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 1,657 records · Page 92Linked to original sources
PubMed2005

Mutational analysis of the Trypanosoma vivax alternative oxidase: the E(X)6Y motif is conserved in both mitochondrial alternative oxidase and plastid terminal oxidase and is indispensable for enzyme activity.

Based on amino acid sequence similarity and the ability to catalyze the four-electron reduction of oxygen to water using a quinol substrate, mitochondrial alternative oxidase (AOX) and plastid terminal oxidase (PTOX) appear to be two closely related members of the membrane-bound diiron carboxylate group of proteins. In the current studies, we took advantage of the high activity of Trypanosoma vivax AOX (TvAOX) to examine the importance of the conserved Glu and the Tyr residues around the predicted third helix region of AOXs and PTOXs. We first compared the amino acid sequences of TvAOX with AOXs and PTOXs from various taxa and then performed alanine-scanning mutagenesis of TvAOX between amino acids Y(199) and Y(247). We found that the ubiquinol oxidase activity of TvAOX is completely lost in the E214A mutant, whereas mutants E215A and E216A retained more than 30% of the wild-type activity. Among the Tyr mutants, a complete loss of activity was also observed for the Y221A mutant, whereas the activities were equivalent to wild-type for the Y199A, Y212A, and Y247A mutants. Finally, residues Glu(214) and Tyr(221) were found to be strictly conserved among AOXs and PTOXs. Based on these findings, it appears that AOXs and PTOXs are a novel subclass of diiron carboxylate proteins that require the conserved motif E(X)(6)Y for enzyme activity.

Amino Acid Motifs↗
PubMed1989

[Analysis of inquiry responses related to visits of stomatological patients depending on age, sex and educational level].

The purpose of the study was demonstration of possible relationships between the frequency of visits to stomatological office and the age, the sex and the educational level of the patients. The analysis covered 776 responses to an inquiry obtained from the patients visiting the Department of Conservative Stomatology. Comparative statistical analysis showed that these parameters had no effect on the frequency of visits to stomatological surgery. With a high likelihood one can state that this frequency depends on adequately conducted health education, wide network of specialist services, and the health care of the population.

Adolescent↗
PubMedDate not supplied

An analysis of factors determining the use of breast conserving surgery for treating early-stage breast cancer.

To determine the trend of breast conserving surgery (BCS) in West Virginia and to identify patient, hospital and surgeon factors associated with use of BCS, we conducted a study of all cases of Stage I and II invasive breast cancer treated surgically in West Virginia from 1991 through 1995 (N = 2411). These records were obtained from the State Cancer Registry. Multiple logistic regression was used to generate odds ratios (or) and 95% confidence intervals (CI) to determine factors associated with BCS. Our results showed the rate of BCS increased from 25% in 1991 to 37% in 1994 and 33% in 1995, with an overall rate of 33%. Multiple logistic regression identified the following factors associated with BCS: tumor size less than 1 cm (or = 1.47, 95% C1 = 1.4, 1.5), hospital bed size > 300 beds (or = 1.3, 95% C1 = 1.05-1.6) and a surgeon who had graduated from medical school since 1981 (or = 1.2, 95% C1 = 1.0, 1.36). We conclude the rate of BCS in West Virginia still remains low and that the women least likely to have BCS were women with tumors > 2 cm treated at small hospitals by older physicians.

Breast Neoplasms↗
PubMed2004

RNA-dependent RNA polymerase gene analysis of worldwide Newcastle disease virus isolates representing different virulence types and their phylogenetic relationship with other members of the paramyxoviridae.

Nucleotide sequence was determined for the RNA-dependent RNA polymerase (L) gene of 16 Newcastle disease virus (NDV) isolates from diverse geographic and chronological origins. The observed consensus amino acid sequence conformed to the six domains previously identified among paramyxovirus L proteins, and the putative 749QGDNQ753 active site was strictly conserved among all isolates. Analysis of predicted amino acid sequences allowed us to identify a sequencing error in the previously reported L genes for NDV. The correct sequences reported herein provided a more accurate alignment with predicted l-amino acid sequences of other paramyxoviruses. Comparison of L gene coding sequences among isolates revealed that synonymous substitutions dominated non-synonymous substitutions, as observed previously with other NDV genes. However, the overall substitution rate was lower than other genes examined making the L gene the most conserved of the NDV genome. Phylogenetic analysis of L genes among NDV isolates was consistent with previous results that suggested the existence of two major lineages. One group contained strains isolated in North America prior to 1970 and included virulent and vaccine strains, while the second group included virulent viruses isolated worldwide. A comparison of the NDV L coding sequences to other Paramyxoviridae illustrated the unique clustering of the avian-specific paramyxoviruses, further justifying the newly created Avulavirus genus.

Animals↗
PubMed2026

Identification and characterization of the HSP gene family in the Chinese giant salamander: Expression patterns under combined environmental stress.

BACKGROUND: The Chinese giant salamander (Andrias davidianus) is a critically endangered living fossil species that is highly sensitive to changes in water temperature. However, systematic studies on the heat shock protein (HSP) gene family and its response mechanisms to environmental stress in this species remain limited. This study utilized transcriptome data from captive-bred salamanders exposed to combined temperature and pathogen stress. Bioinformatics tools were employed to identify the HSP gene family of A. davidianus (AndHSP) and to analyze their evolution, structure, and function, thereby revealing their regulatory mechanisms in response to environmental stress. RESULTS: A total of 72 AndHSPs were identified and classified into five subfamilies. Phylogenetic analysis revealed that each subfamily is evolutionarily conserved and functionally related. Gene expression analysis demonstrated that pathogen infection induced the expression of AndHSPs, and elevated temperature significantly intensified this response. Nine key differentially expressed genes were identified, predominantly from the AndHSP70 subfamily, with AndHSP70-18 exhibiting rapid heat-induced expression. Tissue-specific analysis showed high expression of AndHSP60 in the spleen. A qPCR validation confirmed the reliability of the transcriptome expression results. CONCLUSIONS: This study presents the first systematic identification of the AndHSP gene family and elucidates its cooperative stress response mechanisms under combined temperature and pathogen stress. These findings provide a molecular basis for understanding the species' environmental adaptation and have important implications for its conservation and artificial breeding.

Animals↗
PubMed1993

Management of severe, early pre-eclampsia: is conservative management justified?

A retrospective analysis was performed to assess the fetal and maternal benefits of allowing women presenting with severe pre-eclampsia between 24 and 32 weeks to continue their pregnancy following treatment of their hypertension. Cases presenting in Oxford (conservative management) and in Birmingham (stabilisation and early intervention) were compared. Patients were considered to require treatment when their systolic blood pressure was > or = 170 mmHg systolic or > or = 110 mmHg diastolic, associated with at least 1+ proteinuria and hyperuricaemia. We compared gestation at delivery, birth weight and neonatal complications for each group, and any maternal morbidity. There were 28 patients in each group. Gestational age at delivery was significantly less in the group managed by early intervention. Those women managed conservatively gained a mean of 9.5 days (range 2-26 days; P < 0.05), and their birthweight was significantly greater (P < 0.05). There was a significant difference between the length of stay in the neonatal intensive care unit between the 2 groups (P < 0.05), the babies of those women managed conservatively staying a mean of 7.4 days less. There were fewer neonatal complications in those cases managed conservatively, the number of newborns with 1 or more complications in the early intervention group being 18 (64.3%), compared with 8 (28.6%) in the expectant management group (P = 0.0001). All of the women in the group managed by early intervention recovered with no severe complications. However, those women managed conservatively had a higher incidence of HELLP (2 cases) and ELLP syndrome (2 cases), 1 case requiring temporary renal dialysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Birth Weight↗
PubMed1997

Comparative analysis in three fungi reveals structurally and functionally conserved regions in the Mig1 repressor.

The Mig1 repressor is a key effector in glucose repression in the yeast Saccharomyces cerevisiae. To gain further insights into structure-function relationships, we have now cloned the MIG1 homologue from the yeast Kluyveromyces marxianus. The amino acid sequence deduced from KmMIG1 differs significantly from ScMig1p outside the highly conserved zinc fingers. However, 12 discrete conserved motifs could be identified in a multiple alignment that also included the K. lactis Mig1p sequence. We further found that KmMig1p is fully functional when expressed in S. cerevisiae. First, it represses the SUC2 promoter almost as well as ScMig1p. This repression requires the Cyc8 and Tup1 proteins and is dependent on a C-terminal region comprising several conserved leucine-proline repeats. Second, KmMig1p is regulated by glucose in S. cerevisiae, and a KmMig1-VP16 hybrid activator is inhibited by the ScSnf1p kinase in the absence of glucose. This suggests that KmMig1p has retained the ability to interact with several S. cerevisiae proteins, and reinforces the notion that the conserved motifs are functionally important. Finally, we found that the physiological role of Mig1p also is conserved in K. marxianus, since KmMig1p represses INU1, the counterpart of SUC2 in this organism.

Amino Acid Sequence↗
PubMed1994

Functional analysis of block 5, one of the highly conserved amino acid sequences in the 130-kDa CryIVA protein produced by Bacillus thuringiensis subsp. israelensis.

There are five amino acid sequences highly conserved among Bacillus thuringiensis delta-endotoxins. We have changed the amino acid residues in block 5, one of the conserved sequences, of CryIVA. When the amino acid residues with charged side chains were replaced by others, the amount of production of the altered CryIVA protein was markedly decreased. It is suggested that the decrease is caused by the unstable conformation of the altered CryIVA protein molecule, as judged by digestion with trypsin and thermolysin. On the other hand, the substitution of amino acid residues in block 5 did not affect the insecticidal activity of CryIVA. These results strongly suggest that block 5 of CryIVA is one of the stability-determining elements of the protoxin molecule.

Amino Acid Sequence↗
PubMed2005

PRR5 encodes a conserved proline-rich protein predominant in kidney: analysis of genomic organization, expression, and mutation status in breast and colorectal carcinomas.

Loss of heterozygosity on chromosome 22q13.31 is a frequent event during human breast and colorectal carcinogenesis. Herein we characterize a novel gene at chromosome 22q13.31 designated PRR5. Alternative promoter usage and splicing converge to generate five PRR5 transcript variants with maximum mRNA expression in kidney. In vitro transcription/translation demonstrated that the five variants generate three protein isoforms differing in their N-terminal length. Mutational analysis of PRR5 in human breast and colorectal tumors did not reveal somatic mutations. However, mRNA expression analyses revealed PRR5 overexpression in a majority of colorectal tumors but substantial downregulation of PRR5 expression in a subset of breast tumors and reduced expression in two breast cancer cell lines. Treatment with trichostatin A increased PRR5 mRNA levels in BT549 and MDA-MB-231 cells, whereas 5'-aza-2'-deoxycytidine induced expression in MDA-MB-231 cells only. Thus, PRR5 may represent a potential candidate tumor suppressor gene in breast cancer.

Alternative Splicing↗
PubMed2004

Analysis of the interaction between piD261/Bud32, an evolutionarily conserved protein kinase of Saccharomyces cerevisiae, and the Grx4 glutaredoxin.

The Saccharomyces cerevisiae piD261/Bud32 protein and its structural homologues, which are present along the Archaea-Eukarya lineage, constitute a novel protein kinase family (the piD261 family) distantly related in sequence to the eukaryotic protein kinase superfamily. It has been demonstrated that the yeast protein displays Ser/Thr phosphotransferase activity in vitro and contains all the invariant residues of the family. This novel protein kinase appears to play an important cellular role as deletion in yeast of the gene encoding piD261/Bud32 results in the alteration of fundamental processes such as cell growth and sporulation. In this work we show that the phosphotransferase activity of Bud32 is relevant to its functionality in vivo, but is not the unique role of the protein, since mutants which have lost catalytic activity but not native conformation can partially complement the disruption of the gene encoding piD261/Bud32. A two-hybrid approach has led to the identification of several proteins interacting with Bud32; in particular a glutaredoxin (Grx4), a putative glycoprotease (Ykr038/Kae1) and proteins of the Imd (inosine monophosphate dehydrogenase) family seem most plausible interactors. We further demonstrate that Grx4 directly interacts with Bud32 and that it is phosphorylated in vitro by Bud32 at Ser-134. The functional significance of the interaction between Bud32 and the putative protease Ykr038/Kae1 is supported by its evolutionary conservation.

Amino Acid Sequence↗
PubMed1995

Sequence analysis and chromosomal localization of human Cap Z. Conserved residues within the actin-binding domain may link Cap Z to gelsolin/severin and profilin protein families.

From a human retinal cDNA library, we have isolated cDNAs that are homologs for the alpha 2 and beta subunits of chicken Cap Z. The derived human alpha subunit shares 95% amino acid identity with the chicken alpha 2 subunit; the beta subunit is 99% identical to the chicken subunit residues 1-243. The remaining portion of the human beta subunit (244-272) diverges significantly with only 8 out of 29 C-terminal amino acids conserved between the two species. This lack of conservation is of particular interest because the chicken C terminus contains an actin-binding domain. Cosedimentation assays with F-actin show that human Cap Z binds actin with an affinity equal that of chicken Cap Z. These results point to the eight shared amino acids as critical for actin binding, three of which are regularly spaced leucines. These apolar residues and one outside the region of divergence align well with those residues of the actin-binding alpha-helix proposed for gelsolin segment 1. The apolar residues as well as three polar amino acids are also conserved in other capping, capping and severing, and monomer-binding proteins. Amino acid substitutions in the chicken beta subunit of the two most highly conserved leucines result in significant decreases in F-actin binding activity. The human alpha 2 gene (CAPZA2) has been mapped to chromosome 7 position q31.2-q31.3 and the beta gene (CAPZB) to chromosome 1 region p36.1.

Actins↗
PubMed2006

Critical analysis of reduction mammaplasty techniques in combination with conservative breast surgery for early breast cancer treatment.

BACKGROUND: Although reduction mammaplasty is a well-described technique for aesthetic purposes, there are few previous reports regarding its application and clinical outcome following conservative breast surgery reconstruction. The purpose of this study was to analyze the feasibility of the technique and its outcome following conservative breast surgery. METHODS: Oncologic data and information on age, body mass index, smoking history, and comorbid conditions were collected. Reconstructed and opposite breast complications were evaluated. Reduction mammaplasty was indicated to reconstruct moderate breast defects in patients with enough remaining breast tissue. Mean follow-up was 22 months. RESULTS: Seventy-four patients underwent immediate reduction mammaplasty following breast-conserving surgery. In 55.4 percent of patients, tumors measured 2 cm or less (T1) and in 47.2 percent they were located in the upper outer quadrants. Breast complications occurred in 13 patients (17.6 percent), with skin necrosis in six (8.1 percent), infection in two (2.7 percent), partial areola necrosis in two (2.7 percent), dehiscence in two, and total areola necrosis in one (1.35 percent). Late complications represented by skin lesions and fat necrosis were observed in five patients (6.8 percent). Obese patients and smokers had a significantly higher rate of reconstructed breast complications compared with the normal/overweight patients (p = 0.002) and nonsmokers (p = 0.043). No significant association between complications and age, hypertension, diabetes, axillary lymph node dissection, or chemotherapy was found. CONCLUSIONS: Reduction mammaplasty is a consistent technique for reconstruction following breast-conserving surgery. Complications are more often observed in the reconstructed breast, and obese patients and smokers are higher risk patients.

Adult↗
PubMed1998

Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning.

Mesodermal development is a multistep process in which cells become increasingly specialized to form specific tissue types. In Drosophila and mammals, proper segregation and patterning of the mesoderm involves the bHLH factor Twist. We investigated the activity of a Twist-related factor, CeTwist, during Caenorhabditis elegans mesoderm development. Embryonic mesoderm in C. elegans derives from a number of distinct founder cells that are specified during the early lineages; in contrast, a single blast cell (M) is responsible for all nongonadal mesoderm formation during postembryonic development. Using immunofluorescence and reporter fusions, we determined the activity pattern of the gene encoding CeTwist. No activity was observed during specification of mesodermal lineages in the early embryo; instead, the gene was active within the M lineage and in a number of mesodermal cells with nonstriated muscle fates. A role for CeTwist in postembryonic mesodermal cell fate specification was indicated by ectopic expression and genetic interference assays. These experiments showed that CeTwist was responsible for activating two target genes normally expressed in specific subsets of nonstriated muscles derived from the M lineage. In vitro and in vivo assays suggested that CeTwist cooperates with the C. elegans E/Daughterless homolog in directly activating these targets. The two target genes that we have studied, ceh-24 and egl-15, encode an NK-2 class homeodomain and an FGF receptor (FGFR) homolog, respectively. Twist activates FGFR and NK-homeodomain target genes during mesodermal patterning of Drosophila and similar target interactions have been proposed to modulate mesenchymal growth during closure of the vertebrate skull. These results suggest the possibility that a conserved pathway may be used for diverse functions in mesodermal specification.

Amino Acid Sequence↗
PubMed1990

Expression of multiple novel Wnt-1/int-1-related genes during fetal and adult mouse development.

The mammary tumor-associated proto-oncogene Wnt-1/int-1 encodes a secreted protein implicated in the regulation of neural development in vertebrates and segmental pattern in Drosophila. Using a PCR-based strategy, we isolated cDNAs encoding six novel, related proteins that are expressed in fetal mice. Predicted proteins are of similar molecular masses (38-42 kD) and share between 50% and 85% of amino acids. All contain a putative hydrophobic signal sequence, and comparative analysis reveals 83 absolutely conserved amino acid residues, including 21 cysteines. Transcripts were detected throughout fetal development by Northern blot analysis. Detailed examination of the expression of two of these genes by in situ hybridization revealed complex temporal and spatial patterns of transcription. All new Wnt family members are expressed in adult tissues, particularly in brain and lung. These data support the view that the Wnt-1/int-1 family constitutes a large family of signaling peptides with diverse roles in mouse development.

Aging↗
PubMed1997

Mutational analysis of the D1/E1 core helices and the conserved N-terminal region of yeast transcription factor IIB (TFIIB): identification of an N-terminal mutant that stabilizes TATA-binding protein-TFIIB-DNA complexes.

The general transcription factor IIB (TFIIB) plays an essential role in transcription of protein-coding genes by RNA polymerase II. We have used site-directed mutagenesis to assess the role of conserved amino acids in several important regions of yeast TFIIB. These include residues in the highly conserved amino-terminal region and basic residues in the D1 and E1 core domain alpha-helices. Acidic substitutions of residues K190 (D1) and K201 (E1) resulted in growth impairments in vivo, reduced basal transcriptional activity in vitro, and an inability to form stable TFIIB-TATA-binding protein-DNA (DB) complexes. Significantly, these mutants retained the ability to respond to acidic activators in vivo and to the Gal4-VP16 activator in vitro, supporting the view that these basic residues play a role in basal transcription. In addition, 14 single-amino-acid substitutions were introduced in the conserved amino-terminal region. Three of these mutants, the L50D, R64E, and R78L mutants, displayed altered growth properties in vivo and were compromised for supporting transcription in vitro. The L50D mutant was impaired for RNA polymerase II interaction, while the R64E mutant exhibited altered transcription start site selection both in vitro and in vivo and, surprisingly, was more active than the wild type in the formation of stable DB complexes. These results support the view that the amino-terminal domain is involved in the direct interaction between yeast TFIIB and RNA polymerase II and suggest that this domain may interact with DNA and/or modulate the formation of a DB complex.

Amino Acid Sequence↗