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PubMed1994

Early indicators of hearing conservation program performance.

Retrospective analysis of initial audiograms from 21 hearing conservation programs (HCPs) revealed several statistical protocols capable of identifying HCPs of known performance. American National Standards Institute (ANSI) and Occupational Safety and Health Administration (OSHA) protocols clearly identified 3 HCPs known to have demonstrated excellent overall programs. ANSI and OSHA outcomes appeared equivalent in ability to provide early warnings of potentially unacceptable HCP practices.

Audiometry↗
PubMed1993

An evaluation of the U.S. Air Force's detailed follow-up audiometric examination program.

The authors used information on individuals demonstrating permanent threshold shifts contained in the United States Air Force Hearing Conservation Data Registry to evaluate the effectiveness of detailed follow-up audiometric examinations as part of the USAF Hearing Conservation Program. Analysis yielded a relative risk of 1.00 with a 95% confidence interval of 0.97-1.03, which indicates a high probability that the true effect of these audiograms on the results of the next annual exam is minuscule, if not zero.

Audiometry, Pure-Tone↗
PubMed1997

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease.

The recent determination of the three-dimensional structure of urease revealed striking similarities of enzyme architecture to adenosine deaminase and phosphotriesterase, evidence of a distant evolutionary relationship that had gone undetected by one-dimensional sequence comparisons. Here, based on an analysis of conservation patterns in three dimensions, we report the discovery of the same active-site architecture in an even larger set of enzymes involved primarily in nucleotide metabolism. As a consequence, we predict the three-dimensional fold and details of the active site architecture for dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases, and proteins involved in animal neuronal development. Two member families are common to archaea, eubacteria, and eukaryota. Thirteen other functions supported by the same structural motif and conserved chemical mechanism apparently represent later adaptations for different substrate specificities in different cellular contexts.

Amidohydrolases↗
PubMed1998

Localization of quantitative trait loci regulating adjuvant-induced arthritis in rats: evidence for genetic factors common to multiple autoimmune diseases.

Adjuvant-induced arthritis (AIA) in rats is a widely used autoimmune experimental model with many features similar to rheumatoid arthritis (RA). To identify potential genetic regulatory mechanisms in RA, we conducted genome-wide linkage analysis in F2 progeny of arthritis-susceptible Dark Agouti (DA) and relatively resistant Fischer 344 (F344) inbred rats. We compared the data with our previously reported investigation of collagen-induced arthritis (CIA), which was expanded in the follow-up study reported in this work. We found two quantitative trait loci (QTLs) in common, i.e., Aia1/Cia1 on chromosome 20, which includes the MHC, and Aia3/Cia3 on chromosome 4. We also identified a second unique QTL in AIA, Aia2, on chromosome 4. Interestingly, the QTL region on chromosome 4 (Aia3/Cia3), like the MHC, appears to be involved in several other autoimmune diseases in rats, including insulin-dependent diabetes, thyroiditis, and experimental autoimmune uveitis. Moreover, an analysis of conserved synteny among rats, mice, and humans suggested that Aia2 and Aia3/Cia3, like Aia1/Cia1, contain candidate genes for several autoimmune/inflammatory diseases in mice and humans, including diabetes, systemic lupus erythematosus, inflammatory bowel disease, asthma/atopy, multiple sclerosis, and RA. The rat models appear to provide a powerful complementary approach to identify and characterize candidate genes that may contribute to autoimmune diseases in several species.

Animals↗
PubMed1999

Distribution of protein folds in the three superkingdoms of life.

A sensitive protein-fold recognition procedure was developed on the basis of iterative database search using the PSI-BLAST program. A collection of 1193 position-dependent weight matrices that can be used as fold identifiers was produced. In the completely sequenced genomes, folds could be automatically identified for 20%-30% of the proteins, with 3%-6% more detectable by additional analysis of conserved motifs. The distribution of the most common folds is very similar in bacteria and archaea but distinct in eukaryotes. Within the bacteria, this distribution differs between parasitic and free-living species. In all analyzed genomes, the P-loop NTPases are the most abundant fold. In bacteria and archaea, the next most common folds are ferredoxin-like domains, TIM-barrels, and methyltransferases, whereas in eukaryotes, the second to fourth places belong to protein kinases, beta-propellers and TIM-barrels. The observed diversity of protein folds in different proteomes is approximately twice as high as it would be expected from a simple stochastic model describing a proteome as a finite sample from an infinite pool of proteins with an exponential distribution of the fold fractions. Distribution of the number of domains with different folds in one protein fits the geometric model, which is compatible with the evolution of multidomain proteins by random combination of domains. [Fold predictions for proteins from 14 proteomes are available on the World Wide Web at. The FIDs are available by anonymous ftp at the same location.]

Algorithms↗
PubMed2003

Prognostic factors for patients with localized soft-tissue sarcoma treated with conservation surgery and radiation therapy: an analysis of 1225 patients.

BACKGROUND: Prognostic factors for patients with soft-tissue sarcoma who are treated with conservative surgery and radiation are documented poorly. METHODS: The clinicopathologic features and disease outcome for 1225 patients with localized sarcoma who were treated with conservative surgery and radiation were reviewed retrospectively. Actuarial univariate and multivariate statistical methods were used to determine significant prognostic factors for local control, metastatic recurrence, and disease specific survival. RESULTS: The median follow-up of surviving patients was 9.5 years. The respective local control rates at 5 years, 10 years, and 15 years were 83%, 80%, and 79%. Factors predictive of local recurrence were positive or uncertain resection margins; tumors located in the head and neck and the deep trunk; presentation with local recurrence; patient age > 64 years; malignant fibrous histiocytoma, neurogenic sarcoma. or epithelioid sarcoma histopathology; tumor measuring > 10 cm in greatest dimension; and high pathologic grade. Freedom from metastasis at 5 years, 10 years, and 15 years was 71%, 68%, and 66%, respectively. Factors that were predictive of metastatic recurrence were high tumor grade; large tumor size (> 5 cm); and leiomyosarcoma, rhabdomyosarcoma, synovial sarcoma, or epithelioid sarcoma. The respective disease specific survival rates at 5 years, 10 years, and 15 years were 73%, 68%, and 65%. Adverse factors for disease specific survival were high tumor grade; large tumor size (> 5 cm); tumors located in the head and neck and deep trunk; rhabdomyosarcoma, epithelioid sarcoma, or clear cell sarcoma; patient age > 64 years; and positive or uncertain resection margins. CONCLUSIONS: Soft-tissue sarcoma comprises a heterogeneous group of diseases. Prognostic factors for local recurrence, metastatic recurrence, lymph node recurrence, disease free survival, and disease specific survival are different, and optimal treatment strategies need to take this complexity into account.

Adolescent↗
PubMed2002

Conservative region of the genes encoding four adhesins of Helicobacter pylori: cloning, sequence analysis and biological information analysis.

OBJECTIVE: To clone the conserved regions of the genes encoding the 4 adhesins (BabA, AlpA, AlpB and HopZ) of Helicobacter pylori (H. pylori) and analyze their sequences and biological information, thus facilitating further research in the molecular mechanism and immunogenicity of H. pylori adhesins. METHODS: Common conserved region (designated as CB) was identified from the confirmed sequences (by ANTHEPROT V4.3c software package) of the 4 adhesin proteins. Their DNA sequences were deduced, according to which primers specific to CB were designed for subsequent PCR, and the products were inserted directionally into pET-22b(+) vector to construct recombinant clones of the conserved region. The DNA sequences were determined with the basic local alignment sequence tool (BLAST) and the biological properties analyzed with ANTHEPROT V4.3c software package. RESULTS: The recombinant plasmid containing the CB sequence was constructed. DNA sequencing showed an open reading frame of 588 bp in length, encoding 195 amino acids. The homogencity of conservative region of the 4 adhesion genes was above 50%. The corresponding protein possessed a relative molecular mass (Mr) of 22 500 as predicted by ANTHEPROT V4.3c software prediction, with excellent antigenicity and hydrophobicity. There were 836 767 sequences analyzed with BLAST, in which those with homogencity of 40% with the identified CB sequence were categorized into H. pylori sequences. CONCLUSION: There are conservative regions in the 4 adhesin genes with similar homogencity, suggesting similar molecular basis for adhesion of the adhesins. Biological information analysis indicates that CB has excellent immunogenicity and strict species specificity.

Adhesins, Bacterial↗
PubMed1990

Analysis of beta-tubulin sequences reveals highly conserved, coordinated amino acid substitutions. Evidence that these 'hot spots' are directly involved in the conformational change required for dynamic instability.

Vertebrate beta-tubulins have been classified into six classes on the basis of their C-terminal sequences [(1987) J. Cell Biol. 105, 1707-1720]. In particular, the sequences starting at residue 430 differ between isotypes of the same animal but are conserved between species. We extend this analysis and show that there are three 'hot spots', at residues 35, 55-57 and 124 which exhibit intra-species heterogeneity but inter-species conservation. There is a remarkable correlation between the identity of these residues and the C-terminal sequences, and suggests that the vertebrate beta-tubulins fall into three broad types. This correlation extends to those non-vertebrate organisms which have the Type 1 C-terminal sequence. We propose that these three 'hot spots' and the C-terminal peptide interact in the tertiary structure. We have also noted that the C-terminal peptide almost always contains a single phenylalanine or tyrosine residue, and that there is a strong correlation between this residue and the amino acids at positions 217/218, in both the vertebrate and non-vertebrate sequences. We propose that the C-terminal aromatic amino acid interacts with residues 217/218 in the tertiary structure. Analysis of conditions which stabilise microtubules and/or lower the steady state critical concentration strongly suggests that these two sets of coordinated amino acid substitutions are directly involved in effecting the conformational change associated with GTP hydrolysis which results in dynamic instability. We propose that there is an interaction between the highly acidic sequence between residue 430 and the aromatic amino acid (termed peptide A) and conserved basic amino acids located close to the 'hot spots'. We suggest that this interaction is altered in response to the assembly-dependent GTP hydrolysis, with the consequential increase in the subunit dissociation rate constant.

Amino Acid Sequence↗
PubMed2001

Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.

The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution, revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserved nucleotides for SRP assembly, we measured the affinity of the M domain for a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein.

Conserved Sequence↗
PubMedDate not supplied

Determinants of wound infections after surgery for breast cancer.

BACKGROUND: There are evident risks factors stemming from any the local post-surgical infection, which merits analysis of morbidity derived from conservative and radical surgery after treatment of the operable breast cancer. STUDY DESIGN: 107 patients with breast cancer recruited between November 1995 and October 1997 were evaluated. From that total, 36 patients were subjected to quadrantectomy, axillary lymphadenectomy and postoperative radiation while 71 patients were subjected to modified radical mastectomy. RESULTS: 7 % percent of patients who underwent modified radical surgery succumbed to postoperative local infection vs. 17 % of patients subjected to breast conserving therapies. Local infections were associated with the older patients (63 vs. 54 years old, p=0.03) and greater obesity (p=0.04). Upon logistic regression analysis conservative surgery exhibited adjusted Odds Ratio of 6.42 (1.27-32.28), p =0.02. In postoperative infection group average hospital stay increased by 6 days (p= 0.0001). CONCLUSION: In the present study main risk factors associated with postsurgical wound infection after breast cancer treatment proved to be advanced age, greater obesity and conservative surgery. Nonetheless, more studies are necessary to confirm current findings.

Breast Neoplasms↗
PubMedDate not supplied

Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation.

DNA sequence analysis is a powerful tool for identifying the source of samples thought to be derived from threatened or endangered species. Analysis of mitochondrial DNA (mtDNA) from retail whale meat markets has shown consistently that the expected baleen whale in these markets, the minke whale, makes up only about half the products analyzed. The other products are either unregulated small toothed whales like dolphins or are protected baleen whales such as humpback, Bryde's, fin, or blue whales. Independent verification of such mtDNA identifications requires analysis of nuclear genetic loci, but this is technically more difficult than standard mtDNA sequencing. In addition, evolution of species-specific sequences (i.e., fixation of sequence differences to produce reciprocally monophyletic gene trees) is slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. When will use of nuclear sequences allow forensic DNA identification? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The "three-times rule" suggests that phylogenetic sorting at nuclear loci is likely to produce species-specific sequences when mitochondrial alleles are reciprocally monophyletic and the branches leading to the mtDNA sequences of a species are three times longer than the average difference observed within species. A preliminary test of the three-times rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback and fin whales should show species-specific sequences at fewer nuclear loci. Partial sequences of actin introns from these species confirm the predictions of the three-times rule and show that blue and fin whales are reciprocally monophyletic at this locus. These intron sequences are thus good tools for the identification of these species and will afford a chance to identify putative hybrid blue/fin whales thought to have entered the retail market after 1989.

Actins↗
PubMed1998

Conserved structural regions involved in the catalytic mechanism of Escherichia coli K-12 WaaO (RfaI).

Escherichia coli K-12 WaaO (formerly known as RfaI) is a nonprocessive alpha-1,3 glucosyltransferase, involved in the synthesis of the R core of lipopolysaccharide. By comparing the amino acid sequence of WaaO with those of 11 homologous alpha-glycosyltransferases, four strictly conserved regions, I, II, III, and IV, were identified. Since functionally related transferases are predicted to have a similar architecture in the catalytic sites, it is assumed that these four regions are directly involved in the formation of alpha-glycosidic linkage from alpha-linked nucleotide diphospho-sugar donor. Hydrophobic cluster analysis revealed a conserved domain at the N termini of these alpha-glycosyltransferases. This domain was similar to that previously reported for beta-glycosyltransferases. Thus, this domain is likely to be involved in the formation of beta-glycosidic linkage between the donor sugar and the enzyme at the first step of the reaction. Site-directed mutagenesis analysis of E. coli K-12 WaaO revealed four critical amino acid residues.

Amino Acid Sequence↗
PubMed1996

The sequence organization of Yp/proximal Xq homologous regions of the human sex chromosomes is highly conserved.

Detailed deletion analysis of patients with breakpoints in Yp has allowed the definition of two distinct intervals on the Y chromosome short arm outside the pseudoautosomal region that are homologous to Xq2l.3. Detailed YAC contigs have been developed over these regions on both the X and Y chromosomes, and the relative order of markers has been compared to assess whether rearrangements on either sex chromosome have occurred since the transposition events creating these patterns of homology. On the X chromosome, the region forms almost one contiguous block of homology, whereas on the Y chromosome, there has been one major rearrangement leading to the two separate Yp-Xq2l blocks of homology. The rearrangement breakpoint has been mapped. Within these separate X-Y homologous blocks on Yp, the order of loci homologous to X has been conserved to a high degree between the sex chromosomes. With the exception of the amelogenin gene (proximal Yp block), all the XY homologous sequences in the two Yp blocks have homolognes in Xq2l.3, with the former having its X counterpart in Xp22.2. This suggests an independent evolutionary event leading to the formation of the amelogenin X-Y homology.

Chromosome Mapping↗
PubMed1993

Identification of a zinc finger encoding gene in Onchocerca volvulus.

Eukaryotic transcription factors can be identified and classified according to conserved DNA-binding motifs and conserved regulatory domains. The functional and structural analysis, and the conservation of these genes among metazoans emphasizes the importance of these DNA-binding proteins in development and differentiation. In order to identify genes with common DNA-binding motifs in the genome of Onchocerca volvulus we have cloned a zinc finger encoding gene of the structure C2-H2. Using the Caenorhabditis elegans sex determining tra-1 gene as a probe we have identified two tra-1 related genes in the genome of O. volvulus. The zinc finger region of one of these genes (OvZf1) was subcloned and sequenced. The predicted protein has at least eight consecutive zinc fingers and each finger possesses the characteristic paired cysteine- and histidine residues and the proper spacing of the amino acids between the conserved residues.

Amino Acid Sequence↗
PubMed1989

Analysis of genomic clones of the murine U1RNA-associated 70-kDa protein reveals a high evolutionary conservation of the protein between human and mouse.

We have isolated and characterised two overlapping lambda EMBL3 clones carrying sequences of the gene for the murine U1RNA-associated 70-kDa protein. The two clones cover around 23 kb of the 70-kDa protein gene including its 3' end. Southern blot hybridisation revealed the existence of a single copy of the 70-kDa protein gene in the mouse genome. The 23-kb-long portion of the 70-kDa protein gene is divided into eight exons. While most of the exons are quite small and are widely scattered throughout the DNA sequence, the last one consists of about 830 bp and encodes 226 amino acids of the 70-kDa protein, including the C-terminus. The predicted amino acid sequence of the region of the 70-kDa protein encoded by the genomic clones reveals high conservation of structure when it is compared with the sequence of the human 70-kDa protein. Interestingly, all deletions, additions and substitutions are localised exclusively within the C-terminus of the protein, accounting for a 5'-3' polarity with respect to protein conservation. Moreover, the analysis of the genomic sequences predicts the existence of multiple subclasses of mRNAs that may arise by alternative pre-mRNA splicing. A 72-bp alternative exon harboring an in-frame termination codon was also found in the mouse 70-kDa gene and shows, surprisingly, 100% nucleotide identity to its human counterpart.

Amino Acid Sequence↗
PubMed2005

A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling.

Physiological, morphological, and transcriptional alterations elicited by ethynyl estradiol in the uteri of Sprague-Dawley rats and C57BL/6 mice were assessed using comparable study designs, microarray platforms, and analysis methods to identify conserved estrogen signaling networks. Comparative analysis identified 153 orthologous gene pairs that were positively correlated, suggesting conserved transcriptional targets important in uterine proliferation. Functional annotation for these responses were associated with angiogenesis, water and solute transport, cell cycle control, redox control, DNA replication, protein synthesis and transport, xenobiotic metabolism, cell-cell communication, energetics, and cholesterol and fatty acid regulation. The identification of conserved temporal expression patterns of these orthologs provides experimental support for the transfer of functional annotation from mouse orthologs to 44 previously unannotated rat expressed sequence tags based on their homology and co-expression patterns. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates the ability of systematic comparative genomic assessments to elucidate important conserved mechanisms in rodent estrogen signaling during uterine proliferation.

Animals↗
PubMed2000

The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold.

We have extended the resolution of the crystal structure of human bactericidal/permeability-increasing protein (BPI) to 1.7 A. BPI has two domains with the same fold, but with little sequence similarity. To understand the similarity in structure of the two domains, we compare the corresponding residue positions in the two domains by the method of 3D-1D profiles. A 3D-1D profile is a string formed by assigning each position in the 3D structure to one of 18 environment classes. The environment classes are defined by the local secondary structure, the area of the residue which is buried from solvent, and the fraction of the area buried by polar atoms. A structural alignment between the two BPI domains was used to compare the 3D-1D environments of structurally equivalent positions. Greater than 31% of the aligned positions have conserved 3D-1D environments, but only 13% have conserved residue identities. Analysis of the 3D-1D environmentally conserved positions helps to identify pairs of residues likely to be important in conserving the fold, regardless of the residue similarity. We find examples of 3D-1D environmentally conserved positions with dissimilar residues which nevertheless play similar structural roles. To generalize our findings, we analyzed four other proteins with similar structures yet dissimilar sequences. Together, these examples show that aligned pairs of dissimilar residues often share similar structural roles, stabilizing dissimilar sequences in the same fold.

Amino Acid Sequence↗
PubMed1987

Selective management of pediatric pelvic fractures: a conservative approach.

An analysis of clinical characteristics and pelvic fracture management in a recent 5-year period is presented. Ninety-eight percent of pelvic fractures were the result of a motor vehicle accident, which included 61% auto-pedestrian accidents. Seventy-nine percent of patients sustained one or more major injuries while 21% sustained an isolated pelvic fracture. Head injury was the most common concomitant injury (23% of patients). Forty-six percent of patients required blood transfusions (mean 15.8 mL/kg). Forty-one (72%) patients were treated with bedrest. The remainder were treated with traction (5), spica cast immobilization (5), open reduction and internal fixation (4), or anterior external fixation (2). Overall mortality was 14%. In comparing nonsurvivors with survivors there were significant differences in Modified Injury Severity Scores and Glasgow Coma Scores. The types of pelvic fractures that occur in children were found to be similar to those of adults. There was no significant difference in mortality among children with different types of pelvic fractures. In contrast to adults, pelvic fracture hemorrhage was not a major contributing cause of death in this series of patients. All eight deaths were secondary to severe closed head injury.

Adolescent↗