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At least 793 records · Page 44Linked to original sources
PubMed2005

Prescribed burning effects on summer elk forage availability in the subalpine zone, Banff National Park, Canada.

The effects of prescribed burning on forage abundance and suitability for elk (Cervus elaphus) during the snow-free season was evaluated in east-central Banff National Park, Canada. Six coniferous forest and mixed shrub-herb plant communities (n=144 plots), and 5223ha of burned (n=131) vegetation <12 years old were sampled using a stratified semi-random design. Sampling units represented various combinations of vegetation, terrain conditions, and stand ages that were derived from digital biophysical data, with plant communities the basic unit of analysis. Burning coniferous forest stands reduced woody biomass, and increased herbaceous forage from 146 to 790 kg/ha. Increases commonly occurred in the percent cover of hairy wild rye (Leymus innovatus (Beal) Pigler) and fireweed (Chamerion angustifolium (L.) Holub.). The herbaceous components of mixed shrub-herb communities increased from 336-747 kg/ha to 517-1104 kg/ha in response to burning (P<0.025, Mann-Whitney U-test). Browse biomass (mostly Salix spp. and Betula nana L.) increased >or=220% (P<or=0.003, Mann-Whitney U-test) from 653 kg/ha in deciduous shrub types. Elk preferences for unburned and burned vegetation-types were assessed as low and moderate, respectively. Potential summer carrying capacity, based on forage availability, increased from eight to 28 elk/100 km2 within burned areas, whereas spring grazing potential rose from 13 to 45 elk/100 km2. Most of the increase (73%) was attributable to changes within burned Engelmann Spruce stands, which composed 58% of the burned area.

Alberta↗
PubMed2006

Mosaic structure of human coronavirus NL63, one thousand years of evolution.

Before the SARS outbreak only two human coronaviruses (HCoV) were known: HCoV-OC43 and HCoV-229E. With the discovery of SARS-CoV in 2003, a third family member was identified. Soon thereafter, we described the fourth human coronavirus (HCoV-NL63), a virus that has spread worldwide and is associated with croup in children. We report here the complete genome sequence of two HCoV-NL63 clinical isolates, designated Amsterdam 57 and Amsterdam 496. The genomes are 27,538 and 27,550 nucleotides long, respectively, and share the same genome organization. We identified two variable regions, one within the 1a and one within the S gene, whereas the 1b and N genes were most conserved. Phylogenetic analysis revealed that HCoV-NL63 genomes have a mosaic structure with multiple recombination sites. Additionally, employing three different algorithms, we assessed the evolutionary rate for the S gene of group Ib coronaviruses to be approximately 3 x 10(-4) substitutions per site per year. Using this evolutionary rate we determined that HCoV-NL63 diverged in the 11th century from its closest relative HCoV-229E.

Algorithms↗
PubMed2005

Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.

The PRECISE database was developed by our laboratory to allow for the systematic study of the ligand interactions common to a set of functionally related enzymes, where an interaction site is defined broadly as any residue(s) that interact with a ligand. During the construction of PRECISE, enzyme chains are extracted from the protein data bank (PDB) and clustered according to functional homology as defined by the enzyme commission (EC) nomenclature system. A sequence representative is chosen from each cluster based on the criterion set forth by the non-redundant PDB set, and pair-wise alignments of each cluster member to the representative are performed. Atom-based residue-ligand interactions are calculated for each cluster member, and the summation of ligand interactions for all cluster members at each aligned position is determined. Although we were able to successfully align most clusters using a simple dynamic programming algorithm, several cluster created exhibited poor pair-wise alignments of each cluster member to its sequence representative. We hypothesized that the observed alignment problems were, in most cases, due to the incorrect separation and alignment of different domains in multi-domain proteins, a mistake that frequently causes error proliferation in functional annotation. Here we present the results of generating primary sequence patterns for each poorly aligned cluster in PRECISE to assess the extent to which multi-domain proteins that are incorrectly aligned contributes to poor pair-wise alignments of each cluster member to its representative. This requires the use of an iterative locally optimal pair-wise alignment algorithm to build a hierarchical similarity-based sequence pattern for a set of functionally related enzymes. Our results show that poor alignments in PRECISE are caused most frequently by the misalignment of multi-domain proteins, and that the generation of primary sequence patterns for the assignment of sequence family membership yields better alignments for the functionally related enzyme clusters in PRECISE than our original alignment algorithm.

Amino Acid Sequence↗
PubMed2003

A genome-wide screen for linkage disequilibrium in Sardinian multiple sclerosis.

Using indirect whole genome association screening, we have searched for multiple sclerosis susceptibility genes in the genetically isolated high risk Sardinian population. Two screens were performed; the first was based on 229 cases and 264 unrelated controls, and the second on 235 trio families. Each screen employed a dense set of microsatellite markers and DNA pooling. Data from both screens were available from 2764 markers. Nine markers showed nominally significant results in both screens independently. Five of these markers-D2S408 (2q36), D6S271 (6p21), D6S344 (6p25), D7S1818 (7p12) and D16S420 (16p12)-remained nominally significant in both studies after conservative refining analysis.

Adult↗
PubMed2006

Differential gene expression in the rat cochlea after exposure to impulse noise.

Understanding the molecular biology of noise trauma is vital to developing effective and timely interventions. In a model of explosion-mediated impulse noise injury, differential gene expression was studied in whole rat cochlea preparations at 3 and 24 h following the exposure. We developed a technique using mRNA from a single cochlea on each oligonucleotide microarray to avoid pooling of mRNA samples. Application of a conservative statistical analysis approach resulted in the identification of 61 differentially expressed genes. Within 3 h after the exposure, there was an up-regulation of immediate early genes, mainly transcription factors and genes involved in the tissue's response to oxidative stress. No genes were found to be significantly down-regulated. At 24 h following the exposure, up-regulated genes included members of inflammatory and antioxidant pathways and one gene involved in glutathione metabolism was down-regulated. A subset of genes was confirmed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The present study demonstrates the power of the microarray technique in providing a global view of the gene regulation following noise exposure, and in identifying genes that may be mechanistically important in hearing loss, and thereby serve as a basis for the development of therapeutic interventions.

Acoustic Stimulation↗
PubMed2006

Expression, purification and biochemical characterization of a single-stranded DNA binding protein from Herbaspirillum seropedicae.

An open reading frame encoding a protein similar in size and sequence to the Escherichia coli single-stranded DNA binding protein (SSB protein) was identified in the Herbaspirillum seropedicae genome. This open reading frame was cloned into the expression plasmid pET14b. The SSB protein from H. seropedicae, named Hs_SSB, was overexpressed in E. coli strain BL21(DE3) and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein. The apparent molecular mass of the native Hs_SSB was estimated by gel filtration, suggesting that the native protein is a tetramer made up of four similar subunits. The purified protein binds to single-stranded DNA (ssDNA) in a similar manner to other SSB proteins. The production of this recombinant protein in good yield opens up the possibility of obtaining its 3D-structure and will help further investigations into DNA metabolism.

Amino Acid Sequence↗
PubMed2004

A multidimensional environmental evaluation of packaging materials.

To reduce environmental damage, the properties of environmental issues must be understood. Most previous research has performed relevant assessment either qualitatively or quantitatively. This paper provides a new comprehensive evaluative framework to integrate these two types of approaches. Three methods are combined: (1) life cycle assessment (LCA), a quantitative method, to assess environmental loading, (2) analytic hierarchy process (AHP), a qualitative method, to obtain opinions from experts, and (3) cluster analysis to integrate the results of the former two methods. This new framework could provide integrated information and avoid a bias towards either qualitative or quantitative approach. To present the process of this new evaluative framework, packaging materials are selected as the case study in this paper.

Beverages↗
PubMed2005

Cloning and comparison of bighorn sheep CD18 with that of domestic sheep, goats, cattle, humans and mice.

Previously, we have shown that CD18, the beta-subunit of beta(2)-integrins, serves as a receptor for leukotoxin (Lkt) secreted by Mannheimia (Pasteurella) haemolytica on bovine leukocytes. Anti-CD18 monoclonal antibodies (mAbs) inhibit Lkt-induced cytolysis of bighorn sheep (Ovis canadensis) leukocytes suggesting that CD18 may serve as a receptor for Lkt on the leukocytes of this species as well. Confirmation of bighorn sheep CD18 as a receptor for Lkt, and elucidation of the enhanced Lkt-susceptibility of bighorn sheep polymorphonuclear leukocytes (PMNs), necessitates the cloning and sequencing of cDNA encoding bighorn sheep CD18. Hence, in this study we cloned and sequenced the cDNA encoding CD18 of bighorn sheep, and compared with that of other animal species. The cDNA of bighorn sheep CD18 has an open reading frame (ORF) of 2310bp. CD18 sequences obtained individually from peripheral blood mononuclear cells (PBMCs) and PMNs were identical to each other. Comparison of the deduced 770-amino acid sequence of CD18 of bighorn sheep with that of domestic sheep, goats, cattle, humans and mice revealed 99, 98, 95, 82 and 80% identity, respectively. Availability of cloned bighorn sheep CD18 cDNA should allow the molecular characterization of M. haemolytica Lkt-receptor interactions in bighorn sheep and other ruminants that are susceptible to this disease.

Amino Acid Sequence↗
PubMed2005

The complete sequence of the bovine torovirus genome.

Viruses in the family Coronaviridae have elicited new interest, with the outbreaks caused by SARS-HCoV in 2003 and the recent discovery of a new human coronavirus, HCoV-NL63. The genus Torovirus, within the family Coronaviridae, is less well characterized, in part because toroviruses cannot yet be grown in cell culture (except for the Berne virus). In this study, we determined the sequence of the complete genome of Breda-1 (BoTV-1), a bovine torovirus. This is the first complete torovirus genome sequence to be reported. BoTV-1 RNA was amplified using long RT-PCR and the amplicons sequenced. The genome has a length of 28.475 kb and consisted mainly of the replicase gene ( approximately 20.2 kb) which contains two large overlapping ORFs, ORF1a and ORF1b, encoding polyproteins pp1a and pp1b, respectively. Sequence analysis identified conserved domains within the predicted sequences of pp1a and pp1b. Sequence alignments and protein secondary structure prediction data suggest the presence of a 3C-like serine protease domain with similarity to the arterivirus 3C-like serine protease and a single papain-like cysteine protease domain with similarity to the picornavirus leader protease. The ADRP (APPR-1'') domain - unique to the Coronaviridae - was also located in BoTV pp1a. In addition, several hydrophobic domains were identified that are typical of a nidovirus replicase. Within the pp1b sequence the polymerase and helicase domains were identified, as well as sequences predicted to be involved in ribosomal frameshifting, including the conserved slippery sequence UUUAAAC and two potential pseudoknot structures.

Amino Acid Sequence↗
PubMed2005

Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6.

On pig chromosome 6, the SW71 microsatellite is located in the region corresponding to several quantitative trait loci (QTL), such as those for intramuscular fat content and for body weight at 4 weeks of age. The genomic sequence of approximately 909 kb was obtained from seven BAC clones encompassing the SW71 region corresponding to human 18q11.21-q11.22. By searching the NCBI GenBank using BLASTX and BLASTN, this 909-kb segment was found to contain eight genes, RAB31, TXNDC2, VAPA, APCDD1, NAPG, FAM38B, C18orf30, and C18orf58, and one putative gene (DN119777). The average G + C content in the sequence of this contig was 45.75% and 33 CpG islands were detected. CpG islands were scattered throughout the region in which most of the putative genes were located. Dense CpG islands of approximately 840 bp were observed, including within the 5' UTR and exon 1 of the orthologs of the RAB31, VAPA, APCDD1, and NAPG genes. Comparative analysis of conserved segments of six species showed that K(a)/K(s) ratios of the TXNDC2 gene in collinear and rearranged segments were significantly different at 4.1 and 1.3, respectively. In conclusion, we demonstrated the genomic organization of pig chromosome 6, including the gene order surrounding SW71, which provides important information for comparative mapping. Moreover, the genes revealed in this study may be positional candidate genes associated with QTL on chromosome 6 that affect fat deposition in pigs.

Adiposity↗
PubMed1999

Improved secondary structure predictions for a nicotinic receptor subunit: incorporation of solvent accessibility and experimental data into a two-dimensional representation.

Abstract A refined prediction of the nicotinic acetylcholine receptor (nAChR) subunits' secondary structure was computed with third-generation algorithms. The four selected programs, PHD, Predator, DSC, and NNSSP, based on different prediction approaches, were applied to each sequence of an alignment of nAChR and 5-HT3 receptor subunits, as well as a larger alignment with related subunit sequences from glycine and GABA receptors. A consensus prediction was computed for the nAChR subunits through a "winner takes all" method. By integrating the probabilities obtained with PHD, DSC, and NNSSP, this prediction was filtered in order to eliminate the singletons and to more precisely establish the structure limits (only 4% of the residues were modified). The final consensus secondary structure includes nine alpha-helices (24.2% of the residues, with an average length of 13.9 residues) and 17 beta-strands (22.5% of the residues, with an average length of 6.6 residues). The large extracellular domain is predicted to be mainly composed of beta-strands, with only two helices at the amino-terminal end. The transmembrane segments are predicted to be in a mixed alpha/beta topology (with a predominance of alpha-helices), with no known equivalent in the current protein database. The cytoplasmic domain is predicted to consist of two well-conserved amphipathic helices joined together by an unfolded stretch of variable length and sequence. In general, the segments predicted to occur in a periodic structure correspond to the more conserved regions, as defined by an analysis of sequence conservation per position performed on 152 superfamily members. The solvent accessibility of each residue was predicted from the multiple alignments with PHDacc. Each segment with more than three exposed residues was assumed to be external to the core protein. Overall, these data constitute an envelope of structural constraints. In a subsequent step, experimental data relative to the extracellular portion of the complete receptor were incorporated into the model. This led to a proposed two-dimensional representation of the secondary structure in which the peptide chain of the extracellular domain winds alternatively between the two interfaces of the subunit. Although this representation is not a tertiary structure and does not lead to predictions of specific beta-beta interaction, it should provide a basic framework for further mutagenesis investigations and for fold recognition (threading) searches.

Algorithms↗
PubMed2006

[Bilateral Chylothorax after delivery: an infrequent case treated with videothoracoscopic talc pleurodesis].

Bilateral chylothorax after delivery is a highly infrequent entity. We present the case of a 28-year-old woman who developed progressive dyspnea due to bilateral milky pleural effusion several months after delivery. The effusion was found to contain chylomicrons in the biochemical analysis. Initial conservative treatment failed twice and the chylothorax was successfully treated through sequential bilateral videothoracoscopy with an interval of 6 days between the two interventions and pleurodesis with spray talc.

Adult↗
PubMed2002

ms1, a novel stress-responsive, muscle-specific gene that is up-regulated in the early stages of pressure overload-induced left ventricular hypertrophy.

We have identified and characterised a cDNA encoding a novel gene, designated myocyte stress 1 (ms1), that is up-regulated within 1 h in the left ventricle following the application of pressure overload by aortic banding in the rat. The deduced ms1 protein of 317 amino acids contains several putative functional motifs, including a region that is evolutionarily conserved. Distribution analysis indicates that rat ms1 mRNA expression is predominantly expressed in striated muscle and progressively increases in the left ventricle from embryo to adulthood. These findings suggest that ms1 may be important in striated muscle biology and the development of pressure-induced left ventricular hypertrophy.

Amino Acid Sequence↗
PubMedDate not supplied

Clinical biochemical parameters of the endangered Catalonian donkey breed: normal values and the influence of sex, age, and management practices effect.

Twelve clinical biochemical parameters were determined in 97 animals of all age groups and both sexes of the endangered Catalonian donkey breed. Significant sex differences were observed for phospholipid concentration (P<0.01). Evaluating the effect of management practices on the various parameters showed significant differences for total bilirubin (P<0.001) and creatinine (P<0.05) concentrations and gamma-glutamyltransferase (P<0.05) activity. Moreover, it was observed that inorganic phosphorus concentration decreased with age (P<0.001), whereas albumin and triglyceride concentrations increased with age (P<0.01 and P<0.001, respectively). Comparison of biochemical ranges obtained for the Catalonian donkey breed with reference ranges for other breeds and populations (Mammoth, USA donkeys, UK donkeys, Indian donkeys and Poitou donkeys), indicated that most values were similar, with the exceptions of enzymatic activities mainly. The results reported in the present study could serve as reference ranges for donkey populations.

Age Factors↗
PubMed2002

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

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

Animals↗
PubMed2002

Isolation and characterization of channel catfish natural resistance associated macrophage protein gene.

Natural resistance associated macrophage protein 1 (Nramp1) affects the ability of macrophages to kill pathogens. We cloned Nramp cDNA of channel catfish to identify potential molecular markers for disease resistance. Three different Nramp transcripts were identified: NrampCa-2912 nucleotides (nt), NrampCb-3245 nt, and NrampCc-3721 nt. At the 5' end, the transcripts have a common 2263 nt sequence containing the open reading frame. The differences are in the 3' untranslated region resulting from alternative splicing and polyadenylation. NrampCc is the predominant form expressed. The deduced 550 amino acid sequence of the channel catfish Nramp (NrampC) has high homology to Nramp from other vertebrates and a predicted conserved structure. The NrampC contains the 12 transmembrane domains, and the consensus transport motif. Post-transcriptional processing is also conserved. Phylogenetic analysis grouped NrampC with other fish Nramps and closer to Nramp2 than to Nramp1 of mammals. However, the catfish transcript does not contain an iron-responsive regulatory-protein binding site, a characteristic of Nramp2, and, like Nramp1, NrampC expression is induced in macrophage-rich tissues after exposure to lipopolysaccharide and in a macrophage cell line when stimulated. Thus NrampC is structurally closer to mammalian Nramp2 but may function similar to Nramp1.

Amino Acid Sequence↗
PubMed1996

Analysis of a cation-transporting ATPase of Plasmodium falciparum.

We have cloned and characterised one gene, PfATPase4 which encodes a P-type ATPase containing all the primary sequence motifs characteristic of this class of transmembrane ion transporters, and also a fragment of a second P. falciparum P-type ATPase pseudogene (PfATPase5). Analysis of conserved domains and motifs of specific ATPases reveals that PfATPase4 is most analogous to Ca2+ ATPases of the endoplasmic reticulum. The PfATPase4 gene gives rise to a transcript of 8 kb shortly after erythrocyte invasion. Although this mRNA is not detected in later stages, the protein detected immunologically at 190 kDa persists throughout and is detected in free merozoites. Immunofluorescence microscopy reveals that the PfATPase4 protein is concentrated in discrete compartments at the periphery of the parasite. Detailed sequence and structural analyses of these and the other P-type ATPases of P. falciparum described previously, reveals that they comprise an unusual family in several respects. Firstly, the large number of non-homologous genes so far characterised reflects the complexities of ionic regulation in the diverse environments encountered by the parasite. Secondly, the plasmodial P-type ATPase family may be classified both at primary sequence and structural levels into two distinct groups-those typical of P-type ATPases (including PfATPase4) and those which are much more divergent. A third complexity is illustrated by the fact that one of the other members [1] here termed PfATPase6, has an even greater similarity to the sarcoplasmic reticulum Ca2+ ATPases than does PfATPase4, which raises questions about the possible functional relationship between these two members.

Adenosine Triphosphatases↗
PubMed1999

Characterization of a cDNA encoding a subtilisin-like serine protease (NC-p65) of Neospora caninum.

The NC-p65 cDNA is the first protease sequence cloned and described for Neospora caninum. The full length cDNA was isolated by 5'- and 3'-rapid amplification of cDNA ends (RACE). NC-p65 was composed of 865 amino acids with a predicted signal sequence, a proposed pro-domain, and an internal region of conserved repeats. Analysis of the deduced amino acid sequence revealed that this protein had homology to the serine proteases of the subtilisin-like superfamily (subtilases) and had a predicted active site made up of the catalytic residues, Asp 253, His 309. and Ser 484. Antibodies to recombinant NC-p65 recognized multiple bands on Neospora lysate immunoblots, but most intensely stained a 65 kDa band. When N. caninum proteins were purified with affinity resins specific for NC-p65 and analyzed for enzyme activity, a single specific band of reaction was observed on gelatin-saturated zymograms.

Amino Acid Sequence↗