The evolution of sex chromosomes in the genus <Emphasis Type="Italic">Rumex</Emphasis> (Polygonaceae): Identification of a new species with heteromorphic sex chromosomes

The structural features and evolutionary state of the sex chromosomes of the XX/XY species of Rumex are unknown. Here, we report a study of the meiotic behaviour of the XY bivalent in Rumex acetosella and R. suffruticosus, a new species which we describe cytogenetically for the first time in this paper, and also that of the XY₁Y₂ trivalent of R. acetosa by both conventional cytogenetic techniques and analysis of synaptonemal complex formation. Fluorescent in situ hybridization with satellite DNA and rDNA sequences as probes was used to analyse the degree of cytogenetic differentiation between the X and Y chromosomes in order to depict their evolutionary stage in the three species. Contrasting with the advanced state of genetic differentiation between the X and the Y chromosomes in R. acetosa, we have found that R. acetosella and R. suffruticosus represent an early stage of genetic differentiation between sex chromosomes. Our findings further demonstrate the usefulness of the genus Rumex as a model for analysing the evolution of sex chromosomes in plants, since within this genus it is now possible to study the different levels of genetic differentiation between the sex chromosomes and to analyse their evolutionary history from their origin.     

Full mitochondrial and nuclear genome comparison confirms that <Emphasis Type="Italic">Onchocerca</Emphasis> sp. “Siisa” is <Emphasis Type="Italic">Onchocerca ochengi</Emphasis>

Onchocerca ochengi is a nodule-forming filarial nematode parasite of cattle. It is the closest known relative of the human parasite Onchocerca volvulus, with which it shares the black fly vector Simulium damnosum. Onchocerca sp. “Siisa” was described in black flies and in cattle and, based on limited mitochondrial sequence information, appeared to be about equally phylogenetically distant from O. ochengi and O. volvulus. Based on molecular genetic markers and apparent interbreeding, we later proposed that O. sp. “Siisa” belongs to the species O. ochengi. However, we did not demonstrate directly that the hybrids were fertile, and we were still unable to resolve the phylogenetic relationship of O. ochengi, O. sp. “Siisa,” and O. volvulus, leaving some concerns with the conclusion mentioned above. Here, we present fully assembled, manually curated mitochondrial genomes of O. ochengi and O. sp. “Siisa,” and we compare multiple individuals of these two taxa with respect to their whole mitochondrial and nuclear genomes. Based on the mitochondrial genomes, O. ochengi and O. sp. “Siisa” are phylogenetically much closer to each other than to O. volvulus. The differences between them are well within the range of what is expected for within-species variation. The nuclear genome comparison provided no indication of genetic separation of O. ochengi and O. sp. “Siisa.” From this, in combination with the earlier literature, we conclude that O. ochengi and O. sp. “Siisa” should be considered one species.     

An Enhanced Method of Transcutaneously Stimulating the Tibial Nerve for the Treatment of Overactive Bladder

Transcutaneous electrical nerve stimulation (TENS) can be used to electrically stimulate the tibial nerve for the purpose of treating overactive bladder. Although clinical benefits can be achieved, the overall therapeutic efficacy of TENS is limited. Inconsistent activation of the intended neural target and co-activation of cutaneous sensory fibers are considered key limiting factors. In this study, we propose a novel approach that combines TENS with an implanted, electrically-conductive nerve cuff to reduce the stimulation amplitude needed to activate the tibial nerve. This enhanced version of TENS (called eTENS) was designed using a computational model of the rat tibial nerve and subsequently tested in anesthetized rats. Our computational model showed that eTENS can reduce the nerve activation threshold by a factor of up to 2.6. Similar effects were also achieved by in vivo experiments (1.4 ± 0.1-fold decrease, n = 5). Among various design parameters, spatial alignment between the surface electrode and the nerve cuff was identified as an important factor. Our results show that eTENS can improve the selective activation of the rat tibial nerve, but further work is needed to evaluate its use in clinical therapies.     

Mitogen-activated protein kinases (MAPKs) are modulated during in vitro and in vivo infection with the intracellular bacterium <Emphasis Type="Italic">Burkholderia pseudomallei</Emphasis>

Burkholderia pseudomallei is a Gram-negative intracellular bacterium that causes the disease melioidosis. The disease can be fatal if left untreated or when antibiotic therapy is delayed and total clearance of the pathogen from the host is often not accomplished with current therapies. Thus, new therapeutic approaches for the treatment of infections caused by B. pseudomallei are required. To better understand host responses to B. pseudomallei infection, the activation of key proteins involved in the TLR inflammatory cascade was measured by western blotting. Activation of the mitogen-activated protein kinases (MAPKs) p38 and ERK were both significantly altered during both in vitro and in vivo infection. In considering an approach for therapy of B. pseudomallei infection the inhibition of ERK was achieved in vitro using the inhibitor PD0325901, along with decreased TNF-α production. However, the reduction in phosphorylated ERK and TNF-α release did not correspond with decreased bacterial replication or enhance clearance from infected macrophages. Despite this apparent lack of effect on the intracellular growth of B. pseudomallei in vitro, it is not clear what effect inhibition of ERK activation might have on outcome of disease in vivo. It may be that decreasing the levels of TNF-α in vivo could aid in reducing the overactive immune response that is known to ensue following B. pseudomallei infection, thereby increasing host survival.     

Reliability of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> semi-automated rep-PCR genotyping in various epidemiological situations

The purpose of this study was to evaluate the possibility of using a semi-automated repetitive DNA sequences-based polymerase chain reaction (rep-PCR) for typing Pseudomonas aeruginosa isolates. rep-PCR profiles obtained by the DiversiLab® system of 84 P. aeruginosa isolates from distinct epidemiological situations were obtained. rep-PCR groupings were in good agreement with the origin of these isolates. Linked rep-PCR profiles were observed for isolates recovered from a same family of cystic fibrosis (CF) patients, for the etiological agents of clustered cases of nosocomial infections, and for some isolates recovered from a same hospital room. rep-PCR and pulsed-field gel electrophoresis SpeI restricted genomic DNA (PFGE-SpeI) profiles were compared. In a few instances, rep-PCR revealed genetic divergences among isolates of a same group of PFGE-SpeI profiles. These divergences could reflect genetic drifts among closely related isolates, as illustrated by those observed between clinical and environmental isolates of a same group of PFGE-SpeI profiles. The interpretation of such differences will require further studies, but the rep-PCR analysis of P. aeruginosa diversity appeared to be an appropriate method to investigate infra-specific genetic relatedness.     

DNA microarray analysis of <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> causing bloodstream infection: bacterial genes associated with mortality?

Providing evidence for microbial genetic determinants’ impact on outcome in Staphylococcus aureus bloodstream infections (SABSI) is challenging due to the complex and dynamic microbe–host interaction. Our recent population-based prospective study reported an association between the S. aureus clonal complex (CC) 30 genotype and mortality in SABSI patients. This follow-up investigation aimed to examine the genetic profiles of the SABSI isolates and test the hypothesis that specific genetic characteristics in S. aureus are associated with mortality. SABSI isolates (n?=?305) and S. aureus CC30 isolates from asymptomatic nasal carriers (n?=?38) were characterised by DNA microarray analysis and spa typing. Fisher’s exact test, least absolute shrinkage and selection operator (LASSO) and elastic net regressions were performed to discern within four groups defined by patient outcome and characteristics. No specific S. aureus genetic determinants were found to be associated with mortality in SABSI patients. By applying LASSO and elastic net regressions, we found evidence suggesting that agrIII and cna were positively and setC (=selX) and seh were negatively associated with S. aureus CC30 versus non-CC30 isolates. The genes chp and sak, encoding immune evasion molecules, were found in higher frequencies in CC30 SABSI isolates compared to CC30 carrier isolates, indicating a higher virulence potential. In conclusion, no specific S. aureus genes were found to be associated with mortality by DNA microarray analysis and state-of-the-art statistical analyses. The next natural step is to test the hypothesis in larger samples with higher resolution methods, like whole genome sequencing.     

Multilocus Sequence Analysis of “Atypical” <Emphasis Type="Italic">Borrelia burgdorferi</Emphasis> sensu lato Isolated in Russia

Seventeen isolates of Borrelia burgdorferi sensu lato with an unclear genetic characteristic isolated in Russia from various species of Ixodes ticks (I. persulcatus, I. ricinus, and I. pavlovskyi) have been studied by multilocus sequencing analysis. According to the results of typing, these isolates were identified as B. bavariensis (n = 7), B. garinii (n = 6), B. finlandensis (n = 3), and B. spielmanii (n = 1), that is, species that can cause ixodid tick-borne borreliosis diseases in human beings. The allelic polymorphism of five genes (rrs, fla, groEL, recA, and ospA) and spacer rrfA–rrlB of B. bavariensis and B. garinii isolates was analyzed in comparison with their diversity in the International Nucleotide Sequence Database Collaboration.     

High frequency of occupied <Emphasis Type="Italic">attB</Emphasis> regions in Norwegian <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> isolates supports a two-step MRSA screening algorithm

Rapid nucleic acid amplification tests for methicillin-resistant Staphylococcus aureus (MRSA) diagnostics commonly target the mec resistance gene, genes specific for S. aureus, and the integration site for the SCCmec resistance cassette, orfX. Due to poor specificity when these target genes are used individually, additional culture is required to verify positive results. The combination of these targets is useful, but the optimal algorithm may depend on the presence of the genetic markers in S. aureus isolates, as well as the prevalence of MRSA in a population. The aim of the present study was to identify a rapid, low-cost, and functional screening algorithm in order to reduce the response time for MRSA diagnostics. An in-house orfX-SCCmec polymerase chain reaction (PCR) assay was established and evaluated. The results were compared with an existing mec/nuc PCR assay and traditional culture. Methicillin-sensitive S. aureus (MSSA) that tested false-positive in the orfX-SCCmec PCR assay were further investigated with full genome sequencing using the Ion PGM? System to verify results and causality. Based on these data, a two-step screening algorithm with initial mec/nuc PCR followed by orfX-SCCmec PCR on positive samples was suggested and tested on 1443 patient samples. 22.5 % of MSSA isolates tested false-positive with the orfX-SCCmec PCR. Full genome sequencing of these isolates identified genetic variation in the attB region of S. aureus, including empty cassette variants and non-mec SCC. The suggested two-step MRSA screening algorithm allowed us to report MRSA results for 95.6 % of all samples and 99 % of MRSA-negative samples after one day.     

<Emphasis Type="Italic">ACTA2</Emphasis> mutation and postpartum hemorrhage: a case report

Background

ACTA2 encodes smooth muscle specific α-actin, a critical component or the contractile complex of vascular smooth muscle. Mutations in ACTA2 are the most common genetic cause of thoracic aortic aneurysm, and are also the cause of other disorders, including Moyamoya disease, coronary artery disease and stroke as well as Multisystemic Smooth Muscle Dysfunction Syndrome. We note that ACTA2 is also expressed in uterine smooth muscle, and this raises the possibility that women harboring ACTA2 mutations might exhibit uterine smooth muscle dysfunction.

Case presentation

We present a young woman whose ACTA2 mutation was ascertained during pregnancy because of her father’s history of dissecting aneurysms. She was delivered at full term by cesarean section and subsequently had severe uterine hemorrhage due to uterine atony. Although her atony was successfully treated with uterotonic medications, she required blood transfusion.

Conclusions

This case raises the possibility that women with ACTA2 mutations may be at risk of uterine muscle dysfunction and hemorrhage. Obstetricians should be alerted to and prepared for this possibility.

     

The virus-induced HSPs regulate the apoptosis of <Emphasis Type="Italic">operatus</Emphasis> APCs that result in autoimmunity,not in homeostasis

The viruses stand salient as environmental factors that trigger autoimmunity. The virus realizes its effects through induction of heat-shock proteins (HSPs) as well as by the viral IE-axis-mediated conversion of organ epithelial cells into virgin de novo professional antigen-presenting cells (APCs). The HSP is the accomplished operator in homeostasis by the logic of it being the regulator of apoptosis. By virtue of its regulation of apoptosis, the HSP is also involved in autoimmunity: (1) adornment of viral IE-axis-generated virgin de novo professional APCs with HSP-induced co-stimulatory molecules which transform these otherwise epithelial cells to competent antigen presenters, the operatus APCs, liable to apoptosis that becomes the initiator of organ damages; (2) molecular mimicry mechanism: epitopes on the HSP may be mistaken for viral peptides and be presented by operatus APCs to autoreactive TCRs resulting in the apoptosis of the operatus APCs; (3) regulation of MHC class II DR-mediated apoptosis of operatus APCS which can result in organ-specific autoimmune syndromes. We should remember, however, that Nature’s intended purpose for apoptosis of the professional APCs is benevolence: as a principal regulator of immune homeostasis. But the apoptosis of our postulated operatus APCs can result in autoimmunity. The transformation of virgin de novo professional APCs to operatus APCs mirrors the maturation of DCs through their acquisition of HSP-induced costimulatory molecules. What happens to mature DCs as antigen presenters that end in homeostasis is replicated by what happens to operatus APCs that ends instead in autoimmunity.     

Genetic makeup of Shiga toxin-producing <Emphasis Type="BoldItalic">Escherichia coli</Emphasis> in relation to clinical symptoms and duration of shedding: a microarray analysis of isolates from Swedish children

Shiga toxin (Stx)-producing Escherichia coli (STECs) cause non-bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome, and are the primary cause of acute renal failure in children worldwide. This study investigated the correlation of genetic makeup of STEC strains as revealed by DNA microarray to clinical symptoms and the duration of STEC shedding. All STEC isolated (n?=?96) from patients <10 years of age in Jönköping County, Sweden from 2003 to 2015 were included. Isolates were characterized by DNA microarray, including almost 280 genes. Clinical data were collected through a questionnaire and by reviewing medical records. Of the 96 virulence genes (including stx) in the microarray, 62 genes were present in at least one isolate. Statistically significant differences in prevalence were observed for 21 genes when comparing patients with bloody diarrhea (BD) and with non-bloody stool (18 of 21 associated with BD). Most genes encode toxins (e.g., stx2 alleles, astA, toxB), adhesion factors (i.e. espB_O157, tir, eae), or secretion factors (e.g., espA, espF, espJ, etpD, nleA, nleB, nleC, tccP). Seven genes were associated with prolonged stx shedding; the presence of three genes (lpfA, senB, and stx1) and the absence of four genes (espB_O157, espF, astA, and intI1). We found STEC genes that might predict severe disease outcome already at diagnosis. This can be used to develop diagnostic tools for risk assessment of disease outcome. Furthermore, genes associated with the duration of stx shedding were detected, enabling a possible better prediction of length of STEC carriage after infection.     

Human Genetic Variation and HIV/AIDS in Papua New Guinea: Time to Connect the Dots

Purpose of Review

Human genetic polymorphisms known to influence HIV acquisition and disease progression occur in Papua New Guinea (PNG). However, no genetic association study has been reported so far. In this article, we review research findings, with a view to stimulate genotype-to-phenotype research.

Recent Findings

PNG, a country in Oceania, has a high prevalence of HIV and many sexually transmitted infections. While limited data is available from this country regarding the distribution of human genetic polymorphisms known to influence clinical outcomes of HIV/AIDS, genetic association studies are lacking. Our studies, in the past decade, have revealed that polymorphisms in chemokine receptor-ligand (CCR2-CCR5, CXCL12), innate immune (Toll-like receptor, β-defensin), and antiretroviral drug-metabolism enzyme (CYP2B6, UGT2B7) genes are prevalent in PNG.

Summary

Although our results need to be validated in further studies, it is urgent to pursue large-scale, comprehensive genetic association studies that include these as well as additional genetic polymorphisms.

     

The relationship between polymorphism of four serotonic genes (<Emphasis Type="Italic">5-HTTL, 5-HT1A, 5-HT2A</Emphasis>, and <Emphasis Type="Italic">MAOA</Emphasis>) and personality traits in wrestlers and control group

The molecular genetic analysis of serotonin system genes (5-HTTL, 5-HT1A, 5-HT2A, and MAOA) in male and female wrestlers and in a control group has been performed. Comparative population genetics analysis of the 5-HTTL gene showed the highest frequency of the SS genotype 5-HTTLPR in athletes (p = 0.04), as well as a trend to higher frequencies of united genotypes of the locus 5-HTTLPR VNTR and SNP rs25531—S _A S _A (p = 0.06) compared to the control group. As for the markers of 5-HT1A (rs6295), 5-HT2A (rs6311), and MAOA (VNTR), we found no significant differences between the groups tested. Using an NEO PI-R questionnaire, possible correlations between the genotypes and psychological traits were analyzed in the studied samples. It was demonstrated that the athletic achievements of upper-tier athletes are associated with their lower openness to experience and higher conscientiousness. It was revealed that the factors of gender and 5-HT1A genotype should influence the self-rating for openness to experience. Furthermore, a combined effect of the level of sports achievements and 5-HT2A genotypes was found, as well as gender and 5-HT1A genotypes, on the self-rating for conscientiousness.     

Identification of a new turncurtovirus in the leafhopper <Emphasis Type="Italic">Circulifer haematoceps</Emphasis> and the host plant species <Emphasis Type="Italic">Sesamum indicum</Emphasis>

Turncurtoviruses (family: Geminiviridae; genus: Turncurtovirus) appear to have a high degree of genetic variation in Iran. Leafhoppers of the species Circulifer haematoceps (Mulsant and Rey, 1855) (family: Cicadellidae) were collected in 2014 from three geographical regions in south-eastern Iran (Orzoeyeh, Jiroft and Sirjan; Kerman province) and screened for the presence of turncurtoviruses using a combination of PCR and rolling circle amplification (RCA) methods. Eleven genomes of turncurtovirus were recovered and sequenced. Leafhoppers were sampled off sesame (S. indicum L.) and turnip (Brassica rapa sub sp. rapa). Thus, we identified three symptomatic sesame plants (yellowing, boat-shaped leaf curling, vein swelling on the lower leaf surfaces) from sesame farms in Jiroft. In these samples, we identified the same turncurtovirus as in the leafhoppers and have named it sesame curly top virus (SeCTV). Collectively, these SeCTV share?>?98% genome-wide pairwise identity and ~?87.3% to a recently identified turncurtovirus (sesame yellow mosaic virus; SeYMV) from sesame in Pakistan (GenBank accession MF344550). The SeCTV and SeYMV sequences share?<?70% genome-wide pairwise identity with isolates of Turnip curly top virus and Turnip leaf roll virus, the two species in the genus Turncurtovirus. Based on the pairwise identities and phylogenetic analysis, SeCTV (n?=?12) and SeYMV (n?=?1) represent two strains of a new species in the genus Turncurtovirus.     

Determinants for persistence of Pseudomonas aeruginosa in hospitals: interplay between resistance,virulence and biofilm formation

Pseudomonas aeruginosa (Pa) is one of the major bacterial pathogens causing nosocomial infections. During the past few decades, multidrug-resistant (MDR) and extensively drug-resistant (XDR) lineages of Pa have emerged in hospital settings with increasing numbers. However, it remains unclear which determinants of Pa facilitated this spread. A total of 211 clinical XDR and 38 susceptible clinical Pa isolates (nonXDR), as well as 47 environmental isolates (EI), were collected at the Heidelberg University Hospital. We used RAPD PCR to identify genetic clusters. Carriage of carbapenamases (CPM) and virulence genes were analyzed by PCR, biofilm formation capacity was assessed, in vitro fitness was evaluated using competitive growth assays, and interaction with the host’s immune system was analyzed using serum killing and neutrophil killing assays. XDR isolates showed significantly elevated biofilm formation (p?<?0.05) and higher competitive fitness compared to nonXDR and EI isolates. Thirty percent (62/205) of the XDR isolates carried a CPM. Similarities in distribution of virulence factors, as well as biofilm formation properties, between CPM+ Pa isolates and EI and between CPM- and nonXDR isolates were detected. Molecular typing revealed two distinct genetic clusters within the XDR population, which were characterized by even higher biofilm formation. In contrast, XDR isolates were more susceptible to the immune response than nonXDR isolates. Our study provides evidence that the ability to form biofilms is an outstanding determinant for persistence and endemic spread of Pa in the hospital setting.     

Collinearity of homoeologous group 3 chromosomes in the genus <Emphasis Type="Italic">Hordeum</Emphasis> and <Emphasis Type="Italic">Secale cereale</Emphasis> as revealed by 3H-derived FISH analysis

Crop wild relatives are considered as important genetic resources of allelic diversity for domesticated crop species. Their utilization in breeding programs, however, is often limited due to crossing barriers and genome incompatibilities. Wild relatives of barley possess attractive properties and hence allelic diversity for adapting barley better to changing environmental conditions. Therefore, gaining a better knowledge about genomic synteny between cultivated barley and wild relatives of the same genus is an important task. To visualize genomic collinearity in related species, 22 genomic single-copy and 14 complementary DNA (cDNA) chromosome 3H-specific probes were mapped to the chromosomes of Hordeum bulbosum, Hordeum marinum, Hordeum pubiflorum, Hordeum murinum, and Secale cereale by fluorescent in situ hybridization (FISH). Most probes showed reliable signals confirming homoeology between cultivated barley and related species. Differences in order and position of FISH markers demonstrated sequence movements or small-scale chromosomal rearrangements within genus Hordeum and confirmed interchromosomal rearrangements between barley and rye. Comparison between repeat-free genomic and cDNA probes showed that gene-containing single-copy genomic DNA (gDNA) probes are performing more reliably for FISH-based analysis of synteny.     

Resting Heart Rate Variability (HRV) in Adolescents and Young Adults from a Genetically-Informed Perspective

Reduced heart rate variability (HRV) is associated with cardiac morbidity, mortality, and negative psychopathology. Most research concerning genetic influences on HRV has focused on adult populations, with fewer studies investigating the developmental period of adolescence and emerging adulthood. The current study estimated the genetic and environmental contributions to resting HRV in a sample of twins using various HRV time domain metrics to assess autonomic function across two different time measurement intervals (2.5- and 10-min). Five metrics of resting HRV [mean interbeat interval (IBI), the standard deviation of normal IBIs (SDNN), root square mean of successive differences between IBIs (RMSSD), cardiac vagal index (CVI), and cardiac sympathetic index (CSI)] were assessed in 421 twin pairs aged 14–20 during a baseline electrocardiogram. This was done for four successive 2.5-min intervals as well as the overall 10-min interval. Heritability (h²) appeared consistent across intervals within each metric with the following estimates (collapsed across time intervals): mean IBI (h²?=?0.36–0.46), SDNN (h²?=?0.23–0.30), RMSSD (h²?=?0.36–0.39), CVI (h²?=?0.37–0.42), CSI (h²?=?0.33–0.46). Beyond additive genetic contributions, unique environment also was an important influence on HRV. Within each metric, a multivariate Cholesky decomposition further revealed evidence of genetic stability across the four successive 2.5-min intervals. The same models showed evidence for both genetic and environmental stability with some environmental attenuation and innovation. All measures of HRV were moderately heritable across time, with further analyses revealing consistent patterns of genetic and environmental influences over time. This study confirms that in an adolescent sample, the time interval used (2.5- vs. 10-min) to measure HRV time domain metrics does not affect the relative proportions of genetic and environmental influences.     

Dismantling the theory of planned behavior: evaluating the relative effectiveness of attempts to uniquely change attitudes,norms, and perceived behavioral control

The current study compares the effectiveness of interventions that attempted to uniquely influence hypothesized determinants of behavior in the Theory of Planned Behavior versus some optimal combination of constructs (three constructs vs. four) to increase condom use among intentions and behavior college students. 317 participants (M_age?=?19.31; SD_age?=?1.31; 53.3% female; 74.1% Caucasian) were randomly assigned to one of seven computer-based interventions. Interventions were designed using the Theory of Planned Behavior as the guiding theoretical framework. 196 (61.8%) completed behavioral follow-up assessments 3-month later. We found that the four construct intervention was marginally better at changing intentions (estimate?=???.06, SE?=?.03, p?=?.06), but the single construct interventions were more strongly related to risky sexual behavior at follow-up (estimate?=?.04, SE?=?.02, p?=?.05). This study suggests that these constructs may work together synergistically to produce change (ClinicalTrials.gov Number NCT# 02855489).     

Genetic factors associated with patient-specific warfarin dose in ethnic Indonesians

Background

CYP2C9 and VKORC1 are two major genetic factors associated with inter-individual variability in warfarin dose. Additionally, genes in the warfarin metabolism pathway have also been associated with dose variance. We analyzed Single Nucleotide Polymorphisms (SNPs) in these genes to identify genetic factors that might confer warfarin sensitivity in Indonesian patients.

Methods

Direct sequencing method was used to identify SNPs in CYP2C9, VKORC1, CYP4F2, EPHX1, PROC and GGCX genes in warfarin-treated patients. Multiple linear regressions were performed to model the relationship warfarin daily dose requirement with genetic and non-genetic variables measured and used to develop a novel algorithm for warfarin dosing.

Results

From the 40 SNPs analyzed, CYP2C9 rs17847036 and VKORC1 rs9923231 showed significant association with warfarin sensitivity. In our study population, no significant correlation could be detected between CYP2C9*3, CYP2C9C-65 (rs9332127), CYP4F2 rs2108622, GGCX rs12714145, EPHX1 rs4653436 and PROC rs1799809 with warfarin sensitivity.

Conclusions

VKORC1 rs9923231 AA and CYP2C9 rs17847036 GG genotypes were associated with low dosage requirements of most patients (2.05 ± 0.77 mg/day and 2.09 ± 0.70 mg/day, respectively). CYP2C9 and VKORC1 genetic variants as well as non-genetic factors such as age, body weight and body height account for 15.4% of variance in warfarin dose among our study population. Additional analysis of this combination could allow for personalized warfarin treatment in ethnic Indonesians.

     

Associations of VCAM-1 gene polymorphisms with obesity and inflammation markers

Objective

Among the inflammatory mediators involved in the pathogenesis of obesity, cell adhesion molecules such as intercellular adhesion molecule-1 (ICAM-1) and vascular adhesion molecule-1 (VCAM-1) stand out. The aim of this study was to investigate the associations of ICAM-1 and VCAM-1 gene variants with obesity and to investigate the associations between these genetic polymorphisms and CRP, UA, and WBC count.

Method

Four SNPs of the VCAM-1 gene (rs3176860, rs2392221, rs3917010 and rs3176879) and two SNPs of the ICAM-1 gene (rs281432 and rs5498) were analyzed in 181 control (18 < BMI < 23) and 144 obese (BMI ≥ 25) subjects. The SNPs were genotyped by direct sequencing.

Results

In allele frequency analysis, the G allelic frequency of rs3176860 in the VCAM-1 gene was lower in the obese group (30.9%) than in the controls (41.2%) (P = 0.007). The C allelic frequency of rs3917010 was lower in the obese group (18.1%) than in the control (25.1%) (P = 0.03). In the haplotype analysis of VCAM-1 gene, the ht1 (ACA) was higher and ht2 (GCC) was lower in the obese subjects than in the controls (P = 0.0057 and P = 0.037, respectively). In the obese group, participants carrying the G allele of rs3176860 of the VCAM-1 gene showed a higher percentage of segmented neutrophils and CRP levels than those carrying only the A allele (P = 0.028 and P = 0.042, respectively).

Conclusions

The results of this study suggest that VCAM-1 gene variants may be related to obesity and inflammatory markers in the Korean population.