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At least 1,207 records · Page 67Linked to original sources
PubMed2003

Determination of the charge state distribution of a highly ionized coronal Au plasma.

We present the first definitive measurement of the charge state distribution of a highly ionized gold plasma in coronal equilibrium. The experiment utilized the Livermore electron beam ion trap EBIT-II in a novel configuration to create a plasma with a Maxwellian temperature of 2.5 keV. The charge balance in the plasma was inferred from spectral line emission measurements which accounted for charge exchange effects. The measured average ionization state was 46.8+/-0.75. This differs from the predictions of two modeling codes by up to four charge states.

Journal Article↗
PubMed2005

Experimental benchmark for an improved simulation of absolute soft-x-ray emission from polystyrene targets irradiated with the Nike laser.

Absolutely calibrated, time-resolved spectral intensity measurements of soft-x-ray emission (hnu approximately 0.1-1.0 keV) from laser-irradiated polystyrene targets are compared to radiation-hydrodynamic simulations that include our new postprocessor, Virtual Spectro. This new capability allows a unified, detailed treatment of atomic physics and radiative transfer in nonlocal thermodynamic equilibrium conditions for simple spectra from low-Z materials as well as complex spectra from high-Z materials. The excellent agreement (within a factor of approximately 1.5) demonstrates the powerful predictive capability of the codes for the complex conditions in the ablating plasma. A comparison to data with high spectral resolution (E/deltaE approximately 1000) emphasizes the importance of including radiation coupling in the quantitative simulation of emission spectra.

Journal Article↗
PubMed2002

Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase.

The spontaneous occurrence of resistance to the herbicide glyphosate in weed species has been an extremely infrequent event, despite over 20 years of extensive use. Recently, a glyphosate-resistant biotype of goosegrass (Eleusine indica) was identified in Malaysia exhibiting an LD(50) value approximately 2- to 4-fold greater than the sensitive biotype collected from the same region. A comparison of the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity by glyphosate in extracts prepared from the resistant (R) and sensitive (S) biotypes revealed an approximately 5-fold higher IC(50)(glyphosate) for the (R) biotype. Sequence comparisons of the predicted EPSPS mature protein coding regions from both biotypes revealed four single-nucleotide differences, two of which result in amino acid changes. One of these changes, a proline to serine substitution at position 106 in the (R) biotype, corresponds to a substitution previously identified in a glyphosate-insensitive EPSPS enzyme from Salmonella typhimurium. Kinetic data generated for the recombinant enzymes suggests that the second substitution identified in the (R) EPSPS does not contribute significantly to its reduced glyphosate sensitivity. Escherichia coli aroA- (EPSPS deficient) strains expressing the mature EPSPS enzyme from the (R) biotype exhibited an approximately 3-fold increase in glyphosate tolerance relative to strains expressing the mature EPSPS from the (S) biotype. These results provide the first evidence for an altered EPSPS enzyme as an underlying component of evolved glyphosate resistance in any plant species.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed1992

Cloning and characterization of a phospholipase gene from Erwinia chrysanthemi EC16.

A single gene (plcA) was cloned from a cosmid library of Erwinia chrysanthemi EC16 DNA that encoded an extracellular phospholipase. The gene was subcloned and DNA sequence data showed the presence of a single open reading frame encoding a protein with a predicted size of 39 kDa. The coding region was G+C-rich and the protein had a predicted basic isoelectric point. The protein showed no significant homology with others in the PIR library, including other phospholipases. When overexpressed in Escherichia coli cells, the plcA gene directed production of a c. 39 kDa protein that was largely localized in the periplasm, but its N-terminal amino acid sequence was that of the native protein predicted from DNA sequence data. Unlike the wild-type bacterium, an E. chrysanthemi EC16 marker exchange mutant of the plcA gene did not secrete extracellular phospholipase activity in the medium. However, no detectable change was observed in terms of the virulence of the mutant strain on potato tubers or chrysanthemum stems.

Amino Acid Sequence↗
PubMed2004

Quantifying headache symptoms and other headache features from chart notes.

OBJECTIVES: To describe a method for quantifying headache symptoms/features in family practice charts for patients diagnosed with headache NOS (not otherwise specified, ICD-9: 784) and to determine the share of NOS headache diagnoses with clinical data strongly suggestive of migraine or probable migraine headache. BACKGROUND: Headache is one of the most common pain symptoms that brings patients to a family physician. However, the majority of headache sufferers do not receive a specific headache diagnosis when they visit physicians. METHODS: We examined the chart notes of 454 patients exclusively diagnosed with one or more ICD-9 coded headache NOS diagnoses from July 1, 1995 through December 31, 1999 at a large suburban, university-affiliated practice. We developed a template containing 20 headache items combining International Headache Society diagnostic criteria and additional headache symptoms/features, and decision rules for coding symptoms/features and collected data from patient charts. We then developed decision rules and reclassified NOS headaches into categories strongly suggestive of migraine, probable migraine headache, or other diagnosis. Our main outcome measure is the consistency in the application of decision rules and diagnostic criteria. RESULTS: With this method we estimate 3 in 10 (29%) headache NOS patients may have had migraine (8%) or probable migraine headache (21%). Reclassified migraine visits averaged 6.5 migraine symptoms and reclassified probable migraine headache visits 4.7 migraine symptoms. Logistic regression analysis supports the consistency of diagnostic criteria for classifying headache based on coded symptoms/features--our model correctly predicted 96% of visits. Evidence of physical examination was recorded at 75% of visits suggesting that physician attention is focused on elimination of secondary headache. CONCLUSIONS: We think the use of our rigorous procedures reveals that a substantial amount of migraine and probable migraine headache may be missed in everyday practice. We hope our findings will provide a basis for the development of diagnostic methods more closely suited to the needs of nonspecialists, and contribute to a better standard of care for headache patients seen in primary care practice. Finally, we are hopeful that other researchers will consider using our template and guideline procedures in their efforts to identify diagnostic patterns and study headache and other health problems.

Adult↗
PubMed1998

Codon usage in Actinobacillus actinomycetemcomitans.

The codon usage patterns of 21 genes encompassing 5800 codons from Actinobacillus actinomycetemcomitans were analyzed. A. actinomycetemcomitans genes could be divided into two groups based on their function and G + C content. One group included those genes encoding basic cellular functions. This group displayed an average G + C content of 48%. A second group comprised genes encoding the leukotoxin determinant, an insertion sequence and a plasmid. This group displayed an average G + C content of 36%. These findings suggest that portions of the A. actinomycetemcomitans genome may have been acquired by horizontal gene transfer from one or more distantly related species. We present a table of A. actinomycetemcomitans codon usage. These data may be used to establish standards for computer programs that predict A. actinomycetemcomitans protein coding regions and may be useful in designing degenerate oligonucleotide probes.

Adolescent↗
PubMed2004

PF15p is the chlamydomonas homologue of the Katanin p80 subunit and is required for assembly of flagellar central microtubules.

Numerous studies have indicated that the central apparatus plays a significant role in regulating flagellar motility, yet little is known about how the central pair of microtubules or their associated projections assemble. Several Chlamydomonas mutants are defective in central apparatus assembly. For example, mutant pf15 cells have paralyzed flagella that completely lack the central pair of microtubules. We have cloned the wild-type PF15 gene and confirmed its identity by rescuing the motility and ultrastructural defects in two pf15 alleles, the original pf15a mutant and a mutant generated by insertional mutagenesis. Database searches using the 798-amino-acid polypeptide predicted from the complete coding sequence indicate that the PF15 gene encodes the Chlamydomonas homologue of the katanin p80 subunit. Katanin was originally identified as a heterodimeric protein with a microtubule-severing activity. These results reveal a novel role for the katanin p80 subunit in the assembly and/or stability of the central pair of flagellar microtubules.

Adenosine Triphosphatases↗
PubMed1994

Molecular analysis of urease genes from a newly identified uncultured species of Helicobacter.

"Gastrospirillum hominis" is an uncultured gastric spiral bacterium that has recently been shown by 16S rDNA sequence analysis to be a newly recognized species of Helicobacter that infects humans, and it has been provisionally designated "Helicobacter heilmannii." We used PCR to directly amplify the urease structural genes of "H. heilmannii" from infected gastric tissue. DNA sequence analysis identified two open reading frames, ureA and ureB, which code for polypeptides with predicted molecular weights of 25,729 and 61,831, respectively. The urease subunit genes from "H. heilmannii" were cloned and expressed in Escherichia coli. Western blot (immunoblot) analysis showed that antiserum directed against the ureA and ureB gene products from H. pylori was cross-reactive with the corresponding polypeptides from "H. heilmannii." Analysis of the derived amino acid sequences of "H. heilmannii" UreA and UreB demonstrated that "H. heilmannii" urease is more highly related to the urease from H. felis (found in the stomachs of cats and dogs) than to the urease from H. pylori. These data are consistent with 16S rDNA sequence analysis and suggest that "H. heilmannii" is phylogenetically most closely related to H. felis.

Amino Acid Sequence↗
PubMed2005

Expression library immunization confers protection against Mycobacterium avium subsp. paratuberculosis infection.

Currently, paratuberculosis vaccines are comprised of crude whole-cell preparations of Mycobacterium avium subsp. paratuberculosis. Although effective in reducing clinical disease and fecal shedding, these vaccines have severe disadvantages as well, including seroconversion of vaccinated animals and granulomatous lesions at the site of vaccination. DNA vaccines can offer an alternative approach that may be safer and elicit more protective responses. In an effort to identify protective M. avium subsp. paratuberculosis sequences, a genomic DNA expression library was generated and subdivided into pools of clones (approximately 1,500 clones/pool). The clone pools were evaluated to determine DNA vaccine efficacy by immunizing mice via gene gun delivery and challenging them with live, virulent M. avium subsp. paratuberculosis. Four clone pools resulted in a significant reduction in the amount of M. avium subsp. paratuberculosis recovered from mouse tissues compared to mice immunized with other clone pools and nonvaccinated, infected control mice. One of the protective clone pools was further partitioned into 10 clone arrays of 108 clones each, and four clone arrays provided significant protection from both spleen and mesenteric lymph node colonization by M. avium subsp. paratuberculosis. The nucleotide sequence of each clone present in the protective pools was determined, and coding region functions were predicted by computer analysis. Comparison of the protective clone array sequences implicated 26 antigens that may be responsible for protection in mice. This study is the first study to demonstrate protection against M. avium subsp. paratuberculosis infection with expression library immunization.

Animals↗
PubMed2006

Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens.

The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.

Base Composition↗
PubMed1994

An amplifiable DNA region from the Mycoplasma hyorhinis genome.

A novel amplifiable genomic region that displays variability in the number of tandem copies of a 1,368-bp DNA sequence (designated RS-2) was discovered among individual clonal derivatives within Mycoplasma hyorhinis broth-grown cell populations. Clonal isolates representing variant subpopulations from the original broth culture were of a single size variant, and although continued culture under a variety of growth conditions did not result in further amplification of RS-2, evidence for deletion events which reduced RS-2 copy number, presumably by homologous recombination, was obtained. RS-2 homologous sequences were identified in all M. hyorhinis strains tested, but only the tissue culture-derived strains GDL-1 and GDL-2 showed variability in genomic dosage. The RS-2 nucleotide sequence established that each tandem copy is flanked by direct repeats of a 20-bp sequence and suggested a possible mechanism for its original duplication as the initial phase of a genetic amplification process. The coding strand was defined by PCR amplification of a reverse transcriptase-generated cDNA, and its sequence revealed that RS-2 encodes a 456-residue internal, highly cysteine-rich domain of a larger M. hyorhinis protein whose coding sequence initiates and terminates in unique genomic sequences several hundred base pairs from RS-2 on either side of it. Changes in RS-2 copy number maintain the reading frame, and therefore the coding capacity, for this predicted size-variant protein.

Amino Acid Sequence↗
PubMed1998

The bldB gene encodes a small protein required for morphogenesis, antibiotic production, and catabolite control in Streptomyces coelicolor.

Mutants blocked at the earliest stage of morphological development in Streptomyces species are called bld mutants. These mutants are pleiotropically defective in the initiation of development, the ability to produce antibiotics, the ability to regulate carbon utilization, and the ability to send and/or respond to extracellular signals. Here we report the identification and partial characterization of a 99-amino-acid open reading frame (ORF99) that is capable of restoring morphogenesis, antibiotic production, and catabolite control to all of the bldB mutants. Of the existing bld mutants, bldB is of special interest because the phenotype of this mutant is the most pleiotropic. DNA sequence analysis of ORF99 from each of the existing bldB mutants identified base changes either within the coding region of the predicted protein or in the regulatory region of the gene. Primer extension analysis identified an apparent transcription start site. A promoter fusion to the xylE reporter gene showed that expression of bldB is apparently temporally regulated and that the bldB gene product is involved in the regulation of its own expression.

Amino Acid Sequence↗
PubMed1985

Evidence for at least two dominant neutralization antigens on human rhinovirus 14.

A collection of 28 mutants of human rhinovirus 14, selected for resistance to 10 individual neutralizing monoclonal antibodies, was used to identify two major neutralization antigens, N-Ag I and N-Ag II. Isoelectric analysis showed that all 16 of the N-Ag I mutants analyzed were charge altered in VP1;8 of 12 N-Ag II mutants were altered in VP3. These results suggest that N-Ag I resides on VP1, whereas N-Ag II lies on VP3. The frequency of charge alterations was much higher than predicted by the genetic code, suggesting that charged amino acids on the antigenic sites play an important role in interaction with neutralizing antibody. Antibodies against N-Ag I and N-Ag II neutralize with widely different efficiencies.

Amino Acids↗
PubMed1995

Isolation and characterization of a low-abundance splice variant from the human cytomegalovirus major immediate-early gene region.

The major immediate-early (IE) gene region of human cytomegalovirus (HCMV) encodes several proteins as a result of differential RNA splicing events. By expression vector cloning of HCMV IE mRNA, we isolated and characterized a cDNA for a novel splice variant from the major IE gene region. The RNA product is a derivative of the IE55 mRNA and contains an additional splice from nucleotides 170,635 to 170,307 in the IE2 gene region (UL122), resulting in a 1.4-kb mRNA. The predicted open reading frame codes for a 164-amino-acid protein with a calculated molecular mass of 18 kDa (IE18). Mung bean nuclease analysis and PCR were used to characterize expression of IE18 mRNA in HCMV-infected cells. While the 1.4-kb mRNA was detected in infected human fibroblasts in the presence of a protein synthesis inhibitor, it was not detectable during a normal infection. However, the 1.4-kb mRNA was readily detected in infected human monocyte-derived macrophages at IE times. These results suggest that the novel IE18 mRNA exhibits cell type-specific expression indicating differential regulation of the major IE gene region in different permissive cell types.

Amino Acid Sequence↗
PubMed2025

Genomic and stress resistance characterization of Lactiplantibacillus plantarum GX17, a potential probiotic for animal feed applications.

UNLABELLED: Lactobacilli, recognized as beneficial bacteria within the human body, are celebrated for their multifaceted probiotic functions, including the regulation of intestinal flora, enhancement of body immunity, and promotion of nutrient absorption. This study comprehensively analyzed the genotypic and phenotypic characteristics of Lactiplantibacillus plantarum (L. plantarum) strains isolated from the intestines of healthy chicks and assessed their potential as probiotics. The assembled genome consists of 29,521,986 bp, and a total of 1,771 coding sequences (CDSs) were predicted. Based on the entire genome sequence analysis, 50 stress resistance genes and seven virulence factors were identified. The results of the phenotypic experiments showed that the strain had good resistance to high temperature, low temperature, acid, alkali, salt, artificial gastrointestinal fluid, and strong antioxidant capacity. Additionally, transcriptomic analysis confirmed that under stress conditions, the expression levels of key genes were significantly upregulated. Therefore, the phenotypic characteristics of L. plantarum GX17 align well with its genotypic features, demonstrating promising probiotic properties. This strain holds great potential as a probiotic candidate, and further investigation into its beneficial effects on human health is warranted. IMPORTANCE: In humans, Lactiplantibacillus plantarum may synergize with host microbiota to ameliorate dysbiosis-related pathologies, enhance immunomodulation, and facilitate micronutrient bioavailability. For livestock, its application could improve feed conversion ratios, suppress enteric pathogens through competitive exclusion, and mitigate antibiotic overuse, "a critical strategy in One Health frameworks." Further investigations into strain-specific mechanisms (e.g., postbiotic metabolites, quorum sensing regulation) are warranted to translate these genomic-phenotypic advantages into sustainable health solutions across species.

Probiotics↗
PubMed2004

Investigation of crystallin genes in familial cataract, and report of two disease associated mutations.

AIMS: Mutations of seven crystallin genes have been shown to cause familial cataract. The authors aimed to identify disease causing crystallin mutations in paediatric cataract families from south eastern Australia. METHODS: 38 families with autosomal dominant or recessive paediatric cataract were examined. Three large families were studied by linkage analysis. Candidate genes at regions providing significant LOD scores were sequenced. Single stranded conformational polymorphism (SSCP) analysis was used to screen five crystallin genes in the probands, followed by direct sequencing of observed electrophoretic shifts. Mutations predicted to affect the coding sequence were subsequently investigated in the entire pedigree. RESULTS: A LOD score of 3.72 was obtained at the gamma-crystallin locus in one pedigree. Sequencing revealed a P23T mutation of CRYGD, found to segregate with disease. A splice site mutation at the first base of intron 3 of the CRYBA1/A3 gene segregating with disease was identified by SSCP in another large family. Five polymorphisms were also detected. CONCLUSIONS: Although mutations in the five crystallin genes comprehensively screened in this study account for 38% of paediatric cataract mutations in the literature, only two causative mutations were detected in 38 pedigrees, suggesting that crystallin mutations are a relatively rare cause of the cataract phenotype in this population.

Cataract↗
PubMedDate not supplied

[Validation of colorectal cancer diagnostic codes in a hospital administration data set].

OBJECTIVES: To validate the ability of a hospital administration data set (minimum data set [MDS]) to detect incident cases of colorectal cancer using the Murcia Cancer Registry (MCR) as the gold standard and to measure agreement between the MDS and registration of colorectal cancer. MATERIAL AND METHOD: A cross sectional validation study of the MDS of the main hospital in the region of Murcia (Spain) was conducted. The study population consisted of incident cases of colorectal cancer in 2000 obtained from the MCR and cases in the MDS of the above-mentioned hospital for the same year with an ICD-9 diagnostic code between 153.0 and 154.1, eliminating readmissions. During the process, two analyses were performed: one analysis with the principal diagnosis only and another with all the diagnostic codes. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and agreement was calculated with their 95% confidence intervals (CI). RESULTS: With the first diagnosis only, the MDS detected 80% of the incident cases of colorectal cancer with a PPV of 75%. With all the diagnoses, the MDS detected 85% of the cases with a PPV of 64%. The agreement in codification was high at three digits (kappa 88% [95% CI, 0.79-0.97] first diagnosis, 89% [95% CI, 0.80-0.97] all diagnoses) as well as at four digits (kappa 77% [IC, 0.68-0.85] first diagnosis, 78% [95% CI, 0.70-0.86] all diagnoses) in both analyses. CONCLUSIONS: Because of its high sensitivity, the MDS is a good source for detecting incident cases of cancer. The high agreement found in the site of colorectal cancer helps to consolidate the MDS as a data source for cancer registration.

Colorectal Neoplasms↗
PubMed1998

A finite element study of ultrasonic wave propagation in a tooth phantom.

Ultrasound is used extensively in industry for the detection and characterization of defects in critical engineering structures. Similar techniques could be used in dentistry if a thorough understanding of ultrasonic wave propagation in teeth were available. This paper presents a hypothesis that finite element analysis can be used to solve the hyperbolic partial differential equation which governs ultrasonic wave propagation in teeth. A three-layer tooth phantom based on the geometry of a human second molar is used to illustrate the validity of this hypothesis. Simulated wave propagation studies are described for the tooth phantom with a gold crown layer, with an amalgam restoration insertion, and containing a cavity. Results clearly show the finite element code's ability to predict and visualize ultrasonic wave propagation in complex dental structures.

Algorithms↗