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At least 1,063 records · Page 59Linked to original sources
PubMed2005

Tryptophanyl-tRNA synthetase gene polymorphisms and risk of incident myocardial infarction.

Tryptophanyl-tRNA synthetase (WARS) gene polymorphisms have been associated with the patho-physiology of vascular angiogenesis and homeostasis. Data from a recent genome-wide linkage analysis suggested a potential role of WARS in the risk of myocardial infarction. However, no genetic-epidemiological data are available. From a prospective cohort of 14,916 initially healthy American men, we evaluated five common polymorphisms within or close to the WARS locus, all with a minor allele frequency >0.10, amongst 386 individuals who subsequently developed myocardial infarction and 386 matched individuals who remained free of reported cardiovascular events during follow-up. The polymorphisms were: a G > C substitution in the 5'-flanking region (dbSNP rs2273804), an A > G substitution in intron 1 (dbSNP rs941931), a 335T > C substitution in exon 10 (dbSNP rs9453), a C > T substitution in intron 10 (dbSNP rs1570305), and a C > T substitution in the C14orf68 region (dbSNP rs3736951). The observed genotypes were in Hardy-Weinberg equilibrium in the control group. Genotype- and haplotype-frequency distributions were similar between cases and controls. Further investigation using a haplotype-based matched logistic regression analysis, adjusting for age, smoking, randomized treatment-assignment (likelihood ratio test: chi(3)(2) = 3.20, p = 0.36) or with additional adjustment for BMI, hypertension, and diabetes (likelihood ratio test: chi(3)(2) = 2.38, p = 0.50) yielded similar null findings. An alternative haplotype analysis based on evolutionary arguments again yielded null results. In conclusion, we found no evidence for an association between the common polymorphisms or haplotypes of the tryptophanyl-tRNA synthetase gene tested and risk of myocardial infarction.

Case-Control Studies↗
PubMed2006

Rat 22kHz ultrasonic vocalizations as alarm cries.

Rats incorporate circa 22kHz ultrasonic alarm cries into their defense pattern in response to a predator threat. These calls are dependent on conspecific presence, show gender differences, and tend to be emitted from a place of relative safety. Rats emit sonic defensive threat vocalizations when approached by a potential threat. These are emitted regardless of conspecific presence, and increase as a function of threat proximity, eventually culminating in defensive attack at close distances. Ample data from field studies suggest a similar division of vocalizations into alarm or warning cries, and defensive threat vocalizations, although both are often subsumed under the rubric of "alarm cries". A clear distinction between these types of calls is necessary for proper analysis of the evolutionary mechanisms responsible for the development and maintenance of each of them. Furthermore, the integration of data from field studies and laboratory experiments may prove useful in evaluation of the relationship between each type of cry and emotional (fear or anxiety-like) states in mammals.

Animals↗
PubMed2006

How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews.

Plant parasitism has independently evolved as a nutrition strategy in both true fungi and Oomycetes (stramenopiles). A large number of species within phytopathogenic Oomycetes, the so-called downy mildews, are defined as obligate biotrophs since they have not, to date, been cultured on any artificial medium. Other genera like Phytophthora and Pythium can in general be cultured on standard or non-standard agar media. Within all three groups there are many important plant pathogens responsible for severe economic losses as well as damage to natural ecosystems. Although they are important model systems to elucidate the evolution of obligate parasites, the phylogenetic relationships between these genera have not been clearly resolved. Based on the most comprehensive sampling of downy mildew genera to date and a representative sample of Phytophthora subgroups, we inferred the phylogenetic relationships from a multi-gene dataset containing both coding and non-coding nuclear and mitochondrial loci. Phylogenetic analyses were conducted under several optimality criteria and the results were largely consistent between all the methods applied. Strong support is achieved for monophyly of a clade comprising both the genus Phytophthora and the obligate biotrophic species. The facultatively parasitic genus Phytophthora is shown to be at least partly paraphyletic. Monophyly of a cluster nested within Phytophthora containing all obligate parasites is strongly supported. Within the obligate biotrophic downy mildews, four morphologically or ecologically well-defined subgroups receive statistical support: (1) A cluster containing all species with brownish-violet conidiosporangia, i.e., the genera Peronospora and Pseudoperonospora; (2) a clade comprising the genera with vesicular to pyriform haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, Protobremia); (3) a group containing species included in Hyaloperonospora and Perofascia which almost exclusively infect Brassicaceae; (4) a clade including the grass parasites Viennotia oplismeni and Graminivora graminicola. Phylogenetic relationships between these four clades are not clearly resolved, and neither is the position of Sclerospora graminicola within the downy mildews. Character analysis indicates an evolutionary scenario of gradually increasing adaptation to plant parasitism in Peronosporales and that at least the most important of these adaptive steps occurred only once, including major host shifts within downy mildews.

Animals↗
PubMed2006

Cloning and characterization of the astaxanthin biosynthesis gene cluster from the marine bacterium Paracoccus haeundaensis.

Carotenoids are important natural pigments produced by many microorganisms and plants. In a previous study, we isolated and characterized a marine bacterium, Paracoccus haeundaensis, which produces carotenoids, mainly astaxanthin. In the present study, a carotenoid biosynthesis gene cluster involved in the production of astaxanthin was isolated and characterized from this marine bacterium. The cluster contained six carotenogenic genes, five of which, with the same orientation, were designated crtW, crtZ, crtY, crtI, and crtB, and one of which, with the opposite orientation, was designated crtE. The crtW, crtZ, crtY, crtI, crtB, and crtE genes contained 726, 486, 1158, 1503, 912, and 879 base pairs, respectively, and encoded polypeptides of 242, 162, 386, 501, 304, and 293 amino acid residues, respectively. The stop codon of each crt gene, except crtE, overlapped the start codon of the following crt gene. Comparisons of the structures and nucleotide sequences of the crt genes showed that the signature domains of the carotenoid biosynthesis genes are highly conserved. The molecular phylogenetic tree analysis showed the evolutionary relationships among the carotenoid biosynthesis genes of various organisms. An expression vector (pCR-XR-TOPO-Crt-full vector) containing the astaxanthin biosynthesis genes was constructed and transformed into Escherichia coli BL21(DE3) Codon Plus cells. The E. coli transformants produced 400 microg astaxanthin per gram of dry cell weight.

Base Sequence↗
PubMed2006

Applying hybrid reasoning to mine for associative features in biological data.

We develop the means to mine for associative features in biological data. The hybrid reasoning schema for deterministic machine learning and its implementation via logic programming is presented. The methodology of mining for correlation between features is illustrated by the prediction tasks for protein secondary structure and phylogenetic profiles. The suggested methodology leads to a clearer approach to hierarchical classification of proteins and a novel way to represent evolutionary relationships. Comparative analysis of Jasmine and other statistical and deterministic systems (including Explanation-Based Learning and Inductive Logic Programming) are outlined. Advantages of using deterministic versus statistical data mining approaches for high-level exploration of correlation structure are analyzed.

Algorithms↗
PubMed2005

Structural and evolutionary division of phosphotyrosine binding (PTB) domains.

Proteins encoding phosphotyrosine binding (PTB) domains function as adaptors or scaffolds to organize the signaling complexes involved in wide-ranging physiological processes including neural development, immunity, tissue homeostasis and cell growth. There are more than 200 proteins in eukaryotes and nearly 60 human proteins having PTB domains. Six PTB domain encoded proteins have been found to have mutations that contribute to inherited human diseases including familial stroke, hypercholesteremia, coronary artery disease, Alzheimer's disease and diabetes, demonstrating the importance of PTB scaffold proteins in organizing critical signaling complexes. PTB domains bind both peptides and headgroups of phosphatidylinositides, utilizing two distinct binding motifs to mediate spatial organization and localization within cells. The structure of PTB domains confers specificity for binding peptides having a NPXY motif with differing requirements for phosphorylation of the tyrosine within this recognition sequence. In this review, we use structural, evolutionary and functional analysis to divide PTB domains into three groups represented by phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like and phosphotyrosine-independent Dab-like PTBs, with the Dab-like PTB domains representing nearly 75% of proteins encoding PTB domains. In addition, we further define the binding characteristics of the cognate ligands for each group of PTB domains. The signaling complexes organized by PTB domain encoded proteins are largely unknown and represents an important challenge in systems biology for the future.

Amino Acid Sequence↗
PubMed2005

The human HERC family of ubiquitin ligases: novel members, genomic organization, expression profiling, and evolutionary aspects.

The HERC family of ubiquitin ligases is characterized by the presence of a HECT domain and one or more RCC1-like domains. We report the identification of two novel members, HERC4 and HERC6, and subdivide the family into one group of two large and one group of four small members according to protein size and domain structure. The small members share a similar genomic organization, three of them mapping to chromosomal region 4q22, indicating strong evolutionary cohesions. Phylogenetic analysis reveals that the HERC ancestor emerged in nematodes and that the family expanded throughout evolution. The mRNA expression pattern of the small human members was found to be diverse in selected tissues and cells; overexpressed proteins display a similar cytosolic distribution. These data indicate that the HERC family members exhibit similarities in many aspects, but also sufficient differences indicating functional diversity.

Adaptor Proteins, Signal Transducing↗
PubMed2006

The first radiation hybrid map of a perch-like fish: the gilthead seabream (Sparus aurata L).

Among Teleosts, Perciformes are the largest order of fishes and include numerous species of commercial importance. Perciformes also comprise species of primary interest for evolutionary studies and analysis of the sex determination systems and sex chromosome plasticity. Unfortunately, genomics tools and resources for Perciformes remain to be developed. Here, we report the production of a seabream whole-genome radiation hybrid (RH) panel in which quality was ascertained by the construction of a 2-Mb-resolution RH map. The map encompasses 440 markers (288 microsatellites, 82 gene-based markers, and 70 STS) suitable for linkage analysis and comparative mapping studies. Achievement of a RH panel and a whole-genome RH map should contribute to establishing seabream as a fish model among the Perciformes and should be of importance in aquaculture for marker-assisted selection, improvement of growth performance, and disease management. Development of RH maps in a cost-effective manner for other fishes with the described methodology will offer a powerful approach in aquaculture and will provide extended capabilities for comparing vertebrate genome evolution.

Animals↗
PubMed1999

The concept of disorder as a foundation for the DSM's theory-neutral nosology: response to Follette and Houts, Part 2.

Follette and Houts [Follette, W. C., Houts, A. C. (1996). Models of scientific progress and the role of theory in taxonomy development: a case study of the DSM. Journal of Consulting and Clinical Psychology, 64, 1120-1132] argue that 'mental disorder' and 'function' are value concepts that offer no scientific basis for the DSM's theory-neutral nosology or for distinguishing disorders from other behavioral problems. They also claim that the DSM presupposes a biological theory of etiology, thus is not really theory-neutral. They recommend replacing the DSM by theory-laden diagnostic manuals. I argue: (1) DSM criteria do not imply a biological model of disorder, (2) 'mental disorder' and 'function' have scientific content that allows one to distinguish disorder from nondisorder, (3) the evolutionary 'harmful dysfunction' analysis of disorder [Wakefield, J. C. (1992a). The concept of mental disorder: on the boundary between biological facts and social values. American Psychologist, 47, 373-388] coherently demarcates disorder from nondisorder, (4) the proposed behaviorist alternative to the DSM illustrated by the articles in Follette's special section [Follette, W. C. (Ed.) (1996a). Special section on the development of theoretically coherent alternatives to the DSM system. Journal of Consulting and Clinical Psychology, 64, 1117-1201] is incoherent because it does not distinguish disorder from nondisorder.

Humans↗
PubMed2002

Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences.

When protein sequences divergently evolve under functional constraints, some individual amino acid replacements that reverse the charge (e.g. Lys to Asp) may be compensated by a replacement at a second position that reverses the charge in the opposite direction (e.g. Glu to Arg). When these side-chains are near in space (proximal), such double replacements might be driven by natural selection, if either is selectively disadvantageous, but both together restore fully the ability of the protein to contribute to fitness (are together "neutral"). Accordingly, many have sought to identify pairs of positions in a protein sequence that suffer compensatory replacements, often as a way to identify positions near in space in the folded structure. A "charge compensatory signal" might manifest itself in two ways. First, proximal charge compensatory replacements may occur more frequently than predicted from the product of the probabilities of individual positions suffering charge reversing replacements independently. Conversely, charge compensatory pairs of changes may be observed to occur more frequently in proximal pairs of sites than in the average pair. Normally, charge compensatory covariation is detected by comparing the sequences of extant proteins at the "leaves" of phylogenetic trees. We show here that the charge compensatory signal is more evident when it is sought by examining individual branches in the tree between reconstructed ancestral sequences at nodes in the tree. Here, we find that the signal is especially strong when the positions pairs are in a single secondary structural unit (e.g. alpha helix or beta strand) that brings the side-chains suffering charge compensatory covariation near in space, and may be useful in secondary structure prediction. Also, "node-node" and "node-leaf" compensatory covariation may be useful to identify the better of two equally parsimonious trees, in a way that is independent of the mathematical formalism used to construct the tree itself. Further, compensatory covariation may provide a signal that indicates whether an episode of sequence evolution contains more or less divergence in functional behavior. Compensatory covariation analysis on reconstructed evolutionary trees may become a valuable tool to analyze genome sequences, and use these analyses to extract biomedically useful information from proteome databases.

Amino Acid Sequence↗
PubMed2002

Role of glycogen synthase kinase-3 in cancer: regulation by Wnts and other signaling pathways.

Although glycogen synthase kinase-3 (GSK-3) is but one of more than a thousand distinct serine/threonine kinases present in the mammalian genome, this enzyme has attracted attention for its role in a diverse range of cellular processes and its positioning at a nexus of several signaling pathways that are important in cancer and other human diseases. The association of GSK-3 with widely different functions, from glycogen metabolism to fruit fly segmentation and slime mold differentiation, was initially perplexing. However, as the context of the biological processes involving this enzyme has been clarified, unifying themes have emerged that begin to explain its pleiotropic nature. Unlike most protein kinases involved in signaling, GSK-3 is active in unstimulated, resting cells. Its activity is inactivated during cellular responses and its substrates therefore tend to be dephosphorylated. As more of these targets have been identified and the effects of their modification by GSK-3 determined, most have been found to be functionally inhibited by GSK-3. Hence, this kinase appears to act as a general repressor, keeping its targets switched off or inaccessible under resting conditions. The rarity of this form of regulation is perhaps related to the diversity of its targets. Over the past decade, the importance of GSK-3 has been established by three significant properties: its remarkable evolutionary conservation, allowing analysis in genetically tractable organisms; its involvement in the Wnt/wingless signaling pathway; and its inhibition by agonists of the prosurvival phosphatidylinositol 3' kinase (P13'K) pathway. This review covers recent advances in understanding the physiological roles of this enzyme, particularly in the context of cancer.

Animals↗
PubMed1995

Frequency and characterization of p53 mutations in clinically localized prostate cancer.

OBJECTIVES: To determine the frequency of abnormal p53 expression and to characterize confirmed p53 mutations in tumors from patients with clinically localized adenocarcinoma of the prostate. METHODS: p53 protein nuclear accumulation was determined immunohistochemically in the initial diagnostic tumor specimens from 37 patients with clinically localized prostate carcinoma. Two primary antibodies were used on all specimens. Structural analysis of the p53 gene was performed using the methods of polymerase chain reaction (PCR)/single-strand conformation polymorphism (SSCP) and DNA sequencing. RESULTS: In 1 of the 37 (2.7%) tumor specimens, intense p53 nuclear staining was demonstrated using either antibody PAb 1801 or CM-1. The staining in this case was heterogeneous, with approximately 40% of tumor nuclei staining for p53. This tumor specimen was microdissected and DNA was extracted. Following PCR amplification, abnormally migrating bands were noted on SSCP analysis of exon 8. DNA sequencing confirmed the mutation as a C-->A transversion in codon 281 (asp-->glu). PCR/SSCP analysis of exons 5 through 8 was also performed for seven additional tumors that were negative for p53 nuclear accumulation by immunohistochemical (IHC) methods. All of these specimens demonstrated wild-type p53. CONCLUSIONS: The results of this study confirm and extend our previous findings that p53 mutations are rare in clinically localized adenocarcinoma of the prostate. In detecting clonal p53 mutations, standard immunohistochemical technique correlates reliably with structural p53 gene analysis of the evolutionary conserved domains encompassing exons 5-8. Importantly, most reports have demonstrated that p53 mutations detected by IHC are a late step in the progression of prostate cancer and are associated with advanced disease, dedifferentiation, and the acquisition of androgen independence.

Adenocarcinoma↗
PubMedDate not supplied

The differences between the structural repertoires of VH germ-line gene segments of mice and humans: implication for the molecular mechanism of the immune response.

Although human and murine antibodies are similar when considering their diversification strategies, they differ in the proportion by which kappa and lambda type chains are present in their receptive V, repertoires. It has been shown that this difference implies a divergence in the structural repertoire of the kappa and lambda genes of these species. Nonetheless, the differences in VH have not been systematically studied. In this paper a systematic characterization of the VH structural repertoire of mice is made, so that a comparison with the VH structural repertoire of humans, described in detail elsewhere, could be properly accomplished. Our study shows the structural repertoire of mice to be dominated by canonical structure class 1-2 (approximately 60%), while in humans the dominant one is class 1-3 (approximately 40%). Analysis of the evolutionary relationships between human and mice suggest that this divergence may have a functional meaning. The implications of such findings are discussed.

Amino Acid Sequence↗
PubMed2002

Gene structure and expression of cg-ALR1, a type I activin-like receptor from the bivalve mollusc Crassostrea gigas.

Members of the transforming growth factor beta superfamily of cell signaling polypeptides have attracted much attention because of their ability, from nematodes to mammals, to control cellular functions that in turn, regulate embryo development and tissue homeostasis (the transforming growth factors betas 95 (1990) 419). To understand the divergent evolution of the structures and functions of the transforming growth factor beta receptors (superfamily) we report here the cloning and characterization of an activin-like type I receptor gene from the oyster Crassostrea gigas (cgALR1). This 6 Kb gene encodes a 534 amino acid long protein consisting of a signal peptide, an extracellular ligand binding domain, a transmembrane region and an intracellular domain. The intracellular domain contains sequence motifs such as the GS box and EIF/V and RIKKTL boxes that are thought to be hallmarks of activin type I receptors. The protein sequence shares 67% amino acid identity with other serine/threonine kinase receptors in the most conserved kinase domain and 47-49% similarity with vertebrate type I receptors. The temporal expression pattern of cgALR1 transcripts was examined during early larval developmental stages. To gain insight into evolutionary diversification, phylogenetic analysis as well as an investigation of the genomic structure, including the promoter region of the cgALR1 gene were carried out.

Activin Receptors↗
PubMed1997

Evolution of community mental health case management: considerations for clinical practice.

Case management has been the preferred method of helping persons with mental illness live in the community. This report examines the historical development of case management practice over the past 30 years. The analysis revealed that evolutionary growth in case management developed in response to expansion of community mental health services rather than consumer interests to improve their quality of life. Consequently, this reveals itself in the lack of outcome criteria needed to measure case management effectiveness. Currently, the concept of case management is undergoing a revolutionary paradigm shift that is "consumer-driven" and responds to consumer concerns. However, as mental health care costs rise within a rapidly growing community mental health care system, managed care is being implemented as a method to contain these rising costs. Because of major differences in philosophical underpinnings, developments in support of public mental health managed care may jeopardize the genesis of consumer-driven case management by supporting case management models that reflect managed care ideology.

Case Management↗
PubMed2004

Functional adaptations in the craniofacial morphology of Malagasy primates: shape variations associated with gummivory in the family Cheirogaleidae.

The infraorder Lemuriformes is characterized by a high level of homoplasy that clouds the evolutionary signal. The analysis of the morphological disparity of the Malagasy primates' crania and mandibles demonstrates the high determinism of functional specializations and developmental constraints, regardless of the phylogeny. In the present work, the weight of functional constraints linked to diet--a putative source of homoplasy--is analyzed first at the level of the infraorder Lemuriformes as a whole, and secondly at the level of a single family, the Cheirogaleidae, chosen because it contains taxa with two different diets (omnivory and gummivory). Malagasy primates are characterized by a great variety of dietary habits: some of them are omnivores, folivores, frugivores, gummivores, insectivores or even specialized hard-object feeders. All cheirogaleids feed on tree exudates, but while gum consumption is occasional or limited for Microcebus, Cheirogaleus and Mirza, gums are the dominant food source for Phaner and Allocebus. Craniofacial shape variations are analyzed using geometric morphometrics: methods based on landmark identification (Procrustes superimpositions) are chosen for cranium shape analysis, and methods based on outline decomposition (elliptical Fourier functions) for study of mandible shape. The morphospaces obtained at the level of the infraorder appear to be highly constrained by dietary habits, especially in the case of the mandibles. At the finer level of the family Cheirogaleidae, the analyses permit (1) separation of craniomandibular shape variation associated with the two dietary categories and (2) among the omnivorous category, to distinguish variation associated with the percentage of gum consumption.

Adaptation, Biological↗
PubMed2002

Function of the alternative oxidase: is it still a scavenger?

The alternative oxidase is a respiratory chain protein found in all higher plants, fungi, non-fermentative yeasts and trypanosomes. Its primary structure suggests that it is a new member of the di-iron carboxylate protein family. Recent sequence analysis indicates an evolutionary relationship between primitive members of this protein family and the alternative oxidase, suggesting that its early function was to scavenge di-oxygen. However, modelling of plant growth kinetics suggests a different function.

Electron Transport↗
PubMed2004

Natural variation in the response of Caenorhabditis elegans towards Bacillus thuringiensis.

Almost nothing is known about the natural ecology of the nematode Caenorhabditis elegans, including its interactions with parasites. To help rectify this discrepancy, we assessed natural variation in the response of C. elegans towards a potential parasite, the soil bacterium Bacillus thuringiensis. Our results show that 10 isolates from across the world differ significantly in survival rate and infection level when confronted with a parasitic strain of B. thuringiensis. Furthermore, behavioural responses are identified as an important component of C. elegans defence, including evasion and possibly reduced ingestion of parasites. Again, the natural isolates show significant differences in these traits. In conclusion, worm defence is indicated to be complex and variable across space, implying that parasites play an important role in the ecology of this species. Based on these results, we expect C. elegans to be a promising model host for future analysis of the evolutionary dynamics of parasite-host interactions.

Animals↗