Nonsense Polymorphism Research Articles

The ACTN3 p.Arg577Ter Genetic Variants Biomarker of the Fitness Performance, in Oaxaca Amerindian Population

Backgrond. ACTN3 is primarily expressed in fast skeletal muscle fibres. A common nonsense polymorphism in this gene is ACTN3 R577X (rs1815739:C>T) results in replacement of an arginine (R) with a premature stop codon (X) at amino acid 577 in the fast muscle protein α-actinin-3, which causes an absolute deficiency of α-actinin-3 protein and alterations in muscle metabolism. A common null polymorphism in the ACTN3 gene The ACTN3 p.Arg577Ter allele (p.R577* or R577X) has undergone positive selection, with an increase in the X allele frequency as modern humans migrated out of Africa into the colder, less species-rich Eurasian climates Aim. Analized the frequency of allele or genotypes from ACTN3 p.Arg577Ter genetic variants biomarker of the fitness performance, in Oaxaca Amerindian population. Methods. From people of different ethnic groups the State of Oaxaca, DNA was extracted from peripheral blood to extract DNA using the geneKatcher kit (invitrogene), to amplify the polymorphism p.Arg577Ter was realized by qRT_PCR, using tqman probes by determined by allelic discrimination. Results. The more frequency allele is wild type R in all populations, more tan 50%. The Genotype more prevalent is heterocygote RX. In afromexican population Genotype XX o ter-X/ter-X is a allelic variant. Distribution allelic and genotype is verry heterogenus in the populations. In conclusión the ACTN3 R577X gene variant can be used as a clinical marker for the selection of sports talents in the state of Oaxaca, considering that it has already been validated at the population level, with the R allele being more frequent in the state, which is the one associated with a greater selective advantage in sports that require muscular strength and greater physical performance.

Large-scale epidemiological study on feline autosomal dominant polycystic kidney disease and identification of novel PKD1 gene variants.

Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited disease in cats. In most cases, the responsible abnormality is a nonsense single nucleotide polymorphism in exon 29 of the PKD1 gene (chrE3:g.42858112C>A, the conventional PKD1 variant). The aim of this study was to conduct a large-scale epidemiological study of ADPKD caused by the conventional PKD1 variant in Japan and to search for novel polymorphisms by targeted resequencing of the PKD1 using a next-generation sequencer. A total of 1281 cats visiting the Veterinary Medical Center of the University of Tokyo were included in this study. DNA was extracted from the blood of each cat. We established a novel TaqMan real-time PCR genotyping assay for the conventional PKD1 variant, and all cases were examined for the presence of this variant. Targeted resequencing of all exons of the PKD1 was performed on the DNA of 23 cats with the conventional PKD1 variant, six cats diagnosed with cystic kidneys but without this variant, and 61 wild-type normal cats. Among the 1281 cats examined in this study, 23 (1.8%) harboured the conventional PKD1 variant. The odds of having the conventional PKD1 variant were significantly higher in Persian cats, Scottish Folds and Exotic Shorthairs than in the other breeds, although the number of cases in each breed was small. Furthermore, we identified four variants unique to cats with cystic kidneys that were not found in wild-type normal cats, all of which were in exon 15. In particular, two (chrE:g.42848725delC, pGly1641fs and chrE:g.42850283C>T, pArg2162Trp) were candidate variants. This study revealed that the conventional PKD1 variant was prevalent in Scottish Fold, Persian and Exotic Shorthair breeds in Japan, and variants in exon 15 of PKD1, in addition to the conventional variant in exon 29, would be key factors in the pathogenesis of ADPKD in cats.

Wnt10a missense gene polymorphism association with obesity risk: List of literature and a case-control study with Roc analysis for serum β-catenin level in Egypt

BackgroundGenome-wide association studies have been implicated in the pathogenesis of several diseases including obesity. Few Recent studies reported wnt10a protein as a negative regulator for the adipogenesis process. However, to our knowledge, no studies discussed the role of SNP in the mechanism through which wnt10a gene mediate its role in adipogenesis suppression. Objectiveswe intended to investigate the association between missense and non-sense pathogenic polymorphisms of wnt10a gene and obesity risk in the Egyptian population. In addition, we aimed to determine the diagnostic accuracy of serum β-catenin level, an important modulator of Wnt/β-catenin signaling in the obesity pathogenesis. It is worth noting, that it is the first study to discuss wnt10a gene polymorphisms and serum β-catenin level with obesity risk. MethodsOur study included 96 obese and 102 non-obese of unrelated Egyptian volunteers. All the subjects underwent measurement the level of serum fasting glucose level, lipid profile, serum β-catenin, and CBC. RFLP-PCR method was used to genotype both wnt10a gene polymorphisms (rs121908119-rs141074983). ResultsOur results showed that missense polymorphism of arginine to cysteine (rs141074983) SNP may be associated with obesity risk under different genetic models. The minor allele carrier (CT and TT) was highly associated with obesity (OR = 3.7 (1.3–7.07), p = 0.006). In contrast, the decrease in serum β-catenin level in obese than non-obese volunteers lacked the required statistical confidence (p > 0.05). ConclusionThe substitution of arginine to cysteine (rs141074983) in wnt10a gene is strongly associated with increased risk for obesity in the Egyptian population and larger studies can confirm our results.

Molecular profiling of individual FDA-approved clinical drugs identifies modulators of nonsense-mediated mRNA decay

Nonsense-mediated mRNA decay (NMD) degrades transcripts with premature stop codons. Given the prevalence of nonsense single nucleotide polymorphisms (SNPs) in the general population, it is urgent to catalog the effects of clinically approved drugs on NMD activity: any interference could alter the expression of nonsense SNPs, inadvertently inducing adverse effects. This risk is higher for patients with disease-causing nonsense mutations or an illness linked to dysregulated nonsense transcripts. On the other hand, hundreds of disorders are affected by cellular NMD efficiency and may benefit from NMD-modulatory drugs. Here, we profiled individual FDA-approved drugs for their impact on cellular NMD efficiency using a sensitive method that directly probes multiple endogenous NMD targets for a robust readout of NMD modulation. We found most FDA-approved drugs cause unremarkable effects on NMD, while many elicit clear transcriptional responses. Besides several potential mild NMD modulators, the anticancer drug homoharringtonine (HHT or omacetaxine mepesuccinate) consistently upregulates various endogenous NMD substrates in a dose-dependent manner in multiple cell types. We further showed translation inhibition mediates HHT's NMD effect. In summary, many FDA drugs induce transcriptional changes, and a few impact global NMD, and direct measurement of endogenous NMD substrate expression is robust to monitor cellular NMD.

The ACTN3 R577X polymorphism is associated with metabolic alterations in a sex-dependent manner in subjects from western Mexico.

The ACTN3 gene is primarily expressed in fast skeletal muscle fibres. A common nonsense polymorphism in this gene is ACTN3 R577X (rs1815739), which causes an absolute deficiency of α-actinin-3 protein and alterations in muscle metabolism. Considering metabolic alterations are influenced by nutrition and genetic factors, as well as lifestyle factors, we hypothesise a possible association of the ACTN3 R577X polymorphism with metabolic alterations. In this cross-sectional study, 397 adults met the inclusion criteria. Body composition was measured by electrical bioimpedance. Dietary data were analysed using Nutritionist Pro™ software. Biochemical variables were determined by dry chemistry. Genomic DNA was extracted from peripheral leukocytes and genotyping of the ACTN3 R577X polymorphism was determined by allelic discrimination using TaqMan probes. The statistical analyses were performed using SPSS statistical software. p<0.05 was considered statistically significant. The ACTN3 577XX genotype was associated with high glucose, triglyceride and very low density lipoprotein-cholesterol levels and a higher frequency of hypertriglyceridaemia and insulin resistance in women. In males, the genetic variant showed a trend towards significance for insulin resistance. The ACTN3 R577X polymorphism was associated with metabolic alterations in women and a tendency was observed in men variant carriers. Thus, this common genetic variant could be implicated in the development of chronic metabolic diseases.

Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation

SummaryThe protein α-actinin-3 expressed in fast-twitch skeletal muscle fiber is absent in 1.5 billion people worldwide due to homozygosity for a nonsense polymorphism in ACTN3 (R577X). The prevalence of the 577X allele increased as modern humans moved to colder climates, suggesting a link between α-actinin-3 deficiency and improved cold tolerance. Here, we show that humans lacking α-actinin-3 (XX) are superior in maintaining core body temperature during cold-water immersion due to changes in skeletal muscle thermogenesis. Muscles of XX individuals displayed a shift toward more slow-twitch isoforms of myosin heavy chain (MyHC) and sarcoplasmic reticulum (SR) proteins, accompanied by altered neuronal muscle activation resulting in increased tone rather than overt shivering. Experiments on Actn3 knockout mice showed no alterations in brown adipose tissue (BAT) properties that could explain the improved cold tolerance in XX individuals. Thus, this study provides a mechanism for the positive selection of the ACTN3 X-allele in cold climates and supports a key thermogenic role of skeletal muscle during cold exposure in humans.

Polymorphisms in RocA contribute to the molecular pathogenesis of serotype M28 group A streptococcus

Two‐component systems (TCSs) are signal transduction proteins that enable bacteria to respond to external stimuli by altering the global transcriptome. Accessory proteins interact with TCSs to fine‐tune their activity. In group A streptococcus (GAS), RocA (regulator of Cov) is an accessory protein that functions with the CovRS (control of virulence regulator/sensor) TCS. Previous data suggest that the N‐terminal predicted transmembrane domains are important for RocA function and interaction with the CovRS TCS. Whole‐genome sequencing analysis of serotype M28 GAS strains collected from invasive infections in humans identified a higher number of missense (amino acid altering) and nonsense (protein truncating) polymorphisms in rocA than expected. We hypothesized that polymorphisms in RocA alter the global transcriptome and virulence of serotype M28 GAS. We used naturally‐occurring clinical isolates with rocA polymorphisms, an isogenic rocA deletion mutant strain, and isogenic rocA polymorphism mutant strains to perform genome‐wide transcript analysis (RNA‐seq), in vitro virulence factor assays, and mouse and nonhuman primate pathogenesis studies to test this hypothesis. Results demonstrated that polymorphisms in rocA result in either a subtle transcriptome change causing a wild‐type‐like virulence phenotype, or a substantial transcriptome change leading to a significantly increased virulence phenotype. Each polymorphism had a unique effect on the global GAS transcriptome. Additionally, in contrast to previously published data on functional domains of RocA, polymorphisms in both the N‐terminal transmembrane domains and the C‐terminal predicted non‐functional histidine kinase ATPase domain result in an altered virulence phenotype suggestive of loss of RocA activity. Taken together, our data show that naturally‐occurring polymorphisms in one gene encoding an accessory protein can significantly alter the global transcriptome and virulence phenotype of GAS, an important human pathogen.Support or Funding InformationFondren Foundation, Houston Methodist Hospital and Research Institute (to JMM and PEB)American Heart Association Predoctoral Fellowship award 19PRE34380820 (to PEB)NIH grants R21AI139369‐01A1 and R21AI146771‐01 (to JMM)

Infection with different strains of SARS-COV-2 in patients with COVID-19

The biological diversity of SARS-CoV-2 was assessed by investigating the genetic variations of the spike glycoprotein of patients with COVID-19 in Iraq. Sequencing identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all identified variations showed obvious co-infections with two different viral strains per sample. Most samples exhibited three nonsense single nucleotide polymorphism (SNPs), p.301Cdel, p.380Ydel and p.436del, which yielded three truncated spike glycoproteins, respectively. Network and phylogenetic analyses indicated that all viral infections were derived from multiple viral origins. Results inferred from the specific clade-based tree showed that some viral strains were derived from European G-clade sequences. Our data demonstrated the absence of single-strain infection among all investigated samples in the studied area, which entails a higher risk of SARS-CoV-2 in this country. The identified high frequency of truncated spike proteins suggests that defective SARS-CoV-2 depend on helper strains possessing intact spikes during infection. Alternatively, another putative ACE2-independent route of viral infection is suggested. To the best of our knowledge, this is the first report to describe co-infection with multiple strains of SARS-CoV-2 in patients with COVID-19.

Clinical, histopathological and genetic characterisation of oculoskeletal dysplasia in the Northern Inuit Dog.

Seven Northern Inuit Dogs (NID) were diagnosed by pedigree analysis with an autosomal recessive inherited oculoskeletal dysplasia (OSD). Short-limbed dwarfism, angular limb deformities and a variable combination of macroglobus, cataracts, lens coloboma, microphakia and vitreopathy were present in all seven dogs, while retinal detachment was diagnosed in five dogs. Autosomal recessive OSD caused by COL9A3 and COL9A2 mutations have previously been identified in the Labrador Retriever (dwarfism with retinal dysplasia 1—drd1) and Samoyed dog (dwarfism with retinal dysplasia 2—drd2) respectively; both of those mutations were excluded in all affected NID. Nine candidate genes were screened in whole genome sequence data; only one variant was identified that was homozygous in two affected NID but absent in controls. This variant was a nonsense single nucleotide polymorphism in COL9A3 predicted to result in a premature termination codon and a truncated protein product. This variant was genotyped in a total of 1,232 dogs. All seven affected NID were homozygous for the variant allele (T/T), while 31/116 OSD-unaffected NID were heterozygous for the variant (C/T) and 85/116 were homozygous for the wildtype allele (C/C); indicating a significant association with OSD (p = 1.41x10-11). A subset of 56 NID unrelated at the parent level were analysed to determine an allele frequency of 0.08, estimating carrier and affected rates to be 15% and 0.6% respectively in NID. All 1,109 non-NID were C/C, suggesting the variant is rare or absent in other breeds. Expression of retinal mRNA was similar between an OSD-affected NID and OSD-unaffected non-NID. In conclusion, a nonsense variant in COL9A3 is strongly associated with OSD in NID, and appears to be widespread in this breed.

Polymorphisms in Regulator of Cov Contribute to the Molecular Pathogenesis of Serotype M28 Group A Streptococcus

Two-component systems (TCSs) are signal transduction proteins that enable bacteria to respond to external stimuli by altering the global transcriptome. Accessory proteins interact with TCSs to fine-tune their activity. In group A Streptococcus (GAS), regulator of Cov (RocA) is an accessory protein that functions with the control of virulence regulator/sensor TCS, which regulates approximately 15% of the GAS transcriptome. Whole-genome sequencing analysis of serotype M28 GAS strains collected from invasive infections in humans identified a higher number of missense (amino acid-altering) and nonsense (protein-truncating) polymorphisms in rocA than expected. We hypothesized that polymorphisms in RocA alter the global transcriptome and virulence of serotype M28 GAS. We used naturally occurring clinical isolates with rocA polymorphisms (n=48), an isogenic rocA deletion mutant strain, and five isogenic rocA polymorphism mutant strains to perform genome-wide transcript analysis (RNA sequencing), invitro virulence factor assays, and mouse and nonhuman primate pathogenesis studies to test this hypothesis. Results demonstrated that polymorphisms in rocA result in either a subtle transcriptome change, causing a wild-type-like virulence phenotype, or a substantial transcriptome change, leading to a significantly increased virulence phenotype. Each polymorphism had a unique effect on the global GAS transcriptome. Taken together, our data show that naturally occurring polymorphisms in one gene encoding an accessory protein can significantly alter the global transcriptome and virulence phenotype of GAS, an important human pathogen.

Flagellin-independent effects of a Toll-like receptor 5 polymorphism in the inflammatory response to Burkholderia pseudomallei.

BackgroundToll-like receptors (TLRs) are sentinel receptors of the innate immune system. TLR4 detects bacterial lipopolysaccharide (LPS) and TLR5 detects bacterial flagellin. A common human nonsense polymorphism, TLR5:c.1174C>T, results in a non-functional TLR5 protein. Individuals carrying this variant have decreased mortality from melioidosis, infection caused by the flagellated Gram-negative bacterium Burkholderia pseudomallei. Although impaired flagellin-dependent signaling in carriers of TLR5:c.1174C>T is well established, this study tested the hypothesis that a functional effect of TLR5:c.1174C>T is flagellin-independent and involves LPS-TLR4 pathways.Methodology/Principal findingsWhole blood from two independent cohorts of individuals genotyped at TLR5:c.1174C>T was stimulated with wild type or aflagellated B. pseudomallei or purified bacterial motifs followed by plasma cytokine measurements. Blood from individuals carrying the TLR5:c.1174C>T variant produced less IL-6 and IL-10 in response to an aflagellated B. pseudomallei mutant and less IL-8 in response to purified B. pseudomallei LPS than blood from individuals without the variant. TLR5 expression in THP1 cells was silenced using siRNA; these cells were stimulated with LPS before cytokine levels in cell supernatants were quantified by ELISA. In these cells following LPS stimulation, silencing of TLR5 with siRNA reduced both TNF-α and IL-8 levels. These effects were not explained by differences in TLR4 mRNA expression or NF-κB or IRF activation.Conclusions/SignificanceThe effects of the common nonsense TLR5:c.1174C>T polymorphism on the host inflammatory response to B. pseudomallei may not be restricted to flagellin-driven pathways. Moreover, TLR5 may modulate TLR4-dependent cytokine production. While these results may have broader implications for the role of TLR5 in the innate immune response in melioidosis and other conditions, further studies of the mechanisms underlying these observations are required.

Do Greenlandic Carriers of the TBC1D4 p.Arg684Ter Variant Have Increased Risk of Cardiovascular Disease?

Background: The nonsense polymorphism p.Arg684Ter in the TBC1D4 gene is associated with severe skeletal muscle insulin resistance and postprandial hyperglycemia in the Greenlandic population. Homozygous carriers have an increased risk for type 2 diabetes (odds ratio of 10.3) and the variant has an allele frequency of 17% with 4% homozygous carriers in the population. However, we do not know, if p.Arg684Ter carrier status also confers a greater risk of cardiovascular disease (CVD). Thus the aim is to investigate if carriers of the variant are more at risk of CVD than non-carriers. Materials and Methods: The study included adult participants in the Inuit Health in Transition study completed in the years 2005-2010 with sampling from 12 regions in Greenland (n= 3115) and the B99 study conducted from 1999-2001 (n=1401). Outcome was a first time CVD event from the Greenlandic Patien Register or the Causes of Death Register. Incidence rates of CVD were estimated by Poisson regression for wild type, heterozygous and homozygous carriers followed until the end of 2013, adjusted for European admixture proportion, age, sex, smoking, lipids, blood pressure, lipid- and blood pressure lowering drugs, blood glucose and known diabetes. Results: During a median follow-up time of 7 years [IQR: 5.0, 10.0], 273 had an incident CVD event, 13 events among homozygous (HO), and 78 events among heterozygous (HE) carriers. Both in crude and adjusted analyses, there was a higher risk of incident CVD with p.Arg684Ter carrier status, although not statistically significant, with unadjusted incidence rate ratios (IRR) of 2.2 [CI 0.3- 15.5] for HO vs. WT; multivariable adjusted IRR 1.6 [0.12-19.5] for HO vs. WT. The same pattern was seen for HE vs. WT. Conclusions: Overall, there was a trend towards increased risk of incident CVD with the TBC1D4 p.Arg684Ter variant although not statistically significant. Lack of statistical power may partly explain this, and replication in a larger sample or longer follow-up is needed. Disclosure M.E. Jørgensen: Stock/Shareholder; Self; Novo Nordisk A/S. Research Support; Self; AstraZeneca, Amgen Inc.. M. Tvermosegaard: None. P.F. Rønn: Employee; Spouse/Partner; Novo Nordisk A/S. Stock/Shareholder; Spouse/Partner; Novo Nordisk A/S. P. Bjerregaard: None. I.K. Dahl-Petersen: None. C.V. Larsen: None. M.L. Pedersen: None. A. Albrechtsen: None. I. Moltke: None. N. Grarup: None. T. Hansen: None.

APOBEC and ADAR deaminases may cause many single nucleotide polymorphisms curated in the OMIM database

Cytosine and adenosine deamination events (DNA, RNA substrates) account for most codon-context Targeted Somatic Mutation (TSM) patterns observed in immunoglobulin (Ig) somatic hypermutation (SHM), and in cancer exomes following Ig-SHM-like responses. TSM refers to the process of somatic mutagenesis involving deamination events that results on a dominant type of mutation (e.g., C-to-T), and co-incident at a particular motif (e.g., WRC), and preferentially targeting the first, second or third nucleotide position within the mutated codon (e.g. MC1, MC2 or MC3, read 5-prime to 3-prime). It is now widely accepted that if left uncorrected, the accumulation of uncorrected TSMs involving the deaminases, may lead to a diagnosis of cancer or other degenerative disease. Our hypothesis is that many missense, nonsense and synonymous single nucleotide polymorphisms (SNPs) associated with clinically significant diseases may have arisen in the population by similar highly targeted deamination events. The OMIM database was searched for disease-associated SNPs on the X chromosome, and for all chromosomes. The nucleotide substitution patterns for disease-associated SNPs were analyzed by the TSM method to identify the likely deaminase source for C-to-U (C-to-T/G-to-A) and A-to-I (A-to-G/T-to-C) derived gene mutations preferentially targeting known sequence motifs associated with the deaminases: AID, APOBEC3G, APOBEC3B and ADAR 1/2. Of the 789 OMIM SNPs analysed. In both data sets, the mutation targeting preferences within the mutated codon reveal a statistically significant bias (p < 0.001). The results imply that a deamination of C-site and A-site targets are written into the human germline for the chromosome wide exomic SNPs analysed. This is consistent with previously observed mutation patterns arising in cancer genomes and hypermutated Ig genes during SHM. The results imply that similar types of deaminase-mediated molecular processes that occur in somatic hypermutation and cancer, may be contributing causative drivers of human exomic SNPs.

Pilot screening study of targeted genetic polymorphisms for association with seasonal influenza hospital admission.

Host response to influenza is highly variable, suggesting a potential role of host genetic variation. To investigate the host genetics of severe influenza in a targeted fashion, 32 single nucleotide polymorphisms (SNPs) within viral immune response genes were evaluated for association with seasonal influenza hospitalization in an adult study population with European ancestry. SNP allele and genotype frequencies were compared between hospitalized influenza patients (cases) and population controls in a case-control study that included a discovery group (26 cases and 993 controls) and two independent, validation groups (1 with 84 cases and 4076 controls; the other with 128 cases and 9187 controls). Cases and controls had similar allele frequencies for variant rs12252 in interferon-inducible transmembrane protein 3 (IFITM3) (P > 0.05), and the study did not replicate the previously reported association of rs12252 with hospitalized influenza. In the discovery group, the preliminary finding of an association with a nonsense polymorphism (rs8072510) within the schlafen family member 13 (SFLN13) gene (P = 0.0099) was not confirmed in either validation group. Neither rs12252 nor rs8072510 showed an association according to the presence of clinical risk factors for influenza complications (P > 0.05), suggesting that these factors did not modify associations between the SNPs and hospitalized influenza. No other SNPs showed a statistically significant association with hospitalized influenza. Further research is needed to identify genetic factors involved in host response to seasonal influenza infection and to assess whether rs12252, a low-frequency variant in Europeans, contributes to influenza severity in populations with European ancestry.

Comparative Genomics of Mycoplasma bovis Strains Reveals That Decreased Virulence with Increasing Passages Might Correlate with Potential Virulence-Related Factors.

Mycoplasma bovis is an important cause of bovine respiratory disease worldwide. To understand its virulence mechanisms, we sequenced three attenuated M. bovis strains, P115, P150, and P180, which were passaged in vitro 115, 150, and 180 times, respectively, and exhibited progressively decreasing virulence. Comparative genomics was performed among the wild-type M. bovis HB0801 (P1) strain and the P115, P150, and P180 strains, and one 14.2-kb deleted region covering 14 genes was detected in the passaged strains. Additionally, 46 non-sense single-nucleotide polymorphisms and indels were detected, which confirmed that more passages result in more mutations. A subsequent collective bioinformatics analysis of paralogs, metabolic pathways, protein-protein interactions, secretory proteins, functionally conserved domains, and virulence-related factors identified 11 genes that likely contributed to the increased attenuation in the passaged strains. These genes encode ascorbate-specific phosphotransferase system enzyme IIB and IIA components, enolase, L-lactate dehydrogenase, pyruvate kinase, glycerol, and multiple sugar ATP-binding cassette transporters, ATP binding proteins, NADH dehydrogenase, phosphate acetyltransferase, transketolase, and a variable surface protein. Fifteen genes were shown to be enriched in 15 metabolic pathways, and they included the aforementioned genes encoding pyruvate kinase, transketolase, enolase, and L-lactate dehydrogenase. Hydrogen peroxide (H2O2) production in M. bovis strains representing seven passages from P1 to P180 decreased progressively with increasing numbers of passages and increased attenuation. However, eight mutants specific to eight individual genes within the 14.2-kb deleted region did not exhibit altered H2O2 production. These results enrich the M. bovis genomics database, and they increase our understanding of the mechanisms underlying M. bovis virulence.

A sequence-specific polymerase chain reaction method for HNA-2 genotyping: homozygous c.843A>T mutation predicts the absence of CD177.

Human neutrophil antigen-2 is located on a glycosylphosphatidylinositol-anchored receptor, CD177. Humans not expressing CD177 on their neutrophils may, under defined conditions, form isoantibodies. The genetic background for the absence of CD177 is not fully understood, and genetic screening of patients and donors is currently unavailable. A recent study has documented two mutations associated with CD177 absence: a nonsense polymorphism c.843A>T and a single-base deletion c.1011delG. First, we aimed to demonstrate that these newly described mutations are indeed associated with the absence of CD177. DNA fragments from isoimmunized, CD177-negative individuals were sequenced (n = 5). An additional five negative and 10 positive individuals were also analyzed. Second, we aimed to establish a sequence-specific primer (SSP) polymerase chain reaction method for easy and rapid detection of these mutations. None of 10 CD177-positive individuals, but four of 10 CD177-negative individuals were homozygous for the A>T mutation at Position c.843, including three of five isoimmunized individuals. This finding is supportive for the reported association. Surprisingly, and in contrast to the initial report, c.1011delG was not detected in our cohort. Furthermore, a two-step SSP method for c.843A>G was successfully established. c.843A>T, but not c.1011delG, is associated with the absence of CD177 in a significant number of individuals, including CD177-isoimmunized women. The c.843A>T mutation is easily detectable by a newly established SSP, but screening for this mutation will only provide sufficient evidence for a final diagnosis in case of homozygosity for the c.843T allele.

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

The ACTN3 R577X genotype is associated with muscle function in a Japanese population.

Homozygosity for the common nonsense polymorphism R577X in the α-actinin-3 gene (ACTN3) causes complete α-actinin-3 deficiency in fast-twitch skeletal muscle fibers. This study investigated whether the ACTN3 R577X polymorphism affects fitness status using a battery of tests in a large Japanese cohort. In the present study, 1227 subjects (age: 25-85 years) were genotyped for the ACTN3 R577X polymorphism (rs1815739) using a TaqMan SNP genotyping assay (Applied Biosystems). All subjects were divided into 2 groups based on their age (<55 years and ≥55 years). All subjects completed a questionnaire about exercise habits and were subjected to a battery of tests to assess their fitness status (including grip strength test, chair stand test, and 8-foot walking test). A significant association between the ACTN3 R577X genotype and chair stand test performance was observed in the group of men ≥55 using ANCOVA adjusted for age and exercise habits (p = 0.036). The ACTN3 R577X genotype accounted for 2.5% of the variability in the results of the chair stand test among men in the ≥55 age group. Moreover, for the ≥55 age group, performance in the chair stand test was lower among those with the XX genotype than among those with the RR genotype (p = 0.024) or RX genotype (p = 0.005), unlike results for the <55 age group. No significant difference was noted for hand grip strength or 8-foot walking time. Thus, our results suggest that the ACTN3 R577X genotype is associated with lower-extremity muscle function in the Japanese population.

Association of MOV10L1 gene polymorphisms and male infertility in azoospermic men with complete maturation arrest.

The present research was undertaken to study probable genetic variations of MOV10L1 in 30 infertile men that had complete maturation arrest in their spermatocyte levels and 70 fertile men as the control group. We performed polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) on extracted DNAs and sequencing was used to confirm the results. Identified polymorphisms in the MOV10L1 were further subjected to a haplotype analysis. We identified eight single nucleotide polymorphisms (SNPs): one missense (rs2272837) and four nonsense polymorphisms (rs2272836, rs11704548, rs2272838, rs138271) in the exonic sequences and three polymorphisms (rs12170772, rs2272840, rs17248147) in the intronic regions. With the exception of rs2272838, there was a statistically significant association in all polymorphisms between study population (P < 0.05). The result of haplotyping analysis showed ten possible haplotypes, from which five were significantly increased in infertile patients compared with the control group. Our results suggest that MOV10L1 gene polymorphisms in the studied infertile males with complete maturation arrest are linked to infertility.

Screen of whole blood responses to flagellin identifies TLR5 variation associated with outcome in melioidosis

Melioidosis is a severe infection caused by the flagellated bacterium Burkholderia pseudomallei. The nonsense polymorphism TLR51174C>T is associated with improved outcome in Thais with melioidosis. We hypothesized that other TLR5 variants may modulate the host response and determine outcome in melioidosis. We genotyped 12 TLR5 variants selected de novo from the HapMap database and examined the association of each with cytokines induced by flagellin stimulation of whole blood from healthy Thai subjects. We found a blunted cytokine response for three related markers that were in linkage disequilibrium with a non-synonymous variant, TLR51846T>C. Carriers of TLR51846T>C had broadly impaired cytokine responses induced by flagellin. TLR51846T>C was associated with protection against death in melioidosis patients (OR 0.62, 95% CI: 0.42-0.93, p=0.021). We observed no impairment in TLR51846C-dependent NF-κB activation, however, suggesting an alternative mechanism for the effect. We found that TLR51846T>C was in strong linkage disequilibrium with TLR51174C>T. Many of the blunted cytokine responses observed and the association of TLR51846T>C with survival in melioidosis patients may be attributable to TLR51174C>T, but we could not exclude an independent effect of TLR51846T>C. These data identify novel associations for TLR51846T>C, enhance our understanding of TLR5 genetic architecture in Thais, and provide future directions of study.