Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family

<p>Abstract</p> <p>Background</p> <p>Beta-N-acetylhexosaminidases belonging to the glycosyl hydrolase 20 (GH20) family are involved in the removal of terminal β-glycosidacally linked N-acetylhexosamine residues. These enzymes, widely distributed in microorganisms, animals and plants, are involved in many important physiological and pathological processes, such as cell structural integrity, energy storage, pathogen defence, viral penetration, cellular signalling, fertilization, development of carcinomas, inflammatory events and lysosomal storage diseases. Nevertheless, only limited analyses of phylogenetic relationships between GH20 genes have been performed until now.</p> <p>Results</p> <p>Careful phylogenetic analyses of 233 inferred protein sequences from eukaryotes and prokaryotes reveal a complex history for the GH20 family. In bacteria, multiple gene duplications and lineage specific gene loss (and/or horizontal gene transfer) are required to explain the observed taxonomic distribution. The last common ancestor of extant eukaryotes is likely to have possessed at least one GH20 family member. At least one gene duplication before the divergence of animals, plants and fungi as well as other lineage specific duplication events have given rise to multiple paralogous subfamilies in eukaryotes. Phylogenetic analyses also suggest that a second, divergent subfamily of GH20 family genes present in animals derive from an independent prokaryotic source. Our data suggest multiple convergent changes of functional roles of GH20 family members in eukaryotes.</p> <p>Conclusion</p> <p>This study represents the first detailed evolutionary analysis of the glycosyl hydrolase GH20 family. Mapping of data concerning physiological function of GH20 family members onto the phylogenetic tree reveals that apparently convergent and highly lineage specific changes in substrate specificity have occurred in multiple GH20 subfamilies.</p

Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics

<p>Abstract</p> <p>Background</p> <p>The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined, discrimination between conserved coding and non-coding sequences is a topic of considerable interest. Additionally, it should be considered desirable to discriminate between coding and non-coding conserved sequences without recourse to the use of sequence similarity searches of protein databases as such approaches exclude the identification of novel conserved proteins without characterized homologs and may be influenced by the presence in databases of sequences which are erroneously annotated as coding.</p> <p>Results</p> <p>Here we present a machine learning-based approach for the discrimination of conserved coding sequences. Our method calculates various statistics related to the evolutionary dynamics of two aligned sequences. These features are considered by a Support Vector Machine which designates the alignment coding or non-coding with an associated probability score.</p> <p>Conclusion</p> <p>We show that our approach is both sensitive and accurate with respect to comparable methods and illustrate several situations in which it may be applied, including the identification of conserved coding regions in genome sequences and the discrimination of coding from non-coding cDNA sequences.</p

Positive correlation of employment and psychological well-being for veterans with major abdominal surgery

Background Intestinal stomas (ostomies) have been associated negatively with multiple aspects of health-related quality of life. This article examines the relationship between employment status and psychological well-being (PWB) in veterans who underwent major bowel procedures with or without ostomy. Methods Veterans from 3 Veterans Affairs (VA) medical centers were surveyed using the City of Hope ostomy-specific questionnaire and the Short Form 36 item Veteran’s version (SF-36V). Response rate was 48% (511 of 1,063). Employment and PWB relationship was assessed using multiple regression with age, income, SF-36V physical component summary (PCS), and employment status as independent variables. Results Employed veterans reported higher PWB compared with unemployed veterans (P = .003). Full-time workers also reported higher PWB than part-time or unemployed workers (P = .001). Ostomy was not an independent predictor of PWB. Conclusions Employment among veterans after major abdominal surgery may have intrinsic value for PWB. Patients should be encouraged to return to work, or do volunteer work after recovery

The Full-sky Astrometric Mapping Explorer -- Astrometry for the New Millennium

FAME is designed to perform an all-sky, astrometric survey with unprecedented accuracy. It will create a rigid astrometric catalog of 4x10^7 stars with 5 < m_V < 15. For bright stars, 5 < m_V < 9, FAME will determine positions and parallaxes accurate to < 50 microarcseconds, with proper motion errors < 50 microarcseconds/year. For fainter stars, 9 < m_V < 15, FAME will determine positions and parallaxes accurate to < 500 microarcseconds, with proper motion errors < 500 microarcseconds/year. It will also collect photometric data on these 4 x 10^7 stars in four Sloan DSS colors.Comment: 6 pages, 4 figures, to appear in "Working on the Fringe

Common Avian Infection Plagued the Tyrant Dinosaurs

Abstract Background: Tyrannosaurus rex and other tyrannosaurid fossils often display multiple, smooth-edged full-thickness erosive lesions on the mandible, either unilaterally or bilaterally. The cause of these lesions in the Tyrannosaurus rex specimen FMNH PR2081 (known informally by the name &apos;Sue&apos;) has previously been attributed to actinomycosis, a bacterial bone infection, or bite wounds from other tyrannosaurids

The maize fused leaves1 (fdl1) gene controls organ separation in the embryo and seedling shoot and promotes coleoptile opening

The fdl1-1 mutation, caused by an Enhancer/Suppressor mutator (En/Spm) element insertion located in the third exon of the gene, identifies a novel gene encoding ZmMYB94, a transcription factor of the R2R3-MYB subfamily. The fdl1 gene was isolated through co-segregation analysis, whereas proof of gene identity was obtained using an RNAi strategy that conferred less severe, but clearly recognizable specific mutant traits on seedlings. Fdl1 is involved in the regulation of cuticle deposition in young seedlings as well as in the establishment of a regular pattern of epicuticular wax deposition on the epidermis of young leaves. Lack of Fdl1 action also correlates with developmental defects, such as delayed germination and seedling growth, abnormal coleoptile opening and presence of curly leaves showing areas of fusion between the coleoptile and the first leaf or between the first and the second leaf. The expression profile of ZmMYB94 mRNA\u2014determined by quantitative RT-PCR\u2014 overlaps the pattern of mutant phenotypic expression and is confined to a narrow developmental window. High expression was observed in the embryo, in the seedling coleoptile and in the first two leaves, whereas RNA level, as well as phenotypic defects, decreases at the third leaf stage. Interestingly several of the Arabidopsis MYB genes most closely related to ZmMYB94 are also involved in the activation of cuticular wax biosynthesis, suggesting deep conservation of regulatory processes related to cuticular wax deposition between monocots and dicots