Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Conservation analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources
PubMed1999

The fission yeast rpa17+ gene encodes a functional homolog of AC19, a subunit of RNA polymerases I and III of Saccharomyces cerevisiae.

Eukaryotic RNA polymerases I and III consist of multiple subunits. Each of these enzymes includes two distinct and evolutionarily conserved subunits called alpha-related subunits which are shared only by polymerases I and III. The alpha-related subunits show limited homology with the alpha-subunit of prokaryotic RNA polymerase. To gain further insight into the structure and function of alpha-related subunits, we cloned and characterized a gene from Schizosaccharomyces pombe that encodes a protein of 17 kDa which can functionally replace AC19 - an alpha-related subunit of RNA polymerases I and III of Saccharomyces cerevisiae - and was thus named rpa17+. RPA17 has 125 amino acids and shows 63% identity to AC19 over a 108-residue stretch, whereas the N-terminal regions of the two proteins are highly divergent. Disruption of rpa17+ shows that the gene is essential for cell growth. Sequence comparison with other alpha-related subunits from different species showed that RPA17 contains an 81-amino acid block that is evolutionarily conserved. Deletion analysis of the N- and C-terminal regions of RPA17 and AC19 confirms that the 81-amino acid block is important for the function of the alpha-related subunits.

Amino Acid Sequence↗
PubMed2005

Predation regulation of sedimentary faunal structure: potential effects of a fishery-induced switch in predators in a Newfoundland sub-Arctic fjord.

The collapse of the cod fishery in Newfoundland has coincided with marked increases in abundances of snow crab, pandalid shrimp, and other crustaceans that prey on sedimentary infauna. A 3-year sampling program in Bonne Bay, Newfoundland indicates differences in composition and number of these predators in the two main arms of the fjord that coincide with strong differences in benthic community structure. To test whether predation pressure contributes to the observed patterns in sedimentary fauna, exclusion field experiments with full and partial cages were deployed in both arms at 30-m depth and sampled along with ambient sediments at 0-, 4-, and 8-week periods. Predation significantly influenced species composition, abundance and, in some cases, diversity. The most striking changes included increases in the polychaetes Phöloe tecta and Ophelina cylindricaudata in exclusions relative to controls, and concurrent declines in the polychaete Paradoneis lyra and the cumacean Lamphros fuscata. In laboratory experiments, fresh non-disturbed sediment cores from each experimental area were either protected or exposed to snow crab, the most abundant predator in the bay. A snow crab inclusion experiment was also carried out in the field, using cages similar to those used for exclusions. Despite differences in sedimentary faunas in the two arms, both types of experiments detected a predator effect that was very similar to that documented in exclusion experiments. Thus, despite differences in the scales associated with each type of manipulation, our results suggest that crab predation is a significant structuring force in Newfoundland sedimentary communities. Given the historical changes that have occurred in predator composition as a result of cod over-fishing, we hypothesize that broad-scale community changes may be taking place in North Atlantic benthic ecosystems.

Analysis of Variance↗
PubMed2005

Genetic structure of an endangered Portuguese semiferal pony breed, the Garrano.

The present study intends to survey the genetic variability of an endangered semiferal Portuguese native pony breed, the Garrano. Thirteen microsatellite markers were examined in 277 animals born in 1998, belonging to eight subpopulations corresponding to eight northern Portuguese geographic regions. Mean heterozygosity (H(o)) in the Garrano breed was 0.732, ranging from 0.531 to 0.857 across subpopulations. Allelic frequencies and diversity differed significantly between regions, suggesting the existence of genetic differentiation within the breed confirmed by the population differentiation estimator F(ST). Allele sharing genetic distance (Dps) was used to determine the relationship between the analyzed subpopulations, some of which are diverging significantly from the others. Relationships among six Iberian horse breeds (including the Garrano) were assessed through the restricted maximum likelihood method, which clusters the Garrano with another Celtic pony, the Spanish Asturcon, traditionally bred in geographical continuity with the Garrano. Results reveal a statistically significant deficit of heterozygotes within the Garrano breed (F(IT) = 0.031, p < 0.05). Regular monitoring should therefore be implemented so that the effect of genetic drift within subpopulations, enhanced by inbreeding, may be successfully minimized.

Alleles↗
PubMed1990

Subunit delta of H(+)-ATPases: at the interface between proton flow and ATP synthesis.

The ATP synthases in photophosphorylation and respiration are of the F-type with a membrane-bound proton channel, F0, and an extrinsic catalytic portion, F1. The properties of one particular subunit, delta (in chloroplasts and Escherichia coli) and OSCP (in mitochondria), are reviewed and the role of this subunit at the interface between F0 and F1 is discussed. Delta and OSCP from the three sources have in common the molecular mass (approximately 20 kDa), an elongated shape (axial ratio in solution about 3:1), one high-affinity binding site to F1 (Kd approximately 100 nM) plus probably one or two further low-affinity sites. When isolated delta is added to CF1-depleted thylakoid membranes, it can block proton flow through exposed CF0 channels, as do CF1 or CF1(-delta)+ delta. This identifies delta as part of the proton conductor or, alternatively, conformational energy transducer between F0 (proton flow) and F1 (ATP). Hybrid constructs as CF1(-delta)+ E. coli delta and EF1(-delta)+ chloroplast delta diminish proton flow through CF0.CF1(-delta) + E. coli delta does the same on EF0. Impairment of proton leaks either through CF0 or through EF0 causes "structural reconstitution' of ATP synthesis by remaining intact F0F1. Functional reconstitution (ATP synthesis by fully reconstructed F0F1), however, is absolutely dependent on the presence of subunit delta and is therefore observed only with CF1 or CF1(-delta) + chloroplast delta on CF0 and EF1 or EF1(-delta) + E. coli delta on EF0. The effect of hybrid constructs on F0 channels is surprising in view of the limited sequence homology between chloroplast and E. coli delta (36% conserved residues including conservative replacements). An analysis of the distribution of the conserved residues at present does not allow us to discriminate between the postulated conformational or proton-conductive roles of subunit delta.

Adenosine Triphosphatases↗
PubMed1992

Schistosoma mansoni: cloning of a complementary DNA encoding a cytosolic Cu/Zn superoxide dismutase and high-yield expression of the enzymatically active gene product in Escherichia coli.

We recently purified a 16-kDa cytosolic Cu/Zn superoxide dismutase (CT Cu/Zn-SOD) from Schistosoma mansoni, a human parasite. Three peptide sequences were obtained, one from the unblocked N-terminal and two from internal peptides which were generated by digestions with trypsin and cyanogen bromide. These sequences were aligned to the corresponding sequences of 19 cytosolic Cu/Zn-SODs from various species. Degenerate oligonucleotides were then designed according to the sequence and the position of each peptide. The oligonucleotides were used to amplify a complete cDNA using the polymerase chain reaction with either adult schistosome total RNA or a cercariae lambda gt11 phage cDNA library as the template. The protein encoded by the cDNA has 153 amino acids with a calculated molecular weight of 15,693. It also has 60-65% homology to 19 cytosolic Cu/Zn-SOD from various species. All of the copper/zinc binding sites and SOD activity sites are conserved. Computer analysis predicts that the Cu/Zn-SOD has a pI value of 6.6, which is very close to the experimental results of IEF analysis (6.0 and 6.3). The entire coding sequence from the cDNA was cloned into a bacterial alkaline phosphatase cytosolic expression vector and a large amount of soluble product was expressed and purified to homogeneity. We compared the bacterially expressed Cu/Zn-SOD with the native enzyme derived from schistosomes and found that they are identical by the following criteria: (1) They focus at the same positions on IEF gels; (2) they form dimers in solution as measured by gel filtration; (3) they have the same unblocked N-terminal sequence; (4) they both are enzymatically active with comparable specific activities. The specific activity of the bacterially derived enzyme was increased somewhat (approximately 10%) by incubation with copper and zinc ions.

Amino Acid Sequence↗
PubMed1992

Anatomy and evolution of proteins displaying the viral capsid jellyroll topology.

In this paper the anatomy of 25 structures containing a jellyroll motif, consisting of eight antiparallel beta-strands forming a so-called beta-barrel, was investigated. This involved performing a careful structural alignment based on hydrogen bonds for the equivalent regions of the tertiary folds and a subsequent analysis of conserved amino acids, equivalenced residue-residue contacts, and various parameters describing the size, shape and other geometrical characteristics of these regions. It was found that the jellyroll motif is best viewed as a two-sheet wedge structure rather than a barrel. The more conserved parameters are discussed. A model of evolutionary development for the jellyroll fold in the various protein and viral structures is proposed.

Amino Acid Sequence↗
PubMed1992

Structure determination and analysis of yeast iso-2-cytochrome c and a composite mutant protein.

As part of a study of protein folding and stability, the three-dimensional structures of yeast iso-2-cytochrome c and a composite protein (B-2036) composed of primary sequences of both iso-1 and iso-2-cytochromes c have been solved to 1.9 A and 1.95 A resolutions, respectively, using X-ray diffraction techniques. The sequences of iso-1 and iso-2-cytochrome c share approximately 84% identity and the B-2036 composite protein has residues 15 to 63 from iso-2-cytochrome c with the rest being derived form the iso-1 protein. Comparison of these structures reveals that amino acid substitutions result in alterations in the details of intramolecular interactions. Specifically, the substitution Leu98Met results in the filling of an internal cavity present in iso-1-cytochrome c. Further substitutions of Val20Ile and Cys102Ala alter the packing of secondary structure elements in the iso-2 protein. Blending the isozymic amino acid sequences in this latter area results in the expansion of the volume of an internal cavity in the B-2036 structure to relieve a steric clash between Ile20 and Cys102. Modification of hydrogen bonding and protein packing without disrupting the protein fold is illustrated by the His26Asn and Asn63Ser substitutions between iso-1 and iso-2-cytochromes c. Alternatively, a change in main-chain fold is observed at Gly37 apparently due to a remote amino acid substitution. Further structural changes occur at Phe82 and the amino terminus where a four residue extension is present in yeast iso-2-cytochrome c. An additional comparison with all other eukaryotic cytochrome c structures determined to date is presented, along with an analysis of conserved water molecules. Also determined are the midpoint reduction potentials of iso-2 and B-2036 cytochromes c using direct electrochemistry. The values obtained are 286 and 288 mV, respectively, indicating that the amino acid substitutions present have had only a small impact on the heme reduction potential in comparison to iso-1-cytochrome c, which has a reduction potential of 290 mV.

Amino Acid Sequence↗
PubMed1991

Duct carcinoma in situ of the breast: an analysis of local control after conservation surgery and radiotherapy.

Patients with duct carcinoma-in-situ are being treated with increasing frequency at our center. Between 1977 and 1988, 54 patients, including one with bilateral disease, opted for breast conserving surgery and radiation therapy. The median follow-up was 3 years (range 2-13 years). During this period, 10 patients (18%) had a recurrence in the breast; the local failure probability was 22% at 6 years (Kaplan-Meier). All patients had pre-biopsy mammograms, and in 67% this was the presenting abnormality. Thirty-three lesions (60%) required needle localization. Size, as determined by mammogram or pathology, was 2 cm or less in 60%, 2.1 to 4 cm. in 2%, and not measurable in the remainder. Close or involved margins were noted in 30% of patients who locally recurred, despite the fact that 50% had had a re-excision after their initial biopsy. Breasts which maintained local control had only 4% involved margins and re-excision was performed in only 20%. Radiation doses ranged from 4600 to 5200 cGy to the entire breast with tangential fields, followed by a boost dose in 73% of patients. No patient in the study has developed distant metastasis or died of breast carcinoma, but the local failure rate is of concern and has alerted our group to reexamine its treatment policy in patients with evidence of margin involvement. We continue to consider residual microcalcifications after surgery to be a contraindication to breast conservation.

Adult↗
PubMed1992

Cloning and sequencing of the alcohol oxidase-encoding gene (AOD1) from the formaldehyde-producing asporogeneous methylotrophic yeast, Candida boidinii S2.

Alcohol oxidase (AOD) is the first key enzyme for methanol metabolism in methylotrophic yeasts. AOD activity is strictly regulated by carbon source. The AOD1 gene was cloned from a gene library of the asporogenous formaldehyde-producing methylotrophic yeast, Candida boidinii S2. The complete nucleotide sequence of the gene and its 5'- and 3'-flanking regions (4174 bp) were determined. To identify the conserved and divergent sequences of the AOD1 gene and its 5'-flanking sequences among different species of methylotrophic yeasts, the AOD-encoding genes from C. boidinii S2 (AOD1), Hansenula polymorpha (MOX) and Pichia pastoris (AOX1 and AOX2) were compared. In addition to conserved amino acid sequences, several DNA segments in the G+C-rich region of 5'-flanking sequences were also found to be conserved. Northern analysis showed that the AOD1 gene transcript was induced by methanol, but was not detected when cells were grown on ethanol or glucose. Thus, as in ascosporogenous methylotrophic yeasts, AOD1 gene expression in C. boidinii appears to be controlled at the RNA level.

Alcohol Oxidoreductases↗
PubMed2006

Generation of a homology model for the human cytochrome P450, CYP24A1, and the testing of putative substrate binding residues by site-directed mutagenesis and enzyme activity studies.

A systematic analysis of conserved H-bonding patterns and tertiary structural motifs from 13 crystal structures was used to create a homology model for the human multicatalytic cytochrome P450, CYP24A1, involved in catabolism of 1alpha,25-dihydroxyvitamin D3. The substrate was docked in the active site and used to identify potential substrate contact residues in the B' helix, B'/C loop, F-helix and the beta-5 hairpin. Seven CYP24A1 mutants were created and studied by mammalian cell transfection and CYP24A1 activity assay. Mutants showed reduced metabolic rates and altered metabolite patterns compared to wild-type. We conclude that: Ile-131 positions substrate via A-ring and cis-triene contacts; Trp-134 and Gly-499 are determinants of substrate access; Leu-148 contacts the substrate side-chain; Met-246 is important in mediating regioselectivity. Our findings validate the new model of CYP24A1, which can now be used to predict structural modifications for rational vitamin D drug design.

Amino Acid Substitution↗
PubMed2004

Characterisation of 11 beta-hydroxysteroid dehydrogenases in feline kidney and liver.

11 Beta-hydroxysteroid dehydrogenases type 1 and 2 (11 beta-HSD1 and 11 beta-HSD2) are microsomal enzymes responsible for the interconversion of cortisol into the inactive form cortisone and vice versa. 11 beta-HSD1 is mainly present in the liver, and has predominantly reductase activity although its function has not yet been elucidated. 11 beta-HSD2, present in mineralocorticoid target tissues such as the kidney, converts cortisol into cortisone. Reduced activity due to inhibition or mutations of 11 beta-HSD2 leads to hypertension and hypokalemia resulting in the Apparent Mineralocorticoid Excess Syndrome (AMES). Like humans, cats are highly susceptible for hypertension. As large species differences exist with respect to the kinetic parameters (K(m) and V(max)) and amino acid sequences of both enzymes, we determined these characteristics in the cat. Both enzyme types were found in the kidneys. 11 beta-HSD1 in the feline kidney showed bidirectional activity with predominantly dehydrogenase activity (dehydrogenase: K(m) 1959+/-797 nM, V(max) 766+/-88 pmol/mg*min; reductase: K(m) 778+/-136 nM, V(max) 112+/-4 pmol/mg*min). 11 beta-HSD2 represents a unidirectional dehydrogenase with a higher substrate affinity (K(m) 184+/-24 nM, V(max) 74+/-3 pmol/mg*min). In the liver, only 11 beta-HSD1 is detected exerting reductase activity (K(m) 10462 nM, V(max) 840 pmol/mg*min). Sequence analysis of conserved parts of 11 beta-HSD1 and 11 beta-HSD2 revealed the highest homology of the feline enzymes with the correspondent enzymes found in man. This suggests that the cat may serve as a suitable model species for studies directed to the pathogenesis and treatment of human diseases like AMES and hypertension.

11-beta-Hydroxysteroid Dehydrogenase Type 1↗
PubMed2004

LEPREL1, a novel ER and Golgi resident member of the Leprecan family.

We have identified a novel protein, Leprecan-like 1 (LEPREL1), with profound similarity to the Leprecan family of proteoglycans. The genomic organization of the Leprecan gene family was found to be highly conserved. Expression analysis shows that LEPREL1 is expressed in most tissues as a 3.4 kb transcript encoding an 80 kDa protein. A LEPREL1 specific antibody stains many cell types including adipocytes and neuroendocrine cells of the gastrointestinal epithelium. Muscle tissue contains a specific 6.5 kb transcript and a 200 kDa protein. The 3.4 kb LEPREL1 transcript encodes a 708 amino acid protein containing a signal sequence, four tetratricopeptide repeats (TPRs), a leucine zipper, a P-loop, a prolyl 4-hydroxylase alpha domain (P4Halpha), and a C-terminal KDEL ER-retention motif. LEPREL1 is localized to the ER and Golgi network and over-expressing it affects normal protein disulfide isomerase staining patterns in the ER.

Amino Acid Sequence↗
PubMed2005

High-level expression and characterization of two chitinases, ChiCH and ChiCW, of Bacillus cereus 28-9 in Escherichia coli.

Many chitinase genes have been cloned and sequenced from prokaryotes and eukaryotes but overexpression of chitinases in Escherichia coli cells was less reported. ChiCH and ChiCW of Bacillus cereus 28-9 belong to two distinct groups based on their amino acid sequences of catalytic domains, and in addition, domain structures of two enzymes are different. In this study, we established an ideal method for high-level expression of chitinases in E. coli as glutathione-S-transferase fusion proteins using pGEX-6P-1 vector. Both ChiCH and ChiCW were successfully highly expressed in E. coli cells as soluble GST-chitinase fusion proteins, and recombinant native ChiCH and ChiCW could be purified after cleavage with PreScission protease to remove GST tag. Purified chitinases were used for biochemical characterization of kinetics, hydrolysis products, and binding activities. The results indicate that ChiCW is an endo-chitinase and effectively hydrolyzes chitin and chito-multimers to chito-oligomers and the end product chitobiose, and ChiCH is an exo-chitinase and degrades chito-oligomers to produce chitobiose. Furthermore, due to higher affinity of ChiCW toward colloidal chitin than Avicel, C-terminal domain of ChiCW should be classified as a chitin-binding domain not a cellulose-binding domain although that was revealed as a cellulose-binding domain by conserved domain analysis. Therefore, the method of high-level expression of chitinases is helpful to studies and applications of chitinases.

Bacillus cereus↗
PubMed2006

How reliable is the structural prediction of IgE-binding epitopes of allergens? The case study of plant lipid transfer proteins.

The linear IgE-binding epitopes of non-specific lipid transfer proteins (nsLTP) from plants were predicted using a combination of predictive tools including (1) the hydropathic profiles based on different scales of hydrophilicity, flexibility and exposure to the solvent, (2) the hydrophobic cluster analysis plots, (3) the occurrence of charged residues in the predicted amino acid sequence stretches and, (4) the exposition of the predicted linear IgE-binding epitopes checked on the three-dimensional models built for the nsLTP. A reliable prediction was obtained for nsLTP as compared with the previously characterized IgE-binding epitopes of various proteins. A consensual IgE-binding epitope occurring in other plant nsLTP and responsible for some IgE-binding cross-reactivity among fruit nsLTP has been identified and characterized. Despite some discrepancies, a fairly good prediction resulted in applying our combination of predictive methods to longer nsLTP or plant profilins.

Amino Acid Sequence↗
PubMed2006

Morbidity, mortality, and long-term survival after sleeve lobectomy for non-small cell lung cancer.

OBJECTIVE: Sleeve lobectomy is a widely accepted procedure for central tumors for which the alternative is pneumonectomy. The purpose of this study is to assess operative mortality, morbidity, and long-term results of sleeve lobectomies performed for non-small cell lung carcinoma (NSCLC). METHODS: A retrospective review of 218 patients who underwent sleeve lobectomy for NSCLC between 1981 and 2005 was undertaken. There were 186 (85%) men and 32 women with a mean age of 61.9 years (range, 19-82 years). Eighty patients (36.6%) had a preoperative contraindication to pneumonectomy. Right upper lobectomy was the most common operation (45.4%). Vascular sleeve resection was performed in 28 patients (12.8%) and was commonly associated with left upper lobectomy (n=20; 9.1%; p=0.0001). The histologic type was predominantly squamous cell carcinoma (n=164; 75%), followed by adenocarcinoma (n=46; 21%). Resection was incomplete in nine (4.1%) patients. RESULTS: There were nine operative deaths; the operative mortality and the morbidity rates were 4.1% and 22.9%, respectively. A total of 14 (6.4%) patients presented with bronchial anastomotic complications: two were fatal postoperatively, seven patients required reoperation, three required a stent insertion, and two were managed conservatively. Multivariate analysis showed that compromised patients (p=0.001), current smoking (p=0.01), right sided resections (p=0.003), bilobectomy (p=0.03), squamous cell carcinoma (p=0.03), and presence of N1 or N2 disease (p=0.01) were risk factors for mortality and morbidity. Follow-up was complete in 208 patients (95.4%). Overall 5-year and 10-year survival rates were 53% and 28.6%, respectively. After complete resection, recurrence was local in 10 patients, mediastinal in 20, and distant in 25. By multivariate analysis, two factors significantly and independently influenced survival: nodal status (N0-N1 vs N2; p=0.01) and the stage of the lung cancer (stage I-II vs III, p=0.02). CONCLUSIONS: For patients with NSCLC, sleeve lobectomy achieves local tumor control, even in patients with preoperative contraindication to pneumonectomy and is associated with low mortality and bronchial anastomotic complication rates. Postoperative complications are higher in compromised patients, smokers, N disease, right sided resections, bilobectomies, and squamous cell cancers. The presence of N2 disease and stage III significantly worsen the prognosis.

Adult↗
PubMed2004

The "Sym'Previus" software, a tool to support decisions to the foodstuff safety.

Describing the Sym'Previus project, the software and its deliverable facilities is the aim of this present paper. This software concerns all the partners of the food industry who are involved in the management of food safety and allows food-borne pathogen behaviour in food to be predicted, as function of the environment (nature of the food, manufacturing process, conditions of conservation). This analysis of microbial behaviour has been possible thanks to the progress made in predictive microbiology since the 1980s. Sym'Previus offers to food industry professionals and their partners the possibility of applying this progress, by giving access to a database, to simulation systems and expertise.

Computer Simulation↗
PubMed2005

Analysis of local perspectives on sustainable forest management: an Indonesian case studyThis study was funded through a collaborative project between the University of Illinois and the Center for International Forestry Research (CIFOR). The ideas contained herein are solely of the authors and do not necessarily reflect official views of CIFOR.

Despite widespread acceptance of sustainability as the ultimate goal of forest management, perspectives about its meaning, significance, and relevant indicators may still differ. This paper examines local perspectives on sustainability, and evaluates their similarities and differences. A systematic procedure based on criteria of proximity, pre-existing rights, dependency, knowledge of forest management, forestry spirit, daily activity, and legal rights was used to identify a small group of relevant stakeholders representing different groups, institutions, and organizations. Using participatory action research (PAR), stakeholders were asked to identify relevant indicators of sustainable forest management. The indicators identified by each stakeholder were then compared to a consolidated list assembled by field facilitators with respect to whether relevant indicators are present or not. Based on the resulting presence/absence matrix, a statistical tool called the simple matching coefficient was used to estimate the similarity measures among the stakeholders' perspectives. In addition, cluster analysis was used to classify groups of stakeholders depending on their similarities to each other. Finally, hypotheses related to the 'closeness' of perspectives among local communities, non-governmental organizations, a timber company, and government organizations, as revealed by their selection of indicators, were tested. Results show that: (a) local communities have different perceptions in terms of what they consider to be important indicators compared to the NGOs, (b) there are significantly different perceptions between the government and the timber companies, and (c) there are also different perceptions between urban and field-based personnel of the same organization.

Cluster Analysis↗