An EEG-based machine learning method to screen alcohol use disorder

Screening alcohol use disorder (AUD) patients has been challenging due to the subjectivity involved in the process. Hence, robust and objective methods are needed to automate the screening of AUD patients. In this paper, a machine learning method is proposed that utilized resting-state electroencephalography (EEG)-derived features as input data to classify the AUD patients and healthy controls and to perform automatic screening of AUD patients. In this context, the EEG data were recorded during 5 min of eyes closed and 5 min of eyes open conditions. For this purpose, 30 AUD patients and 15 aged-matched healthy controls were recruited. After preprocessing the EEG data, EEG features such as inter-hemispheric coherences and spectral power for EEG delta, theta, alpha, beta and gamma bands were computed involving 19 scalp locations. The selection of most discriminant features was performed with a rank-based feature selection method assigning a weight value to each feature according to a criterion, i.e., receiver operating characteristics curve. For example, a feature with large weight was considered more relevant to the target labels than a feature with less weight. Therefore, a reduced set of most discriminant features was identified and further be utilized during classification of AUD patients and healthy controls. As results, the inter-hemispheric coherences between the brain regions were found significantly different between the study groups and provided high classification efficiency (Accuracy = 80.8, sensitivity = 82.5, and specificity = 80, F-Measure = 0.78). In addition, the power computed in different EEG bands were found significant and provided an overall classification efficiency as (Accuracy = 86.6, sensitivity = 95, specificity = 82.5, and F-Measure = 0.88). Further, the integration of these EEG feature resulted into even higher results (Accuracy = 89.3 %, sensitivity = 88.5 %, specificity = 91 %, and F-Measure = 0.90). Based on the results, it is concluded that the EEG data (integration of the theta, beta, and gamma power and inter-hemispheric coherence) could be utilized as objective markers to screen the AUD patients and healthy controls.     

Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes

Interaction of DNA methylation and sequence variants that are methylation quantitative trait loci (mQTLs) may influence susceptibility to diseases such as alcohol dependence (AD). We used genome-wide genotype data from 268 African Americans (AAs: 129 AD cases and 139 controls) and 143 European Americans (EAs: 129 AD cases and 14 controls) to identify mQTLs that were associated with promoter CpGs in 82 AD risk genes. 282 significant mQTL–CpG pairs (9.9 × 10^?100 ≤ P _nominal ≤ 7.7 × 10^?8) in AAs and 313 significant mQTL–CpG pairs (2.7 × 10^?53 ≤ P _nominal ≤ 9.9 × 10^?8) in EAs were identified [i.e., mQTL–CpG associations survived multiple-testing correction, q values (false discovery rate) ≤ 0.05]. The most significant mQTL was rs1800759, which was strongly associated with CpG cg12011299 in both AAs (P _nominal = 9.9 × 10^?100; q = 6.7 × 10^?91) and EAs (P _nominal = 2.7 × 10^?53; q = 1.4 × 10^?44). Rs1800759 (previously known to be associated to AD) and CpG cg12011299 (distance: 37 bp) are both located in alcohol dehydrogenase (ADH) 4 gene (ADH4) promoter region. In general, the strength of association between mQTLs and CpGs was inversely correlated with the distance between them. Association was also influenced by race and AD. Additionally, 48.3 % of the mQTLs identified in AAs and 65.6 % of the mQTLs identified in EAs were predicted to be expression QTLs. Three mQTLs (rs2173201, rs4147542, and rs4147541 in ADH1B-AHD1C gene cluster region) found in AAs were previously identified by our genome-wide association studies as being significantly associated with AD in AAs. Thus, DNA methylation, which can be influenced by sequence variants and is implicated in gene expression regulation, appears to at least partially underlie the association of genetic variation with AD.     

Association of the HTR2A gene with alcohol and heroin abuse

Positive genetic associations of rs6313 (102T/C at exon 1) and rs6311 (?1438A/G) on the 5-hydroxytryptamine (serotonin) 2A receptor gene (HTR2A or 5-HT2A) were reported for alcohol and drug abuse; however, other association studies failed to produce consistent results supporting the susceptibility of the two single nucleotide polymorphisms (SNPs). To clarify the associations of the HTR2A gene with substance use disorders, we performed a meta-analysis based on the genotypes from the available candidate gene association studies of the two SNPs with alcohol and drug abuse from multiple populations. Evidence of association was found for HTR2A rs6313 in all the combined studies (e.g., allelic P = 0.0048 and OR 0.86, 95 % CI 0.77–0.95) and also in the combined studies of alcohol dependence (abuse) (e.g., allelic P = 0.0001 and OR 0.71, 95 % CI 0.59–0.85). The same association trend was also observed in the Study of Addiction: Genetics and Environment datasets. The meta-analysis supports a contribution of the HTR2A gene to the susceptibility to substance use disorders, particularly alcohol dependence.     

The influence of goethite and gibbsite on soluble nutrient dynamics and microbial community composition

Iron and aluminum (oxyhydr)oxides are ubiquitous in the soil environment and have the potential to strongly affect the properties of dissolved organic matter. We examined the effect of oxide surfaces on soluble nutrient dynamics and microbial community composition using an incubation of forest floor material in the presence of (1) goethite and quartz, (2) gibbsite and quartz, and (3) quartz surfaces. Forest floor material was incubated over a period of 154 days. Aqueous extracts of the incubations were harvested on days 5, 10, 20, 30, 60, 90, and 154, and concentrations of P, N, PO₄ ^3?, NO₂ ^?, NO₃ ^?, and organic C were measured in the solutions. Microbial community composition was examined through pyrosequencing of bacterial and fungal small subunit ribosomal RNA genes on selected dates throughout the incubation. Results indicated that oxide surfaces exerted strong control on soluble nutrient dynamics and on the composition of the decomposer microbial community, while possibly having a small impact on system-level respiration. Goethite and gibbsite surfaces showed preferential adsorption of P-containing and high molar mass organic solutes, but not of N-containing compounds. On average, organic C concentrations were significantly lower in water extractable organic matter (WEOM) solutions from oxide treatments than from the control treatment (P = 0.0037). Microbial community composition varied both among treatments and with increasing time of incubation. Variation in bacterial and fungal community composition exhibited strong-to-moderate correlation with length of incubation, and several WEOM physiochemical characteristics including apparent (weight averaged) molar mass, pH and electrical conductivity. Additionally, variation in bacterial community composition among treatments was correlated with total P (r = 0.60, P < 0.0001), PO₄ ^3? (r = 0.79, P < 0.0001), and organic C (r = 0.36, P = 0.015) concentrations; while variation in fungal communities was correlated with organic C concentrations (r = ?0.48, P = 0.0008) but not with phosphorus concentrations. The relatively small impact of oxide surfaces on system-level microbial respiration of organic matter despite their significant effects on microbial community composition and WEOM dynamics lends additional support to the theory of microbial functional redundancy.     

Association between the rs6950982 polymorphism near the SERPINE1 gene and blood pressure and lipid parameters in a high-cardiovascular-risk population: interaction with Mediterranean diet

The SERPINE1 (serpin peptidase inhibitor, clade E, member 1) gene, better known by its previous symbol PAI-1 (plasminogen activator inhibitor 1), has been associated with cardiovascular phenotypes with differing results. Our aim was to examine the association between the rs6950982 (G > A) near the SERPINE1 gene, blood pressure (BP) and plasma lipid concentrations as well as the modulation of the polymorphism effects by adherence to Mediterranean diet (AMD). We studied 945 high-cardiovascular-risk subjects. Biochemical, clinical, dietary and genetic data (rs6950982) were obtained. We also determined the common rs1799768 (4G/5G), for checking independent effects. AMD was measured by a validated questionnaire, and four groups were considered. rs6950982 (A > G) and rs1799768 (4G/5G) were only in moderate–low linkage disequilibrium (D′ = 0.719; r ² = 0.167). The most significant associations we obtained were with rs6950982 (A > G). In males, the G allele was nominally associated with higher diastolic BP (AA: 81.5 ± 10.9, AG: 82.1 ± 11.4, GG: 85.7 ± 10.5 mmHg; P _additive = 0.030) and systolic BP (AA + AG: 141.4 ± 6.9 mmHg vs. GG: 149.8 ± 8.0 mmHg; P _recessive = 0.036). In the whole population, the rs6950982 was also associated with plasma lipids. Subject with the G allele presented higher total cholesterol (P _additive = 0.016, P _recessive = 0.011), low-density lipoprotein cholesterol (P _additive = 0.032, P _recessive = 0.031) and triglycerides (P _additive = 0.040, P _recessive = 0.029). AMD modulated the effect of rs6950982 on triglyceride concentrations (P for interaction = 0.036). Greater AMD reduced the higher triglyceride concentrations in GG subjects. No significant interactions were found for the other parameters. The rs6950982 was associated with higher BP in men and higher triglycerides in the whole population, this association being modulated by AMD.     

Aortic Pulse Wave Velocity is Associated with Measures of Subclinical Target Organ Damage in Patients with Mild Hypertension

We evaluated the temporal association between aortic arterial stiffness and subclinical target organ damage, including renal function decline, left ventricular geometric remodeling, and left ventricular diastolic dysfunction in patients with mild hypertension. Automatic pulse wave velocity (PWV) measuring system was applied to examine carotid-femoral PWV (CFPWV) reflecting aortic arterial stiffness in 644 essential hypertensive patients. Clinical data were collected, and cardiac structure and function were assessed by echocardiography. CFPWV was significantly and positively associated with left ventricular mass index (r = 0.153, P = 0.018), relative wall thickness (r = 0.235, P < 0.001), and left atrial diameter (r = 0.192, P = 0.003), and negatively with E/A ratio (r = ?0.361, P < 0.001) and creatinine clearance (r = ?0.248, P < 0.001). Logistic regression analysis demonstrated that CFPWV remained significantly correlated with renal function decline (P = 0.011), left ventricular diastolic dysfunction (P = 0.009) and left ventricular geometric remodeling (P = 0.020). Higher CFPWV was independently associated with greater burden of subclinical disease in renal impairment, left ventricular geometric remodeling and diastolic dysfunction.     

Ordered subset linkage analysis based on admixture proportion identifies new linkage evidence for alcohol dependence in African-Americans

Genetic heterogeneity could reduce the power of linkage analysis to detect risk loci for complex traits such as alcohol dependence (AD). Previously, we performed a genomewide linkage analysis for AD in African-Americans (AAs) (Biol Psychiatry 65:111–115, 2009). The power of that linkage analysis could have been reduced by the presence of genetic heterogeneity owing to differences in admixture among AA families. We hypothesized that by examining a study sample whose genetic ancestry was more homogeneous, we could increase the power to detect linkage. To test this hypothesis, we performed ordered subset linkage analysis in 384 AA families using admixture proportion as a covariate to identify a more homogeneous subset of families and determine whether there is increased evidence for linkage with AD. Statistically significant increases in lod scores in subsets relative to the overall sample were identified on chromosomes 4 (P = 0.0001), 12 (P = 0.021), 15 (P = 0.026) and 22 (P = 0.0069). In a subset of 44 families with African ancestry proportions ranging from 0.858 to 0.996, we observed a genomewide significant linkage at 180 cM on chromosome 4 (lod = 4.24, pointwise P < 0.00001, empirical genomewide P = 0.008). A promising candidate gene located there, GLRA3, which encodes a subunit of the glycine neurotransmitter receptor. Our results demonstrate that admixture proportion can be used as a covariate to reduce genetic heterogeneity and enhance the detection of linkage for AD in an admixed population such as AAs. This approach could be applied to any linkage analysis for complex traits conducted in an admixed population.     

Relationship of self-mutilative behaviour with history of childhood trauma and adult ADHD symptoms in a sample of inpatients with alcohol use disorder

The aim of the present study was to evaluate relationship of self-mutilative behaviour (SMB) with the severity of childhood trauma and adult attention-deficit/hyperactivity disorder (ADHD) symptoms in a sample of inpatients with alcohol use disorder (AUD). Participants included 188 inpatients with AUD. Participants were evaluated with the Self-mutilative Behaviour Questionnaire, the Childhood Trauma Questionnaire (CTQ-28) and the Adult ADD/ADHD DSM-IV Based Diagnostic Screening and Rating Scale (Adult ADHD Scale). Among inpatients with AUD those who have a history of SMB constituted the SMB group (n = 57, 30.3%), and those without a history of SMB constituted the group without SMB (n = 131, 69.7%). Risk of high ADHD risk was 2.5 times higher among those with SMB. Adult ADHD Scale and CTQ-28 scores were also higher in the group with SMB. In the first backward logistic regression model, the severity of ADHD symptoms predicted the presence of SMB, together with the severity of childhood trauma, whereas in the second model, physical neglect and inattentive (IN) dimension of ADHD predicted the presence of SMB. These findings suggest that the higher severity of physical neglect and adult IN dimension of ADHD may be related to SMB among inpatients with AUD.     

Size at maturity of Mediterranean marine fishes

In this review we collected data on the length at maturity (L_m) and maximum reported total length (L_max) of 565 Mediterranean marine fish stocks, representing 150 species, 68 families, 24 orders and 3 classes. Overall, L_m ranged from 2 cm, for the males of the toothcarp Aphanius fasciatus, to 350 cm, for the females of the bluntnose sixgill shark Hexanchus griseus. L_m was positively linearly related with L_max for Actinopterygii (logL_m = ?0.123 + 0.92 × logL_max; r ² = 0.87, n = 471, P < 0.001) and Elasmobranchii (logL_m = ?0.008 + 0.922 × logL_max; r ² = 0.90, n = 92, P < 0.001) with the two slopes being significantly different (ANCOVA: F = 2,904, P < 0.001). The reproductive load (L_m/L_max) ranged between 0.23 (sand steenbras Lithognathus mormyrus) and 0.94 (angular roughshark Oxynotus centrina and thornback ray Raja clavata). The mean L_m/L_max was significantly (ANOVA, F = 34.14, P < 0.001) lower for Actinopterygii (mean = 0.59, SD = 0.122, n = 471) compared to Elasmobranchii (mean = 0.70, SD = 0.132, n = 92) and Holocephali (mean = 0.77, SD = 0.077, n = 2). The L_m/L_max was significantly (ANOVA, F = 43.80, P < 0.001) higher for species providing some form of parental care, i.e. guarders, bearers, nesters (mean L_m/L_max ± SD = 0.68 ± 0.141, n = 111) compared to non-guarders (mean L_m/L_max ± SD = 0.59 ± 0.123, n = 454). The mean L_m/L_max displayed a remarkable constancy with longitude (northern and southern Mediterranean coastline: ANOVA, F = 0.01, P = 0.93), latitude (western, central and eastern regions: ANOVA, F = 1.25, P = 0.29) and habitat (ANOVA, F = 0.85, P = 0.51).     

Polymorphisms of Genes in Neurotransmitter Systems Were Associated with Alcohol Use Disorders in a Tibetan Population

Studies of linkage and association in various ethnic populations have revealed many predisposing genes of multiple neurotransmitter systems for alcohol use disorders (AUD). However, evidence often is contradictory regarding the contribution of most candidate genes to the susceptibility of AUD. We, therefore, performed a case-control study to investigate the possible associations of genes selected from multiple neurotransmitter systems with AUD in a homogeneous Tibetan community population in China. AUD cases (N = 281) with an alcohol use disorder identification test (AUDIT) score ≥10, as well as healthy controls (N = 277) with an AUDIT score ≤5, were recruited. All participants were genotyped for 366 single nucleotide polymorphisms (SNPs) of 34 genes selected from those involved in neurotransmitter systems. Association analyses were performed using PLINK version 1.07 software. Allelic analyses before adjustment for multiple tests showed that 15 polymorphisms within seven genes were associated with AUD (p<0.05). After adjustment for the number of SNPs genotyped within each gene, only the association of a single marker (rs10044881) in HTR4 remained statistically significant. Haplotype analysis for two SNPs in HTR4 (rs17777298 and rs10044881) showed that the haplotype AG was significantly associated with the protective effect for AUD. In conclusion, the present study discovered that the HTR4 gene may play a marked role in the pathogenesis of AUD. In addition, this Tibetan population sample marginally replicated previous evidence regarding the associations of six genes in AUD.     

Flow Cytometry Analysis of Neural Differentiation Markers Expression in Human Glioblastomas May Predict Their Response to Chemotherapy

Glioblastoma multiforme (GBM) represents an extremely chemoresistant tumour type. Here, authors analysed the immunophenotype of GBM tumours by flow cytometry and correlated the immunophenotypic characteristics with sensitivity to chemotherapy. The expression of selected neural and non-neural differentiation markers including A2B5, CD34, CD45, CD56, CD117, CD133, EGFR, GFAP, Her-2/neu, LIFR, nestin, NGFR, Pgp and vimentin was analysed by flow cytometry in eleven GBM (WHO gr.IV) patients. The sensitivity of tumour cells to a panel of chemotherapeutic agents was tested by the MTT assay. All tumours were positive for A2B5, CD56, nestin and vimentin. CD133, EGFR, LIFR, NGFR and Pgp were expressed only by minor tumour cell subpopulations. CD34, CD45, CD117, GFAP and Her-2/neu were constantly negative. Direct correlations were found between the immunophenotypic markers and chemosensitivity: A2B5 vs lomustine (r² = 0.642, P = 0.033), CD56 vs cisplatin (r² = 0.745, P = 0.013), %Pgp⁺ vs vincristine (r² = 0.846, P = 0.008), and %NGFR⁺ vs daunorubicine (r² = 0.672, P = 0.047) and topotecan (r² = 0.792, P = 0.011). In contrast, inverse correlations were observed between: EGFR vs paclitaxel (r² = ?0.676, P = 0.046), CD133 vs dacarbazine (r² = ?0.636, P = 0.048) and LIFR vs daunorubicine (r² = ?0.878, P = 0.004). Finally, significant associations were also found among sensitivities to different chemotherapeutic agents and among different immunophenotypic markers. In conclusion, histopathologically identical GBM tumours displayed a marked immunophenotypic heterogeneity. The expression of A2B5, CD56, NGFR and Pgp appeared to be associated with chemoresistance whereas CD133, EGFR and LIFR expression was characteristic of chemosensitive tumours. We suggest that flow cytometric imunophenotypic analysis of GBM may predict chemoresponsiveness and help to identify patients who could potentially benefit from chemotherapy.     

ELISA examining urinary angiotensinogen as a potential indicator of intrarenal renin–angiotensin system (RAS) activity: a clinical study of 128 chronic kidney disease patients

In the current study, we measured urinary angiotensinogen (AGT) through enzyme-linked immunoadsordent assay (ELISA) and analyzed its correlation with intrarenal renin–angiotensin system (RAS) activity in 128 chronic kidney disease (CKD) patients. Urinary and plasma renin activity, AGT, angiotensin II (Ang II) and aldosterone levels were also measured by radioimmunoassay (RIA) or ELISA in these participants. Further, the expression level of intrarenal renin, AGT, Ang II and Ang II receptors were examined by immunohistochemistry staining (IHCS) in 72 CKD patients. Their correlations with urinary AGT were also analyzed. We found that the urinary AGT level was positively correlated with hypertension (ρ = 0.28, P < 0.01), urinary protein (r = 0.38, P < 0.01), urinary Ang II (r = 0.29, P < 0.05), urinary type IV collagen (Col IV) (r = 0.56, P < 0.01), and was negatively correlated with estimated glomerular filtration rate (eGFR) (r = ?0.28, P < 0.01), urinary sodium (r = ?0.22, P < 0.05) and serum AGT (r = ?0.27, P < 0.01). Multiple regression analysis indicated low serum AGT (P < 0.01), high urinary protein (P < 0.01), high urinary Ang II (P < 0.05) and high urinary Col IV (P < 0.01) were correlated significantly with high urinary AGT. Urinary AGT level was positively correlated with intrarenal expression level of AGT (ρ = 0.46, P < 0.01), Ang II (ρ = 0.56, P < 0.01) and Ang II type 1 receptor (ρ = 0.32, P < 0.01), as detected by IHCS. Together, these data suggest that urinary AGT might be a potential biomarker of intrarenal RAS and Ang II activities in CKD patients.     

Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat

Wheat production is currently threatened by widely virulent races of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, that are part of the TTKSK (also known as ‘Ug99’) race group. The diploid D genome donor species Aegilops tauschii (2n = 2x = 14, DD) is a readily accessible source of resistance to TTKSK and its derivatives that can be transferred to hexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD). To expedite transfer of TTKSK resistance from Ae. tauschii, a direct hybridization approach was undertaken that integrates gene transfer, mapping, and introgression into one process. Direct crossing of Ae. tauschii accessions with an elite wheat breeding line combines the steps of gene transfer and introgression while development of mapping populations during gene transfer enables the identification of closely linked markers. Direct crosses were made using TTKSK-resistant Ae. tauschii accessions TA1662 and PI 603225 as males and a stem rust-susceptible T. aestivum breeding line, KS05HW14, as a female. Embryo rescue enabled recovery of F₁ (ABDD) plants that were backcrossed as females to the hexaploid recurrent parent. Stem rust-resistant BC₁F₁ plants from each Ae. tauschii donor source were used as males to generate BC₂F₁ mapping populations. Bulked segregant analysis of BC₂F₁ genotypes was performed using 70 SSR loci distributed across the D genome. Using this approach, stem rust resistance genes from both accessions were located on chromosome arm 1DS and mapped using SSR and EST-STS markers. An allelism test indicated the stem rust resistance gene transferred from PI 603225 is Sr33. Race specificity suggests the stem rust resistance gene transferred from TA1662 is unique and this gene has been temporarily designated SrTA1662. Stem rust resistance genes derived from TA1662 and PI 603225 have been made available with selectable molecular markers in genetic backgrounds suitable for stem rust resistance breeding.     

Genetic diversity and genetic structure in wild populations of Mexican oregano (Lippia graveolens H.B.K.) and its relationship with the chemical composition of the essential oil

Mexican oregano is an aromatic plant traditionally harvested from wild populations by rural communities; however, there is little information about population genetics aspects of this species. Moreover, considering that the variation in essential oil production of aromatic plants has been attributed to several environmental as well as genetic factors, in this study we estimated the genetic diversity and genetic structure from 14 wild populations of L. graveolens located in four different bioclimatic regions in southeastern Mexico using AFLP markers. The overall genetic diversity of L. graveolens described as the percentage of polymorphic loci (PPL = 60.9 %) and Nei’s gene diversity (H _j  = 0.17) was moderate, but not associated with the bioclimatic conditions. Genetic variation was analyzed at chemotype and population levels. Regarding chemotypes, thymol had the highest genetic diversity (PPL = 82.8 % and H _j  = 0.22). PCoA revealed that chemotypes exhibit a certain level of genetic differentiation. Maximum parsimony dendrogram showed a grouping of individuals with a predominant chemotype. Bayesian analyses revealed a low, but significant differentiation among chemotypes (θ _ΙΙ = 0.008). Regarding populations, gene diversity showed significant differences (F _13,1204 = 22.8, P < 0.001); populations dominated by individuals from the thymol chemotype showed the highest gene diversity (H _j  = 0.31–0.25), while populations with exclusively sesquiterpene chemotype showed the lowest value (H _j  = 0.058). Cluster and Bayesian analyses (θ _ΙΙ = 0.027) revealed a low level of genetic differentiation among populations. Correlation analysis showed a significant association between the distance matrices based on the genetic markers (AFLP) and chemical compounds of essential oil (r = 0.06, P < 0.001). Our results suggest an important genetic influence on the observed chemical profiles. Nevertheless, other biotic and abiotic environmental pressures also play an important role in determining the chemotype and structure found in this aromatic species.     

Association, interaction, and replication analysis of genes encoding serotonin transporter and 5-HT3 receptor subunits A and B in alcohol dependence

On the basis of the converging evidence showing regulation of drinking behavior by 5-HT_3AB receptors and the serotonin transporter, we hypothesized that the interactive effects of genetic variations in the genes HTR3A, HTR3B, and SLC6A4 confer greater susceptibility to alcohol dependence (AD) than do their effects individually. We examined the associations of AD with 22 SNPs across HTR3A, HTR3B, and two functional variants in SLC6A4 in 500 AD and 280 healthy control individuals of European descent. We found that the alleles of the low-frequency SNPs rs33940208:T in HTR3A and rs2276305:A in HTR3B were inversely and nominally significantly associated with AD with odds ratio (OR) and 95 % confidence interval of 0.212 and 0.073, 0.616 (P = 0.004) and 0.261 and 0.088, 0.777 (P = 0.016), respectively. Further, our gene-by-gene interaction analysis revealed that two four-variant models that differed by only one SNP carried a risk for AD (empirical P < 1 × 10^?6 for prediction accuracy of the two models based on 10⁶ permutations). Subsequent analysis of these two interaction models revealed an OR of 2.71 and 2.80, respectively, for AD (P < 0.001) in carriers of genotype combinations 5′-HTTLPR:LL/LS(SLC6A4)–rs1042173:TT/TG(SLC6A4)–rs1176744:AC(HTR3B)–rs3782025:AG(HTR3B) and 5′-HTTLPR:LL/LS(SLC6A4)–rs10160548:GT/TT(HTR3A)–rs1176744:AC(HTR3B)–rs3782025:AG(HTR3B). Combining all five genotypes resulted in an OR of 3.095 (P = 2.0 × 10^?4) for AD. Inspired by these findings, we conducted the analysis in an independent sample, OZ-ALC-GWAS (N = 6699), obtained from the NIH dbGAP database, which confirmed the findings, not only for all three risk genotype combinations (Z = 4.384, P = 1.0 × 10^?5; Z = 3.155, P = 1.6 × 10^?3; and Z = 3.389, P = 7.0 × 10^?4, respectively), but also protective effects for rs33940208:T (χ ² = 3.316, P = 0.0686) and rs2276305:A (χ ² = 7.224, P = 0.007). These findings reveal significant interactive effects among variants in SLC6A4–HTR3A–HTR3B affecting AD. Further studies are needed to confirm these findings and characterize the molecular mechanisms underlying these effects.     

Analyses of longitudinal effects of gene-environment interactions on plasma C-reactive protein levels: the Hallym Aging Study

High C-reactive protein (CRP) level (above 3 mg/L), an inflammatory biomarker, is a well-known risk factor for cardiovascular disease. We investigated the longitudinal effects of interaction between genetic variants of seven candidate loci (i.e., IL6R, CRP, GCKR, IL6, CYP17A1, HNF1A, and APOE) and eight non-genetic factors (i.e., body mass index (BMI), total cholesterol to high density lipoprotein cholesterol ratio (T/HDL), systolic blood pressure, diastolic blood pressure (DBP), current smoking, alcohol consumption, regular exercise, and sleeping hours) on plasma hsCRP levels in a community-based cohort composed of 1,051 elderly Korean participants with a 6-year follow up. We applied a recently developed nonparametric approach, Survival Dimensionality Reduction (SDR) to evaluate gene-environment interactions using follow up data, and compared the results to those of conventional statistical approaches, Cox proportional hazard (CPH) regression model and log-rank test. Four gene variants significantly interacted with three non-genetic factors: SNPs rs2293571 (GCKR), rs1004467 (CYP17A1) and high DBP (HR = 3.22 and 2.95, P _G×E = 0.013 and 0.017, respectively); rs2464196 (HNF1A) and two non-genetic factors, regular exercise (HR = 3.78, P _G×E = 0.043) and high T/HDL (HR = 4.54, P _G×E = 0.042); and rs439401 (APOE) and regular exercise (HR = 3.01, P _G×E = 0.049). The interaction between the rs2464196 and T/HDL was consistently observed in both CPH model and SDR model (Accuracy = 0.86, P = 0.011). Investigating the effects of gene-environment interactions on baseline plasma hsCRP concentrations will provide clues to identify the pathway involved in increasing hsCRP level and the risks of related diseases.     

Genetic diversity of the endangered Chinese endemic herb Saruma henryi Oliv. (Aristolochiaceae) and its implications for conservation

Saruma henryi Oliv., the only representative of the monotypic genus Saruma Oliv. (Aristolochiaceae), is an endangered perennial herb endemic to China. It is a phylogenetically, ecologically, and medicinally important species. In the present study, inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 14 populations. A total of 16 selected primers yielded 175 bright and discernible bands, with an average of 10.94 per primer. POPGENE analysis showed that the genetic diversity was quite low at the population level (h = 0.0447–0.1243; I = 0.0642–0.1853; PPB = 10.29–36.57%), but pretty high at the species level (h = 0.2603; I = 0.3857; PPB = 73.71%). The hierarchical analysis of molecular variance (AMOVA) revealed a high level of genetic differentiation among populations (67.18% of total variance components, P < 0.001), in line with the gene differentiation coefficient (G _ST = 0.6903) and the limited among-population gene flow (N _m = 0.2243). Both Principal Coordinates Analysis (PCoA) and UPGMA cluster analysis supported the grouping of all 14 populations into three geographic groups, among which there occurred a moderate level of genetic differentiation (33.18% of total variance components, P < 0.001) as shown by AMOVA analysis. In addition, Mantel test revealed a significant correlation between genetic and geographic distances among populations (r = 0.7792, P = 0.001), indicating the role of geographic isolation in shaping its present population genetic structure. The present levels and patterns of genetic diversity of S. henryi were assumed to result largely from its breeding system, geographic isolation, clonal growth, its unique biological traits and evolutionary history. The high genetic differentiation among populations implies that the conservation efforts should aim to preserve all the extant populations of this endangered herb.     

Is high prevalence of vitamin D deficiency a correlate for attention deficit hyperactivity disorder?

The aim of the study was to determine the association between vitamin D and attention deficit hyperactivity disorder (ADHD), and difference in the level of vitamin D in ADHD children and control. This a case–control study carried out in school health and primary health care clinics. A total of 1,331 children and adolescents who were diagnosed with ADHD based on clinical criteria and standardized questionnaires were enrolled in this study and were matched with 1,331 controls, aged 5–18 years old. Data on body mass index (BMI), clinical biochemistry variables including serum 25-hydroxyvitamin D were collected. The study found significant association between ADHD and vitamin D deficiency after adjusting for BMI and sex (adj. OR 1.54; 95 % CI 1.32–1.81; P < 0.001). Majority of the ADHD children were in the age group 5–10 years (40.7 %), followed by 11–13 years (38.4 %). The proportion of BMI <85th percentile was significantly over represented in ADHD group as compared to healthy control (87.8 vs. 83 %; P < 0.001, respectively), while on the other hand, BMI >95th percentile was over represented in the control than ADHD group (7.6 vs. 4.6 %; P < 0.001, respectively). Mean values of vitamin D (ng/mL) were significantly lower in ADHD children (16.6 ± 7.8) than in healthy children (23.5 ± 9.0) (P < 0.001). There was significant correlation between vitamin D deficiency and age (r = ?0.191, P = 0.001); calcium (r = 0.272, P = 0.001); phosphorous (r = 0.284, P = 0.001); magnesium (r = 0.292, P = 0.001); and BMI (r = 0.498, P = 0.001) in ADHD children. The vitamin D deficiency was higher in ADHD children compared to healthy children.