Allele Research Papers - Academia.edu (original) (raw)

We evaluated the clinical features, molecular defects, and problems associated with the management of two patients who had type-VII Ehlers-Danlos syndrome and reviewed the cases of eighteen patients with this condition who had been reported on previously. The typical clinical features associated with this syndrome include bilateral congenital dislocation of the hip; severe generalized hypermobility of the joints; multiple dislocations of joints other than the hip; muscular hypotonia; and hyperelasticity, fragility, and a doughy texture of the skin.

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- Biomedical Engineering, DNA, Mutation, Exploration

Recently, we reported an almost intact human endogenous retrovirus (HERV-K(HML-2.HOM); HGMWapproved symbol ERVK6) located on human chromosome 7, with open reading frames for all retroviral genes and a mutation only within the reverse transcriptase. We further characterized the genomic organization of this endogenous retrovirus by subcloning and sequencing of the proviral insert contained within a chromosome 7-specific cosmid clone and found HERV-K(HML-2.HOM) to be organized as a tandem repeat. Examination of various human DNA samples for this specific proviral repeat suggests a relatively ubiquitous distribution of the HERV-K(HML-2.HOM) tandem structure. However, we identified two human samples having only a single provirus at this locus. In addition, we investigated the presence of HERV-K(HML-2.HOM) alleles having an intact YXDD motif within the reverse transcriptase domain by sequencing the corresponding polymerase gene from various human DNA samples. We identified a HERV-K(HML-2.HOM) polymerase with an intact YXDD motif in two samples, thus potentially coding for an active reverse transcriptase. Our results show for the first time an endogenous retrovirus tandem repeat in human populations and suggest the existence of alleles harboring an intact human endogenous retrovirus including an intact polymerase gene.

- by Jens Mayer
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- Information Systems, Genetics, Genomics, Endogenous Retroviruses

HLA-DQAl typing of 227 randomly selected Northern Italian people by the use of polymeraae chain reaction are reported. The combined use of commercial Amplitype HLA-DQalpha system and four sequence-specific oligonucleotide probes allows the definition of 8 alleles and 36 genotypes, arranged according to World Health Organisation nomenclature. Seven of these genotypes are not observed among the analyzed samples. Allele frequencies range from 1.5 to 35.7% and genotype observations do not deviate significantly from Hardy-Weinberg equilibrium; observed heterozygosity is 0.8238 with an allelic diversity value of 0.79 and the power of discrimination is 0.925. Our Italian population sample shows differences from other Caucasian samples both for allele and genotype frequencies. This locus typing for the 8 defined alleles provides a rapid and sensitive method in individual iden.tification and paternity investigation.

- by Armando Mannucci and +1
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- Forensic Science, Population Genetics, Multidisciplinary, Italy

Molecular markers based on single nucleotide polymorphisms (SNPs) are abundant and evenly distributed in a whole genome enough to distinguish individuals in a population. In recent years, sets of SNP markers have been designed and applied for cultivar identification in various crop species. This paper is the first to report the development of a panel of SNP markers for variety identification in peppers. We used conserved ortholog set II (COSII) markers developed from conserved unigenes between tomato and Arabidopsis to identify SNPs in peppers. We tested 438 COSII primer sets amplified as single PCR products out of a total 600 COSII primer sets. Among the 438 COSII primers, 170 primer sets (38.8%) showed polymorphisms between Capsicum annuum ‘RNaky (RN)’and C. chinense ‘PI 159234 (234)’. In contrast, only 48 primer sets (11.0%) out of 438 primers sets were polymorphic between C. annuum ‘Perennial (PER), and ‘Dempsey (DEMP)’. The average frequency of SNPs plus InDels between C. annuum and C. chinense was 1/189 bp and between C. annuum spp. was 1/948 bp. Primer sets showing SNP between C. annuum PER and DEMP were re-designed to Allele Specific PCR (AS-PCR) primers and we finally selected a total of 40 SNP markers for cultivar identification. As the result, we were able to discriminate 97.5% of the 81 commercial hot cultivars and 100% of the 17 sweet pepper cultivars. We conclude the paper by discussing the use of the SNP marker set for cultivar identification and other applications.

- by Byoung-Cheorl Kang
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- Technology, Polymorphism, Pepper, Biological Sciences

Morphological, physiological and molecular changes were investigated in in vitro salt-stressed barley (Hordeum vulgare L. cv. Tokak). Mature embryos were cultured in Murashige and Skoog medium containing 0 (control), 50 and 100 mM NaCl for 20 days. Both concentrations inhibited shoot growth, decreased fresh weight and protein content, and increased SOD (EC 1.15.1.1) activity in a dose-dependent manner. The lower concentration increased root growth. Salinity caused nucleotide variations in roots, but did not affect shoot DNAs. The higher concentration caused methylation changes, mainly hypermethylation in shoots. This is the first study on genetic and epigenetic effects of salinity in barley.

- by Ángel-Luis García-Otín
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- Genetics, Demography, Molecular Biology, Polymorphism
- by Sonia Bojorquez
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- Genetics, Trait, Genome, Phenotype

Marked interindividual variability in expression of CYP3A4 in¯uences the disposition of many endo-and xenobiotics, including the metabolism of steroids, environmental toxins and therapeutically useful drugs. The present study was designed to determine the genetic basis of CYP3A4 variability. We analysed DNA from 82 individuals with known CYP3A4 phenotype including 53 Caucasians and 21 African-American liver donors, seven individuals who were outliers in CYP3A4 metabolism and ®ve individuals in a family of a poor nifedipine metabolizer. In addition, we analysed DNA from the eight person DNA Polymorphism Discovery Resource subset (Coriell Institute) and 89 individuals representing nine ethnic groups. Five nonsynonymous mutations in the coding region of CYP3A4 were observed. CYP3A4 Ã 14 (T44C) in exon 1 resulted in an L15P change; CYP3A4 Ã 15 (G14387A) in exon 6 resulted in a R162Q substitution; CYP3A4 Ã 10 (G14422C) in exon 6 resulted in a D174H substitution; CYP3A4 Ã 16 (C15721G) in exon 7 resulted in a T185S amino acid substitution; and CYP3A4 Ã 12 (C22002T) in exon 11 resulted in a L373F change in the CYP3A4 protein. An additional six single nucleotide polymorphisms (SNPs) in the 59-UTR, 13 SNPs in the introns and three SNPs in the 39-UTR were observed. Extensive population differences were observed in the frequencies of various CYP3A4 alleles. None of the 28 CYP3A4 SNPs identi®ed in CYP3A4 phenotyped persons (most individuals being heterozygous for any CYP3A4 variant) was associated with low hepatic CYP3A4 protein expression or low CYP3A4 activity in vivo.

- by Erin Schuetz and +1
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- Genetics, Western blotting, DNA, Population

Single nucleotide polymorphisms and restriction digestion-based haplotype variations among 160 flood prone rice varieties were analyzed with enzymes Alu I and Cac8 I to generate polymorphisms at Sub1A and Sub1C loci (conferring submergence tolerance), respectively. Haplotype associated with phenotype was used to study the haplotype variations at Sub1A and Sub1C loci and to determine their functional influence on submergence tolerance and stem elongation. Three patterns at Sub1A locus, Sub1A0 (null allele), Sub1A1 (does not cut) and Sub1A2 (one SNP), and four patterns at Sub1C locus, Sub1C1, Sub1C2, Sub1C3 and Sub1C4, were generated. Both tolerant Sub1A1 and intolerant Sub1A2 had the same length, but the difference was presence of a restriction site in the Sub1A2, but absent at the Sub1A1. Further, two types of polymorphism were detected at the Sub1C, one included major length polymorphisms (165, 170 and 175 bp) and the other was a single restriction site at different position. Eight haplotypes (different combinations of the two loci), A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4, were detected among 160 varieties. Haplotype A1C1 was comparatively more related to haplotypes A1C2 and A1C4, having the same Sub1A allele, and these haplotypes were found only in Bangladeshi, Sri Lankan and Indian varieties. Most tolerant varieties in A1C1 haplotype showed slow elongation, having tolerant specific Sub1A1 and Sub1C1 alleles. Further, the varieties Madabaru and Kottamali (A2C2) also showed moderate level of tolerance without Sub1A1 allele. These varieties were different with FR13A and also suspected to carry different novel tolerant genes at other loci. These materials could be used for hybridization with Sub1 varieties for pyramiding additional tolerant specific alleles into a single genotype for improving submergence tolerance in rice.

- by Maksudul Haque
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- Single Nucleotide Polymorphisms (SNPs), Haplotypes, Submergence, Allele

The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one "former" Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/ biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.

- by Xavier Nesme and +1
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- Microbiology, Microbial Ecology, Ecology, Sequence Analysis
- by J. Huerta-espino
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- Biology, Innate immunity, Medicine, Multidisciplinary

The resistant Rdl allele for dieldrin insecticide was detected on the Hypothenemus hampei populations from Colombia using conventional PCR methods. Based on this sequence, a melting temperature (T m ) shift genotyping method that relies on allele-specific PCR is described for insecticide resistance-associated single nucleotide polymorphism (SNP) at the H. hampei Rdl gene. The method reported here uses GC-rich tails of unequal length attached to allele-specific primers containing 3 0 terminal bases that correspond to SNP allelic variants. Specific PCR products are identified by inspection of a melting curve on a real-time PCR thermocycler using SYBR Green DNA binding dye. Resistant and susceptible alleles resulted in specific PCR products with T m of 83.3 ± 0.1°C and 86.0 ± 0.2°C, respectively. The Rdl T m -shift genotyping method is a new method to identify the Rdl gene in the coffee berry borer H. hampei, the principal pest of coffee that in general show low genetic diversity and very few genetic strategies for control of this pest have been developed. The method supplies a high-throughput tool for dieldrin resistance-associated SNP diagnostic in the coffee berry borer which will be useful for resistance-management strategies and as genetic marker in the colombian insect populations for genetics research.

- by LUCIO NAVARRO
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- Genetics, Molecular Biology, Genetic Diversity, Biological Sciences

A single nucleotide polymorphism or SNP is a site of the genome where variation occurs within a population. Almost all SNPs have only two alleles (variants). In this work, we consider a statistical method based on a likelihood ratio test... more

- by David Ramsey
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- Single Nucleotide Polymorphisms (SNPs), Genome Sequencing, Allele

This study used proteomic and transcriptomic techniques to understand the molecular basis of the phenotypic variability in the bone disorder osteogenesis imperfecta (OI). Calvarial bone mRNA expression was evaluated by microarray, real-time, and comparative RT-PCR and the bone proteome profile was analyzed by 2-DE, MS, and immunoblotting in the OI murine model BrtlIV, which has either a moderate or a lethal OI outcome. Differential expression analysis showed significant changes for eight proteins. The expression of the ER stress-related protein Gadd153 was increased in lethal mice, whereas expression of the chaperone aB crystallin was increased in nonlethal mice, suggesting that the intracellular machinery is involved in the modulation of the OI phenotype. Furthermore, in lethal BrtlIV, the increased expression of the cartilaginous proteins Prelp, Bmp6, and Bmp7 and the lower expression of the bone matrix proteins matrilin 4, microfibril-associated glycoprotein 2, and thrombospondin 3 revealed that both a delay in skeletal development and an alteration in extracellular matrix composition influence OI outcomes. Differentially expressed proteins identified in this model offer a starting point for elucidating the molecular basis of phenotypic variability, a characteristic common to many genetic disorders. The first reference 2-DE map for murine calvarial tissue is also reported.

- by Elena Campari
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- Proteomics, Western blotting, Biological Sciences, Microarray

The Latvian and the Swedish sweet cherry (Prunus avium L.) genetic resources collections comprise valuable material for breeding. The collections represent local Latvian and Scandinavian genetic resources: semi-wild samples, landraces, and cultivars developed in local breeding programmes, as well as diverse germplasm from the northern temperate zone. The objective of this investigation was to determine which S 1 –S 6 alleles are most important in the sweet cherry genetic resources collections and to compare the identified allelic and genotypic frequencies in material of different origin. Accessions in the two collections were screened for the presence of the self-incompatibility (S) S 1 to S 6 alleles, using PCR based typing. Significant differences (P < 0.05) between screened collections were found in frequencies of S 4 and S 5 alleles. Analysis of allele combinations identified the high occurrence of selections with the S-genotype S 3 S 6 in both collections. Compared to the S-allele frequencies published for over 250 sweet cherry cultivars from Western and Southern Europe, the Latvian and Swedish germplasm appeared to have a high frequency of the S 6 allele in both collections, and a relatively high frequency of the S 5 allele in Latvian germplasm. This study represents the first comprehensive S-allele screening for the sweet cherry genetic resources collections in Latvia and Sweden. Both sweet cherry collections contain high proportion of accessions adapted to north central European growing conditions, not typical for the majority of the documented sweet cherry genetic resources, which explains differences in certain S-allele occurrence.

- by Isaak Rashal
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- Technology, Biological Sciences, High Frequency, Allele
- by Roger Paredes
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- Microbiology, Medical Microbiology, Virology, HIV
- by Prida Malasit
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- Biology, Risk, Regulation, Medicine

Preliminary studies of historical sources and remote sensing were used to identify ancient olive trees near archaeological sites and heritage buildings in the Orcia Valley (Siena, Italy). Distinctive characters were assessed by traditional pomological observation. Trees with similar characters were selected on the basis of the features of endocarps, the only structure that survives aerobic deterioration and conserves useful botanical information for centuries. Non-invasive morphometric analysis of endocarp size and shape established morphological variations in individuals of different populations. Plastid organization in the endocarp and location of DNA in the endocarp tegument were detected by morphological and ultrastructural observations using light and electron microscopy. Cytoplasmic markers with high polymorphism were used to test similarity of endocarp and leaf DNA within individuals and to confirm low variability and minimal divergence between individuals. The ancient trees studied showed the same allelic profiles and therefore belonged to a distinct cultivar. The traditional pomological descriptions of the trees, leaves and fruits, morphometric analysis of size, and shape elliptic Fourier analysis of endocarp outline, ultrastructural observations and allelic profiles of endocarp tegument delineated the general species-specific qualities of the cultivar “olivastra Seggianese” of the Orcia Valley.Des études préliminaires sur sources historiques et de télédétection ont été utilisées pour identifier les oliviers centenaires à proximité des sites archéologiques et des édifices historiques du patrimoine dans le Val d’Orcia (Sienne, Italie). Les caractères distinctifs des oliviers ont été évalués au travers d’observations pomologiques traditionnelles. Arbres aux caractères similaires ont été sélectionnés sur la base des caractéristiques de l’endocarpe, la seule structure qui survit à la dégradation aérobie et conserve pendant des siècles des informations botaniques utiles. Avec l’étude morphométrique non-invasive de la taille et l’analyse de la forme de l’endocarpe, des changements morphologiques étaient établis chez les individus de populations différentes. L’organisation des plates dans le tégument de l’endocarpe et la localisation du DNA ont été détectées par des observations morphologiques et ultrastructurales avec microscopie optique et électrique. Marqueurs cytoplasmiques avec haut niveau de polymorphisme ont été utilisés pour tester des similitudes du DNA entre endocarpe et feuilles, et pour confirmer la faible variabilité et des divergences minimes entre les individus. Les vieux arbres étudiés présentaient les mêmes profils alléliques et donc appartenaient à un cultivar spécifique. Les descriptions pomologiques des arbres, des feuilles et des fruits, les analyses morphométriques avec l’étude de la taille et la forme de l’endocarpe d’olive, les observations ultrastructurales et les profils alléliques des endocarpes tégument, ont définit les qualités générales spécifiques à l’espèce de la variété « olivastra Seggianese » du Val d’Orcia.

- by Claudio Milanesi
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- Archaeology, Remote Sensing, Electron Microscopy, Polymorphism

The major outer-membrane protein (MOMP) of Campylobacter jejuni and Campylobacter coli, encoded by the porA gene, is extremely genetically diverse. Conformational MOMP epitopes are important in host immunity, and variation in surface-exposed regions probably occurs as a result of positive immune selection during infection. porA diversity has been exploited in genotyping studies using highly discriminatory nucleotide sequences to identify potentially epidemiologically linked cases of human campylobacteriosis. To understand the overall nature and extent of porA diversity and stability in C. jejuni and C. coli we investigated sequences in isolates (n=584) obtained from a defined human population (approx. 600 000) over a defined time period (1 year). A total of 196 distinct porA variants were identified. Regions encoding putative extracellular loops were the most variable in both nucleotide sequence and length. Phylogenetic analysis identified three porA allele clusters that originated ...

- by Martin Maiden
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- Genetics, Microbiology, Multidisciplinary, Genetic Diversity

Frequent and broad application of anthelmintic drugs for treatment of intestinal parasite infection has led to drug resistance that often renders whole populations of livestock unresponsive to treatment. Therefore, it is important to detect mutations associated with drug resistance before it becomes clinically manifest. To monitor developing drug resistance against benzimidazoles (BZ), we developed real-time PCR assays and applied them to analyse the beta-tubulin isotype-1 gene of the hookworm Ancylostoma caninum, an important parasite of dogs. Previously, we developed PCR assays to monitor codon positions 167 and 200. Here, we describe an assay which is able to detect resistance alleles in codon 198. These realtime PCR assays were subsequently applied to screen hookworm specimens recovered from dogs in Georgia. No elevated levels of polymorphisms at the investigated loci were found, suggesting that selection for resistance in the tested samples did not occur.

- by Ray Kaplan
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- Microbiology, Polymorphism, real time PCR, Dogs

The spread of plasmid-mediated quinolone resistance determinants (qnr-like determinants) was evaluated in a collection of 232 ciprofloxacin-resistant or extended-spectrum -lactamase (ESBL)-producing enterobacterial isolates recovered between . qnr genes were mainly found in Klebsiella pneumoniae (68%) and to a lesser extent in Escherichia coli (5.1%). Among the qnrA1, qnrS1 and qnrB19 alleles found, the latter was by far the most frequent. Genetic environment analysis revealed that one qnrB19 gene in E. coli was embedded in an ISCR1 complex class 1 integron. All other qnrB19 genes were flanked by an ISEcp1C region as part of the Tn2012 transposon.

- by Sara Richter
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- Genetics, Medical Microbiology, Italy, Escherichia coli
- by Sanaa Haroon
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- Tissue culture, ROOT, PEST, Genotype

Neo-Darwinists have long held that random mutations produce genetic differences among individuals, and selection increases the frequency of advantageous alleles. 1 In 1988, Cairns et al. claimed that an environmental pressure can cause advantageous mutations to occur in specific genes to alleviate that particular pressure. Directed mutation, as proposed by Cairns, has been all but eradicated from evolutionary thinking. However, more than a decade of research spurred by the Cairns et al. paper has cast doubt on three neo-Darwinian principles: (1) mutations occur independently of the environment, (2) mutations are due to replication errors, and (3) mutation rates are constant. This mini-review explores the history of the controversy and the decade of research that followed so as to place it in an evolutionary context. Several of the cellular mechanisms and models that explain the increased genetic diversity in populations experiencing adverse environmental pressure are described. In most cases it is clear that the increased genetic diversity is due to breakdowns of cellular machinery or alleles evolved for a purpose other than increasing genetic diversity, rather than to cellular systems that have been evolutionarily selected to increase the genetic diversity in times of stress.

- by Dustin Brisson
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- Genetics, Microbiology, Population Genetics, Molecular Evolution
- by When Rama
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- Multidisciplinary, Nature, Colorectal cancer, Mutation
- by Gail Jarvik
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- Gene expression, Biological Sciences, Mutation, Exploration
- by Daniel Grinberg
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- Genetics, Gene expression, Spain, Child

The hyaluronate lyase (HL) gene of Staphylococcus aureus 8325-4 (hysA) was inactivated in vitro with the insertion of the erythromycin determinant, ermC, from plasmid pE194. The hysA : : ermC mutation was introduced into S. aureus via a temperature-sensitive shuttle vector, where it underwent homologous recombination with the wild-type (w.t.) allele. The insertion of ermC in the chromosomal hysA locus was confirmed by Southern blot hybridization and the loss of HL activity was demonstrated macroscopically by a plate assay. The importance of HL for pathogenicity was assessed by comparing the virulence of the HL " mutant strain to that of the w.t. in an established mouse abscess model of S. aureus infection. A significantly higher cell recovery was obtained from lesions infected with the w.t. strain compared to the lesions infected with the HL " strain (P =0?01). Although the lesion areas from both groups were not significantly different (P=0?9) they were of different morphology. A colorimetric assay was used to measure HL activity from culture supernatants of the S. aureus 8325-4 strains w.t., WA250 (agr) and PC1839 (sar) grown in a chemically defined medium. HL activity reached a maximum in the w.t. strain during mid-exponential phase (t=5 h) and while it showed a 16-fold decrease in the agr mutant it increased 35-fold in the sar mutant background. These results strongly suggest that HL is a virulence factor which is important in the early stages of subcutaneous infections.

- by George Makris
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- Microbiology, Hybridization, Multidisciplinary, Virulence
- by Revista Agronomía Costarricense and +2
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- Susceptibility, Allele, Severity
- by Nick Patterson
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- Genetic Drift, Biological Sciences, Frequency, Spectrum

The aim of this study was to assess the association between the loss-of-function cytochrome P450 2C19 (CYP2C19)*2 variant (10 studies, 11,959 patients) or the use of proton pump inhibitors (PPIs) (13 studies, 48,674 patients) and ischemic... more

- by Ana Peña
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- Genetics, Cardiology, Treatment, Stents
- by A. Murphree
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- Genetics, Polymorphism, Multidisciplinary, Nature

Many species of Prunus display an S-RNase-based gametophytic self-incompatibility (SI), controlled by a single highly polymorphic multigene complex termed the S-locus. This comprises tightly linked stylar- and pollen-expressed genes that determine the specificity of the SI response. We investigated SI of Prunus tenella, a wild species found in small, isolated populations on the Balkan peninsula, initially by pollination experiments and identifying stylar-expressed RNase alleles. Nine P. tenella S-RNase alleles (S1–S9) were cloned; their sequence analysis showed a very high ratio of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) and revealed that S-RNase alleles of P. tenella, unlike those of Prunus dulcis, show positive selection in all regions except the conserved regions and that between C2 and RHV. Remarkably, S8-RNase, was found to be identical to S1-RNase from Prunus avium, a species that does not interbreed with P. tenella and, except for just one amino acid, to S11 of P. dulcis. However, the corresponding introns and S-RNase–SFB intergenic regions showed considerable differences. Moreover, protein sequences of the pollen-expressed SFB alleles were not identical, harbouring 12 amino-acid replacements between those of P. tenella SFB8 and P. avium SFB1. Implications of this finding for hypotheses about the evolution of new S-specificities are discussed.

- by Vesna Maksimović
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- Reproduction, Plant Biology, Fluorescence Microscopy, Pollination

Background-Artemether-lumefantrine (AL) is a major and highly effective artemisinin-based combination therapy that is becoming increasingly important as a new first-line therapy against Plasmodium falciparum malaria. However, recrudescences occurring after AL treatment have been reported. Identification of drug-specific parasite determinants that contribute to treatment failures will provide important tools for the detection and surveillance of AL resistance.

- by David Fidock
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- Microbiology, Treatment, Infectious Diseases, Molecular Genetics

Scapuloperoneal spinal muscular atrophy (SPSMA) and hereditary motor and sensory neuropathy type IIC (HMSN IIC, also known as HMSN2C or Charcot-Marie-Tooth disease type 2C (CMT2C)) are phenotypically heterogeneous disorders involving topographically distinct nerves and muscles. We originally described a large New England family of French-Canadian origin with SPSMA and an American family of English and Scottish descent with CMT2C ,2 . We mapped SPSMA and CMT2C risk loci to 2q24.-q24.3 with an overlapping region between the two diseases 3,4 . Further analysis reduced the CMT2C risk locus to a 4-Mb region 5 . Here we report that SPSMA and CMT2C are allelic disorders caused by mutations in the gene encoding the transient receptor potential cation channel, subfamily V, member 4 (TRPV4). Functional analysis revealed that increased calcium channel activity is a distinct property of both SPSMA- and CMT2C-causing mutant proteins. Our findings link mutations in TRPV4 to altered calcium homeostasis and peripheral neuropathies, implying a pathogenic mechanism and possible options for therapy for these disorders.

- by Han-Xiang Deng
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- Biological Sciences, Cell line, Spinal Muscular Atrophy, Mutation

Czechs (CZ) and Gypsies (GY) have lived in the same country for several centuries but seem to have different migratory origins. We have studied 99 CZ and compared them with 34 GY from an isolated group living in Czechoslovakia. DRBI, DRB3, DRB4, DRB5, DQAI, DQBl and DPBl alleles were determined by PCR followed by oligonucleotide hybridization. DRB1*0701 was the most frequent DR allele in CZ (af=36.3%,). In GY, after DRB1*0701, DRBI*I404 was the second most frequent allele (af=29.4%), while in CZ this allele was not found.

- by Marie Cerna
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- Immunology, Comparative Study, DNA, Haplotypes

- by Ray Kaplan
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- Microbiology, Polymorphism, real time PCR, Dogs

The development of human breast cancer is a complex multi-step process that depends on various exogenous and endogenous factors that modulate the transformation of normal human breast epithelial cells into neoplastic ones. Using a spontaneously-immortalized human breast epithelial (MCF-10F) cell line, we have shown previously that radiation, in combination with estrogen, induces a stepwise neoplastic transformation of this cell line. In the present study, we investigate the incidence of microsatellite instability and loss of heterozygosity using a battery of markers on chromosomes 6 and 17, we correlate the genetic alteration with the malignant transformation of the MCF-10F cell line ranging from altered morphology to increase in proliferative rate, anchorage independent growth and tumorigenicity in nude mice. Microsatellite markers were selected from the hot spot regions (6q21-q27, 17p12-p13.3 and 17q12-q21) of both chromosomes. We found that the frequency of allelic imbalance occurs at the different stages of tumor progression with a range of 21 to 50% depending on the marker studied. The relatively high rate of allele imbalance at all these loci suggests the presence and inactivation of one or more tumor suppressor genes in these regions. Thus, the present data will be useful for systematic studies to identify the cellular and molecular changes associated with radiation-induced breast carcinogenesis.

- by Debasish Roy
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- Genetics, Breast Cancer, Cell line, In Vitro

To investigate the origin of European spelt (Triticum spelta L., genome AABBDD) and its relation to bread wheat (Triticum aestivum L., AABBDD), we analysed an approximately 1-kb sequence, including a part of the promoter and the coding region, of the high-molecular-weight (HMW) glutenin B1-1 and A1-2 subunit genes in 58 accessions of hexa- and tetraploid wheat from different geographical regions. Six Glu-B1-1 and five Glu-A1-2 alleles were identified based on 21 and 19 informative sites, respectively, which suggests a polyphyletic origin of the A- and B-genomes of hexaploid wheat. In both genes, a group of alleles clustered in a distinct, so-called beta subclade. High frequencies of alleles from the Glu-B1-1 and Glu-A1-2 beta subclades differentiated European spelt from Asian spelt and bread wheat. This indicates different origins of European and Asian spelt, and that European spelt does not derive from the hulled progenitors of bread wheat. The conjoint differentiation of alleles of the A- and B-genome in European spelt suggests the introgression of a tetraploid wheat into free-threshing hexaploid wheat as the origin of European spelt.

- by Stefanie Jacomet
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- Genetics, Technology, Agriculture, Biological Sciences

Group A rotaviruses (RVA) are double stranded RNA viruses that are a significant cause of acute pediatric gastroenteritis. Beginning in 2006 and 2008, respectively, two vaccines, Rotarix™ and RotaTeq®, have been approved for use in the USA for prevention of RVA disease. The effects of possible vaccine pressure on currently circulating strains in the USA and their genome constellations are still under investigation. In this study we report 33 complete RVA genomes (ORF regions) collected in multiple cities across USA during 2006-2009, including 8 collected from children with verified receipt of 3 doses of rotavirus vaccine. The strains included 16 G1P[8], 10 G3P[8], and 7 G9P[8]. All 33 strains had a Wa like backbone with the consensus genotype constellation of G(1/3/9)-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. From maximum likelihood based phylogenetic analyses, we identified 3-7 allelic constellations grouped mostly by respective G types, suggesting a possible allelic segregation based on th...

- by Mathew Esona
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- Genetics, Allele

The dopamine D4 receptor gene (DRD4) has an expressed polymorphism in the third exon that may have functional relevance. The polymorphism exists at two levels. At the higher level there is an imperfect tandem repeat of 48 base pairs (bp) coding for 16 amino acids; alleles have been identified with 2 (32 amino acids) to 10 (160 amino acids) repeats. The imperfect nature of the repeats is responsible for a more subtle level of variation since alleles with the same number of repeats can differ in the exact sequences or in the order of the variants of the 48-bp unit. We have undertaken a global survey of this expressed polymorphism as one approach to understanding the evolutionary significance and origins of the polymorphism as well as understanding what selective forces, if any, may be operating at this locus. As the first step, we have determined the repeat number genotype of the DRD4 repeat polymorphism in 1,327 individuals from 36 different populations. The allele frequencies differ considerably among the different populations. The 4-repeat allele was the most prevalent (global mean allele frequency = 64.3%) and appeared in every population with a frequency ranging from 0.16 to 0.96. The 7-repeat allele was the second most common (global mean = 20.6%), appearing quite frequently in the Americas (mean frequency = 48.3%) but only occasionally in East and South Asia (mean frequency = 1.9%). The 2-repeat allele was the third most common (global mean frequency = 8.2%) and was quite frequent in East and South Asia (mean frequency = 18.1%) while uncommon in the Americas (mean frequency = 2.9%) and Africa (mean frequency = 1.7%). The universality of the polymorphism with only three common repeat-number alleles (4, 7, and 2) indicates that the polymorphism is ancient and arose before the global dispersion of modern humans. The diversity of actual allele frequencies for this expressed polymorphism among different populations emphasizes the importance of population considerations in the design and interpretation of any association studies carried out with this polymorphism.

- by Kenneth Kidd
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- Genetics, Human Genetics, Complementary and Alternative Medicine, Africa

- by Kenneth Kidd
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- Genetics, Human Genetics, Complementary and Alternative Medicine, Africa

This report aims to genetically characterize the relationships between geographically targeted human populations covering an expanse from east sub-Saharan Africa northeastward into northern India with an emphasis on the Near East. A number of parameters of population genetics interest were examined based on allele frequencies from 15 forensic autosomal STR markers [D8S1179,

- by Rene Herrera
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- Genetics, Geography, Genetic Epidemiology, Human Genetics
- by Michael Neale
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- Genetics, Research Design, Biology, Medicine

Background-The viral load setpoint (VLS) is an important predictor of HIV disease progression, but there is a lack of information regarding the VLS and its possible determinants in African populations. Methods-Initially HIV negative adults from three distinct groups (female barworkers, females and males from the general population) were followed for up to four years. The VLS was calculated for 108 seroconverters and associations of the VLS with possible risk factors were analyzed using univariate and multivariate regression. Results-The median VLS for female barworkers, females and males from the general population were 69,850, 28,600 and 158,000 RNA copies/ml respectively. Significant associations with an elevated viral load were observed for male gender (Risk Ratio (RR)=1.83, 95% confidence interval (95%CI)=1.14-2.93), the expression of harmful HLA I alleles (RR=1.73, 95%CI=1.13-2.66) and multiple infection with different HIV-1 subtypes (RR=1.65, 95%CI =1.03-2.66). Barworkers were considerably more often infected with different HIV-1 subtypes than participants from the general population.

- by Miguel Arroyo
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- Biology, Adolescent, Tanzania, Medicine

The ability to detect quantitative trait loci (QTLs) in a bi-allelic population is often limited. The power of QTL detection and identification of the most beneficial allele at each QTL could be greatly improved by comparing QTLs among different populations derived from connecting multi-parents. In this study, three sets of connected recombinant inbred lines (RILs) derived from the crosses between Zhenshan 97 and Minghui 63 (PZM), Zhenshan 97 and Teqing (PZT), and Minghui 63 and Teqing (PMT), respectively, were used. QTL analyses for the number of spikelets per panicle (SPP) and 1,000grain weight (TGW) were performed in PZT, and five SPP QTLs on chromosomes 1, 6, and 7 and two TGW QTLs on chromosome 1 were detected. QTL for SPP was also identified in PMT, and six QTLs were detected on chromosomes 1, 2, 3, 6, and 7 in this population. In an earlier study, we identified five SPP QTLs and four TGW QTLs in PMT and nine TGW QTLs in PZM. Comparison of the QTL mapping results of these two studies showed that one QTL was common to the three populations, 11 QTLs were detected in two populations, and six QTLs were found in only one population. Comparison of genetic effect and the action direction of the QTLs detected in the three populations showed that additive effects of QTLs estimated in different populations were also expressed additively among three parental alleles. Additive effects of SPP7a estimated in three nearisogenic line F 2 populations supported this finding. Based on these results, we suggest that pyramiding the most beneficial alleles among the three parents could efficiently improve rice yield.

- by Yongzhong Xing
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- Technology, Biological Sciences, Population, Inflorescence

Background. Previous genomewide association studies (GWASs) of AIDS have targeted end points based on the control of viral load and disease nonprogression. The discovery of genetic factors that predispose individuals to rapid progression to AIDS should also reveal new insights into the molecular etiology of the pathology. Methods. We undertook a case-control GWAS of a unique cohort of 85 human immunodeficiency virus type 1 (HIV-1)-infected patients who experienced rapid disease progression, using Illumina HumanHap300 BeadChips. The case group was compared with a control group of 1352 individuals for the 291,119 autosomal single-nucleotide polymorphisms (SNPs) passing the quality control tests, using the false-discovery rate (FDR) statistical method for multitest correction. Results. Novel associations with rapid progression (FDR, р25%) were identified for PRMT6 (P p ; odds ratio [OR], 0.24), SOX5 (; OR, 0.45), RXRG (; OR, 3.29), and Ϫ7 Ϫ6 Ϫ6

- by Jean Spadoni
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- Infectious Diseases, Biological Sciences, Association study, Identification

One hundred and twenty four microsatellites were isolated from analysis of 5000 Vitis expressed sequence tags (ESTs). A diversity of dinucleotide and trinucleotide simple sequence repeat (SSR) motifs were present. Primers were designed for 16 of these SSRs and they were tested on seven accessions. Ten of the sixteen primer pairs resulted in PCR products of the expected size. All ten functional primers were polymorphic across the accessions studied. Polymorphisms were evident at the level of cultivars, Vitis species, and between related genera. SSRs that were from the 3′ untranslated region (3′UTR) were most polymorphic at the cultivar level, the 5′ untranslated region (5′ UTR) SSRs were most polymorphic between cultivars and species, and those SSRs within coding sequence were most polymorphic between species and genera. These results show that EST-derived SSRs in Vitis are useful as they are polymorphic and highly transferable. With EST SSRs being applicable to studies at several taxonomic levels, the large number of SSRs (approximately 1000) that will be available from an expanded EST database of 45 000 will have many potential applications in mapping and identity research.

- by Robert Henry
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- Technology, Polymorphism, Biological Sciences, DNA
- by Malcolm Collins
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- Mechanical Engineering, Genetics, Sports Medicine, Epidemiology

In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from ge-nomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome.

- by Leonard Lipovich
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- Technology, Polymorphism, Biotechnology, Biological Sciences