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PubMed2005

Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops revealed by nucleotide sequence analysis.

The second largest BamHI fragment (B2) of the chloroplast DNA in Triticum (wheat) and Aegilops contains a highly variable region (a hotspot), resulting in four types of B2 of different size, i.e. B2l (10.5kb), B2m (10.2kb), B2 (9.6kb) and B2s (9.4kb). In order to gain a better understanding of the molecular nature of the variations in length and explain unexpected identity among B2 of Ae. ovata, Ae. speltoides and common wheat (T. aestivum), the nucleotide sequence between a stop codon of rbcL and a HindIII site in cemA in the hotspot was determined for Ae. ovata, Ae. speltoides, Ae. caudata and Ae. mutica. The total number of nucleotides in the region was 2808, 2810, 3302, and 3594 bp, for Ae. speltoides, Ae. ovata, Ae. caudata and Ae. mutica, respectively, and the sequences were compared with the corresponding ones of Ae. crassa 4x, T. aestivum and Ae. squarrosa. Compared with the largest B2l fragment of Ae. mutica, a 791bp and a 793 bp deletion were found in Ae. speltoides and Ae. ovata, respectively, and the possible site of deletion in the two species is the same as that of T. aestivum. However, a deleted segment in Ae. ovata is 2 bp longer than that of Ae. speltoides (and T. aestivum), demonstrating that recurrent deletions had occurred in the chloroplast genomes of both species. Comparison of the sequences from Ae. caudata and Ae. crassa 4x with that of Ae. mutica revealed a 289 bp and a 61 bp deletion at the same site in Ae. caudata and Ae. crassa 4x, respectively. Sequence comparison using wild Aegilops plants showed that the large length variations in a hotspot are fixed to each species. A considerable number of polymorphisms are observed in a loop in the 3' of rbcL. The study reveals the relative importance of the large and small indels and minute inversions to account for variations in the chloroplast genomes among closely related species.

Base Sequence↗
PubMed2006

Pharmacogenomics in inflammatory bowel disease.

Inherited variations in the nucleotide sequence of genes influence how individual patients respond to drugs. Most commonly, clinically significant genetic variations consist of single nucleotide polymorphisms (SNPs) within genes that affect drug disposition or drug targets. Up to now, relatively few clinically important examples of inherited traits that affect drug responses have been studied in detail. However, one of the well-characterized examples is highly relevant to inflammatory bowel disease therapeutics, that of thiopurine methyltransferase pharmacogenetics. Individuals with 2 normal alleles of the gene encoding thiopurine methyltransferase metabolize and clear thiopurines such as azathioprine and 6-mercaptopurine rapidly. Individuals with 1 normal and 1 variant allele are intermediate, whereas those with 2 variant alleles clear thiopurines very slowly. Intermediate and slow metabolizers are predisposed to have high active thiopurine drug levels and develop bone marrow suppression. Genomic era technology permits determination of large numbers of SNPs in large numbers of individuals. This capability is allowing the field of pharmacogenomics to become one of the most productive interfaces in translational biomedical research at present. By using high-throughput SNP genotyping, combined with careful phenotypic characterization of disease, pharmacogenomic research carries the potential of identifying individual biomarkers that predict the relative likelihood of benefit or risk from a therapeutic intervention. If this promise can be realized, pharmacogenomics will deliver the opportunity for personalized medicine.

Anti-Inflammatory Agents↗
PubMed2003

Variation in a repeat sequence determines whether a common variant of the cystic fibrosis transmembrane conductance regulator gene is pathogenic or benign.

An abbreviated tract of five thymidines (5T) in intron 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is found in approximately 10% of individuals in the general population. When found in trans with a severe CFTR mutation, 5T can result in male infertility, nonclassic cystic fibrosis, or a normal phenotype. To test whether the number of TG repeats adjacent to 5T influences disease penetrance, we determined TG repeat number in 98 patients with male infertility due to congenital absence of the vas deferens, 9 patients with nonclassic CF, and 27 unaffected individuals (fertile men). Each of the individuals in this study had a severe CFTR mutation on one CFTR gene and 5T on the other. Of the unaffected individuals, 78% (21 of 27) had 5T adjacent to 11 TG repeats, compared with 9% (10 of 107) of affected individuals. Conversely, 91% (97 of 107) of affected individuals had 12 or 13 TG repeats, versus only 22% (6 of 27) of unaffected individuals (P<.00001). Those individuals with 5T adjacent to either 12 or 13 TG repeats were substantially more likely to exhibit an abnormal phenotype than those with 5T adjacent to 11 TG repeats (odds ratio 34.0, 95% CI 11.1-103.7, P<.00001). Thus, determination of TG repeat number will allow for more accurate prediction of benign versus pathogenic 5T alleles.

Base Sequence↗
PubMedDate not supplied

Computerized breast thermography: study of image segmentation and temperature cyclic variations.

Breast cancer is a common and dreadful disease in women. The surface temperature and the vascularization pattern of the breast could indicate breast diseases. Establishing the surface isotherm pattern of the breast and the normal range of cyclic variations of temperature distribution can assist in identifying the abnormal infrared images of diseased breasts. This paper investigates the cyclic variation of temperature and vascularization of the normal breast thermograms under a controlled environment. More than 50 Asian women, were examined and some of them have been examined continuously for two month. All together, not less than 800 thermograms were obtained. Before these thermograms can be analysed objectively via a computer algorithm, they must be digitized and segmented. The authors present a method to segment thermograms and extract the useful region from the background. After the image processing, these thermograms can be analysed and then the best time to perform an examination can be chosen. All these results are important for establishing a data bank of normal breast thermography, to choose the best time for an examination and as a systematic methodology for evaluating and analysing the abnormal breast thermography in the future.

Adult↗
PubMed1993

Variation in physicians' recommendations about revisit interval for three common conditions.

BACKGROUND: The appropriate revisit interval for most conditions is uncertain. This survey was done to gather information about physicians' recommendations on revisit intervals for three common conditions. METHODS: Data were gathered in a mailed survey of 116 primary care physicians in the University of California at San Francisco Collaborative Research Network. Physicians were given descriptions of three hypothetical patients, one with diabetes mellitus, one with angina, and one with hypertension, and were asked when they would recommend a follow-up visit for the condition. RESULTS: There were great variations in physicians' recommendations about revisit intervals for each hypothetical patient. Internists were significantly more likely than family physicians to recommend a longer revisit interval for the hypothetical patient with diabetes mellitus; a similar revisit pattern was found for the patient with hypertension. There were no significant associations with recommended revisit interval and many other physician characteristics. CONCLUSIONS: As interest in containing the cost and improving the efficiency of medical care increases, knowing how often patients ought to be seen will be a topic of increasing importance. A rational, information-based approach to the choice of revisit interval for common conditions could yield substantial savings in medical care costs. The existence of great variation in recommended revisit interval suggests that physicians are uncertain about what interval is best.

Aged↗
PubMed2004

Comparative anatomy of the superfamily Myliobatoidea (Chondrichthyes) with some comments on phylogeny.

The anatomy of species belonging to the superfamily Myliobatoidea was examined with the aim of better determining their phylogenetic relationships. A wide variation among genera was observed in skeletal anatomy, despite the fact that they all share a common morphological pattern. However, variation among species of the same genus was low, excepting Mobula. Dorsal musculature showed a substantial consistency, except for the epiaxialis muscle, which was larger in rhinopterids and mobulids. Variation in the ventral muscles was low among species of the same genus, but considerable among different genera. Mobulids have a reduction in ventral muscles, while rhinopterids and myliobatoids show an increase in muscular mass. A consensus tree shows a basal split into two groups. The first includes the family Gymnuridae with the genera Gymnura and Aetoplatea; this group is supported by seven synapomorphies, including: 27(1) ceratobranchialis fused proximally, 36(1) anterior lateral processes present in the synarcual, 52(0) quadratomandibularis internal muscle present. The second group is composed of the family Myliobatidae (Myliobatis, Aetomylaeus, Aetobatus, Rhinoptera, Mobula, and Manta), this group is supported by 11 synapomorphies, including: 5(1) first postorbital process fused with the second, 21(1) fused mandibular symphysis, 24(1) first hypobranchial cartilage absent, 48(2) epiaxialis muscle inserted in the cranial orbital region, 73(1) pectoral fins joined behind the orbital region. This study concluded that myliobatoids (Myliobatis, Aetomylaeus, and Aetobatus) integrate a monophyletic group which, unlike other phylogenies previously obtained, is the sister group of rhinopterids (Rhinoptera). Mobulids (Mobula and Manta) are the sister group of myliobatoids-rhinopterids.

Anatomy, Comparative↗
PubMed1994

Seasonal variation in heavy metal levels in tissues of common guillemots, Uria aalge from northwest Scotland.

Mercury, cadmium, zinc, and copper concentrations were analyzed in three samples of common guillemot (in April, June, and November). Levels measured were uniformly low, and not enough to have any toxic effects. Adult guillemots had significantly more cadmium in their livers and kidneys than juveniles, with juvenile levels ranging from 25% to 89% of adult levels. Mercury concentrations in liver and kidney were also higher in adults. Juvenile levels represented from 80% to 94% of adults, but there were no age differences in feather and muscle mercury. Mercury levels declined throughout the year in internal tissues from April through June to November. There was a strong seasonal fluctuation in cadmium levels in liver and kidney, rising significantly between April and June and declining in both adult and juvenile birds. The influences of seasonal processes (namely breeding and moult) and seasonal dietary differences as causative factors in the changes in metal burdens are discussed. These findings have implications for the use of seabirds as monitors of heavy metals in the marine environment.

Animals↗
PubMed2003

Somaclonal variation in Coffea arabica: effects of genotype and embryogenic cell suspension age on frequency and phenotype of variants.

We determined how age of embryogenic cell suspensions affects somaclonal variation in five F1 hybrids of Coffea arabica L. Batches of plants were produced either directly from embryogenic callus, or after 3, 6, 9 and 12 months of embryogenic cell suspension culture. Seven phenotypic variants were characterized. Based on vigor and productivity of the regenerated plants, we classified the variants in order of increasing severity of physiological disorders as: Juvenile leaf color, Giant, Dwarf, Thick leaf (Bullata), Variegata, Angustifolia, and Multi-stem. The Dwarf, Angustifolia and Multi-stem variants were the most frequent among the regenerated plants (1.4, 4.8 and 2.9%, respectively). The frequency (f) of variants increased exponentially with the age (t) of the embryogenic suspension, in accordance with the function f = 0.99e(0.267t). For all genotypes, somaclonal variation was low (1.3%) in plants produced from embryogenic callus or 3-month-old cell suspensions and increased in frequency with increasing suspension age (6, 10 and 25% in plants produced from cell suspensions aged 6, 9 and 12 months, respectively). Large differences in somaclonal variation among genotypes were found only in plants produced from 12-month-old cell suspensions. For two genotypes, the oldest suspensions produced a majority of somaclonal variants (80-90%), whereas somaclonal variation ranged between 8 and 18% in the other genotypes. Cell suspension age and genotype also affected the type of variant produced. The severity of somaclonal variations increased with cell suspension age. For all genotypes combined, the Angustifolia variant was the most common. The other somaclonal variations were specific to certain genotypes or distributed randomly among the genotypes.

Cells, Cultured↗
PubMed1998

Diurnal variation on the excretion patterns of fecal steroids in common marmoset (Callithrix jacchus) females.

The use of fecal steroid analysis to assess gonadal and adrenal function in primates has rapidly increased in recent years due to the ability to collect feces from nonhuman primates living in wild conditions. These techniques offer an exciting new potential for enhancing our knowledge of the endocrine status of free-living animals. Prior to using these techniques under field conditions, it is important to determine the diurnal variation of fecal excreted steroids for assessing possible time limitations on fecal collections. The following study investigates the diurnal frequency of defecation and patterns of steroid levels excreted in feces from four female common marmosets, Callithrix jacchus, living in a family group. These females represented three reproductive conditions: early pregnancy, ovarian cycling, and noncycling (postpubertal). Cortisol, estradiol, and progesterone were extracted and analyzed by enzyme immunoassay. Diurnal variations in steroid levels were found by ANOVA for cortisol and progesterone but not for estradiol. Significantly higher levels of cortisol were found in the afternoon, while the reverse was found for progesterone. All females showed the same pattern of steroid level change, except for cortisol in the pregnant female. Since all females defecated within the first hour after they awoke in the morning, this time was determined to be the most effective time to collect feces. The consistency of our findings reinforces the usefulness of this approach for studying reproductive and adrenocortical function in marmosets and also indicates that fecal collection should be limited to either morning or afternoon collections.

Adrenal Cortex↗
PubMed2005

Common polymorphisms in the CYP7A1 gene do not contribute to variation in rates of bile acid synthesis and plasma LDL cholesterol concentration.

Transcriptional regulation of the cholesterol 7alpha-hydroxylase (CYP7AI) gene is of critical importance for bile acid and cholesterol metabolism. We evaluated the physiological significance of two common polymorphisms (-203C/A and -469T/C) in the promoter region of the CYP7AI gene. No evidence was found for physiological differences between either the -203C and -203A alleles or the -469T and -469C alleles in transient transfection studies using native 834bp promoter constructs. Moreover, no association was observed between the CYP7AI promoter polymorphisms and the hepatic cholesterol 7alpha-hydroxylase activity and parameters of bile acid synthesis rates, as analyzed in subjects with gallstone disease. In addition, no relationships were found between the promoter polymorphisms and plasma LDL cholesterol concentration in association studies conducted in three different groups of middle-aged Swedish men. Finally, near complete allelic association was found between the two promoter polymorphisms and the IVS6+363G/A polymorphism at the 3' end of the CYP7AI gene (|D'|=0.98), indicating strong linkage disequilibrium across the whole CYP7AI gene. It is concluded that common polymorphisms of the CYP7A1 gene do not contribute to variation in cholesterol 7alpha-hydroxylase activity, rates of bile acid synthesis and plasma LDL cholesterol concentration in humans.

Bile Acids and Salts↗
PubMed2001

Variability and predictors of mental disorder rates and medical practitioner responses across Australian general practices.

OBJECTIVE: To determine the variation in prevalence of common mental disorders and general practitioner (GP) responses across Australian general practices, and to identify practice characteristics that predict these rates. DESIGN: Cross-sectional national audit of general practices throughout Australia in 1998-1999. PARTICIPANTS: 46515 ambulatory care patients attending 386 GPs. MAIN OUTCOME MEASURES: Practice-based prevalence of mental disorders (based on patient-reported symptoms) and GP-reported rates of psychological diagnoses and treatment (median and range, excluding the upper and lower 10% of practices); practice characteristics (patient, doctor and organisational) that predict prevalences and rates, determined by multiple regression analysis. RESULTS: Even after omitting the upper and lower 10% of practices, there were large variations between practices in prevalence of common mental disorders (range, 39% to 59% of patients; median, 48%), and substance misuse (range, 3%-13%; median, 7%). There were also large variations between practices in rates at which GPs made psychological diagnoses in each practice (range, 12%-51%; median, 27%), judged patients to be at risk to self or others (range, 6%-54%; median, 23%), provided psychological treatments (range, 8%-41%; median, 22%) and referred patients to specialist services (range, 1%-10%; median, 4%). Practice-based rates of disorders and GP responses were predicted not only by sociodemographic characteristics of patients in each practice (eg, mean age or proportion of unemployed people), but also by doctor characteristics (eg, age and sex) and practice organisation characteristics (eg, urban versus regional or rural location). CONCLUSION: We identified patient, GP and practice characteristics that predict rates of mental disorder and treatments provided. These could be used to guide mental health service reform in general practice and assist with targeting relevant education and practice support programs.

Adult↗
PubMed1999

Geographic variations in utilization rates in Veterans Affairs hospitals and clinics.

BACKGROUND: In the United States, geographic variation in hospital use is common. It is uncertain whether there are similar geographic variations in the health care system of the Department of Veterans Affairs (VA), which differs from the private sector because it predominantly serves men with annual incomes below $20,000, has a central system of administration, and uses salaried physicians. Thus, it might be less likely to have geographic variations. METHODS: We used VA data bases to obtain information on patients treated for eight diseases (chronic obstructive pulmonary disease, pneumonia, congestive heart failure, angina, diabetes, chronic renal failure, bipolar disorder, and major depression). We analyzed their use of hospital and outpatient services by assessing the risk-adjusted numbers of hospital days (the average number of days a patient spent in the hospital per 12 months of follow-up, regardless of the number of hospital stays), hospital-discharge rates, and clinic-visit rates from 1991 through 1995 for the entire system and within the 22 geographically based health care networks. RESULTS: We found substantial geographic variation in hospital use for all eight cohorts of patients and all the years studied. Variations in the numbers of hospital days per person-year among the networks were greatest among patients with chronic obstructive pulmonary disease (ranging from a factor of 2.7 to a factor of 3.1) during a given year and smallest among patients with angina (ranging from a factor of 1.5 to a factor of 2.1). Levels of hospital use were highest in the Northeast and lowest in the West. The variation in the rates of clinic visits for principal medical care among the networks ranged from a factor of approximately 1.6 to a factor of 4.0; variations in the rates were greatest among patients with chronic renal failure and smallest among patients with chronic obstructive pulmonary disease. There was no clear geographic pattern in the rates of outpatient-clinic use. CONCLUSIONS: There are significant geographic variations in the use of hospital and outpatient services in the VA health care system. Because VA physicians are unable to increase their income by changing their patterns of practice, our findings suggest that their practice styles are similar to those of other physicians in their geographic regions.

Chronic Disease↗
PubMed1995

Small repeating units within the Ureaplasma urealyticum MB antigen gene encode serovar specificity and are associated with antigen size variation.

Ureaplasma urealyticum is a common commensal of the female lower urogenital tract, yet it has been shown to be an important cause of chorioamnion infection, respiratory and central nervous system disease, and death in premature infants. It has been suggested that only certain serovars are capable of producing invasive disease. However, we previously showed that many serotypes are invasive and that perhaps antigen variability and host factors are more important determinants of ureaplasma infections than are different serotypes per se. The molecular characterization in this report describes a mechanism available to ureaplasmas for producing antigen variation. That antigen, designated MB and previously identified on U. urealyticum, contains serovar-specific and cross-reactive epitopes, is produced both in vitro and in vivo, is a predominant antigen recognized during ureaplasma infections of humans, undergoes a high rate of size variation in vitro, and is size variable on invasive ureaplasma isolates. In the present study, we cloned and sequenced the gene of the MB antigen from serovar 3, the serovar most commonly isolated from humans. The 3' two-thirds of the gene was shown to contain identical 18-nucleotide tandem repeats. PCR analysis and direct sequencing of two variants indicated that alterations within this repeat region are responsible for the size variation of the MB antigen. Intact recombinant serovar 3 MB antigen and truncated products, expressed by coupled in vitro transcription and translation of the cloned gene, were immunoprecipitated by both a serovar-specific monoclonal antibody and the serum of a U. urealyticum-infected patient, and these results identified the repeat region of the MB antigen as serovar defining. Resolution of the precise amino acids responsible for specific epitopes and characterization of similar genes in the other serovars should yield reagents useful in elucidating the role of antigen size variants in disease production and the role of specific antibody in protection from ureaplasma disease.

Amino Acid Sequence↗
PubMed2005

Performance of variations of carbolfuchsin staining of sputum smears for AFB under field conditions.

SETTING: A field project in Bangladesh. OBJECTIVE: To compare the effectiveness of commonly used carbolfuchsin staining variations. DESIGN: Routine hot Ziehl-Neelsen (ZN) 1% basic fuchsin staining for 15 min in 75 field clinics. Blind reading of duplicate smears stained by ZN 1% vs. 0.3% basic fuchsin applied for 5 min, or by ZN 1% 5 min vs. Kinyoun cold staining. Rechecking of discordant series. RESULTS: For comparable numbers of false positives, sensitivity was significantly lower with Kinyoun than with ZN 1% 5 min (85.6% vs. 93.0%, P < 0.001). Sensitivity with ZN 1% 5 min was not significantly higher than with 0.3% 5 min staining (89.9% vs. 86.5%). Routine examination using 1% 15 min ZN identified more positives than any of the study techniques. CONCLUSIONS: Kinyoun cold staining sensitivity was unsatisfactory in field clinics. The sensitivity of the WHO/IUATLD recommended 0.3% fuchsin for 5 min was not significantly different from the original 1% ZN for 5 min, but 1% 15 min hot staining might be superior. A reduced fuchsin concentration together with a short staining time may leave too narrow a margin for error. TB programmes using hot ZN with a concentrated stain or longer staining time should not be urged to change.

Bangladesh↗