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Open reading frames on plus strand genome of duck hepatitis B virus.

Hepadnaviruses have open reading frames of surface, core, polymerase and X protein on the minus strand of the genome. We analyzed a plus strand of duck hepatitis B virus (DHBV) for the presence of open reading frame with a computer program. We found one frame on the area that is complement to 3' end of polymerase gene and 5' end of precore gene. That open reading frame is conserved in three strains of DHBV, and the predicted protein is about 80 amino acids.

Amino Acid Sequence↗

The LYS5 gene of Saccharomyces cerevisiae.

The LYS2 and LYS5 genes of Saccharomyces cerevisiae together encode the 180-kDa alpha-aminoadipate reductase (AAR) in the biosynthetic pathway of lysine. The 4.8-kb LYS2 gene encodes the 155-kDa subunit of AAR. The complete nucleotide (nt) sequence of the 1.1-kb LYS5 gene is presented in this report. It contains a single continuous open reading frame of 816 nt encoding a 272-amino-acid, 30.6-kDa polypeptide.

Aldehyde Oxidoreductases↗

Cloning and genetic organization of the bacteriocin 31 determinant encoded on the Enterococcus faecalis pheromone-responsive conjugative plasmid pYI17.

The conjugative plasmid pYI17 (57.5 kb) isolated from Enterococcus faecalis YI717 confers a pheromone response on the host and encodes the bacteriocin 31 gene. Bacteriocin 31 is active against E. hirae 9790, E. faecium, and Listeria monocytogenes. pYI17 was mapped physically by restriction enzyme analysis and the relational clone method. Deletion mutant and sequence analyses of the EcoRI fragment B cloned from pYl17 revealed that a 1.0-kb fragment contained the bacteriocin gene (bacA) and an immunity gene (bacB). This fragment induced bacteriocin activity in E. faecalis OG1X and E. hirae 9790. The bacA gene is located on the pYI17 physical map between 3.37 and 3.57 kb, and bacB is located between 3.59 kb and 3.87 kb, bacA encodes 67 amino acids, and bacB encodes 94 amino acids. The deduced amino acid sequence of the bacA protein contained a series of hydrophobic residues typical of a signal sequence at its amino terminus. The predicted mature bacA protein (43 amino acids) showed sequence homology with the membrane-active class II bacteriocins of lactic acid bacteria. Analysis of Tn5 insertion mutants and the resulting transcripts indicated that these genes are transcribed as an operon composed of bacA, bacB, and an open reading frame located downstream of bacB designated ORF3.

Amino Acid Sequence↗

Identification and expression of rpo19, a vaccinia virus gene encoding a 19-kilodalton DNA-dependent RNA polymerase subunit.

The vaccinia virus DNA-dependent RNA polymerase subunit gene rpo19 was identified, and its expression was examined at RNA and protein levels. Antibody to the multisubunit RNA polymerase purified from virions reacted with a polypeptide with an apparent Mr of 21,000 that was synthesized in reticulocyte lysates programmed with (i) mRNA from infected cells that was isolated by hybridization to DNA subclones of the viral genomic HindIII A fragment and (ii) mRNA made in vitro by transcription of the viral open reading frame A6R. Polyclonal antiserum, raised to a recombinant protein product of the A6R open reading frame which could encode an 18,996-Da protein with an acidic N terminus, reacted with Mr-21,000 and -22,000 polypeptides that cosedimented with purified RNA polymerase. Internal sequencing of the two polypeptides confirmed that both were encoded by A6R, and the gene was named rpo19 to indicate the predicted molecular mass of the polypeptide in kilodaltons. Immunoblotting and metabolic labeling of infected cell proteins indicated that synthesis of the Mr-21,000 polypeptide started early and continued throughout virus infection, whereas the Mr-22,000 form appeared late following DNA replication. RNA analyses suggested that the rpo19 mRNA was expressed from a dual early/late promoter and that the protein-coding region of the mRNA was directly preceded by a short 5' poly(A) leader, apparently initiated within the TAAATG motif at the beginning of the open reading frame.

Amino Acid Sequence↗

Sequence and transcriptional analysis of the Escherichia coli rnt gene encoding RNase T.

The Escherichia coli rnt gene encoding the enzyme RNase T, which is responsible for the end-turnover of tRNA, was cloned on a 1.5-kilobase DNA fragment. When placed in pUC18 and pUC19 vectors this fragment led to approximately a 40-fold overexpression of RNase T activity. The cloned fragment was sequenced and was found to contain an open reading frame sufficient to encode a protein of 215 amino acids with a molecular weight of 23,521, which is close to the subunit molecular weight of RNase T; the fragment also contains a second incomplete open reading frame with some sequence similarity to RNA helicases. The derived sequence of RNase T showed no similarity to any of the other E. coli exoribonucleases sequenced to date. Primer extension analysis and deletion of part of the upstream region were used to identify the transcription start point and the promoter of the rnt gene. Northern and primer extension analysis revealed that the rnt message also included the second open reading frame, suggesting that rnt is part of an operon.

Amino Acid Sequence↗

Sequence of the open reading frame of the FLO1 gene from Saccharomyces cerevisiae.

The cloned part of the flocculation gene FLO1 of Saccharomyces cerevisiae (Teunissen, A.W.R.H., van den Berg, J.A. and Steensma, H.Y. (1993). Physical localization of the flocculation gene FLO1 on chromosome I of Saccharomyces cerevisiae, Yeast, in press) has been sequenced. The sequence contains a large open reading frame of 2685 bp. The amino acid sequence of the putative protein reveals a serine- and threonine-rich C-terminus (46%), the presence of repeated sequences and a possible secretion signal at the N-terminus. Although the sequence is not complete (we assume the missing fragment consists of repeat units), these data strongly suggest that the protein is located in the cell wall, and thus may be directly involved in the flocculation process.

Amino Acid Sequence↗

A new skatepark: the impact on the local hospital.

BACKGROUND: There has been a resurgence of skateboarding, rollerblading and BMX riding in recent years and in response dedicated skateparks have opened in many cities across the UK. It is acknowledged that these sports are associated with risk of injury and it is recommended that participants wear protective clothing. OBJECTIVE: We aimed to determine if the opening of a skatepark near our hospital had any effect on the number of skatepark related injuries attending the emergency department and to describe the types of injuries sustained. METHODS: All patients attending the emergency department with sports injuries were identified over 24 consecutive weeks. At the end of the 12th week a skatepark opened nearby. Data recorded prospectively included age and sex of subjects, the delay from injury to presenting to hospital, whether or not protective equipment was worn and if first aid was administered before attending hospital. The investigations performed in the emergency department, the diagnosis, treatment received and disposal from the hospital were also recorded. RESULTS: After the skatepark opened there was a significant increase in the number of skatepark related attendances from 7 to 32. Protective clothing was only worn by 9 out of 39 of those with injuries. The commonest injuries were musculoskeletal and the limbs were injured more frequently than the head and trunk. CONCLUSION: We demonstrated a significant increase in the number of skatepark related injuries attending the emergency department following the opening of a nearby skatepark.

Adolescent↗

The clients' perspective on change during treatment for an alcohol problem: qualitative analysis of follow-up interviews in the UK Alcohol Treatment Trial.

AIM: To develop a model of change during and following professional treatment for drinking problems, grounded in clients' accounts. PARTICIPANTS: Subsets of consecutively selected clients of the UK Alcohol Treatment Trial (UKATT), followed-up at 3 months (n = 211) and 12 months (n = 198) after randomization. Location Five statutory and non-statutory alcohol problems treatment agencies in three areas of England and Wales. Data Open-ended interviews conducted according to a brief interview guide, leading to 400-800-word post-interview reports used for analysis (tape-recordings used for auditing purposes). ANALYSIS: Reports analysed by a team according to grounded theory principles, involving an iterative process with successive refinement of interviewing and analysis with each successive batch of data. FINDINGS: A model of change from the clients' perspective was developed. Treatment was seen by clients as facilitating various changes in ways of thinking and/or increased support of various kinds from family and friends, along with new ways of acting in relation to drinking or more generally. For many those changes had led to an appreciation of the benefits accruing to them. Treatment was seen as part of a broader treatment system which included pretreatment assessment, forms of help additional to the trial treatment, plus an element of self-directed change during and following treatment. Taken with awareness of worsening alcohol-related harms, triggering events and external influence to seek treatment (the catalyst system), to which clients continued to refer following treatment, the change process is depicted as a complex, ongoing set of systems in which a trial treatment is embedded. CONCLUSIONS: Models of change should be broadened so that treatment is seen as a complex system of parts, facilitating a nexus of cognitive, social and behavioural changes, embedded within a broader system of events and processes catalysing change. Such a model helps explain the relative absence of between-treatments outcome differences in UKATT and in the alcohol problems treatment and more general psychotherapy research literatures.

Adaptation, Psychological↗

Characterization of the left 4 kb of conjugative transposon Tn916: determinants involved in excision.

The rate-limiting step in movement of the conjugative transposon Tn916, originally identified in Enterococcus faecalis, is believed to be an excision event that generates a non-replicative circular intermediate. When present on a plasmid vector in Escherichia coli, Tn916 generally excises at a high frequency. It was reported previously that insertion of Tn5 in a region near the left end of Tn916 eliminated the ability to excise; and the mutation could be complemented in trans. In this communication the nucleotide sequence of 4 kb of Tn916 DNA connecting the recently sequenced tet(M) determinant (Su et al., 1992; Burdett, 1990) with the left end of the transposon. Ten open reading frames (ORFs) were deduced, two of which (ORF3 and ORF4) were encoded in-frame within a third (ORF2). Mutants with Tn5 insertions in the ORF1 or ORF2 (ORF3 and ORF4) were defective in excision, but could be complemented in vivo by a co-resident plasmid containing the ORF1 or ORF2 determinant, respectively. The data support the view that both ORF1 and ORF2 are essential for excision. ORF1 and ORF2 are essentially identical to determinants designated xis-Tn and int-Tn, respectively, in the closely related Tn1545. A Tn5 insertion in ORF5 eliminated conjugative transfer between E. faecalis strains. Functions for the remaining ORFs (ORF6 through ORF10) remain unknown; however, nucleotide sequences within ORF6 and ORF9 had significant homology with sequence downstream of other tet(M) determinants.

Amino Acid Sequence↗

Identification and characterisation of a cDNA sequence encoding a glutamic acid-rich protein specifically transcribed in Trichinella spiralis newborn larvae and recognised by infected swine serum.

Presently, little is known of the mechanism by which Trichinella penetrates and modulates reprogramming of muscle cells. In light of evidence demonstrating strong protective characteristics of antigens derived from this stage, understanding this process may shed light on potential targets for effective abatement of infection. To this end, a PCR-derived cDNA expression library was constructed using 0.5 micro g of total RNA from Trichinella spiralis newborn larvae. The library consisted of >125000 insert-containing clones. Approximately 40-50 x 10(3) clones were screened immunologically using sera from pigs experimentally infected with 7000 Trichinella L1. Multiple clones reacting positively with the swine infection serum and encoding portions of a glutamic acid-rich protein were identified. Northern and Southern blots indicated at least two distinct genes that encoded the glutamic acid-rich proteins and that these genes were transcribed specifically in the newborn larvae stage. cDNA sequence data predicted open reading frames of 1497 and 1,716 bp generating proteins of 498 amino acids and 571 amino acids, respectively. Both sequences consisted of approximately 39% glutamic acid and 16% serine residues, and differed by the presence of a 219 bp fragment present in the 1716 bp sequence that was absent from the 1497 bp sequence. PCR data indicated that additional isoforms exist within this gene family that are different in length from those described above. In addition, it was found that more than one isoform can exist within a single worm and that this pattern can vary between individual worms within a population. Mouse antibodies to recombinant antigen localised the glutamic acid-rich proteins to the periphery of the developing stichocyte cells within the newborn larvae consistent with the hypothesis that the newborn larval antigens are secreted.

Amino Acid Sequence↗

Is more choice always desirable? Evidence and arguments from leks, food selection, and environmental enrichment.

Recent studies on humans show that too much choice can make subjects less likely to choose any item. I consider general adaptive and non-adaptive explanations of why such choice aversion, or its converse, might occur in animals. There are three questions: is more choice always preferred, does it ever lead to less consumption (or a lower probability of consumption), and may it result in worse items being selected ? A preference for choice is one of the main explanations for lek formation and I draw attention to previously unrecognised parallels with models of human shopping behaviour. There is indeed evidence of female preference for larger leks, although much of the observational data are open to other interpretations. Unfortunately nobody has looked for choice aversion where it is most to be expected, in leks larger than normally occur. Evidence that too much choice of males confuses females is strongest in acoustically advertising frogs, but the widespread decrease of mating skew in larger leks might also have this explanation. A model reanalyses data on skew in black grouse Tetrao tetrix and suggests that considering only a random subset of a large lek may increase the chances of selecting the better males: larger leks are more likely to include better males, but these are less likely to be selected. These opposing effects may lead to an optimum lek size, but only with a sufficient decline in choice accuracy with size. With food choice, very few studies have avoided confounding choice with food quality, by manipulating only flavour. The widespread phenomena of stimulus-specific satiety and novelty seeking imply that monotonous diets are aversive, but no studies test whether animals choose sites where they know food diversity to be greater. Operant experiments that demonstrate mild preferences for free choice concern choice about the means to get food rather than the food itself. In some insect species even moderate choice of diet can be deleterious, and studies on search images and the confusion effect may be evidence of this in vertebrates. Environmental enrichment of captive animals often relies on increasing the options available, but it need not be the choice itself that is beneficial. I consider briefly further areas in biology where choice preference or aversion are potentially important.

Adaptation, Biological↗

Identification and mapping of a chromosomal gene cluster of Borrelia burgdorferi containing genes expressed in vivo.

A clone containing a 6.4 kb Borrelia burgdorferi chromosomal DNA insert reacted only with sera from patients with Lyme disease and not with any normal human or rabbit sera. Restriction enzyme analysis indicated that this DNA fragment was located on the B. burgdorferi chromosomal map between rpoB and p22A; its direction of transcription was towards p22A. Sequence analysis suggests that LA006 encodes six proteins: three previously described immunodominant lipoproteins of the 39 kDa Bmp protein family, BmpA, BmpB and BmpC; a 51 kDa MgtE magnesium transporter protein; a 16 kDa protein kinase C inhibitor; and a 56 kDa protein with similarity to an uncharacterized Escherichia coli chromosomal open reading frame.

Amino Acid Sequence↗

Acoustic scattering by benthic and planktonic shelled animals.

Acoustic backscattering measurements and associated scattering modeling were recently conducted on a type of benthic shelled animal that has a spiral form of shell (Littorina littorea). Benthic and planktonic shelled animals with this shape occur on the seafloor and in the water column, respectively, and can be a significant source of acoustic scattering in the ocean. Modeling of the scattering properties allows reverberation predictions to be made for sonar performance predictions as well as for detection and classification of animals for biological and ecological applications. The studies involved measurements over the frequency range 24 kHz to 1 MHz and all angles of orientation in as small as 1 degree increments. This substantial data set is quite revealing of the physics of the acoustic scattering by these complex shelled bodies and served as a basis for the modeling. Specifically, the resonance structure of the scattering was strongly dependent upon angle of orientation and could be traced to various types of rays (e.g., subsonic Lamb waves and rays entering the opercular opening). The data are analyzed in both the frequency and time domain (compressed pulse processing) so that dominant scattering mechanisms could be identified. Given the complexity of the animal body (irregular elastic shell with discontinuities), approximate scattering models are used with only the dominant scattering properties retained. Two models are applied to the data, both approximating the body as a deformed sphere: (1) an averaged form of the exact modal-series-based solution for the spherical shell, which is used to estimate the backscattering by a deformed shell averaged over all angles of orientation, and produces reasonably accurate predictions over all k1a(esr) (k1 is the acoustic wave number of the surrounding water and a(esr) is the equivalent spherical radius of the body), and (2) a ray-based formula which is used to estimate the scattering at fixed angle of orientation, but only for high k1a(esr). The ray-based model is an extension of a model recently developed for the shelled zooplankton Limacina retroversa that has a shape similar to that of the Littorina littorea but swims through the water [Stanton et al., J. Acoust. Soc. Am. 103, 236-253 (1998b)]. Applications of remote detection and classification of the seafloor and water column in the presence of shelled animals are discussed.

Acoustics↗

Analysis of a region from the bacteriophage resistance plasmid pCI528 involved in its conjugative mobilization between Lactococcus strains.

A 10-kb HindIII fragment of pCI528 cloned into the nonconjugative shuttle vector pCI3340 could be transferred by conjugative mobilization from Lactococcus lactis subsp. lactis MG1363, whereas other HindIII fragments of pCI528 or the vector alone were nonmobilizable. Subcloning of this 10-kb region identified a 4.4-kb BglII-EcoRI fragment which contained all the DNA essential for transfer. Sequence analysis of a 2-kb region within this 4.4 kb-segment revealed a region rich in inverted repeats and two potential overlapping open reading frames, one of which demonstrated homology to mobilization proteins of two nonconjugative staphylococcal plasmids.

Amino Acid Sequence↗

[Sequence and structure analysis of cryptic plasmid pN30 from oil-oxidizing strain Rhodococcus erythropolis 30].

Nucleotide sequence of cryptic plasmid pN30 from a Rhodococcus erythropolis 30 soil isolate was determined. Plasmid DNA consists of 5403 nucleotide pairs and contains about 62% GC pairs, which is typical of Rhodococcus DNA. No significant homology was determined between the pN30 DNA sequence and those of known plasmids. Computer-aided analysis of pN30 sequence revealed open reading frames that encode proteins strongly homologous to replicative proteins encoded by small cryptic plasmids of different actinomycetes.

Amino Acid Sequence↗

Identification of a T4 gene required for bacteriophage mRNA processing.

A ribonucleolytic activity that cleaves within the Shine/Dalgarno sequences of the bacteriophage T4 motA and ORF2 mRNAs was recently described. We have identified additional sites of processing within several other ribosome binding sites, including two sites in the polycistronic frd transcript. Deletion mutants (farP) that overproduce the product of frd are defective in this mRNA processing. The mutants were used to identify processing events dependent on the T4 activity including attack at nuclease-sensitive sites within the coding sequences of some genes and within the intercistronic region 5' of gene 43. All known processing sites lie within similar sequences. Another mutant in mRNA processing carries a point mutation in one of the open reading frames (orf61.9) removed by the farP deletions. Introduction of a cloned copy of this open reading frame into a unique site in the chromosome of farP phage is sufficient to restore mRNA processing capability. The open reading frame probably encodes the T4 regB protein.

Base Sequence↗

Isolation of a yeast tropomyosin-related cDNA clone that encodes a novel transmembrane protein having a C-terminal highly basic region.

A novel cDNA clone was isolated from a yeast Saccharomyces cerevisiae lambda gt11 cDNA library using rabbit anti-rat tropomyosin (TM30nm) polyclonal antibody (RTM8-2). It consists of an open reading frame of 951 bp, encoding 317 amino acid residues. The putative sequence recognized by RTM8-2 was present in Asn-235 to Thr-250. The deduced amino acid sequence and hydropathy plot suggested that this protein has a tropomyosin-homologous sequence, a predicted transmembrane, and a C-terminal basic region. A search of the data bases (EMBL and GenBank) revealed that the 128bp sequence in the 3' untranslated region (3'UTR) is almost identical (96.9%) to the human cDNA clone 54E05 sequence (EMBL accession number Z15978).

Amino Acid Sequence↗