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Significant Similarity (significant + similarity)
Selected AbstractsMetagenomic signatures of 86 microbial and viral metagenomesENVIRONMENTAL MICROBIOLOGY, Issue 7 2009Dana Willner Summary Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa. [source] AAA+ superfamily ATPases: common structure,diverse functionGENES TO CELLS, Issue 7 2001Teru Ogura The AAA+ superfamily of ATPases, which contain a homologous ATPase module, are found in all kingdoms of living organisms where they participate in diverse cellular processes including membrane fusion, proteolysis and DNA replication. Recent structural studies have revealed that they usually form ring-shaped oligomers, which are crucial for their ATPase activities and mechanisms of action. These ring-shaped oligomeric complexes are versatile in their mode of action, which collectively seem to involve some form of disruption of molecular or macromolecular structure; unfolding of proteins, disassembly of protein complexes, unwinding of DNA, or alteration of the state of DNA,protein complexes. Thus, the AAA+ proteins represent a novel type of molecular chaperone. Comparative analyses have also revealed significant similarities and differences in structure and molecular mechanism between AAA+ ATPases and other ring-shaped ATPases. [source] Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolutionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2009R. J. BUTLER Abstract Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to poor sampling in the Turonian,Santonian interval. Stegosauria shows a significant negative correlation with flowering plants and a significant positive correlation with the nonflowering cycadophytes (cycads, Bennettitales). This interesting pattern is worthy of further investigation, and it reflects the decline of both stegosaurs and cycadophytes during the Early Cretaceous. [source] Is there a ,New Managerial Work'?JOURNAL OF MANAGEMENT STUDIES, Issue 7 2006A Comparison with Henry Mintzberg's Classic Study 30 Years Later abstract This comparative study of top executives' work aimed at examining the stability of top managerial behaviour reveals a relatively different pattern of behaviour compared with the study by Henry Mintzberg. The main differences are a much larger workload, a contact pattern to a larger degree oriented towards subordinates in group-settings, a greater emphasis on giving information, and less preoccupation with administrative work. One important finding is that fragmentation of time , in previous studies highlighted as a central tenet of managerial work , was not as prevalent in the new study. The different results can be attributed (with caution) to the impact of the management discourse about leadership and corporate culture, and to factors such as organizational structure and geographical dispersion of companies. However, there are also significant similarities between the two studies which indicate that claims of the emergence of a radically different managerial work are much exaggerated. Instead the empirical data shows that new work-practices are combined with older practices, both in a complex and context-specific ways. Therefore, there is a need for better integration between theoretical development and empirical investigations in this field of inquiry. [source] Mechanistic comparison of blood undergoing laser photocoagulation at 532 and 1,064 nmLASERS IN SURGERY AND MEDICINE, Issue 2 2005John F. Black PhD Abstract Background and Objectives We seek to compare and contrast the mechanisms of blood photocoagulation under 532 and 1,064 nm laser irradiation in vitro in order to better understand the in vivo observations. We also seek to validate a finite element model (FEM) developed to study the thermodynamics of coagulation. Study Design/Materials and Methods We study the photocoagulation of whole blood in vitro at 532 and 1,064 nm using time-domain spectroscopic and optical coherence tomography (OCT)-based imaging techniques. We model the coagulation using an FEM program that includes the latent heat of vaporization (LHV) of water, consideration of the pulse shape of the laser, and the bathochromic shift in the hemoglobin absorption spectrum. Results We find significant similarities in the spectroscopic, chemical, and structural changes occurring in hemoglobin and in the blood matrix during photocoagulation despite the very large difference in the absorption coefficients. The more uniform temperature profile developed by the deeper-penetrating 1,064 nm laser allows us to resolve the structural phase transition in the red blood cells (going from biconcave disc to spherocyte) and the chemical transition creating met-hemoglobin. We find that the RBC morphology transition happens first, and that the met-Hb transition happens at a much higher temperature (,>,90°C) than is found in slow bath heating. The FEM analysis with the LHV constraint and bathochromic shift predicts accurately the imaging results in both cases, and can be used to show that at 1,064 nm there is the potential for a runaway increase in absorption during the laser pulse. Conclusions Photothermally mediated processes dominate the in vitro coagulation dynamics in both regimes despite the difference in absorption coefficients. There is a significant risk under 1,064 nm irradiation of vascular lesions in vivo that the dynamic optical properties of blood will cause runaway absorption and heating. This may in turn explain some recent results at this wavelength where full-thickness burns resulted from laser treatment. Lasers Surg. Med. 36:155,165, 2005. © 2005 Wiley-Liss, Inc. [source] Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genesPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 10 2010Chance W Riggins Abstract BACKGROUND: Waterhemp is a model for weed genomics research in part because it possesses many interesting biological characteristics, rapidly evolves resistance to herbicides and has a solid foundation of previous genetics work. To develop further the genomics resources for waterhemp, the transcriptome was sequenced using Roche GS-FLX 454 pyrosequencing technology. RESULTS: Pyrosequencing produced 483 225 raw reads, which, after quality control and assembly, yielded 44 469 unigenes (contigs + singletons). A total of 49% of these unigenes displayed highly significant similarities to Arabidopsis proteins and were subsequently grouped into gene ontology categories. Blast searches against public and custom databases helped in identifying and obtaining preliminary sequence data for all of the major target-site genes for which waterhemp has documented resistance. Moreover, sequence data for two other herbicide targets [4-hydroxyphenylpyruvate dioxygenase (HPPD) and glutamine synthetase], where resistance has not yet been reported in any plant, were also investigated in waterhemp and six related weedy Amaranthus species. CONCLUSION: These results demonstrate the enormous value of 454 sequencing for gene discovery and polymorphism detection in a major weed species and its relatives. Furthermore, the merging of the 454 transcriptome data with results from a previous whole genome 454 sequencing experiment has made it possible to establish a valuable genomic resource for weed science research. Copyright © 2010 Society of Chemical Industry [source] Is the Rehydrin TrDr3 from Tortula ruralis Associated with Tolerance to Cold, Salinity, and Reduced pH?PLANT BIOLOGY, Issue 3 2005HdeD from Escherichia coli in Response to Abiotic Stress, Physiological Evaluation of the TrDr3 -Orthologue Abstract: We have employed EST analysis in the resurrection moss Tortula ruralis to discover genes that control vegetative desiccation tolerance and describe the characterization of the EST-derived cDNA TrDr3 (Tortula ruralis desiccation-stress related). The deduced polypeptide TRDR3 has a predicted molecular mass of 25.5 kDa, predicted pI of 6.7, and six transmembrane helical domains. Preliminary expression analyses demonstrate that the TrDr3 transcript ratio increases in response to slow desiccation relative to the hydrated control in both total and polysomal mRNA (mRNP fraction), which classifies TrDr3 as a rehydrin. Bioinformatic searches of the electronic databases reveal that Tortula TRDR3 shares significant similarities to the hdeD gene product (HNS-dependent expression) from Escherichia coli. The function of the HdeD protein in E. coli is unknown, but it is postulated to be involved in a mechanism of acid stress defence. To establish the role of E. coli HdeD in abiotic stress tolerance, we determined the log survival percentage from shaking cultures of wild-type bacteria and the isogenic hdeD deletion strain (,hdeD) in the presence of low temperature (28 °C), elevated NaCl (5 % (w/v)), or decreased pH (4.5), or all treatments simultaneously. The ,hdeD deletion strain was less sensitive, as compared to wild-type E. coli, in response to decreased pH (p > 0.009), and the combination of all three stresses (p > 0.0001). [source] Identification of RSVP14 and RSVP20 Components by Two-dimensional Electrophoresis and Western-blottingREPRODUCTION IN DOMESTIC ANIMALS, Issue 1 2008JA Cardozo Contents We have already shown that RSVP14 and RSVP20, two ram seminal plasma (SP) proteins postulated to be involved in sperm capacitation and gamete interaction can protect spermatozoa against cold-shock. In this study, we use two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for the analysis of SP proteins of Rasa Aragonesa rams, using enhanced protein solubilization in the presence of tributyl phosphine (TBP) and a polyacrylamide linear gradient gel with a narrow pH range (4,7). The image analysis of the 2D map detected 195 protein spots, with isoelectric points (pIs) ranging from 4.5 to 6.6, and molecular weight (Mr) from 11.7 to 90.4. Staining of 2D gels with Pro-Q Emerald 300 Glycoprotein Stain revealed that most significant proteins in ram SP are glycosylated. The removing of protein N-linked oligosaccharides improved the gel resolution. 2D-PAGE analysis of the whole fraction 6 (F6) separated from ram SP by exclusion chromatography showed six main protein spots, four (a, b, c, d) in the 14 kDa and two (e, f) in the 20 kDa region. Western-blot analyses indicated that the anti-P14 antibody recognized four spots on the SP map, 4, 5, 6 and 7, that matched with spots a, b, c, d of F6 map. The anti-P20 antibody recognized spots 13 and 14 of SP map that corresponded to spots e, f of F6 map. The deduced sequences by de novo sequencing evidenced that protein spots 7 and 13 have significant similarities to BSP family, while protein spots 4 and 14 did not appear to be homologous with any reported protein in the current mammalian Proteinbank databases. [source] The few virus-like genes of Cotesia congregata bracovirus ,ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 3 2006J-M. Drezen Abstract The origin of the symbiotic association between parasitoid wasps and bracoviruses is still unknown. From phylogenetic analyses, bracovirus-associated wasp species constitute a monophyletic group, the microgastroid complex. Thus all wasp,bracovirus associations could have originated from the integration of an ancestral virus in the genome of the ancestor of the microgastroids. In an effort to identify a set of virus genes that would give clues on the nature of the ancestral virus, we have recently performed the complete sequencing of the genome of CcBV, the bracovirus of the wasp Cotesia congregata. We describe here the putative proteins encoded by CcBV genome having significant similarities with sequences from known viruses and mobile elements. The analysis of CcBV gene content does not lend support to the hypothesis that bracoviruses originated from a baculovirus. Moreover, no consistent homology was found between CcBV genes and any set of genes constituting the core genome of a known free-living virus. We discuss the significance of the scarce homology found between proteins from CcBV and other viruses or mobile elements. Arch. Insect Biochem. Physiol. 61:110,122, 2006. © 2006 Wiley-Liss, Inc. [source] The effect of oestrogen and testosterone on the urethral seam of the developing male mouse genital tubercleBJU INTERNATIONAL, Issue 9 2003S. Yucel OBJECTIVES To describe the effects of exogenous oestrogens and androgens on urethral formation in the mouse, as the development of the mouse and human urethra have significant similarities, and understanding normal male urethral development may help to identify the causes of abnormal development, e.g. hypospadias. MATERIALS AND METHODS Timed-pregnant C57/6 mice were exposed to synthetic oestrogens and androgens. The morphology of the genital tubercles was examined histologically and with three-dimensional computer reconstruction. Specific attention was focused on the developing urethral seam. RESULTS Microscopic serial analysis confirmed the presence of an arrest in seam formation in about half of oestrogen-treated male fetuses. In contrast, there was acceleration of urethral fold fusion and a longer urethral tube in those treated with androgens. Oestrogen-treated fetuses had a thin periurethral spongiosa, in contrast to androgen-treated fetuses which developed a thicker periurethral spongiosa. The effect of oestrogens on seam area formation did not depend on the dose, but in contrast, in the androgen-treated fetuses it was. CONCLUSION Oestrogens and androgens have a direct effect on the fusion of the urethral fold that leads to seam formation. Normal urethral development depends on the delicate balance of these complementary hormones. [source] Correlation between sea surface topography and bathymetry in shallow shelf waters in the Western MediterraneanGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2002G. Rodríguez Velasco Summary In this paper, gravimetric and altimetric data are used to assess an estimation of the sea surface topography in the Western Mediterranean Sea. This is a complex area from different points of view, due to the presence of several islands, coastal lines, shallow waters and a peculiar hydrologic equilibrium due to its proximity to the Atlantic water exchange area. First, a gravimetric geoid was computed using the least-squares collocation (LSC) procedure with the classical remove-restore technique. We also present a local mean sea surface generated from repeat ERS-1 altimeter data fitted to TOPEX. We chose this satellite because it offers a better spatial resolution than the TOPEX data. The time span used in the computations is one year. This is a useful interval for averaging out the regular seasonal variations, which are very large in this area. We present the comparisons between the gravimetric geoidal heights and the adjusted sea surface. This is a way to obtain a rough estimation of the sea surface topography (SST) since we also include the errors in the two surfaces and other oceanic signals. The differences obtained are physically reasonable with a mean of 17 cm and standard deviation (s.d.) of 39 cm. A significant similarity is observed between the features reproduced by these differences and the bathymetry in the area, suggesting some sort of correlation between both magnitudes for the studied region. If we accept such correlation, the SST may be described as a function of depth. This procedure lets us filter out the short wavelength part of the geoid from the first SST estimation. [source] Analysis of expressed sequence tags for Frankliniella occidentalis, the western flower thripsINSECT MOLECULAR BIOLOGY, Issue 4 2010D. Rotenberg Abstract Thrips are members of the insect order Thysanoptera and Frankliniella occidentalis (the western flower thrips) is the most economically important pest within this order. F. occidentalis is both a direct pest of crops and an efficient vector of plant viruses, including Tomato spotted wilt virus (TSWV). Despite the world-wide importance of thrips in agriculture, there is little knowledge of the F. occidentalis genome or gene functions at this time. A normalized cDNA library was constructed from first instar thrips and 13 839 expressed sequence tags (ESTs) were obtained. Our EST data assembled into 894 contigs and 11 806 singletons (12 700 nonredundant sequences). We found that 31% of these sequences had significant similarity (E, 10,10) to protein sequences in the National Center for Biotechnology Information nonredundant (nr) protein database, and 25% were functionally annotated using Blast 2GO. We identified 74 sequences with putative homology to proteins associated with insect innate immunity. Sixteen sequences had significant similarity to proteins associated with small RNA-mediated gene silencing pathways (RNA interference; RNAi), including the antiviral pathway (short interfering RNA-mediated pathway). Our EST collection provides new sequence resources for characterizing gene functions in F. occidentalis and other thrips species with regards to vital biological processes, studying the mechanism of interactions with the viruses harboured and transmitted by the vector, and identifying new insect gene-centred targets for plant disease and insect control. [source] Molecular characterization of a peroxiredoxin from the hard tick Haemaphysalis longicornisINSECT MOLECULAR BIOLOGY, Issue 2 2001N. Tsuji Abstract Antioxidant enzymes in eukaryotes play an important role in protection against the oxygen radicals generated during aerobic metabolism. Here we report the cloning and characterization of a cDNA encoding the antioxidant enzyme peroxiredoxin from the hard tick Haemaphysalis longicornis (HlPrx). HlPrx is 939 bp long and contains a 101 bp non-translated sequence at the 5, end and a polyadenylation singnal followed by a poly(A) tail at the 3, end. HlPrx encodes a full-length protein with a predicted molecular mass of 26 kDa that possesses one cysteine residue at amino acid 49 that is conserved among Prx proteins of various species. GenBankÔ analysis showed that the deduced amino acid sequence had significant similarity to mammalian and plant Prxs at the amino acid level. A DNA-nicking assay revealed that Escherichia coli,expressed recombinant HlPrx (rHlPrx) inhibited oxidative-nicking of supercoiled plasmid DNA. Two-dimensional immunoblot analysis with mouse antirHlPrx serum showed reaction with a major constituent protein spot in extracts of adult ticks. In addition, immunoblot analysis showed that rHlPrx was immunoreacted with serum from rabbits repeatedly infested with H. longicornis. Localization analysis using mouse antirHlPrx serum revealed that native HlPrx was highly expressed in the salivary gland of the tick. Moreover, Northern blot analysis showed that the level of HlPrx transcripts was increased during blood sucking. The present results indicate that HlPrx may be an important detoxifying enzyme during the normal life span as well as during blood sucking in ticks. [source] Updating Geographic Distribution of Artemia urmiana Günther, 1890 (Branchiopoda: Anostraca) in Europe: An Integrated and Interdisciplinary ApproachINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 5 2009Theodore J. Abatzopoulos Abstract Artemia urmiana (a species previously considered endemic of Lake Urmia, NW Iran) has been found in Lake Koyashskoe, a hypersaline lake on the Black Sea coast of the Crimean peninsula (Ukraine). Therefore, this is the first record of A. urmiana in Europe which updates its distribution. The species identification was based on an integrated and interdisciplinary approach using discriminant analysis of the morphometric characters, scanning electron microscopy, and molecular profile analysis. The data derived from the above mentioned approaches converge to significant similarity of the population under investigation with A. urmiana. The updated geographic distribution of the species, deriving from the present report, asks for additional contribution of other disciplines (e.g., avian dispersal of cysts, history of salt trade) to be finally clarified. At present we suggest that the punctuated geographic distribution of A. urmiana is probably linked to its low dispersal capability, and we suppose that its presence in two distant sites could be explained by historical human salt trade between Lake Urmia and the ancient port of Kimmerik, whose remains have been found in the present Lake Koyashskoe. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Potential of ,flat' fibre evanescent wave spectroscopy to discriminate between normal and malignant cells in vitroJOURNAL OF MICROSCOPY, Issue 2 2007Z. HAMMODY Summary The present study focuses on evaluating the potential of flattened AgClBr fibre-optic evanescent wave spectroscopy (FTIR-FEWS) technique for detection and identification of cancer cells in vitro using cell culture as a model system. The FTIR-FEWS results are compared to those from FTIR-microspectroscopy (FTIR-MSP) method extensively used to identify spectral properties of intact cells. Ten different samples of control and malignant cells were measured in parallel by the above two methods. Our results show a significant similarity between the results obtained by the two methodologies. The absorbance level of Amide I/Amide II, phosphates and carbohydrates were significantly altered in malignant compared to the normal cells using both systems. Thus, common biomarkers such as Amide I/Amide II, phosphate and carbohydrate levels can be derived to discern between normal and cancer cells. However, marked differences are also noted between the two methodologies in the protein bands due to CH3 bending vibration (1480,1350 cm,1). The spectral differences may be attributed to the variation in the penetration depth of the two methodologies. The use of flattened fibre rather than the standard cylindrical fibre has several practical advantages and is considered as an important step towards in vivo measurements in real time, such as that of skin nevi and melanoma using special designs of fibre-optic,based sensors. [source] REPRODUCTIVE ISOLATION BY SEX PHEROMONES IN THE CLOSTERIUM PERACEROSUM,STRIGOSUM,LITTORALE COMPLEX (ZYGNEMATALES, CHAROPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 5 2008Yuki Tsuchikane The Closterium peracerosum,strigosum,littorale (C. psl.) complex consists of unicellular algae and is known to be composed of several reproductively isolated mating groups of heterothallic strains. Group I-E is completely isolated from mating groups II-A and II-B, groups II-A and II-B are partially isolated from each other, and only mating-type plus (mt+) cells of group II-A and mating-type minus (mt,) cells of group II-B form zygotes. Based on the alignment of 1506 group I introns, significant phylogenetic relationships were observed among mating groups II-A and II-B, while mating group I-E was distant from groups II-A and II-B. Sexual cell division in both mating-type cells of group II-A was stimulated in conditioned media in which cells of group II-B had been cultured. When mt, cells of group II-B were stimulated in conditioned medium derived from group II-A, mt+ cells of group II-B did not respond to the conditioned medium. Conditioned media derived from group I-E did not exhibit sexual cell division (SCD),inducing activity against any strain except those within its own group. From the alignment of deduced amino acid sequences from orthologous protoplast-release-inducing protein (PR-IP) Inducer genes, we detected a significant similarity among groups II-A and II-B, and mating group I-E had low similarity to other mating groups. The existing degree of reproductive isolation can be partially explained by differences in molecular structures and physiological activities of sex pheromones of these heterothallic mating groups. [source] ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM THE MARINE MICROALGA NANNOCHLOROPSIS OCULATA (EUSTIGMATOPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 1 2008Juan Shi Nannochloropsis oculata (Droop) D. J. Hibberd (Eustigmatophyceae), a marine eukaryotic unicellular alga, is widely used in mariculture as live feed. It is considered to be of high nutritional value owing to its high content of proteins; polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA, C20:5n3); and diverse pigments. Previous studies of this microalga focused on its taxonomy, culture, and biochemistry, but little is known at the molecular level. Establishing a molecular base is vital to understand the biological processes of this alga. Therefore, we constructed a cDNA library using algal cells grown at exponential growth phase and carried out expressed sequence tag (EST) analysis. A total of 1,960 nonredundant sequences (NRSs) were generated for N. oculata clone CS-179. Only 32.5% of NRSs showed significant similarity (E < 1e-04) to proteins registered in the GenBank nonredundant protein database. The KOG (clusters of euKaryotic Orthologous Groups) profile database returned significant hits for 490 NRSs. Analysis revealed that a large proportion of NRSs could be unique to this microalga. [source] Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta),JOURNAL OF PHYCOLOGY, Issue 6 2007Fan Xiaolei Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) is cultivated in China and widely consumed in Asia. To gain more insight into its physiological and biochemical properties, we generated 5318 expressed sequence tags (ESTs) from the sporophyte of P. haitanensis, and upon assembling into a nonredundant set, 2535 sequences were obtained, among which only 32.2% (816) shared certain similarity with published sequences (Nr and KOG). Functional classification of such ESTs revealed that most of the transcripts were related to its conservative biological metabolism, and P. haitanensis most likely possesses cyanide-resistant respiration and a C4-like carbon-fixation pathway, both of which have never been reported in a rhodophyte before. Twenty-eight percent of the nonredundant gene clusters exhibited significant similarity to those from P. yezoensis Ueda sporophytes, and 16 genes up-regulated in P. yezoensis sporophytes were also expressed abundantly in P. haitanensis. Codon usage analysis indicated that exposure to high GC pressure might occur during evolution of P. haitanensis. These findings represent the most extensive collection of ESTs from P. haitanensis to date, and all the ESTs in this study have been submitted to GenBank (accession nos. DN604790,DN608469, EG016226,EG018540). [source] ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM THE GREEN ALGA ULVA LINZA (CHLOROPHYTA),JOURNAL OF PHYCOLOGY, Issue 6 2005Michele S. Stanley There is a general lack of genomic information available for chlorophyte seaweed genera such as Ulva, and in particular there is no information concerning the genes that contribute to adhesion and cell wall biosynthesis for this organism. Partial sequencing of cDNA libraries to generate expressed sequence tags (ESTs) is an effective means of gene discovery and characterization of expression patterns. In this study, a cDNA library was created from sporulating tissue of Ulva linza L. Initially, 650 ESTs were randomly selected from a cDNA library and sequenced from their 5, ends to obtain an indication of the level of redundancy of the library (21%). The library was normalized to enrich for rarer sequences, and a further 1920 ESTs were sequenced. These sequences were subjected to contig assembly that resulted in a unigene set of approximately 1104 ESTs. Forty-eight percent of these sequences exhibited significant similarity to sequences in the databases. Phylogenetic comparisons are made between selected sequences with similarity in the databases to proteins involved in aspects of extracellular matrix/cell wall assembly and adhesion. [source] Consumer health information on the Web: The relationship of visual design and perceptions of credibilityJOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY, Issue 1 2010David Robins Consumer health information has proliferated on the Web. However, because virtually anyone can publish this type of information on the Web, consumers cannot always rely on traditional credibility cues such as reputation of a journal. Instead, they must rely on a variety of cues, including visual presentation, to determine the veracity of information. This study is an examination of the relationship of people's visual design preferences to judgments of credibility of information on consumer health information sites. Subjects were asked to rate their preferences for visual designs of 31 health information sites after a very brief viewing. The sites were then reordered and subjects rated them according to the extent to which they thought the information on the sites was credible. Visual design judgments bore a statistically significant similarity to credibility ratings. Sites with known brands were also highly rated for both credibility and visual design. Theoretical implications are discussed. [source] An updated view of hemostasis: mechanisms of hemostatic dysfuntion associated with sepsisJOURNAL OF VETERINARY EMERGENCY AND CRITICAL CARE, Issue 2 2005DACVECC, Kate Hopper BVSc Abstract Objective: To review the current understanding of mechanisms involved in normal hemostasis and to describe the changes associated with pro-inflammatory disease processes such as sepsis. Data sources: Original research articles and scientific reviews. Human data synthesis: Organ damage caused by sepsis is created in part by the interdependent relationship between hemostasis and inflammation. Markers of coagulation have been found to have prognostic value in human patients with sepsis and there are both experimental and clinical investigations of the therapeutic potential of modulating the hemostatic system in sepsis. Improvement of 28-day all-cause mortality in severe sepsis by treatment with recombinant human activated Protein C strongly supports the interdependence of hemostasis and inflammation in the pathophysiology of sepsis. Veterinary data synthesis: Publications reporting clinical evaluation of the hemostatic changes occurring in septic dogs or cats are minimal. Experimental animal models of sepsis reveal significant similarity between human and animal sepsis and may provide relevance to clinical veterinary medicine until prospective clinical evaluations are published. Conclusions: It is now apparent that inflammation and the coagulation system are intimately connected. Understanding this relationship provides some insight into the pathogenesis of the hemostatic changes associated with sepsis. This new updated view of hemostasis may lead to the development of novel therapeutic approaches to sepsis and disseminated intravascular coagulation in veterinary medicine. [source] Identification of cyanobacterial cell division genes by comparative and mutational analysesMOLECULAR MICROBIOLOGY, Issue 1 2005Shin-ya Miyagishima Summary We performed comparative and mutational analyses to define more comprehensively the repertoire of genes involved in cyanobacterial cell division. Genes ftsE, ftsI, ftsQ, ftsW, and (previously recognized) ftsZ, minC, minD, minE and sulA were identified as homologues of cell division genes of Gram-negative and Gram-positive bacteria. Transposon mutagenesis of Synechococcus elongatus PCC 7942 identified five additional genes, cdv1, cdv2, cdv3, ftn6 and cikA, involved in cell division. cdv1 encodes a presumptive periplasmic peptidyl-prolyl cis - trans isomerase. cdv2 has similarity to ylmF which, like divIVA, lies within the Gram-positive bacterial ylm gene cluster whose members have functions associated with division. Conservation of other ylm genes in cyanobacteria suggests that cyanobacteria and Gram-positive bacteria share specific division proteins. Two ylm homologues are also found in algal and plant genomes. cdv3 has low but significant similarity to divIVA, suggesting that minE and cdv3 both mediate division-site determination in cyanobacteria. In contrast, Gram-positive bacteria lack minE, and (Gram-negative) proteobacteria lack divIVA. ftn6, of unknown function, and the circadian input kinase, cikA, are specific to cyanobacteria. In S. elongatus, unlike in other bacteria, FtsZ rings are formed at sites occupied by nucleoids. Thus, the division machinery of cyanobacteria differs in its composition and regulation from that of Gram-negative and Gram-positive bacteria. [source] SREA is involved in regulation of siderophore biosynthesis, utilization and uptake in Aspergillus nidulansMOLECULAR MICROBIOLOGY, Issue 5 2001Harald Oberegger Under conditions of low iron availability, most fungi excrete siderophores in order to mobilize extracellular iron. We show that lack of the GATA-type transcription factor SREA in Aspergillus nidulans not only leads to derepression of siderophore biosynthesis but also to deregulation of siderophore-bound iron uptake and ornithine esterase expression. Furthermore, SREA deficiency causes increased accumulation of ferricrocin, the siderophore responsible for intracellular iron storage. In sreA deletion strains, extracellular siderophore production is derepressed but still regulated negatively by iron availability, indicating the presence of an additional iron-regulatory mechanism. In contrast, iron affects ferricrocin accumulation in a positive way, suggesting a protective role for this siderophore in detoxification of intracellular iron excess. The harmfulness of deregulated iron uptake in this mutant is demonstrated by increased expression of genes encoding the antioxidative enzymes catalase CATB and the superoxide dismutases SODA and SODB. It is noteworthy that iron starvation was found to repress catB expression in wild-type (wt) and SREA-deficient strains, consistent with catB being subject to SREA-independent iron regulation. Differential display led to the identification of putative SREA target genes amcA and mirA. The deduced MIRA amino acid sequence displays significant similarity to recently characterized siderophore permeases of Saccharomyces cerevisiae. amcA encodes a putative mitochondrial carrier for the siderophore precursor ornithine, indicating cross-regulation of siderophore and ornithine metabolism. [source] When similars do not attract: Tests of a prediction from the self-expansion modelPERSONAL RELATIONSHIPS, Issue 4 2006ARTHUR ARON This study tested the hypothesis from the self-expansion model that the usual effect of greater attraction to a similar (vs. dissimilar) stranger will be reduced or reversed when a person is given information that a relationship would be likely to develop (i.e., that they would be very likely to get along) with the other person. The study employed the "bogus stranger" paradigm and focused on similarity/dissimilarity of interests in the context of attraction to a same-gender other. The effect for similarity under conditions in which no information is given about relationship likelihood replicated the usual pattern of greater attraction to similars. However, as predicted, a significant similarity by information interaction demonstrated that this effect was significantly reduced (and slightly reversed) when participants had been given information that the partner will like self. In analyses for each gender separately, both of these effects were significant only for men, suggesting that the focus on interest similarity may have been less relevant for women. [source] Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 GenesPLANT BIOLOGY, Issue 6 2004U. Egertsdotter Abstract: The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy-one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process. [source] LiveBench-1: Continuous benchmarking of protein structure prediction serversPROTEIN SCIENCE, Issue 2 2001Janusz M. Bujnicki Abstract We present a novel, continuous approach aimed at the large-scale assessment of the performance of available fold-recognition servers. Six popular servers were investigated: PDB-Blast, FFAS, T98-lib, GenTHREADER, 3D-PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one-half of the targets, but significantly accurate sequence-structure alignments were produced for only one-third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets,where standard methods such as PSI-BLAST fail,the most sensitive fold-recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence-structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An "ideally combined consensus" prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join. [source] Heritability of different measures of smooth pursuit eye tracking dysfunction: A study of normal twinsPSYCHOPHYSIOLOGY, Issue 6 2000Joanna Katsanis Research studies have found that smooth pursuit eye movement dysfunction may serve as an index of genetic liability to develop schizophrenia. The heritability of various measures of smooth pursuit eye tracking proficiency and the saccades that occur during smooth pursuit was examined in 64 monozygotic (MZ) and 48 dizygotic (DZ) twin pairs. Two age cohorts were assessed (11,12 and 17,18 years of age). Intraclass correlations indicated significant similarity in the MZ twins for almost all measures in both age cohorts, whereas few of the DZ twin correlations attained significance. Biometrical modeling indicated that genetic mechanisms influence performance on both global and specific eye tracking measures, accounting for about 40% to 60% of the variance. These findings suggest that the underlying brain systems responsible for smooth pursuit and saccade generation during pursuit are under partial genetic control. [source] Transcriptionally active transposable elements in recent hybrid sugarcaneTHE PLANT JOURNAL, Issue 5 2005Paula G. de Araujo Summary Transposable elements (TEs) are considered to be important components of the maintenance and diversification of genomes. The recent increase in genome sequence data has created an opportunity to evaluate the impact of these active mobile elements on the evolution of plant genomes. Analysis of the sugarcane transcriptome identified 267 clones with significant similarity to previously described plant TEs. After full cDNA sequencing, 68 sugarcane TE clones were assigned to 11 families according to their best sequence alignment against a fully characterized element. Expression was further investigated through a combined study utilizing electronic Northerns, macroarray, transient and stable sugarcane transformation. Newly synthesized cDNA probes from flower, leaf roll, apical meristem and callus tissues confirm previous results. Callus was identified as the tissue with the highest number of TEs being expressed, revealing that tissue culture drastically induced the expression of different elements. No tissue-specific family was identified. Different representatives within a TE family displayed differential expression patterns, showing that each family presented expression in almost every tissue. Transformation experiments demonstrated that most Hopscotch clone-derived U3 regions are, indeed, active promoters, although under a strong transcriptional regulation. This is a large-scale study about the expression pattern of TEs and indicates that mobile genetic elements are transcriptionally active in the highly polyploid and complex sugarcane genome. [source] Linkage mapping of gene-associated SNPs to pig chromosome 11ANIMAL GENETICS, Issue 3 2006M. Sawera Summary Single nucleotide polymorphisms (SNPs) were discovered in porcine expressed sequence tags (ESTs) orthologous to genes from human chromosome 13 (HSA13) and predicted to be located on pig chromosome 11 (SSC11). The SNPs were identified as sequence variants in clusters of EST sequences from pig cDNA libraries constructed in the Sino,Danish pig genome project. In total, 312 human gene sequences from HSA13 were used for similarity searches in our pig EST database. Pig ESTs showing significant similarity with HSA13 genes were clustered and candidate SNPs were identified. Allele frequencies for 26 SNPs were estimated in a group of 80 unrelated pigs from Danish commercial pig breeds: Duroc, Hampshire, Landrace and Large White. Eighteen of the 26 SNPs genotyped in the PiGMaP Reference Families were mapped by linkage analysis to SSC11. The EST-based SNPs published here are new genetic markers useful for linkage and association studies in commercial and experimental pig populations. This study represents the first gene-associated SNP linkage map of pig chromosome 11 and adds new comparative mapping information between SSC11 and HSA13. Furthermore, our data facilitate future studies aimed at the identification of interesting regions on pig chromosome 11, positional cloning and fine mapping of quantitative trait loci in pig. [source] | ||||||||||||||||||||||