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PubMed2006

The distribution of species diversity across a flora's component lineages: dating the Cape's 'relicts'.

The Cape Floristic Region is exceptionally species-rich both for its area and latitude, and this diversity is highly unevenly distributed among genera. The modern flora is hypothesized to result largely from recent (post-Oligocene) speciation, and it has long been speculated that particular species-poor lineages pre-date this burst of speciation. Here, we employ molecular phylogenetic data in combination with fossil calibrations to estimate the minimum duration of Cape occupation by 14 unrelated putative relicts. Estimates vary widely between lineages (7-101 Myr ago), and when compared with the estimated timing of onset of the modern flora's radiation, it is clear that many, but possibly not all, of these lineages pre-date its establishment. Statistical comparisons of diversities with lineage age show that low species diversity of many of the putative relicts results from a lower rate of diversification than in dated Cape radiations. In other putative relicts, however, we cannot reject the possibility that they diversify at the same underlying rate as the radiations, but have been present in the Cape for insufficient time to accumulate higher diversity. Although the extremes in diversity of currently dated Cape lineages fall outside expectations under a constant underlying diversification rate, sampling of all Cape lineages would be required to reject this null hypothesis.

Base Sequence↗

PubMed2004

Tracheoesophageal diversion versus total laryngectomy for intractable aspiration.

This study evaluates the outcome and surgical stress associated with surgery for intractable aspiration. A retrospective review was conducted to compare the results between tracheoesophageal diversion and total laryngectomy. The operative time, intra-operative bleeding, time until drain removal, feeding conditions and surgical complications were compared between the two groups. Of the 19 patients, 31.6 per cent underwent tracheoesophageal diversion and 68.4 per cent received total laryngectomy. The operative time and drain insertion periods were statistically shorter in the tracheoesophageal diversion group, while the amount of intra-operative blood loss was smaller in the tracheoesophageal diversion group. The complication rate and the feeding conditions before and after surgery for the two groups did not show any statistically significant difference. Tracheoesophageal diversion was thus found to be a simple, safe, and reliable therapeutic modality for the control of intractable aspiration. Moreover, it induced less surgical stress than total laryngectomy.

Adult↗

PubMed2005

Lay health workers in primary and community health care.

BACKGROUND: Lay health workers (LHWs) are widely used to provide care for a broad range of health issues. However, little is known about the effectiveness of LHW interventions. OBJECTIVES: To assess the effects of LHW interventions in primary and community health care on health care behaviours, patients' health and wellbeing, and patients' satisfaction with care. SEARCH STRATEGY: We searched the Cochrane Effective Practice and Organisation of Care and Consumers and Communication specialised registers (to August 2001); the Cochrane Central Register of Controlled Trials (to August 2001); MEDLINE (1966- August 2001); EMBASE (1966-August 2001); Science Citations (to August 2001); CINAHL (1966-June 2001); Healthstar (1975-2000); AMED (1966-August 2001); the Leeds Health Education Effectiveness Database and the reference lists of articles. SELECTION CRITERIA: Randomised controlled trials of any intervention delivered by LHWs (paid or voluntary) in primary or community health care and intended to promote health, manage illness or provide support to patients. A 'lay health worker' was defined as any health worker carrying out functions related to health care delivery; trained in some way in the context of the intervention; and having no formal professional or paraprofessional certificated or degreed tertiary education. There were no restrictions on the types of consumers. DATA COLLECTION AND ANALYSIS: Two reviewers independently extracted data onto a standard form and assessed study quality. Studies that compared broadly similar types of interventions were grouped together. Where feasible, the results of included studies were combined and an estimate of effect obtained. MAIN RESULTS: Forty three studies met the inclusion criteria, involving more than 210,110 consumers. These showed considerable diversity in the targeted health issue and the aims, content and outcomes of interventions. Most were conducted in high income countries (n=35), but nearly half of these focused on low income and minority populations (n=15). Study diversity limited meta-analysis to outcomes for five subgroups (n=15 studies) (LHW interventions to promote the uptake of breast cancer screening, immunisation and breastfeeding promotion [before two weeks and between two weeks and six months post partum] and to improve diagnosis and treatment for selected infectious diseases). Promising benefits in comparison with usual care were shown for LHW interventions to promote immunisation uptake in children and adults (RR=1.30 [95% CI 1.14, 1.48] p=0.0001) and LHW interventions to improve outcomes for selected infectious diseases (RR=0.74 [95% CI 0.58, 0.93) p=0.01). LHWs also appear promising for breastfeeding promotion. They appear to have a small effect in promoting breast cancer screening uptake when compared with usual care. For the remaining subgroups (n=29 studies), the outcomes were too diverse to allow statistical pooling. We can therefore draw no general conclusions on the effectiveness of these subgroups of interventions. AUTHORS' CONCLUSIONS: LHWs show promising benefits in promoting immunisation uptake and improving outcomes for acute respiratory infections and malaria, when compared to usual care. For other health issues, evidence is insufficient to justify recommendations for policy and practice. There is also insufficient evidence to assess which LHW training or intervention strategies are likely to be most effective. Further research is needed in these areas.

Allied Health Personnel↗

PubMed2003

On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles.

DNA microarrays provide for unprecedented large-scale views of gene expression and, as a result, have emerged as a fundamental measurement tool in the study of diverse biological systems. Statistical questions abound, but many traditional data analytic approaches do not apply, in large part because thousands of individual genes are measured with relatively little replication. Empirical Bayes methods provide a natural approach to microarray data analysis because they can significantly reduce the dimensionality of an inference problem while compensating for relatively few replicates by using information across the array. We propose a general empirical Bayes modelling approach which allows for replicate expression profiles in multiple conditions. The hierarchical mixture model accounts for differences among genes in their average expression levels, differential expression for a given gene among cell types, and measurement fluctuations. Two distinct parameterizations are considered: a model based on Gamma distributed measurements and one based on log-normally distributed measurements. False discovery rate and related operating characteristics of the methodology are assessed in a simulation study. We also show how the posterior odds of differential expression in one version of the model is related to the ratio of the arithmetic mean to the geometric mean of the two sample means. The methodology is used in a study of mammary cancer in the rat, where four distinct patterns of expression are possible.

Animals↗

PubMed1995

Development and familiality of sexual orientation in females.

The development and familial clustering of sexual orientation were studied in 358 heterosexual, bisexual, and homosexual women. Sexual orientation, as measured by the Kinsey scales, was diverse yet showed statistical congruity and stability over a 1- to 1.5-year time span. Developmental patterns, as measured by retrospective reports on the ages of first sexual or romantic attraction and of self-acknowledgement of sexual orientation were very similar in the heterosexual and lesbian subjects except for the difference in object choice. The bisexual subjects displayed intermediate patterns that were more similar to the heterosexuals' on most facets yet closer to the lesbian subjects' on other dimensions. Familial clustering of nonheterosexual orientation was significant. Using two criteria, elevated rates of nonheterosexuality were found in four classes of relatives: sisters, daughters, nieces, and female cousins through a paternal uncle. The current data are not sufficient to distinguish between genetic and shared environmental sources of this familial aggregation. We discuss the possibility of using developmental criteria to differentiate between inherited and cultural sources of variation in female sexual orientation.

Adolescent↗

PubMed2026

Oral and gut microbiota profiles in patients with locally advanced rectal cancer with varying responses to neoadjuvant chemoradiotherapy.

Recent research has focused on gut bacteria in colorectal cancer, but the influence of other microbiota, including oral and nonbacterial gut microbiota, on treatment efficacy remains insufficiently explored. This study aimed to investigate their relationship with the efficacy of neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancer (LARC). Saliva and fecal samples were collected from patients with LARC before treatment. Shotgun metagenomic sequencing was used to profile bacterial, archaeal, eukaryotic, and viral taxonomic groups and to examine oral and gut microbial functions. An artificial intelligence-based prediction model was developed by integrating oral and gut microbiome data with clinical information. Statistical analyses compared diversity and response-associated microbial features between responders and non-responders to nCRT. Response-associated differences were observed in bacterial and nonbacterial taxonomic profiles and in oral and gut microbial functional profiles. In the internal test subset, the integrated analysis yielded an observed AUC of 0.917. Given the small cohort and the exploratory comparison of candidate classifiers, this estimate requires confirmation in larger, independent cohorts. Baseline oral and gut microbiome profiles were associated with response to nCRT. Integrating microbiome and clinical features showed potential for response prediction, but the model remains exploratory and requires validation in larger, independent cohorts before clinical application. Retrospectively registered on 01/08/2026, NCT07346729.

Aged↗

PubMed2005

Molecular analysis of divergence in tachinid Uzi (Exorista sorbillans) populations in India.

Exorista sorbillans is a tachinid endoparasitoid of silkworm, Bombyx mori, and is globally known as uzi. It causes economic injury to the cocoon crop in silkworm cultivating areas of India, except those above 400 m above mean sea level (AMSL) in the foothills of the Himalayas (Darjeeling). It is reported that the sericulture tract of south India became infected with this pest only since 1980 through an accidental transportation of cocoons from West Bengal. To ascertain whether the genome of this parasitoid is differentiating into discrete gene pools in contrasting geo-climatic conditions, molecular profiling of four populations (Es (Annatapur), Es(Ramanagaram), Es (Channapatna) and Es(Kodathi) from south India and Es(Murshidabad) from Murshidabad, West Bengal was undertaken with 13 ISSR, 3 RAPD and six non-random primers designed from various repeat sequences of B. mori . MANOVA indicated significance for the Roy's largest root estimate (55.4; F =18.47; p = 0.002) for the variability contributed by the replication. Further, hierarchical clustering done on the basis of Euclidean distance matrix and Nei's unbiased Phylip clustering put Es(Murshidabad) at the maximum distance from those of south India and 29 markers could also be identified which significantly differentiateEs(Murshidabad) from others. However, Nei's statistics for gene diversity in sub-populations reveal considerably high gene-flow (3.44 and 2.51) among the populations around Bangalore. The gene-flow between Es(Murshidabad) and other population is lowest but cannot be ignored. The comparison of endosymbiont specific 16SrRNA and fts Z gene (partial) sequences through clustalW (gcgMSF) revealed a closer relationship of Es(Murshidabad) with Es(Annatapur) and Es (Ramanagaram) and is not congruent with the relationships discussed above. The significance of this maiden study with a tachinid fly-pest is discussed in the context of understanding the diversification of Uzi fly-pest and also establishing this pest as a relevant biological material for studying microevolution in future.

Animals↗

PubMed2006

Nuclear receptors in human immune cells: expression and correlations.

Nuclear receptors (NR) are key modulators of gene transcription. Their activity is ligand induced and modulates a large variety of tissue-specific cellular functions. However, for many NR little is known about their role in cells of the immune system. In this study, expression patterns and distribution of 24 NR were investigated in human peripheral blood mononuclear cells. We provide the first evidence of the expression of the 12 receptors CAR, CoupTFalpha, CoupTFbeta, FXR, GCNF, HNF4alpha, PPARbeta/delta, PXR, RevErbbeta, TR2, TR4 and TLX in highly purified CD4, CD8, CD19, CD14 cells. The expression profile of RevErbalpha and LXRalpha previously observed in B cell and macrophages, respectively, has been extended to CD4, CD8 and CD14 cells. Except for RARbeta, which was absence in any of the cells tested, our results suggest an almost ubiquitous expression of the NR in the different cell lineages of the immune system. The expression of CAR, CoupTFalpha, FXR was also confirmed at a protein level and despite conspicuous mRNA levels of HNF4alpha, only low levels of this receptor were detectable in the nuclear fraction of PBMCs. Expression of the latter receptors was mostly only a fraction (4-20%) of their expression in the thyroid gland, the adrenal gland, the lung or subcutaneous adipose tissue. The Spearman rank order correlation test was performed to examine the correlation in expression between individual nuclear receptor pairs in the four cell types for several donors. Distinct correlation patterns were observed between receptor pairs in the individual cell types. In CD4 T cells four NR, GCNF, PPARgamma, PPARalpha7 and RevErbbeta are perfectly correlated with each other (P> or =0.0167). In the other cell types correlations between NR pairs were more diverse, but also statistically highly significant. Interestingly, the relative expression level of a number of receptor pairs ranked identical or similar in at least three (CoupTFalpha and PPARbeta/delta, CoupTFbeta and HNF4alpha as well as RORbeta and PXR) or four cell types (CoupTFalpha and CoupTFbeta, PPARgamma and RevErbbeta). Despite the variability of NR expression in immune cells, these results suggest that some of the NR may be co-regulated in human immune cells.

Female↗

PubMedDate not supplied

Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring.

Docking and scoring are critical issues in virtual drug screening methods. Fast and reliable methods are required for the prediction of binding affinity especially when applied to a large library of compounds. The implementation of receptor flexibility and refinement of scoring functions for this purpose are extremely challenging in terms of computational speed. Here we propose a knowledge-based multiple-conformation docking method that efficiently accommodates receptor flexibility thus permitting reliable virtual screening of large compound libraries. Starting with a small number of active compounds, a preliminary docking operation is conducted on a large ensemble of receptor conformations to select the minimal subset of receptor conformations that provides a strong correlation between the experimental binding affinity (e.g., Ki, IC50) and the docking score. Only this subset is used for subsequent multiple-conformation docking of the entire data set of library (test) compounds. In conjunction with the multiple-conformation docking procedure, a two-step scoring scheme is employed by which the optimal scoring geometries obtained from the multiple-conformation docking are re-scored by a molecular mechanics energy function including desolvation terms. To demonstrate the feasibility of this approach, we applied this integrated approach to the estrogen receptor alpha (ERalpha) system for which published binding affinity data were available for a series of structurally diverse chemicals. The statistical correlation between docking scores and experimental values was significantly improved from those of single-conformation dockings. This approach led to substantial enrichment of the virtual screening conducted on mixtures of active and inactive ERalpha compounds.

Protein Binding↗

PubMed1999

Artificial neural networks in urology: Update 2000.

Artificial neural networks (ANNs) are widely available and have been demonstrated to be superior to standard empirical methods of detecting, staging and monitoring prostate cancer. These algorithms have been statistically validated in diverse, well-characterized patient groups and are now being evaluated for clinical use worldwide. New variables based on demographic data, tissue and serum markers show promise for improving our ability to predict disease extent and outcome and may be integrated in future ANN models. This review focuses on recently developed neural networks for detecting, staging and monitoring prostate cancer.

Journal Article↗

PubMed2003

The Eating Behavior Patterns Questionnaire predicts dietary fat intake in African American women.

OBJECTIVE: To develop a behavioral assessment of eating that would be predictive of fat intake in African American women. DESIGN: Questionnaires were developed using a three-stage design, involving item generation, item refinement, and questionnaire validation. SUBJECTS: Focus groups sessions were conducted with 40 African American women, initial questionnaire development employed 80 African American women, and questionnaire validation involved 310 African American women from diverse socioeconomic backgrounds. Statistical analyses Transcripts of focus groups were used to generate 113 behavioral questionnaire items. The initial questionnaire was administered along with a food frequency questionnaire, and the item pool was reduced to 51 items. Factor analysis was used to create subscales. Correlation (r) and multiple regression analysis (R) were used to evaluate construct validity. RESULTS: Factor analysis revealed six subscales: low-fat eating, emotional eating, snacking on sweets, cultural/ethnic, haphazard planning, and meal skipping. The scales are significant predictors of micronutrient (R values from 0.22 to 0.47) and macronutrient intakes (R values from 0.33 to 0.58) assessed using a food frequency questionnaire and show construct validity in relationship to other measures of eating behavior (r values from 0.22 to 0.65). APPLICATIONS: The Eating Behavior Patterns Questionnaire (EBPQ) may be a useful tool for clinical assessment, clinical and community nutrition intervention studies, and epidemiologic research with African American women.

Adult↗

PubMed2005

A convenient fluorometric method to study sulfur mustard-induced apoptosis in human epidermal keratinocytes monolayer microplate culture.

Sulfur mustard [SM; bis-(2-chloroethyl) sulfide], which causes skin blistering or vesication [(1991). Histo- and cytopathology of acute epithelial lesions. In: Papirmeister, B., Feister, A. J., Robinson, S. I., Ford, R. D., eds. Medical Defense Against Mustard Gas: Toxic Mechanisms and Pharmacological Implications. Boca Raton: CRC Press, pp. 43-78.], is a chemical warfare agent as well as a potential terrorism agent. SM-induced skin blistering is believed to be due to epidermal-dermal detachment as a result of epidermal basal cell death via apoptosis and/or necrosis. Regarding the role of apoptosis in SM pathology in animal skin, the results obtained in several laboratories, including ours, suggest the following: 1) cell death due to SM begins via apoptosis that proceeds to necrosis via an apoptotic-necrotic continuum and 2) inhibiting apoptosis decreases SM-induced microvesication in vivo. To study the mechanisms of SM-induced apoptosis and its prevention in vitro, we have established a convenient fluorometric apoptosis assay using monolayer human epidermal keratinocytes (HEK) adaptable for multiwell plates (24-, 96-, or 384-well) and high-throughput applications. This assay allows replication and multiple types of experimental manipulation in sister cultures so that the apoptotic mechanisms and the effects of test compounds can be compared statistically. SM affects diverse cellular mechanisms, including endoplasmic reticulum (ER) Ca2+ homeostasis, mitochondrial functions, energy metabolism, and death receptors, each of which can independently trigger apoptosis. However, the biochemical pathway in any of these apoptotic mechanisms is characterized by a pathway-specific sequence of caspases, among which caspase-3 is a key member. Therefore, we exposed 80-90% confluent HEK cultures to SM and monitored apoptosis by measuring the fluorescence generated due to hydrolysis of a fluorogenic caspase-3 substrate (acetyl- or benzyl oxycarbonyl-Asp-Glu-Val-Asp-fluorochrome, also designated as AC-or Z-DEVD- fluorochrome) added to the assay medium. Fluorescence was measured using a plate reader. We used two types of substrates, one (Sigma-Aldrich, CASP-3-F) required cell disruption and the other (Beckman-Coulter CellProbe HT Caspase-3/7 Whole Cell Assay Kit) was cell permeable. The latter substrate was useful in experiments such as determining the time-course of apoptosis immediately following SM exposure without disruption (e.g., due to cell processing). In SM-exposed HEK, fluorescence generated from the fluorogenic caspase-3 substrate hydrolysis increased in a time (0-24 h) and concentration (0.05, 0.1, 0.15, 0.2, 0.3, 0.5 mM) dependent manner. SM caused maximum fluorescence at about 0.5 mM. However, at 2 mM SM, fluorescence decreased compared with 0.5 mM, which remains to be explained. Following 0.3 mM SM exposure, which is considered to be the in vitro equivalent of a vesicating dose in vivo (Smith, W. J., Sanders, K. M., Ruddle, S. E., Gross, C. L. (1993). Cytometric analysis of DNA changes induced by sulfur mustard. J. Toxicol.-Cut. Ocular Toxicol. 12(4):337-347.), a small fluorescence increase was observed at 6 to 8 h, which was markedly higher at 12 h. At 24 h, all SM concentrations increased fluorescence. Fluorescence increase due to SM was prevented 100% by a caspase-3-specific peptide inhibitor AC-DEVD-CHO (acetyl-Asp-Glu-Val-Asp-aldehyde, 0.1 mM), but less effectively by a general caspase inhibitor Z-VAD-FMK (benzyl oxycarbonyl-Val-Ala-Asp-fluoromethylketone, 0.01 mM), indicating that the fluorescence increase was due to caspase-3-mediated apoptosis. These results suggest potential applications of this method to study apoptosis mechanisms involving caspase-3 substrates and possibly those involving other caspase substrates.

Apoptosis↗

PubMed2004

Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block.

To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.

Africa↗

PubMed2006

Teamwork in the operating room: frontline perspectives among hospitals and operating room personnel.

BACKGROUND: The Joint Commission on Accreditation of Healthcare Organizations is proposing that hospitals measure culture beginning in 2007. However, a reliable and widely used measurement tool for the operating room (OR) setting does not currently exist. METHODS: OR personnel in 60 US hospitals were surveyed using the Safety Attitudes Questionnaire. The teamwork climate domain of the survey uses six items about difficulty speaking up, conflict resolution, physician-nurse collaboration, feeling supported by others, asking questions, and heeding nurse input. To justify grouping individual-level responses to a single score at each hospital OR level, the authors used a multilevel confirmatory factor analysis, intraclass correlations, within-group interrater reliability, and Cronbach's alpha. To detect differences at the hospital OR level and by caregiver type, the authors used multivariate analysis of variance (items) and analysis of variance (scale). RESULTS: The response rate was 77.1%. There was robust evidence for grouping individual-level respondents to the hospital OR level using the diverse set of statistical tests, e.g., Comparative Fit Index = 0.99, root mean squared error of approximation = 0.05, and acceptable intraclasss correlations, within-group interrater reliability values, and Cronbach's alpha = 0.79. Teamwork climate differed significantly by hospital (F59, 1,911 = 4.06, P < 0.001) and OR caregiver type (F4, 1,911 = 9.96, P < 0.001). CONCLUSIONS: Rigorous assessment of teamwork climate is possible using this psychometrically sound teamwork climate scale. This tool and initial benchmarks allow others to compare their teamwork climate to national means, in an effort to focus more on what excellent surgical teams do well.

Anesthesiology↗

PubMed1995

Evaluation of the Interaction Model of Client Health Behavior through the first decade of research.

The Interaction Model of Client Health Behavior was proposed in 1982 as a prescriptive nursing framework. The model is grounded in multidisciplinary perspectives, and early research suggests that the model may be useful for research and practice. The elements of client singularity and health outcomes have been the primary focus of research during the past decade. Statistical analyses have been exploratory. This article concludes that the model is ready for hypothesis testing with more rigorous statistical procedures, more diversity in samples, and more comprehensive use of the model, including the elements of client-professional interaction.

Bias↗

PubMed2025

Genetic predisposition to systemic inflammatory proteins is causally associated with inflammatory bowel disease: Insights from multi-omics association study and single-cell RNA-sequencing analysis.

Systemic inflammatory proteins have been reported to be related to inflammatory bowel disease (IBD) in previous observational research. However, their causal links remain obscure. Herein, we performed a Mendelian randomization (MR) analysis to analyze the causality between systemic inflammatory proteins and IBD. Genetic variants related to systemic inflammatory proteins were extracted from a meta-analysis of genome-wide association study (GWAS) data of 8293 European participants. Summary statistics of IBD diverse subtypes were obtained from the international IBD genetic consortium (IIBDGC). We conducted multi-omics method and MR study to detect the causal links through integrating GWAS and protein quantity trait loci (pQTL) data. Inverse variance weighted (IVW) approach was utilized as the dominated analysis method. Moreover, complementary approaches such as MR-Egger intercept test, Cochran Q test and leave-one-out analysis were utilized to validate pleiotropy and heterogeneity. Finally, single-cell RNA-sequencing analysis was performed to detect the expression of significant genes. For IBD, IVW estimates suggested that genetically predicted IL-10 and IL-13 were suggestively associated with an elevated risk of IBD (IL-10: OR: 1.12, 95% CI: 1.00-1.24, P = .04; IL-13: OR: 1.09, 95% CI: 1.01-1.18, P = .023), while CXCL10 was suggestively linked to a lower risk of IBD (CXCL10: OR: 0.90, 95% CI: 0.82-0.99, P = .037). For Crohn disease (CD), the IVW approach provided evidence to sustain that genetically determined IL-13 and CCL3 had a suggestive association with a higher risk of CD (IL-13: OR: 1.13, 95% CI: 1.02-1.26, P = .023; CCL3: OR: 1.22, 95% CI: 1.03-1.45, P = .018). Sensitivity analysis did not explore any heterogeneity and pleiotropy. Our findings supported the causal relationships between 4 specific inflammatory proteins (IL-10, IL-13, CXCL10, and CCL3) and the risk of IBD and CD, thereby providing promising biomarkers of various subtypes stratification and new insights for the prevention and therapeutic target of IBD.

Humans↗

PubMed1997

Screening of the TAP1 gene by denaturing gradient gel electrophoresis in insulin-dependent diabetes mellitus: detection and comparison of new polymorphisms between patients and controls.

New protective or disease-associated polymorphisms in the TAP1 gene were sought in insulin-dependent diabetes mellitus (IDDM) patients with the use of denaturing gradient gel electrophoresis (DGGE) screening of genomic DNA. The TAP1 gene is located in the human leukocyte antigen (HLA) class II region of the genome and encodes components of a peptide transporter essential for antigen presentation by HLA class I molecules. Fragments of TAP1 corresponding to the 5' promoter, each of the 11 exons (with portions of adjacent intronic regions) and the 3' flanking region were amplified by the polymerase chain reaction and then subjected to DGGE. DNA fragments of TAP1 yielded DGGE bands with patterns whose frequencies differed between IDDM patients and controls. Specific DGGE band patterns with fragments corresponding to the promoter, exons or introns 3, 6, 7, 8, 9 or 10 of TAP1 were detected exclusively in either patients or controls. Sequencing of TAP1 fragments encompassing exon 7 gave rise to a DGGE band pattern exclusively observed in an IDDM patient and sequencing revealed a previously unidentified polymorphisms at codon 518 (GTC-->ATC, Val-->Ile). Another unique polymorphism uncovered by DGGE revealed by sequencing a polymorphism in intron 2 in a diabetic patient. The genotypes of additional HLA class II matched patients and controls were determined with regard to five exonic and one intronic TAP1 polymorphism. A 10 base pair intronic insertion in intron 9 was exclusively identified in controls and missing from patients (P = 0.017). Further large population-based studies may reveal whether these newly identified at risk or protective TAP1 variants confer markers of statistical risk in diverse population groups.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2005

Local genetic differentiation among populations of the mass-flowering tropical shrub Erythroxylum havanense (Erythroxylaceae).

This study is aimed to understand the role of life-history traits in determining the genetic structure of populations. We used Erythroxylum havanense, a distylous shrub with synchronous and massive patterns of flowering and fruiting. We suggest that the high concentration of ephemeral resources produced by mass flowering satiates both pollinators and frugivores, restricting gene flow and leading to genetic differentiation among populations. Using random amplified polymorphic DNAs as genetic markers, we estimated genetic diversity and structure statistics to quantify the amount and distribution of genetic variation within and among five populations from the Pacific coast of Mexico. High levels of genetic variation within populations and significant differentiation among populations located very near to each other were found. Furthermore, spatial autocorrelation analysis indicated the presence of significant genetic structure at short spatial distances. We suggest that by influencing the foraging behavior of pollinators and frugivores, mass flowering may produce the observed patterns of genetic structure, while small differences in flowering or fruiting phenology could further reinforce the isolation of nearby populations.

Animals↗