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At least 1,099 records · Page 61Linked to original sources
PubMed2001

A novel plasmid-mediated beta-lactamase that hydrolyzes broad-spectrum cephalosporins in a clinical isolate of Klebsiella pneumoniae.

A new extended-spectrum beta-lactamase with an isoelectric point (pI) of 6.2 was detected in Klebsiella pneumoniae F161 that was isolated from a patient with infection. This strain was highly resistant to the third or fourth generation cephalosporins such as ceftazidime, ceftriaxone, cefoperazone, and cefpirome. Analysis of this strain by the double disk diffusion test showed synergies between amoxicillin-clavulanate (AMX-CA) and cefotaxime, and AMX-CA and aztreonam, which suggested that this strain produced a extended-spectrum beta-lactamase (ESBL). Genetic analysis revealed that the resistance was due to the presence of a 9.4-kb plasmid, designated as pKP161, encoding for new beta-lactamase gene (bla). Sequence analysis showed that a new bla gene of pKP161 differed from bla(TEM-1) by three mutations leading to the following amino acid substitutions: Val84 --> Ile, Ala184 --> Val, and Gly238 --> Ser. These mutations have not been reported previously in the TEM type beta-lactamases produced by clinical strains. The novel beta-lactamase was overexpressed in E. coli and purified by ion exchange chromatography on Q-Sepharose and CM-Sepharose, and then further purified by gel filtration on Sehadex G-200. The catalytic activity of the purified beta-lactamase was confirmed by the nitrocefin disk.

Amino Acid Sequence↗
PubMed2005

New developments in the treatment of postmenopausal breast cancer.

In recent years, new agents have challenged tamoxifen as the standard endocrine therapy for postmenopausal breast cancer. This article reviews developments with regard to the third-generation aromatase inhibitors (AIs)--anastrozole, letrozole and exemestane--and fulvestrant, the first of a new type of estrogen receptor antagonist that, unlike tamoxifen, has no partial agonist activity. The final results of the "Arimidex", Tamoxifen, Alone or in Combination (ATAC) trial, at a median follow-up of more than five years, and recent results from switching studies with anastrozole and exemestane, strengthen the position of these AIs as adjuvant treatment for hormone receptor-positive early breast cancer. Sequencing options for the future are also discussed because non-steroidal AIs are increasingly used early in the treatment sequence.

Anastrozole↗
PubMed2004

KCNJ11 polymorphisms and sudden cardiac death in patients with acute myocardial infarction.

PURPOSE: Patients with an acute myocardial infarction (AMI) are of high risk to develop ischemia-induced ventricular arrhythmias, leading to sudden cardiac death (SCD) in about one third of all AMI patients. The individual susceptibility to ischemia-induced arrhythmias may be modified by polymorphisms in genes encoding ion channels. The cardiac ATP-dependent potassium channel (K(ATP)) current is generated by ion channels encoded by the KCNJ11 gene and the SUR2a gene. Opening of the K(ATP) channel during ischemia results in action potential shortening in various studies and may therefore influence the outcome of AMI patients. METHODS: Using a three-primer strategy, we sequenced the complete coding and adjacent 5' and 3' sequences of the intronless KCNJ11 gene (1.3 kb) prospectively in two groups. Patients of group 1 (n = 84) survived three or more transmyocardial infarctions without developing any ventricular arrhythmias. Patients of group 2 died suddenly from their first myocardial infarction (n = 86), most of them witnessed SCDs. RESULTS: We identified a total of six known polymorphisms (K23E, A190A, L267V, L270V, I337V, and K281K) and two new polymorphisms (L267L, 3'UTR +62 G/A). The allele, genotype, and haplotype frequencies did not differ between the two groups. All polymorphisms were found to be in Hardy-Weinberg equilibrium. In addition, we identified two novel missense mutations in a highly conserved region of the gene in two patients of group 2 (P266T and R371H) with yet unknown functional consequences. CONCLUSION: In this study of AMI patients, SCD was not related to polymorphisms in the KCNJ11 gene.

Aged↗
PubMed2004

Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences.

We developed an automated pipeline for the detection of single nucleotide polymorphisms (SNPs) in expressed sequence tag (EST) data sets, by combining three DNA sequence analysis programs: Phred, Phrap and PolyBayes. This application requires access to the individual electrophoregram traces. First, a reference set of 65 SNPs was obtained from the sequencing of 30 gametes in 13 maritime pine (Pinus pinaster Ait.) gene fragments (6671 bp), resulting in a frequency of 1 SNP every 102.6 bp. Second, parameters of the three programs were optimized in order to retrieve as many true SNPs, while keeping the rate of false positive as low as possible. Overall, the efficiency of detection of true SNPs was 83.1%. However, this rate varied largely as a function of the rare SNP allele frequency: down to 41% for rare SNP alleles (frequency < 10%), up to 98% for allele frequencies above 10%. Third, the detection method was applied to the 18498 assembled maritime pine (Pinus pinaster Ait.) ESTs, allowing to identify a total of 1400 candidate SNPs, in contigs containing between 4 and 20 sequence reads. These genetic resources, described for the first time in a forest tree species, were made available at http://www.pierroton.inra/genetics/Pinesnps. We also derived an analytical expression for the SNP detection probability as a function of the SNP allele frequency, the number of haploid genomes used to generate the EST sequence database, and the sample size of the contigs considered for SNP detection. The frequency of the SNP allele was shown to be the main factor influencing the probability of SNP detection.

Algorithms↗
PubMed2000

Evolution of the neuropeptide Y receptor family: gene and chromosome duplications deduced from the cloning and mapping of the five receptor subtype genes in pig.

Neuropeptide Y (NPY) receptors mediate a variety of physiological responses including feeding and vasoconstriction. To investigate the evolutionary events that have generated this receptor family, we have sequenced and determined the chromosomal localizations of all five presently known mammalian NPY receptor subtype genes in the domestic pig, Sus scrofa (SSC). The orthologs of the Y(1) and Y(2) subtypes display high amino acid sequence identities between pig, human, and mouse (92%-94%), whereas the Y(4), Y(5), and y(6) subtypes display lower identities (76%-87%). The lower identity of Y(5) is due to high sequence divergence in the large third intracellular loop. The NPY1R, NPY2R, and NPY5R receptor genes were localized to SSC8, the NPY4R to SSC14, and NPY6R to SSC2. Our comparisons strongly suggest that the tight cluster of NPY1R, NPY2R, and NPY5R on human chromosome 4 (HSA4) represents the ancestral configuration, whereas the porcine cluster has been split by two inversions on SSC8. These 3 genes, along with adjacent genes from 14 other gene families, form a cluster on HSA4 with extensive similarities to a cluster on HSA5, where NPY6R and >13 other paralogs reside, as well as another large cluster on HSA10 that includes NPY4R. Thus, these gene families have expanded through large-scale duplications. The sequence comparisons show that the NPY receptor triplet NPY1R-NPY2R-NPY5R existed before these large-scale duplications.

Animals↗
PubMed2003

Cytadherence-deficient mutants of Mycoplasma gallisepticum generated by transposon mutagenesis.

Cytadherence-related molecules of Mycoplasma gallisepticum strain R-low were identified by Tn4001 transposon mutagenesis with the hemadsorption (HA) assay as an indicator for cytadherence. Three Gm(r) HA-negative (HA(-)) colonies displaying a stable HA(-) phenotype through several successive generations in which gentamicin selection was maintained were isolated from four independent transformation experiments and characterized. Southern blot analysis showed that the transposon was inserted as a single copy within the genome of each of the HA(-) mutants, suggesting that the transposon insertion was directly responsible for their inability to attach to erythrocytes. Sequence analysis of the transposon insertion sites revealed that in two mutants, the transposon was inserted at two distinct sites within the gapA structural gene. In the third mutant, the insertion was mapped within the crmA gene, which is located immediately downstream of the gapA gene as part of the same operon. In vitro attachment experiments with the MRC-5 human lung fibroblast cell line showed that the cytadherence capabilities of the HA(-) mutants were less than 25% those of original strain R. Experimental infection of chickens, the natural host of M. gallisepticum, with each of the three mutants demonstrated significantly impaired colonization and host responses. These data demonstrate conclusively the role of both GapA and CrmA proteins in the adherence of M. gallisepticum to host cells in model systems and in vivo colonization. Furthermore, these results underscore the relevance of in vitro cytadherence model systems for studying the pathogenesis of natural infections in chickens.

Adhesins, Bacterial↗
PubMed1999

Structural elements within the methylation loop (residues 112-117) and EF hands III and IV of calmodulin are required for Lys(115) trimethylation.

Calmodulin is trimethylated by a specific methyltransferase on Lys115, a residue located in a six amino acid loop (LGEKLT) between EF hands III and IV. To investigate the structural requirements for methylation, domain exchange mutants as well as single point mutations of conserved methylation loop residues (E114A, Glu114-->Ala; L116T, Leu116-->Thr) were generated. E114A and L116T activated cyclic nucleotide phosphodiesterase (PDE) and NAD+ kinase (NADK) similar to wild-type calmodulin, but lost their ability to be methylated. Domain exchange mutants in which EF hand III or IV was replaced by EF hand I or II respectively (CaM1214 and CaM1232 respectively) showed a modest effect on PDE and NADK activation (50 to 100% of wild-type), but calmodulin methylation was abolished. A third domain exchange mutant, CaMEKL, has the methylation loop sequence placed at a symmetrical position between EF hands I and II in the N-terminal lobe [residues QNP(41-43) replaced by EKL]. CaMEKL activated PDE normally, but did not activate NADK. However, CaMEKL retained the ability to bind to NADK and inhibited activation by wild-type calmodulin. Site-directed mutagenesis of single residues showed that Gln41 and Pro43 substitutions had the strongest effect on NADK activation. Additionally, CaMEKL was not methylated, suggesting that the introduction of the methylation loop between EF hands I and II is not adequate for methyltransferase recognition. Overall the data indicate that residues in the methylation loop are essential but not sufficient for methyltransferase recognition, and that additional residues unique to EF hands III and IV are required. Secondly, the QNP sequence in the loop between EF hands I and II is necessary for NADK activation.

Base Sequence↗
PubMed1993

The phylogenetic utility of cytochrome b: lessons from bufonid frogs.

The mitochondrial cytochrome b gene is widely used in systematic studies to resolve divergences of many different ages. To investigate phylogenetic relationships among frogs of the large family Bufonidae, and to explore the utility of cytochrome b for this purpose, approximately one-third of the gene was sequenced from representatives of this group. Samples were chosen to represent a range of divergence levels within Bufonidae: (1) deep (= old), among species from around the world; (2) middle, among North American species; and (3) shallow (= young), within a single species group (the Bufo boreas group). The inferred amino acid sequences of cytochrome b are highly similar in these frogs although most pairwise comparisons of the nucleotide sequences are 15-20% different. Consequently insufficient information is available to generate robust phylogenetic hypotheses for the older divergences; silent differences are saturated and yet almost no informative replacement differences exist. Among the younger divergences, silent differences are not saturated and some resolution is possible. These results show that (1) the amino acid sequence of cytochrome b evolves differently in Bufonidae than expected based on other vertebrates (2) it consequently provides surprisingly little information about old divergences in Bufonidae, and (3) phylogenetic studies applying particular genes to new groups should begin with preliminary surveys of exemplar taxa representing the range of divergence times within the group to estimate the likely phylogenetic utility of that gene in that group.

Amino Acid Sequence↗
PubMed1989

Allelic variation linked to adenine phosphoribosyltransferase locus in mouse teratocarcinoma cell line and feral-derived mouse strains.

Southern blot analysis reveals two distinct adenine phosphoribosyltransferase (APRT) alleles in the P-19 mouse teratocarcinoma cell line. One allele is identical to that observed in common laboratory mouse strains (Mus musculus domesticus). The restriction enzyme site variations between the two alleles occur in sequences located both upstream and downstream of the APRT gene, but not within it. Although the P-19 cell line was established from a C3H strain embryo (Mus musculus domesticus), a sixth generation ancestor of this embryo was a feral mouse (Mus musculus musculus). The restriction pattern of the variant APRT allele in P-19 is identical to that of a feral-derived Mus musculus musculus animal, establishing the origin of this allele in the P-19 cell line. A third, distinct APRT allele was found in a Mus spretus feral-derived mouse. Exploiting the differences between the two APRT alleles in the P-19 cell line, we have demonstrated their sequential loss in APRT-deficient clones.

Adenine Phosphoribosyltransferase↗
PubMed1997

Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination.

One-third of humans are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. Sequence analysis of two megabases in 26 structural genes or loci in strains recovered globally discovered a striking reduction of silent nucleotide substitutions compared with other human bacterial pathogens. The lack of neutral mutations in structural genes indicates that M. tuberculosis is evolutionarily young and has recently spread globally. Species diversity is largely caused by rapidly evolving insertion sequences, which means that mobile element movement is a fundamental process generating genomic variation in this pathogen. Three genetic groups of M. tuberculosis were identified based on two polymorphisms that occur at high frequency in the genes encoding catalase-peroxidase and the A subunit of gyrase. Group 1 organisms are evolutionarily old and allied with M. bovis, the cause of bovine tuberculosis. A subset of several distinct insertion sequence IS6110 subtypes of this genetic group have IS6110 integrated at the identical chromosomal insertion site, located between dnaA and dnaN in the region containing the origin of replication. Remarkably, study of approximately 6,000 isolates from patients in Houston and the New York City area discovered that 47 of 48 relatively large case clusters were caused by genotypic group 1 and 2 but not group 3 organisms. The observation that the newly emergent group 3 organisms are associated with sporadic rather than clustered cases suggests that the pathogen is evolving toward a state of reduced transmissability or virulence.

Alleles↗
PubMed1993

The third human homolog of a murine gene encoding an inhibitor of stem cell proliferation is truncated and linked to a CpG island-containing upstream sequence.

The murine gene, MIP1 alpha, encodes a cytokine (macrophage inflammatory protein 1 alpha) that inhibits the proliferation of bone marrow stem cells. Two human homologs have been characterized, G0S19-1 and G0S19-2. Like MIP1 alpha, these genes contain three exons, the first of which encodes a hydrophobic signal sequence. The existence of a third human G0S19 gene, present in one in four individuals, has been predicted from restriction enzyme analyses. This paper reports that a previously identified human genomic clone containing a G0S19 sequence (G0S19-3), corresponds to the third gene. However, the first G0S19 exon is missing. The sequence differs from those of G0S19-1 and G0S19-2 upstream of a point 31 nucleotides from the junction of the first intron with the second exon. This upstream sequence contains a CpG island and is named "CpG island-containing upstream sequence," CUS. Apart from the G0S19-3-associated copy found only in individuals with the third G0S19 gene, all individuals have one DNA species hybridizing strongly to a CUS-specific probe and at least two less strongly hybridizing species. The CUS has potential binding sites for transcription factors AP-1, AP-2, AP-3, AP-4, and Sp1, a Donehower conserved repetitive element, and motifs characteristic of cytokine, oncogene, and retroviral promoters. Thus, the CUS might promote the transcription of sequences with which it became associated. We suggest that the CUS-G0S19-3 sequence was generated by recombination between a G0S19-2 gene and a member of a novel CUS-associated gene family.

Base Sequence↗
PubMed1996

Two different RNA binding activities for the AU-rich element and the poly(A) sequence of the mouse neuronal protein mHuC.

HuC is one of the RNA binding proteins which are suggested to play important roles in neuronal differentiation and maintenance. We cloned and sequenced cDNAs encoding a mouse protein which is homologous to human HuC (hHuC). The longest cDNA encodes a 367 amino acid protein with three RNA recognition motifs (RRMs) and displays 96% identity to hHuC. Northern blot analysis showed that two different mRNAs, of 5.3 and 4.3 kb, for mouse HuC (mHuC) are expressed specifically in brain tissue. Comparison of cDNA sequences with the corresponding genomic sequence revealed that alternative 3' splice site selection generates two closely related mHuC isoforms. Iterative in vitro RNA selection and binding analyses showed that both HuC isoforms can bind with almost identical specificity to sequences similar to the AU-rich element (ARE), which is involved in the regulation of mRNA stability. Functional domain mapping using mHuC deletion mutants showed that the first RRM binds to ARE, that the second RRM has no RNA binding activity by itself, but facilitates ARE binding by the first RRM and that the third RRM has specific binding activity for the poly(A) sequence.

Alternative Splicing↗
PubMed2000

Isolation and characterization of Francisella novicida mutants defective in lipopolysaccharide biosynthesis.

In order to identify genes involved in LPS biosynthesis we isolated random mutants generated by transposon insertion in Francisella novicida. The resulting mutant bank yielded mutants with three distinct LPS phenotypes, and three representative mutants were chosen for further study. One mutant that had short O-antigen chains was sensitive to serum; this mutant and one other were more sensitive to killing by deoxycholate than control strains. The third mutant was resistant to deoxycholate killing but slightly sensitive to serum. The three mutants varied in their ability to grow in macrophages. The DNA sequences interrupted by the transposon in two of the three mutants showed similarity to known LPS biosynthetic genes at the deduced amino acid level.

Animals↗
PubMed1988

Biliary obstruction after cholecystectomy: diagnosis with quantitative cholescintigraphy.

Fifty patients with recurrent post-cholecystectomy pain underwent hepatobiliary scintigraphy. Time-activity curves were generated from regions of interest over the liver, bile duct, duodenum, and bowel. Patients were divided into obstructed and unobstructed groups with endoscopic retrograde cholangiopancreatography criteria. Measurements from the liver, duodenum, and bowel curves contributed little to the analysis. The washout phase of the bile duct curve showed intermittent emptying in both obstructed and unobstructed groups. Less than one-third of peak activity remained in both groups at 90 minutes. Retention fell more rapidly in the later portion of the sequence in patients with obstruction. Quantification was essential, since differences were subtle and could not be appreciated visually. In the absence of hepatocellular disease, the most reliable criterion was the time at which maximal bile duct activity occurred. A cutoff level of 29 minutes or more was used in the diagnosis of obstruction. A sensitivity of 93% with an adequate specificity of 64% and an overall accuracy of 80% was achieved in the prediction of obstruction.

Adult↗
PubMed2004

Central control of electric signaling behavior in the mormyrid Brienomyrus brachyistius: segregation of behavior-specific inputs and the role of modifiable recurrent inhibition.

Like all mormyrid fish, Brienomyrus brachyistius produces an electric organ discharge (EOD) with a constant waveform and variable sequence of pulse intervals (SPI). Periodic bursts fall into two display categories termed 'scallops' and 'accelerations', with a third category termed 'rasps' that appears to combine the two. The medullary EOD command nucleus (CN) receives excitatory input from the midbrain precommand nucleus (PCN) and the thalamic dorsal posterior nucleus (DP), both of which are regulated by a recurrent inhibitory projection from the ventroposterior nucleus of the torus semicircularis (VP). We tested the following hypotheses: (1) PCN and DP are responsible for generating different burst types (scallops and accelerations, respectively), (2) differences in the strength of recurrent inhibition are related to physiological differences between PCN and DP and (3) recurrent inhibition regulates the resting electromotor rhythm, while disinhibition releases PCN and DP, allowing them to generate bursts. Iontophoresis of the excitatory neurotransmitter L-glutamate (L-Glu) into DP led to acceleration-like output patterns, while in PCN it led to scallop-like output patterns. Iontophoresis of the inhibitory neurotransmitter gamma-amino-butyric acid (GABA) into DP and PCN led to an elongation of intervals, as did iontophoresis of L-Glu into VP. Iontophoresis of the GABA(A) receptor blocker bicuculline methiodide (BMI) into DP and PCN induced repetitive bursting behavior and eliminated differences in the effects of L-Glu iontophoresis in the two nuclei. These results support our three hypotheses, suggesting that production of different communication behaviors may be regulated by spatially distinct groups of neurons, and recurrent inhibition and disinhibition may play an active role in driving and shaping such behaviors.

Animal Communication↗
PubMed2004

Structural and conformational aspects of the anticoagulant and anti-thrombotic activity of heparin and dermatan sulfate.

Heparin and other iduronic acid-containing glycosaminoglycans (GAG) such as dermatan sulfate exert their anticoagulant properties primarily by accelerating the rate of inhibition of the natural protease inhibitors antithrombin III (AT, which inhibits both factor Xa and thrombin) and heparin cofactor II (HCII, which selectively inhibits thrombin). Although AT and HCII are structural homologs, only heparin binds to AT, and HCII has different binding sites for heparin and dermatan sulfate. Whereas the binding site of heparin for AT is a unique pentasaccharide sequence contained in only about one third of the chains of this GAG, HCII-binding sequences of heparin and dermatan sulfate are less specific and contained in practically all the GAG chains. Protein binding and associated biological activities of heparin and dermatan sulfate are modulated by the "plasticity" of their iduronic acid residues due to the availability of up to three equienergetic conformation among which the protein selects the one favouring the most stable complex. Glycol-splitting of nonsulfated uronic acid residues, a device for generating flexible joints along the GAG chains, has different effects on different binding domains. Whereas it inactivates the binding site for AT causing a drop of the anticoagulant activity, it enhances the HCII-associated activity of both heparin and dermatan sulfate.

Anticoagulants↗
PubMed1999

Pac1p, an RNase III homolog, is required for formation of the 3' end of U2 snRNA in Schizosaccharomyces pombe.

Like its homologs in higher eukaryotes, the U2 snRNA in Schizosaccharomyces pombe is transcribed by RNA polymerase II and is not polyadenylated. Instead, an RNA stem-loop structure located downstream of the U2 snRNA coding sequence and transcribed as part of a 3' extended precursor serves as a signal for 3'-end formation. We have identified three mutants that have temperature-sensitive defects in U2 snRNA 3'-end formation. In these mutants, the synthesis of the major snRNAs is also affected and unprocessed rRNA precursors accumulate at the restrictive temperature. Two of these mutants contain the same G-to-A transition within the pac1 gene, whereas the third contains a lesion outside the pac1 locus, indicating that at least two genes are involved. The pac1+ gene is codominant with the mutant allele and can rescue the temperature-sensitive phenotype and the defects in snRNA and rRNA synthesis, if overexpressed. In vitro, Pac1p, an RNase III homolog, can cleave a synthetic U2 precursor within the signal for 3'-end formation, generating a product that is a few nucleotides longer than mature U2 snRNA. In addition, U2 precursors are cleaved and trimmed to the mature size in extracts made from wild-type S. pombe cells. However, extracts made from pac1 mutant cells are unable to do so unless they are supplemented with purified recombinant Pac1p. Thus, the 3' end of S. pombe U2 snRNA is generated by a processing reaction that requires Pac1p and an additional component, and can be dissociated from transcription in vitro.

Amino Acid Sequence↗
PubMed1997

Localization of ligand-binding domains of human corticotropin-releasing factor receptor: a chimeric receptor approach.

Two CRF receptors, CRFR1 and CRFR2, have recently been cloned and characterized. CRFR1 shares 70% sequence identity with CRFR2, yet has much higher affinity for rat/human CRF (r/hCRF) than CRFR2. As a first step toward understanding the interactions between rat/human CRF and its receptor, the regions that are involved in receptor-ligand binding and/or receptor activation were determined by using chimeric receptor constructs of the two human CRFR subtypes, CRFR1 and CRFR2, followed by generating point mutations of the receptor. The EC50 values in stimulation of intracellular cAMP of the chimeric and mutant receptors for the peptide ligand were determined using a cAMP-dependent reporter system. Three regions of the receptor were found to be important for optimal binding of r/hCRF and/or receptor activation. The first region was mapped to the junction of the third extracellular domain and the fifth transmembrane domain; substitution of three amino acids of CRFR1 in this region (Val266, Tyr267, and Thr268) by the corresponding CRFR2 amino acids (Asp266, Leu267, and Val268) increased the EC50 value by approximately 10-fold. The other two regions were localized to the second extracellular domain of the CRFR1 involving amino acids 175-178 and His189 residue. Substitutions in these two regions each increased the EC50 value for r/hCRF by approximately 7- to 8-fold only in the presence of the amino acid 266-268 mutation involving the first region, suggesting that their roles in peptide ligand binding might be secondary.

Amino Acid Sequence↗