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Fragment Length (fragment + length)
Terms modified by Fragment Length Selected AbstractscagA gene variants in Malaysian Helicobacter pylori strains isolated from patients of different ethnic groupsFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 2 2005Mohamed Ramelah Abstract Helicobacter pylori infection of a distinct subtype of cagA may lead to different pathological manifestation. The aim of this study is to determine the presence of cagA gene and its variants in H. pylori infection among different ethnic groups and its effect on gastroduodenal diseases. Overall detection of cagA among the 205 clinical isolates of H. pylori was 94%. Variations in size of the 3, region of cagA gene were examined among 192 Malaysian H. pylori cagA -positive strains. Results showed that three cagA variants differing in fragment length of PCR products were detected and designated as type A (621,651 bp), type B (732,735 bp) and type C (525 bp). Although there was no association between any of the cagA subtypes with peptic ulcer disease (p > 0.05), an association between cagA subtypes with a specific ethnic group was observed. Specific- cagA subtype A strains were predominantly isolated from Chinese compared to Malays and Indians (p < 0.0005), and cagA subtype B strains were predominantly isolated from Malays and Indians compared to Chinese (p < 0.05). The cagA type A strains of H. pylori is commonly found in the Chinese patients who have a higher risk of peptic ulcer disease, thus indicating that it could be used as an important clinical biomarker for a more severe infection. [source] The effects of social status on biological aging as measured by white-blood-cell telomere lengthAGING CELL, Issue 5 2006L. F. Cherkas Summary Low socio-economic status (SES) is associated with a shortened life expectancy, but its effect on aging is unknown. The rate of white-blood-cell (WBC) telomere attrition may be a biological indicator of human aging. We tested the hypothesis that SES is associated with telomere attrition independent of known risk factors influencing the aging process. We studied 1552 female twins. A venous blood sample was taken from each twin and isolated WBCs used for extraction of DNA. Terminal restriction fragment length (TRFL) was measured. Questionnaire data were collected on occupation, education, income, smoking, exercise, height and weight. Standard multiple linear regression and multivariate analyses of variance tested for associations between SES and TRFL, adjusting for covariates. A discordant twin analysis was conducted on a subset to verify findings. WBC telomere length was highly variable but significantly shorter in lower SES groups. The mean difference in TRFL between nonmanual and manual SES groups was 163.2 base pairs (bp) of which 22.9 bp (,14%) was accounted for by body mass index, smoking and exercise. Comparison of TRFL in the 17 most discordant SES twin pairs confirmed this difference. Low SES, in addition to the harmful effects of smoking, obesity and lack of exercise, appears to have an impact on telomere length. [source] A phylogenetic framework for wing pattern evolution in the mimetic Mocker Swallowtail Papilio dardanusMOLECULAR ECOLOGY, Issue 18 2009REBECCA CLARK Abstract The Batesian mimetic swallowtail butterfly Papilio dardanus exhibits numerous distinct wing colour morphs whose evolutionary origins require large phenotypic shifts. A phylogenetic framework to study the history of these morphs was established by DNA sequencing of representative subspecies from sub-Saharan Africa and Indian Ocean islands. Two mitochondrial genes and the nuclear internal transcribed spacer marker revealed deeply separated eastern and western African mainland lineages, plus one lineage each on Madagascar and Grande Comore. These markers showed very little polymorphism within lineages. In contrast, markers genetically linked to the mimicry locus H, including the transcription factor invected and two adjacent amplified fragment length polymorphisms-derived sequences, showed high nucleotide diversity but were not geographically structured. Variation in the unlinked wingless gene showed a similar pattern, rejecting the hypothesis that high level of variation in the H region is due to balancing selection exerted by the phenotypes. The separation from a common ancestor with Papilio phorcas estimated at 2.9 Ma coincides with the origin of a mimicry model, Danaus chrysippus. However, the model reached Africa only at the time of the internal splits of P. dardanus mtDNA groups, here estimated at 0.55,0.94 Ma. The nuclear genome shows less geographic structure and may not track recent population differentiation, suggesting that widespread mimicry morphs have arisen early in the evolution of the P. dardanus lineage, although after the male,female dimorphism which is ancestral. The current wide distribution of P. dardanus and population subdivision evident from mtDNA may have been achieved only with the spread of the models across Africa. [source] Automated binning of microsatellite alleles: problems and solutionsMOLECULAR ECOLOGY RESOURCES, Issue 1 2007W. AMOS Abstract As genotyping methods move ever closer to full automation, care must be taken to ensure that there is no equivalent rise in allele-calling error rates. One clear source of error lies with how raw allele lengths are converted into allele classes, a process referred to as binning. Standard automated approaches usually assume collinearity between expected and measured fragment length. Unfortunately, such collinearity is often only approximate, with the consequence that alleles do not conform to a perfect 2-, 3- or 4-base-pair periodicity. To account for these problems, we introduce a method that allows repeat units to be fractionally shorter or longer than their theoretical value. Tested on a large human data set, our algorithm performs well over a wide range of dinucleotide repeat loci. The size of the problem caused by sticking to whole numbers of bases is indicated by the fact that the effective repeat length was within 5% of the assumed length only 68.3% of the time. [source] Molecular sexing and sources of CHD1-Z/W sequence variation in Hawaiian birdsMOLECULAR ECOLOGY RESOURCES, Issue 4 2006SUSAN I. JARVI Abstract Sequence information from 28 CHD1 gene fragments reveals that a primary source of variability in CHD1-W genes is a variable intron microsatellite; a single-codon deletion was found in the 3, exon in one species. Sequence variation of CHD1-Z genes was detected in males that altered polymerase chain reaction (PCR) fragment length. Three sets of CHD1-based primers were evaluated for sex determination in 12 endemic and 8 alien Hawaiian species, including one of the last po'o-uli. Combined, these primers provide a reliable means of sex determination in most species (including the po'o-uli), and have produced a valuable reference database for future expanded population-level studies. [source] Amplified fragment length polymorphism-derived microsatellite sequence linked to the Pch1 and Ep-D1 loci in common wheatPLANT BREEDING, Issue 1 2003J. Z. Groenewald Abstract Amplified fragment length polymorphism (AFLP) markers linked to the Aegilops ventricosa -derived chromosome segment in ,VPM1' on which the eyespot resistance gene, Pch1, and the endopeptidase gene, Ep-D1b, occur were identified. One marker was isolated from the gel, cloned and sequenced. Sequence analysis revealed a microsatellite repeat motif. Sequence-specific primers were designed to amplify a product containing the repeat motif, and the microsatellite marker was tested for cosegregation with the Ep-D1b allele. Distinct alleles were produced by the Pch1 sources, normal wheat and wheat containing the Lr19 translocation. A recombination frequency of 0.02 was calculated between the microsatellite marker and Ep-D1. [source] Strain rate effect in the single-fiber-fragmentation testPOLYMER COMPOSITES, Issue 3 2001X. J. Gong The single fiber fragmentation test (SFVU) has been widely used to characterize the interface it fiber-reinforced polymers. The purpose of the work reported here was to determine the effect of strain rate on the fiber fragment lengths obtained in the SFFT. Three materials systems were used to make single-fiber-composite specimens: E-glass fiber/polycarbonate matrix, AS4-carbon fiber/polycarbonate matrix, and AS4-carbon fiber/polycarbonate matrix. The fiber-matrix adhesion in all three systems is based on physisorption rather than chemisorption. Each system was tested at strain rates ranging over four orders of magnitude. Results are reported in terms of fragment length, the dependent variable in this study, which is inversely related to the quality of the Interface. It was expected that the fragment length would show a systematic decrease with Increasing strain rate, but the expected trend was not found. Although the polycarbonate matrix exhibited rate-dependent viscoelastic behavior typical of amorphous polymers below Tg, the fragment length at saturation did not show a statistically significant variation with strain rate for any of the three materials systems. A major contributor to the lack of observed effect was the inherent random variability associated with the SFFT; random variability in average fragment length was equal or greater than the 19% effect of rate predicted for ideal elastic systems with no debonding at the interface. In addition, considerable interfacial debonding occurred during the SFFT, not surprising for Interfaces based on physisorption alone. Debonding Interferes with transfer of applied load from matrix to fiber, and would thus interfere with transfer of the effect of rate from matrix to fiber. A tensile Impact test developed previously was also performed on single-fiber composite specimens made from the same three materials systems. The results of the Impact tests differed from those obtained at controlled strain-rates for only two of the materials systems. [source] New polymorphic microsatellite loci for different camel speciesMOLECULAR ECOLOGY RESOURCES, Issue 3 2003D. Evdotchenko Abstract New microsatellite loci were screened and sequenced from the genomic DNA of male Camelus bactrianus. Among 32 loci, 23 were amplified in bactrian and dromedary species, 19 in llama and 20 in alpaca. The different species had similar fragment lengths per locus, with more striking similarities between bactrian and dromedary and between llama and alpaca, respectively. Seven loci had more than 10 alleles each, nine were monomorphic in all species, and one was monomorphic in Old World and polymorphic in New World camels. The results show that the informative microsatellite loci can be widely applied to several species. [source] Underground primary succession of ectomycorrhizal fungi in a volcanic desert on Mount FujiNEW PHYTOLOGIST, Issue 3 2003Kazuhide Nara Summary , , Ectomycorrhizal (ECM) fungi are indispensable symbionts for the normal growth of many tree species. Here, we report the underground primary succession of ECM fungi in a volcanic desert on Mt. Fuji, Japan. , , We identified all the underground fungal constituents by comparing the fragment lengths of the internal transcribed spacer (ITS) regions in nuclear r-DNA with those of sporocarps, considering intraspecific variation of each species at the research site. ITS sequences were also used for identification. , , In total, 21 ECM fungi associated with Salix reinii were identified. Species recorded as sporocarps dominated the underground ECM community. The sere of underground ECM fungi was initiated by one or two of three first-stage fungi, and additional species were recruited with host growth, especially in the soil that developed within a vegetation patch. The species richness of ECM fungi increased significantly with host growth. , , The underground ECM community associated with unhealthy hosts differed from that of normally growing hosts. The underground ECM communities and their successional patterns might influence plant growth and plant communities during early primary succession. [source] Strain rate effect in the single-fiber-fragmentation testPOLYMER COMPOSITES, Issue 3 2001X. J. Gong The single fiber fragmentation test (SFVU) has been widely used to characterize the interface it fiber-reinforced polymers. The purpose of the work reported here was to determine the effect of strain rate on the fiber fragment lengths obtained in the SFFT. Three materials systems were used to make single-fiber-composite specimens: E-glass fiber/polycarbonate matrix, AS4-carbon fiber/polycarbonate matrix, and AS4-carbon fiber/polycarbonate matrix. The fiber-matrix adhesion in all three systems is based on physisorption rather than chemisorption. Each system was tested at strain rates ranging over four orders of magnitude. Results are reported in terms of fragment length, the dependent variable in this study, which is inversely related to the quality of the Interface. It was expected that the fragment length would show a systematic decrease with Increasing strain rate, but the expected trend was not found. Although the polycarbonate matrix exhibited rate-dependent viscoelastic behavior typical of amorphous polymers below Tg, the fragment length at saturation did not show a statistically significant variation with strain rate for any of the three materials systems. A major contributor to the lack of observed effect was the inherent random variability associated with the SFFT; random variability in average fragment length was equal or greater than the 19% effect of rate predicted for ideal elastic systems with no debonding at the interface. In addition, considerable interfacial debonding occurred during the SFFT, not surprising for Interfaces based on physisorption alone. Debonding Interferes with transfer of applied load from matrix to fiber, and would thus interfere with transfer of the effect of rate from matrix to fiber. A tensile Impact test developed previously was also performed on single-fiber composite specimens made from the same three materials systems. The results of the Impact tests differed from those obtained at controlled strain-rates for only two of the materials systems. [source] | ||||||||||