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PubMed2004

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.

The analysis of conservation between the human and mouse genomes resulted in the identification of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic conservation remains unknown, however. The availability of the sequence of a third mammalian genome, the dog, allows for a large-scale analysis of evolutionary attributes of CNGs in mammals. We have aligned 1638 previously identified CNGs and 976 conserved exons (CODs) from human chromosome 21 (Hsa21) with their orthologous sequences in mouse and dog. Attributes of selective constraint, such as sequence conservation, clustering, and direction of substitutions were compared between CNGs and CODs, showing a clear distinction between the two classes. We subsequently performed a chromosome-wide analysis of CNGs by correlating selective constraint metrics with their position on the chromosome and relative to their distance from genes. We found that CNGs appear to be randomly arranged in intergenic regions, with no bias to be closer or farther from genes. Moreover, conservation and clustering of substitutions of CNGs appear to be completely independent of their distance from genes. These results suggest that the majority of CNGs are not typical of previously described regulatory elements in terms of their location. We propose models for a global role of CNGs in genome function and regulation, through long-distance cis or trans chromosomal interactions.

Animals↗
PubMed1984

Evaluation of conservative therapeutic modalities for hepatocellular carcinoma--analysis of 206 cases.

The clinical effectiveness of conservative therapeutic modalities for hepatocellular carcinoma (HCC) was evaluated in terms of extension of survival. The therapeutic methods included one-shot therapy (OST) using Mitomycin C (MMC), Adriamycin (ADM), simultaneous ADM & MMC, with or without transcatheter arterial embolization (TAE). Prior to estimating the effectiveness, the subjects were graded into three stages according to the pretreatment severity of their residual liver function, based on total bilirubin, aspartate aminotransferase/alanine aminotransferase ratio, and ascites as constituent factors. OST with or without TAE significantly prolonged the mean survival time in stage I cases in good condition and in stage II cases in fair condition, but not in stage III cases in poor condition. Concerning OST without TAE, the results of ADM were slightly better than MMC in terms of extension of survival. OST combined with TAE was far more effective than OST without TAE. Extension of survival by simultaneous ADM & MMC is now under observation, but the toxicity of the modality has so far not proved serious. The long-term influence of repeated TAE on liver function was revealed to be mild within an average observation period of approximately one year. This study confirmed the validity of the present staging system in evaluating the efficacy of OST and TAE in terms of extension of survival.

Adult↗
PubMed1998

Glutamate-459 is important for Escherichia coli branching enzyme activity.

The branching enzyme belongs to the amylolytic family, a group of enzymes that cleave and/or transfer chains of glucan. The amylolytic enzymes are homologous and all contain four conserved regions, proposed to contain the active site. By primary structure analysis, a conserved position unique to branching enzymes has been identified. This residue, which is either Asp or Glu, depending on the species, is located immediately after the putative catalytic Glu-458 (Escherichia coli numbering). Branching enzymes differ from other amylolytic enzymes in having this acid pair, and we asked if this motif could be essential for branching enzyme action. We used site-directed mutagenesis of the Glu-459 residue in the E. coli branching enzyme in order to determine the significance of the conserved Asp/Glu in branching enzymes. A substitution of Glu-459 to Asp resulted in increased specific activity compared to wild-type, suggesting that the mutation had created a more efficient enzyme. Changing Glu-459 to Ala, Lys, or Gln lowered the specific activities and altered the preferred substrate from amylose to amylopectin.

1,4-alpha-Glucan Branching Enzyme↗
PubMed2004

Raman spectroscopic analysis of a tembetá: a resin archaeological artefact in need of conservation.

The Raman spectroscopic analysis of a Brazilian tembetá, a lip-plug which signifies the attainment of manhood in tribal cultures, and dated to about 1600 years BP is reported. Tembetá are usually made of wood or stone but this lip-plug is very rare in that it is made of resin, which has been severely degraded in the burial environment; the brownish-red fragmented remains are in an extremely fragile condition and information about the chemical composition was required before urgent conservation was undertaken. Raman spectra excited at 1064 nm showed the presence of triterpenoid materials in the main body of the artefact, and indicated that the red-brown coating was not iron(III) oxide as suspected but rather degraded resin. Comparison with contemporary resins has facilitated the partial identification of the material in this important artefact as a triterpenoid-rich material, which is closely similar to the Pistacia species. A possible archaeological link to the Jatobá do Cerrado (Hymenaea stigonocarpa Mart.) resin has been excluded as the Raman spectra of this resin specimen and the tembetá do not match; indeed, the Jatobá do Cerrado resin specimen belongs to a diterpenoid-rich classification as befits its Hymenaea species.

Archaeology↗
PubMed2001

Surgical or conservative treatment for chronic rotator cuff calcifying tendinitis--a matched-pair analysis of 100 patients.

Conservative or operative treatment for rotator cuff calcifying tendinitis was investigated in 100 patients in a matched-pair analysis. They were examined clinically and ultrasonographically 35-60 months after the initial visit. The mean Patte score was 91.8 for the patients who underwent surgical treatment and 81 for the ones who received conservative therapy (p < 0.004), while the age-related Constant-score was 103.4 and 95, respectively. Ultrasonography showed 28% calcifications in the surgical group, 18% newly formed and 10% that did not resolve after surgery. In the conservatively treated group, 33% calcifications were seen, of which 67% resolved. The number of rotator cuff ruptures was significantly higher in the conservative group. In the surgical group, 2% of partial tears and in the conservative group 5% of partial and 4% of complete cuff ruptures were found. Conservative treatment for calcifying tendinitis leads to less favourable pain results in the long term than surgical treatment. Surgery shortens the painful period and may reduce the number of future rotator cuff ruptures. Finally, the subjective functional outcome is significantly better after surgery.

Activities of Daily Living↗
PubMed1999

Chloroplast small heat shock proteins: evidence for atypical evolution of an organelle-localized protein.

Knowledge of the origin and evolution of gene families is critical to our understanding of the evolution of protein function. To gain a detailed understanding of the evolution of the small heat shock proteins (sHSPs) in plants, we have examined the evolutionary history of the chloroplast (CP)-localized sHSPs. Previously, these nuclear-encoded CP proteins had been identified only from angiosperms. This study reveals the presence of the CP sHSPs in a moss, Funaria hygrometrica. Two clones for CP sHSPs were isolated from a F. hygrometrica heat shock cDNA library that represent two distinct CP sHSP genes. Our analysis of the CP sHSPs reveals unexpected evolutionary relationships and patterns of sequence conservation. Phylogenetic analysis of the CP sHSPs with other plant CP sHSPs and eukaryotic, archaeal, and bacterial sHSPs shows that the CP sHSPs are not closely related to the cyanobacterial sHSPs. Thus, they most likely evolved via gene duplication from a nuclear-encoded cytosolic sHSP and not via gene transfer from the CP endosymbiont. Previous sequence analysis had shown that all angiosperm CP sHSPs possess a methionine-rich region in the N-terminal domain. The primary sequence of this region is not highly conserved in the F. hygrometrica CP sHSPs. This lack of sequence conservation indicates that sometime in land plant evolution, after the divergence of mosses from the common ancestor of angiosperms but before the monocot-dicot divergence, there was a change in the selective constraints acting on the CP sHSPs.

Amino Acid Sequence↗
PubMed2005

Nested genes in the human genome.

Here we studied one special type of gene, i.e., the nested gene, in the human genome. We collected 373 reliably annotated nested genes. Two-thirds of them were on the strand opposite that of their host gene. About 58% coding nested gene pairs were conserved in mouse and some were even maintained in chicken and fish, while nested pseudogenes were poorly conserved. Ka/Ks analysis revealed that nested genes were under strong selection, although they did not demonstrate greater conservation than other genes. With microarray data we observed that two partners of one nested pair seemed to be expressed reciprocally. A significant proportion of nested genes were tissue-specifically expressed. Gene ontology analysis demonstrated that quite a number of nested genes participated in cellular signal transduction. Based on these observations, we think that nested genes are a group of genes with important physiological functions.

Animals↗
PubMed2002

Identification and functional characterization of the novel BM-motif in the murine phosphoadenosine phosphosulfate (PAPS) synthetase.

PAPS synthetase (SK) catalyzes the two sequential reactions of phosphoadenosine phosphosulfate (PAPS) synthesis. A functional motif in the kinase domain of mouse SK, designated the BM-motif ((86) LDGDNhRxhh(N/S)(K/R)(97)), was defined in the course of identifying the brachymorphic (bm) defect. Sequence comparison and the secondary structure predicted for APS kinase suggest that the BM-motif consists of a DGD-turn sequence flanked by other conserved residues. Mutational analysis of the DGD-turn revealed that a flexible and neutral amino acid is preferred at residue 88, that negatively charged residues are strictly required at positions 87 and 89, and that the active site is rigid. The reduction in kinase activity for all DGD-turn mutants, except G88A, was much less severe than the reduction in overall activity, indicating that the BM-motif may also be playing a role in adenosine phosphosulfate (APS) channeling. Two switch mutations, LD86DL and DN89ND, designed to test the positional constraints of Asp(87) and Asp(89), exhibited complete loss of both kinase and overall activities, while LD86DL also exhibited a significant (60%) loss of reverse sulfurylase activity, suggesting that this peptide region is interacting with the sulfurylase domain as well as functioning in the kinase reaction. Other residues targeted for mutational analysis were the highly conserved flanking Asn(90), Arg(92), and Lys(97). N90A resulted in a partial (30%) loss in kinase and overall activities, R92A exhibited total loss of kinase and overall activities, and K97A had no effect on any of the three activities. The complexity of the bifunctional SK in catalyzing the kinase reaction and channeling APS is illustrated by the strict requirements of this novel structural motif in the kinase active site.

Amino Acid Motifs↗
PubMed1998

Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements.

The expression of a heat-inducible cct1 (chaperonin-containing Tcp-1) family member gene is regulated at the transcription level in the archaeon Haloferax volcanii. Transcriptional fusions of the cct1 promoter region with a yeast proline tRNA reporter gene were constructed to analyse the functional domains of this archaeal heat shock promoter. Both basal and heat-induced transcription of the reporter gene was directed by an archaeal consensus TATA element (5'-TTTATA-3') centred 25bp upstream of the transcription start site. Deletion mutagenesis indicated that the 5' boundary of the cct1 regulatory region mapped to position -37. Nucleotide alignment with the 5' flanking regions of two additional cct-related genes identified in H. volcanii showed a high degree of sequence conservation between positions +1 and -37, especially in and immediately surrounding the TATA element of the putative core promoter. Mutational analysis of conserved sequences demonstrated that basal and heat-induced transcription required sequence elements located upstream and downstream of the TATA-box. These findings indicate that the regulatory sequences involved in heat-induced transcription lie within the core promoter region and suggest that the mechanism controlling heat shock gene expression in H. volcanii differs from the bacterial and eukaryal strategies.

Archaeal Proteins↗
PubMed1997

Characterization of the phosphoglucose isomerase gene from crickets: an analysis of phylogeny, amino acid conservation and nucleotide composition.

Although electrophoretic variation in phosphoglucose isomerase (PGI) is often detected in allozyme studies, the Pgi gene has rarely been characterized. Here, I present the cDNA sequence of the Pgi gene from two species of field cricket, Gryllus pennsylvanicus (U65475) and G. veletis (U65476), in which the PGI protein is suspected of being under balancing selection. Phylogenetic analyses support the conclusion that these sequences are truly cricket Pgi. The cricket amino acid sequences are compared to sequences from other taxa to determine conserved residues that may be essential for the function of the protein. Such analysis is necessary as there is no well-resolved structure of the PGI protein. In addition, the compositional bias of cricket Pgi is different from the other animal Pgi genes characterized to date.

Amino Acid Sequence↗
PubMed1997

[Laparoscopic interventions in gastroesophageal reflux--a cost-benefit analysis].

On the basis of a cost analysis of conservative and surgical therapy of gastroesophageal reflux disease in 70 patients health economic aspects are discussed. In a prospective documented series of reflux patients a retrolective analysis of medication cost and duration of conservative therapy is performed. In addition, the costs for surgical therapy including preoperative diagnostic workup, cost during hospitalization as well as costs for complications with necessary additional treatment and readmissions are assessed. For the conservative treatment of 70 reflux patients a total of more than DM < 700,000 had to be spent during preoperative 5 years. A major part of this sum was spent for patients who needed to increase the initial 20 mg dosage of Omeprazol within 5 years. A mean of approximately DM 2,000 per patient was spent for conservative treatment. Surgical treatment without complications was calculated with DM 5,425 per case. However, in 7 patients complications occurred causing prolonged or even rehospitalization with necessary further treatment summing up to about DM 486,000 for surgical therapy in 70 patients including complications. Cost relevant factors are therefore in conservative treatment patients who need increasing dosages, while, in surgical treatment, the cost relevant patients are those with complications and necessary additional treatment.

Adolescent↗
PubMed2006

Disease risk analysis: a tool for primate conservation planning and decision making.

Concern about emerging and re-emerging diseases plays an increasing role in conservation and management of both captive and free-ranging nonhuman primates (NHPs). Managers and policy makers must formulate conservation plans in an arena plagued by uncertainty, complexity, emotion, and politics. The risk analysis paradigm provides a framework that brings together scientists and policy experts to make better decisions for both people and animals. Risk analysis is a multidisciplinary, science-based process that provides an organized and logical approach for incorporating scientific information into policy development in the real world. By blending four specific goal-oriented stages-hazard identification, risk assessment, risk management, and risk communication-one can logically assess the probability that an adverse event, such as the introduction of an emerging disease into a naïve population, will occur. The following is a review of this process as it pertains to NHP conservation and risks associated with infectious diseases.

Animals↗
PubMed2004

Genetic divergence, population structure and historical demography of rare springsnails (Pyrgulopsis) in the lower Colorado River basin.

Springsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.

Animals↗
PubMed2005

Phylogenic analysis of rickettsial patatin-like protein with conserved phospholipase A2 active sites.

Genome analysis of Rickettsia felis highlighted the presence of three patatin-like protein (PLP) genes (pat1, pat2A, and pat2B), whereas only one PLP gene (pat1) is found in the other sequenced rickettsial genomes. Here, we aligned the rickettsial PLPs with characterized patatins from plants and found that they possess all the conserved amino acid residues identified as important for phospholipase A(2) activity. We also carried out a phylogenic analysis of the rickettsial PLPs together with bacterial and eukaryotic homologs. The phylogeny of the rickettsial Pat1 proteins is in conflict with the currently recognized Rickettsia phylogeny. Possible scenarios that might explain this incongruence are discussed and involve either gene conversion or gene duplication events.

Amino Acid Sequence↗
PubMed2006

Risk of facial palsy and severe Frey's syndrome after conservative parotidectomy for benign disease: analysis of 610 operations.

CONCLUSIONS: Advanced age, long operation time and large specimen volume were significant risk factors for transient facial palsy after conservative parotidectomy. Revision operation was the only risk factor for development of a permanent palsy. Risk factors for Frey's syndrome were not found. The incidence of Frey's syndrome was not altered by the use of a sternocleidomastoid muscle flap or other implantation material. OBJECTIVES: The results of studies identifying risk factors for facial palsy and Frey's syndrome after parotidectomy are contradictory. This study attempted to identify these risk factors by performing a retrospective review of a large series of patients. PATIENTS AND METHODS: A total of 610 standardized conservative parotidectomies for benign diseases performed between 1989 and 2004 were studied retrospectively. The risk factors for facial palsy and Frey's syndrome were determined by univariate and if possible by multivariate analysis of variables related to patient demographics and operation characteristics. RESULTS: The rates of transient facial palsies, permanent facial palsies and Frey's syndrome were 18%, 4%, and 4%, respectively. Significant univariate and multivariate risk factors for development of a transient facial palsy were age>70 years, operation time>260 min, and a specimen volume>70 cm3. The only significant risk factor for the development of a permanent palsy was prior surgery. A significant risk factor for the development of Frey's syndrome could not be estimated.

Adenolymphoma↗
PubMed2005

A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes.

A long-standing question in molecular biology is whether interfaces of protein-protein complexes are more conserved than the rest of the protein surfaces. Although it has been reported that conservation can be used as an indicator for predicting interaction sites on proteins, there are recent reports stating that the interface regions are only slightly more conserved than the rest of the protein surfaces, with conservation signals not being statistically significant enough for predicting protein-protein binding sites. In order to properly address these controversial reports we have studied a set of 28 well resolved hetero complex structures of proteins that consists of transient and non-transient complexes. The surface positions were classified into four conservation classes and the conservation index of the surface positions was quantitatively analyzed. The results indicate that the surface density of highly conserved positions is significantly higher in the protein-protein interface regions compared with the other regions of the protein surface. However, the average conservation index of the patches in the interface region is not significantly higher compared with other surface regions of the protein structures. This finding demonstrates that the number of conserved residue positions is a more appropriate indicator for predicting protein-protein binding sites than the average conservation index in the interacting region. We have further validated our findings on a set of 59 benchmark complex structures. Furthermore, an analysis of 19 complexes of antigen-antibody interactions shows that there is no conservation of amino acid positions in the interacting regions of these complexes, as expected, with the variable region of the immunoglobulins interacting mostly with the antigens. Interestingly, antigen interacting regions also have a higher number of non-conserved residue positions in the interacting region than the rest of the protein surface.

Amino Acid Sequence↗
PubMed2000

Analysis of the levels of conservation of the J domain among the various types of DnaJ-like proteins.

DnaJ-like proteins are defined by the presence of an approximately 73 amino acid region termed the J domain. This region bears similarity to the initial 73 amino acids of the Escherichia coli protein DnaJ. Although the structures of the J domains of E coli DnaJ and human heat shock protein 40 have been solved using nuclear magnetic resonance, no detailed analysis of the amino acid conservation among the J domains of the various DnaJ-like proteins has yet been attempted. A multiple alignment of 223 J domain sequences was performed, and the levels of amino acid conservation at each position were established. It was found that the levels of sequence conservation were particularly high in 'true' DnaJ homologues (ie, those that share full domain conservation with DnaJ) and decreased substantially in those J domains in DnaJ-like proteins that contained no additional similarity to DnaJ outside their J domain. Residues were also identified that could be important for stabilizing the J domain and for mediating the interaction with heat shock protein 70.

Amino Acid Sequence↗
PubMed2026

Genome-wide characterization of BraABCB transporters reveals their potential roles in hormone responses in Brassica rapa var. parachinensis.

Thirty-six BraABCB genes were identified in Brassica rapa var. parachinensis; expression and interaction analyses suggest BraABCB27 and BraABCB28 as hormone-responsive candidates associated with BRI1-related proteins. ABCB transporters are ATP-dependent membrane proteins that mediate the transport of diverse substrates, including phytohormones, and play important roles in plant development and environmental adaptation. Previous studies in Arabidopsis have shown that several ABCB proteins participate in phytohormone transport, including auxin and brassinosteroid transport, whereas the functions of their homologs in Brassica rapa var. parachinensis remain poorly understood. In this study, 36 BraABCB genes were identified and classified into four phylogenetic groups. Conserved domain analysis showed that BraABCB proteins contain typical nucleotide-binding domains and transmembrane domains. Chromosomal distribution, collinearity, and Ka/Ks analyses suggested that the BraABCB family is evolutionarily conserved and mainly subject to purifying constraints. Promoter analysis and RT-qPCR assays of selected Group IV BraABCB genes revealed diverse expression patterns and responses to drought, high temperature, brassinolide, and indole-3-acetic acid treatments. Subcellular localization assays showed that selected Group IV BraABCB proteins exhibited predominant plasma membrane localization. Notably, BraABCB27 and BraABCB28, two close AtABCB1/AtABCB19-related homologs, showed detectable physical associations with BRI1-related proteins in BiFC and split-ubiquitin yeast two-hybrid assays. Together, these results provide a genome-wide characterization of the BraABCB gene family and identify BraABCB27 and BraABCB28 as candidate genes for future studies of their possible associations with BR-related membrane processes and hormone-regulated growth responses in B. rapa var. parachinensis.

Plant Growth Regulators↗