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Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures.

The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure. First, the structure of an approximate model was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, an analysis of orientations of water in the first coordination shell, and the free energy of hydration of the chloride ion are reported for both state points. The most common water structure has one hydrogen close to the chloride ion and one pointing away (46% at 573 K and 57% at 723 K). Waters in the first coordination shell that are not strongly bound to the chloride ions are common. Several variations of the method were tested. Models in which the water-water interaction is calculated with ab initio methods predict only a slightly different structure than models in which water-water interactions are determined from the approximate models. Similarly, using the approximate model for solute-water interactions when the water is far from the chloride ion did not affect the results. Uncertainties due to the limited sample of configurations are estimated and found to be small. The results are in qualitative agreement with X-ray and neutron diffraction experiments and with simulations of approximate models.

Journal Article↗

A cross-cultural and developmental analysis of self-esteem in Chinese and Western children.

In this review, we examine the construct of self-esteem from a cross-cultural perspective in Chinese and Western children and adolescents. We also explore the role of childrearing practices in the development of self-esteem in these different cultures. In doing so, we first review the concepts of emic (i.e., variations in patterns of behavior within a given culture) and etic research (i.e., variations in common patterns of behavior or activities across cultures). Then, we invoke Berry's notions of "imposed-etic" and "derived-etic" approaches (J. Berry, 1989) in understanding crucial cross-cultural differences that are evident in the literature. We pose basic questions such as: (1) What does self-esteem "look" like in Chinese children? (2) How do childrearing practices in China influence the development of self-esteem in children? And, (3) what are the limitations of cross-cultural research in understanding a phenomenon such as self-esteem? We suggest that self-esteem does not "mean" the same things across these collectivist and individualistic cultures. We conclude our discourse with specific recommendations for clinical theory, research, and practice.

Adolescent↗

High throughput detection of small genomic insertions or deletions by Pyrosequencing.

Small insertions or deletions of nucleotides are common polymorphic variations in the human genome and can result in a predisposition to disease. However, high throughput methods for detecting these variations are limited. This report describes a method to detect this variation based on sequencing the boundaries of nucleotide alterations using the Pyrosequencing technique. This method can optimally detect up to 100 base pair nucleotide insertions and deletions, and also complicated genomic rearrangements.

Algorithms↗

Inherited thrombophilia: impact on human reproduction.

The development of thrombotic disorders is a major threat for young women during pregnancy. It is one of the main causes of pregnancy-related disorders, which may also result in harm for the conceptus. Successful pregnancies require an even balance of coagulation and fibrinolysis, in order to secure stabilization of the basal plate as well as adequate placental perfusion. Thrombophilia is a laboratory definition for pre-disposing factors of thrombosis, which can be inherited or acquired. Many individuals, who carry a thrombotic defect remain asymptomatic, at least until additional boosting factors arise. The documentation of thrombophilic causes of recurrent miscarriage or pregnancy-related disorders is important, because of availability of effective early treatment. There is a rapidly growing awareness on the relationship of genetic factors influencing hemostasis and pregnancy-related disorders. The aim of our review is to summarize this knowledge, focusing on common genetic variations.

Blood Coagulation↗

Cancer genetics.

Cancer genetics has for many years focused on mutational events that have their primary effect within the cancer cell. Recently that focus has widened, with evidence of the importance of epigenetic events and of cellular interactions in cancer development. The role of common genetic variation in determining the range of individual susceptibility within the population is increasingly recognized, and will be addressed using information from the Human Genome Project. These new research directions will highlight determinants of cancer that lie outside the cancer cell, suggest new targets for intervention, and inform the design of strategies for prevention in groups at increased risk.

Animals↗

Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease.

Genes and mechanisms involved in common complex diseases, such as the autoimmune disorders that affect approximately 5% of the population, remain obscure. Here we identify polymorphisms of the cytotoxic T lymphocyte antigen 4 gene (CTLA4)--which encodes a vital negative regulatory molecule of the immune system--as candidates for primary determinants of risk of the common autoimmune disorders Graves' disease, autoimmune hypothyroidism and type 1 diabetes. In humans, disease susceptibility was mapped to a non-coding 6.1 kb 3' region of CTLA4, the common allelic variation of which was correlated with lower messenger RNA levels of the soluble alternative splice form of CTLA4. In the mouse model of type 1 diabetes, susceptibility was also associated with variation in CTLA-4 gene splicing with reduced production of a splice form encoding a molecule lacking the CD80/CD86 ligand-binding domain. Genetic mapping of variants conferring a small disease risk can identify pathways in complex disorders, as exemplified by our discovery of inherited, quantitative alterations of CTLA4 contributing to autoimmune tissue destruction.

Abatacept↗

A road map for efficient and reliable human genome epidemiology.

Networks of investigators have begun sharing best practices, tools and methods for analysis of associations between genetic variation and common diseases. A Network of Investigator Networks has been set up to drive the process, sponsored by the Human Genome Epidemiology Network. A workshop is planned to develop consensus guidelines for reporting results of genetic association studies. Published literature databases will be integrated, and unpublished data, including 'negative' studies, will be captured by online journals and through investigator networks. Systematic reviews will be expanded to include more meta-analyses of individual-level data and prospective meta-analyses. Field synopses will offer regularly updated overviews.

Databases, Factual↗

Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9.

The low-density lipoprotein receptor (LDLR) prevents hypercholesterolemia and atherosclerosis by removing low-density lipoprotein (LDL) from circulation. Mutations in the genes encoding either LDLR or its ligand (APOB) cause severe hypercholesterolemia. Missense mutations in PCSK9, encoding a serine protease in the secretory pathway, also cause hypercholesterolemia. These mutations are probably gain-of-function mutations, as overexpression of PCSK9 in the liver of mice produces hypercholesterolemia by reducing LDLR number. To test whether loss-of-function mutations in PCSK9 have the opposite effect, we sequenced the coding region of PCSK9 in 128 subjects (50% African American) with low plasma levels of LDL and found two nonsense mutations (Y142X and C679X). These mutations were common in African Americans (combined frequency, 2%) but rare in European Americans (<0.1%) and were associated with a 40% reduction in plasma levels of LDL cholesterol. These data indicate that common sequence variations have large effects on plasma cholesterol levels in selected populations.

Adult↗

Fine-mapping the CYP2A6 regional association with nicotine metabolism among African American smokers.

The nicotine metabolite ratio (NMR; 3'hydroxycotinine/cotinine) is a stable biomarker for CYP2A6 enzyme activity and nicotine clearance, with demonstrated clinical utility in personalizing smoking cessation treatment. Common genetic variation in the CYP2A6 region is strongly associated with NMR in smokers. Here, we investigated this regional association in more detail. We evaluated the association of CYP2A6 single-nucleotide polymorphisms (SNPs) and * alleles with NMR among African American smokers (N&#x2009;=&#x2009;953) from two clinical trials of smoking cessation. Stepwise conditional analysis and Bayesian fine-mapping were undertaken. Putative causal variants were incorporated into an existing African ancestry-specific genetic risk score (GRS) for NMR, and the performance of the updated GRS was evaluated in both African American (n&#x2009;=&#x2009;953) and European ancestry smokers (n&#x2009;=&#x2009;933) from these clinical trials. Five independent associations with NMR in the CYP2A6 region were identified using stepwise conditional analysis, including the deletion variant CYP2A6*4 (beta&#x2009;=&#x2009;-0.90, p&#x2009;=&#x2009;1.55&#x2009;&#xd7;&#x2009;10-11). Six putative causal variants were identified using Bayesian fine-mapping (posterior probability, PP&#x2009;=&#x2009;0.67), with the top causal configuration including CYP2A6*4, rs116670633, CYP2A6*9, rs28399451, rs8192720, and rs10853742 (PP&#x2009;=&#x2009;0.09). Incorporating these putative causal variants into an existing ancestry-specific GRS resulted in comparable prediction of NMR within African American smokers, and improved trans-ancestry portability of the GRS to European smokers. Our findings suggest that both * alleles and SNPs underlie the association of the CYP2A6 region with NMR among African American smokers, identify a shortlist of variants that may causally influence nicotine clearance, and suggest that portability of GRSs across populations can be improved through inclusion of putative causal variants.

Adult↗

Treatment-resistant depression: role of genetic factors in the perspective of clinical stratification and treatment personalisation.

Treatment-resistant depression (TRD) is associated with chronic depression, suicidal behaviours, and reduced quality of life. TRD has a demonstrated genetic component, estimated around 8% based on common genetic variation in unrelated individuals. However, only six genome-wide association studies of TRD were published, and no replicated signals at locus or gene level have been identified; furthermore, apparently opposite results were reported in terms of genetic overlap between TRD and other traits. Other than limited power, an important issue of previous studies was the scarce consideration of TRD heterogeneity, as TRD likely comprises different groups and talking about TRDs could be more appropriate. This review points out important issues in the definition of TRD and differences across samples included in previous studies, which can be partly responsible for the inconsistency across results. Different definitions of TRD should not be expected to have similar genetic profiles, and the whole TRD group can partitioned into subgroups, based on clinical and biological features, to increase reproducibility, as exemplified by recent findings. This can be a key factor to develop/repurpose targeted treatments, or simply to aid a more personalised prescription of available medications compared to current clinical practice, that is largely concentrated on the prescription of a limited number of antidepressants compared to those available.

Humans↗

Chronotype and cellular circadian rhythms predict the clinical response to lithium maintenance treatment in patients with bipolar disorder.

Bipolar disorder (BD) is a serious mood disorder associated with circadian rhythm abnormalities. Risk for BD is genetically encoded and overlaps with systems that maintain circadian rhythms. Lithium is an effective mood stabilizer treatment for BD, but only a minority of patients fully respond to monotherapy. Presently, we hypothesized that lithium-responsive BD patients (Li-R) would show characteristic differences in chronotype and cellular circadian rhythms compared to lithium non-responders (Li-NR). Selecting patients from a prospective, multi-center, clinical trial of lithium monotherapy, we examined morning vs. evening preference (chronotype) as a dimension of circadian rhythm function in 193 Li-R and Li-NR BD patients. From a subset of 59 patient&#xa0;donors, we measured circadian rhythms in skin&#xa0;fibroblasts longitudinally over 5 days using a bioluminescent reporter (Per2-luc). We then estimated circadian rhythm parameters (amplitude, period, phase) and the pharmacological effects of lithium on rhythms in cells from Li-R and Li-NR donors. Compared to Li-NRs, Li-Rs showed a difference in chronotype, with higher levels of morningness. Evening chronotype was associated with increased mood symptoms at baseline, including depression, mania, and insomnia. Cells from Li-Rs were more likely to exhibit a short circadian period, a linear relationship between period and phase, and period shortening effects of lithium. Common genetic variation in the IP3 signaling pathway may account for some of the individual differences in the effects of lithium on cellular rhythms. We conclude that circadian rhythms may influence response to lithium in maintenance treatment of BD.

Adult↗

Polymorphisms of genes coding for insulin-like growth factor 1 and its major binding proteins, circulating levels of IGF-I and IGFBP-3 and breast cancer risk: results from the EPIC study.

Insulin-like growth factor I (IGF-I) stimulates cell proliferation and can enhance the development of tumours in different organs. Epidemiological studies have shown that an elevated level of circulating IGF-I is associated with increased risk of breast cancer, as well as of other cancers. Most of circulating IGF-I is bound to an acid-labile subunit and to one of six insulin-like growth factor binding proteins (IGFBPs), among which the most important are IGFBP-3 and IGFBP-1. Polymorphisms of the IGF1 gene and of genes encoding for the major IGF-I carriers may predict circulating levels of IGF-I and have an impact on cancer risk. We tested this hypothesis with a case-control study of 807 breast cancer patients and 1588 matched control subjects, nested within the European Prospective Investigation into Cancer and Nutrition. We genotyped 23 common single nucleotide polymorphisms in IGF1, IGFBP1, IGFBP3 and IGFALS, and measured serum levels of IGF-I and IGFBP-3 in samples of cases and controls. We found a weak but significant association of polymorphisms at the 5' end of the IGF1 gene with breast cancer risk, particularly among women younger than 55 years, and a strong association of polymorphisms located in the 5' end of IGFBP3 with circulating levels of IGFBP-3, which confirms previous findings. Common genetic variation in these candidate genes does not play a major role in altering breast cancer risk in Caucasians.

Adult↗

Allelic association of sequence variants in the herpes virus entry mediator-B gene (PVRL2) with the severity of multiple sclerosis.

Discrepant findings have been reported regarding an association of the apolipoprotein E (APOE) gene with the clinical course of multiple sclerosis (MS). To resolve these discrepancies, we examined common sequence variation in six candidate genes residing in a 380-kb genomic region surrounding and including the APOE locus for an association with MS severity. We genotyped at least three polymorphisms in each of six candidate genes in 1,540 Caucasian MS families (729 single-case and multiple-case families from the United States, 811 single-case families from the UK). By applying the quantitative transmission/disequilibrium test to a recently proposed MS severity score, the only statistically significant (P=0.003) association with MS severity was found for an intronic variant in the Herpes Virus Entry Mediator-B Gene PVRL2. Additional genotyping extended the association to a 16.6 kb block spanning intron 1 to intron 2 of the gene. Sequencing of PVRL2 failed to identify variants with an obvious functional role. In conclusion, the analysis of a very large data set suggests that genetic polymorphisms in PVRL2 may influence MS severity and supports the possibility that viral factors may contribute to the clinical course of MS, consistent with previous reports.

3' Untranslated Regions↗

The SREBF-1 locus is associated with type 2 diabetes and plasma adiponectin levels in a middle-aged Austrian population.

CONTEXT: The sterol regulatory element-binding protein-1c (SREBP-1c) is a transcription factor involved in the regulation of lipid and glucose metabolism and has been implicated in the pathophysiology of type 2 diabetes mellitus (T2DM). OBJECTIVE: We aimed to confirm associations of the SREBF-1 gene with T2DM in an Austrian population and to study possible associations with diabetes-related quantitative traits. DESIGN, SETTINGS AND PARTICIPANTS: We genotyped a diabetic cohort (n=446) along with a control group (n=1524) for a common C/G variation that is located in exon 18c (rs2297508) and has been associated with obesity and T2DM in French populations. MAIN OUTCOME MEASURES: Body mass index (BMI), indices of insulin sensitivity and beta-cell function, plasma adiponectin, T2DM and single-nucleotide polymorphism rs2297508. RESULTS: Genotype distributions associated with rs2297508 differed by T2DM status (P=0.0045), but not by BMI. The variant G allele was associated with a modest, but significant, increase in the prevalence of T2DM after adjustment for age, sex and BMI (G/G: odds ratios (OR) (95% confidence intervals)=1.45 (0.99-2.11) and G/C: OR=1.37 (1.04-1.81)). In a cross-sectional population of non-diabetic subjects, associations of rs2297508 genotypes with plasma adiponectin levels adjusted for age, sex and BMI (P=0.0017) were observed in that the risk G/G genotype displayed the lowest adiponectin levels. CONCLUSIONS: We observed associations of rs2297508 with T2DM prevalence and plasma adiponectin. SREBP-1c has been implicated in the regulation of adiponectin gene expression. Our results therefore raise the possibility that sequence variations at the SREBF-1 gene locus might contribute to T2DM risk, at least in part, by altering circulating adiponectin levels.

Adiponectin↗

Vitamin D receptor gene polymorphism in men and its effect on bone density and calcium absorption.

OBJECTIVE: Previous studies have suggested that polymorphism of the alleles of the vitamin D receptor (VDR) gene may account for the major part of the heritable component of bone density in women, possibly mediated in part by impaired calcium absorption from the bowel. In view of the increasing importance of osteoporosis in men, we have now investigated the association between common allelic variations in the vitamin D receptor gene, calcium absorption and bone density in men. SUBJECTS: Forty-eight men (median age 64, range 27-77) with a wide range of bone density measurements, comprising 20 men with vertebral crush fractures and 28 male control subjects. MEASUREMENTS: Analysis of the VDR gene polymorphism and measurement of fractional radiocalcium absorption and bone mineral density was performed in all subjects. RESULTS: The distribution of the three genotypes (TT, tt, Tt) was comparable to that reported previously. There was no significant difference in femoral neck bone density Z-scores between the three genotypes (mean +/- SD TT -0.31 +/- 1.19, tt -0.08 +/- 1.28 and Tt -0.37 +/- 1.17). There were also no significant differences in mean femoral neck bone density T-scores or lumbar spine bone density Z or T-scores between the three genotypes. Fractional radiocalcium absorption was 0.59 +/- 0.27 for TT, 0.69 +/- 0.30 for tt and 0.60 +/- 0.30 for Tt, showing no significant difference between the genotypes. CONCLUSIONS: This study shows no association between vitamin D receptor gene polymorphism and bone density or fractional calcium absorption in a group of men with a range of bone density values. We conclude that the vitamin D receptor gene alleles probably account at most for only a small part of the genetic component of bone density in men.

Adult↗

Quantitative genetics of ultrasonic advertisement signalling in the lesser waxmoth Achroia grisella (Lepidoptera: pyralidae).

Males of the lesser waxmoth Achroia grisella (Lepidoptera: Pyralidae) produce ultrasonic advertisement signals attractive to females within several metres. Previous studies showed that females prefer male signals that are louder, delivered at a faster rate, and have a greater asynchrony between pulses produced by the right and left wings. These three signal characters vary considerably within populations but are repeatable within individuals. Breeding experiments employing half-sib designs were conducted on both collectively and individually reared moths to determine genetic variance within and covariance among these signal characters. Heritabilities of all signal characters were significant among collectively reared moths. Heritabilities for signal rate and right-left wing asynchrony interval were not significant, however, among individually reared moths, suggesting the presence of significant nonadditive genetic variance or common environmental variation. Development time was also significantly heritable, but only under individual rearing. The only significant genetic correlation was between signal rate and length of the right-left wing asynchrony and this was negative. Our findings on heritability of signal characters are consistent with a coevolutionary sexual selection mechanism, but the absence of signal x development genetic correlation fails to support specifically a good-genes mechanism. The variation in heritability among conditions suggests that environmental variance may be high, and may render selection on signal characters by female choice ineffective. Thus, additive genetic variance for these characters may be maintained in the presence of directional female choice.

Animals↗

Cutaneous sarcoidosis in black South Africans.

BACKGROUND: It has been observed that, in the USA, sarcoidosis is more common in African-Americans than in other races. It has also been noted that sarcoidosis in African-Americans is characterized by more severe extrapulmonary involvement and more exuberant skin lesions. There is little information on sarcoidosis in black Africans. METHODS: Fifty-four black South African patients with cutaneous lesions of sarcoidosis proven by biopsy were prospectively studied. Dermatologic and ophthalmologic examinations and chest X-rays were performed in all patients. Other investigations relevant in the diagnosis of extracutaneous sarcoidosis were also performed in a variable number of patients. RESULTS: In 40 patients (71%), systemic sarcoidosis was found with lung, eye, and acral bone involvement being most common. Great variations in the morphology of skin lesions were observed. In one-quarter of patients, atypical cutaneous lesions (hypopigmented, ichthyosiform, lymphedematous, mutilating, ulcerative, verrucous) were found. Lupus pernio, once thought to be confined to Northern Europe, was observed in five patients in the subtropical milieu of South African Transvaal. Sarcoidal dactylitis with nail changes was seen in eight patients. Fibrinoid necrosis was found in 12% of the biopsies. CONCLUSIONS: Sarcoidosis in black South Africans is characterized by extensive cutaneous involvement. The lesions are morphologically extremely variable, frequently atypical, and often demonstrate fibrinoid necrosis on histology.

Adult↗

Phenotypic, genotypic and pathogenic variation among streptomycetes implicated in common scab disease.

This study examines the diversity of streptomycetes causing potato scab using phenotypic identification, 16S rRNA sequence, and pathogenicity measurements. Pathogenicity did not correlate well with taxonomic identification, nor with phylogenetic position. This result suggests that neither phenotypic nor 16S characteristics are diagnostic for scab-causing strains. Additionally, phenotypic characterizations were not fully consistent with phylogenetic relationships. This incongruency highlights the difficulties of taxonomy within the streptomycetes and affirms the need for better integration of genetic and phenotypic characters in the systematics of this group.

DNA, Bacterial↗