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At least 1,369 records · Page 76Linked to original sources
PubMed2005

Gene expression in the salivary complexes from Haementeria depressa leech through the generation of expressed sequence tags.

A survey of the transcriptional profile of Haementeria depressa Ringuelet, 1972 (Annelida, Hirudinea) salivary complexes was produced through expressed sequence tag (EST). Sequences from 898 independent clones were assembled in 555 clusters, representing the transcript profile of this tissue. The repertoire of possible proteins involved in feeding and host interaction processes of the leech corresponded to 10.6% of all identified transcripts (67 clusters), being the carbonic anhydrases (30%), several coagulation inhibitors (25%) and hemerythrin-like molecules (19%), the major components. Among the 387 clusters matching cellular proteins, the majority represents molecules involved in gene and protein expression, reflecting a high specialization of this tissue for protein synthesis. Our H. depressa dbEST was also compared to those from other blood-feeding organisms, providing evidences that among the secreted proteins, the coagulation inhibitors present a profile very characteristic of this animal class.

Amino Acid Sequence↗
PubMed1997

A survey of polypeptide deformylase function throughout the eubacterial lineage.

N-terminal formylation of ribosome-synthesized polypeptides is assumed to be among the most conserved features that distinguish the eubacterial line of descent from other living phyla. In order to assess the ancientness of this trait, def genes encoding polypeptide deformylase were characterized from four eubacterial species, Lactococcus lactis, Bacillus subtilis, Calothrix PCC7601 and Thermotoga maritima, taking advantage of the conditional viability of the def mutants of Escherichia coli. Altogether, eight sequences of polypeptide deformylase have been obtained from all the eubacterial sources which were investigated, either through systematic genome sequence analysis or through genetic screening, yielding a highly homologous family. A gene putatively encoding Met-tRNAi formyltransferase, fmt, was found downstream of the deformylase gene except in L. lactis, Mycoplasma genitalium, Calothrix PCC7601 and T. maritima. These results argue strongly for the ancestral character of N-terminal formylation in eubacteria. Most of the wide deviations of amino acid usage observed in def- and fmt-encoded proteins among species is best accounted for by the nucleotide composition of genomes. Furthermore, the species of origin of each protein appears to be more recognizable than its function, considering only its amino acid composition.

Amidohydrolases↗
PubMed2004

Isolation of Hox and Parahox genes in the hemichordate Ptychodera flava and the evolution of deuterostome Hox genes.

Because of their importance for proper development of the bilaterian embryo, Hox genes have taken center stage for investigations into the evolution of bilaterian metazoans. Taxonomic surveys of major protostome taxa have shown that Hox genes are also excellent phylogenetic markers, as specific Hox genes are restricted to one of the two great protostome clades, the Lophotrochozoa or the Ecdysozoa, and thus support the phylogenetic relationships as originally deduced by 18S rDNA studies. Deuterostomes are the third major group of bilaterians and consist of three major phyla, the echinoderms, the hemichordates, and the chordates. Most morphological studies have supported Hemichordata+Chordata, whereas molecular studies support Echinodermata+Hemichordata, a clade known as Ambulacraria. To test these competing hypotheses, complete or near complete cDNAs of eight Hox genes and four Parahox genes were isolated from the enteropneust hemichordate Ptychodera flava. Only one copy of each Hox gene was isolated suggesting that the Hox genes of P. flava are arranged in a single cluster. Of particular importance is the isolation of three posterior or Abd-B Hox genes; these genes are only shared with echinoderms, and thus support the monophyly of Ambulacraria.

Amino Acid Motifs↗
PubMed2004

Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profiling.

Sugarcane accumulates high concentrations of sucrose in the mature stem and a number of physiological processes on-going in maturing stem tissue both directly and indirectly allow this process. To identify transcripts that are associated with stem maturation, we compared patterns of gene expression in maturing and immature stem tissue by expression profiling and bioinformatic analysis of sets of stem ESTs. This study complements a previous study of gene expression associated directly with sugar metabolism in sugarcane. A survey of sequences derived from stem tissue identified an abundance of several classes of sequence that are associated with fibre biosynthesis in the maturing stem. A combination of EST analyses and microarray hybridization revealed that genes encoding homologues of the dirigent protein, a protein that assists in the stereospecificity of lignin assembly, were the most abundant and most strongly differentially expressed transcripts in maturing stem tissue. There was also evidence of coordinated expression of other categories of fibre biosynthesis and putative defence- and stress-related transcripts in the maturing stem. This study has demonstrated the utility of genomic approaches using large-scale EST acquisition and microarray hybridization techniques to highlight the very significant transcriptional investment the maturing stem of sugarcane has placed in fibre biosynthesis and stress tolerance, in addition to its already well-documented role in sugar accumulation.

Amino Acid Sequence↗
PubMed2001

Evolution and characterization of tetraonine endogenous retrovirus: a new virus related to avian sarcoma and leukosis viruses.

In a previous study, we found avian sarcoma and leukosis virus (ASLV) gag genes in 19 species of birds in the order Galliformes including all grouse and ptarmigan (Tetraoninae) surveyed. Our data suggested that retroviruses had been transmitted horizontally among some host species. To further investigate these elements, we sequenced a replication-defective retrovirus, here named tetraonine endogenous retrovirus (TERV), from Bonasa umbellus (ruffed grouse). This is the first report of a complete, replication-defective ASLV provirus sequence from any bird other than the domestic chicken. We found a replication-defective proviral sequence consisting of putative Gag and Env proteins flanked by long terminal repeats. Reverse transcription-PCR analysis showed that retroviral gag sequences closely related to TERV are transcribed, supporting the hypothesis that TERV is an active endogenous retrovirus. Phylogenetic analyses suggest that TERV may have arisen via recombination between different retroviral lineages infecting birds. Southern blotting using gag probes showed that TERV occurs in tetraonines but not in chickens or ducks, suggesting that integration occurred after the earliest phasianid divergences but prior to the radiation of tetraonine birds.

Amino Acid Sequence↗
PubMed2005

Expressed sequence tag (EST) survey of the highly adapted green algal parasite, Helicosporidium.

Helicosporidia are obligate invertebrate pathogens with a unique and highly adapted mode of infection. The evolutionary history of Helicosporidia has been uncertain, but several recent molecular phylogenetic studies have shown an unexpectedly close relationship to green algae, and specifically to the opportunistic pathogen Prototheca. To date, molecular sequences from Helicosporidia are restricted to those genes used for phylogenetic reconstruction and genes related to the existence and function of its cryptic plastid. We have therefore conducted a small expressed sequence tag (EST) project on Helicosporidium sp., yielding about 700 unique sequences. We have examined the functional distribution of known genes, the distribution of EST abundance, and the prevalence of previously unknown gene sequences. To demonstrate the potential utility of large amounts of data, we have used ribosomal proteins to test whether the phylogenetic position of Helicosporidium inferred from a small number of genes is broadly supported by a large number of genes. We conducted phylogenetic analyses on 69 ribosomal proteins and found that 98% supported the green algal origin of Helicosporidia and 80% support a specific relationship with Prototheca. Overall, these data multiply the available molecular information from Helicosporidium 100-fold, which should provide the basis for new insights into these unusual but interesting parasites.

Chlorophyta↗
PubMed2001

Hand hygiene--comparison of international recommendations.

The value of hand hygiene for the prevention of cross-infection was first observed in the middle of the 19th century. Since then, which procedure is the most suitable for hand hygiene has been repeatedly discussed and several different guidelines and recommendations have been published. The aim of this review is to compare different recommendations for hand hygiene regarding technique and indication. Medline, the internet and a personal library were searched to obtain as many written recommendations as possible. In addition, a small questionnaire was sent by e-mail to 20 international colleagues. As a result, written recommendations from 10 countries could be compared. Recommended methods of hand hygiene include handwashing (washing hands with plain soap), hygienic handwash (washing hands with medicated soap) and hygienic hand-rub (use of antiseptic rubs). In most countries handwashing and hygienic handwash are the methods of choice and only in central European countries is hygienic hand-rub the preferred technique. Situations in which performance of hand hygiene is recommended are comparable. However, no single indication is recommended in all guidelines. Hand hygiene is most often recommended before performing invasive procedures and after microbial contamination. Guidelines should be clear and easy to follow for them to become standard of care. Thus, guidelines are needed that do not leave to the health care worker a decision as to whether hand hygiene is indicated.

Attitude of Health Personnel↗
PubMed2003

Understanding uncertainty and minimizing families' anxiety at the time of transfer from intensive care.

When general ward registered nurses (RN) receive patients from an intensive care unit (ICU) they report that much of their time in the initial phases revolves around meeting family needs (Farvis, 2002). Families experience anxiety when leaving the security of the close monitoring seen in ICU (Leith, 1999) and their anxiety reduces their ability to play a key role in the patient's recovery (McShane, 1991; Leske, 1992) as it can impair their decision-making (Cagan, 1988; Halm et al., 1993). By reducing a family's anxiety, they may be more able to cope with the necessary transition to a general ward and support the patient's recovery. A literature search from 1990 onwards was performed within the CINAHL, Medline and Cochrane databases using the key words: intensive care, family, General System Theory, uncertainty, anxiety and transfer. Further articles were retrieved from citation references from the Web of Science or through the reference lists of retrieved literature. Library catalogues were searched using the same key words for books and book chapters. von Bertalanffy's General System Theory provides a framework for understanding the importance of family in a critical illness situation. Critical illness permits little or no time to adapt, thus reducing the family's ability to cope with the situation. Transfer out of ICU is a significant anxiety-producing event for families. Uncertainty in illness is reported in other illness situations to reduce family's adaptation to illness events, but has not been researched with an ICU cohort of families. Seven out of the top 10 needs of ICU families are information needs, highlighting the importance of communication regarding progress and future plans. Nurses require an increased awareness that transfer anxiety exists for families and to be knowledgeable about ways to reduce its occurrence. Research is required to evaluate the efficacy of interventions to reduce anxiety for families and examine the level of uncertainty in illness in this cohort.

Anxiety↗
PubMed2005

Exploring the genome of Trypanosoma vivax through GSS and in silico comparative analysis.

A survey of the Trypanosoma vivax genome was carried out by the genome sequence survey (GSS) approach resulting in 1,086 genomic sequences. A total of 455 high-quality GSS sequences were generated, consisting of 331 non-redundant sequences distributed in 264 singlets and 67 clusters in a total of 135.5 Kb of the T. vivax genome. The estimation of the overall G+C content, and the prediction of the presence of ORFs and putative genes were carried out using the Glimmer and Jemboss packages. Analysis of the obtained sequences was carried out by BLAST programs against 12 different databases and also using the Conserved Domain Database, InterProScan, and tRNAscan-SE. Along with the existing 23 T. vivax entries in the GenBank, the 32 putative genes predicted and the 331 non-redundant GSS sequences reported herein represent new potential markers for the development of PCRbased assays for specific diagnosis and typing of Trypanosoma vivax.

Algorithms↗
PubMed1997

A brief descriptive catalogue of Ayurvedic palm leaves manuscripts procured and preserved in the Indian Institute of Medicine.

It seems the survey for medical manuscripts has not been done thoroughly so far in India particularly in Andhra Pradesh. Though few Researchers toured many important places and collected a number of manuscripts, but still there are many villages and several families of physicians and scholars possessing many manuscripts, are not covered. One of the aims and objects of the Indian Institute of History of Medicine is to procure and study the rare and uncared medical manuscripts. There are many difficulties in this task as many of the families in possession of the manuscripts are generally not prepared to hand over the ancestry property i.e., manuscripts to any individual or institution due to their sentiments, though they are not able to preserve or make use of same properly. However, efforts were made by the Institute in this direction, visiting several families of hereditary physicians residing in different part of Andhra Pradesh, and procured 12 such valuable palm leaves manuscripts pertaining to Ayurveda and preserved in the Institute. A brief descriptive catalogue of these manuscripts is presented here.

Academies and Institutes↗
PubMed1982

Being there: the effect of the user's presence on MEDLINE search results.

An evaluation was conducted at the University of Iowa Health Sciences Library to determine what effect the user's presence had on MEDLINE search results. One hundred users participated over a four-month period. Three main criteria were used: search precision, search recall, and user satisfaction. Each MEDLINE search was processed twice, once prior to the user's arrival and a second time during the scheduled appointment with the user. The two searches for each user were processed by different searchers, and four searchers alternated processing the user-absent or the user-present search. Users were asked to compare the citations on the two searchers by checking each printout for relevant citations. A short questionnaire was administered to determine general information about users and satisfaction measures for each search. The extensiveness of the interview for the user-absent search was varied in order to determine if the depth of the initial interview would affect the search results. Evaluation of the findings indicated an increase in precision, recall, and user satisfaction for the user-present search. Some difficulties in designing the experiment are discussed and implications of the evaluation results are considered.

Consumer Behavior↗
PubMed2000

Identification of a novel DNA probe for strain typing Mycobacterium bovis by restriction fragment length polymorphism analysis.

Bovine tuberculosis caused by Mycobacterium bovis remains a significant disease of farmed cattle in many countries despite ongoing tuberculosis eradication programs. Molecular typing methods such as restriction fragment length polymorphism (RFLP) analysis and spoligotyping have been used to identify related herd breakdowns in an attempt to identify more precisely the route of infection into cattle herds and to trace the transmission of bovine tuberculosis. A recent geographical survey of Irish M. bovis isolates demonstrated that a significant proportion of isolates ( approximately 20%) exhibit a common strain type, limiting the value of current strain typing methods as an epidemiological tool. We have identified and cloned a region of the M. bovis genome, pUCD, which generates a clear, highly polymorphic banding pattern when used as an RFLP probe on AluI restriction-digested M. bovis genomic DNA and which effectively subdivides this common strain type. When used to type 60 Irish M. bovis isolates, pUCD exhibited greater discriminatory power than the commonly used mycobacterial RFLP probes IS6110, PGRS, and DR and detected an equivalent number of strain types to a combination of these three probes. pUCD also detected significantly more strain types than the spoligotyping technique, while maintaining a high level of concordance between epidemiologically related and unrelated herd breakdowns. The polymorphic element within pUCD remains to be fully characterized, however the potential for this probe to greatly decrease the workload necessary to genotype M. bovis by RFLP analysis is compelling.

Animals↗
PubMed1995

Construction of a transcription map surrounding the BRCA1 locus of human chromosome 17.

We have used a combination of methods (exon amplification, direct selection, direct screening, evolutionary conservation, island rescue-PCR, and direct sequence analysis) to survey approximately 600 kb of genomic DNA surrounding the BRCA1 gene for transcribed sequences. We have cloned a set of fragments representing at least 26 genes. The DNA sequence of these clones reveals that 5 are previously cloned genes; the precise chromosomal location of 2 was previously unknown, and 3 have been cloned and mapped by others to this interval. Three other genes, including BRCA1 itself, have recently been mapped independently to this region. Sequences from 11 genes are similar but not identical matches to known genes; 5 of these appear to be the human homologues of genes cloned from other species. Another 7 genes have no similarity with known genes. In addition, 39 putative exons and 14 expressed sequence tags have been identified and mapped to individual cosmids. This transcript map provides a detailed description of gene organization for this region of the genome.

Animals↗
PubMed2004

Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space.

Maize (Zea mays) possesses a large, highly repetitive genome, and subsequently a number of reduced-representation sequencing approaches have been used to try and enrich for gene space while eluding difficulties associated with repetitive DNA. This article documents the ability of publicly available maize expressed sequence tag and Genome Survey Sequences (GSSs; many of which were isolated through the use of reduced representation techniques) to recognize and provide coverage of 78 maize full-length cDNAs (FLCs). All 78 FLCs in the dataset were identified by at least three GSSs, indicating that the majority of maize genes have been identified by at least one currently available GSS. Both methyl-filtration and high-Cot enrichment methods provided a 7- to 8-fold increase in gene discovery rates as compared to random sequencing. The available maize GSSs aligned to 75% of the FLC nucleotides used to perform searches, while the expressed sequence tag sequences aligned to 73% of the nucleotides. Our data suggest that at least approximately 95% of maize genes have been tagged by at least one GSS. While the GSSs are very effective for gene identification, relatively few (18%) of the FLCs are completely represented by GSSs. Analysis of the overlap of coverage and bias due to position within a gene suggest that RescueMu, methyl-filtration, and high-Cot methods are at least partially nonredundant.

Base Sequence↗
PubMed2006

Pyruvate formate-lyase and a novel route of eukaryotic ATP synthesis in Chlamydomonas mitochondria.

Pyruvate formate-lyase (PFL) catalyzes the non-oxidative conversion of pyruvate to formate and acetyl-CoA. PFL and its activating enzyme (PFL-AE) are common among strict anaerobic and microaerophilic prokaryotes but are very rare among eukaryotes. In a proteome survey of isolated Chlamydomonas reinhardtii mitochondria, we found several PFL-specific peptides leading to the identification of cDNAs for PFL and PFL-AE, establishing the existence of a PFL system in this photosynthetic algae. Anaerobiosis and darkness led to increased PFL transcripts but had little effect on protein levels, as determined with antiserum raised against C. reinhardtii PFL. Protein blots revealed the occurrence of PFL in both chloroplast and mitochondria purified from aerobically grown cells. Mass spectrometry sequencing of C. reinhardtii mitochondrial proteins, furthermore, identified peptides for phosphotransacetylase and acetate kinase. The phosphotransacetylase-acetate kinase pathway is a common route of ATP synthesis or acetate assimilation among prokaryotes but is novel among eukaryotes. In addition to PFL and pyruvate dehydrogenase, the algae also expresses pyruvate:ferredoxin oxidoreductase and bifunctional aldehyde/alcohol dehydrogenase. Among eukaryotes, the oxygen producer C. reinhardtii has the broadest repertoire of pyruvate-, ethanol-, and acetate-metabolizing enzymes described to date, many of which were previously viewed as specific to anaerobic eukaryotic lineages.

Acetylesterase↗
PubMed2006

An evaluation of a collaborative model for preparing evidence-based medicine teachers.

PURPOSE: The authors studied the effectiveness of a train-the-trainer collaboration model between librarians and medical faculty to instruct librarians and health professionals in teaching evidence-based medicine (EBM) principles. METHODS: A telephone survey was administered to graduates of an EBM course who agreed to participate in the study. They were asked if and how they taught EBM on returning to their institutions, if they felt competent to critically appraise an article, if their skill in searching PubMed improved, and if they collaborated with others in teaching EBM. RESULTS: Most respondents were librarians. The class was successful in that most taught EBM on return to their home institutions. Most initiated collaboration with health professionals. The goals of improving PubMed searching and achieving statistical competency had less success. CONCLUSION: This model is effective in preparing librarians to teach EBM. Modeling and encouraging collaboration between librarians and health professionals were successful techniques. Librarians would like more instruction in statistical concepts and less in searching PubMed. conclusions cannot be made for health professionals because of the low response rate from this group. As evidence-based health care continues to extend to other disciplines, librarians can position themselves to participate fully in the EBM educational process.

Consumer Behavior↗
PubMed2001

Identification of bacteria responsible for ammonia oxidation in freshwater aquaria.

Culture enrichments and culture-independent molecular methods were employed to identify and confirm the presence of novel ammonia-oxidizing bacteria (AOB) in nitrifying freshwater aquaria. Reactors were seeded with biomass from freshwater nitrifying systems and enriched for AOB under various conditions of ammonia concentration. Surveys of cloned rRNA genes from the enrichments revealed four major strains of AOB which were phylogenetically related to the Nitrosomonas marina cluster, the Nitrosospira cluster, or the Nitrosomonas europaea-Nitrosococcus mobilis cluster of the beta subdivision of the class Proteobacteria. Ammonia concentration in the reactors determined which AOB strain dominated in an enrichment. Oligonucleotide probes and PCR primer sets specific for the four AOB strains were developed and used to confirm the presence of the AOB strains in the enrichments. Enrichments of the AOB strains were added to newly established aquaria to determine their ability to accelerate the establishment of ammonia oxidation. Enrichments containing the Nitrosomonas marina-like AOB strain were most efficient at accelerating ammonia oxidation in newly established aquaria. Furthermore, if the Nitrosomonas marina-like AOB strain was present in the original enrichment, even one with other AOB, only the Nitrosomonas marina-like AOB strain was present in aquaria after nitrification was established. Nitrosomonas marina-like AOB were 2% or less of the cells detected by fluorescence in situ hybridization analysis in aquaria in which nitrification was well established.

Ammonia↗
PubMed2003

The rate of peptidyl-tRNA dissociation from the ribosome during minigene expression depends on the nature of the last decoding interaction.

The expression of some very short open reading frames (ORFs) in Escherichia coli results in peptidyl-tRNA accumulation that is lethal to cells defective in peptidyl-tRNA hydrolase activity. In an attempt to understand the factors that affect this phenotype, we have surveyed the toxicity of a complete set of two-codon ORFs cloned as minigenes in inducible expression vectors. The minigenes were tested in hydrolase-defective hosts and classified according to their degree of toxicity. In general, minigenes harboring codons belonging to the same box in the standard table of the genetic code mediated similar degrees of toxicity. Moreover, the levels of peptidyl-tRNA accumulation for synonymous minigenes decoded by the same tRNA were comparable. However, two exceptions were observed: (i) expression of minigenes harboring the Arg codons CGA, CGU, and CGC, resulted in the accumulation of different levels of the unique peptidyl-tRNAArg-2 and (ii) the toxicity of minigenes containing CUG and UCU codons, each recognized by two different tRNAs, depended on peptidyl-tRNA accumulation of only one of them. Non-toxic, or partly toxic, minigenes prompted higher accumulation levels of peptidyl-tRNA upon deprivation of active RF1, implying that translation termination occurred efficiently. Our data indicate that the nature of the last decoding tRNA is crucial in the rate of peptidyl-tRNA release from the ribosome.

Blotting, Northern↗