion of ecologically distinct species across environmental gradients. Molecular (mitochondrial DNA, allozymes), morphological, and bioclimatic data were obtained for two avian sibling species (Baeolophus inornatus and B. ridgwayi) that exist in recent, narrow secondary contact in northern California. These species are broadly allopatric and occupy rangewide associations of oak and pinyon-juniper woodlands, respectively, although B. inornatus also inhabits mixed or juniper woodlands locally. Patterns of molecular variation generally were congruent with morphological and bioclimatic data, and support prior evidence for a history of isolation, adaptation, and divergence in distinctive, species-specific vegetation-climate associations. However, molecular and morphological clines fall east of the limit of oaks, and individuals of B. inornatus in this juniper-associated contact zone experience bioclimates that are more similar to B. ridgwayi than to B. inornatus in oak habitat. Thus, B. inornatus is able to adapt and expand locally into the range of its close relative, but not vice versa. These data support the hypothesis that gene flow is asymmetrical where peripheral populations meet at range boundaries. Physiological differences between species may play an important role in influencing these patterns. Empirical studies that highlight the importance of local adaptation and patterns of gene flow in which closely related species contact across ecotones are central to understanding limits on geographic ranges, sympatry, and introgression-a cornerstone of biogeographic and speciation theory.

Analysis of Variance↗

Drosophila DJ-1 mutants are selectively sensitive to environmental toxins associated with Parkinson's disease.

Parkinson's disease (PD) is a common neurodegenerative disorder that displays both sporadic and inherited forms. Exposure to several common environmental toxins acting through oxidative stress has been shown to be associated with PD. One recently identified inherited PD gene, DJ-1, may have a role in protection from oxidative stress, thus potentially linking a genetic cause with critical environmental risk factors. To develop an animal model that would allow integrative study of genetic and environmental influences, we have generated Drosophila lacking DJ-1 function. Fly DJ-1 homologs exhibit differential expression: DJ-1beta is ubiquitous, while DJ-1alpha is predominantly expressed in the male germline. DJ-1alpha and DJ-1beta double knockout flies are viable, fertile, and have a normal lifespan; however, they display a striking selective sensitivity to those environmental agents, including paraquat and rotenone, linked to PD in humans. This sensitivity results primarily from loss of DJ-1beta protein, which also becomes modified upon oxidative stress. These studies demonstrate that fly DJ-1 activity is selectively involved in protection from environmental oxidative insult in vivo and that the DJ-1beta protein is biochemically responsive to oxidative stress. Study of these flies will provide insight into the critical interplay of genetics and environment in PD.

Amino Acid Sequence↗