Science.gov

Sample records for high allelic diversity

  1. High levels of MHC class II allelic diversity in lake trout from Lake Superior

    USGS Publications Warehouse

    Dorschner, M.O.; Duris, T.; Bronte, C.R.; Burnham-Curtis, M. K.; Phillips, R.B.

    2000-01-01

    Sequence variation in a 216 bp portion of the major histocompatibility complex (MHC) II B1 domain was examined in 74 individual lake trout (Salvelinus namaycush) from different locations in Lake Superior. Forty-three alleles were obtained which encoded 71-72 amino acids of the mature protein. These sequences were compared with previous data obtained from five Pacific salmon species and Atlantic salmon using the same primers. Although all of the lake trout alleles clustered together in the neighbor-joining analysis of amino acid sequences, one amino acid allelic lineage was shared with Atlantic salmon (Salmo salar), a species in another genus which probably diverged from Salvelinus more than 10-20 million years ago. As shown previously in other salmonids, the level of nonsynonymous nucleotide substitution (d(N)) exceeded the level of synonymous substitution (d(S)). The level of nucleotide diversity at the MHC class II B1 locus was considerably higher in lake trout than in the Pacific salmon (genus Oncorhynchus). These results are consistent with the hypothesis that lake trout colonized Lake Superior from more than one refuge following the Wisconsin glaciation. Recent population bottlenecks may have reduced nucleotide diversity in Pacific salmon populations.

  2. Transposon-based high sequence diversity in Avr-Pita alleles increases the potential for pathogenicity of Magnaporthe oryzae populations.

    PubMed

    Singh, P K; Thakur, S; Rathour, R; Variar, M; Prashanthi, S K; Singh, A K; Singh, U D; Sharma, V; Singh, N K; Sharma, T R

    2014-06-01

    Magnaporthe oryzae causes rice blast that is one of the most devastating diseases of rice worldwide. Highly variable nature of this fungus has evolved itself against major resistance genes in newly released rice varieties. Understanding the population structure of this fungus is essential for proper utilization of the rice blast resistance genes in rice crop plants. In the present study, we analyzed 133 isolates of M. oryzae from ten countries to find the allelic variation of Avr-Pita gene that is triggering Pita-mediated resistance in rice plant. The diversity analysis of these alleles showed higher level of nucleotide variation in the coding regions than the noncoding regions. Evolutionary analysis of these alleles indicates that Avr-Pita gene is under purifying selection to favor its major alleles in 133 isolates analyzed in this study. We hypothesize that the selection of favorable Avr-Pita allele in these isolates may occur through a genetic mechanism known as recurrent selective sweeps. A total of 22 functional Avr-Pita protein variants were identified in this study. Insertion of Pot3 transposable element into the promoter of Avr-Pita gene was identified in virulent isolates and was suggested that mobility of repeat elements in avirulence genes of M. oryzae seems to help in emergence of new virulent types of the pathogen. Allele-specific markers developed in this study will be helpful to identify a particular type of Avr-Pita allele from M. oryzae population which can form the basis for the deployment of Pita gene in different epidemiological regions. PMID:24633351

  3. Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea

    PubMed Central

    Bajaj, Deepak; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

    2015-01-01

    We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66–85%) and broader natural allelic diversity (6–64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools. PMID:26208313

  4. Several different lactase persistence associated alleles and high diversity of the lactase gene in the admixed Brazilian population.

    PubMed

    Friedrich, Deise C; Santos, Sidney E B; Ribeiro-dos-Santos, Ândrea K C; Hutz, Mara H

    2012-01-01

    Adult-type hypolactasia is a common phenotype caused by the lactase enzyme deficiency. The -13910 C>T polymorphism, located 14 Kb upstream of the lactase gene (LCT) in the MCM6 gene was associated with lactase persistence (LP) in Europeans. This polymorphism is rare in Africa but several other variants associated with lactase persistence were observed in Africans. The aims of this study were to identify polymorphisms in the MCM6 region associated with the lactase persistence phenotype and to determine the distribution of LCT gene haplotypes in 981 individuals from North, Northeast and South Brazil. These polymorphisms were genotyped by PCR based methods and sequencing. The -13779*C,-13910*T, -13937*A, -14010*C, -14011*T LP alleles previously described in the MCM6 gene region that acts as an enhancer for the LCT gene were identified in Brazilians. The most common LP allele was -13910*T. Its frequency was highly correlated with European ancestry in the Brazilian populations investigated. The -13910*T was higher (0.295) in southern Brazilians of European ancestry and lower (0.175) in the Northern admixed population. LCT haplotypes were derived from the 10 LCT SNPs genotyped. Overall twenty six haplotypes previously described were identified in the four Brazilian populations studied. The Multidimensional Scaling analysis showed that Belém, in the north, was closer to Amerindians. Northeastern and southern Afro-descendants were more related with Bantu-speaking South Africans whereas the Southern population with European ancestry grouped with Southern and Northern Europeans. This study shows a high variability considering the number of LCT haplotypes observed. Due to the highly admixed nature of the Brazilian populations, the diagnosis of hypolactasia in Brazil, based only in the investigation of the -13910*T allele is an oversimplification. PMID:23029545

  5. High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes.

    PubMed

    Mishra, S K; Niranjan, S K; Banerjee, B; Dubey, P K; Gonge, D S; Mishra, B P; Kataria, R S

    2016-07-01

    In this study, genetic diversity analysis of MHC class II-DQA locus helped in identification of 25 new Bubu-DQA nucleotide sequences in swamp buffaloes (Bubalus bubalis carabanesis, Bubu). Phylogenetic analysis revealed the distribution of the buffalo DQA sequences in two major clusters of DQA1 and DQA2 genes, sharing common lineages with corresponding cattle alleles, possibly due to trans-species evolution. However, a highly divergent sequence, Bubu-DQA*2501, homologous to cattle (BoLA) DQA3 allele, was identified, indicating the existence of an additional locus; putative DQA3 in buffalo. PCR-RFLP analysis revealed extensive duplication of DQA locus in swamp buffaloes, sharing DQA1, DQA2, and DQA3 alleles in different combinations in duplicated haplotypes. Higher dN than dS values and Wu-Kabat variability at peptide-binding regions in Bubu-DQA indicated high polymorphism with balancing selection. Levels of genetic diversity within DQA sequences and duplication in a small population of swamp buffalo indicate the genetic richness of the species, important for fitness. PMID:27177904

  6. HLA-B allele and haplotype diversity among Thai patients identified by PCR-SSOP: evidence for high risk of drug-induced hypersensitivity

    PubMed Central

    Puangpetch, Apichaya; Koomdee, Napatrupron; Chamnanphol, Montri; Jantararoungtong, Thawinee; Santon, Siwalee; Prommas, Santirhat; Hongkaew, Yaowaluck; Sukasem, Chonlaphat

    2015-01-01

    Background: There are 3 classes of HLA molecules; HLA class I, II and III, of which different classes have different functions. HLA-B gene which belongs to HLA class I play an important role predicting drug hypersensitivity. Materials and Methods: Nine hundred and eighty-six Thai subjects who registered at a pharmacogenomics laboratory were determined for HLA-B genotype using a two-stage sequence-specific oligonucleotide probe system (PCR-SSOP). Results: In this study, HLA-B alleles did not deviate from Hardy-Weinberg equilibrium (P > 0.05). The most common HLA-B alleles observed in this population were HLA-B*46:01 (11.51%), HLA-B*58:01 (8.62%), HLA-B*40:01 (8.22%), HLA-B*15:02 (8.16%) and HLA-B*13:01 (6.95%). This finding revealed that HLA-B allele frequency in the Thai population was consistent with the Chinese population (p > 0.05), however, differed from the Malaysian population (p < 0.05). The top five HLA-B genotypes were HLA-B*40:01/46:01 (2.13%), HLA-B*46:01/46:01 (2.03%), HLA-B*40:01/58:01 (2.03%), HLA-B*46:01/58:01 (1.93%) and HLA-B*15:02/46:01 (1.83%). This study found that 15.92% of Thai subjects carry HLA-B*15:02, which has been associated with carbamazepine-induced severe cutaneous adverse drug reactions (SCARs). Moreover, 16.33% of Thai subjects carry the HLA-B*58:01 allele, which has been associated with allopurinol-induced SCARs. Conclusion: This study demonstrates a high diversity of HLA-B polymorphisms in this Thai population. The high frequency of HLA-B pharmacogenomic markers in the population emphasizes the importance of such screening to predict/avoid drug hypersensitivity. PMID:25657656

  7. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited.

    PubMed

    Ross, P; Buntzman, A S; Vincent, B G; Grover, E N; Gojanovich, G S; Collins, E J; Frelinger, J A; Hess, P R

    2012-08-01

    In the dog, previous analyses of major histocompatibility complex class I genes suggest a single polymorphic locus, dog leukocyte antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds, DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

  8. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited

    PubMed Central

    Ross, Peter; Buntzman, Adam S.; Vincent, Benjamin G.; Grover, Elise N.; Gojanovich, Gregory S.; Collins, Edward J.; Frelinger, Jeffrey A.; Hess, Paul R.

    2012-01-01

    In the dog, previous analyses of major histocompatibility complex (MHC) class I genes suggest a single polymorphic locus, Dog Leukocyte Antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

  9. MHC class II DR allelic diversity in bighorn sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA...

  10. Extensive Allelic Diversity of MHC Class I in Wild Mallard Ducks.

    PubMed

    Fleming-Canepa, Ximena; Jensen, Shawna M; Mesa, Christine M; Diaz-Satizabal, Laura; Roth, Alexa J; Parks-Dely, Julie A; Moon, Debra A; Wong, Janet P; Evseev, Danyel; Gossen, Desolie A; Tetrault, David G; Magor, Katharine E

    2016-08-01

    MHC class I is critically involved in defense against viruses, and diversity from polygeny and polymorphism contributes to the breadth of the immune response and health of the population. In this article, we examine MHC class I diversity in wild mallard ducks, the natural host and reservoir of influenza A viruses. We previously showed domestic ducks predominantly use UAA, one of five MHC class I genes, but whether biased expression is also true for wild mallards is unknown. Using RT-PCR from blood, we examined expressed MHC class I alleles from 38 wild mallards (Anas platyrhynchos) and identified 61 unique alleles, typically 1 or 2 expressed alleles in each individual. To determine whether expressed alleles correspond to UAA adjacent to TAP2 as in domestic ducks, we cloned and sequenced genomic UAA-TAP2 fragments from all mallards, which matched transcripts recovered and allowed us to assign most alleles as UAA Allelic differences are primarily located in α1 and α2 domains in the residues known to interact with peptide in mammalian MHC class I, suggesting the diversity is functional. Most UAA alleles have unique residues in the cleft predicting distinct specificity; however, six alleles have an unusual conserved cleft with two cysteine residues. Residues that influence peptide-loading properties and tapasin involvement in chicken are fixed in duck alleles and suggest tapasin independence. Biased expression of one MHC class I gene may make viral escape within an individual easy, but high diversity in the population places continual pressure on the virus in the reservoir species. PMID:27342841

  11. DRD4 dopamine receptor allelic diversity in various primate species

    SciTech Connect

    Adamson, M.; Higley, D.; O`Brien, S.

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  12. High prevalence and diversity of pre-CTXΦ alleles in the environmental Vibrio cholerae O1 and O139 strains in the Zhujiang River estuary.

    PubMed

    Wang, Duochun; Wang, Xiaomei; Li, Baisheng; Deng, Xiaoling; Tan, Hailing; Diao, Baowei; Chen, Jingdiao; Ke, Bixia; Zhong, Haojie; Zhou, Haijian; Ke, Changwen; Kan, Biao

    2014-06-01

    Toxigenic conversion of environmental Vibrio cholerae strains through lysogenic infection by the phage CTXΦ is an important step in the emergence of new pathogenic clones. The precursor form of the CTXΦ phage, pre-CTXΦ, does not carry the cholera toxin gene. During our investigation, we frequently found pre-CTXΦ prophages in non-toxigenic isolates in the serogroups of O1 and O139 strains in the Zhujiang estuary. We observed high amounts of sequence variation of rstR and gIII(CTX) in the pre-CTXΦ alleles as well as in the tcpA sequences within the strains. In addition, a new pre-CTXΦ allele, with a novel rstR sequence type and hybrid RS2, was identified. Our findings show that active, complicated gene recombination and horizontal transfer of pre-CTXΦs occurs within V. cholerae environmental strains, which creates a complex intermediate pool for the generation of toxigenic clones in the estuarine environment. PMID:24983529

  13. Puroindoline allelic diversity in Indian wheat germplasm and identification of new allelic variants

    PubMed Central

    Kumar, Rohit; Arora, Shaweta; Singh, Kashmir; Garg, Monika

    2015-01-01

    Grain hardness is an important quality trait that influences product development in wheat. This trait is governed by variation in puroindoline proteins (PINA and PINB). Our study evaluated 551 Indian wheat germplasm lines for diversity in Pina and Pinb genes. Eighty-two lines were shortlisted for full length sequencing and grain hardness studies. Sequencing studies identified six unknown alleles: two for the Pina gene and four for the Pinb gene. Five of them were novel with non-synonymous changes in the corresponding amino acid sequences. Identified mutations in the deduced mature proteins and their pre- and pro-peptides influenced the hardness characteristics of the grain. We classified these 82 varieties into different hardness categories with reference to international and Indian systems of classification. The majority of Indian wheat varieties were categorized as hard. This study revealed that unexplored Indian wheat germplasm can be a good source of genetic variability for both Pina and Pinb genes, helping in marker-assisted breeding and in obtaining wheat with different textural properties. PMID:26366114

  14. Facultative cheating supports the coexistence of diverse quorum-sensing alleles

    PubMed Central

    Pollak, Shaul; Omer-Bendori, Shira; Even-Tov, Eran; Lipsman, Valeria; Bareia, Tasneem; Ben-Zion, Ishay; Eldar, Avigdor

    2016-01-01

    Bacterial quorum sensing enables bacteria to cooperate in a density-dependent manner via the group-wide secretion and detection of specific autoinducer molecules. Many bacterial species show high intraspecific diversity of autoinducer–receptor alleles, called pherotypes. The autoinducer produced by one pherotype activates its coencoded receptor, but not the receptor of another pherotype. It is unclear what selection forces drive the maintenance of pherotype diversity. Here, we use the ComQXPA system of Bacillus subtilis as a model system, to show that pherotype diversity can be maintained by facultative cheating—a minority pherotype exploits the majority, but resumes cooperation when its frequency increases. We find that the maintenance of multiple pherotypes by facultative cheating can persist under kin-selection conditions that select against “obligate cheaters” quorum-sensing response null mutants. Our results therefore support a role for facultative cheating and kin selection in the evolution of quorum-sensing diversity. PMID:26787913

  15. Allele mining across DREB1A and DREB1B in diverse rice genotypes suggest a highly conserved pathway inducible by low temperature.

    PubMed

    Challam, Clarissa; Ghosh, Tapu; Rai, Mayank; Tyagi, Wricha

    2015-06-01

    Low temperature stress is one of the major limiting factors affecting rice productivity in higher altitudes. DREB1A and DREB1B, are two transcription factors that have been reported to play key regulatory role in low temperature tolerance. In order to understand whether natural genetic variation in these two loci leads to cold tolerance or susceptibility, OsDREB1A and OsDREB1B were targeted across several rice genotypes showing differential response to low temperature. Expression data suggests induction of gene expression in shoots in response to low temperature in both tolerant and susceptible genotypes. Upon sequence analysis of 20 rice genotypes, eight nucleotide changes were identified including two in the coding region and six in the 5'UTR. None of the discovered novel variations lie in the conserved region of the genes under study, thereby causing little or no changes in putative function of the corresponding proteins. In silico analysis using a diverse set of 400 O. sativa revealed much lower nucleotide diversity estimates across two DREB loci and one other gene (MYB2) involved in DREB pathway than those observed for other rice genes. None of the changes showed association with seedling stage cold tolerance, suggesting that nucleotide changes in DREB loci are unlikely to contribute to low temperature tolerance. So far, data concerning the physiological role and regulation of DREB1 in different genetic background are very limited; it is to be expected that they will be studied extensively in the near future. PMID:26174670

  16. Estimating allelic diversity generated by excision of different transposon types.

    PubMed

    Nordborg, M; Walbot, V

    1995-05-01

    Methods are presented for calculating the number and type of different DNA sequences generated by base excision and insertion events at a given site in a known DNA sequence. We calculate, for example, that excision of the Mu1 transposon from the bz1::Mu1 allele of maize should generate more than 500,000 unique alleles given the extent of base deletion (up to 34 bases removed) and base insertion (0-5 bases) observed thus far in sequenced excision alleles. Analysis of this universe of potential alleles can, for example, be used to predict the frequency of creation of stop codons or repair-generated duplications. In general, knowledge of the distribution of alleles can be used to evaluate models of both excision and repair by determining whether particular events occur more frequently than expected. Such quantitative analysis complements the qualitative description provided by the DNA sequence of individual events. Similar methods can be used to evaluate the outcome of other cases of DNA breakage and repair such as programmed V(D)J recombination in immunoglobin genes. PMID:24172918

  17. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure.

    PubMed Central

    Go, M F; Kapur, V; Graham, D Y; Musser, J M

    1996-01-01

    Genetic diversity and relationships in 74 Helicobacter pylori isolates recovered from patients assigned to distinct clinical categories were estimated by examination of allelic variation in six genes encoding metabolic housekeeping enzymes by multilocus enzyme electrophoresis. Seventy-three distinct allele profiles, representing multilocus chromosomal genotypes, were identified. All six loci were highly polymorphic, with an average of 11.2 alleles per locus. The mean genetic diversity in the sample was 0.735, a value that exceeds the level of diversity recorded in virtually all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles (lack of enzyme activity) was identified and warrants further investigation at the molecular level. Lack of linkage disequilibrium (nonrandom association (of alleles over loci) indicates that horizontal transfer and recombination of metabolic enzyme genes have contributed to the generation of chromosomal diversity in H. pylori. In this sample of isolates, there was no statistically significant association of multilocus enzyme electrophoretic types or cluster of related chromosomal types and disease category. PMID:8682800

  18. Naturally occurring allele diversity allows potato cultivation in northern latitudes.

    PubMed

    Kloosterman, Bjorn; Abelenda, José A; Gomez, María del Mar Carretero; Oortwijn, Marian; de Boer, Jan M; Kowitwanich, Krissana; Horvath, Beatrix M; van Eck, Herman J; Smaczniak, Cezary; Prat, Salomé; Visser, Richard G F; Bachem, Christian W B

    2013-03-14

    Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world's most important food crops. This annual plant originates from the Andean regions of South America. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets. PMID:23467094

  19. Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes.

    PubMed

    Norman, Paul J; Abi-Rached, Laurent; Gendzekhadze, Ketevan; Hammond, John A; Moesta, Achim K; Sharma, Deepti; Graef, Thorsten; McQueen, Karina L; Guethlein, Lisbeth A; Carrington, Christine V F; Chandanayingyong, Dasdayanee; Chang, Yih-Hsin; Crespí, Catalina; Saruhan-Direskeneli, Güher; Hameed, Kamran; Kamkamidze, Giorgi; Koram, Kwadwo A; Layrisse, Zulay; Matamoros, Nuria; Milà, Joan; Park, Myoung Hee; Pitchappan, Ramasamy M; Ramdath, D Dan; Shiau, Ming-Yuh; Stephens, Henry A F; Struik, Siske; Tyan, Dolly; Verity, David H; Vaughan, Robert W; Davis, Ronald W; Fraser, Patricia A; Riley, Eleanor M; Ronaghi, Mostafa; Parham, Peter

    2009-05-01

    Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here is KIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the 3DL1 and 3DL2 genes produced a deleted KIR haplotype in which the telomeric "half" was reduced to a single fusion gene with functional properties distinct from its 3DL1 and 3DL2 parents. Conversely, in Eurasian populations, duplication of the KIR3DL1/S1 locus by unequal crossing over has enabled individuals to carry and express alleles of all three KIR3DL1/S1 lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving human KIR gene family. PMID:19411600

  20. Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes

    PubMed Central

    Norman, Paul J.; Abi-Rached, Laurent; Gendzekhadze, Ketevan; Hammond, John A.; Moesta, Achim K.; Sharma, Deepti; Graef, Thorsten; McQueen, Karina L.; Guethlein, Lisbeth A.; Carrington, Christine V.F.; Chandanayingyong, Dasdayanee; Chang, Yih-Hsin; Crespí, Catalina; Saruhan-Direskeneli, Güher; Hameed, Kamran; Kamkamidze, Giorgi; Koram, Kwadwo A.; Layrisse, Zulay; Matamoros, Nuria; Milà, Joan; Park, Myoung Hee; Pitchappan, Ramasamy M.; Ramdath, D. Dan; Shiau, Ming-Yuh; Stephens, Henry A.F.; Struik, Siske; Tyan, Dolly; Verity, David H.; Vaughan, Robert W.; Davis, Ronald W.; Fraser, Patricia A.; Riley, Eleanor M.; Ronaghi, Mostafa; Parham, Peter

    2009-01-01

    Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here is KIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the 3DL1 and 3DL2 genes produced a deleted KIR haplotype in which the telomeric “half” was reduced to a single fusion gene with functional properties distinct from its 3DL1 and 3DL2 parents. Conversely, in Eurasian populations, duplication of the KIR3DL1/S1 locus by unequal crossing over has enabled individuals to carry and express alleles of all three KIR3DL1/S1 lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving human KIR gene family. PMID:19411600

  1. Evolution of Functionally Diverse Alleles Associated with PTC Bitter Taste Sensitivity in Africa

    PubMed Central

    Campbell, Michael C.; Ranciaro, Alessia; Froment, Alain; Hirbo, Jibril; Omar, Sabah; Bodo, Jean-Marie; Nyambo, Thomas; Lema, Godfrey; Zinshteyn, Daniel; Drayna, Dennis; Breslin, Paul A. S.; Tishkoff, Sarah A.

    2012-01-01

    Although human bitter taste perception is hypothesized to be a dietary adaptation, little is known about genetic signatures of selection and patterns of bitter taste perception variability in ethnically diverse populations with different diets, particularly from Africa. To better understand the genetic basis and evolutionary history of bitter taste sensitivity, we sequenced a 2,975 bp region encompassing TAS2R38, a bitter taste receptor gene, in 611 Africans from 57 populations in West Central and East Africa with diverse subsistence patterns, as well as in a comparative sample of 132 non-Africans. We also examined the association between genetic variability at this locus and threshold levels of phenylthiocarbamide (PTC) bitterness in 463 Africans from the above populations to determine how variation influences bitter taste perception. Here, we report striking patterns of variation at TAS2R38, including a significant excess of novel rare nonsynonymous polymorphisms that recently arose only in Africa, high frequencies of haplotypes in Africa associated with intermediate bitter taste sensitivity, a remarkably similar frequency of common haplotypes across genetically and culturally distinct Africans, and an ancient coalescence time of common variation in global populations. Additionally, several of the rare nonsynonymous substitutions significantly modified levels of PTC bitter taste sensitivity in diverse Africans. While ancient balancing selection likely maintained common haplotype variation across global populations, we suggest that recent selection pressures may have also resulted in the unusually high level of rare nonsynonymous variants in Africa, implying a complex model of selection at the TAS2R38 locus in African populations. Furthermore, the distribution of common haplotypes in Africa is not correlated with diet, raising the possibility that common variation may be under selection due to their role in nondietary biological processes. In addition, our data

  2. Geographical patterns of turnover and nestedness-resultant components of allelic diversity among populations.

    PubMed

    Diniz-Filho, Jose Alexandre Felizola; Collevatti, Rosane Garcia; Soares, Thannya Nascimento; Telles, Mariana Pires de Campos

    2012-06-01

    The analysis of geographical patterns in population divergence has always been a powerful way to infer microevolutionary processes involved in population differentiation, and several approaches have been used to investigate such patterns. Most frequently, multivariate spatial patterns of population differentiation are analyzed by computing pairwise genetic distances or F(ST) (or related statistics, such as ϕ(ST) from AMOVA), which are then correlated with geographical distances or landscape features. However, when calculating distances, especially based on presence-absence of alleles in local populations, there would be a confounding effect of allelic richness differences in the population differentiation. Moreover, the relative magnitude of these components and their spatial patterns can help identifying microevolutionary processes driving population differentiation. Here we show how recent methodological advances in ecological community analyses that allows partitioning dissimilarity into turnover (turnover) and richness differences, or nestedness-resultant dissimilarity, can be applied to allelic variation data, using an endemic Cerrado tree (Dipteryx alata) as a case study. Individuals from 15 local populations were genotyped for eight microsatellite loci, and pairwise dissimilarities were computed based on presence-absence of alleles. The turnover of alleles among populations represented 69 % of variation in dissimilarity, but only the richness difference component shows a clear spatial structure, appearing as a westward decrease of allelic richness. We show that decoupling richness difference and turnover components of allelic variation reveals more clearly how similarity among populations reflects geographical patterns in allelic diversity that can be interpreted in respect to historical range expansion in the species. PMID:22886007

  3. Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep.

    PubMed

    Jones, Bryony L; Raga, Tamiru O; Liebert, Anke; Zmarz, Pawel; Bekele, Endashaw; Danielsen, E Thomas; Olsen, Anders Krüger; Bradman, Neil; Troelsen, Jesper T; Swallow, Dallas M

    2013-09-01

    The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(∗)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(∗)G, rs41525747; -13915(∗)G, rs41380347; -14010(∗)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(∗)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep. PMID:23993196

  4. Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program

    PubMed Central

    Gragert, Loren; Maiers, Martin; Chatterjee, Ansu; Albrecht, Mark

    2015-01-01

    Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions. These measures are of particular interest in the field of hematopoietic stem cell transplant (HSCT). Donor/Recipient suitability for HSCT is determined by Human Leukocyte Antigen (HLA) similarity. Match predictions rely upon a precise description of HLA diversity, yet classical estimates are inaccurate given the heavy-tailed nature of the distribution. This directly affects HSCT matching and diversity measures in broader fields such as species richness. We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions. Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual. Indeed, our discovery rate of all U.S. European American haplotypes is estimated at 23.45% based upon sampling 3.97% of the population, leaving a large number of unobserved haplotypes. Population coverage, however, is much higher at 99.4% given that 90% of European Americans carry one of the 4.5% most frequent haplotypes. Alleles were found to be less diverse suggesting the current registry represents most alleles in the population. Thus, for HSCT registries, haplotype discovery will remain high with continued recruitment to a very deep level of sampling, but population coverage will not. Finally, we compared the convergence of our power-law versus classical diversity estimators such as Capture recapture, Chao, ACE and Jackknife methods. When fit to the haplotype data, our estimator displayed favorable properties in terms of convergence (with respect to sampling depth) and accuracy (with respect to diversity estimates). This

  5. Power laws for heavy-tailed distributions: modeling allele and haplotype diversity for the national marrow donor program.

    PubMed

    Slater, Noa; Louzoun, Yoram; Gragert, Loren; Maiers, Martin; Chatterjee, Ansu; Albrecht, Mark

    2015-04-01

    Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions. These measures are of particular interest in the field of hematopoietic stem cell transplant (HSCT). Donor/Recipient suitability for HSCT is determined by Human Leukocyte Antigen (HLA) similarity. Match predictions rely upon a precise description of HLA diversity, yet classical estimates are inaccurate given the heavy-tailed nature of the distribution. This directly affects HSCT matching and diversity measures in broader fields such as species richness. We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions. Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual. Indeed, our discovery rate of all U.S. European American haplotypes is estimated at 23.45% based upon sampling 3.97% of the population, leaving a large number of unobserved haplotypes. Population coverage, however, is much higher at 99.4% given that 90% of European Americans carry one of the 4.5% most frequent haplotypes. Alleles were found to be less diverse suggesting the current registry represents most alleles in the population. Thus, for HSCT registries, haplotype discovery will remain high with continued recruitment to a very deep level of sampling, but population coverage will not. Finally, we compared the convergence of our power-law versus classical diversity estimators such as Capture recapture, Chao, ACE and Jackknife methods. When fit to the haplotype data, our estimator displayed favorable properties in terms of convergence (with respect to sampling depth) and accuracy (with respect to diversity estimates). This

  6. Analysis of the vomeronasal receptor repertoire, expression and allelic diversity in swine.

    PubMed

    Dinka, Hunduma; Le, Minh Thong; Ha, Heekyun; Cho, Hyesun; Choi, Min-Kyeung; Choi, Hojun; Kim, Jin-Hoi; Soundarajan, Nagasundarapandian; Park, Jin-Ki; Park, Chankyu

    2016-05-01

    Here we report a comprehensive analysis of the vomeronasal receptor repertoire in pigs. We identified a total of 25 V1R sequences consisting of 10 functional genes, 3 pseudogenes, and 12 partial genes, while functional V2R and FPR genes were not present in the pig genome. Pig V1Rs were classified into three subfamilies, D, F, and J. Using direct high resolution sequencing-based typing of all functional V1Rs from 10 individuals of 5 different breeds, a total of 24 SNPs were identified, indicating that the allelic diversity of V1Rs is much lower than that of the olfactory receptors. A high expression level of V1Rs was detected in the vomeronasal organ (VNO) and testes, while a low expression level of V1Rs was observed in all other tissues examined. Our results showed that pigs could serve as an interesting large animal model system to study pheromone-related neurobiology because of their genetic simplicity. PMID:26482471

  7. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic seq...

  8. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

    PubMed Central

    Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

    2015-01-01

    The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93–96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13–89%)/functional allelic diversity (18–77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54–0.68) and extended LD decay (400–500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically

  9. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  10. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  11. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    DOE PAGESBeta

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-06-08

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed basedmore » on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non -redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp, diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

  12. Global phylogeography of the avian malaria pathogen Plasmodium relictum based on MSP1 allelic diversity

    USGS Publications Warehouse

    Hellgren, Olof; Atkinson, Carter T.; Bensch, Staffan; Albayrak, Tamer; Dimitrov, Dimitar; Ewen, John G.; Kim, Kyeong Soon; Lima, Marcos R.; Martin, Lynn; Palinauskas, Vaidas; Ricklefs, Robert; Sehgal, Ravinder N. M.; Gediminas, Valkiunas; Tsuda, Yoshio; Marzal, Alfonso

    2015-01-01

    Knowing the genetic variation that occurs in pathogen populations and how it is distributed across geographical areas is essential to understand parasite epidemiology, local patterns of virulence, and evolution of host-resistance. In addition, it is important to identify populations of pathogens that are evolutionarily independent and thus ‘free’ to adapt to hosts and environments. Here, we investigated genetic variation in the globally distributed, highly invasive avian malaria parasite Plasmodium relictum, which has several distinctive mitochondrial haplotyps (cyt b lineages, SGS1, GRW11 and GRW4). The phylogeography of P. relictum was accessed using the highly variable nuclear gene merozoite surface protein 1 (MSP1), a gene linked to the invasion biology of the parasite. We show that the lineage GRW4 is evolutionarily independent of GRW11 and SGS1 whereas GRW11 and SGS1 share MSP1 alleles and thus suggesting the presence of two distinct species (GRW4 versus SGS1 and GRW11). Further, there were significant differences in the global distribution of MSP1 alleles with differences between GRW4 alleles in the New and the Old World. For SGS1, a lineage formerly believed to have both tropical and temperate transmission, there were clear differences in MSP1 alleles transmitted in tropical Africa compared to the temperate regions of Europe and Asia. Further, we highlight the occurrence of multiple MSP1 alleles in GRW4 isolates from the Hawaiian Islands, where the parasite has contributed to declines and extinctions of endemic forest birds since it was introduced. This study stresses the importance of multiple independent loci for understanding patterns of transmission and evolutionary independence across avian malaria parasites.

  13. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

    PubMed Central

    Muir, William M.; Wong, Gane Ka-Shu; Zhang, Yong; Wang, Jun; Groenen, Martien A. M.; Crooijmans, Richard P. M. A.; Megens, Hendrik-Jan; Zhang, Huanmin; Okimoto, Ron; Vereijken, Addie; Jungerius, Annemieke; Albers, Gerard A. A.; Lawley, Cindy Taylor; Delany, Mary E.; MacEachern, Sean; Cheng, Hans H.

    2008-01-01

    Breed utilization, genetic improvement, and industry consolidation are predicted to have major impacts on the genetic composition of commercial chickens. Consequently, the question arises as to whether sufficient genetic diversity remains within industry stocks to address future needs. With the chicken genome sequence and more than 2.8 million single-nucleotide polymorphisms (SNPs), it is now possible to address biodiversity using a previously unattainable metric: missing alleles. To achieve this assessment, 2551 informative SNPs were genotyped on 2580 individuals, including 1440 commercial birds. The proportion of alleles lacking in commercial populations was assessed by (1) estimating the global SNP allele frequency distribution from a hypothetical ancestral population as a reference, then determining the portion of the distribution lost, and then (2) determining the relationship between allele loss and the inbreeding coefficient. The results indicate that 50% or more of the genetic diversity in ancestral breeds is absent in commercial pure lines. The missing genetic diversity resulted from the limited number of incorporated breeds. As such, hypothetically combining stocks within a company could recover only preexisting within-breed variability, but not more rare ancestral alleles. We establish that SNP weights act as sentinels of biodiversity and provide an objective assessment of the strains that are most valuable for preserving genetic diversity. This is the first experimental analysis investigating the extant genetic diversity of virtually an entire agricultural commodity. The methods presented are the first to characterize biodiversity in terms of allelic diversity and to objectively link rate of allele loss with the inbreeding coefficient. PMID:18981413

  14. High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces

    PubMed Central

    Alexander, William G.; Doering, Drew T.; Hittinger, Chris Todd

    2014-01-01

    Current genome editing techniques available for Saccharomyces yeast species rely on auxotrophic markers, limiting their use in wild and industrial strains and species. Taking advantage of the ancient loss of thymidine kinase in the fungal kingdom, we have developed the herpes simplex virus thymidine kinase gene as a selectable and counterselectable marker that forms the core of novel genome engineering tools called the Haploid Engineering and Replacement Protocol (HERP) cassettes. Here we show that these cassettes allow a researcher to rapidly generate heterogeneous populations of cells with thousands of independent chromosomal allele replacements using mixed PCR products. We further show that the high efficiency of this approach enables the simultaneous replacement of both alleles in diploid cells. Using these new techniques, many of the most powerful yeast genetic manipulation strategies are now available in wild, industrial, and other prototrophic strains from across the diverse Saccharomyces genus. PMID:25209147

  15. Allelic diversity of a beer haze active protein gene in cultivated and Tibetan wild barley and development of allelic specific markers.

    PubMed

    Ye, Lingzhen; Dai, Fei; Qiu, Long; Sun, Dongfa; Zhang, Guoping

    2011-07-13

    The formation of haze is a serious quality problem in beer production. It has been shown that the use of silica elute (SE)-ve malt (absence of molecular weight (MW) ∼14000 Da) for brewing can improve haze stability in the resultant beer, and the protein was identified as a barley trypsin inhibitor of the chloroform/methanol type (BTI-CMe). The objectives of this study were to determine (1) the allelic diversity of the gene controlling BTI-CMe in cultivated and Tibetan wild barley and (2) allele-specific (AS) markers for screening SE protein type. A survey of 172 Tibetan annual wild barley accessions and 71 cultivated barley genotypes was conducted, and 104 wild accessions and 35 cultivated genotypes were identified as SE+ve and 68 wild accessions and 36 cultivated genotypes as SE-ve. The allelic diversity of the gene controlling BTI-CMe was investigated by cloning, alignment, and association analysis. It was found that there were significant differences between the SE+ve and SE-ve types in single-nucleotide polymorphisms at 234 (SNP(234)), SNP(313), and SNP(385.) Furthermore, two sets of AS markers were developed to screen SE protein type based on SNP(313). AS-PCR had results very similar to those obtained by immunoblot method. Mapping analysis showed that the gene controlling the MW∼14 kDa band was located on the short arm of chromosome 3H, at the position of marker BPB-0527 (33.302 cM) in the Franklin/Yerong DH population. PMID:21608526

  16. Allelic Diversity and Geographical Distribution of the Gene Encoding Plasmodium falciparum Merozoite Surface Protein-3 in Thailand

    PubMed Central

    Sawaswong, Vorthon; Simpalipan, Phumin; Siripoon, Napaporn; Harnyuttanakorn, Pongchai; Pattaradilokrat, Sittiporn

    2015-01-01

    Merozoite surface proteins (MSPs) of malaria parasites play critical roles during the erythrocyte invasion and so are potential candidates for malaria vaccine development. However, because MSPs are often under strong immune selection, they can exhibit extensive genetic diversity. The gene encoding the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum displays 2 allelic types, K1 and 3D7. In Thailand, the allelic frequency of the P. falciparum msp-3 gene was evaluated in a single P. falciparum population in Tak at the Thailand and Myanmar border. However, no study has yet looked at the extent of genetic diversity of the msp-3 gene in P. falciparum populations in other localities. Here, we genotyped the msp-3 alleles of 63 P. falciparum samples collected from 5 geographical populations along the borders of Thailand with 3 neighboring countries (Myanmar, Laos, and Cambodia). Our study indicated that the K1 and 3D7 alleles coexisted, but at different proportions in different Thai P. falciparum populations. K1 was more prevalent in populations at the Thailand-Myanmar and Thailand-Cambodia borders, whilst 3D7 was more prevalent at the Thailand-Laos border. Global analysis of the msp-3 allele frequencies revealed that proportions of K1 and 3D7 alleles of msp-3 also varied in different continents, suggesting the divergence of malaria parasite populations. In conclusion, the variation in the msp-3 allelic patterns of P. falciparum in Thailand provides fundamental knowledge for inferring the P. falciparum population structure and for the best design of msp-3 based malaria vaccines. PMID:25925176

  17. Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

    PubMed Central

    de las Rivas, Blanca; Marcobal, Ángela; Muñoz, Rosario

    2004-01-01

    Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria. PMID:15574919

  18. Copy number variation and genetic diversity of MHC Class IIb alleles in an alien population of Xenopus laevis.

    PubMed

    Mable, Barbara K; Kilbride, Elizabeth; Viney, Mark E; Tinsley, Richard C

    2015-10-01

    Xenopus laevis (the African clawed frog), which originated through hybridisation and whole genome duplication, has been used as a model for genetics and development for many years, but surprisingly little is known about immune gene variation in natural populations. The purpose of this study was to use an isolated population of X. laevis that was introduced to Wales, UK in the past 50 years to investigate how variation at the MHC compares to that at other loci, following a severe population bottleneck. Among 18 individuals, we found nine alleles based on exon 2 sequences of the Class IIb region (which includes the peptide binding region). Individuals carried from one to three of the loci identified from previous laboratory studies. Genetic variation was an order of magnitude higher at the MHC compared with three single-copy nuclear genes, but all loci showed high levels of heterozygosity and nucleotide diversity and there was not an excess of homozygosity or decrease in diversity over time that would suggest extensive inbreeding in the introduced population. Tajima's D was positive for all loci, which is consistent with a bottleneck. Moreover, comparison with published sequences identified the source of the introduced population as the Western Cape region of South Africa, where most commercial suppliers have obtained their stocks. These factors suggest that despite founding by potentially already inbred individuals, the alien population in Wales has maintained substantial genetic variation at both adaptively important and neutral genes. PMID:26329765

  19. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping

    PubMed Central

    Edzesi, Wisdom M.; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U.; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes. PMID:27375646

  20. Status of allele frequency and diversity of Plasmodium falciparum msp1, msp2 and glurp before implementation of an artemisinin-based combined therapy in Northwestern Colombia.

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

    Introduction: The status of msp1, msp2 and glurp allele frequency and the diversity of Plasmodium falciparum in Northwestern Colombia before the implementation of an artemisinin-combined therapy have been explored only by a few authors and in a relatively small number of samples from this highly endemic region. Objective: To evaluate the frequency of msp1, msp2, and glurp alleles and the diversity of P. falciparum in two Colombian regions before the use of an artemisinin-combined therapy. Methods: This study was part of a major anti-malarial efficacy trial designed as a random, clinically-controlled study for which 224 subjects were recruited. Region 2 of msp1 and msp2 (central region) were amplified by a nested PCR; glurp (region R2) was amplified by a semi-nested PCR. Results: For msp1, five genotypes were observed, representing the K1, MAD20, and RO33 allelic families. All samples corresponded to a MAD20 150 bp allele. For msp2 (IC family), two alleles were detected and for glurp, eight were observed. A total 33 haplotypes were detected. Conclusions: Analysis of glurpcan be used to successfully genotype parasite populations in the new studies in Colombia aimed at exploring Plasmodium spp population dynamics. In addition, analysis of msp1 and msp2 can also be of value for comparisons with past studies, but not when the objective is to study parasites obtained from the same patient in a reduced period of time; for instance, during treatment efficacy studies. PMID:24892236

  1. Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers

    PubMed Central

    Roorkiwal, Manish; Nayak, Spurthi N.; Thudi, Mahendar; Upadhyaya, Hari D.; Brunel, Dominique; Mournet, Pierre; This, Dominique; Sharma, Prakash C.; Varshney, Rajeev K.

    2014-01-01

    Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding. PMID:24926299

  2. High throughput automated allele frequency estimation by pyrosequencing.

    PubMed

    Doostzadeh, Julie; Shokralla, Shadi; Absalan, Farnaz; Jalili, Roxana; Mohandessi, Sharareh; Langston, James W; Davis, Ronald W; Ronaghi, Mostafa; Gharizadeh, Baback

    2008-01-01

    Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis. PMID:18628978

  3. High Throughput Automated Allele Frequency Estimation by Pyrosequencing

    PubMed Central

    Absalan, Farnaz; Jalili, Roxana; Mohandessi, Sharareh; Langston, James W.; Davis, Ronald W.; Ronaghi, Mostafa; Gharizadeh, Baback

    2008-01-01

    Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis. PMID:18628978

  4. A loss-of-function allele of OsHMA3 associated with high cadmium accumulation in shoots and grain of Japonica rice cultivars.

    PubMed

    Yan, Jiali; Wang, Peitong; Wang, Peng; Yang, Meng; Lian, Xingming; Tang, Zhong; Huang, Chao-Feng; Salt, David E; Zhao, Fang Jie

    2016-09-01

    Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non-functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380(th) position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F1 test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root-to-shoot Cd translocation and a shift in root Cd speciation from Cd-S to Cd-O bonding determined by synchrotron X-ray absorption spectroscopy. Our study has identified a new loss-of-function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain. PMID:27038090

  5. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

    PubMed Central

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

  6. Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

    PubMed Central

    Gadala-Maria, Daniel; Yaari, Gur; Uduman, Mohamed; Kleinstein, Steven H.

    2015-01-01

    Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses. PMID:25675496

  7. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches.

    PubMed

    Marmesat, Elena; Soriano, Laura; Mazzoni, Camila J; Sommer, Simone; Godoy, José A

    2016-01-01

    The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele's amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications. PMID:27294261

  8. Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast.

    PubMed

    Pasino, Serena; Caratti, Stefano; Del Pero, Massimiliano; Santovito, Alfredo; Torre, Carlo; Robino, Carlo

    2011-09-01

    Twenty-one X-chromosomal short tandem repeat (STR) loci, including the six clusters of linked markers DXS10148-DXS10135-DXS8378 (Xp22), DXS7132-DXS10079-DXS10074 (Xq12), DXS6801-DXS6809-DXS6789 (Xq21), DXS7424-DXS101 (Xq22), DXS10103-HPRTB-DXS10101 (Xq26), DXS8377-DXS10146-DXS10134-DXS7423 (Xq28) and the loci DXS6800, GATA172D05 and DXS10011 were typed in a population sample from Ivory Coast (n=125; 51 men and 74 women). Allele and haplotype frequencies as well as linkage disequilibrium data for kinship calculations are provided. On the whole, no significant differences in the genetic variability of X-STR markers were observed between Ivorians and other sub-Saharan African populations belonging to the Niger-Kordofanian linguistic group. PMID:21717153

  9. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches

    PubMed Central

    Marmesat, Elena; Soriano, Laura; Mazzoni, Camila J.; Sommer, Simone

    2016-01-01

    The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele’s amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications. PMID:27294261

  10. Inborn errors of human STAT1: allelic heterogeneity governs the diversity of immunological and infectious phenotypes

    PubMed Central

    Boisson-Dupuis, Stephanie; Kong, Xiao-Fei; Okada, Satoshi; Cypowyj, Sophie; Puel, Anne; Abel, Laurent; Casanova, Jean-Laurent

    2012-01-01

    The genetic dissection of various human infectious diseases has led to the definition of inborn errors of human STAT1 immunity of four types, including (i) autosomal recessive (AR) complete STAT1 deficiency, (ii) AR partial STAT1 deficiency, (iii) autosomal dominant (AD) STAT1 deficiency, and (iv) AD gain of STAT1 activity. The two types of AR STAT1 defect give rise to a broad infectious phenotype with susceptibility to intramacrophagic bacteria (mostly mycobacteria) and viruses (herpes viruses at least), due principally to the impairment of IFN-γ-mediated and IFN-α/β-mediated immunity, respectively. Clinical outcome depends on the extent to which the STAT1 defect decreases responsiveness to these cytokines. AD STAT1 deficiency selectively predisposes individuals to mycobacterial disease, owing to the impairment of IFN-γ-mediated immunity, as IFN-α/β-mediated immunity is maintained. Finally, AD gain of STAT1 activity is associated with autoimmunity, probably owing to an enhancement of IFN-α/β-mediated immunity. More surprisingly, it is also associated with chronic mucocutaneous candidiasis, through as yet undetermined mechanisms involving an inhibition of the development of IL-17-producing T cells. Thus, germline mutations in human STAT1 define four distinct clinical disorders. Various combinations of viral, mycobacterial and fungal infections are therefore allelic at the human STAT1 locus. These experiments of Nature neatly highlight the clinical and immunological impact of the human genetic dissection of infectious phenotypes. PMID:22651901

  11. The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles

    PubMed Central

    Boone, Philip M.; Yuan, Bo; Campbell, Ian M.; Scull, Jennifer C.; Withers, Marjorie A.; Baggett, Brett C.; Beck, Christine R.; Shaw, Christine J.; Stankiewicz, Pawel; Moretti, Paolo; Goodwin, Wendy E.; Hein, Nichole; Fink, John K.; Seong, Moon-Woo; Seo, Soo Hyun; Park, Sung Sup; Karbassi, Izabela D.; Batish, Sat Dev; Ordóñez-Ugalde, Andrés; Quintáns, Beatriz; Sobrido, María-Jesús; Stemmler, Susanne; Lupski, James R.

    2014-01-01

    Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects’ genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional—and possibly phenotypic—consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci. PMID:25065914

  12. Cytochrome P450 2C8*2 allele in Botswana: Human genetic diversity and public health implications.

    PubMed

    Motshoge, Thato; Tawe, Leabaneng; Muthoga, Charles Waithaka; Allotey, Joel; Romano, Rita; Quaye, Isaac; Paganotti, Giacomo Maria

    2016-05-01

    Human cytochrome P450 2C8 is a highly polymorphic gene and shows variation according to ethnicity. The CYP2C8*2 is a slow drug metabolism allele and shows 10-24% frequency in Black populations. The objective of this study was to assess the prevalence of CYP2C8*2 allele in Botswana among the San (or Bushmen) and the Bantu ethnic groups. For that purpose we recruited 544 children of the two ethnicities in three districts of Botswana from primary schools, collected blood samples, extracted DNA and genotyped them through PCR-based restriction fragment length polymorphism analysis. The results demonstrated that in the San the prevalence of the CYP2C8*2 allele is significantly higher than among the Bantu-related ethnic groups (17.5% and 8.5% for San and Bantu, respectively; P=0.00002). These findings support the evidence of a different genetic background of the San with respect to Bantu-related populations, and highlight a possible higher risk of longer drug clearance or poor level of activation of pro-drugs among the San group. PMID:26836270

  13. Allele- and Tir-Independent Functions of Intimin in Diverse Animal Infection Models

    PubMed Central

    Mallick, Emily M.; Brady, Michael J.; Luperchio, Steven A.; Vanguri, Vijay K.; Magoun, Loranne; Liu, Hui; Sheppard, Barbara J.; Mukherjee, Jean; Donohue-Rolfe, Art; Tzipori, Saul; Leong, John M.; Schauer, David B.

    2012-01-01

    Upon binding to intestinal epithelial cells, enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli (EPEC), and Citrobacter rodentium trigger formation of actin pedestals beneath bound bacteria. Pedestal formation has been associated with enhanced colonization, and requires intimin, an adhesin that binds to the bacterial effector translocated intimin receptor (Tir), which is translocated to the host cell membrane and promotes bacterial adherence and pedestal formation. Intimin has been suggested to also promote cell adhesion by binding one or more host receptors, and allelic differences in intimin have been associated with differences in tissue and host specificity. We assessed the function of EHEC, EPEC, or C. rodentium intimin, or a set of intimin derivatives with varying Tir-binding abilities in animal models of infection. We found that EPEC and EHEC intimin were functionally indistinguishable during infection of gnotobiotic piglets by EHEC, and that EPEC, EHEC, and C. rodentium intimin were functionally indistinguishable during infection of C57BL/6 mice by C. rodentium. A derivative of EHEC intimin that bound Tir but did not promote robust pedestal formation on cultured cells was unable to promote C. rodentium colonization of conventional mice, indicating that the ability to trigger actin assembly, not simply to bind Tir, is required for intimin-mediated intestinal colonization. Interestingly, streptomycin pre-treatment of mice eliminated the requirement for Tir but not intimin during colonization, and intimin derivatives that were defective in Tir-binding still promoted colonization of these mice. These results indicate that EPEC, EHEC, and C. rodentium intimin are functionally interchangeable during infection of gnotobiotic piglets or conventional C57BL/6 mice, and that whereas the ability to trigger Tir-mediated pedestal formation is essential for colonization of conventional mice, intimin provides a Tir-independent activity during colonization

  14. Y chromosome STR allelic and haplotype diversity in a Rwanda population from East Central Africa.

    PubMed

    Balamurugan, Kuppareddi; Duncan, George

    2012-03-01

    We have analyzed 17 Y-chromosomal STR loci in a population sample of 69 unrelated male individuals of the Rwanda-Hutu population from East Central Africa using an AmpFlSTR® Yfiler™ PCR amplification kit. A total of 62 unique haplotypes were identified among the 69 individuals studied. The haplotype diversity was found to be 0.9970 for this population. The gene diversity ranged from 0.1130 (DYS392) to 0.7722 (DYS385). Comparison of populations in this study with twenty-five other national and global populations using Principal Co-ordinate Analysis (PCA) and phylogenetic molecular analysis using a genetic distance matrix indicates a delineation of all the African populations from other unrelated populations. The results of population pair-wise Fst p values indicate statistically significant differentiation of the Rwandan population when compared with 25 other global populations including four African populations (p=0.0000). Analysis of Molecular Variance (AMOVA) of the Rwanda population with four other African populations indicated a 93% variance within populations and 7% variance among the five populations. A data base search of the 62 haplotypes yielded only one non-African haplotype match, suggesting these haplotypes are unique to the African continent. PMID:22285642

  15. Compensatory Aspects of Allele Diversity at Immunoglobulin Loci: Gene Correlations in Rabbit Populations Devoid of Light Chain Diversity (Oryctolagus Cuniculus L.; Kerguelen Islands)

    PubMed Central

    van-der-Loo, W.; Bousses, P.; Arthur, C. P.; Chapuis, J. L.

    1996-01-01

    Is there a selective advantage of increased diversity at one immunoglobulin locus when diversity at another locus is low? A previous paper demonstrated excess heterozygosity at the rabbit light chain b locus when heterozygosity was low at the heavy chain constant region e locus. Here we consider the reverse situation by analyzing allele distributions at heavy chain loci in populations fixed for the light chain b locus. We analyzed the a locus that encodes the predominantly expressed heavy chain variable region, and the d and e loci that control different parts of the Ig gamma class constant region. While there was excess heterozygosity, genetic differentiation between localities was extensive and was most pronounced for females. This was in marked contrast with observations in areas where b-locus diversity was important and confirms a negative correlation between e- and b-locus heterozygosity. Trigenic disequilibria corresponded to a significant negative correlation between e- and a-locus heterozygosity due mainly to strong variation among localities within the context of pronounced (digenic) linkage disequilibria. Although substantial, the average increase in a/e-locus single heterozygosity implemented by higher order disequilibria within localities was not significant. PMID:8913759

  16. Diversity in High Schools and Diversity Management: A Qualitative Study

    ERIC Educational Resources Information Center

    Ordu, Aydan

    2015-01-01

    The purpose of the present study is to present the diversities in high schools and opinions of teachers about management of these diversities. The sample of the study is from nine teachers working at the official high schools in the center of Denizli in Turkey. In this qualitative study, the data are collected with a semi-structured interview form…

  17. Allelic and haplotypic diversity at the rp1 rust resistance locus of maize.

    PubMed Central

    Smith, Shavannor M; Pryor, Anthony J; Hulbert, Scot H

    2004-01-01

    The maize Rp1 rust resistance locus is a complex consisting of a family of closely related resistance genes. The number of Rp1 paralogs in different maize lines (haplotypes) varied from a single gene in some stocks of the inbred A188 to >50 genes in haplotypes carrying the Rp1-A and Rp1-H specificities. The sequences of paralogs in unrelated haplotypes differ, indicating that the genetic diversity of Rp1-related genes is extremely broad in maize. Two unrelated haplotypes with five or nine paralogs had identical resistance phenotypes (Rp1-D) encoded in genes that differed by three nucleotides resulting in a single amino acid substitution. Genes in some haplotypes are more similar to each other than to any of the genes in other haplotypes indicating that they are evolving in a concerted fashion. PMID:15342531

  18. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism.

    PubMed

    Hammond, John A; Guethlein, Lisbeth A; Norman, Paul J; Parham, Peter

    2012-12-01

    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals' classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

  19. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

    PubMed Central

    Norman, Paul J.; Parham, Peter

    2012-01-01

    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals’ classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

  20. Allelic Diversity of the Plasmodium falciparum Erythrocyte Membrane Protein 1 Entails Variant-Specific Red Cell Surface Epitopes

    PubMed Central

    Vigan-Womas, Inès; Guillotte, Micheline; Juillerat, Alexandre; Vallieres, Cindy; Lewit-Bentley, Anita; Tall, Adama; Baril, Laurence; Bentley, Graham A.; Mercereau-Puijalon, Odile

    2011-01-01

    The clonally variant Plasmodium falciparum PfEMP1 adhesin is a virulence factor and a prime target of humoral immunity. It is encoded by a repertoire of functionally differentiated var genes, which display architectural diversity and allelic polymorphism. Their serological relationship is key to understanding the evolutionary constraints on this gene family and rational vaccine design. Here, we investigated the Palo Alto/VarO and IT4/R29 and 3D7/PF13_003 parasites lines. VarO and R29 form rosettes with uninfected erythrocytes, a phenotype associated with severe malaria. They express an allelic Cys2/group A NTS-DBL1α1 PfEMP1 domain implicated in rosetting, whose 3D7 ortholog is encoded by PF13_0003. Using these three recombinant NTS-DBL1α1 domains, we elicited antibodies in mice that were used to develop monovariant cultures by panning selection. The 3D7/PF13_0003 parasites formed rosettes, revealing a correlation between sequence identity and virulence phenotype. The antibodies cross-reacted with the allelic domains in ELISA but only minimally with the Cys4/group B/C PFL1955w NTS-DBL1α. By contrast, they were variant-specific in surface seroreactivity of the monovariant-infected red cells by FACS analysis and in rosette-disruption assays. Thus, while ELISA can differentiate serogroups, surface reactivity assays define the more restrictive serotypes. Irrespective of cumulated exposure to infection, antibodies acquired by humans living in a malaria-endemic area also displayed a variant-specific surface reactivity. Although seroprevalence exceeded 90% for each rosetting line, the kinetics of acquistion of surface-reactive antibodies differed in the younger age groups. These data indicate that humans acquire an antibody repertoire to non-overlapping serotypes within a serogroup, consistent with an antibody-driven diversification pressure at the population level. In addition, the data provide important information for vaccine design, as production of a vaccine

  1. Allelic Associations between 100 DNA Markers and High versus Low IQ.

    ERIC Educational Resources Information Center

    Plomin, Robert; And Others

    1995-01-01

    For DNA markers in or near genes of neurological relevance, allelic frequencies were compared for groups of high- and low-IQ children (total sample of 86). This study adds 40 markers to the 60 already studied. Only one showed a significant association with IQ in original and replication samples. (SLD)

  2. Estimating copy numbers of alleles from population-scale high-throughput sequencing data

    PubMed Central

    2015-01-01

    Background With the recent development of microarray and high-throughput sequencing (HTS) technologies, a number of studies have revealed catalogs of copy number variants (CNVs) and their association with phenotypes and complex traits. In parallel, a number of approaches to predict CNV regions and genotypes are proposed for both microarray and HTS data. However, only a few approaches focus on haplotyping of CNV loci. Results We propose a novel approach to infer copy unit alleles and their numbers in each sample simultaneously from population-scale HTS data by variational Bayesian inference on a generative probabilistic model inspired by latent Dirichlet allocation, which is a well studied model for document classification problems. In simulation studies, we evaluated concordance between inferred and true copy unit alleles for lower-, middle-, and higher-copy number dataset, in which precision and recall were ≥ 0.9 for data with mean coverage ≥ 10× per copy unit. We also applied the approach to HTS data of 1123 samples at highly variable salivary amylase gene locus and a pseudogene locus, and confirmed consistency of the estimated alleles within samples belonging to a trio of CEPH/Utah pedigree 1463 with 11 offspring. Conclusions Our proposed approach enables detailed analysis of copy number variations, such as association study between copy unit alleles and phenotypes or biological features including human diseases. PMID:25707811

  3. Ongoing Horizontal and Vertical Transmission of Virulence Genes and papA Alleles among Escherichia coli Blood Isolates from Patients with Diverse-Source Bacteremia

    PubMed Central

    Johnson, James R.; O'Bryan, Timothy T.; Kuskowski, Michael; Maslow, Joel N.

    2001-01-01

    The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process. PMID:11500406

  4. Drift Rather than Selection Dominates MHC Class II Allelic Diversity Patterns at the Biogeographical Range Scale in Natterjack Toads Bufo calamita

    PubMed Central

    Zeisset, Inga; Beebee, Trevor J. C.

    2014-01-01

    Study of major histocompatibility complex (MHC) loci has gained great popularity in recent years, partly due to their function in protecting vertebrates from infections. This is of particular interest in amphibians on account of major threats many species face from emergent diseases such as chytridiomycosis. In this study we compare levels of diversity in an expressed MHC class II locus with neutral genetic diversity at microsatellite loci in natterjack toad (Bufo (Epidalea) calamita) populations across the whole of the species’ biogeographical range. Variation at both classes of loci was high in the glacial refugium areas (REF) and much lower in postglacial expansion areas (PGE), especially in range edge populations. Although there was clear evidence that the MHC locus was influenced by positive selection in the past, congruence with the neutral markers suggested that historical demographic events were the main force shaping MHC variation in the PGE area. Both neutral and adaptive genetic variation declined with distance from glacial refugia. Nevertheless, there were also some indications from differential isolation by distance and allele abundance patterns that weak effects of selection have been superimposed on the main drift effect in the PGE zone. PMID:24937211

  5. MAIZE ALLELIC DIVERSITY PROJECT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Of the estimated 250-300 races of maize, only 24 races are represented in materials utilized by the Germplasm Enhancement of Maize (GEM) project, a collaborative effort between USDA-ARS and public and private sector research scientists. This is largely a result of poor performance of many races in ...

  6. Testing for High-Risk APOL1 Alleles in Potential Living Kidney Donors.

    PubMed

    Riella, Leonardo V; Sheridan, Alice M

    2015-09-01

    Accurate risk assessment is critical when evaluating potential living kidney donors. High-risk kidney APOL1 variants have been associated with end-stage renal disease of multiple causes among African Americans, though the predictive power of these variants in population-based studies is small. No studies have looked at the effect of high-risk APOL1 alleles on donor outcomes, though few transplantation centers in the United States offer screening for APOL1 among African American donors. Screening all African Americans for high-risk APOL1 alleles may result in the exclusion of many potential donors (∼13% of African Americans). Such an exclusion may have a large effect on the availability of transplants for African Americans, who are already less likely to undergo transplantation. Nephrologists should be prepared to discuss with potential African American donors the relative increase in risk that is likely conferred by carrying 2 high-risk APOL1 alleles and how additional factors such as environmental exposures (eg, viral infections) and/or other genetic susceptibilities may be required for developing kidney disease. In this Perspective, we review the use of APOL1 testing for risk stratification of potential African American kidney donors. PMID:26049628

  7. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

    PubMed Central

    2012-01-01

    Background High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. Conclusions The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons. PMID:22866951

  8. Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1.

    PubMed

    Zhang, Wenqiong; Xiao, Chao; Wei, Tian; Pan, Chao; Yi, Shaohua; Huang, Daixin

    2016-07-01

    Rapidly mutating Y-STRs (RM Y-STRs) have been paid much attention in recent years. The 13 RM Y-STRs have been proved to have substantially higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, indicating the considerable power in paternal lineage differentiation. To investigate the haplotype diversity in Chinese Han population, we collected 252 unrelated male samples and tested the genotype of the 13 RM Y-STRs. Among 252 male individuals, a total of 250 haplotypes were observed in which only 2 haplotypes were shared by 2 males respectively. The haplotype diversity reached 0.999937 and the discrimination capacity was 99.21%, showing a great discrimination power in Chinese Han population. In addition, an update on the allele designation of DYF403S1 was proposed. PMID:27217255

  9. Associations of high-grade glioma with glioma risk alleles and histories of allergy and smoking.

    PubMed

    Lachance, Daniel H; Yang, Ping; Johnson, Derek R; Decker, Paul A; Kollmeyer, Thomas M; McCoy, Lucie S; Rice, Terri; Xiao, Yuanyuan; Ali-Osman, Francis; Wang, Frances; Stoddard, Shawn M; Sprau, Debra J; Kosel, Matthew L; Wiencke, John K; Wiemels, Joseph L; Patoka, Joseph S; Davis, Faith; McCarthy, Bridget; Rynearson, Amanda L; Worra, Joel B; Fridley, Brooke L; O'Neill, Brian Patrick; Buckner, Jan C; Il'yasova, Dora; Jenkins, Robert B; Wrensch, Margaret R

    2011-09-01

    Glioma risk has consistently been inversely associated with allergy history but not with smoking history despite putative biologic plausibility. Data from 855 high-grade glioma cases and 1,160 controls from 4 geographic regions of the United States during 1997-2008 were analyzed for interactions between allergy and smoking histories and inherited variants in 5 established glioma risk regions: 5p15.3 (TERT), 8q24.21 (CCDC26/MLZE), 9p21.3 (CDKN2B), 11q23.3 (PHLDB1/DDX6), and 20q13.3 (RTEL1). The inverse relation between allergy and glioma was stronger among those who did not (odds ratio(allergy-glioma) = 0.40, 95% confidence interval: 0.28, 0.58) versus those who did (odds ratio(allergy-glioma) = 0.76, 95% confidence interval: 0.59, 0.97; P(interaction) = 0.02) carry the 9p21.3 risk allele. However, the inverse association with allergy was stronger among those who carried (odds ratio(allergy-glioma) = 0.44, 95% confidence interval: 0.29, 0.68) versus those who did not carry (odds ratio(allergy-glioma) = 0.68, 95% confidence interval: 0.54, 0.86) the 20q13.3 glioma risk allele, but this interaction was not statistically significant (P = 0.14). No relation was observed between glioma risk and smoking (odds ratio = 0.92, 95% confidence interval: 0.77, 1.10; P = 0.37), and there were no interactions for glioma risk of smoking history with any of the risk alleles. The authors' observations are consistent with a recent report that the inherited glioma risk variants in chromosome regions 9p21.3 and 20q13.3 may modify the inverse association of allergy and glioma. PMID:21742680

  10. Associations of High-Grade Glioma With Glioma Risk Alleles and Histories of Allergy and Smoking

    PubMed Central

    Lachance, Daniel H.; Yang, Ping; Johnson, Derek R.; Decker, Paul A.; Kollmeyer, Thomas M.; McCoy, Lucie S.; Rice, Terri; Xiao, Yuanyuan; Ali-Osman, Francis; Wang, Frances; Stoddard, Shawn M.; Sprau, Debra J.; Kosel, Matthew L.; Wiencke, John K.; Wiemels, Joseph L.; Patoka, Joseph S.; Davis, Faith; McCarthy, Bridget; Rynearson, Amanda L.; Worra, Joel B.; Fridley, Brooke L.; O’Neill, Brian Patrick; Buckner, Jan C.; Il’yasova, Dora; Jenkins, Robert B.; Wrensch, Margaret R.

    2011-01-01

    Glioma risk has consistently been inversely associated with allergy history but not with smoking history despite putative biologic plausibility. Data from 855 high-grade glioma cases and 1,160 controls from 4 geographic regions of the United States during 1997–2008 were analyzed for interactions between allergy and smoking histories and inherited variants in 5 established glioma risk regions: 5p15.3 (TERT), 8q24.21 (CCDC26/MLZE), 9p21.3 (CDKN2B), 11q23.3 (PHLDB1/DDX6), and 20q13.3 (RTEL1). The inverse relation between allergy and glioma was stronger among those who did not (odds ratioallergy-glioma = 0.40, 95% confidence interval: 0.28, 0.58) versus those who did (odds ratioallergy-glioma = 0.76, 95% confidence interval: 0.59, 0.97; Pinteraction = 0.02) carry the 9p21.3 risk allele. However, the inverse association with allergy was stronger among those who carried (odds ratioallergy-glioma = 0.44, 95% confidence interval: 0.29, 0.68) versus those who did not carry (odds ratioallergy-glioma = 0.68, 95% confidence interval: 0.54, 0.86) the 20q13.3 glioma risk allele, but this interaction was not statistically significant (P = 0.14). No relation was observed between glioma risk and smoking (odds ratio = 0.92, 95% confidence interval: 0.77, 1.10; P = 0.37), and there were no interactions for glioma risk of smoking history with any of the risk alleles. The authors’ observations are consistent with a recent report that the inherited glioma risk variants in chromosome regions 9p21.3 and 20q13.3 may modify the inverse association of allergy and glioma. PMID:21742680

  11. High-Throughput Carrier Screening Using TaqMan Allelic Discrimination

    PubMed Central

    Fedick, Anastasia; Su, Jing; Jalas, Chaim; Northrop, Lesley; Devkota, Batsal; Ekstein, Josef; Treff, Nathan R.

    2013-01-01

    Members of the Ashkenazi Jewish community are at an increased risk for inheritance of numerous genetic diseases such that carrier screening is medically recommended. This paper describes the development and evaluation of 30 TaqMan allelic discrimination qPCR assays for 29 mutations on 2 different high-throughput platforms. Four of these mutations are in the GBA gene and are successfully examined using short amplicons due to the qualitative nature of TaqMan allelic discrimination. Two systems were tested for their reliability (call rate) and consistency with previous diagnoses (diagnostic accuracy) indicating a call rate of 99.04% and a diagnostic accuracy of 100% (+/−0.00%) from one platform, and a call rate of 94.66% and a diagnostic accuracy of 93.35% (+/−0.29%) from a second for 9,216 genotypes. Results for mutations tested at the expected carrier frequency indicated a call rate of 97.87% and a diagnostic accuracy of 99.96% (+/−0.05%). This study demonstrated the ability of a high throughput qPCR methodology to accurately and reliably genotype 29 mutations in parallel. The universally applicable nature of this technology provides an opportunity to increase the number of mutations that can be screened simultaneously, and reduce the cost and turnaround time for accommodating newly identified and clinically relevant mutations. PMID:23555759

  12. Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.).

    PubMed

    Kim, Sunggil; Park, Jee Young; Yang, Tae-Jin

    2015-06-01

    Intact retrotransposon and DNA transposons inserted in a single gene were characterized in onions (Allium cepa) and their transcription and copy numbers were estimated in this study. While analyzing diverse onion germplasm, large insertions in the DFR-A gene encoding dihydroflavonol 4-reductase (DFR) involved in the anthocyanin biosynthesis pathway were found in two accessions. A 5,070-bp long terminal repeat (LTR) retrotransposon inserted in the active DFR-A (R4) allele was identified from one of the large insertions and designated AcCOPIA1. An intact ORF encoded typical domains of copia-like LTR retrotransposons. However, AcCOPIA1 contained atypical 'TG' and 'TA' dinucleotides at the ends of the LTRs. A 4,615-bp DNA transposon was identified in the other large insertion. This DNA transposon, designated AcCACTA1, contained an ORF coding for a transposase showing homology with the CACTA superfamily transposable elements (TEs). Another 5,073-bp DNA transposon was identified from the DFR-A (TRN) allele. This DNA transposon, designated AchAT1, belonged to the hAT superfamily with short 4-bp terminal inverted repeats (TIRs). Finally, a 6,258-bp non-autonomous DNA transposon, designated AcPINK, was identified in the ANS-p allele encoding anthocyanidin synthase, the next downstream enzyme to DFR in the anthocyanin biosynthesis pathway. AcPINK also possessed very short 3-bp TIRs. Active transcription of AcCOPIA1, AcCACTA1, and AchAT1 was observed through RNA-Seq analysis and RT-PCR. The copy numbers of AcPINK estimated by mapping the genomic DNA reads produced by NextSeq 500 were predominantly high compared with the other TEs. A series of evidence indicated that these TEs might have transposed in these onion genes very recently, providing a stepping stone for elucidation of enormously large-sized onion genome structure. PMID:25515665

  13. Effects of Glutenin Loci Allelic Diversity and Rye Translocations on Dough Properties Within U.S. Hard Winter Wheat Breeding Programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Allelic variation at the Glu-1 and Glu-3 loci is known to contribute to end-use qualities in wheat (Triticum aestivum L.). The Glu-1 loci, which encodes high molecular weight glutenin subunits (HMW-GS), and the Glu-3 loci, which encodes low molecular weight glutenin subunits (LMW-GS), are polymorph...

  14. Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles

    PubMed Central

    2014-01-01

    Abstracts Background Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers. Results 23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed betweenthe two species. Conclusions Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc-DQB1 genes in these

  15. The serodominant secreted effector protein of Salmonella, SseB, is a strong CD4 antigen containing an immunodominant epitope presented by diverse HLA class II alleles

    PubMed Central

    Reynolds, Catherine J; Jones, Claire; Blohmke, Christoph J; Darton, Thomas C; Goudet, Amelie; Sergeant, Ruhena; Maillere, Bernard; Pollard, Andrew J; Altmann, Daniel M; Boyton, Rosemary J

    2014-01-01

    Detailed characterization of the protective T-cell response in salmonellosis is a pressing unmet need in light of the global burden of human Salmonella infections and the likely contribution of CD4 T cells to immunity against this intracellular infection. In previous studies screening patient sera against antigen arrays, SseB was noteworthy as a serodominant target of adaptive immunity, inducing significantly raised antibody responses in HIV-seronegative compared with seropositive patients. SseB is a secreted protein, part of the Espa superfamily, localized to the bacterial surface and forming part of the translocon of the type III secretion system (T3SS) encoded by Salmonella pathogenicity island 2. We demonstrate here that SseB is also a target of CD4 T-cell immunity, generating a substantial response after experimental infection in human volunteers, with around 0·1% of the peripheral repertoire responding to it. HLA-DR/peptide binding studies indicate that this protein encompasses a number of peptides with ability to bind to several different HLA-DR alleles. Of these, peptide 11 (p11) was shown in priming of both HLA-DR1 and HLA-DR4 transgenic mice to contain an immunodominant CD4 epitope. Analysis of responses in human donors showed immunity focused on p11 and another epitope in peptide 2. The high frequency of SseB-reactive CD4 T cells and the broad applicability to diverse HLA genotypes coupled with previous observations of serodominance and protective vaccination in mouse challenge experiments, make SseB a plausible candidate for next-generation Salmonella vaccines. PMID:24891088

  16. Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka).

    PubMed

    McClelland, Erin K; Ming, Tobi J; Tabata, Amy; Kaukinen, Karia H; Beacham, Terry D; Withler, Ruth E; Miller, Kristina M

    2013-09-01

    The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations. PMID:24033436

  17. Bloomfield High School: Diversity Spurs Growth

    ERIC Educational Resources Information Center

    Principal Leadership, 2012

    2012-01-01

    Changing the culture of a large, diverse high school from a place of teaching to a place of learning requires determination and the commitment of the entire school staff. Documented academic growth for all students and reduced achievement gaps over the last five years have demonstrated that Bloomfield (New Jersey) High School has made this…

  18. High Producing Tumor Necrosis Factor Alpha Gene Alleles in Protection against Severe Manifestations of Dengue

    PubMed Central

    Sam, Sing-Sin; Teoh, Boon-Teong; Chinna, Karuthan; AbuBakar, Sazaly

    2015-01-01

    Dengue virus (DENV) infection usually presents with mild self-limiting dengue fever (DF). Few however, would present with the more severe form of the disease, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). In the present study, the association between IL-12B, IL-10 and TNF-α gene polymorphisms and dengue severity was investigated. Methods: A case-control study was performed on a total of 120 unrelated controls, 86 DF patients and 196 DHF/DSS patients. The polymorphisms in IL-12B, IL-10 and TNF-α genes were genotyped using PCR-RFLP and PCR-sequencing methods. Results: A protective association of TNF-α -308A allele and -308GA genotype against DHF/DSS was observed, while TNF-α -238A allele and -238GA genotype were associated with DHF/DSS. A combination of TNF-α -308GA+AA genotype and IL-10 non-GCC haplotypes, IL-12B pro homozygotes (pro1/pro1, pro2/pro2) and IL-12B 3'UTR AC were significantly correlated with protective effects against DHF/DSS. An association between the cytokine gene polymorphisms and protection against the clinical features of severe dengue including thrombocytopenia and increased liver enzymes was observed in this study. Conclusion: The overall findings of the study support the correlation of high-producer TNF-α genotypes combined with low-producer IL-10 haplotypes and IL-12B genotypes in reduced risk of DHF/DSS. PMID:25589894

  19. Dissecting Allele Architecture of Early Onset IBD Using High-Density Genotyping

    PubMed Central

    Prahalad, Sampath; Walters, Thomas; Guthery, Stephen L.; Dubinsky, Marla; Baldassano, Robert; Crandall, Wallace V.; Rosh, Joel; Markowitz, James; Stephens, Michael; Kellermayer, Richard; Pfefferkorn, Marian; Heyman, Melvin B.; LeLeiko, Neal; Mack, David; Moulton, Dedrick; Kappelman, Michael D.; Kumar, Archana; Prince, Jarod; Bose, Promita; Mondal, Kajari; Ramachandran, Dhanya; Bohnsack, John F.; Griffiths, Anne M.; Haberman, Yael; Essers, Jonah; Thompson, Susan D.; Aronow, Bruce; Keljo, David J.; Hyams, Jeffrey S.; Denson, Lee A.; Kugathasan, Subra

    2015-01-01

    Background The inflammatory bowel diseases (IBD) are common, complex disorders in which genetic and environmental factors are believed to interact leading to chronic inflammatory responses against the gut microbiota. Earlier genetic studies performed in mostly adult population of European descent identified 163 loci affecting IBD risk, but most have relatively modest effect sizes, and altogether explain only ~20% of the genetic susceptibility. Pediatric onset represents about 25% of overall incident cases in IBD, characterized by distinct disease physiology, course and risks. The goal of this study is to compare the allelic architecture of early onset IBD with adult onset in population of European descent. Methods We performed a fine mapping association study of early onset IBD using high-density Immunochip genotyping on 1008 pediatric-onset IBD cases (801 Crohn’s disease; 121 ulcerative colitis and 86 IBD undetermined) and 1633 healthy controls. Of the 158 SNP genotypes obtained (out of the 163 identified in adult onset), this study replicated 4% (5 SNPs out of 136) of the SNPs identified in the Crohn’s disease (CD) cases and 0.8% (1 SNP out of 128) in the ulcerative colitis (UC) cases. Replicated SNPs implicated the well known NOD2 and IL23R. The point estimate for the odds ratio (ORs) for NOD2 was above and outside the confidence intervals reported in adult onset. A polygenic liability score weakly predicted the age of onset for a larger collection of CD cases (p< 0.03, R2= 0.007), but not for the smaller number of UC cases. Conclusions The allelic architecture of common susceptibility variants for early onset IBD is similar to that of adult onset. This immunochip genotyping study failed to identify additional common variants that may explain the distinct phenotype that characterize early onset IBD. A comprehensive dissection of genetic loci is necessary to further characterize the genetic architecture of early onset IBD. PMID:26098103

  20. Blood group genotyping in a population of highly diverse ancestry.

    PubMed

    Pellegrino, J; Castilho, L; Rios, M; De Souza, C A

    2001-01-01

    Accurate phenotyping of red blood cells (RBCs) can be difficult in transfusion-dependent patients such as those with thalassemia and sickle cell anemia because of the presence of previously transfused RBCs in the patient's circulation. Recently, the molecular basis associated with the expression of many blood group antigens was established. This allowed the development of a plethora of polymerase chain reaction (PCR)-based tests for identification of the blood group antigens by testing DNA. The new technologies complement phenotyping and overcome some of the limitations of hemagglutination assays. These molecular assays were developed on the basis of DNA sequences of individuals of Caucasian ancestry. The present study addresses the concern that these genotyping assays may not be applicable to populations of highly diverse ancestry because of variability in intronic regions or because of unrecognized alleles. We determined both phenotype and genotype for RH D, K 1/K 2, JK A/JK B, FY A/ FY B-GATA in 250 normal blood donors using PCR. Phenotype and genotype results agreed in 100% of the cases, indicating that molecular genotyping protocols can be effectively applied to populations with a highly diverse genetic background. However, genotyping for Duffy antigens provided information that could not be obtained by phenotyping. Essentially, 30.5 % of the donors with the FY B gene typed as Fy(b-) because of mutations in the GATA box. This information is very useful for the management of transfusion dependent patients. PMID:11170227

  1. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques.

    PubMed

    Onda, Yoshihiko; Mochida, Keiichi

    2016-08-01

    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study. PMID:27499684

  2. The induction of nitric oxide response of carp macrophages by transferrin is influenced by the allelic diversity of the molecule.

    PubMed

    Jurecka, Patrycja; Irnazarow, Ilgiz; Stafford, James L; Ruszczyk, Aleksandra; Taverne, Nico; Belosevic, Miodrag; Savelkoul, Huub F J; Wiegertjes, Geert F

    2009-04-01

    The central role of transferrin (Tf) as an iron transporting protein has been extended by observations that modified versions of Tf also participate in the regulation of innate immunity. We report on the isolation of two carp Tf proteins (alleles D and G) to purity using rivanol precipitation and ion-exchange chromatography, and describe the activation of head kidney-derived carp macrophages by cleaved Tf. We demonstrate the superiority of the D-type over the G-type Tf in inducing nitric oxide (NO) and confirm previous observations that full-length Tf cannot induce NO in fish macrophages. We believe that cleaved Tf fragments should be considered to be "alarmins". We discuss the possibility that parasites such as Trypanoplasma borreli cleave Tf and use Tf fragments to their advantage by modulating the NO induction in carp macrophages. PMID:18996204

  3. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breed utilization, genetic improvement, and industry consolidation are predicted to have major impacts on the genetic composition of commercial chickens. Consequently, the question arises as to whether sufficient genetic diversity remains within industry stocks to address future needs. With the ch...

  4. Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation

    PubMed Central

    2013-01-01

    Background Genetic engineering of industrial microorganisms often suffers from undesirable side effects on essential functions. Reverse engineering is an alternative strategy to improve multifactorial traits like low glycerol/high ethanol yield in yeast fermentation. Previous rational engineering of this trait always affected essential functions like growth and stress tolerance. We have screened Saccharomyces cerevisiae biodiversity for specific alleles causing lower glycerol/higher ethanol yield, assuming higher compatibility with normal cellular functionality. Previous work identified ssk1E330N…K356N as causative allele in strain CBS6412, which displayed the lowest glycerol/ethanol ratio. Results We have now identified a unique segregant, 26B, that shows similar low glycerol/high ethanol production as the superior parent, but lacks the ssk1E330N…K356N allele. Using segregants from the backcross of 26B with the inferior parent strain, we applied pooled-segregant whole-genome sequence analysis and identified three minor quantitative trait loci (QTLs) linked to low glycerol/high ethanol production. Within these QTLs, we identified three novel alleles of known regulatory and structural genes of glycerol metabolism, smp1R110Q,P269Q, hot1P107S,H274Y and gpd1L164P as causative genes. All three genes separately caused a significant drop in the glycerol/ethanol production ratio, while gpd1L164P appeared to be epistatically suppressed by other alleles in the superior parent. The order of potency in reducing the glycerol/ethanol ratio of the three alleles was: gpd1L164P > hot1P107S,H274Y ≥ smp1R110Q,P269Q. Conclusions Our results show that natural yeast strains harbor multiple specific alleles of genes controlling essential functions, that are apparently compatible with survival in the natural environment. These newly identified alleles can be used as gene tools for engineering industrial yeast strains with multiple subtle changes, minimizing the risk of

  5. Newborn screening strategy for cystic fibrosis: a field study in an area with high allelic heterogeneity.

    PubMed

    Castellani, C; Bonizzato, A; Cabrini, G; Mastella, G

    1997-05-01

    To verify to what extent mutation analysis on blood spot could improve cystic fibrosis neonatal screening in an area with high allelic heterogeneity, we designed a special protocol. Spot trypsin estimation at birth, trypsin re-testing after 1 month, meconium lactase testing and mutation analysis of delta F508, R1162X and N1303K, were retrospectively clustered according to different patterns (trypsin/lactase/mutation; trypsin/lactase/re-testing; trypsin/mutation) and compared. The programme, which lasted 2 years (1993-94) and covered most of North-eastern Italy, included 95,553 screened newborns. Thirty-four affected babies were detected by screening and one by meconium ileus (incidence 1/2730). The combined use of trypsin, lactase and mutation analysis in cystic fibrosis neonatal screening permits a better sensitivity compared to the two other combinations (34 diagnoses vs 32 in both cases). Moreover, the higher specificity of the former method (false positives 42 vs 148) allows a reduction of recalls, which cause considerable anxiety. We confirm in trypsin-positive newborns an increased frequency of cystic fibrosis heterozygotes (1/17). PMID:9183489

  6. Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure

    PubMed Central

    Field, Wesley; Hershberg, Ruth

    2015-01-01

    Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have focused on characterizing the frequencies with which horizontally acquired resistance genes segregate within natural bacterial populations. Yet, very little is currently understood regarding the frequency of segregation of resistance alleles occurring within the housekeeping targets of antibiotics. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non host-associated environments for such alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles occurring within the target genes of each of the three antibiotics, with quinolone resistance alleles being the most frequent and rifamycin resistance alleles being the least frequent. Resistance allele frequencies varied greatly between different phyla and as a function of environment. The frequency of quinolone resistance alleles was especially high within host-associated environments, where it averaged an alarming ∼40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. High frequencies of quinolone resistance alleles were also found within hosts that were not directly treated with antibiotics. Therefore, the high segregation frequency of quinolone resistance alleles occurring within the housekeeping targets of antibiotics in host-associated environments does not seem to be the sole result of clinical antibiotic usage. PMID:26019163

  7. Functionally Divergent Alleles and Duplicated Loci Encoding an Acyltransferase Contribute to Acylsugar Metabolite Diversity in Solanum Trichomes[OPEN

    PubMed Central

    Schilmiller, Anthony L.; Moghe, Gaurav D.; Fan, Pengxiang; Ghosh, Banibrata; Ning, Jing; Jones, A. Daniel; Last, Robert L.

    2015-01-01

    Glandular trichomes from tomato (Solanum lycopersicum) and other species in the Solanaceae produce and secrete a mixture of O-acylsugars (aliphatic esters of sucrose and glucose) that contribute to insect defense. Despite their phylogenetic distribution and diversity, relatively little is known about how these specialized metabolites are synthesized. Mass spectrometric profiling of acylsugars in the S. lycopersicum x Solanum pennellii introgression lines identified a chromosome 11 locus containing a cluster of BAHD acyltransferases with one gene (named Sl-ASAT3) expressed in tip cells of type I trichomes where acylsugars are made. Sl-ASAT3 was shown to encode an acyl-CoA-dependent acyltransferase that catalyzes the transfer of short (four to five carbons) branched acyl chains to the furanose ring of di-acylsucrose acceptors to produce tri-acylsucroses, which can be further acetylated by Sl-ASAT4 (previously Sl-AT2). Among the wild tomatoes, diversity in furanose ring acyl chains on acylsucroses was most striking in Solanum habrochaites. S. habrochaites accessions from Ecuador and northern Peru produced acylsucroses with short (≤C5) or no acyl chains on the furanose ring. Accessions from central and southern Peru had the ability to add short or long (up to C12) acyl chains to the furanose ring. Multiple ASAT3-like sequences were found in most accessions, and their in vitro activities correlated with observed geographical diversity in acylsugar profiles. PMID:25862303

  8. MHC variability supports dog domestication from a large number of wolves: high diversity in Asia

    PubMed Central

    Niskanen, A K; Hagström, E; Lohi, H; Ruokonen, M; Esparza-Salas, R; Aspi, J; Savolainen, P

    2013-01-01

    The process of dog domestication is still somewhat unresolved. Earlier studies indicate that domestic dogs from all over the world have a common origin in Asia. So far, major histocompatibility complex (MHC) diversity has not been studied in detail in Asian dogs, although high levels of genetic diversity are expected at the domestication locality. We sequenced the second exon of the canine MHC gene DLA–DRB1 from 128 Asian dogs and compared our data with a previously published large data set of MHC alleles, mostly from European dogs. Our results show that Asian dogs have a higher MHC diversity than European dogs. We also estimated that there is only a small probability that new alleles have arisen by mutation since domestication. Based on the assumption that all of the currently known 102 DLA–DRB1 alleles come from the founding wolf population, we simulated the number of founding wolf individuals. Our simulations indicate an effective population size of at least 500 founding wolves, suggesting that the founding wolf population was large or that backcrossing has taken place. PMID:23073392

  9. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    PubMed

    Noreen, Annika M E; Webb, Edward L

    2013-01-01

    Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss. PMID:24367531

  10. High Frequency of Pathogenic Rearrangements in SPG11 and Extensive Contribution of Mutational Hotspots and Founder Alleles.

    PubMed

    Günther, Sven; Elert-Dobkowska, Ewelina; Soehn, Anne S; Hinreiner, Sophie; Yoon, Grace; Heller, Raoul; Hellenbroich, Yorck; Hübner, Christian A; Ray, Peter N; Hehr, Ute; Bauer, Peter; Sulek, Anna; Beetz, Christian

    2016-07-01

    Biallelic loss-of-function mutations in SPG11 cause a wide spectrum of recessively inherited, neurodegenerative disorders including hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis, and Charcot-Marie-Tooth disease. By comprehensive screening of three large cohorts of HSP index patients, we identified 83 alleles with "small" mutations and 13 alleles that carry large genomic rearrangements. Including relevant data from previous studies, we estimate that copy number variants (CNVs) account for ∼19% of pathogenic SPG11 alleles. The breakpoints for all novel and some previously reported CNVs were determined by long-range PCR and sequencing. This revealed several Alu-associated recombination hotspots. We also found evidence for additional mutational mechanisms, including for a two-step event in which an Alu retrotransposition preceded the actual rearrangement. Apparently independent samples with identical breakpoints were analyzed by microsatellite PCRs. The resulting haplotypes suggested the existence of two rearrangement founder alleles. Our findings widen the spectra of mutations and mutational mechanisms in SPG11, underscore the pivotal role played by Alus, and are of high diagnostic relevance for a wide spectrum of clinical phenotypes including the most frequent form of recessive HSP. PMID:27071356

  11. High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

    PubMed Central

    2010-01-01

    Background Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. Results Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs) were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%). Conclusions Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes in the human term

  12. A Computer Simulation Study of Vntr Population Genetics: Constrained Recombination Rules Out the Infinite Alleles Model

    PubMed Central

    Harding, R. M.; Boyce, A. J.; Martinson, J. J.; Flint, J.; Clegg, J. B.

    1993-01-01

    Extensive allelic diversity in variable numbers of tandem repeats (VNTRs) has been discovered in the human genome. For population genetic studies of VNTRs, such as forensic applications, it is important to know whether a neutral mutation-drift balance of VNTR polymorphism can be represented by the infinite alleles model. The assumption of the infinite alleles model that each new mutant is unique is very likely to be violated by unequal sister chromatid exchange (USCE), the primary process believed to generate VNTR mutants. We show that increasing both mutation rates and misalignment constraint for intrachromosomal recombination in a computer simulation model reduces simulated VNTR diversity below the expectations of the infinite alleles model. Maximal constraint, represented as slippage of single repeats, reduces simulated VNTR diversity to levels expected from the stepwise mutation model. Although misalignment rule is the more important variable, mutation rate also has an effect. At moderate rates of USCE, simulated VNTR diversity fluctuates around infinite alleles expectation. However, if rates of USCE are high, as for hypervariable VNTRs, simulated VNTR diversity is consistently lower than predicted by the infinite alleles model. This has been observed for many VNTRs and accounted for by technical problems in distinguishing alleles of neighboring size classes. We use sampling theory to confirm the intrinsically poor fit to the infinite alleles model of both simulated VNTR diversity and observed VNTR polymorphisms sampled from two Papua New Guinean populations. PMID:8293988

  13. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGESBeta

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; et al

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcriptionmore » factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.« less

  14. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    SciTech Connect

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; Ziebell, Angela L.; Klapste, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry; Douglas, Carl; Mansfield, Shawn; Martin, Joel; Schackwitz, Wendy; Evans, Luke M.; Czarnecki, Olaf; Tuskan, Gerald A.

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.

  15. Impacts of kafirin allelic diversity, starch content, and protein digestibility on ethanol conversion efficiency in grain sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seed protein and starch composition determines the efficiency of ethanol conversion in the production of grain-based biofuels. Sorghum, highly water- and nutrient-efficient, has the potential to replace fuel crops with greater irrigation and fertiliser requirements, such as maize. However, sorghum g...

  16. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    NASA Astrophysics Data System (ADS)

    Shan, Tifeng; Pang, Shaojun; Liu, Feng; Xu, Na; Zhao, Xiaobo; Gao, Suqin

    2012-03-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation. To better understand the genetic relationships of different gametophyte cultures isolated from different sources, 20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U. pinnatifida isolated from wild sporophytes in Vladivostok, Russia and from cultivated sporophytes from Dalian and Qingdao, China. One locus was abandoned because of poor amplification. At the sex-linked locus of Up-AC-2A8, 3 alleles were detected in 25 female gametophyte clones, with sizes ranging from 307 to 316 bp. At other loci, 3 to 7 alleles were detected with an average of 4.5 alleles per locus. The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones, respectively. The average gene diversity for Russian, Chinese, and for the combined total of gametophyte clones was 0.1, 0.4, and 0.5, respectively. Russian gametophyte clones had unique alleles at 7 out of the 19 loci. In cluster analysis, Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance. Overall, high genetic diversity was detected in gametophyte clones isolated from the two countries. These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  17. A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages.

    PubMed

    Lau, Q; Yasukochi, Y; Satta, Y

    2015-11-01

    Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co-evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide-binding and pathogen-recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non-peptide-binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non-exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time. PMID:26392055

  18. High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program

    PubMed Central

    Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

    2015-01-01

    Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis

  19. Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish.

    PubMed

    Chen, Ailu; Wang, Ruijia; Liu, Shikai; Peatman, Eric; Sun, Luyang; Bao, Lisui; Jiang, Chen; Li, Chao; Li, Yun; Zeng, Qifan; Liu, Zhanjiang

    2016-06-01

    Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE). In this work, we analyzed ASE in F1 hybrid catfish using RNA-Seq datasets. While the vast majority of genes were expressed with both alleles, 7-8 % SNPs exhibited significant differences in allele ratios of expression. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5420 (8.2 %) and 13,390 (7.5 %) SNPs were identified as significant ASE-SNPs, respectively. With these SNPs, a total of 1519 and 3075 ASE-genes were identified. Gene Ontology analysis revealed that genes encoding cytoplasmic ribosomal proteins (RP) were highly enriched among ASE genes. Parent-of-origin was determined for 27 and 30 ASE RP genes in the liver and gill, respectively. The results indicated that genes from both channel catfish and blue catfish were involved in ASE. However, each RP gene appeared to be almost exclusively expressed from only one parent, indicating that ribosomes in the hybrid catfish were in the "hybrid" form. Overall representation of RP transcripts among the transcriptome appeared lower in the F1 hybrid catfish than in channel catfish or blue catfish, suggesting that the "hybrid" ribosomes may work more efficiently for translation in the F1 hybrid catfish. PMID:26747053

  20. High Resolution Human Leukocyte Antigen Class I Allele Frequencies and HIV-1 Infection Associations in Chinese Han and Uyghur Cohorts

    PubMed Central

    Liu, Yanhou; Zhao, Zhongfang; Li, Tianyi; Liao, Qi; Kushner, Nicholas; Touzjian, Neal Y.; Shao, Yiming; Sun, Yongtao; Strong, Amie J.; Lu, Yichen

    2012-01-01

    Background Host immunogenetic factors such as HLA class I polymorphism are important to HIV-1 infection risk and AIDS progression. Previous studies using high-resolution HLA class I profile data of Chinese populations appeared insufficient to provide information for HIV-1 vaccine development and clinical trial design. Here we reported HLA class I association with HIV-1 susceptibility in a Chinese Han and a Chinese Uyghur cohort. Methodology/Principal Findings Our cohort included 327 Han and 161 Uyghur ethnic individuals. Each cohort included HIV-1 seropositive and HIV-1 seronegative subjects. Four-digit HLA class I typing was performed by sequencing-based typing and high-resolution PCR-sequence specific primer. We compared the HLA class I allele and inferred haplotype frequencies between HIV-1 seropositive and seronegative groups. A neighbor-joining tree between our cohorts and other populations was constructed based on allele frequencies of HLA-A and HLA-B loci. We identified 58 HLA-A, 75 HLA-B, and 32 HLA-Cw distinct alleles from our cohort and no novel alleles. The frequency of HLA-B*5201 and A*0301 was significantly higher in the Han HIV-1 negative group. The frequency of HLA-B*5101 was significantly higher in the Uyghur HIV-1 negative group. We observed statistically significant increases in expectation-maximization (EM) algorithm predicted haplotype frequencies of HLA-A*0201-B*5101 in the Uyghur HIV-1 negative group, and of Cw*0304-B*4001 in the Han HIV-1 negative group. The B62s supertype frequency was found to be significantly higher in the Han HIV-1 negative group than in the Han HIV-1 positive group. Conclusions At the four-digit level, several HLA class I alleles and haplotypes were associated with lower HIV-1 susceptibility. Homogeneity of HLA class I and Bw4/Bw6 heterozygosity were not associated with HIV-1 susceptibility in our cohort. These observations contribute to the Chinese HLA database and could prove useful in the development of HIV-1 vaccine

  1. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  2. Swine Leukocyte Antigen (SLA) class I allele typing of Danish swine herds and identification of commonly occurring haplotypes using sequence specific low and high resolution primers.

    PubMed

    Pedersen, Lasse Eggers; Jungersen, Gregers; Sorensen, Maria Rathmann; Ho, Chak-Sum; Vadekær, Dorte Fink

    2014-12-15

    The swine major histocompatibility complex (MHC) genomic region (SLA) is extremely polymorphic comprising high numbers of different alleles, many encoding a distinct MHC class I molecule, which binds and presents endogenous peptides to circulating T cells of the immune system. Upon recognition of such peptide-MHC complexes (pMHC) naïve T cells can become activated and respond to a given pathogen leading to its elimination and the generation of memory cells. Hence SLA plays a crucial role in maintaining overall adaptive immunologic resistance to pathogens. Knowing which SLA alleles that are commonly occurring can be of great importance in regard to future vaccine development and the establishment of immune protection in swine through broad coverage, highly specific, subunit based vaccination against viruses such as swine influenza, porcine reproductive and respiratory syndrome virus, vesicular stomatitis virus, foot-and-mouth-disease virus and others. Here we present the use of low- and high-resolution PCR-based typing methods to identify individual and commonly occurring SLA class I alleles in Danish swine. A total of 101 animals from seven different herds were tested, and by low resolution typing the top four most frequent SLA class I alleles were those of the allele groups SLA-3*04XX, SLA-1*08XX, SLA-2*02XX, and SLA-1*07XX, respectively. Customised high resolution primers were used to identify specific alleles within the above mentioned allele groups as well as within the SLA-2*05XX allele group. Our studies also suggest the most common haplotype in Danish pigs to be Lr-4.0 expressing the SLA-1*04XX, SLA-2*04XX, and SLA-3*04XX allele combination. PMID:25457547

  3. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

    PubMed Central

    2012-01-01

    Background The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total). Conclusions The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post

  4. High resolution human leukocyte antigen (HLA) class I and class II allele typing in Mexican mestizo women with sporadic breast cancer: case-control study

    PubMed Central

    2009-01-01

    Background The development of breast cancer is multifactorial. Hormonal, environmental factors and genetic predisposition, among others, could interact in the presentation of breast carcinoma. Human leukocyte antigen (HLA) alleles play an important role in immunity (cellular immunity) and may be important genetic traits. HLAAllele-specific interaction has not been well established. Recently, several studies had been conducted in order to do so, but the results are controversial and in some instances contradictory. Methods We designed a case-control study to quantify the association of HLA class I and II genes and breast cancer. HLA typing was performed by high resolution sequence-specific oligotyping after DNA amplification (PCR-SSOP) of 100 breast cancer Mexican mestizo patients and 99 matched healthy controls. Results HLA-A frequencies that we were able to observe that there was no difference between both groups from the statistical viewpoint. HLA-B*1501 was found three times more common in the case group (OR, 3.714; p = 0.031). HLA-Cw is not a marker neither for risk, nor protection for the disease, because we did not find significant statistical differences between the two groups. DRB1*1301, which is expressed in seven cases and in only one control, observing an risk increase of up to seven times and DRB1*1602, which behaves similarly in being present solely in the cases (OR, 16.701; 95% CI, 0.947 – 294.670). DQ*0301-allele expression, which is much more common in the control group and could be protective for the presentation of the disease (OR, 0.078; 95% CI, 0.027–0.223, p = 0.00001). Conclusion Our results reveal the role of the MHC genes in the pathophysiology of breast cancer, suggesting that in the development of breast cancer exists a disorder of immune regulation. The triggering factor seems to be restricted to certain ethnic groups and certain geographical regions since the relevant MHC alleles are highly diverse. This is the first study in Mexican

  5. Diverse microbial species survive high ammonia concentrations

    NASA Astrophysics Data System (ADS)

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  6. End-use quality and agronomic characteristics associated with the Glu-B1al high-molecular-weight glutenin allele in U.S. hard winter wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High molecular weight glutenin subunits (HMW-GS) conferred by alleles at the Glu-B1 and Glu-D1 loci confer unique end-use quality properties for wheat (Triticum aestivum L.). The Glu-B1al allele at the Glu-B1 locus has not been widely used for cultivar development in the U.S. hard winter wheat regio...

  7. High Genetic Diversity in a Potentially Vulnerable Tropical Tree Species Despite Extreme Habitat Loss

    PubMed Central

    Noreen, Annika M. E.; Webb, Edward L.

    2013-01-01

    Over the last 150 years, Singapore’s primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843–0.854), high allelic richness (R = 16.7–19.5), low inbreeding co-efficients (FIS = 0.013–0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0–10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss. PMID

  8. High frequency of the apolipoprotein E *4 allele in African pygmies and most of the African populations in sub-Saharan Africa.

    PubMed

    Zekraoui, L; Lagarde, J P; Raisonnier, A; Gérard, N; Aouizérate, A; Lucotte, G

    1997-08-01

    Apolipoprotein E genotypes (alleles *2, *3, and *4) have been determined in 70 Aka Pygmies and 470 unrelated African sub-Saharan subjects. Allele frequencies for Pygmies are 5.7% for APOE*2, 53.6% for APOE*3, and 40.7% for APOE*4, and the global proportions for sub-Saharan subjects are 11.6% for APOE*2, 70.6% for APOE*3, and 17.8% for APOE*4. The frequencies in some ethnic groups are statistically different from the overall mean in the Afar and the Isa, the Ewe (Togo), the Malinke (Guinea), and the Mossi; three ethnic groups have a higher allele frequency of APOE*4 (Fon, 29.4%; Zairians, 33.3%; Tutsi, 38.5%). The APOE*4 allele is considered the ancestral form because of its high frequency in African Pygmies and other aboriginal populations. PMID:9198315

  9. Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

    PubMed Central

    Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

    2016-01-01

    Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays. PMID:27171472

  10. Effect of Rht alleles on wheat grain yield and quality under high temperature and drought stress during booting and anthesis.

    PubMed

    Alghabari, Fahad; Ihsan, Muhammad Zahid; Hussain, Saddam; Aishia, Ghulam; Daur, Ihsanullah

    2015-10-01

    The present study examined the effects of gibberellin semi-sensitive reduced height (Rht) alleles on wheat grain yield and quality under high temperature and drought stress during booting and anthesis stages. Near-isogenic lines (NILs) of winter wheat (Rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-8c, Rht-D1c, Rht-12) having background of Mercia and Maris Widgeon cultivars were compared under variable temperatures (day/night: 20/12, 27/19, 30/22, 33/25, 36/28, and 39/31 °C) and irrigation regimes. Pots were transferred to controlled thermal conditions (Saxcil growth chamber) during booting and anthesis stages and were maintained at field capacity (FC) or had water withheld. High temperature (>30 °C) and drought stress for seven consecutive days during booting and anthesis stages reduced the grain yield, while increased nitrogen (N) and sulphur (S) concentrations. A 50 % reduction in grain yield was fitted to have occurred at 37.4 °C for well-watered plants and at 31.4 °C for drought-stressed plants. The N and S concentrations were higher for severe dwarfs, whereas no significant differences were observed between tall and semi-dwarfs in Mercia. In the taller background (Maris Widgeon), N and S concentrations were significantly higher compared with that in Mercia. In Mercia, the severe dwarf Rht-D1c had higher Hagberg falling number (HFN) and sodium dodecyl sulphate (SDS) sedimentation volume. In both backgrounds, semi-dwarfs and severe dwarfs had higher HFN. Moreover, the SDS sedimentation volumes in Maris Widgeon were also higher than that in Mercia. Greater adaptability and improved grain quality traits suggested that severe dwarf Rht alleles are better able to enhance tolerance to high temperature and drought stress in wheat. PMID:26006072

  11. High Risks of Losing Genetic Diversity in an Endemic Mauritian Gecko: Implications for Conservation

    PubMed Central

    Buckland, Steeves; Cole, Nik C.; Groombridge, Jim J.; Küpper, Clemens; Burke, Terry; Dawson, Deborah A.; Gallagher, Laura E.; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID

  12. High mycobacterial diversity in recreational lakes.

    PubMed

    Roguet, A; Therial, C; Saad, M; Boudahmane, L; Moulin, L; Lucas, F S

    2016-05-01

    Although nontuberculous mycobacteria (NTM) are natural inhabitants of freshwater ecosystems, few studies have focused on their distribution in these habitats. Thus, the knowledge about the abundance as well as the composition of NTM remains limited and patchy in these environments. In this context, a prospective study was performed to identify favourable habitats for mycobacteria in two recreational lakes. Mycobacterial density and diversity were measured using quantitative real-time PCR and the MiSeq Illumina platform. For both lakes, five compartments were investigated, i.e. water column, air-water interface, sediment, epilithon and epiphyton biofilms. Nontuberculous mycobacteria were detected in all compartments in large densities and displayed a remarkable diversity. NTM were dominated by fast-growing species. Lakes and compartments appeared to shape mycobacteria assemblage composition as well as their densities. In both lakes, some OTUs assigned to the species level were identified as related to known opportunistic pathogens. PMID:26873594

  13. Assessment of Immune Interference, Antagonism and Diversion following Human Immunization with Bi-Allelic Blood-Stage Malaria Viral Vectored Vaccines and Controlled Malaria Infection

    PubMed Central

    Elias, Sean C.; Collins, Katharine A.; Halstead, Fenella D.; Choudhary, Prateek; Bliss, Carly M.; Ewer, Katie J.; Sheehy, Susanne H.; Duncan, Christopher J. A.; Biswas, Sumi; Hill, Adrian V. S.; Draper, Simon J.

    2012-01-01

    Overcoming antigenic variation is one of the major challenges in the development of an effective vaccine against Plasmodium falciparum, a causative agent of human malaria. Inclusion of multiple antigen variants in subunit vaccine candidates is one strategy that has aimed to overcome this problem for the leading blood-stage malaria vaccine targets, merozoite surface protein 1 (MSP1) and apical membrane antigen 1 (AMA1). However previous studies, utilizing malaria antigens, have concluded that inclusion of multiple allelic variants, encoding altered peptide ligands (APL), in such a vaccine may be detrimental to both the priming and in vivo re-stimulation of antigen-experienced T cells. Here we analyze the T cell responses to two alleles of MSP1 and AMA1 induced by vaccination of malaria-naïve adult volunteers with bi-valent viral vectored vaccine candidates. We show a significant bias to the 3D7/MAD20 allele compared to the Wellcome allele for the 33kDa region of MSP1, but not for the 19kDa fragment or the AMA1 antigen. Whilst this bias could be caused by ‘immune interference’ at priming, the data don’t support a significant role for ‘immune antagonism’ during memory T cell re-stimulation, despite observation of the latter at a minimal epitope level in vitro. A lack of class I HLA epitopes in the Wellcome allele that are recognized by vaccinated volunteers may in fact contribute to the observed bias. We also show that controlled infection with 3D7 strain P. falciparum parasites neither boosts existing 3D7-specific T cell responses nor appears to ‘immune divert’ cellular responses towards the Wellcome allele. PMID:23293353

  14. High frequency of allelic imbalance at chromosome region 16q22-23 in human breast cancer: correlation with high PgR and low S phase.

    PubMed

    Skirnisdottir, S; Eiriksdottir, G; Baldursson, T; Barkardottir, R B; Egilsson, V; Ingvarrson, S

    1995-04-21

    The loss of genetic material from a specific chromosome region in tumors suggests that presence of tumor-suppressor genes. Loss of heterozygosity (LOH) or allelic imbalance (AI) on the long arm of chromosome 16 is a known event in sporadic breast cancer. To locate the commonly deleted regions, and therefore (a) candidate tumor-suppressor gene(s), a deletion map of chromosome 16 was made, using 10 microsatellite markers on 150 sporadic breast tumors. The 3 smallest regions of overlap (SRO) were detected on the long arm of chromosome 16. Allelic imbalance was observed with at least one marker in 67% of the tumors. One marker, D16S421, at the 16q22-23 region, showed the highest allelic imbalance, 58%. Tumors with and without AI on 16q were tested for correlation with clinico-pathological features of the tumors such as estrogen- and progesterone-receptor content (ER and PgR), age at diagnosis, tumor size, node status, histological type, S-phase fraction, AI on chromosome 3p, and ploidy. A correlation was found between AI on 16q and high PgR content, also low S-phase fraction (99% confidence limits). A comparison of tumors with and without AI at the D16S421 marker locus revealed a slight correlation with high PgR content. The survival data showed no difference between patients with AI on 16q and those with a normal allele pattern on the long arm of chromosome 16. PMID:7615353

  15. Diversity and High Academic Expectations without Tracking: Inclusively Responsive Instruction

    ERIC Educational Resources Information Center

    Murata, Aki

    2013-01-01

    This article presents an instructional model (inclusively responsive instruction) that takes advantage of student diversity in order to differentiate student learning while maintaining high expectations. In the history of U.S. education, diversity and academic rigor were often considered at odds, and educators tried to emphasize one at the expense…

  16. High diversity of magnetotactic deltaproteobacteria in a freshwater niche.

    PubMed

    Wang, Yinzhao; Lin, Wei; Li, Jinhua; Pan, Yongxin

    2013-04-01

    Knowledge of the diversity of magnetotactic bacteria in natural environments is crucial for understanding their contribution to various biological and geological processes. Here we report a high diversity of magnetotactic bacteria in a freshwater site. Ten out of 18 operational taxonomic units (OTUs) were affiliated with the Deltaproteobacteria. Some rod-shaped bacteria simultaneously synthesized greigite and magnetite magnetosomes. PMID:23377941

  17. High Diversity of Magnetotactic Deltaproteobacteria in a Freshwater Niche

    PubMed Central

    Wang, Yinzhao; Lin, Wei; Li, Jinhua

    2013-01-01

    Knowledge of the diversity of magnetotactic bacteria in natural environments is crucial for understanding their contribution to various biological and geological processes. Here we report a high diversity of magnetotactic bacteria in a freshwater site. Ten out of 18 operational taxonomic units (OTUs) were affiliated with the Deltaproteobacteria. Some rod-shaped bacteria simultaneously synthesized greigite and magnetite magnetosomes. PMID:23377941

  18. Allelic variation contributes to bacterial host specificity

    SciTech Connect

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

  19. Allelic variation contributes to bacterial host specificity

    DOE PAGESBeta

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; et al

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population andmore » functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.« less

  20. Allelic variation contributes to bacterial host specificity

    PubMed Central

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  1. Allelic variation contributes to bacterial host specificity.

    PubMed

    Yue, Min; Han, Xiangan; De Masi, Leon; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S; Fraser, George P; Zhao, Shaohua; McDermott, Patrick F; Weill, François-Xavier; Mainil, Jacques G; Arze, Cesar; Fricke, W Florian; Edwards, Robert A; Brisson, Dustin; Zhang, Nancy R; Rankin, Shelley C; Schifferli, Dieter M

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  2. High diversity and no significant selection signal of human ADH1B gene in Tibet

    PubMed Central

    2012-01-01

    Background ADH1B is one of the most studied human genes with many polymorphic sites. One of the single nucleotide polymorphism (SNP), rs1229984, coding for the Arg48His substitution, have been associated with many serious diseases including alcoholism and cancers of the digestive system. The derived allele, ADH1B*48His, reaches high frequency only in East Asia and Southwest Asia, and is highly associated with agriculture. Micro-evolutionary study has defined seven haplogroups for ADH1B based on seven SNPs encompassing the gene. Three of those haplogroups, H5, H6, and H7, contain the ADH1B*48His allele. H5 occurs in Southwest Asia and the other two are found in East Asia. H7 is derived from H6 by the derived allele of rs3811801. The H7 haplotype has been shown to have undergone significant positive selection in Han Chinese, Hmong, Koreans, Japanese, Khazak, Mongols, and so on. Methods In the present study, we tested whether Tibetans also showed evidence for selection by typing 23 SNPs in the region covering the ADH1B gene in 1,175 individuals from 12 Tibetan populations representing all districts of the Tibet Autonomous Region. Multiple statistics were estimated to examine the gene diversities and positive selection signals among the Tibetans and other populations in East Asia. Results The larger Tibetan populations (Qamdo, Lhasa, Nagqu, Nyingchi, Shannan, and Shigatse) comprised mostly farmers, have around 12% of H7, and 2% of H6. The smaller populations, living on hunting or recently switched to farming, have lower H7 frequencies (Tingri 9%, Gongbo 8%, Monba and Sherpa 6%). Luoba (2%) and Deng (0%) have even lower frequencies. Long-range haplotype analyses revealed very weak signals of positive selection for H7 among Tibetans. Interestingly, the haplotype diversity of H7 is higher in Tibetans than in any other populations studied, indicating a longer diversification history for that haplogroup in Tibetans. Network analysis on the long-range haplotypes revealed

  3. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep.

    PubMed

    Vahidi, S M F; Faruque, M O; Falahati Anbaran, M; Afraz, F; Mousavi, S M; Boettcher, P; Joost, S; Han, J L; Colli, L; Periasamy, K; Negrini, R; Ajmone-Marsan, P

    2016-08-01

    Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7-22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72-0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST  = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes, are discussed. PMID:26953226

  4. Effect of high molecular weight glutenin subunit allelic composition on wheat flour tortilla quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat cultivars possessing quality attributes needed to produce optimum quality tortillas have not been identified. This study investigated the effect of variations in high molecular weight glutenin subunits encoded at the Glu-1 loci (Glu-A1, Glu-B1, Glu-D1) on dough properties and tortilla quality....

  5. High Spatial Genetic Structure and Genetic Diversity in Chinese Populations of Sitobion miscanthi (Hemiptera: Aphididae).

    PubMed

    Wang, Yongmo; Hereward, James P; Zhang, Guoan

    2016-02-01

    The wheat aphid, Sitobion miscanthi Takahashi, a serious wheat pest, was previously considered to be highly migratory and anholocyclic in China. We recorded 69 alleles and 346 multilocus genotypes among 708 aphid individuals from 12 populations in China using 5 microsatellite loci. This genotypic diversity indicates that at least some holocyclic lineages exist. Bayesian clustering analysis revealed that there are two differentiated genetic groups of S. misanthi, one northern and one southern, in China. Principal coordinates analysis of population genetic distance, pairwise F(ST)'s, and network analysis of individual minimum spanning distance also supported the division. Low levels of migration were detected between the northern and southern sampling sites, but the high genetic differentiation does not support the hypothesis S. miscanthi overwinters in the south and migrates to the north in the spring annually. PMID:26487744

  6. Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation

    PubMed Central

    Watson, Corey T.; Steinberg, Karyn M.; Huddleston, John; Warren, Rene L.; Malig, Maika; Schein, Jacqueline; Willsey, A. Jeremy; Joy, Jeffrey B.; Scott, Jamie K.; Graves, Tina A.; Wilson, Richard K.; Holt, Robert A.; Eichler, Evan E.; Breden, Felix

    2013-01-01

    The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3–0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested. PMID:23541343

  7. Mitochondrial DNA genetic diversity and LCT-13910 and deltaF508 CFTR alleles typing in the medieval sample from Poland.

    PubMed

    Płoszaj, T; Jerszyńska, B; Jędrychowska-Dańska, K; Lewandowska, M; Kubiak, D; Grzywnowicz, K; Masłowska, A; Witas, H W

    2015-06-01

    We attempted to confirm the resemblance of a local medieval population and to reconstruct their contribution to the formation of the modern Polish population at the DNA level. The HVR I mtDNA sequence and two nuclear alleles, LCT-13910C/T SNP and deltaF508 CFTR, were chosen as markers since the distribution of selected nuclear alleles varies among ethnic groups. A total of 47 specimens were selected from a medieval cemetery in Cedynia (located in the western Polish lowland). Regarding the HVR I profile, the analyzed population differed from the present-day population (P = 0.045, F(st) = 0.0103), in contrast to lactase persistence (LP) based on the LCT-13910T allele, thus indicating the lack of notable frequency changes of this allele during the last millennium (P = 0.141). The sequence of the HVR I mtDNA fragment allowed to identify six major haplogroups including H, U5, T, K, and HV0 within the medieval population of Cedynia which are common in today's central Europe. An analysis of haplogroup frequency and its comparison with modern European populations shows that the studied medieval population is more closely related to Finno-Ugric populations than to the present Polish population. Identification of less common haplogroups, i.e., Z and U2, both atypical of the modern Polish population and of Asian origin, provides evidence for some kind of connections between the studied and foreign populations. Furthermore, a comparison of the available aDNA sequences from medieval Europe suggests that populations differed from one another and a number of data from other locations are required to find out more about the features of the medieval gene pool profile. PMID:25896719

  8. DRD4 long allele carriers show heightened attention to high-priority items relative to low-priority items.

    PubMed

    Gorlick, Marissa A; Worthy, Darrell A; Knopik, Valerie S; McGeary, John E; Beevers, Christopher G; Maddox, W Todd

    2015-03-01

    Humans with seven or more repeats in exon III of the DRD4 gene (long DRD4 carriers) sometimes demonstrate impaired attention, as seen in attention-deficit hyperactivity disorder, and at other times demonstrate heightened attention, as seen in addictive behavior. Although the clinical effects of DRD4 are the focus of much work, this gene may not necessarily serve as a "risk" gene for attentional deficits, but as a plasticity gene where attention is heightened for priority items in the environment and impaired for minor items. Here we examine the role of DRD4 in two tasks that benefit from selective attention to high-priority information. We examine a category learning task where performance is supported by focusing on features and updating verbal rules. Here, selective attention to the most salient features is associated with good performance. In addition, we examine the Operation Span (OSPAN) task, a working memory capacity task that relies on selective attention to update and maintain items in memory while also performing a secondary task. Long DRD4 carriers show superior performance relative to short DRD4 homozygotes (six or less tandem repeats) in both the category learning and OSPAN tasks. These results suggest that DRD4 may serve as a "plasticity" gene where individuals with the long allele show heightened selective attention to high-priority items in the environment, which can be beneficial in the appropriate context. PMID:25244120

  9. Allele-specific expression assays using Solexa

    PubMed Central

    Main, Bradley J; Bickel, Ryan D; McIntyre, Lauren M; Graze, Rita M; Calabrese, Peter P; Nuzhdin, Sergey V

    2009-01-01

    Background Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans regulatory variation. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation. While ASE is commonly measured via relative fluorescence at a SNP, next generation sequencing provides an opportunity to measure ASE in an accurate and high-throughput manner using read counts. Results We introduce a Solexa-based method to perform large numbers of ASE assays using only a single lane of a Solexa flowcell. In brief, transcripts of interest, which contain a known SNP, are PCR enriched and barcoded to enable multiplexing. Then high-throughput sequencing is used to estimate allele-specific expression using sequencing counts. To validate this method, we measured the allelic bias in a dilution series and found high correlations between measured and expected values (r>0.9, p < 0.001). We applied this method to a set of 5 genes in a Drosophila simulans parental mix, F1 and introgression and found that for these genes the majority of expression divergence can be explained by cis-regulatory variation. Conclusion We present a new method with the capacity to measure ASE for large numbers of assays using as little as one lane of a Solexa flowcell. This will be a valuable technique for molecular and population genetic studies, as well as for verification of genome-wide data sets. PMID:19740431

  10. Highly frequent allelic loss of chromosome 6q16-23 in osteosarcoma: involvement of cyclin C in osteosarcoma.

    PubMed

    Ohata, Norihide; Ito, Sachio; Yoshida, Aki; Kunisada, Toshiyuki; Numoto, Kunihiko; Jitsumori, Yoshimi; Kanzaki, Hirotaka; Ozaki, Toshifumi; Shimizu, Kenji; Ouchida, Mamoru

    2006-12-01

    The molecular pathogenesis of osteosarcoma is very complicated and associated with chaotic abnormalities on many chromosomal arms. We analyzed 12 cases of osteosarcomas with comparative genomic hybridization (CGH) to identify chromosomal imbalances, and detected highly frequent chromosomal alterations in chromosome 6q, 8p, 10p and 10q. To define the narrow rearranged region on chromosome 6 with higher resolution, loss of heterozygosity (LOH) analysis was performed with 21 microsatellite markers. Out of 31 cases, 23 cases (74%) showed allelic loss at least with one marker on chromosome 6q. We identified two distinct commonly deleted regions on chromosome 6 using markers D6S1565 located at 6q16 and 6q23MS1 at 6q23. The expression analysis of genes located at the deleted region was performed, and the decreased mRNA expression of the CCNC gene, one of the regulators of cell cycle, was detected. Growth of osteosarcoma cell line was significantly suppressed after the CCNC cDNA transfection. Fine mapping of the deleted region containing a possible tumor suppressor gene and the transfection assay suggest that the CCNC is a candidate tumor suppressor gene. PMID:17089020

  11. High functional diversity stimulates diversification in experimental microbial communities

    PubMed Central

    Jousset, Alexandre; Eisenhauer, Nico; Merker, Monika; Mouquet, Nicolas; Scheu, Stefan

    2016-01-01

    There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available. PMID:27386573

  12. High functional diversity stimulates diversification in experimental microbial communities.

    PubMed

    Jousset, Alexandre; Eisenhauer, Nico; Merker, Monika; Mouquet, Nicolas; Scheu, Stefan

    2016-06-01

    There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available. PMID:27386573

  13. High incidence of lung, bone, and lymphoid tumors in transgenic mice overexpressing mutant alleles of the p53 oncogene.

    PubMed Central

    Lavigueur, A; Maltby, V; Mock, D; Rossant, J; Pawson, T; Bernstein, A

    1989-01-01

    We have investigated the role of the p53 gene in oncogenesis in vivo by generating transgenic mice carrying murine p53 genomic fragments isolated from a mouse Friend erythroleukemia cell line or BALB/c mouse liver DNA. Elevated levels of p53 mRNA were detected in several tissues of two transgenic lines tested. Increased levels of p53 protein were also detected in most of the tissues analyzed by Western blotting (immunoblotting). Because both transgenes encoded p53 proteins that were antigenically distinct from wild-type p53, it was possible to demonstrate that overexpression of the p53 protein was mostly, if not entirely, due to the expression of the transgenes. Neoplasms developed in 20% of the transgenic mice, with a high incidence of lung adenocarcinomas, osteosarcomas, and lymphomas. Tissues such as ovaries that expressed the transgene at high levels were not at higher risk of malignant transformation than tissues expressing p53 protein at much lower levels. The long latent period and low penetrance suggest that overexpression of p53 alone is not sufficient to induce malignancies and that additional events are required. These observations provide direct evidence that mutant alleles of the p53 oncogene have oncogenic potential in vivo and that different cell types show intrinsic differences in susceptibility to malignant transformation by p53. Since recent data suggest that p53 may be a recessive oncogene, it is possible that the elevated tumor incidence results from functional inactivation of endogenous p53 by overexpression of the mutant transgene. The high incidence of lung and bone tumors suggests that p53 transgenic mice may provide a useful model to investigate the molecular events that underlie these malignancies in humans. Images PMID:2476668

  14. Mississippian coral latitudinal diversity gradients (western interior United States): Testing the limits of high resolution diversity data

    USGS Publications Warehouse

    Webb, G.E.; Sando, W.J.; Raymond, A.

    1997-01-01

    Analysis of high resolution diversity data for Mississippian corals in the western interior United States yielded mild latitudinal diversity gradients despite the small geographic area covered by samples and a large influence on diversity patterns by geographic sampling intensity (sample bias). Three competing plate tectonic reconstructions were tested using the diversity patterns. Although none could be forcefully rejected, one reconstruction proved less consistent with diversity patterns than the other two and additional coral diversity data from farther north in Canada would better discriminate the two equivalent reconstructions. Despite the relatively high sampling intensity represented by the analyzed database, diversity patterns were greatly affected by sample abundance and distribution. Hence, some effort at recognizing and accounting for sample bias should be undertaken in any study of latitudinal diversity gradients. Small-scale geographic lumping of sample localities had only small effects on geographic diversity patterns. However, large-scale (e.g., regional) geographic lumping of diversity data may not yield latitudinally sensitive diversity patterns. Temporal changes in coral diversity in this region reflect changes in eustacy, local tectonism, and terrigenous sediment flux, far more than they do shifting latitude. Highest regional diversity occurred during the interval when the studied region occupied the highest latitude. Therefore, diversity data from different regions may not be comparable, in terms of latitudinal inference. Small-scale stratigraphic lumping of the data caused a nearly complete loss of the latitudinal diversity patterns apparent prior to lumping. Hence, the narrowest possible stratigraphic resolution should be maintained in analyzing latitudinal diversity gradients.

  15. High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding.

    PubMed

    Mengistu, Dejene Kassahun; Kidane, Yosef Gebrehawaryat; Catellani, Marcello; Frascaroli, Elisabetta; Fadda, Carlo; Pè, Mario Enrico; Dell'Acqua, Matteo

    2016-09-01

    Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome-specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome-wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker-assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat. PMID:26853077

  16. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    PubMed

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists. PMID:23487323

  17. Maintaining High Challenge and High Support for Diverse Learners

    ERIC Educational Resources Information Center

    Athanases, Steven

    2012-01-01

    As teachers, schools and school leaders work to better prepare California's culturally and linguistically diverse students, methods for doing so vary widely. One approach prioritizes safe spaces, welcoming environments, well-structured routines--school and classroom culture features essential for students' well-being. A second key priority, often…

  18. High-resolution HLA-DRB1 genotyping in an Australian inclusion body myositis (s-IBM) cohort: an analysis of disease-associated alleles and diplotypes.

    PubMed

    Rojana-udomsart, Arada; James, Ian; Castley, Alison; Needham, Merrilee; Scott, Adrian; Day, Timothy; Kiers, Lynette; Corbett, Alastair; Sue, Carolyn; Witt, Campbell; Martinez, Patricia; Christiansen, Frank; Mastaglia, Frank

    2012-09-15

    We performed high-resolution (4-digit) HLA-DRB1 genotyping in an Australian cohort of 105s-IBM patients and 189 controls. Our findings showed that whilst the strongest association was with the HLA-DRB1*03:01 allele and the HLA-DRB1*03:01/*01:01 diplotype, HLA-DRB1*01:01 and HLA-DRB1*13:01 are also risk alleles. A number of other alleles, HLA-DRB1*04:01, *04:04, *07:01, *09:01, *11:01 and *15:01, as well as the HLA-DRB1*03:01/*04:01 and HLA-DRB1*03:01/*07:01 diplotypes were reduced in s-IBM cases and may be protective. The HLA-DRB1*03:01 and HLA-DRB1*13:01 alleles also appear to have an influence on the age at onset of the disease and severity of muscle weakness. Our findings indicate that the influence of HLA-DRB1 in s-IBM is complex and that epistatic interactions at the HLA-DRB1 locus contribute both to disease susceptibility and to the clinical phenotype. PMID:22633068

  19. Global marine bacterial diversity peaks at high latitudes in winter

    PubMed Central

    Ladau, Joshua; Sharpton, Thomas J; Finucane, Mariel M; Jospin, Guillaume; Kembel, Steven W; O'Dwyer, James; Koeppel, Alexander F; Green, Jessica L; Pollard, Katherine S

    2013-01-01

    Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms. PMID:23514781

  20. High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region

    PubMed Central

    Douaihy, Bouchra; Vendramin, Giovanni G.; Boratyński, Adam; Machon, Nathalie; Bou Dagher-Kharrat, Magda

    2011-01-01

    Background and aims Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation. Methodology Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine. Principal results Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were Na=8.78 and He=0.76, respectively. The fixation index showed a significant deviation from Hardy–Weinberg equilibrium and an excess of homozygotes (FIS=0.27–0.56). A moderate level of genetic differentiation was observed among the populations (FST=0.075, P<0.001). The most differentiated populations corresponded to old vestigial stands found at the tree line (>2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters. Conclusions High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish–southeastern European populations. PMID:22476474

  1. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigers to Bt Soybean in Brazil.

    PubMed

    Dourado, Patrick M; Bacalhau, Fabiana B; Amado, Douglas; Carvalho, Renato A; Martinelli, Samuel; Head, Graham P; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL-1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  2. High Susceptibility to Cry1Ac and Low Resistance Allele Frequency Reduce the Risk of Resistance of Helicoverpa armigers to Bt Soybean in Brazil

    PubMed Central

    Bacalhau, Fabiana B.; Amado, Douglas; Carvalho, Renato A.; Martinelli, Samuel; Head, Graham P.; Omoto, Celso

    2016-01-01

    The Old World bollworm, Helicoverpa armigera (Hübner), was recently introduced into Brazil, where it has caused extensive damage to cotton and soybean crops. MON 87701 × MON 89788 soybean, which expresses the Bt protein Cry1Ac, was recently deployed in Brazil, providing high levels of control against H. armigera. To assess the risk of resistance to the Cry1Ac protein expressed by MON 87701 × MON 89788 soybean in Brazil, we conducted studies to evaluate the baseline susceptibility of H. armigera to Cry1Ac, in planta efficacy including the assessment of the high-dose criterion, and the initial resistance allele frequency based on an F2 screen. The mean Cry1Ac lethal concentration (LC50) ranged from 0.11 to 1.82 μg·mL−1 of diet among all H. armigera field populations collected from crop seasons 2013/14 to 2014/15, which indicated about 16.5-fold variation. MON 87701 × MON 89788 soybean exhibited a high level of efficacy against H. armigera and most likely met the high dose criterion against this target species in leaf tissue dilution bioassays up to 50 times. A total of 212 F2 family lines of H. armigera were established from field collections sampled from seven locations across Brazil and were screened for the presence of MON 87701 × MON 89788 soybean resistance alleles. None of the 212 families survived on MON 87701 × MON 89788 soybean leaf tissue (estimated allele frequency = 0.0011). The responses of H. armigera to Cry1Ac protein, high susceptibility to MON 87701 × MON 89788 soybean, and low frequency of resistance alleles across the main soybean-producing regions support the assumptions of a high-dose/refuge strategy. However, maintenance of reasonable compliance with the refuge recommendation will be essential to delay the evolution of resistance in H. armigera to MON 87701 × MON 89788 soybean in Brazil. PMID:27532632

  3. Common chimpanzees have greater diversity than humans at two of the three highly polymorphic MHC class I genes.

    PubMed

    Adams, E J; Cooper, S; Thomson, G; Parham, P

    2000-05-01

    MHC class I polymorphism improves the defense of vertebrate species against viruses and other intracellular pathogens. To see how polymorphism at the same class I genes can evolve in different species we compared the MHC-A, MHC-B, and MHC-C loci of common chimpanzees and humans. Diversity in 23 Patr-A, 32 Patr-B, and 18 Patr-C alleles obtained from study of 48 chimpanzees was compared to diversity in 66 HLA-A, 149 HLA-B, and 41 HLA-C alleles obtained from a study of over 1 million humans. At each locus, alleles group hierarchically into families and then lineages. No alleles or families are shared by the two species, commonality being seen only at the lineage level. The overall nucleotide sequence diversity of MHC class I is estimated to be greater for modern chimpanzees than humans. Considering the numbers of lineages, families, and alleles, Patr-B and Patr-C have greater diversity than the HLA-B and HLA-C, respectively. In contrast, Patr-A has less polymorphism than HLA-A, due to the absence of A2 lineage alleles. The results are consistent with ancestral humans having passed through a narrower population bottleneck than chimpanzees, and with pathogen-mediated selection having favored either preservation of A2 lineage alleles on the human line and/or their extinction on the chimpanzee line. PMID:10866107

  4. Melting Curve Analysis after T Allele Enrichment (MelcaTle) as a Highly Sensitive and Reliable Method for Detecting the JAK2V617F Mutation

    PubMed Central

    Morishita, Soji; Takahashi, Kochi; Araki, Marito; Hironaka, Yumi; Sunami, Yoshitaka; Edahiro, Yoko; Tsutsui, Miyuki; Ohsaka, Akimichi; Tsuneda, Satoshi; Komatsu, Norio

    2015-01-01

    Detection of the JAK2V617F mutation is essential for diagnosing patients with classical myeloproliferative neoplasms (MPNs). However, detection of the low-frequency JAK2V617F mutation is a challenging task due to the necessity of discriminating between true-positive and false-positive results. Here, we have developed a highly sensitive and accurate assay for the detection of JAK2V617F and named it melting curve analysis after T allele enrichment (MelcaTle). MelcaTle comprises three steps: 1) two cycles of JAK2V617F allele enrichment by PCR amplification followed by BsaXI digestion, 2) selective amplification of the JAK2V617F allele in the presence of a bridged nucleic acid (BNA) probe, and 3) a melting curve assay using a BODIPY-FL-labeled oligonucleotide. Using this assay, we successfully detected nearly a single copy of the JAK2V617F allele, without false-positive signals, using 10 ng of genomic DNA standard. Furthermore, MelcaTle showed no positive signals in 90 assays screening healthy individuals for JAK2V617F. When applying MelcaTle to 27 patients who were initially classified as JAK2V617F-positive on the basis of allele-specific PCR analysis and were thus suspected as having MPNs, we found that two of the patients were actually JAK2V617F-negative. A more careful clinical data analysis revealed that these two patients had developed transient erythrocytosis of unknown etiology but not polycythemia vera, a subtype of MPNs. These findings indicate that the newly developed MelcaTle assay should markedly improve the diagnosis of JAK2V617F-positive MPNs. PMID:25794279

  5. [Agrobacterium rubi strains from blueberry plants are highly diverse].

    PubMed

    Abrahamovich, Eliana; López, Ana C; Alippi, Adriana M

    2014-01-01

    The diversity of a collection of Agrobacterium rubi strains isolated from blueberries from different regions of Argentina was studied by conventional microbiological tests and molecular techniques. Results from biochemical and physiological reactions, as well as from rep-PCR and RFLP analysis of PCR-amplified 23S rDNA showed high phenotypic and genotypic intraspecific variation. PMID:25444133

  6. 132. FORKS DIVERSION, HIGH LINE AND LOW LINE CANALS, TWIN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    132. FORKS DIVERSION, HIGH LINE AND LOW LINE CANALS, TWIN FALLS COUNTY, SOUTH OF HANSEN, IDAHO; POWER GATES FOR HYDRO-ELECTRIC. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

  7. High plant diversity in Eocene South America: Evidence from Patagonia

    USGS Publications Warehouse

    Wilf, P.; Cuneo, N.R.; Johnson, K.R.; Hicks, J.F.; Wing, S.L.; Obradovich, J.D.

    2003-01-01

    Tropical South America has the highest plant diversity of any region today, but this richness is usually characterized as a geologically recent development (Neogene or Pleistocene). From caldera-lake beds exposed at Laguna del Hunco in Patagonia, Argentina, paleolatitude ???47??S, we report 102 leaf species. Radioisotopic and paleomagnetic analyses indicate that the flora was deposited 52 million years ago, the time of the early Eocene climatic optimum, when tropical plant taxa and warm, equable climates reached middle latitudes of both hemispheres. Adjusted for sample size, observed richness exceeds that of any other Eocene leaf flora, supporting an ancient history of high plant diversity in warm areas of South America.

  8. Cohabitation promotes high diversity of clownfishes in the Coral Triangle.

    PubMed

    Camp, Emma F; Hobbs, Jean-Paul A; De Brauwer, Maarten; Dumbrell, Alex J; Smith, David J

    2016-03-30

    Global marine biodiversity peaks within the Coral Triangle, and understanding how such high diversity is maintained is a central question in marine ecology. We investigated broad-scale patterns in the diversity of clownfishes and their host sea anemones by conducting 981 belt-transects at 20 locations throughout the Indo-Pacific. Of the 1508 clownfishes encountered, 377 fish occurred in interspecific cohabiting groups and cohabitation was almost entirely restricted to the Coral Triangle. Neither the diversity nor density of host anemone or clownfish species alone influenced rates of interspecific cohabitation. Rather cohabitation occurred in areas where the number of clownfish species exceeds the number of host anemone species. In the Coral Triangle, cohabiting individuals were observed to finely partition their host anemone, with the subordinate species inhabiting the periphery. Furthermore, aggression did not increase in interspecific cohabiting groups, instead dominant species were accepting of subordinate species. Various combinations of clownfish species were observed cohabiting (independent of body size, phylogenetic relatedness, evolutionary age, dentition, level of specialization) in a range of anemone species, thereby ensuring that each clownfish species had dominant reproductive individuals in some cohabiting groups. Clownfishes are obligate commensals, thus cohabitation is an important process in maintaining biodiversity in high diversity systems because it supports the persistence of many species when host availability is limiting. Cohabitation is a likely explanation for high species richness in other obligate commensals within the Coral Triangle, and highlights the importance of protecting these habitats in order to conserve unique marine biodiversity. PMID:27030417

  9. Dissemination of the highly expressed Bx7 glutenin subunit (Glu-B1al allele) in wheat as revealed by novel PCR markers and RP-HPLC.

    PubMed

    Butow, B J; Gale, K R; Ikea, J; Juhász, A; Bedö, Z; Tamás, L; Gianibelli, M C

    2004-11-01

    Increased expression of the high molecular weight glutenin subunit (HMW-GS) Bx7 is associated with improved dough strength of wheat (Triticum aestivum L.) flour. Several cultivars and landraces of widely different genetic backgrounds from around the world have now been found to contain this so-called 'over-expressing' allelic form of the Bx7 subunit encoded by Glu-B1al. Using three methods of identification, SDS-PAGE, RP-HPLC and PCR marker analysis, as well as pedigree information, we have traced the distribution and source of this allele from a Uruguayan landrace, Americano 44D, in the mid-nineteenth century. Results are supported by knowledge of the movement of wheat lines with migrants. All cultivars possessing the Glu-B1al allele can be identified by the following attributes: (1) the elution of the By sub-unit peak before the Dx sub-unit peak by RP-HPLC, (2) high expression levels of Bx7 (>39% Mol% Bx), (3) a 43 bp insertion in the matrix-attachment region (MAR) upstream of the gene promoter relative to Bx7 and an 18 bp nucleotide duplication in the coding region of the gene. Evidence is presented indicating that these 18 and 43 bp sequence insertions are not causal for the high expression levels of Bx7 as they were also found to be present in a small number of hexaploid species, including Chinese Spring, and species expressing Glu-B1ak and Glu-B1a alleles. In addition, these sequence inserts were found in different isolates of the tetraploid wheat, T. turgidum, indicating that these insertion/deletion events occurred prior to hexaploidization. PMID:15340686

  10. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes

    PubMed Central

    2014-01-01

    Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our

  11. Allele mining and enhanced genetic recombination for rice breeding.

    PubMed

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources. PMID:26606925

  12. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi

    PubMed Central

    Telleria, Jenny; Biron, David G.; Brizard, Jean-Paul; Demettre, Edith; Séveno, Martial; Barnabé, Christian; Ayala, Francisco J.; Tibayrenc, Michel

    2010-01-01

    We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi–subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10−4) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens. PMID:21059959

  13. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi.

    PubMed

    Telleria, Jenny; Biron, David G; Brizard, Jean-Paul; Demettre, Edith; Séveno, Martial; Barnabé, Christian; Ayala, Francisco J; Tibayrenc, Michel

    2010-11-23

    We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi-subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10(-4)) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens. PMID:21059959

  14. A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

    PubMed Central

    Harrang, Estelle; Lapègue, Sylvie; Morga, Benjamin; Bierne, Nicolas

    2013-01-01

    Marine bivalves show among the greatest allozyme diversity ever reported in Eukaryotes, putting them historically at the heart of the neutralist−selectionist controversy on the maintenance of genetic variation. Although it is now acknowledged that this high diversity is most probably a simple consequence of a large population size, convincing support for this explanation would require a rigorous assessment of the silent nucleotide diversity in natural populations of marine bivalves, which has not yet been done. This study investigated DNA sequence polymorphism in a set of 37 nuclear loci in wild samples of the flat oyster Ostrea edulis. Silent diversity was found to be only moderate (0.7%), and there was no departure from demographic equilibrium under the Wright-Fisher model, suggesting that the effective population size might not be as large as might have been expected. In accordance with allozyme heterozygosity, nonsynonymous diversity was comparatively very high (0.3%), so that the nonsynonymous to silent diversity ratio reached a value rarely observed in any other organism. We estimated that one-quarter of amino acid-changing mutations behave as neutral in O. edulis, and as many as one-third are sufficiently weakly selected to segregate at low frequency in the polymorphism. Finally, we inferred that one oyster is expected to carry more than 4800 non-neutral alleles (or 4.2 cM−1). We conclude that a high load of segregating non-neutral amino-acid polymorphisms contributes to high protein diversity in O. edulis. The high fecundity of marine bivalves together with an unpredictable and highly variable success of reproduction and recruitment (sweepstakes reproduction) might produce a greater decoupling between Ne and N than in other organisms with lower fecundities, and we suggest this could explain why a higher segregating load could be maintained for a given silent mutation effective size. PMID:23390609

  15. Diversity in a Variable-Number Tandem Repeat from Yersinia pestis

    PubMed Central

    Adair, D. M.; Worsham, P. L.; Hill, K. K.; Klevytska, A. M.; Jackson, P. J.; Friedlander, A. M.; Keim, P.

    2000-01-01

    We have identified a tetranucleotide repeat sequence, (CAAA)N, in the genome of Yersinia pestis, the causative agent of plague. This variable-number tandem repeat (VNTR) region has nine alleles and great diversity (calculated as 1 minus the sum of the squared allele frequencies) (diversity value, 0.82) within a set of 35 diverse Y. pestis strains. In contrast, the nucleotide sequence of the lcrV (low-calcium-response) gene differed only slightly among these strains, having a haplotype diversity value of 0.17. Replicated cultures, phenotypic variants of particular strains, and extensively cultured replicates within strains did not differ in VNTR allele type. Thus, while a high mutation rate must contribute to the great diversity of this locus, alleles appear stable under routine laboratory culture conditions. The classic three plague biovars did not have single identifying alleles, although there were allelic biases within biovar categories. The antiqua biovar was the most diverse, with four alleles observed in 5 strains, while the orientalis and mediaevalis biovars exhibited five alleles in 21 strains and three alleles in 8 strains, respectively. The CAAA VNTR is located immediately adjacent to the transcriptional promoters for flanking open reading frames and may affect their activity. This VNTR marker may provide a high-resolution tool for epidemiological analyses of plague. PMID:10747136

  16. The 894T allele of endothelial nitric oxide synthase gene is related to left ventricular mass in African Americans with high-normal blood pressure.

    PubMed Central

    Lapu-Bula, Rigobert; Quarshie, Alexander; Lyn, Deborah; Oduwole, Adefisayo; Pack, Cheryl; Morgan, Jan; Nkemdiche, Sunday; Igho-Pemu, Priscilla; Onwuanyi, Anekwe; Li, Rongling; Ofili, Elizabeth

    2005-01-01

    BACKGROUND AND OBJECTIVES: The 894T allele in exon 7 of the endothelial nitric oxide synthase (eNOS) gene has been inconsistently associated with hypertension in different racial groups. Because high-normal blood pressure (BP) confers an increased risk for the development of hypertension and other cardiovascular disorders, including left ventricular hypertrophy (LVH), we tested the hypothesis that the allelic variation (894T) in the eNOS gene would directly correlate with alterations in LV mass (LVM) in individuals with high-normal BP. METHODS: Genotype distribution of G894T was compared between 20 African Americans (10 females/10 males) with high-normal BP (systolic BP of 130-139 and/or diastolic BP of 85-89 mmHg) and 64 counterparts (37 females/27 males) with normal BP (<130/85 mmHg). Echocardiographic LVM was calculated (Devereux formula) and indexed to body surface area to define the presence of LVH (LVMI >134/110 g/m2 for men/women). RESULTS: For the entire group, the 894T allelic frequencies (15, 48%) and G894T genotype distributions were consistent with the Hardy-Weinberg equilibrium expectations (estimated disequilibrium coefficient = 0.0118, P=0.40). LVMI was significantly higher in homozygous carriers (TT) of the rare 894T allele (n = 3 females/0 males) than in heterozygous GT (n = 13 females/7 males) and individuals bearing the GG (n=34 females/27 males) variant (124 +/- 70 vs. 82 +/- 24 and 82 +/- 19 g/m2, respectively, P < 0.05). The observed relationship between eNOS 894T allele and LVMI was restricted to individuals with high-normal BP (r = 0.94, P = 0.03) but not in those with normal BP (r = 0.39, P =0.64), by analysis of variance (ANOVA) after adjusting for age, gender, body mass index, smoking and systolic BP. CONCLUSION: These findings, not previously described, provide important preliminary evidence to suggest an increased susceptibility to LVH in African Americans who carry the 894T variant of the eNOS gene and have high-normal blood pressure

  17. Allele-specific extension allows base-pair neutral homozygotes to be discriminated by high-resolution melting of small amplicons.

    PubMed

    Cai, Yanning; Yuan, Yanpeng; Lin, Qingling; Chan, Piu

    2010-11-01

    Not all single-nucleotide polymorphisms (SNPs) can be determined using high-resolution melting (HRM) of small amplicons, especially class 3 and 4 SNPs. This is due mainly to the small shift in the melting temperature (Tm) between two types of homozygote. Choosing rs1869458 (a class 4 SNP) as a sample, we developed a modified small amplicon HRM assay. An allele-specific extension (ASE) primer, which ended at an SNP site and matched only one of the alleles, was added to the reaction as well as additional thermal steps for ASE. Following asymmetric polymerase chain reaction and melting curve analysis, heterozygotes were easily identified. Two types of homozygote were also distinguishable, indicating that extension primers 11 to 13 bases in length worked efficiently in an allele-specific way. Modification of the limiting amplification primer with locked nucleic acid increased the Tm difference between extension and amplification peaks and facilitated subsequent genotyping. In addition, 194 human genomic DNA samples were genotyped with the developed assay and by direct sequencing, with the different methods providing identical genotyping results. In conclusion, ASE-HRM is a simple, inexpensive, closed-tube genotyping method that can be used to examine all types of SNP. PMID:20599636

  18. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib

    PubMed Central

    Vasudevan, Kumar; Vera Cruz, Casiana M.; Gruissem, Wilhelm; Bhullar, Navreet K.

    2016-01-01

    Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level. PMID:27446145

  19. High-order species interactions shape ecosystem diversity.

    PubMed

    Bairey, Eyal; Kelsic, Eric D; Kishony, Roy

    2016-01-01

    Classical theory shows that large communities are destabilized by random interactions among species pairs, creating an upper bound on ecosystem diversity. However, species interactions often occur in high-order combinations, whereby the interaction between two species is modulated by one or more other species. Here, by simulating the dynamics of communities with random interactions, we find that the classical relationship between diversity and stability is inverted for high-order interactions. More specifically, while a community becomes more sensitive to pairwise interactions as its number of species increases, its sensitivity to three-way interactions remains unchanged, and its sensitivity to four-way interactions actually decreases. Therefore, while pairwise interactions lead to sensitivity to the addition of species, four-way interactions lead to sensitivity to species removal, and their combination creates both a lower and an upper bound on the number of species. These findings highlight the importance of high-order species interactions in determining the diversity of natural ecosystems. PMID:27481625

  20. High-order species interactions shape ecosystem diversity

    PubMed Central

    Bairey, Eyal; Kelsic, Eric D.; Kishony, Roy

    2016-01-01

    Classical theory shows that large communities are destabilized by random interactions among species pairs, creating an upper bound on ecosystem diversity. However, species interactions often occur in high-order combinations, whereby the interaction between two species is modulated by one or more other species. Here, by simulating the dynamics of communities with random interactions, we find that the classical relationship between diversity and stability is inverted for high-order interactions. More specifically, while a community becomes more sensitive to pairwise interactions as its number of species increases, its sensitivity to three-way interactions remains unchanged, and its sensitivity to four-way interactions actually decreases. Therefore, while pairwise interactions lead to sensitivity to the addition of species, four-way interactions lead to sensitivity to species removal, and their combination creates both a lower and an upper bound on the number of species. These findings highlight the importance of high-order species interactions in determining the diversity of natural ecosystems. PMID:27481625

  1. Allele and haplotype diversity of new multiplex of 19 ChrX-STR loci in Han population from Guanzhong region (China).

    PubMed

    Zhang, Yu-Dang; Shen, Chun-Mei; Meng, Hao-Tian; Guo, Yu-Xin; Dong, Qian; Yang, Guang; Yan, Jiang-Wei; Liu, Yao-Shun; Mei, Ting; Huang, Rui-Zhe; Zhu, Bo-Feng

    2016-07-01

    X-chromosomal short tandem repeats (X-STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X-STR loci (DXS10148-DXS10135-DXS8378, DXS10159-DXS10162-DXS10164, DXS7132-DXS10079-DXS10074-DXS10075, DXS6809-DXS6789, DXS7424-DXS101, DXS10103-HPRTB-DXS10101 and DXS7423-DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy-Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X-STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa. PMID:27063464

  2. Sousse, Tunisia: tumultuous history and high Y-STR diversity.

    PubMed

    Fadhlaoui-Zid, Karima; Chennakrishnaiah, Shilpa; Zemni, Ramzi; Grinberg, Sagy; Herrera, Rene J; Benammar-Elgaaied, Amel

    2012-12-01

    In the present study, 17 Y-chromosomal STR (Y-STR) loci were typed in 218 unrelated males from Sousse, Central-East Tunisia, to evaluate forensic and population genetic applications of the data. A total of 154 different haplotypes were identified, 127 (82.5%) of which were unique, with the most frequent haplotype occurring in 14 individuals (6.4%). The locus diversity ranged from 0.2050 at DYS392 to 0.8760 at DYS385. The haplotype diversity at the 17-loci resolution was calculated to be 0.9916, while the corresponding values for the extended (11 loci) and minimal (9 loci) haplotypes were estimated at 0.9735 and 0.9710, respectively. Comparison with 29 regional and global populations using correspondence analysis, neighbor joining (NJ) tree, and Rst genetic distance revealed that the Sousse population is highly diverse. This finding is consistent with historical data. Furthermore, the results of this study indicate a distinct genetic substructure among Tunisian populations. In conclusion, the present study demonstrated that the 17 Y-STRs analyzed are highly informative for individual identification, parentage analysis, and population genetic studies. PMID:23160959

  3. High plant diversity in Eocene South America: evidence from Patagonia.

    PubMed

    Wilf, Peter; Cúneo, N Rubén; Johnson, Kirk R; Hicks, Jason F; Wing, Scott L; Obradovich, John D

    2003-04-01

    Tropical South America has the highest plant diversity of any region today, but this richness is usually characterized as a geologically recent development (Neogene or Pleistocene). From caldera-lake beds exposed at Laguna del Hunco in Patagonia, Argentina, paleolatitude approximately 47 degrees S, we report 102 leaf species. Radioisotopic and paleomagnetic analyses indicate that the flora was deposited 52 million years ago, the time of the early Eocene climatic optimum, when tropical plant taxa and warm, equable climates reached middle latitudes of both hemispheres. Adjusted for sample size, observed richness exceeds that of any other Eocene leaf flora, supporting an ancient history of high plant diversity in warm areas of South America. PMID:12677065

  4. Rare Species Support Vulnerable Functions in High-Diversity Ecosystems

    PubMed Central

    Mouillot, David; Bellwood, David R.; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C. E. Timothy; Renaud, Julien; Thuiller, Wilfried

    2013-01-01

    Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

  5. Diversion assumptions for high-powered research reactors

    SciTech Connect

    Binford, F.T.

    1984-01-01

    This study deals with diversion assumptions for high-powered research reactors -- specifically, MTR fuel; pool- or tank-type research reactors with light-water moderator; and water, beryllium, or graphite reflectors, and which have a power level of 25 MW(t) or more. The objective is to provide assistance to the IAEA in documentation of criteria and inspection observables related to undeclared plutonium production in the reactors described above, including: criteria for undeclared plutonium production, necessary design information for implementation of these criteria, verification guidelines including neutron physics and heat transfer, and safeguards measures to facilitate the detection of undeclared plutonium production at large research reactors.

  6. High-Level Genetic Diversity among Invasive Streptococcus pneumoniae Isolates in Turkey.

    PubMed

    Guldemir, Dilek; Acar, Sumeyra; Otgun, Selin Nar; Unaldi, Ozlem; Gozalan, Aysegul; Ertek, Mustafa; Durmaz, Riza

    2016-05-20

    This study obtained information on the serotypes and molecular typing characteristics of Streptococcus pneumoniae strains causing invasive diseases in Turkey. Sixty-eight S. pneumoniae isolates causing invasive pneumococcal diseases were collected from different regions of Turkey from 2009 to 2011. The isolates were characterized by performing multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and capsular serotyping, and 25 different serotypes were identified. Serotypes 19F, 23F, 1, 14, and 7F were common and accounted for 52.9% of all the serotypes. In addition, 54 different PFGE profiles (pulsotypes) were observed. Twenty-three of the 68 (33.8%) isolates were clustered into 9 pulsotypes. MLST analysis yielded 36 sequence types, of which 12 (33.3%) were novel. A comparison of results with the global pneumococcal MLST database by performing eBURST analysis showed that our strains belonged to 20 different clonal complexes and 5 singletons. In addition, we identified 4 new alleles: 2 gdh, 1 xpt, and 1 ddl. Thus, the results of this study highlighted a high level of diversity among pneumococcal isolates. In addition, the study identified a case of possible capsular switching. PMID:26255730

  7. Understanding Students' Precollege Experiences with Racial Diversity: The High School as Microsystem

    ERIC Educational Resources Information Center

    Park, Julie J.; Chang, Stephanie H.

    2015-01-01

    Few qualitative studies consider how high school experiences affect readiness for diversity engagement in college. Using data from an ethnographic case study, three central trends (student experiences within homogeneous high schools, racial divisions within diverse high schools, and students who attended diverse high schools but had little…

  8. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

    PubMed Central

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A.; Catenacci, Daniel V. T.; Hudson, Richard R.; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-01-01

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 “polymorphic” SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors. PMID:26561581

  9. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

    PubMed

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A; Catenacci, Daniel V T; Hudson, Richard R; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-11-24

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors. PMID:26561581

  10. Uncommon HLA alleles identified by hemizygous ultra-high Sanger sequencing: haplotype associations and reconsideration of their assignment in the Common and Well-Documented catalogue.

    PubMed

    Voorter, Christina E M; Groeneweg, Mathijs; Groeneveld, Lisette; Tilanus, Marcel G J

    2016-02-01

    Although the number of HLA alleles still increases, many of them have been reported being uncommon. This is partly due to lack of full length gene sequencing, especially for those alleles belonging to an allele ambiguity in which the first discovered allele has been assigned as the most frequent one. As members of the working group on Common and Well Documented (CWD) alleles and since we implemented full length group-specific sequencing as standard method routinely, we have investigated the presence of presumably rare alleles in our collection of HLA typing data. We identified 50 alleles, that were not previously encountered as Common or Well Documented. Sixteen of them should be added to the CWD catalogue, since we encountered them in 5 or more unrelated individuals. Another 11 could be added, based upon our results and the data present in the IMGT database and the rare allele section of the allele frequencies database. Furthermore, tight associations were observed between several different alleles even at the level of synonymous and non-coding sequences. In addition, in several cases the uncommon allele was found to be more frequent than its common counterpart. PMID:26610902

  11. Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC)

    PubMed Central

    Michelacci, Valeria; Orsini, Massimiliano; Knijn, Arnold; Delannoy, Sabine; Fach, Patrick; Caprioli, Alfredo; Morabito, Stefano

    2016-01-01

    Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC. PMID:26941726

  12. Highly specialized microbial diversity in hyper-arid polar desert

    PubMed Central

    Pointing, Stephen B.; Chan, Yuki; Lacap, Donnabella C.; Lau, Maggie C. Y.; Jurgens, Joel A.; Farrell, Roberta L.

    2009-01-01

    The McMurdo Dry Valleys in Antarctica are a cold hyperarid polar desert that present extreme challenges to life. Here, we report a culture-independent survey of multidomain microbial biodiversity in McKelvey Valley, a pristine example of the coldest desert on Earth. We demonstrate that life has adapted to form highly-specialized communities in distinct lithic niches occurring concomitantly within this terrain. Endoliths and chasmoliths in sandstone displayed greatest diversity, whereas soil was relatively depauperate and lacked a significant photoautotrophic component, apart from isolated islands of hypolithic cyanobacterial colonization on quartz rocks in soil contact. Communities supported previously unreported polar bacteria and fungi, but archaea were absent from all niches. Lithic community structure did not vary significantly on a landscape scale and stochastic moisture input due to snowmelt resulted in increases in colonization frequency without significantly affecting diversity. The findings show that biodiversity near the cold-arid limit for life is more complex than previously appreciated, but communities lack variability probably due to the high selective pressures of this extreme environment. PMID:19850879

  13. High Diversity of Fungi in Air Particulate Matter

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Despres, V. R.; Pöschl, U.

    2009-04-01

    Fungal spores account for large proportions of air particulate matter, and they influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, hardly known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse and more human pathogens and allergens in the respirable fine particle fraction (< 3 µm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere. References: Després, V.R., J.F. Nowoisky, M. Klose, R. Conrad, M.O. Andreae, U. Pöschl, Characterization of primary biogenic aerosol particles in urban, rural, and high-alpine air by DNA sequence and restriction fragment analysis of ribosomal RNA genes, Biogeosciences, 4, 1127-1141, 2007. Elbert, W., P. E. Taylor, M. O. Andreae, U. Pöschl, Contribution of fungi to primary biogenic aerosols in the atmosphere: wet and dry discharged spores, carbohydrates, and inorganic ions, Atmospheric Chemistry and Physics, 7, 4569-4588, 2007. Fröhlich-Nowoisky, J. Despres, V.R., Pöschl, U.: High diversity of fungi in air particulate matter, Proceedings of the National Academy of Sciences, submitted, 2008.

  14. Predator Diversity and Abundance Provide Little Support for the Enemies Hypothesis in Forests of High Tree Diversity

    PubMed Central

    Schuldt, Andreas; Both, Sabine; Bruelheide, Helge; Härdtle, Werner; Schmid, Bernhard; Zhou, Hongzhang; Assmann, Thorsten

    2011-01-01

    Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity—and thus information on the relevance of experimental findings—for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25–69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes) of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis—derived from studies in less diverse ecosystems—of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species-rich forest

  15. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  16. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

    PubMed Central

    Hodgson, Jason A.; Pickrell, Joseph K.; Pearson, Laurel N.; Quillen, Ellen E.; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D.; Perry, George H.

    2014-01-01

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  17. High herbivore density associated with vegetation diversity in interglacial ecosystems

    PubMed Central

    Sandom, Christopher J.; Ejrnæs, Rasmus; Hansen, Morten D. D.; Svenning, Jens-Christian

    2014-01-01

    The impact of large herbivores on ecosystems before modern human activities is an open question in ecology and conservation. For Europe, the controversial wood–pasture hypothesis posits that grazing by wild large herbivores supported a dynamic mosaic of vegetation structures at the landscape scale under temperate conditions before agriculture. The contrasting position suggests that European temperate vegetation was primarily closed forest with relatively small open areas, at most impacted locally by large herbivores. Given the role of modern humans in the world-wide decimations of megafauna during the late Quaternary, to resolve this debate it is necessary to understand herbivore–vegetation interactions before these losses. Here, a synthetic analysis of beetle fossils from Great Britain shows that beetles associated with herbivore dung were better represented during the Last Interglacial (132,000–110,000 y B.P., before modern human arrival) than in the early Holocene (10,000–5,000 y B.P.). Furthermore, beetle assemblages indicate closed and partially closed forest in the early Holocene but a greater mixture of semiopen vegetation and forest in the Last Interglacial. Hence, abundant and diverse large herbivores appear to have been associated with high structural diversity of vegetation before the megafauna extinctions at the end of the Pleistocene. After these losses and in the presence of modern humans, large herbivores generally were less abundant, and closed woodland was more prevalent in the early Holocene. Our findings point to the importance of the formerly rich fauna of large herbivores in sustaining structurally diverse vegetation in the temperate forest biome and provide support for recent moves toward rewilding-based conservation management. PMID:24591633

  18. Two allelic isoforms of the serotonin transporter from Schistosoma mansoni display electrogenic transport and high selectivity for serotonin

    PubMed Central

    Fontana, Andréia C. K.; Sonders, Mark S.; Pereira-Junior, Olavo S.; Knight, Matty; Javitch, Jonathan A.; Rodrigues, Vanderlei; Amara, Susan G.; Mortensen, Ole V.

    2009-01-01

    The human blood fluke Schistosoma mansoni is the primary cause of schistosomiasis, a debilitating disease that affects 200 million individuals in over 70 countries. The biogenic amine serotonin is essential for the survival of the parasite and serotonergic proteins are potential novel drug targets for treating schistosomiasis. Here we characterize two novel serotonin transporter gene transcripts, SmSERT-A and SmSERT-B, from Schistosoma mansoni. Southern blot analysis shows that the two mRNAs are the products of different alleles of a single SmSERT gene locus. The two SmSERT forms differ in three amino acid positions near the N-terminus of the protein. Both SmSERTs are expressed in the adult form and in the sporocyst form (infected snails) of the parasite, but are absent from all other stages of the parasite’s complex life cycle. Heterologous expression of the two cDNAs in mammalian cells resulted in saturable, sodium-dependent serotonin transport activity with an apparent affinity for serotonin comparable to that of the human serotonin transporter. Although the two SmSERTs are pharmacologically indistinguishable from each other, efflux experiments reveal notably higher substrate selectivity for serotonin compared with their mammalian counterparts. Several well-established substrates for human SERT including (±)MDMA, S-(+)amphetamine, RU 24969, and m-CPP are not transported by SmSERTs, underscoring the higher selectivity of the schistosomal isoforms. Voltage clamp recordings of SmSERT substrate-elicited currents confirm the substrate selectivity observed in efflux experiments and suggest that it may be possible to exploit the electrogenic nature of SmSERT to screen for compounds that target the parasite in vivo. PMID:19549517

  19. Vip3A Resistance Alleles Exist at High Levels in Australian Targets before Release of Cotton Expressing This Toxin

    PubMed Central

    Mahon, Rod J.; Downes, Sharon J.; James, Bill

    2012-01-01

    Crops engineered to produce insecticidal crystal (Cry) proteins from the soil bacterium Bacillus thuringiensis (Bt) have revolutionised pest control in agriculture. However field-level resistance to Bt has developed in some targets. Utilising novel vegetative insecticidal proteins (Vips), also derived from Bt but genetically distinct from Cry toxins, is a possible solution that biotechnical companies intend to employ. Using data collected over two seasons we determined that, before deployment of Vip-expressing plants in Australia, resistance alleles exist in key targets as polymorphisms at frequencies of 0.027 (n = 273 lines, 95% CI = 0.019–0.038) in H. armigera and 0.008 (n = 248 lines, 0.004–0.015) in H. punctigera. These frequencies are above mutation rates normally encountered. Homozygous resistant neonates survived doses of Vip3A higher than those estimated in field-grown plants. Fortunately the resistance is largely, if not completely, recessive and does not confer resistance to the Bt toxins Cry1Ac or Cry2Ab already deployed in cotton crops. These later characteristics are favourable for resistance management; however the robustness of Vip3A inclusive varieties will depend on resistance frequencies to the Cry toxins when it is released (anticipated 2016) and the efficacy of Vip3A throughout the season. It is appropriate to pre-emptively screen key targets of Bt crops elsewhere, especially those such as H. zea in the USA, which is not only closely related to H. armigera but also will be exposed to Vip in several varieties of cotton and corn. PMID:22761737

  20. Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra).

    PubMed

    Keever, Carson C; Puritz, Jonathan B; Addison, Jason A; Byrne, Maria; Grosberg, Richard K; Toonen, Robert J; Hart, Michael W

    2013-10-23

    We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allele at nearly all nuclear loci; heterozygotes were extremely rare (0.18%); mitochondrial DNA sequences were more variable, but few populations shared haplotypes in common. Isolation-with-migration models suggest that these patterns are caused by population bottlenecks (relative to ancestral population size) and low gene flow. Loss of genetic diversity and low potential for dispersal between high-intertidal habitats may have dire consequences for extinction risk and potential for future adaptive evolution in response to climate and other selective agents. PMID:23925835

  1. IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors.

    PubMed

    Aouinti, Safa; Malouche, Dhafer; Giudicelli, Véronique; Kossida, Sofia; Lefranc, Marie-Paule

    2015-01-01

    The adaptive immune responses of humans and of other jawed vertebrate species (gnasthostomata) are characterized by the B and T cells and their specific antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) (up to 2.1012 different IG and TR per individual). IMGT, the international ImMunoGeneTics information system (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc (Montpellier University and CNRS) to manage the huge and complex diversity of these antigen receptors. IMGT built on IMGT-ONTOLOGY concepts of identification (keywords), description (labels), classification (gene and allele nomenclature) and numerotation (IMGT unique numbering), is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. IMGT/HighV-QUEST, the first web portal, and so far the only one, for the next generation sequencing (NGS) analysis of IG and TR, is the paradigm for immune repertoire standardized outputs and immunoprofiles of the adaptive immune responses. It provides the identification of the variable (V), diversity (D) and joining (J) genes and alleles, analysis of the V-(D)-J junction and complementarity determining region 3 (CDR3) and the characterization of the 'IMGT clonotype (AA)' (AA for amino acid) diversity and expression. IMGT/HighV-QUEST compares outputs of different batches, up to one million nucleotide sequencesfor the statistical module. These high throughput IG and TR repertoire immunoprofiles are of prime importance in vaccination, cancer, infectious diseases, autoimmunity and lymphoproliferative disorders, however their comparative statistical analysis still remains a challenge. We present a standardized statistical procedure to analyze IMGT/HighV-QUEST outputs for the evaluation of the significance of the IMGT clonotype (AA) diversity differences in proportions, per gene of a given group, between NGS IG and TR repertoire immunoprofiles. The procedure is generic and

  2. A very small and isolated population of the green Oak Leaf Roller, Tortrix viridana L., with high genetic diversity--how does this work?

    PubMed

    Schroeder, Hilke; Yanbaev, Yulai; Degen, Bernd

    2010-01-01

    A geographically isolated population of an herbivorous insect (Tortrix viridana, Lepidoptera: Tortricidae) in the Bashkir Transural region and 5 further populations were investigated for genetic variation using eight microsatellite markers. The sample size per population was between 48 and 62 individuals. The genetic variation was higher within the isolated population than within populations in the center of the distribution area. No bottleneck effects were discovered during analyses that could have formatted the gene pool of this population. Balancing or directed selection toward preservation of specific alleles or promotion of heterozygous individuals could be an explanation for the unexpected high genetic diversity within this small and isolated population. PMID:20511381

  3. Female sticklebacks count alleles in a strategy of sexual selection explaining MHC polymorphism.

    PubMed

    Reusch, T B; Häberli, M A; Aeschlimann, P B; Milinski, M

    2001-11-15

    The origin and maintenance of polymorphism in major histocompatibility complex (MHC) genes in natural populations is still unresolved. Sexual selection, frequency-dependent selection by parasites and pathogens, and heterozygote advantage have been suggested to explain the maintenance of high allele diversity at MHC genes. Here we argue that there are two (non-exclusive) strategies for MHC-related sexual selection, representing solutions to two different problems: inbreeding avoidance and parasite resistance. In species prone to inadvertent inbreeding, partners should prefer dissimilar MHC genotypes to similar ones. But if the goal is to maximize the resistance of offspring towards potential infections, the choosing sex should prefer mates with a higher diversity of MHC alleles. This latter strategy should apply when there are several MHC loci, as is the case in most vertebrates. We tested the relative importance of an 'allele counting' strategy compared to a disassortative mating strategy using wild-caught three-spined sticklebacks (Gasterosteus aculeatus) from an interconnected system of lakes. Here we show that gravid female fish preferred the odour of males with a large number of MHC class-IIB alleles to that of males with fewer alleles. Females did not prefer male genotypes dissimilar to their own. PMID:11713527

  4. Novel rapid genotyping assays for neuronal ceroid lipofuscinosis in Border Collie dogs and high frequency of the mutant allele in Japan.

    PubMed

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Kawahara, Natsuko; Hayashi, Daisuke; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2011-11-01

    Neuronal ceroid lipofuscinosis (NCL) constitutes a group of recessively inherited lysosomal storage diseases that primarily affect neuronal cells. Such diseases share certain clinical and pathologic features in human beings and animals. Neuronal ceroid lipofuscinosis in Border Collie dogs was first detected in Australia in the 1980s, and the pathogenic mutation was shown to be a nonsense mutation (c.619C>T) in exon 4 in canine CLN5 gene. In the present study, novel rapid genotyping assays including polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR primer-induced restriction analysis, mutagenically separated PCR, and real-time PCR with TaqMan minor groove binder probes, were developed. The utility of microchip electrophoresis was also evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies in Japan using these assays to determine the current allele frequency in Japan, providing information to control and prevent this disease in the next stage. All assays developed in the current study are available to discriminate these genotypes, and microchip electrophoresis showed a timesaving advantage over agarose gel electrophoresis. Of all assays, real-time PCR was the most suitable for large-scale examination because of its high throughput. The genotyping survey demonstrated that the carrier frequency was 8.1%. This finding suggested that the mutant allele frequency of NCL in Border Collies is high enough in Japan that measures to control and prevent the disease would be warranted. The genotyping assays developed in the present study could contribute to the prevention of NCL in Border Collies. PMID:22362793

  5. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

    PubMed Central

    Vina, Marcelo A. Fernandez; Hollenbach, Jill A.; Lyke, Kirsten E.; Sztein, Marcelo B.; Maiers, Martin; Klitz, William; Cano, Pedro; Mack, Steven; Single, Richard; Brautbar, Chaim; Israel, Shosahna; Raimondi, Eduardo; Khoriaty, Evelyne; Inati, Adlette; Andreani, Marco; Testi, Manuela; Moraes, Maria Elisa; Thomson, Glenys; Stastny, Peter; Cao, Kai

    2012-01-01

    The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans. PMID:22312049

  6. Patterns of Neutral Diversity Under General Models of Selective Sweeps

    PubMed Central

    Coop, Graham; Ralph, Peter

    2012-01-01

    Two major sources of stochasticity in the dynamics of neutral alleles result from resampling of finite populations (genetic drift) and the random genetic background of nearby selected alleles on which the neutral alleles are found (linked selection). There is now good evidence that linked selection plays an important role in shaping polymorphism levels in a number of species. One of the best-investigated models of linked selection is the recurrent full-sweep model, in which newly arisen selected alleles fix rapidly. However, the bulk of selected alleles that sweep into the population may not be destined for rapid fixation. Here we develop a general model of recurrent selective sweeps in a coalescent framework, one that generalizes the recurrent full-sweep model to the case where selected alleles do not sweep to fixation. We show that in a large population, only the initial rapid increase of a selected allele affects the genealogy at partially linked sites, which under fairly general assumptions are unaffected by the subsequent fate of the selected allele. We also apply the theory to a simple model to investigate the impact of recurrent partial sweeps on levels of neutral diversity and find that for a given reduction in diversity, the impact of recurrent partial sweeps on the frequency spectrum at neutral sites is determined primarily by the frequencies rapidly achieved by the selected alleles. Consequently, recurrent sweeps of selected alleles to low frequencies can have a profound effect on levels of diversity but can leave the frequency spectrum relatively unperturbed. In fact, the limiting coalescent model under a high rate of sweeps to low frequency is identical to the standard neutral model. The general model of selective sweeps we describe goes some way toward providing a more flexible framework to describe genomic patterns of diversity than is currently available. PMID:22714413

  7. DISPERSAL AS A MECHANISM LIMITING DIVERSITY OF HIGH LATITUDES

    EPA Science Inventory

    The pervasiveness acress taxa, space, and time of the latitudinal gradient in species diversity is conventionally thought to suggest a common cause that is not yet identified. Conventionally, the cause of the gradient is thought to originate in the tropics where diversity is hig...

  8. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages

    PubMed Central

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-01-01

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth (Lepidoptera: Geometridae) assemblages in the mature temperate forest on Changbai Mountain. A total of 9285 geometrid moths representing 131 species were collected, with many species displaying wide elevational distribution ranges. Moth α-diversity decreased monotonously, while the standardized effect size of mean pairwise phylogenetic distances (MPD) and phylogenetic diversity (PD) increased significantly with increasing elevation. At high elevations, the insect assemblages consisted largely of habitat generalists that were individually more phylogenetically distinct from co-occurring species than species in assemblages at lower altitudes. This could hint at higher speciation rates in more favourable low-elevation environments generating a species-rich geometrid assemblage, while exclusion of phylogenetically closely related species becomes increasingly important in shaping moth assemblages at higher elevations. Overall, it appears likely that high-elevation temperate moth assemblages are strongly resilient to environmental change, and that they contain a much larger proportion of the genetic diversity encountered at low-elevation assemblages in comparison to tropical geometrid communities. PMID:26979402

  9. High phylogenetic diversity is preserved in species-poor high-elevation temperate moth assemblages.

    PubMed

    Zou, Yi; Sang, Weiguo; Hausmann, Axel; Axmacher, Jan Christoph

    2016-01-01

    Understanding the diversity and composition of species assemblages and identifying underlying biotic and abiotic determinants represent great ecological challenges. Addressing some of these issues, we investigated the α-diversity and phylogenetic composition of species-rich geometrid moth (Lepidoptera: Geometridae) assemblages in the mature temperate forest on Changbai Mountain. A total of 9285 geometrid moths representing 131 species were collected, with many species displaying wide elevational distribution ranges. Moth α-diversity decreased monotonously, while the standardized effect size of mean pairwise phylogenetic distances (MPD) and phylogenetic diversity (PD) increased significantly with increasing elevation. At high elevations, the insect assemblages consisted largely of habitat generalists that were individually more phylogenetically distinct from co-occurring species than species in assemblages at lower altitudes. This could hint at higher speciation rates in more favourable low-elevation environments generating a species-rich geometrid assemblage, while exclusion of phylogenetically closely related species becomes increasingly important in shaping moth assemblages at higher elevations. Overall, it appears likely that high-elevation temperate moth assemblages are strongly resilient to environmental change, and that they contain a much larger proportion of the genetic diversity encountered at low-elevation assemblages in comparison to tropical geometrid communities. PMID:26979402

  10. Population analysis of Vibrio parahaemolyticus originating from different geographical regions demonstrates a high genetic diversity

    PubMed Central

    2014-01-01

    Background Vibrio parahaemolyticus is frequently isolated from environmental and seafood samples and associated with gastroenteritis outbreakes in American, European, Asian and African countries. To distinguish between different lineages of V. parahaemolyticus various genotyping techniques have been used, incl. multilocus sequence typing (MLST). Even though some studies have already applied MLST analysis to characterize V. parahaemolyticus strain sets, these studies have been restricted to specific geographical areas (e.g. U.S. coast, Thailand and Peru), have focused exclusively on pandemic or non-pandemic pathogenic isolates or have been based on a limited strain number. Results To generate a global picture of V. parahaemolyticus genotype distribution, a collection of 130 environmental and seafood related V. parahaemolyticus isolates of different geographical origins (Sri Lanka, Ecuador, North Sea and Baltic Sea as well as German retail) was subjected to MLST analysis after modification of gyrB and recA PCRs. The V. parahaemolyticus population was composed of 82 unique Sequence Types (STs), of which 68 (82.9%) were new to the pubMLST database. After translating the in-frame nucleotide sequences into amino acid sequences, less diversity was detectable: a total of 31 different peptide Sequence Types (pSTs) with 19 (61.3%) new pSTs were generated from the analyzed isolates. Most STs did not show a global dissemination, but some were supra-regionally distributed and clusters of STs were dependent on geographical origin. On peptide level no general clustering of strains from specific geographical regions was observed, thereby the most common pSTs were found on all continents (Asia, South America and Europe) and rare pSTs were restricted to distinct countries or even geographical regions. One lineage of pSTs associated only with strains from North and Baltic Sea strains was identified. Conclusions Our study reveals a high genetic diversity in the analyzed V

  11. Allelic isoforms of the H+/nucleoside co-transporter (CaCNT) from Candida albicans reveal separate high- and low-affinity transport systems for nucleosides.

    PubMed

    Slugoski, Melissa D; Loewen, Shaun K; Ng, Amy M L; Baldwin, Stephen A; Cass, Carol E; Young, James D

    2004-11-01

    Contigs 19-10196 and 19-20196 of the Stanford Candida albicans genome sequence databank encode two putative allelic isoforms of C. albicans CaCNT, a recently characterized 608 amino acid residue H+-coupled fungal member of the CNT family of concentrative nucleoside transport proteins. The single Ser/Gly difference between CaCNT/19-20196 and CaCNT occurs at position 328 in putative TM 7, and corresponds to a Ser/Gly substitution previously shown to contribute to the contrasting pyrimidine and purine nucleoside selectivities of human (h) and rat (r) Na+-dependent CNT1 and CNT2. CaCNT/19-10196 differs from CaCNT by four amino acids, but has Gly at position 328. These new proteins were recreated by site-directed mutagenesis of CaCNT and characterized functionally by heterologous expression in Xenopus laevis oocytes. In marked contrast to h/rCNT1/2, both CaCNT/19-10196 and CaCNT/19-20196 exhibited permeant selectivities for purine nucleosides (adenosine, guanosine and inosine) and uridine similar to that of CaCNT. However, although H+-coupled, CaCNT/19-20196 exhibited a approximately 10-fold higher apparent Km for uridine than either CaCNT or CaCNT/19-10196. CaCNT/19-20196 also exhibited a low apparent affinity for inosine. We conclude that the three proteins correspond to high-affinity (CaCNT, CaCNT/19-10196) and low-affinity (CaCNT/19-20196) allelic isoforms of the C. albicans CNT nucleoside transporter. This is the first example of a single amino acid residue substitution altering a CNT protein's overall apparent affinity for nucleosides. PMID:15543539

  12. Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe.

    PubMed

    Ścieżyńska, Aneta; Oziębło, Dominika; Ambroziak, Anna M; Korwin, Magdalena; Szulborski, Kamil; Krawczyński, Maciej; Stawiński, Piotr; Szaflik, Jerzy; Szaflik, Jacek P; Płoski, Rafał; Ołdak, Monika

    2016-04-01

    Variation in the ABCA4 locus has emerged as the most prevalent cause of monogenic retinal diseases. The study aimed to discover causative ABCA4 mutations in a large but not previously investigated cohort with ABCA4-related diseases originating from Central Europe and to refine the genetic relevance of all identified variants based on population evidence. Comprehensive clinical studies were performed to identify patients with Stargardt disease (STGD, n = 76) and cone-rod dystrophy (CRD, n = 16). Next-generation sequencing targeting ABCA4 was applied for a widespread screening of the gene. The results were analyzed in the context of exome data from a corresponding population (n = 594) and other large genomic databases. Our data disprove the pathogenic status of p.V552I and provide more evidence against a causal role of four further ABCA4 variants as drivers of the phenotype under a recessive paradigm. The study identifies 12 novel potentially pathogenic mutations (four of them recurrent) and a novel complex allele p.[(R152*; V2050L)]. In one third (31/92) of our cohort we detected the p.[(L541P; A1038V)] complex allele, which represents an unusually high level of genetic homogeneity for ABCA4-related diseases. Causative ABCA4 mutations account for 79% of STGD and 31% of CRD cases. A combination of p.[(L541P; A1038V)] and/or a truncating ABCA4 mutation always resulted in an early disease onset. Identification of ABCA4 retinopathies provides a specific molecular diagnosis and justifies a prompt introduction of simple precautions that may slow disease progression. The comprehensive, population-specific study expands our knowledge on the genetic landscape of retinal diseases. PMID:26593885

  13. Ribo HRM--detection of inter- and intra-species polymorphisms within ribosomal DNA by high resolution melting analysis supported by application of artificial allelic standards.

    PubMed

    Masny, Aleksander; Jagiełło, Agata; Płucienniczak, Grażyna; Golab, Elzbieta

    2012-09-01

    Ribo HRM, a single-tube PCR and high resolution melting (HRM) assay for detection of polymorphisms in the large subunit ribosomal DNA expansion segment V, was developed on a Trichinella model. Four Trichinella species: T. spiralis (isolates ISS3 and ISS160), T. nativa (isolates ISS10 and ISS70), T. britovi (isolates ISS2 and ISS392) and T. pseudospiralis (isolates ISS13 and ISS1348) were genotyped. Cloned allelic variants of the expansion segment V were used as standards to prepare reference HRM curves characteristic for single sequences and mixtures of several cloned sequences imitating allelic composition detected in Trichinella isolates. Using the primer pair Tsr1 and Trich1bi, it was possible to amplify a fragment of the ESV and detect PCR products obtained from the genomic DNA of pools of larvae belonging to the four investigated species: T. pseudospiralis, T. spiralis, T. britovi and T. nativa, in a single tube Real-Time PCR reaction. Differences in the shape of the HRM curves of Trichinella isolates suggested the presence of differences between examined isolates of T. nativa, T. britovi and T. pseudospiralis species. No differences were observed between T. spiralis isolates. The presence of polymorphisms within the amplified ESV sequence fragment of T. nativa T. britovi and T. pseudospiralis was confirmed by sequencing of the cloned PCR products. Novel sequences were discovered and deposited in GenBank (GenBank IDs: JN971020-JN971027, JN120902.1, JN120903.1, JN120904.1, JN120906.1, JN120905.1). Screening the ESV region of Trichinella for polymorphism is possible using the genotyping assay Ribo HRM at the current state of its development. The Ribo HRM assay could be useful in phylogenetic studies of the Trichinella genus. PMID:22766326

  14. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation.

    PubMed

    Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel

    2015-12-01

    It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices. PMID:26497875

  15. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Natural variation provides a powerful opportunity to study the genetic basis of biological traits. Brachypodium distachyon is a broadly distributed diploid model grass with a small genome and a large collection of diverse inbred lines. As a step towards understanding the genetic basis of the natura...

  16. High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia.

    PubMed

    Koban, E; Denizci, M; Aslan, O; Aktoprakligil, D; Aksu, S; Bower, M; Balcioglu, B K; Ozdemir Bahadir, A; Bilgin, R; Erdag, B; Bagis, H; Arat, S

    2012-08-01

    The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia's role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey. PMID:22497212

  17. High-Resolution Genetic Map for Understanding the Effect of Genome-Wide Recombination Rate on Nucleotide Diversity in Watermelon

    PubMed Central

    Reddy, Umesh K.; Nimmakayala, Padma; Levi, Amnon; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Tomason, Yan. R.; Vajja, Gopinath; Reddy, Rishi; Abburi, Lavanya; Wehner, Todd C.; Ronin, Yefim; Karol, Abraham

    2014-01-01

    We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima’s D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication. PMID:25227227

  18. Phenotype of Arabidopsis thaliana semi-dwarfs with deep roots and high growth rates under water-limiting conditions is independent of the GA5 loss-of-function alleles

    PubMed Central

    Barboza-Barquero, Luis; Nagel, Kerstin A.; Jansen, Marcus; Klasen, Jonas R.; Kastenholz, Bernd; Braun, Silvia; Bleise, Birgit; Brehm, Thorsten; Koornneef, Maarten; Fiorani, Fabio

    2015-01-01

    Background and Aims The occurrence of Arabidopsis thaliana semi-dwarf accessions carrying inactive alleles at the gibberellin (GA) biosynthesis GA5 locus has raised the question whether there are pleiotropic effects on other traits at the root level, such as rooting depth. In addition, it is unknown whether semi-dwarfism in arabidopsis confers a growth advantage under water-limiting conditions compared with wild-type plants. The aim of this research was therefore to investigate whether semi-dwarfism has a pleiotropic effect in the root system and also whether semi-dwarfs might be more tolerant of water-limiting conditions. Methods The root systems of different arabidopsis semi-dwarfs and GA biosynthesis mutants were phenotyped in vitro using the GROWSCREEN-ROOT image-based software. Semi-dwarfs were phenotyped together with tall, near-related accessions. In addition, root phenotypes were investigated in soil-filled rhizotrons. Rosette growth trajectories were analysed with the GROWSCREEN-FLUORO setup based on non-invasive imaging. Key Results Mutations in the early steps of the GA biosynthesis pathway led to a reduction in shoot as well as root size. Depending on the genetic background, mutations at the GA5 locus yielded phenotypes characterized by decreased root length in comparison with related wild-type ones. The semi-dwarf accession Pak-3 showed the deepest root system both in vitro and in soil cultivation experiments; this comparatively deep root system, however, was independent of the ga5 loss-of-function allele, as shown by co-segregation analysis. When the accessions were grown under water-limiting conditions, semi-dwarf accessions with high growth rates were identified. Conclusions The observed diversity in root system growth and architecture occurs independently of semi-dwarf phenotypes, and is probably linked to a genetic background effect. The results show that there are no clear advantages of semi-dwarfism at low water availability in arabidopsis

  19. Cerebellum volume in high-risk offspring from multiplex alcohol dependence families: association with allelic variation in GABRA2 and BDNF.

    PubMed

    Hill, Shirley Y; Wang, Shuhui; Carter, Howard; Tessner, Kevin; Holmes, Brian; McDermott, Michael; Zezza, Nicholas; Stiffler, Scott

    2011-12-30

    Offspring from families with multiple cases of alcohol dependence have a greater likelihood of developing alcohol dependence (AD) and related substance use disorders. Greater susceptibility for developing these disorders may be related to structural differences in brain circuits that influence the salience of rewards or modify the efficiency of information processing and AD susceptibility. We examined the cerebellum of 71 adolescent/young adult high-risk (HR) offspring from families with multiple cases of alcohol dependence (multiplex families), and 60 low-risk (LR) controls with no family history of alcohol or drug dependence who were matched for age, gender, socioeconomic status and IQ, with attention given to possible effects of personal use of substances and maternal use during pregnancy. Magnetic resonance images were acquired on a General Electric 1.5-Tesla scanner and manually traced (BRAINS2) blind to clinical information. GABRA2 and BDNF variation were tested for their association with cerebellar volumes. High-risk offspring from multiplex AD families showed greater total volume of the cerebellum and total gray matter (GM), in comparison with LR controls. An interaction between allelic variation in GABRA2 and BDNF genes was associated with GM volumes, suggesting that inherited variation in these genes may promote early developmental differences in neuronal proliferation of the cerebellum. PMID:22047728

  20. Cerebellum volume in high-risk offspring from multiplex alcohol dependence families: Association with allelic variation in GABRA2 and BDNF

    PubMed Central

    Hill, Shirley Y.; Wang, Shuhui; Carter, Howard; Tessner, Kevin; Holmes, Brian; McDermott, Michael; Zezza, Nicholas; Stiffler, Scott

    2012-01-01

    Offspring from families with multiple cases of alcohol dependence have a greater likelihood of developing alcohol dependence (AD) and related substance use disorders. Greater susceptibility for developing these disorders may be related to structural differences in brain circuits that influence the salience of rewards or modify the efficiency of information processing and AD susceptibility. We examined the cerebellum of 71 adolescent/young adult high-risk (HR) offspring from families with multiple cases of alcohol dependence (multiplex families), and 60 low-risk (LR) controls with no family history of alcohol or drug dependence who were matched for age, gender, socioeconomic status and IQ, with attention given to possible effects of personal use of substances and maternal use during pregnancy. Magnetic resonance images were acquired on a General Electric 1.5-Tesla scanner and manually traced (BRAINS2) blind to clinical information. GABRA2 and BDNF variation were tested for their association with cerebellar volumes. High-risk offspring from multiplex AD families showed greater total volume of the cerebellum and total gray matter (GM), in comparison with LR controls. An interaction between allelic variation in GABRA2 and BDNF genes was associated with GM volumes, suggesting that inherited variation in these genes may promote early developmental differences in neuronal proliferation of the cerebellum. PMID:22047728

  1. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    PubMed

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  2. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

    PubMed Central

    Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  3. High Diversity of the Saliva Microbiome in Batwa Pygmies

    PubMed Central

    Schroeder, Roland; Creasey, Jean L.; Li, Mingkun; Stoneking, Mark

    2011-01-01

    We describe the saliva microbiome diversity in Batwa Pygmies, a former hunter-gatherer group from Uganda, using next-generation sequencing of partial 16S rRNA sequences. Microbial community diversity in the Batwa is significantly higher than in agricultural groups from Sierra Leone and the Democratic Republic of Congo. We found 40 microbial genera in the Batwa, which have previously not been described in the human oral cavity. The distinctive composition of the salvia microbiome of the Batwa may have been influenced by their recent different lifestyle and diet. PMID:21858083

  4. Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene

    SciTech Connect

    Pena, S.D.J.; De Souza, K.T. ); De Andrade, M.; Chakraborty, R. )

    1994-01-18

    At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the same alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, the authors observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of cooperative changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

  5. High levels of cryptic species diversity uncovered in Amazonian frogs

    PubMed Central

    Funk, W. Chris; Caminer, Marcel; Ron, Santiago R.

    2012-01-01

    One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador (Engystomops: 252 individuals from 36 localities; Hypsiboas: 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops, the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas, two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought. PMID:22130600

  6. High-level cefixime- and ceftriaxone-resistant Neisseria gonorrhoeae in France: novel penA mosaic allele in a successful international clone causes treatment failure.

    PubMed

    Unemo, Magnus; Golparian, Daniel; Nicholas, Robert; Ohnishi, Makoto; Gallay, Anne; Sednaoui, Patrice

    2012-03-01

    Recently, the first Neisseria gonorrhoeae strain (H041) highly resistant to the expanded-spectrum cephalosporins (ESCs) ceftriaxone and cefixime, which are the last remaining options for first-line gonorrhea treatment, was isolated in Japan. Here, we confirm and characterize a second strain (F89) with high-level cefixime and ceftriaxone resistance which was isolated in France and most likely caused a treatment failure with cefixime. F89 was examined using six species-confirmatory tests, antibiograms (33 antimicrobials), porB sequencing, N. gonorrhoeae multiantigen sequence typing (NG-MAST), multilocus sequence typing (MLST), and sequencing of known gonococcal resistance determinants (penA, mtrR, penB, ponA, and pilQ). F89 was assigned to MLST sequence type 1901 (ST1901) and NG-MAST ST1407, which is a successful gonococcal clone that has spread globally. F89 has high-level resistance to cefixime (MIC = 4 μg/ml) and ceftriaxone (MIC = 1 to 2 μg/ml) and resistance to most other antimicrobials examined. A novel penA mosaic allele (penA-CI), which was penA-XXXIV with an additional A501P alteration in penicillin-binding protein 2, was the primary determinant for high-level ESC resistance, as determined by transformation into a set of recipient strains. N. gonorrhoeae appears to be emerging as a superbug, and in certain circumstances and settings, gonorrhea may become untreatable. Investigations of the biological fitness and enhanced understanding and monitoring of the ESC-resistant clones and their international transmission are required. Enhanced disease control activities, antimicrobial resistance control and surveillance worldwide, and public health response plans for global (and national) perspectives are also crucial. Nevertheless, new treatment strategies and/or drugs and, ideally, a vaccine are essential to develop for efficacious gonorrhea management. PMID:22155830

  7. Allelic background of LEPRE1 mutations that cause recessive forms of osteogenesis imperfecta in different populations

    PubMed Central

    Pepin, Melanie G; Schwarze, Ulrike; Singh, Virendra; Romana, Marc; Jones-LeCointe, Altheia; Byers, Peter H

    2013-01-01

    Biallelic mutations in LEPRE1 result in recessively inherited forms of osteogenesis imperfecta (OI) that are often lethal in the perinatal period. A mutation (c.1080+1G>T, IVS5+1G>T) in African Americans has a carrier frequency of about 1/240. The mutant allele originated in West Africa in tribes of Ghana and Nigeria where the carrier frequencies are 2% and 5%. By examining 200 samples from an African-derived population in Tobago and reviewing hospital neonatal death records, we determined that the carrier frequency of c.1080+1G>T was about one in 200 and did not contribute to the neonatal deaths recorded over a 3-year period of time in Trinidad. In the course of sequence analysis, we found surprisingly high LEPRE1 allelic diversity in the Tobago DNA samples in which there were 11 alleles distinguished by a single basepair variant in or near exon 5. All the alleles found in the Tobago population that were within the sequence analysis region were found in the African American population in the Exome Variant Project. This diversity appeared to reflect the geographic origin of the original population in Tobago. In 44 individuals with biallelic LEPRE1 mutations identified by clinical diagnostic testing, we found the sequence alterations occurred on seven of the 11 variant alleles. All but one of the mutations identified resulted in mRNA or protein instability for the majority of the transcripts from the altered allele. These findings suggest that the milder end of the clinical spectrum could be due to as yet unidentified missense mutations in LEPRE1. PMID:24498616

  8. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers.

    PubMed

    Medhi, K; Sarmah, D K; Deka, M; Bhau, B S

    2014-12-01

    The genetic diversity in Zanthoxylum species viz.  Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454

  9. High-Level Genetic Diversity and Complex Population Structure of Siberian Apricot (Prunus sibirica L.) in China as Revealed by Nuclear SSR Markers

    PubMed Central

    Wang, Zhe; Kang, Ming; Liu, Huabo; Gao, Jiao; Zhang, Zhengdong; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

    2014-01-01

    Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species. PMID:24516551

  10. High-level genetic diversity and complex population structure of Siberian apricot (Prunus sibirica L.) in China as revealed by nuclear SSR markers.

    PubMed

    Wang, Zhe; Kang, Ming; Liu, Huabo; Gao, Jiao; Zhang, Zhengdong; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

    2014-01-01

    Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species. PMID:24516551

  11. Functional Significance of Single Nucleotide Polymorphisms in the Lactase Gene in Diverse United States Subjects and Evidence for a Novel Lactase Persistence Allele at -13909 in Those of European Ancestry

    PubMed Central

    Baffour-Awuah, Nana Yaa; Fleet, Sarah; Baker, Susan S.; Butler, Johannah L.; Campbell, Catarina; Tischfield, Samuel; Mitchell, Paul D.; Moon, Jennifer E.; Allende-Richter, Sophie; Fishman, Laurie; Bousvaros, Athos; Fox, Victor; Kuokkanen, Mikko; Montgomery, Robert K.; Grand, Richard J.; Hirschhorn, Joel N.

    2014-01-01

    Objectives Recent data from mainly homogeneous European and African populations implicate a 140 bp region 5′ to the transcriptional start site of LCT (the lactase gene) as a regulatory site for lactase persistence and non-persistence. As there are no studies of United States non-homogeneous populations, we performed genotype/phenotype analysis of the -13910 and -22018 LCT SNPs in New England children, mostly of European ancestry. Methods Duodenal biopsies were processed for disaccharidase activities, RNA quantification by RT-PCR, allelic expression ratios by PCR, and genotyping and SNP analysis. Results were compared to clinical information. Results Lactase activity and mRNA levels, as well as sucrase-to-lactase ratios of enzyme activity and mRNA, showed robust correlations with genotype. None of the other LCT SNPs showed as strong a correlation with enzyme or mRNA activities as did -13910. Data were consistent with the -13910 being the causal sequence variant rather than -22018. Four individuals heterozygous for -13910T/C had allelic expression patterns similar to individuals with -13910C/C genotypes; of these, 2 showed equal LCT expression from the 2 alleles and a novel variant (-13909C>A) associated with lactase persistence. Conclusion The identification of -13910C/C genotype is very likely to predict lactase non-persistence, consistent with prior published studies. A -13910T/T genotype will frequently, but not perfectly, predict lactase persistence in this mixed European-ancestry population; a -13910T/C genotype will not predict the phenotype. A long, rare haplotype in 2 individuals with -13910T/C genotype but equal allele-specific expression contains a novel lactase persistence allele present at -13909. PMID:25625576

  12. ADZE: a rarefaction approach for counting alleles private to combinations of populations

    PubMed Central

    Szpiech, Zachary A.; Jakobsson, Mattias; Rosenberg, Noah A.

    2008-01-01

    Motivation: Analysis of the distribution of alleles across populations is a useful tool for examining population diversity and relationships. However, sample sizes often differ across populations, sometimes making it difficult to assess allelic distributions across groups. Results: We introduce a generalized rarefaction approach for counting alleles private to combinations of populations. Our method evaluates the number of alleles found in each of a set of populations but absent in all remaining populations, considering equal-sized subsamples from each population. Applying this method to a worldwide human microsatellite dataset, we observe a high number of alleles private to the combination of African and Oceanian populations. This result supports the possibility of a migration out of Africa into Oceania separate from the migrations responsible for the majority of the ancestry of the modern populations of Asia, and it highlights the utility of our approach to sample size correction in evaluating hypotheses about population history. Availability: We have implemented our method in the computer pro-gram ADZE, which is available for download at http://rosenberglab.bioinformatics.med.umich.edu/adze.html. Contact: szpiechz@umich.edu PMID:18779233

  13. Understanding and utilizing crop genome diversity via high-resolution genotyping.

    PubMed

    Voss-Fels, Kai; Snowdon, Rod J

    2016-04-01

    High-resolution genome analysis technologies provide an unprecedented level of insight into structural diversity across crop genomes. Low-cost discovery of sequence variation has become accessible for all crops since the development of next-generation DNA sequencing technologies, using diverse methods ranging from genome-scale resequencing or skim sequencing, reduced-representation genotyping-by-sequencing, transcriptome sequencing or sequence capture approaches. High-density, high-throughput genotyping arrays generated using the resulting sequence data are today available for the assessment of genomewide single nucleotide polymorphisms in all major crop species. Besides their application in genetic mapping or genomewide association studies for dissection of complex agronomic traits, high-density genotyping arrays are highly suitable for genomic selection strategies. They also enable description of crop diversity at an unprecedented chromosome-scale resolution. Application of population genetics parameters to genomewide diversity data sets enables dissection of linkage disequilibrium to characterize loci underlying selective sweeps. High-throughput genotyping platforms simultaneously open the way for targeted diversity enrichment, allowing rejuvenation of low-diversity chromosome regions in strongly selected breeding pools to potentially reverse the influence of linkage drag. Numerous recent examples are presented which demonstrate the power of next-generation genomics for high-resolution analysis of crop diversity on a subgenomic and chromosomal scale. Such studies give deep insight into the history of crop evolution and selection, while simultaneously identifying novel diversity to improve yield and heterosis. PMID:27003869

  14. Do farmers reduce genetic diversity when they domesticate tropical trees? A case study from Amazonia.

    PubMed

    Hollingsworth, P M; Dawson, I K; Goodall-Copestake, W P; Richardson, J E; Weber, J C; Sotelo Montes, C; Pennington, R T

    2005-02-01

    Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high. PMID:15660940

  15. Distribution of CGG repeats and FRAXAC1/DXS548 alleles in South American populations.

    PubMed

    Mingroni-Netto, Regina Célia; Angeli, Claudia B; Auricchio, Maria Teresa B M; Leal-Mesquita, Emygdia R; Ribeiro-dos-Santos, Andrea K C; Ferrari, Iris; Hutz, Mara H; Salzano, Francisco M; Hill, Kim; Hurtado, A Magdalena; Vianna-Morgante, Angela M

    2002-08-15

    In order to assess the molecular variability related to fragile X (FMR1 locus), we investigated the distribution of CGG repeats and DXS548/FRAXAC1 haplotypes in normal South American populations of different ethnic backgrounds. Special attention was given to Amerindian Wai-Wai (Northern Brazil) and Ache (Paraguay), as well as to Brazilian isolated communities of African ancestry, the remnants of quilombos. Comparison of samples from quilombos, Amerindians, and the ethnically mixed, but mainly European-derived population of São Paulo revealed that the 30-copy allele of the fragile X gene is the most frequent in all groups. A second peak at 20 repeats was present in the population of São Paulo only, confirming this as a European peculiarity. The distribution of DXS548 and FRAXAC1 alleles led to a high expected heterozygosity in African Brazilians, followed by that observed in the population of São Paulo. Amerindians showed the lowest diversity in CGG repeats and DXS548/FRAXAC1 haplotypes. Some rare alleles, for example, the 148-bp (FRAXAC1) or 200-bp (DXS548) variants, which seem to be almost absent in Europe, occurred in higher frequencies among African Brazilians. This suggests a general trend for higher genetic diversity among Africans; these rarer alleles could be African in origin and would have been lost or possibly were not present in the groups that gave rise to the Europeans. PMID:12210320

  16. Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

    PubMed Central

    Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

    2013-01-01

    We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

  17. Retention of agronomically important variation in germplasm core collections: implications for allele mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to d...

  18. Local endemicity and high diversity characterise high-latitude coral- Symbiodinium partnerships

    NASA Astrophysics Data System (ADS)

    Wicks, L. C.; Sampayo, E.; Gardner, J. P. A.; Davy, S. K.

    2010-12-01

    Obligate symbiotic dinoflagellates ( Symbiodinium) residing within the tissues of most reef invertebrates are important in determining the tolerance range of their host. Coral communities living at high latitudes experience wide fluctuations in environmental conditions and thus provide an ideal system to gain insights into the range within which the symbiotic relationship can be sustained. Further, understanding whether and how symbiont communities associated with high-latitude coral reefs are different from their tropical counterparts will provide clues to the potential of corals to cope with marginal or changing conditions. However, little is known of the host and symbiont partnerships at high latitudes. Symbiodinium diversity and specificity of high-latitude coral communities were explored using denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA at Lord Howe Island (31°S; Australia), and the Kermadec Islands (29°S; New Zealand). All but one host associated with clade C Symbiodinium, the exception being a soft coral ( Capnella sp.) that contained Symbiodinium B1. Besides ‘host-generalist’ Symbiodinium types C1 and C3, approximately 72% of the Symbiodinium identified were novel C types, and zonation of symbionts in relation to environmental parameters such as depth and turbidity was evident in certain host species. The high-latitude Symbiodinium communities showed little overlap and relatively high diversity compared with communities sampled on the tropical Great Barrier Reef. Although host specificity was maintained in certain species, others shared symbionts and this potential reduction of fidelity at high-latitude locations may be the result of locally challenging and highly variable environmental conditions.

  19. A high-fat diet and the threonine-encoding allele (Thr54) polymorphism of fatty acid–binding protein 2 reduce plasma triglyceride–rich lipoproteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Thr54 allele of the fatty acid binding protein 2 (FABP2) DNA polymorphism is associated with increased triglyceride-rich lipoproteins and insulin resistance. We investigated whether the triglyceride-rich lipoprotein response to diets of varied fat content is affected by the fatty acid binding pr...

  20. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the...

  1. Roles of conserved and allelic regions of the major merozoite surface protein (gp195) in immunity against Plasmodium falciparum.

    PubMed Central

    Hui, G S; Hashimoto, A; Chang, S P

    1992-01-01

    The Plasmodium falciparum major merozoite surface protein gp195 is a candidate antigen for a vaccine against human malaria. The significance of allelism and polymorphism in vaccine-induced immunity to gp195 was investigated in this study. Rabbits were immunized with each of two allelic forms of gp195 that were affinity purified from the FUP and FVO parasite isolates. gp195-specific antibodies raised against one allelic form of gp195 cross-reacted extensively with the gp195 of the heterologous allele in enzyme-linked immunosorbent assays (ELISAs) and immunofluorescence assays. Competitive binding ELISAs with homologous and heterologous gp195s confirmed that a majority of the anti-gp195 antibodies produced against either allelic protein were cross-reactive. Moreover, the biological activities of the gp195 antibody responses were also highly cross-reactive, since anti-gp195 sera inhibited the in vitro growth of the homologous and heterologous parasites with equal efficiency. The degree of cross-reactivity with strain-specific and allele-specific determinants of gp195 in the ELISA was low. These results suggest that the immunological cross-reactivity between the two gp195 proteins is due to recognition of conserved determinants. They also suggest that a gp195-based vaccine may be effective against blood-stage infection with a diverse array of parasite isolates. Images PMID:1548068

  2. Nematode Hsp90: highly conserved but functionally diverse.

    PubMed

    Gillan, Victoria; Devaney, Eileen

    2014-08-01

    Nematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species. PMID:24721950

  3. High diversity of fungi in air particulate matter

    PubMed Central

    Fröhlich-Nowoisky, Janine; Pickersgill, Daniel A.; Després, Viviane R.; Pöschl, Ulrich

    2009-01-01

    Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 μm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere. PMID:19617562

  4. Yellowstone Lake: high-energy geochemistry and rich bacterial diversity.

    PubMed

    Clingenpeel, Scott; Macur, Richard E; Kan, Jinjun; Inskeep, William P; Lovalvo, Dave; Varley, John; Mathur, Eric; Nealson, Kenneth; Gorby, Yuri; Jiang, Hongchen; LaFracois, Toben; McDermott, Timothy R

    2011-08-01

    Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H(2)S, CH(4), CO(2) and H(2), although CH(4) and H(2) levels were also significant throughout the lake. Pyrosequencing and near full-length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size-fractionated by sequentially filtering through 20-µm-, 3.0-µm-, 0.8-µm- and 0.1-µm-pore-size filters, with the >0.1 to <0.8 µm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α- and β-Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α-Proteobacteria clade tightly linked with freshwater SAR11-like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97-100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain. PMID:21450005

  5. Analysis of the distribution of HLA-A alleles in populations from five continents.

    PubMed

    Middleton, D; Williams, F; Meenagh, A; Daar, A S; Gorodezky, C; Hammond, M; Nascimento, E; Briceno, I; Perez, M P

    2000-10-01

    The variation and frequency of HLA-A genotypes were established by PCR-SSOP typing in diverse geographically distributed populations: Brazilian, Colombian Kogui, Cuban, Mexican, Omani, Singapore Chinese, and South African Zulu. HLA-A allelic families with only one allele were identified for HLA-A*01, -A*23, -A*25, -A*31, -A*32, -A*36, -A*43, -A*69, -A*80; and with two alleles for HLA-A*03, -A*11, -A*26, -A*29, -A*33, -A*34, and -A*66. Greater variation was detected for HLA-A*02, -A*24, and -A*68 allele families. Colombian Kogui and Mexican Seris showed the least diversity with respect to HLA-A alleles, albeit with small numbers tested, with only four and five HLA-A alleles identified, respectively. It would appear by their presence in all populations studied, either rural or indigenous, that certain alleles are very important in pathogen peptide presentation. PMID:11082518

  6. Evidence for selection maintaining MHC diversity in a rodent species despite strong density fluctuations.

    PubMed

    Schuster, Andrea C; Herde, Antje; Mazzoni, Camila J; Eccard, Jana A; Sommer, Simone

    2016-07-01

    Strong spatiotemporal variation in population size often leads to reduced genetic diversity limiting the adaptive potential of individual populations. Key genes of adaptive variation are encoded by the immune genes of the major histocompatibility complex (MHC) playing an essential role in parasite resistance. How MHC variation persists in rodent populations that regularly experience population bottlenecks remains an important topic in evolutionary genetics. We analysed the consequences of strong population fluctuations on MHC class II DRB exon 2 diversity in two distant common vole (Microtus arvalis) populations in three consecutive years using a high-throughput sequencing approach. In 143 individuals, we detected 25 nucleotide alleles translating into 14 unique amino acid MHC alleles belonging to at least three loci. Thus, the overall allelic diversity and amino acid distance among the remaining MHC alleles, used as a surrogate for the range of pathogenic antigens that can be presented to T-cells, are still remarkably high. Both study populations did not show significant population differentiation between years, but significant differences were found between sites. We concluded that selection processes seem to be strong enough to maintain moderate levels of MHC diversity in our study populations outcompeting genetic drift, as the same MHC alleles were conserved between years. Differences in allele frequencies between populations might be the outcome of different local parasite pressures and/or genetic drift. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in cyclic populations. PMID:27225422

  7. Plant and Soil Responses to High and Low Diversity Grassland Restoration Practices

    NASA Astrophysics Data System (ADS)

    Bach, Elizabeth M.; Baer, Sara G.; Six, Johan

    2012-02-01

    The USDA's Conservation Reserve Program (CRP) has predominantly used only a few species of dominant prairie grasses (CP2 practice) to reduce soil erosion, but recently has offered a higher diversity planting practice (CP25) to increase grassland habitat quality. We quantified plant community composition in CP25 and CP2 plantings restored for 4 or 8 years and compared belowground properties and processes among restorations and continuously cultivated soils in southeastern Nebraska, USA. Relative to cultivated soils, restoration increased soil microbial biomass ( P = 0.033), specifically fungi ( P < 0.001), and restored soils exhibited higher rates of carbon (C) mineralization ( P = 0.010). High and low diversity plantings had equally diverse plant communities; however, CP25 plantings had greater frequency of cool-season (C3) grasses ( P = 0.007). Older (8 year) high diversity restorations contained lower microbial biomass ( P = 0.026), arbuscular mycorrhizal fungi (AMF) biomass ( P = 0.003), and C mineralization rates ( P = 0.028) relative to 8 year low diversity restorations; older plantings had greater root biomass than 4 year plantings in all restorations ( P = 0.001). Low diversity 8 year plantings contained wider root C:N ratios, and higher soil microbial biomass, microbial community richness, AMF biomass, and C mineralization rate relative to 4 year restorations ( P < 0.050). Net N mineralization and nitrification rates were lower in 8 year than 4 year high diversity plantings ( P = 0.005). We attributed changes in soil C and N pools and fluxes to increased AMF associated with C4 grasses in low diversity plantings. Thus, reduced recovery of AMF in high diversity plantings restricted restoration of belowground microbial diversity and microbially-mediated soil processes over time.

  8. High Diversity of Drosophilidae in High-Altitude Wet Forests in Northeastern Brazil.

    PubMed

    Monteiro, L S; Garcia, A C L; Oliveira, G F; Rohde, C

    2016-06-01

    The high-altitude wet forests of northeastern Brazil, locally known as "Brejos de Altitude," are enclaves of the Atlantic Forest situated above 500 m, surrounded by dryland vegetation, the Caatinga. The aim of this study was to characterize drosophilid communities in these upland forests, since few ecological studies on drosophilid communities have been conducted in northeastern Brazil. Four sites were investigated in three different times of the year throughout standardized traps. The results reveal the presence of 55 different species in a total of 13,064 specimens collected. The data were evaluated using ecological diversity measurements and compared with those obtained for other environments in the same geographic region. As for species composition, the Bonito upland forest, in a boundary forest location, stood out as having high species richness. PMID:26957082

  9. Gay Youth in American Public High Schools: Invisible Diversity.

    ERIC Educational Resources Information Center

    Reed, Donald B.

    Gay youth enter high school with the knowledge that they are different and with the belief that heterosexuality is normal and that homosexuality is not normal. Also, gay youth enter high school with the belief that honesty and integrity are important personal values. Additionally, the gay youth enter high school without family knowledge of their…

  10. High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence

    PubMed Central

    George, Jan-Peter; Konrad, Heino; Collin, Eric; Thevenet, Jean; Ballian, Dalibor; Idzojtic, Marilena; Kamm, Urs; Zhelev, Peter; Geburek, Thomas

    2015-01-01

    Background and Aims Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations. Methods Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods. Key Results Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = –0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted. Conclusions It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria

  11. Huangshan population of Chinese Zacco platypus (Teleostei, Cyprinidae) harbors diverse matrilines and high genetic diversity.

    PubMed

    Zheng, Xin; Zhou, Tian-Qi; Wan, Tao; Perdices, Anabel; Yang, Jin-Quan; Tang, Xin-Sheng; Wang, Zheng-Ping; Huang, Li-Qun; Huang, Song; He, Shun-Ping

    2016-03-18

    Six main mitochondrial DNA (mtDNA) lineages have been described in minnow (Zacco platypus) samples obtained from northern, western and southern China. Perdices et al. (2004) predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b (cytb) sequence variations. Combined with reported data in GenBank, we identified ten matrilines (Zacco A-J) in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus. PMID:27029868

  12. Huangshan population of Chinese Zacco platypus (Teleostei, Cyprinidae) harbors diverse matrilines and high genetic diversity

    PubMed Central

    ZHENG, Xin; ZHOU, Tian-Qi; WAN, Tao; PERDICES, Anabel; YANG, Jin-Quan; TANG, Xin-Sheng; WANG, Zheng-Ping; HUANG, Li-Qun; HUANG, Song; HE, Shun-Ping

    2016-01-01

    Six main mitochondrial DNA (mtDNA) lineages have been described in minnow (Zacco platypus) samples obtained from northern, western and southern China. Perdices et al. (2004) predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b (cytb) sequence variations. Combined with reported data in GenBank, we identified ten matrilines (Zacco A-J) in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus. PMID:27029868

  13. High cryptic soil ciliate (Ciliophora, Hypotrichida) diversity in Australia.

    PubMed

    Kumar, Santosh; Foissner, Wilhelm

    2016-04-01

    The diversity and distribution of soil ciliates from Australia is poorly known. Thus, we studied eight taxa, using the non-flooded Petri dish culture method, live observation, silver impregnation, detailed morphometrics, ontogenesis, and reinvestigation of type slides. At first glance, the Australian taxa looked very similar to described species, however, detailed investigations resulted in the identification of six cryptic species: Afroamphisiella multinucleata minima nov. subspec., Cladotricha similis nov. spec., Erimophrya similis nov. spec., Heterogonostomum salinarum nov. gen., nov. spec., Pseudohemisincirra arabica australiensis nov. subspec., and Pattersoniella (Pattersoniellides) australiensis nov. subgen., nov. spec. This new subgenus is unique among all described hypotrichs in having reduced some anterior paroral dikinetids the fibrillar associates of which are, however, still present. Only two of the eight taxa are possibly cosmopolitans: Apourosomoida halophilaFoissner et al., 2002 and Urosoma karinaeFoissner, 1987. This supports the moderate endemicity model, i.e., that a third of protists have a restricted distribution (Foissner, Chao and Katz 2008). PMID:26844781

  14. A High-Rate Space-Time Block Code with Full Diversity

    NASA Astrophysics Data System (ADS)

    Gao, Zhenzhen; Zhu, Shihua; Zhong, Zhimeng

    A new high-rate space-time block code (STBC) with full transmit diversity gain for four transmit antennas based on a generalized Alamouti code structure is proposed. The proposed code has lower Maximum Likelihood (ML) decoding complexity than the Double ABBA scheme does. Constellation rotation is used to maximize the diversity product. With the optimal rotated constellations, the proposed code significantly outperforms some known high-rate STBCs in the literature with similar complexity and the same spectral efficiency.

  15. Genetic Variability and Distribution of Mating Type Alleles in Field Populations of Leptosphaeria maculans from France

    PubMed Central

    Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

    2006-01-01

    Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

  16. Genetic variability and distribution of mating type alleles in field populations of Leptosphaeria maculans from France.

    PubMed

    Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

    2006-01-01

    Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

  17. High CYP2A6 Enzyme Activity as Measured by a Caffeine Test and Unique Distribution of CYP2A6 Variant Alleles in Ethiopian Population

    PubMed Central

    Djordjevic, Natasa; Carrillo, Juan Antonio; Makonnen, Eyasu; Bertilsson, Leif; Ingelman-Sundberg, Magnus

    2014-01-01

    Abstract CYP2A6 metabolizes clinically relevant drugs, including antiretroviral and antimalarial drugs of major public health importance for the African populations. CYP2A6 genotype–phenotype relationship in African populations, and implications of geographic differences on enzyme activity, remain to be investigated. We evaluated the influence of CYP2A6 genotype, geographical differences, gender, and cigarette smoking on enzyme activity, using caffeine as a probe in 100 healthy unrelated Ethiopians living in Ethiopia, and 72 living in Sweden. CYP2A6 phenotype was estimated by urinary 1,7-dimethyluric acid (17U)/1,7-dimethylxanthine or paraxanthine (17X) ratio. The frequencies of CYP2A6*1B, *1D, *2, *4, *9, and *1x2 in Ethiopians were 31.3, 29.4, 0.6, 0.6, 2.8, and 0.3%, respectively. The overall mean±SD for log 17U/17X was 0.12±0.24 and coefficient of variation 199%. No significant difference in the mean log 17U/17X ratio between Ethiopians living in Sweden versus Ethiopia was observed. Analysis of variance revealed CYP2A6 genotype (p=0.04, F=2.01) but not geographical differences, sex, or cigarette smoking as predictors of CYP2A6 activity. Importantly, the median (interquartile range) of 17U/17X ratio in Ethiopians 1.35 (0.99 to 1.84) was 3- and 11-fold higher than the previously reported value in Swedes 0.52 (0.27 to 1.00) and Koreans 0.13 (0.0 to 0.35), respectively (Djordjevic et al., 2013). Taken together, we report here the relevance of CYP2A6 genotype for enzyme activity in this Ethiopian sample, as well as high CYP2A6 activity and unique distribution of the CYP2A6 variant alleles in Ethiopians as compared other populations described hitherto. Because Omics biomarker research is rapidly accelerating in Africa, CYP2A6 pharmacogenetics and clinical pharmacology observations reported herein for the Ethiopian populations have clinical and biological importance to plan for future rational therapeutics efforts in the African continent as well as therapeutics

  18. Detecting the H3F3A mutant allele found in high-grade pediatric glioma by real-time PCR.

    PubMed

    Zhang, Ray; Han, Jing; Daniels, David; Huang, Haojie; Zhang, Zhiguo

    2016-01-01

    Diffuse intrinsic pontine glioma (DIPG) is an aggressive pediatric brain tumor with a median survival of 1 year after diagnosis. It has been reported recently that about 80% of DIPG cases and 70% of midline glioblastomas contain a mutation at one allele of the H3F3A gene (encoding histone H3 variant H3.3), replacing the lysine 27 with methionine (K27M). In order to facilitate diagnosis of DIPG patients, a quick and reliable method to identify the H3F3A K27M mutation is needed. Here, we describe a real-time PCR-based procedure involving a mutant-specific primer, a blocker oligonucleotide, and a reverse primer that can differentiate samples with H3F3A K27M mutation from those that do not. We first tested four different mutant-specific primers for their ability to selectively amplify H3F3A K27M-mutant allele and found that one primer amplified the mutant allele more efficiently than the rest. We then determined the optimal concentration of blocker oligo that significantly improved amplification of the H3F3A K27M-mutant allele. Using this optimized real-time PCR assay, we analyzed eleven samples, two of which containing H3F3A K27M mutation, and found that these two samples were differentially amplified from the nine others. In addition, we were able to discern the H3F3A K27M mutation in a newly obtained pediatric brainstem glioblastoma sample whose H3.3 status was not known previously, and in three other DIPG samples as well as paraffin embedded samples. These results demonstrate that we have developed a new reliable procedure for detecting the H3F3A K27M mutation in pediatric glioblastoma patient samples. PMID:26376656

  19. Ecosystems with mutually exclusive interactions self-organize to a state of high diversity.

    PubMed

    Mathiesen, Joachim; Mitarai, Namiko; Sneppen, Kim; Trusina, Ala

    2011-10-28

    Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general unknown. Using lichen communities as an example, we propose a model for the evolution of mutually excluding organisms that compete for space. We suggest that chainlike or cyclic invasions open for creation of spatially separated subpopulations that subsequently can lead to increased diversity. In contrast to its nonspatial counterpart, our model predicts robust coexistence of a large number of species. It is demonstrated that large species diversity can be obtained on evolutionary time scales, provided that interactions between species have spatial constraints. In particular, a phase transition to a sustainable state of high diversity is identified. PMID:22107676

  20. Catalogue of alleles of gliadin-coding loci in durum wheat (Triticum durum Desf.).

    PubMed

    Melnikova, N V; Kudryavtseva, A V; Kudryavtsev, A M

    2012-02-01

    Gliadins are seed storage proteins which are characterized by high intervarietal polymorphism and can be used as genetic markers. As a result of our work, a considerably extended catalogue of allelic variants of gliadin component blocks was compiled for durum wheat; 74 allelic variants for four gliadin-coding loci were identified for the first time. The extended catalogue includes a total of 131 allelic variants: 16 for locus Gli-A1(d), 19 for locus Gli-B1(d), 41 for locus Gli-A2(d), and 55 for locus Gli-B2(d). The electrophoretic pattern of the standard cultivar and a diagram are provided for every block identified. The number of alleles per family is quite small for loci Gli-A1(d) and Gli-B1(d) of durum wheat, as contrasted to loci Gli-A2(d) and Gli-B2(d) that are characterized by large families including many alleles. The presence of large block families determines a higher diversity of durum wheat for loci Gli-A2(d) and Gli-B2(d) as compared to Gli-A1(d) and Gli-B1(d). The catalogue of allelic variants of gliadin component blocks can be used by seed farmers to identify durum wheat cultivars and evaluate their purity; by breeders, to obtain homogenous cultivars and control the initial stages of selection; by gene bank experts, to preserve native varieties and the original biotypic composition of cultivars. PMID:21946233

  1. HLA-B alleles of the Cayapa of Ecuador: New B39 and B15 alleles

    SciTech Connect

    Garber, T.L.; Butler, L.M.; Watkins, D.I.

    1995-05-01

    Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles. 70 refs., 2 figs., 2 tabs.

  2. High Schools, Race, and America's Future: What Students Can Teach Us about Morality, Diversity, and Community

    ERIC Educational Resources Information Center

    Blum, Lawrence

    2012-01-01

    In "High Schools, Race, and America's Future", Lawrence Blum offers a lively account of a rigorous high school course on race and racism. Set in a racially, ethnically, and economically diverse high school, the book chronicles students' engagement with one another, with a rich and challenging academic curriculum, and with questions that relate…

  3. High-throughput FACS-based mutant screen identifies a gain-of-function allele of the Fusarium graminearum adenylyl cyclase causing deoxynivalenol over-production.

    PubMed

    Blum, Ailisa; Benfield, Aurélie H; Stiller, Jiri; Kazan, Kemal; Batley, Jacqueline; Gardiner, Donald M

    2016-05-01

    Fusarium head blight and crown rot, caused by the fungal plant pathogen Fusarium graminearum, impose a major threat to global wheat production. During the infection, plants are contaminated with mycotoxins such as deoxynivalenol (DON), which can be toxic for humans and animals. In addition, DON is a major virulence factor during wheat infection. However, it is not fully understood how DON production is regulated in F. graminearum. In order to identify regulators of DON production, a high-throughput mutant screen using Fluorescence Activated Cell Sorting (FACS) of a mutagenised TRI5-GFP reporter strain was established and a mutant over-producing DON under repressive conditions identified. A gain-of-function mutation in the F. graminearum adenylyl cyclase (FAC1), which is a known positive regulator of DON production, was identified as the cause of this phenotype through genome sequencing and segregation analysis. Our results show that the high-throughput mutant screening procedure developed here can be applied for identification of fungal proteins involved in diverse processes. PMID:26932301

  4. Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project

    PubMed Central

    2010-01-01

    Background In the last hundred years, the development of improved wheat cultivars has led to the replacement of landraces and traditional varieties by modern cultivars. This has resulted in a decline in the genetic diversity of agriculturally used wheat. However, the diversity lost in the elite material is somewhat preserved in crop gene banks. Therefore, the gene bank accessions provide the basis for genetic improvement of crops for specific traits and and represent rich sources of novel allelic variation. Results We have undertaken large scale molecular allele mining to isolate new alleles of the powdery mildew resistance gene Pm3 from wheat gene bank accessions. The search for new Pm3 alleles was carried out on a geographically diverse set of 733 wheat accessions originating from 20 countries. Pm3 specific molecular tools as well as classical pathogenicity tests were used to characterize the accessions. Two new functional Pm3 alleles were identified out of the eight newly cloned Pm3 sequences. These new resistance alleles were isolated from accessions from China and Nepal. Thus, the repertoire of functional Pm3 alleles now includes 17 genes, making it one of the largest allelic series of plant resistance genes. The combined information on resistant and susceptible Pm3 sequences will allow to study molecular function and specificity of functional Pm3 alleles. Conclusions This study demonstrates that molecular allele mining on geographically defined accessions is a useful strategy to rapidly characterize the diversity of gene bank accessions at a specific genetic locus of agronomical importance. The identified wheat accessions with new resistance specificities can be used for marker-assisted transfer of the Pm3 alleles to modern wheat lines. PMID:20470444

  5. HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of 10 918 Koreans from bone marrow donor registry in Korea.

    PubMed

    Park, H; Lee, Y-J; Song, E Y; Park, M H

    2016-10-01

    The human leucocyte antigen (HLA) system is the most polymorphic genetic system in humans, and HLA matching is crucial in organ transplantation, especially in hematopoietic stem cell transplantation. We investigated HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies at allelic level in 10 918 Koreans from bone marrow donor registry in Korea. Intermediate resolution HLA typing was performed using Luminex technology (Wakunaga, Japan), and additional allelic level typing was performed using PCR-single-strand conformation polymorphism method and/or sequence-based typing (Abbott Molecular, USA). Allele and haplotype frequencies were calculated by direct counting and maximum likelihood methods, respectively. A total of 39 HLA-A, 66 HLA-B and 47 HLA-DRB1 alleles were identified. High-frequency alleles found at a frequency of ≥5% were 6 HLA-A (A*02:01, *02:06, *11:01, *24:02, *31:01 and *33:03), 6 HLA-B (B*15:01, *35:01, *44:03, *51:01, 54:01 and *58:01) and 8 HLA-DRB1 (DRB1*01:01, *04:05, *04:06, *07:01, *08:03, *09:01, *13:02 and *15:01) alleles. At each locus, A*02, B*15 and DRB1*14 generic groups were most diverse at allelic level, consisting of 9, 12 and 11 different alleles, respectively. A total of 366, 197 and 21 different HLA-A-B-DRB1 haplotypes were estimated with frequencies of ≥0.05%, ≥0.1% and ≥0.5%, respectively. The five most common haplotypes with frequencies of ≥2.0% were A*33:03-B*44:03-DRB1*13:02 (4.97%), A*33:03-B*58:01-DRB1*13:02, A*33:03-B*44:03-DRB1*07:01, A*24:02-B*07:02-DRB1*01:01 and A*24:02-B*52:01-DRB1*15:02. Among 34 serologic HLA-A-B-DR haplotypes with frequencies of ≥0.5%, 17 haplotypes revealed allele-level diversity and majority of the allelic variation was arising from A2, A26, B61, B62, DR4 and DR14 specificities. Haplotype diversity obtained in this study is the most comprehensive data thus far reported in Koreans, and the information will be useful for unrelated stem cell transplantation as well as for disease

  6. Co-occurrence of linguistic and biological diversity in biodiversity hotspots and high biodiversity wilderness areas

    PubMed Central

    Gorenflo, L. J.; Romaine, Suzanne; Mittermeier, Russell A.; Walker-Painemilla, Kristen

    2012-01-01

    As the world grows less biologically diverse, it is becoming less linguistically and culturally diverse as well. Biologists estimate annual loss of species at 1,000 times or more greater than historic rates, and linguists predict that 50–90% of the world’s languages will disappear by the end of this century. Prior studies indicate similarities in the geographic arrangement of biological and linguistic diversity, although conclusions have often been constrained by use of data with limited spatial precision. Here we use greatly improved datasets to explore the co-occurrence of linguistic and biological diversity in regions containing many of the Earth’s remaining species: biodiversity hotspots and high biodiversity wilderness areas. Results indicate that these regions often contain considerable linguistic diversity, accounting for 70% of all languages on Earth. Moreover, the languages involved are frequently unique (endemic) to particular regions, with many facing extinction. Likely reasons for co-occurrence of linguistic and biological diversity are complex and appear to vary among localities, although strong geographic concordance between biological and linguistic diversity in many areas argues for some form of functional connection. Languages in high biodiversity regions also often co-occur with one or more specific conservation priorities, here defined as endangered species and protected areas, marking particular localities important for maintaining both forms of diversity. The results reported in this article provide a starting point for focused research exploring the relationship between biological and linguistic–cultural diversity, and for developing integrated strategies designed to conserve species and languages in regions rich in both. PMID:22566626

  7. Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes

    PubMed Central

    Barnes, Christopher J.; Maldonado, Carla; Frøslev, Tobias G.; Antonelli, Alexandre; Rønsted, Nina

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of −0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's “hidden biodiversity.”

  8. Co-occurrence of linguistic and biological diversity in biodiversity hotspots and high biodiversity wilderness areas.

    PubMed

    Gorenflo, L J; Romaine, Suzanne; Mittermeier, Russell A; Walker-Painemilla, Kristen

    2012-05-22

    As the world grows less biologically diverse, it is becoming less linguistically and culturally diverse as well. Biologists estimate annual loss of species at 1,000 times or more greater than historic rates, and linguists predict that 50-90% of the world's languages will disappear by the end of this century. Prior studies indicate similarities in the geographic arrangement of biological and linguistic diversity, although conclusions have often been constrained by use of data with limited spatial precision. Here we use greatly improved datasets to explore the co-occurrence of linguistic and biological diversity in regions containing many of the Earth's remaining species: biodiversity hotspots and high biodiversity wilderness areas. Results indicate that these regions often contain considerable linguistic diversity, accounting for 70% of all languages on Earth. Moreover, the languages involved are frequently unique (endemic) to particular regions, with many facing extinction. Likely reasons for co-occurrence of linguistic and biological diversity are complex and appear to vary among localities, although strong geographic concordance between biological and linguistic diversity in many areas argues for some form of functional connection. Languages in high biodiversity regions also often co-occur with one or more specific conservation priorities, here defined as endangered species and protected areas, marking particular localities important for maintaining both forms of diversity. The results reported in this article provide a starting point for focused research exploring the relationship between biological and linguistic-cultural diversity, and for developing integrated strategies designed to conserve species and languages in regions rich in both. PMID:22566626

  9. Mutated tumor alleles are expressed according to their DNA frequency

    PubMed Central

    Castle, John C.; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D.; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Türeci, Özlem; Sahin, Ugur

    2014-01-01

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

  10. Mutated tumor alleles are expressed according to their DNA frequency.

    PubMed

    Castle, John C; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Türeci, Özlem; Sahin, Ugur

    2014-01-01

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

  11. High Challenge, High Support: Integrating Language and Content Instruction for Diverse Learners in an English Literature Classroom

    ERIC Educational Resources Information Center

    Hammond, Jennifer

    2006-01-01

    In this paper, I argue for a response to the needs of linguistically and culturally diverse students that is both high challenge and high support. In elaborating this argument I draw on an English literature programme that was designed for a year 7 boys' class (the first year of high school) in an Australian public school. The students in the…

  12. A rare allele combination of the interleukin-1 gene complex is associated with high interleukin-1 beta plasma levels in healthy individuals.

    PubMed

    Hulkkonen, J; Laippala, P; Hurme, M

    2000-06-01

    Increases in the plasma levels of the inflammatory cytokines can be detected in various infectious and inflammatory diseases, but in healthy individuals these levels are in most cases low or undetectable. There is now increasing evidence that genes of the inflammatory cytokines are polymorphic and the various alleles may differ in their capability to produce the cytokine. We have measured the plasma levels IL-1 beta of 400 healthy blood donors and correlated these to the genotype (biallelelic base exchanges at the position - 889 of the IL-1 alpha gene, and at the position - 511 of the IL-1 beta gene and the pentaallelic VNTR in the second intron of the IL-1Ra gene). The median concentration of IL-1 beta was 5.8 pg/ml (upper and lower quartiles 2.2-13.6). The polymorphisms of the IL-1 beta and IL-1 Ra genes did not have any significant influence on the IL-1 beta levels, but the IL-1 alpha 2.2 homozygotes (32/400 blood donors) had significantly elevated levels (median 7.0 pg/ml, quartiles 2.2-22.4, one-way ANOVA p < 0.008 as compared to the IL-1 alpha 1.1 homozygotes and p < 0.02 as compared to the IL-1 alpha 1.2 heterozygotes). This effect of IL-1 alpha 2.2 homozygosity was more pronounced in donors, who also were carriers of the IL-1 beta allele 2. Thus these data suggest that this allele combination has a regulatory effect on basal IL-1 beta production. PMID:10903804

  13. Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)

    USGS Publications Warehouse

    Peters, Jeffrey L.; Sonsthagen, Sarah A.; Lavretsky, Philip; Rezsutek, Michael; Johnson, William P.; McCracken, Kevin G.

    2014-01-01

    Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (Ne). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks (Anas fulvigula) and geographically widespread mallards (A. platyrhynchos), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated Ne of mottled ducks to 33 % of the equilibrium Ne and yielded an estimated Ne consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.

  14. High frequency and founder effect of the CYP3A4*20 loss-of-function allele in the Spanish population classifies CYP3A4 as a polymorphic enzyme.

    PubMed

    Apellániz-Ruiz, M; Inglada-Pérez, L; Naranjo, M E G; Sánchez, L; Mancikova, V; Currás-Freixes, M; de Cubas, A A; Comino-Méndez, I; Triki, S; Rebai, A; Rasool, M; Moya, G; Grazina, M; Opocher, G; Cascón, A; Taboada-Echalar, P; Ingelman-Sundberg, M; Carracedo, A; Robledo, M; Llerena, A; Rodríguez-Antona, C

    2015-06-01

    Cytochrome P450 3A4 (CYP3A4) is a key drug-metabolizing enzyme. Loss-of-function variants have been reported as rare events, and the first demonstration of a CYP3A4 protein lacking functional activity is caused by CYP3A4*20 allele. Here we characterized the world distribution and origin of CYP3A4*20 mutation. CYP3A4*20 was determined in more than 4000 individuals representing different populations, and haplotype analysis was performed using CYP3A polymorphisms and microsatellite markers. CYP3A4*20 allele was present in 1.2% of the Spanish population (up to 3.8% in specific regions), and all CYP3A4*20 carriers had a common haplotype. This is compatible with a Spanish founder effect and classifies CYP3A4 as a polymorphic enzyme. This constitutes the first description of a CYP3A4 loss-of-function variant with high frequency in a population. CYP3A4*20 results together with the key role of CYP3A4 in drug metabolism support screening for rare CYP3A4 functional alleles among subjects with adverse drug events in certain populations. PMID:25348618

  15. High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi.

    PubMed

    Sánchez-Ramírez, Santiago; Etienne, Rampal S; Moncalvo, Jean-Marc

    2015-08-01

    Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity buildup, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well-recognized pattern describing a decline in species richness from the equator polewards. Recent macroecological studies in ectomycorrhizal (EM) fungi have shown that their LDG is shifted, peaking at temperate rather than tropical latitudes. Here we investigate this phenomenon from a macroevolutionary perspective, focusing on a well-sampled group of edible EM mushrooms from the genus Amanita-the Caesar's mushrooms, which follow similar diversity patterns. Our approach consisted in applying a suite of models including (1) nontrait-dependent time-varying diversification (Bayesian analysis of macroevolutionary mixtures [BAMM]), (2) continuous trait-dependent diversification (quantitative-state speciation and extinction [QuaSSE]), and (3) diversity-dependent diversification. In short, results give strong support for high speciation rates at temperate latitudes (BAMM and QuaSSE). We also find some evidence for different diversity-dependence thresholds in "temperate" and "tropical" subclades, and little differences in diversity due to extinction. We conclude that our analyses on the Caesar's mushrooms give further evidence of a temperate-peaking LDG in EM fungi, highlighting the importance and the implications of macroevolutionary processes in explaining diversity gradients in microorganisms. PMID:26179951

  16. Clonal Ordering of 17p and 5q Allelic Losses in Barrett Dysplasia and Adenocarcinoma

    NASA Astrophysics Data System (ADS)

    Blount, Patricia L.; Meltzer, Stephen J.; Yin, Jing; Huang, Ying; Krasna, Mark J.; Reid, Brian J.

    1993-04-01

    Both 17p and 5q allelic losses appear to be involved in the pathogenesis or progression of many human solid tumors. In colon carcinogenesis, there is strong evidence that the targets of the 17p and 5q allelic losses are TP53, the gene encoding p53, and APC, respectively. It is widely accepted that 5q allelic losses precede 17p allelic losses in the progression to colonic carcinoma. The data, however, supporting this proposed order are largely based on the prevalence of 17p and 5q allelic losses in adenomas and unrelated adenocarcinomas from different patients. We investigated the order in which 17p and 5q allelic losses developed during neoplastic progression in Barrett esophagus by evaluating multiple aneuploid cell populations from the same patient. Using DNA content flow cytometric cell sorting and polymerase chain reaction, 38 aneuploid cell populations from 14 patients with Barrett esophagus who had high grade dysplasia, cancer or both were evaluated for 17p and 5q allelic losses. 17p allelic losses preceded 5q allelic losses in 7 patients, both 17p and 5q allelic losses were present in all aneuploid populations of 4 patients, and only 17p (without 5q) allelic losses were present in the aneuploid populations of 3 patients. In no patient did we find that a 5q allelic loss preceded a 17p allelic loss. Our data suggest that 17p allelic losses typically occur before 5q allelic losses during neoplastic progression in Barrett esophagus.

  17. Microbial life at high salt concentrations: phylogenetic and metabolic diversity

    PubMed Central

    Oren, Aharon

    2008-01-01

    Halophiles are found in all three domains of life. Within the Bacteria we know halophiles within the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, and Bacteroidetes. Within the Archaea the most salt-requiring microorganisms are found in the class Halobacteria. Halobacterium and most of its relatives require over 100–150 g/l salt for growth and structural stability. Also within the order Methanococci we encounter halophilic species. Halophiles and non-halophilic relatives are often found together in the phylogenetic tree, and many genera, families and orders have representatives with greatly different salt requirement and tolerance. A few phylogenetically coherent groups consist of halophiles only: the order Halobacteriales, family Halobacteriaceae (Euryarchaeota) and the anaerobic fermentative bacteria of the order Halanaerobiales (Firmicutes). The family Halomonadaceae (Gammaproteobacteria) almost exclusively contains halophiles. Halophilic microorganisms use two strategies to balance their cytoplasm osmotically with their medium. The first involves accumulation of molar concentrations of KCl. This strategy requires adaptation of the intracellular enzymatic machinery, as proteins should maintain their proper conformation and activity at near-saturating salt concentrations. The proteome of such organisms is highly acidic, and most proteins denature when suspended in low salt. Such microorganisms generally cannot survive in low salt media. The second strategy is to exclude salt from the cytoplasm and to synthesize and/or accumulate organic 'compatible' solutes that do not interfere with enzymatic activity. Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range. Most halophilic Bacteria, but also the halophilic methanogenic Archaea use such organic solutes. A variety of such solutes are known, including glycine betaine

  18. Microbial life at high salt concentrations: phylogenetic and metabolic diversity.

    PubMed

    Oren, Aharon

    2008-01-01

    Halophiles are found in all three domains of life. Within the Bacteria we know halophiles within the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, and Bacteroidetes. Within the Archaea the most salt-requiring microorganisms are found in the class Halobacteria. Halobacterium and most of its relatives require over 100-150 g/l salt for growth and structural stability. Also within the order Methanococci we encounter halophilic species. Halophiles and non-halophilic relatives are often found together in the phylogenetic tree, and many genera, families and orders have representatives with greatly different salt requirement and tolerance. A few phylogenetically coherent groups consist of halophiles only: the order Halobacteriales, family Halobacteriaceae (Euryarchaeota) and the anaerobic fermentative bacteria of the order Halanaerobiales (Firmicutes). The family Halomonadaceae (Gammaproteobacteria) almost exclusively contains halophiles. Halophilic microorganisms use two strategies to balance their cytoplasm osmotically with their medium. The first involves accumulation of molar concentrations of KCl. This strategy requires adaptation of the intracellular enzymatic machinery, as proteins should maintain their proper conformation and activity at near-saturating salt concentrations. The proteome of such organisms is highly acidic, and most proteins denature when suspended in low salt. Such microorganisms generally cannot survive in low salt media. The second strategy is to exclude salt from the cytoplasm and to synthesize and/or accumulate organic 'compatible' solutes that do not interfere with enzymatic activity. Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range. Most halophilic Bacteria, but also the halophilic methanogenic Archaea use such organic solutes. A variety of such solutes are known, including glycine betaine

  19. High bat (Chiroptera) diversity in the Early Eocene of India

    NASA Astrophysics Data System (ADS)

    Smith, Thierry; Rana, Rajendra S.; Missiaen, Pieter; Rose, Kenneth D.; Sahni, Ashok; Singh, Hukam; Singh, Lachham

    2007-12-01

    The geographic origin of bats is still unknown, and fossils of earliest bats are rare and poorly diversified, with, maybe, the exception of Europe. The earliest bats are recorded from the Early Eocene of North America, Europe, North Africa and Australia where they seem to appear suddenly and simultaneously. Until now, the oldest record in Asia was from the Middle Eocene. In this paper, we report the discovery of the oldest bat fauna of Asia dating from the Early Eocene of the Cambay Formation at Vastan Lignite Mine in Western India. The fossil taxa are described on the basis of well-preserved fragments of dentaries and lower teeth. The fauna is highly diversified and is represented by seven species belonging to seven genera and at least four families. Two genera and five species are new. Three species exhibit very primitive dental characters, whereas four others indicate more advanced states. Unexpectedly, this fauna presents strong affinities with the European faunas from the French Paris Basin and the German Messel locality. This could result from the limited fossil record of bats in Asia, but could also suggest new palaeobiogeographic scenarios involving the relative position of India during the Early Eocene.

  20. High HIV-1 Genetic Diversity in Patients from Northern Brazil.

    PubMed

    da Costa, Carolina Marinho; Costa de Oliveira, Cintia Mara; Chehuan de Melo, Yonne Francis; Delatorre, Edson; Bello, Gonzalo; Couto-Fernandez, Jose Carlos

    2016-09-01

    The HIV-1 epidemic in Brazil is driven by subtypes B, F1, and C and recombinants forms among those subtypes. The distribution of HIV-1 subtypes, however, may vary across different Brazilian regions and the molecular epidemiologic profile in Northern Brazil remains poorly explored. HIV-1 pol sequences were obtained from 305 patients failing antiretroviral therapy followed at outpatient clinics from five Northern Brazilian states. The most prevalent HIV-1 clade observed in the Northern Brazilian region was subtype B (81%), followed by BF1 recombinants (10%), subtype F1 (4%), subtype C (3%), BC recombinants (2%), and BU recombinants (1%). Although HIV-1 subtype B was the predominant HIV-1 clade in Northern Brazil, its prevalence greatly varies among different states, ranging from 63% in Rondônia to 92% in Acre. Among the 37 HIV-1 recombinant sequences detected in the Northern Brazilian region, nine (24%) displayed a unique recombinant form structure, five (14%) a CRF28/29_BF-like structure, and four (11%) a CRF31_BC-like structure. Two other BF1 recombinant patterns were identified in 16 (43%) and three (8%) samples that may correspond to two potentially new CRFs_BF characteristic of the Northern region. This study reveals that despite the low spatial connectivity with other Brazilian regions, the genetic complexity of the HIV-1 epidemic in Northern Brazil is very high and that the molecular epidemiologic pattern may vary across different northern states, reflecting a complex epidemic with multiple independent viral introductions into this Brazilian region. PMID:27091699

  1. The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca).

    PubMed

    Haag, T; Santos, A S; Sana, D A; Morato, R G; Cullen, L; Crawshaw, P G; De Angelo, C; Di Bitetti, M S; Salzano, F M; Eizirik, E

    2010-11-01

    Habitat fragmentation may disrupt original patterns of gene flow and lead to drift-induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar's high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large-scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars' ability to effectively disperse across the human-dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift. PMID:21040050

  2. RECOVERY OF EXOTIC ALLELES IN ENHANCED TROPICAL YELLOW GERMPLASM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into...

  3. Recovery of Exotic Alleles in Enhanced Tropical Yellow Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into...

  4. Curriculum Diversity and Young Adult Physical Activity: Reflections from High School Physical Education

    ERIC Educational Resources Information Center

    Mears, Derrick

    2008-01-01

    This study was to evaluate if exposure to a diverse curriculum in high school physical education had an impact on young adult physical activity. Students from two universities were surveyed concerning high school physical education content exposure and physical activity in four areas. By investigating relationships between content exposure and…

  5. Nonsyntenic Genes Drive Tissue-Specific Dynamics of Differential, Nonadditive, and Allelic Expression Patterns in Maize Hybrids1[OPEN

    PubMed Central

    2016-01-01

    Distantly related maize (Zea mays) inbred lines display an exceptional degree of genomic diversity. F1 progeny of such inbred lines are often more vigorous than their parents, a phenomenon known as heterosis. In this study, we investigated how the genetic divergence of the maize inbred lines B73 and Mo17 and their F1 hybrid progeny is reflected in differential, nonadditive, and allelic expression patterns in primary root tissues. In pairwise comparisons of the four genotypes, the number of differentially expressed genes between the two parental inbred lines significantly exceeded those of parent versus hybrid comparisons in all four tissues under analysis. No differentially expressed genes were detected between reciprocal hybrids, which share the same nuclear genome. Moreover, hundreds of nonadditive and allelic expression ratios that were different from the expression ratios of the parents were observed in the reciprocal hybrids. The overlap of both nonadditive and allelic expression patterns in the reciprocal hybrids significantly exceeded the expected values. For all studied types of expression - differential, nonadditive, and allelic - substantial tissue-specific plasticity was observed. Significantly, nonsyntenic genes that evolved after the last whole genome duplication of a maize progenitor from genes with synteny to sorghum (Sorghum bicolor) were highly overrepresented among differential, nonadditive, and allelic expression patterns compared with the fraction of these genes among all expressed genes. This observation underscores the role of nonsyntenic genes in shaping the transcriptomic landscape of maize hybrids during the early developmental manifestation of heterosis in root tissues of maize hybrids. PMID:27208302

  6. Nonsyntenic Genes Drive Tissue-Specific Dynamics of Differential, Nonadditive, and Allelic Expression Patterns in Maize Hybrids.

    PubMed

    Baldauf, Jutta A; Marcon, Caroline; Paschold, Anja; Hochholdinger, Frank

    2016-06-01

    Distantly related maize (Zea mays) inbred lines display an exceptional degree of genomic diversity. F1 progeny of such inbred lines are often more vigorous than their parents, a phenomenon known as heterosis. In this study, we investigated how the genetic divergence of the maize inbred lines B73 and Mo17 and their F1 hybrid progeny is reflected in differential, nonadditive, and allelic expression patterns in primary root tissues. In pairwise comparisons of the four genotypes, the number of differentially expressed genes between the two parental inbred lines significantly exceeded those of parent versus hybrid comparisons in all four tissues under analysis. No differentially expressed genes were detected between reciprocal hybrids, which share the same nuclear genome. Moreover, hundreds of nonadditive and allelic expression ratios that were different from the expression ratios of the parents were observed in the reciprocal hybrids. The overlap of both nonadditive and allelic expression patterns in the reciprocal hybrids significantly exceeded the expected values. For all studied types of expression - differential, nonadditive, and allelic - substantial tissue-specific plasticity was observed. Significantly, nonsyntenic genes that evolved after the last whole genome duplication of a maize progenitor from genes with synteny to sorghum (Sorghum bicolor) were highly overrepresented among differential, nonadditive, and allelic expression patterns compared with the fraction of these genes among all expressed genes. This observation underscores the role of nonsyntenic genes in shaping the transcriptomic landscape of maize hybrids during the early developmental manifestation of heterosis in root tissues of maize hybrids. PMID:27208302

  7. What Is a Recessive Allele?

    ERIC Educational Resources Information Center

    American Biology Teacher, 1991

    1991-01-01

    Presents four misconceptions students have concerning the concepts of recessive and dominant alleles. Discusses the spectrum of dominant-recessive relationships, different levels of analysis between phenotype and genotype, possible causes of dominance, and an example involving wrinkled peas. (MDH)

  8. "I Thought I Was Prepared!" Meeting the Challenges of Diversity in High-Need, High-Potential Schools

    ERIC Educational Resources Information Center

    Jung, Eunjoo; Angell, Maureen E.; Moore, Marilyn K.; Lippert, Lance R.; Hunt, Stephen K.; Simonds, Brent

    2010-01-01

    This article reports descriptive findings of a qualitative investigation of early-career teachers' perceptions of their preparedness to teach diverse learners in high-need, high-potential urban schools. Interviews revealed new teachers' insights into their teacher preparation programs and the challenging expectations involved in teaching diverse…

  9. Depth and Breadth: Bridging the Gap between Scientific Inquiry and High-Stakes Testing with Diverse Junior High School Students

    ERIC Educational Resources Information Center

    Kang, Jee Sun Emily

    2009-01-01

    This study explored how inquiry-based teaching and learning processes occurred in two teachers' diverse 8th grade Physical Science classrooms in a Program Improvement junior high school within the context of high-stakes standardized testing. Instructors for the courses examined included not only the two 8th grade science teachers, but also…

  10. Diversity of Sarcocystis spp shed by opossums in Brazil inferred with phylogenetic analysis of DNA coding ITS1, cytochrome B, and surface antigens.

    PubMed

    Valadas, Samantha Y O B; da Silva, Juliana I G; Lopes, Estela Gallucci; Keid, Lara B; Zwarg, Ticiana; de Oliveira, Alice S; Sanches, Thaís C; Joppert, Adriana M; Pena, Hilda F J; Oliveira, Tricia M F S; Ferreira, Helena L; Soares, Rodrigo M

    2016-05-01

    Although few species of Sarcocystis are known to use marsupials of the genus Didelphis as definitive host, an extensive diversity of alleles of surface antigen genes (sag2, sag3, and sag4) has been described in samples of didelphid opossums in Brazil. In this work, we studied 25 samples of Sarcocystis derived from gastrointestinal tract of opossums of the genus Didelphis by accessing the variability of sag2, sag3, sag4, gene encoding cytochrome b (cytB) and first internal transcribed spacer (ITS1). Reference samples of Sarcocystis neurona (SN138) and Sarcocystis falcatula (SF1) maintained in cell culture were also analyzed. We found four allele variants of cytB, seven allele variants of ITS1, 10 allele variants of sag2, 13 allele variants of sag3, and 6 allele variants of sag4. None of the sporocyst-derived sequences obtained from Brazilian opossums revealed 100% identity to SN138 at cytB gene, nor to SN138 or SF1 at ITS1 locus. In addition, none of the sag alleles were found identical to either SF1 or SN138 homologous sequences, and a high number of new sag allele types were found other than those previously described in Brazil. Out of ten sag2 alleles, four are novel, while eight out of 13 sag3 alleles are novel and one out of six sag4 alleles is novel. Further studies are needed to clarify if such a vast repertoire of allele variants of Sarcocystis is the consequence of re-assortments driven by sexual exchange, in order to form individuals with highly diverse characteristics, such as pathogenicity, host spectrum, among others or if it only represents allele variants of different species with different biological traits. PMID:26905780

  11. High nutrient availability reduces the diversity and stability of the equine caecal microbiota

    PubMed Central

    Hansen, Naja C. K.; Avershina, Ekaterina; Mydland, Liv T.; Næsset, Jon A.; Austbø, Dag; Moen, Birgitte; Måge, Ingrid; Rudi, Knut

    2015-01-01

    Background It is well known that nutrient availability can alter the gut microbiota composition, while the effect on diversity and temporal stability remains largely unknown. Methods Here we address the equine caecal microbiota temporal stability, diversity, and functionality in response to diets with different levels of nutrient availability. Hay (low and slower nutrient availability) versus a mixture of hay and whole oats (high and more rapid nutrient availability) were used as experimental diets. Results We found major effects on the microbiota despite that the caecal pH was far from sub-clinical acidosis. We found that the low nutrient availability diet was associated with a higher level of both diversity and temporal stability of the caecal microbiota than the high nutrient availability diet. These observations concur with general ecological theories, suggesting a stabilising effect of biological diversity and that high nutrient availability has a destabilising effect through reduced diversity. Conclusion Nutrient availability does not only change the composition but also the ecology of the caecal microbiota. PMID:26246403

  12. Multitrophic diversity in a biodiverse forest is highly nonlinear across spatial scales

    PubMed Central

    Schuldt, Andreas; Wubet, Tesfaye; Buscot, François; Staab, Michael; Assmann, Thorsten; Böhnke-Kammerlander, Martin; Both, Sabine; Erfmeier, Alexandra; Klein, Alexandra-Maria; Ma, Keping; Pietsch, Katherina; Schultze, Sabrina; Wirth, Christian; Zhang, Jiayong; Zumstein, Pascale; Bruelheide, Helge

    2015-01-01

    Subtropical and tropical forests are biodiversity hotspots, and untangling the spatial scaling of their diversity is fundamental for understanding global species richness and conserving biodiversity essential to human well-being. However, scale-dependent diversity distributions among coexisting taxa remain poorly understood for heterogeneous environments in biodiverse regions. We show that diversity relations among 43 taxa—including plants, arthropods and microorganisms—in a mountainous subtropical forest are highly nonlinear across spatial scales. Taxon-specific differences in β-diversity cause under- or overestimation of overall diversity by up to 50% when using surrogate taxa such as plants. Similar relationships may apply to half of all (sub)tropical forests—including major biodiversity hotspots—where high environmental heterogeneity causes high biodiversity and species turnover. Our study highlights that our general understanding of biodiversity patterns has to be improved—and that much larger areas will be required than in better-studied lowland forests—to reliably estimate biodiversity distributions and devise conservation strategies for the world's biodiverse regions. PMID:26658136

  13. Multitrophic diversity in a biodiverse forest is highly nonlinear across spatial scales.

    PubMed

    Schuldt, Andreas; Wubet, Tesfaye; Buscot, François; Staab, Michael; Assmann, Thorsten; Böhnke-Kammerlander, Martin; Both, Sabine; Erfmeier, Alexandra; Klein, Alexandra-Maria; Ma, Keping; Pietsch, Katherina; Schultze, Sabrina; Wirth, Christian; Zhang, Jiayong; Zumstein, Pascale; Bruelheide, Helge

    2015-01-01

    Subtropical and tropical forests are biodiversity hotspots, and untangling the spatial scaling of their diversity is fundamental for understanding global species richness and conserving biodiversity essential to human well-being. However, scale-dependent diversity distributions among coexisting taxa remain poorly understood for heterogeneous environments in biodiverse regions. We show that diversity relations among 43 taxa-including plants, arthropods and microorganisms-in a mountainous subtropical forest are highly nonlinear across spatial scales. Taxon-specific differences in β-diversity cause under- or overestimation of overall diversity by up to 50% when using surrogate taxa such as plants. Similar relationships may apply to half of all (sub)tropical forests-including major biodiversity hotspots-where high environmental heterogeneity causes high biodiversity and species turnover. Our study highlights that our general understanding of biodiversity patterns has to be improved-and that much larger areas will be required than in better-studied lowland forests-to reliably estimate biodiversity distributions and devise conservation strategies for the world's biodiverse regions. PMID:26658136

  14. Does natural selection organize ecosystems for the maintenance of high productivity and diversity?

    PubMed Central

    Leigh, Egbert Giles; Vermeij, Geerat Jacobus

    2002-01-01

    Three types of evidence suggest that natural ecosystems are organized for high productivity and diversity: (i) changes not previously experienced by a natural ecosystem, such as novel human disturbances, tend to diminish its productivity and/or diversity, just as 'random' changes in a machine designed for a function usually impair its execution of that function; (ii) humans strive to recreate properties of natural ecosystems to enhance productivity of artificial ones, as farmers try to recreate properties of natural soils in their fields; and (iii) productivity and diversity have increased during the Earth's history as a whole, and after every major biotic crisis. Natural selection results in ecosystems organized to maintain high productivity of organic matter and diversity of species, just as competition among individuals in Adam Smith's ideal economy favours high production of wealth and diversity of occupations. In nature, poorly exploited energy attracts more efficient users. This circumstance favours the opening of new ways of life and more efficient recycling of resources, and eliminates most productivity-reducing 'ecological monopolies'. Ecological dominants tend to be replaced by successors with higher metabolism, which respond to more stimuli and engage in more varied interactions. Finally, increasingly efficient predators and herbivores favour faster turnover of resources. PMID:12079531

  15. Geographical Gradient of the eIF4E Alleles Conferring Resistance to Potyviruses in Pea (Pisum) Germplasm

    PubMed Central

    Konečná, Eva; Šafářová, Dana; Navrátil, Milan; Hanáček, Pavel; Coyne, Clarice; Flavell, Andrew; Vishnyakova, Margarita; Ambrose, Mike; Redden, Robert; Smýkal, Petr

    2014-01-01

    Background The eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the eIF4E gene to identify novel genetic diversity. Methodology/Principal findings Germplasm of 2803 pea accessions was screened for eIF4E intron 3 length polymorphism, resulting in the detection of four eIF4EA-B-C-S variants, whose distribution was geographically structured. The eIF4EA variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, eIF4EB, was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The eIF4EC variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The eIF4ES variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (eIF4EA-1-2-3-4-5-6-7, eIF4EB-1, eIF4EC-2) conferred resistance to the P1 PSbMV pathotype. Conclusions/Significance This work identified novel eIF4E alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible eIF4ES1 allele. Despite high variation present in wild Pisum accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis

  16. Consistent role of weak and strong interactions in high- and low-diversity trophic food webs.

    PubMed

    Gellner, Gabriel; McCann, Kevin S

    2016-01-01

    The growing realization of a looming biodiversity crisis has inspired considerable progress in the quest to link biodiversity, structure and ecosystem function. Here we construct a method that bridges low- and high-diversity approaches to food web theory by elucidating the connection between the stability of the basic building block of food webs and the mean stability properties of large random food web networks. Applying this theoretical framework to common food web models reveals two key findings. First, in almost all cases, high-diversity food web models yield a stability relationship between weak and strong interactions that are compatible in every way to simple low-diversity models. And second, the models that generate the recently discovered phenomena of being purely stabilized by increasing interaction strength correspond to the biologically implausible assumption of perfect interaction strength symmetry. PMID:27068000

  17. Consistent role of weak and strong interactions in high- and low-diversity trophic food webs

    PubMed Central

    Gellner, Gabriel; McCann, Kevin S.

    2016-01-01

    The growing realization of a looming biodiversity crisis has inspired considerable progress in the quest to link biodiversity, structure and ecosystem function. Here we construct a method that bridges low- and high-diversity approaches to food web theory by elucidating the connection between the stability of the basic building block of food webs and the mean stability properties of large random food web networks. Applying this theoretical framework to common food web models reveals two key findings. First, in almost all cases, high-diversity food web models yield a stability relationship between weak and strong interactions that are compatible in every way to simple low-diversity models. And second, the models that generate the recently discovered phenomena of being purely stabilized by increasing interaction strength correspond to the biologically implausible assumption of perfect interaction strength symmetry. PMID:27068000

  18. Biased Allelic Expression in Human Primary Fibroblast Single Cells

    PubMed Central

    Borel, Christelle; Ferreira, Pedro G.; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y.; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T.; Antonarakis, Stylianos E.

    2015-01-01

    The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

  19. High diversity of root associated fungi in both alpine and arctic Dryas octopetala

    PubMed Central

    2010-01-01

    Background Dryas octopetala is a widespread dwarf shrub in alpine and arctic regions that forms ectomycorrhizal (ECM) symbiotic relationships with fungi. In this study we investigated the fungal communities associated with roots of D. octopetala in alpine sites in Norway and in the High Arctic on Svalbard, where we aimed to reveal whether the fungal diversity and species composition varied across the Alpine and Arctic regions. The internal transcribed spacer (ITS) region of nuclear ribosomal DNA was used to identify the fungal communities from bulk root samples obtained from 24 plants. Results A total of 137 operational taxonomic units (OTUs) were detected (using 97% similarity cut off during sequence clustering) and well-known ECM genera such as Cenococcum, Cortinarius, Hebeloma, Inocybe and Tomentella occurred frequently. There was no decrease in fungal diversity with increasing latitude. The overall spatial heterogeneity was high, but a weak geographical structuring of the composition of OTUs in the root systems was observed. Calculated species accumulation curves did not level off. Conclusions This study indicates that the diversity of fungi associated with D. octopetala does not decrease in high latitude arctic regions, which contrasts observations made in a wide spectrum of other organism groups. A high degree of patchiness was observed across root systems, but the fungal communities were nevertheless weakly spatially structured. Non-asymptotical species accumulation curves and the occurrence of a high number of singletons indicated that only a small fraction of the fungal diversity was detected. PMID:21070665

  20. Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

    PubMed Central

    Pyron, R. Alexander; Wiens, John J.

    2013-01-01

    Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently. PMID:24026818

  1. A spider species complex revealed high cryptic diversity in South China caves.

    PubMed

    Zhang, Yuanyuan; Li, Shuqiang

    2014-10-01

    Cryptic species, which are an important component of biodiversity, have rarely been studied in South China karst. We investigated cryptic diversity in the cave species complex Telema cucurbitina, which has a narrow niche but widespread distribution among multiple caves. We sampled another 15 populations (caves) in addition to the population from the type locality. Phylogenetic results indicated that individuals from the same cave constituted well-supported clades. Species diversity within this species complex was assessed in a coalescent framework, first with a Bayesian extension of the general mixed Yule coalescent (bGMYC) model and a Bayesian species delimitation method (BPP). Both species delimitation methods identified each cave population as a separate species. We propose that each cave population within this species complex was a separate evolving lineage and therefore 16 OTUs were recovered based on our molecular data despite their high morphological similarities. We also propose that the unrecognized organism's diversity within South China caves might be extremely large considering our case. Furthermore, our work reveals that species discovery of cave organisms by morphological data has a high probability of underestimating hidden diversity. Our work also highlights the need for conservation strategies to protect this largely neglected diversity of cave organisms. PMID:24994029

  2. Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

    PubMed Central

    2010-01-01

    Background Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size. Results The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size) or similar proportions of retained alleles (in a core collection of smaller size) were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed. Conclusions Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection potentially reflects the maximum

  3. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers.

    PubMed

    Kashyap, V K; Ashma, Richa; Gaikwad, Sonali; Sarkar, B N; Trivedi, R

    2004-04-01

    The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic

  4. Evolution of HLA class II molecules: Allelic and amino acid site variability across populations.

    PubMed Central

    Salamon, H; Klitz, W; Easteal, S; Gao, X; Erlich, H A; Fernandez-Viña, M; Trachtenberg, E A; McWeeney, S K; Nelson, M P; Thomson, G

    1999-01-01

    Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations. PMID:10224269

  5. High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Implementation of molecular methods in hop breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. Diversity Arrays Technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of...

  6. Social Justice Education in a Diverse Classroom: Examining High School Discussions about Race, Power, and Privilege

    ERIC Educational Resources Information Center

    Welton, Anjalé D.; Harris, Tiffany Octavia; La Londe, Priya G.; Moyer, Rachel T.

    2015-01-01

    High school students who participate in social justice education have a greater awareness of inequities that impact their school, community, and society, and learn tools for taking action to address these inequities. Also, a classroom that consist of students with a diverse set of identities creates an ideal circumstance in which a teacher can…

  7. Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)

    EPA Science Inventory

    Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

  8. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advances in next-generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restri...

  9. iPad Deployment in a Diverse Urban High School: A Formative Experiment

    ERIC Educational Resources Information Center

    Frey, Nancy; Fisher, Douglas; Lapp, Diane

    2015-01-01

    We explore the use of iPads in a diverse urban high school and the ways in which teachers and students were supported to integrate these tools into their instruction. We provided 4 English teachers with 20 iPads with little or no professional development about how to integrate them into their instruction. Using a formative experiment design, we…

  10. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea

    PubMed Central

    Bajaj, Deepak; Srivastava, Rishi; Nath, Manoj; Tripathi, Shailesh; Bharadwaj, Chellapilla; Upadhyaya, Hari D.; Tyagi, Akhilesh K.; Parida, Swarup K.

    2016-01-01

    The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10–15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea. PMID:27148286

  11. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea.

    PubMed

    Bajaj, Deepak; Srivastava, Rishi; Nath, Manoj; Tripathi, Shailesh; Bharadwaj, Chellapilla; Upadhyaya, Hari D; Tyagi, Akhilesh K; Parida, Swarup K

    2016-01-01

    The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea. PMID:27148286

  12. Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them.

    PubMed

    Zhai, Feifei; Mao, Jinmei; Liu, Junxiang; Peng, Xiangyong; Han, Lei; Sun, Zhenyuan

    2016-01-01

    Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation. PMID:27047511

  13. Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them

    PubMed Central

    Zhai, Feifei; Mao, Jinmei; Liu, Junxiang; Peng, Xiangyong; Han, Lei; Sun, Zhenyuan

    2016-01-01

    Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation. PMID:27047511

  14. Molecular breeding for introgression of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B) enhances oil quality in high and low oil containing peanut genotypes.

    PubMed

    Janila, Pasupuleti; Pandey, Manish K; Shasidhar, Yaduru; Variath, Murali T; Sriswathi, Manda; Khera, Pawan; Manohar, Surendra S; Nagesh, Patne; Vishwakarma, Manish K; Mishra, Gyan P; Radhakrishnan, T; Manivannan, N; Dobariya, K L; Vasanthi, R P; Varshney, Rajeev K

    2016-01-01

    High oleate peanuts have two marketable benefits, health benefits to consumers and extended shelf life of peanut products. Two mutant alleles present on linkage group a09 (ahFAD2A) and b09 (ahFAD2B) control composition of three major fatty acids, oleic, linoleic and palmitic acids which together determine peanut oil quality. In conventional breeding, selection for fatty acid composition is delayed to advanced generations. However by using DNA markers, breeders can reject large number of plants in early generations and therefore can optimize time and resources. Here, two approaches of molecular breeding namely marker-assisted backcrossing (MABC) and marker-assisted selection (MAS) were employed to transfer two FAD2 mutant alleles from SunOleic 95R into the genetic background of ICGV 06110, ICGV 06142 and ICGV 06420. In summary, 82 MABC and 387 MAS derived introgression lines (ILs) were developed using DNA markers with elevated oleic acid varying from 62 to 83%. Oleic acid increased by 0.5-1.1 folds, with concomitant reduction of linoleic acid by 0.4-1.0 folds and palmitic acid by 0.1-0.6 folds among ILs compared to recurrent parents. Finally, high oleate ILs, 27 with high oil (53-58%), and 28 ILs with low oil content (42-50%) were selected that may be released for cultivation upon further evaluation. PMID:26566838

  15. High diversity of methanotrophic bacteria in geothermal soils affected by high methane fluxes

    NASA Astrophysics Data System (ADS)

    D'Alessandro, Walter; Gagliano, Antonina Lisa; Quatrini, Paola; Parello, Francesco

    2014-05-01

    enrichment cultures. The isolates showed a wide range of tolerance to pH (3.5 - 8) and temperatures (18 - 45°C), and an average methane oxidation rate of 450 ppm/h. A larger diversity of proteobacterial and verrucomicrobial methanotrophs was detected by the amplification of the methane mono-oxygenase gene pmoA. This study demonstrates the coexistence of both the methanotrophic phyla Verrucomicrobia and Proteobacteria in the same geothermal site. The presence of proteobacterial methanotrophs was quite unexpected because they are generally considered not adapted to live in such harsh environments. Their presence at Favara Grande could be explained by not so low soil pH values (> 5) of this specific geothermal site and by the high methane availability. Such species could have found their niches in the shallowest part of the soils, were the temperatures are not so high, thriving on the abundant upraising methane. Understanding the ecology of methanotrophy in geothermal sites will increase our knowledge of their role in methane emissions to the atmosphere.

  16. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis

    PubMed Central

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-01-01

    Abstract Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5′- and 3′-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients. Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3′-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5′-UTR polymorphisms). For neither the 3′- nor the 5′-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance. The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold

  17. High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks

    PubMed Central

    Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrão, Ester

    2013-01-01

    The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhizapolyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038

  18. High and distinct range-edge genetic diversity despite local bottlenecks.

    PubMed

    Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Serrão, Ester Alvares

    2013-01-01

    The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038

  19. A and MdMYB1 allele-specific markers controlling apple (Malus x domestica Borkh.) skin color and suitability for marker-assisted selection.

    PubMed

    Zhang, X J; Wang, L X; Chen, X X; Liu, Y L; Meng, R; Wang, Y J; Zhao, Z Y

    2014-01-01

    Pre-selection for fruit skin color at the seedling stage would be highly advantageous, with marker-assisted selection offering a potential method for apple pre-selection. A and MdMYB1 alleles are allele-specific DNA markers that are potentially associated with apple skin color, and co-segregate with the Rf and Rni loci, respectively. Here, we assessed the potential application of these 2 alleles for marker-assisted breeding across 30 diverse cultivars and 2 apple seedling progenies. The red skin color phenotype was usually associated with the MdMYB1-1 allele and A(1) allele, respectively, while the 2 molecular markers provided approximately 91% predictability in the 'Fuji' x 'Cripps Pink' and 'Fuji' x 'Gala' progenies. The results obtained from the 30 cultivars and 2 progenies were consistent for the 2 molecular markers. Hence, the results supported that Rf and Rni could be located in a gene cluster, or even correspond to alleles of the same gene. Our results are consistent with the hypothesis that red/yellow dimorphism is controlled by a monogenic system, with the presence of the red anthocyanin pigmentation being dominant. In addition, our results supported that the practical utilization of the 2 function markers to efficiently and accurately select red-skinned apple cultivars in apple scion breeding programs. PMID:25366802

  20. Analysis of genetic variation and diversity of Rice stripe virus populations through high-throughput sequencing.

    PubMed

    Huang, Lingzhe; Li, Zefeng; Wu, Jianxiang; Xu, Yi; Yang, Xiuling; Fan, Longjiang; Fang, Rongxiang; Zhou, Xueping

    2015-01-01

    Plant RNA viruses often generate diverse populations in their host plants through error-prone replication and recombination. Recent studies on the genetic diversity of plant RNA viruses in various host plants have provided valuable information about RNA virus evolution and emergence of new diseases caused by RNA viruses. We analyzed and compared the genetic diversity of Rice stripe virus (RSV) populations in Oryza sativa (a natural host of RSV) and compared it with that of the RSV populations generated in an infection of Nicotiana benthamiana, an experimental host of RSV, using the high-throughput sequencing technology. From infected O. sativa and N. benthamiana plants, a total of 341 and 1675 site substitutions were identified in the RSV genome, respectively, and the average substitution ratio in these sites was 1.47 and 7.05 %, respectively, indicating that the RSV populations from infected N. benthamiana plant are more diverse than those from infected O. sativa plant. Our result gives a direct evidence that virus might allow higher genetic diversity for host adaptation. PMID:25852724

  1. Rapid anti-pathogen response in ant societies relies on high genetic diversity.

    PubMed

    Ugelvig, Line V; Kronauer, Daniel J C; Schrempf, Alexandra; Heinze, Jürgen; Cremer, Sylvia

    2010-09-22

    Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony. PMID:20444720

  2. Rapid anti-pathogen response in ant societies relies on high genetic diversity

    PubMed Central

    Ugelvig, Line V.; Kronauer, Daniel J. C.; Schrempf, Alexandra; Heinze, Jürgen; Cremer, Sylvia

    2010-01-01

    Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony. PMID:20444720

  3. High diversity of West African bat malaria parasites and a tight link with rodent Plasmodium taxa

    PubMed Central

    Schaer, Juliane; Perkins, Susan L.; Decher, Jan; Leendertz, Fabian H.; Fahr, Jakob; Weber, Natalie; Matuschewski, Kai

    2013-01-01

    As the only volant mammals, bats are captivating for their high taxonomic diversity, for their vital roles in ecosystems—particularly as pollinators and insectivores—and, more recently, for their important roles in the maintenance and transmission of zoonotic viral diseases. Genome sequences have identified evidence for a striking expansion of and positive selection in gene families associated with immunity. Bats have also been known to be hosts of malaria parasites for over a century, and as hosts, they possess perhaps the most phylogenetically diverse set of hemosporidian genera and species. To provide a molecular framework for the study of these parasites, we surveyed bats in three remote areas of the Upper Guinean forest ecosystem. We detected four distinct genera of hemosporidian parasites: Plasmodium, Polychromophilus, Nycteria, and Hepatocystis. Intriguingly, the two species of Plasmodium in bats fall within the clade of rodent malaria parasites, indicative of multiple host switches across mammalian orders. We show that Nycteria species form a very distinct phylogenetic group and that Hepatocystis parasites display an unusually high diversity and prevalence in epauletted fruit bats. The diversity and high prevalence of novel lineages of chiropteran hemosporidians underscore the exceptional position of bats among all other mammalian hosts of hemosporidian parasites and support hypotheses of pathogen tolerance consistent with the exceptional immunology of bats. PMID:24101466

  4. Common alleles contribute to schizophrenia in CNV carriers

    PubMed Central

    Tansey, K E; Rees, E; Linden, D E; Ripke, S; Chambert, K D; Moran, J L; McCarroll, S A; Holmans, P; Kirov, G; Walters, J; Owen, M J; O'Donovan, M C

    2016-01-01

    The genetic architecture of schizophrenia is complex, involving risk alleles ranging from common alleles of weak effect to rare alleles of large effect, the best exemplar of the latter being large copy number variants (CNVs). It is currently unknown whether pathophysiology in those with defined rare mutations overlaps with that in other individuals with the disorder who do not share the same rare mutation. Under an extreme heterogeneity model, carriers of specific high-penetrance mutations form distinct subgroups. In contrast, under a polygenic threshold model, high-penetrance rare allele carriers possess many risk factors, of which the rare allele is the only one, albeit an important, factor. Under the latter model, cases with rare mutations can be expected to share some common risk alleles, and therefore pathophysiological mechanisms, with cases without the same mutation. Here we show that, compared with controls, individuals with schizophrenia who have known pathogenic CNVs carry an excess burden of common risk alleles (P=2.25 × 10−17) defined from a genome-wide association study largely based on individuals without known CNVs. Our finding is not consistent with an extreme heterogeneity model for CNV carriers, but does offer support for the polygenic threshold model of schizophrenia. That this is so provides support for the notion that studies aiming to model the effects of rare variation may uncover pathophysiological mechanisms of relevance to those with the disorder more widely. PMID:26390827

  5. Common alleles contribute to schizophrenia in CNV carriers.

    PubMed

    Tansey, K E; Rees, E; Linden, D E; Ripke, S; Chambert, K D; Moran, J L; McCarroll, S A; Holmans, P; Kirov, G; Walters, J; Owen, M J; O'Donovan, M C

    2016-08-01

    The genetic architecture of schizophrenia is complex, involving risk alleles ranging from common alleles of weak effect to rare alleles of large effect, the best exemplar of the latter being large copy number variants (CNVs). It is currently unknown whether pathophysiology in those with defined rare mutations overlaps with that in other individuals with the disorder who do not share the same rare mutation. Under an extreme heterogeneity model, carriers of specific high-penetrance mutations form distinct subgroups. In contrast, under a polygenic threshold model, high-penetrance rare allele carriers possess many risk factors, of which the rare allele is the only one, albeit an important, factor. Under the latter model, cases with rare mutations can be expected to share some common risk alleles, and therefore pathophysiological mechanisms, with cases without the same mutation. Here we show that, compared with controls, individuals with schizophrenia who have known pathogenic CNVs carry an excess burden of common risk alleles (P=2.25 × 10(-17)) defined from a genome-wide association study largely based on individuals without known CNVs. Our finding is not consistent with an extreme heterogeneity model for CNV carriers, but does offer support for the polygenic threshold model of schizophrenia. That this is so provides support for the notion that studies aiming to model the effects of rare variation may uncover pathophysiological mechanisms of relevance to those with the disorder more widely. PMID:26390827

  6. Highly diverse and seasonally dynamic protist community in a pristine peat bog.

    PubMed

    Lara, Enrique; Mitchell, Edward A D; Moreira, David; López García, Purificación

    2011-01-01

    Culture-independent molecular methods based on the amplification, cloning and sequencing of small-subunit ribosomal RNA genes (SSU rDNAs) are powerful tools to study the diversity of microorganisms. Despite so, the eukaryotic microbial diversity of many ecosystems, including peatlands has not yet received much attention. We analysed the eukaryotic diversity by molecular surveys in water from the centre of a pristineSphagnum-dominated peatland in the Jura Mountains of Switzerland during a complete seasonal cycle. The clone libraries constructed from five different temporal samplings revealed a high diversity of protists with representatives of all major eukaryotic phyla. In addition, four sequence types could not be assigned to any known high-level eukaryotic taxon but branched together with a rather good statistic support, raising the possibility of a novel, deep branching eukaryotic clade. The analysis of seasonal patterns of phylotypes showed a clear change in the eukaryotic communities between the warm period (late spring and summer) and the cold period (autumn and winter). Chrysophytes dominated the samples in the cold period while testate amoebae (Arcellinida and Euglyphida) and a few other groups peaked in summer. A few phylotypes (such as a cryptomonad and a perkinsid) were abundant at given sampling times and then almost disappeared, suggesting bloom-like dynamics. PMID:20692868

  7. High-Pitched Notes during Vocal Contests Signal Genetic Diversity in Ocellated Antbirds

    PubMed Central

    Araya-Ajoy, Yi-men; Chaves-Campos, Johel; Kalko, Elisabeth K. V.; DeWoody, J. Andrew

    2009-01-01

    Animals use honest signals to assess the quality of competitors during aggressive interactions. Current theory predicts that honest signals should be costly to produce and thus reveal some aspects of the phenotypic or genetic quality of the sender. In songbirds, research indicates that biomechanical constraints make the production of some acoustic features costly. Furthermore, recent studies have found that vocal features are related to genetic diversity. We linked these two lines of research by evaluating if constrained acoustic features reveal male genetic diversity during aggressive interactions in ocellated antbirds (Phaenostictus mcleannani). We recorded the aggressive vocalizations of radiotagged males at La Selva Biological Station in Costa Rica, and found significant variation in the highest frequency produced among individuals. Moreover, we detected a negative relationship between the frequency of the highest pitched note and vocalization duration, suggesting that high pitched notes might constrain the duration of vocalizations through biomechanical and/or energetic limitations. When we experimentally exposed wild radiotagged males to simulated acoustic challenges, the birds increased the pitch of their vocalization. We also found that individuals with higher genetic diversity (as measured by zygosity across 9 microsatellite loci) produced notes of higher pitch during aggressive interactions. Overall, our results suggest that the ability to produce high pitched notes is an honest indicator of male genetic diversity in male-male aggressive interactions. PMID:19956580

  8. Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities

    PubMed Central

    Chisholm, Ryan A.; Pacala, Stephen W.

    2010-01-01

    A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function. PMID:20733073

  9. Engineering of bacterial exotoxins for highly efficient and receptor-specific intracellular delivery of diverse cargos.

    PubMed

    Ryou, Jeong-Hyun; Sohn, Yoo-Kyoung; Hwang, Da-Eun; Park, Woo-Yong; Kim, Nury; Heo, Won-Do; Kim, Mi-Young; Kim, Hak-Sung

    2016-08-01

    The intracellular delivery of proteins with high efficiency in a receptor-specific manner is of great significance in molecular medicine and biotechnology, but remains a challenge. Herein, we present the development of a highly efficient and receptor-specific delivery platform for protein cargos by combining the receptor binding domain of Escherichia coli Shiga-like toxin and the translocation domain of Pseudomonas aeruginosa exotoxin A. We demonstrated the utility and efficiency of the delivery platform by showing a cytosolic delivery of diverse proteins both in vitro and in vivo in a receptor-specific manner. In particular, the delivery system was shown to be effective for targeting an intracellular protein and consequently suppressing the tumor growth in xenograft mice. The present platform can be widely used for intracellular delivery of diverse functional macromolecules with high efficiency in a receptor-specific manner. Biotechnol. Bioeng. 2016;113: 1639-1646. © 2016 Wiley Periodicals, Inc. PMID:26773973

  10. Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation

    PubMed Central

    Ægisdóttir, Hafdís Hanna; Kuss, Patrick; Stöcklin, Jürg

    2009-01-01

    Background and Aims Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity. Methods Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure. Key Results High within-population genetic diversity (HE = 0·76) and a relatively low inbreeding coefficient (FIS = 0·022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G′ST = 0·53). A significant isolation-by-distance relationship was found (r = 0·62, P < 0·001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population. Conclusions The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear western–eastern differentiation in this species

  11. Cranial biomechanics underpins high sauropod diversity in resource-poor environments

    PubMed Central

    Button, David J.; Rayfield, Emily J.; Barrett, Paul M.

    2014-01-01

    High megaherbivore species richness is documented in both fossil and contemporary ecosystems despite their high individual energy requirements. An extreme example of this is the Late Jurassic Morrison Formation, which was dominated by sauropod dinosaurs, the largest known terrestrial vertebrates. High sauropod diversity within the resource-limited Morrison is paradoxical, but might be explicable through sophisticated resource partitioning. This hypothesis was tested through finite-element analysis of the crania of the Morrison taxa Camarasaurus and Diplodocus. Results demonstrate divergent specialization, with Camarasaurus capable of exerting and accommodating greater bite forces than Diplodocus, permitting consumption of harder food items. Analysis of craniodental biomechanical characters taken from 35 sauropod taxa demonstrates a functional dichotomy in terms of bite force, cranial robustness and occlusal relationships yielding two polyphyletic functional ‘grades’. Morrison taxa are widely distributed within and between these two morphotypes, reflecting distinctive foraging specializations that formed a biomechanical basis for niche partitioning between them. This partitioning, coupled with benefits associated with large body size, would have enabled the high sauropod diversities present in the Morrison Formation. Further, this provides insight into the mechanisms responsible for supporting the high diversities of large megaherbivores observed in other Mesozoic and Cenozoic communities, particularly those occurring in resource-limited environments. PMID:25297869

  12. Results of Expedicion Humana. I. Analysis of HLA class II (DRB1-DQA1-DPB1) alleles and DR-DQ haplotypes in nine Amerindian populations from Colombia.

    PubMed

    Trachtenberg, E A; Keyeux, G; Bernal, J E; Rhodas, M C; Erlich, H A

    1996-09-01

    HLA class II variation was analyzed in nine Native American populations of Colombia using PCR/SSOP typing methods. Under the auspices of the Expedition Humana, approximately 30 unrelated native Colombia Indian samples each from the Tule (NW Pacific Coast), Kogui (Sierra Nevada). Ijka (Sierra Nevada), Ingano (Amazonas), Coreguaje (Amazonas), Nukak (Amazonas), Waunana (Pacific), Embera (Pacific) and Sikuani (Northeastern Plains) were collected and analyzed at the DRBI, DQA1, DQB1 and DPB1 loci. The number of different DRB1, DQA1, DQB1 and DPB1 alleles in the Colombian Indians is markedly reduced in comparison with neighboring African Colombian populations, which exhibit a very high degree of class II variability, as discussed in an accompanying paper. In the Colombian Amerindian groups, DR2 (DRB1*1602), DR4 (DRB1*0407, *0404, *0403 AND *0411), DR6 (DRB1*1402) and DR8 (DRB1*0802) comprise > 95% of all DRB1 alleles. We also found an absence of DR3 in all populations, and DR1, DR7 and DR9 allelic groups were either very rare or absent. Each Colombian Amerindian population has a predominant DRB1 allele (f = approximately 0.22-0.65) and DRB1-DQA1-DQB1 haplotype. Several novel DR-DQ haplotypes were also found. At the DPB1 locus, DPB1*0402 (f = 0.28-0.82), *1401 (f = 0.03-0.45), and *3501 (f = 0.03-0.27), were the three most prevalent alleles, each population maintaining one of these three alleles as the predominant (f > 0.26) DPB1 allele. The reduction of diversity for the HLA class II alleles in the Colombian Indians is suggestive of a population bottleneck during the colonization of the Americans, with little to no subsequent admixture with neighboring African Colombian populations in the last approximately 300 years. PMID:8896175

  13. Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

    Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

  14. Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity

    PubMed Central

    Cousins, Matthew M.; Ou, San-San; Wawer, Maria J.; Munshaw, Supriya; Swan, David; Magaret, Craig A.; Mullis, Caroline E.; Serwadda, David; Porcella, Stephen F.; Gray, Ronald H.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

    2012-01-01

    Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution. PMID:22785188

  15. Genetic Diversity and mRNA Expression of Porcine MHC Class I Chain-Related 2 (SLA-MIC2) Gene and Development of a High-Resolution Typing Method

    PubMed Central

    Dinka, Hunduma; Nguyen, DinhTruong; Choi, Hojun; Cho, Hyesun; Choi, Minkyeung; Kim, Jin-Hoi; Park, Jin-Ki; Soundrarajan, Nagasundarapandian; Park, Chankyu

    2015-01-01

    The genetic structure and function of MHC class I chain-related (MIC) genes in the pig genome have not been well characterized, and show discordance in available data. Therefore, we have experimentally characterized the exon-intron structure and functional copy expression pattern of the pig MIC gene, SLA-MIC2. We have also studied the genetic diversity of SLA-MIC2 from seven different breeds using a high-resolution genomic sequence-based typing (GSBT) method. Our results showed that the SLA-MIC2 gene has a similar molecular organization as the human and cattle orthologs, and is expressed in only a few tissues including the small intestine, lung, and heart. A total of fifteen SLA-MIC2 alleles were identified from typing 145 animals, ten of which were previously unreported. Our analysis showed that the previously reported and tentatively named SLA-MIC2*05, 07, and 01 alleles occurred most frequently. The observed heterozygosity varied from 0.26 to 0.73 among breeds. The number of alleles of the SLA-MIC2 gene in pigs is somewhat lower compared to the number of alleles of the porcine MHC class I and II genes; however, the level of heterozygosity was similar. Our results indicate the comprehensiveness of using genomic DNA-based typing for the systemic study of the SLA-MIC2 gene. The method developed for this study, as well as the detailed information that was obtained, could serve as fundamental tools for understanding the influence of the SLA-MIC2 gene on porcine immune responses. PMID:26305091

  16. High conopeptide diversity in Conus tribblei revealed through analysis of venom duct transcriptome using two high-throughput sequencing platforms

    PubMed Central

    Barghi, Neda; Concepcion, Gisela P.; Olivera, Baldomero M.; Lluisma, Arturo O.

    2015-01-01

    The venom of each species of Conus contains different kinds of pharmacologically-active peptides which are mostly unique to that species. Collectively, the ~500 – 700 species of Conus produce a large number of these peptides, perhaps exceeding 140,000 different types in total. To date, however, only a small fraction of this diversity has been characterized via transcriptome sequencing. In addition, the sampling of this chemical diversity has not been uniform across the different lineages in the genus. In this study, we used high-throughput transcriptome sequencing approach to further investigate the diversity of Conus venom peptides. We chose a species, Conus tribblei, as a representative of a poorly studied clade of Conus. Using the Roche 454 and Illumina platforms, we discovered 136 unique and novel putative conopeptides belonging to 30 known gene superfamilies and 6 new conopeptide groups, the greatest diversity so far observed from a transcriptome. Most of the identified peptides exhibited divergence from the known conopeptides and some contained cysteine frameworks observed for the first time in cone snails. In addition, several enzymes involved in post-translational modification of conopeptides and also some proteins involved in efficient delivery of the conopeptides to prey were identified as well. Interestingly, a number of conopeptides highly similar to the conopeptides identified in a phylogenetically distant species, the generalist feeder Conus californicus, were observed. The high diversity of conopeptides and the presence of conopeptides similar to those in C. californicus suggest that C. tribblei may have a broad range of prey preferences. PMID:25117477

  17. Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts.

    PubMed

    Haynes, Benjamin T; Marcus, Alan D; Higgins, Damien P; Gongora, Jaime; Gray, Rachael; Šlapeta, Jan

    2014-12-01

    The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h=0.986) and nucleotide diversity (π=0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST=0.007) and a high gene flow (Nm=35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology. PMID:25262830

  18. Unexpected high diversity of galling insects in the Amazonian upper canopy: the savanna out there.

    PubMed

    Julião, Genimar R; Venticinque, Eduardo M; Fernandes, G Wilson; Price, Peter W

    2014-01-01

    A relatively large number of studies reassert the strong relationship between galling insect diversity and extreme hydric and thermal status in some habitats, and an overall pattern of a greater number of galling species in the understory of scleromorphic vegetation. We compared galling insect diversity in the forest canopy and its relationship with tree richness among upland terra firme, várzea, and igapó floodplains in Amazonia, Brazil. The soils of these forest types have highly different hydric and nutritional status. Overall, we examined the upper layer of 1,091 tree crowns. Galling species richness and abundance were higher in terra firme forests compared to várzea and igapó forests. GLM-ANCOVA models revealed that the number of tree species sampled in each forest type was determinant in the gall-forming insect diversity. The ratio between galling insect richness and number of tree species sampled (GIR/TSS ratio) was higher in the terra firme forest and in seasonally flooded igapó, while the várzea presented the lowest GIR/TSS ratio. In this study, we recorded unprecedented values of galling species diversity and abundance per sampling point. The GIR/TSS ratio from várzea was approximately 2.5 times higher than the highest value of this ratio ever reported in the literature. Based on this fact, we ascertained that várzea and igapó floodplain forests (with lower GIA and GIR), together with the speciose terra firme galling community emerge as the gall diversity apex landscape among all biogeographic regions already investigated. Contrary to expectation, our results also support the "harsh environment hypothesis", and unveil the Amazonian upper canopy as similar to Mediterranean vegetation habitats, hygrothermically stressed environments with leaf temperature at lethal limits and high levels of leaf sclerophylly. PMID:25551769

  19. Unexpected High Diversity of Galling Insects in the Amazonian Upper Canopy: The Savanna Out There

    PubMed Central

    Julião, Genimar R.; Venticinque, Eduardo M.; Fernandes, G. Wilson; Price, Peter W.

    2014-01-01

    A relatively large number of studies reassert the strong relationship between galling insect diversity and extreme hydric and thermal status in some habitats, and an overall pattern of a greater number of galling species in the understory of scleromorphic vegetation. We compared galling insect diversity in the forest canopy and its relationship with tree richness among upland terra firme, várzea, and igapó floodplains in Amazonia, Brazil. The soils of these forest types have highly different hydric and nutritional status. Overall, we examined the upper layer of 1,091 tree crowns. Galling species richness and abundance were higher in terra firme forests compared to várzea and igapó forests. GLM-ANCOVA models revealed that the number of tree species sampled in each forest type was determinant in the gall-forming insect diversity. The ratio between galling insect richness and number of tree species sampled (GIR/TSS ratio) was higher in the terra firme forest and in seasonally flooded igapó, while the várzea presented the lowest GIR/TSS ratio. In this study, we recorded unprecedented values of galling species diversity and abundance per sampling point. The GIR/TSS ratio from várzea was approximately 2.5 times higher than the highest value of this ratio ever reported in the literature. Based on this fact, we ascertained that várzea and igapó floodplain forests (with lower GIA and GIR), together with the speciose terra firme galling community emerge as the gall diversity apex landscape among all biogeographic regions already investigated. Contrary to expectation, our results also support the “harsh environment hypothesis”, and unveil the Amazonian upper canopy as similar to Mediterranean vegetation habitats, hygrothermically stressed environments with leaf temperature at lethal limits and high levels of leaf sclerophylly. PMID:25551769

  20. Characterization of a New Pm2 Allele Conferring Powdery Mildew Resistance in the Wheat Germplasm Line FG-1

    PubMed Central

    Ma, Pengtao; Xu, Hongxng; Li, Lihui; Zhang, Hongxia; Han, Guohao; Xu, Yunfeng; Fu, Xiaoyi; Zhang, Xiaotian; An, Diaoguo

    2016-01-01

    Powdery mildew has a negative impact on wheat production. Novel host resistance increases the diversity of resistance genes and helps to control the disease. In this study, wheat line FG-1 imported from France showed a high level of powdery mildew resistance at both the seedling and adult stages. An F2 population and F2:3 families from the cross FG-1 × Mingxian 169 both fit Mendelian ratios for a single dominant resistance gene when tested against multiple avirulent Blumeria tritici f. sp. tritici (Bgt) races. This gene was temporarily designated PmFG. PmFG was mapped on the multi-allelic Pm2 locus of chromosome 5DS using seven SSR, 10 single nucleotide polymorphism (SNP)-derived and two SCAR markers with the flanking markers Xbwm21/Xcfd81/Xscar112 (distal) and Xbwm25 (proximal) at 0.3 and 0.5 cM being the closest. Marker SCAR203 co-segregated with PmFG. Allelism tests between PmFG and documented Pm2 alleles confirmed that PmFG was allelic with Pm2. Line FG-1 produced a significantly different reaction pattern compared to other lines with genes at or near Pm2 when tested against 49 Bgt isolates. The PmFG-linked marker alleles detected by the SNP-derived markers revealed significant variation between FG-1 and other lines with genes at or near Pm2. It was concluded that PmFG is a new allele at the Pm2 locus. Data from seven closely linked markers tested on 31 wheat cultivars indicated opportunities for marker-assisted pyramiding of this gene with other genes for powdery mildew resistance and additional traits. PMID:27200022

  1. What Can Teacher Education Programs Do to Prepare Teachers to Teach High-Achieving Culturally Diverse Male Students?

    ERIC Educational Resources Information Center

    Milner, H. Richard; Tenore, F. Blake; Laughter, Judson

    2008-01-01

    In this article, the authors discuss what teacher education programs can do to prepare teachers to teach high-achieving culturally diverse male students. They suggest that special attention needs to be directed at the educational experiences of high-achieving Black male students. They also believe that diverse male learners, and especially high…

  2. High shrew diversity on Alaska's Seward Peninsula: Community assembly and environmental change

    USGS Publications Warehouse

    Hope, Andrew G.

    2012-01-01

    In September 2010, 6 species of shrews (genus: Sorex) were collected at a single locality on the Seward Peninsula of Alaska. Such high sympatric diversity within a single mammalian genus is seldom realized. This phenomenon at high latitudes highlights complex Arctic community dynamics that reflect significant turnover through time as a consequence of environmental change. Each of these shrew species occupies a broad geographic distribution collectively spanning the entire Holarctic, although the study site lies within Eastern Beringia, near the periphery of all individual ranges. A review of published genetic evidence reflects a depauperate shrew community within ice-free Beringia through the last glaciation, and recent assembly of current diversity during the Holocene.

  3. Rethinking Diversity.

    ERIC Educational Resources Information Center

    Gordon, Jack

    1992-01-01

    Managing diversity is about coping with unassimilated differences, about building systems and a culture that unite different people in a common pursuit without undermining their diversity. The goal of diversity training is a high performance organization rather than a climate in which no one's feathers are ruffled. (SK)

  4. Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.

    PubMed

    Buitrago-Flórez, Francisco Javier; Restrepo, Silvia; Riaño-Pachón, Diego Mauricio

    2014-01-01

    The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles. PMID:25375671

  5. Identification of Transcription Factor Genes and Their Correlation with the High Diversity of Stramenopiles

    PubMed Central

    Buitrago-Flórez, Francisco Javier; Restrepo, Silvia; Riaño-Pachón, Diego Mauricio

    2014-01-01

    The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles. PMID:25375671

  6. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina

    PubMed Central

    2013-01-01

    Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small

  7. Genes associated to lactose metabolism illustrate the high diversity of Carnobacterium maltaromaticum.

    PubMed

    Iskandar, Christelle F; Cailliez-Grimal, Catherine; Rahman, Abdur; Rondags, Emmanuel; Remenant, Benoît; Zagorec, Monique; Leisner, Jorgen J; Borges, Frédéric; Revol-Junelles, Anne-Marie

    2016-09-01

    The dairy population of Carnobacterium maltaromaticum is characterized by a high diversity suggesting a high diversity of the genetic traits linked to the dairy process. As lactose is the main carbon source in milk, the genetics of lactose metabolism was investigated in this LAB. Comparative genomic analysis revealed that the species C. maltaromaticum exhibits genes related to the Leloir and the tagatose-6-phosphate (Tagatose-6P) pathways. More precisely, strains can bear genes related to one or both pathways and several strains apparently do not contain homologs related to these pathways. Analysis at the population scale revealed that the Tagatose-6P and the Leloir encoding genes are disseminated in multiple phylogenetic lineages of C. maltaromaticum: genes of the Tagatose-6P pathway are present in the lineages I, II and III, and genes of the Leloir pathway are present in the lineages I, III and IV. These data suggest that these genes evolved thanks to horizontal transfer, genetic duplication and translocation. We hypothesize that the lac and gal genes evolved in C. maltaromaticum according to a complex scenario that mirrors the high population diversity. PMID:27217362

  8. Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding*

    PubMed Central

    Wang, Jun-mei; Yang, Jian-ming; Zhu, Jing-huan; Jia, Qiao-jun; Tao, Yue-zhi

    2010-01-01

    The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the barley accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 barley accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China. PMID:20872987

  9. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    PubMed

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

  10. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific

    PubMed Central

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

  11. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis

    PubMed Central

    2010-01-01

    Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture of the major distinct gene

  12. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

    PubMed

    Atwell, Susanna; Corwin, Jason A; Soltis, Nicole E; Subedy, Anushryia; Denby, Katherine J; Kliebenstein, Daniel J

    2015-01-01

    How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range. PMID:26441923

  13. High genetic diversity at the regional scale and possible speciation in Sebacina epigaea and S. incrustans

    PubMed Central

    2013-01-01

    Background Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of genetic variation within two morphological species, Sebacina epigaea and S. incrustans, based on 340 DNA haplotype sequences of independent genetic markers from the nuclear (ITS + 5.8S + D1/D2, RPB2) and mitochondrial (ATP6) genomes for 98 population samples. By characterising the genetic population structure within these species, we provide insights into species boundaries and the possible factors responsible for genetic diversity at a regional geographic scale. Results We found that recombination events are relatively common between natural populations within Sebacina epigaea and S. incrustans, and play a significant role in generating intraspecific genetic diversity. Furthermore, we also found that RPB2 and ATP6 genes display higher levels of intraspecific synonymous polymorphism. Phylogenetic and demographic analyses based on nuclear and mitochondrial loci revealed three distinct phylogenetic lineages within of each of the morphospecies S. epigaea and S. incrustans: one major and widely distributed lineage, and two geographically restricted lineages, respectively. We found almost no differential morphological or ecological characteristics that could be used to discriminate between these lineages. Conclusions Our results suggest that recombination and negative selection have played significant roles in generating genetic diversity within these morphological species at small geographical scales. Concordance between gene genealogies identified lineages/cryptic species that have evolved independently for a relatively long period of time. These putative species were not associated with geographic provenance

  14. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  15. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

    PubMed Central

    Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

    2014-01-01

    Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere. PMID:24624126

  16. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes.

    PubMed

    Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

    2014-01-01

    Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere. PMID:24624126

  17. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity

    PubMed Central

    Atwell, Susanna; Corwin, Jason A.; Soltis, Nicole E.; Subedy, Anushryia; Denby, Katherine J.; Kliebenstein, Daniel J.

    2015-01-01

    How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range. PMID:26441923

  18. Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi

    PubMed Central

    Yeo, Matthew; Mauricio, Isabel L.; Messenger, Louisa A.; Lewis, Michael D.; Llewellyn, Martin S.; Acosta, Nidia; Bhattacharyya, Tapan; Diosque, Patricio; Carrasco, Hernan J.; Miles, Michael A.

    2011-01-01

    Background Multilocus sequence typing (MLST) is a powerful and highly discriminatory method for analysing pathogen population structure and epidemiology. Trypanosoma cruzi, the protozoan agent of American trypanosomiasis (Chagas disease), has remarkable genetic and ecological diversity. A standardised MLST protocol that is suitable for assignment of T. cruzi isolates to genetic lineage and for higher resolution diversity studies has not been developed. Methodology/Principal Findings We have sequenced and diplotyped nine single copy housekeeping genes and assessed their value as part of a systematic MLST scheme for T. cruzi. A minimum panel of four MLST targets (Met-III, RB19, TcGPXII, and DHFR-TS) was shown to provide unambiguous assignment of isolates to the six known T. cruzi lineages (Discrete Typing Units, DTUs TcI-TcVI). In addition, we recommend six MLST targets (Met-II, Met-III, RB19, TcMPX, DHFR-TS, and TR) for more in depth diversity studies on the basis that diploid sequence typing (DST) with this expanded panel distinguished 38 out of 39 reference isolates. Phylogenetic analysis implies a subdivision between North and South American TcIV isolates. Single Nucleotide Polymorphism (SNP) data revealed high levels of heterozygosity among DTUs TcI, TcIII, TcIV and, for three targets, putative corresponding homozygous and heterozygous loci within DTUs TcI and TcIII. Furthermore, individual gene trees gave incongruent topologies at inter- and intra-DTU levels, inconsistent with a model of strict clonality. Conclusions/Significance We demonstrate the value of systematic MLST diplotyping for describing inter-DTU relationships and for higher resolution diversity studies of T. cruzi, including presence of recombination events. The high levels of heterozygosity will facilitate future population genetics analysis based on MLST haplotypes. PMID:21713026

  19. Population genetic diversity and fitness in multiple environments

    PubMed Central

    2010-01-01

    Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater) and stressful conditions (diluted seawater). The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and

  20. High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains.

    PubMed

    Kammerlander, Barbara; Breiner, Hans-Werner; Filker, Sabine; Sommaruga, Ruben; Sonntag, Bettina; Stoeck, Thorsten

    2015-04-01

    We analyzed the genetic diversity (V4 region of the 18S rRNA) of planktonic microbial eukaryotes in four high mountain lakes including two remote biogeographic regions (the Himalayan mountains and the European Alps) and distinct habitat types (clear and glacier-fed turbid lakes). The recorded high genetic diversity in these lakes was far beyond of what is described from high mountain lake plankton. In total, we detected representatives from 66 families with the main taxon groups being Alveolata (55.0% OTUs 97%, operational taxonomic units), Stramenopiles (34.0% OTUs 97%), Cryptophyta (4.0% OTUs 97%), Chloroplastida (3.6% OTUs 97%) and Fungi (1.7% OTUs 97%). Centrohelida, Choanomonada, Rhizaria, Katablepharidae and Telonema were represented by <1% OTUs 97%. Himalayan lakes harbored a higher plankton diversity compared to the Alpine lakes (Shannon index). Community structures were significantly different between lake types and biogeographic regions (Fisher exact test, P < 0.01). Network analysis revealed that more families of the Chloroplastida (10 vs 5) and the Stramenopiles (14 vs 8) were found in the Himalayan lakes than in the Alpine lakes and none of the fungal families was shared between them. Biogeographic aspects as well as ecological factors such as water turbidity may structure the microbial eukaryote plankton communities in such remote lakes. PMID:25764458

  1. High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains

    PubMed Central

    Kammerlander, Barbara; Breiner, Hans-Werner; Filker, Sabine; Sommaruga, Ruben; Sonntag, Bettina; Stoeck, Thorsten

    2015-01-01

    We analyzed the genetic diversity (V4 region of the 18S rRNA) of planktonic microbial eukaryotes in four high mountain lakes including two remote biogeographic regions (the Himalayan mountains and the European Alps) and distinct habitat types (clear and glacier-fed turbid lakes). The recorded high genetic diversity in these lakes was far beyond of what is described from high mountain lake plankton. In total, we detected representatives from 66 families with the main taxon groups being Alveolata (55.0% OTUs97%, operational taxonomic units), Stramenopiles (34.0% OTUs97%), Cryptophyta (4.0% OTUs97%), Chloroplastida (3.6% OTUs97%) and Fungi (1.7% OTUs97%). Centrohelida, Choanomonada, Rhizaria, Katablepharidae and Telonema were represented by <1% OTUs97%. Himalayan lakes harbored a higher plankton diversity compared to the Alpine lakes (Shannon index). Community structures were significantly different between lake types and biogeographic regions (Fisher exact test, P < 0.01). Network analysis revealed that more families of the Chloroplastida (10 vs 5) and the Stramenopiles (14 vs 8) were found in the Himalayan lakes than in the Alpine lakes and none of the fungal families was shared between them. Biogeographic aspects as well as ecological factors such as water turbidity may structure the microbial eukaryote plankton communities in such remote lakes. PMID:25764458

  2. High-demand jobs: age-related diversity in work ability?

    PubMed

    Sluiter, Judith K

    2006-07-01

    High-demand jobs include 'specific' job demands that are not preventable with state of the art ergonomics knowledge and may overburden the bodily capacities, safety or health of workers. An interesting question is whether the age of the worker is an important factor in explanations of diversity in work ability in the context of high-demand jobs. In this paper, the work ability of ageing workers is addressed according to aspects of diversity in specific job demands and the research methods that are needed to shed light upon the relevant associated questions. From the international literature, a body of evidence was elicited concerning rates of chronological ageing in distinct bodily systems and functions. Intra-age-cohort differences in capacities and work ability, however, require (not yet existing) valid estimates of functional age or biological age indices for the specific populations of workers in high-demand jobs. Many studies have drawn on the highly demanding work of fire-fighters, ambulance workers, police officers, medical specialists, pilots/astronauts and submarine officers. Specific job demands in these jobs can be physical, mental or psychosocial in origin but may cause combined task-level loadings. Therefore, the assessment of single demands probably will not reveal enough relevant information about work ability in high-demand jobs and there will be a call for more integrated measures. Existing studies have used a variety of methodologies to address parts of the issue: task analyses for quantifying physical work demands, observations of psychological and physiological parameters, measures of psychosocial work demands and health complaints. Specific details about the work ability of ageing workers in high-demand jobs are scarce. In general, specific demands are more likely to overtax the capacities of older workers than those of younger workers in high-demand jobs, implying greater repercussions for health, although these effects also vary considerably

  3. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    NASA Astrophysics Data System (ADS)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  4. Competition-based cellular peptide binding assays for 13 prevalent HLA class I alleles using fluorescein-labeled synthetic peptides.

    PubMed

    Kessler, Jan H; Mommaas, Bregje; Mutis, Tuna; Huijbers, Ivo; Vissers, Debby; Benckhuijsen, Willemien E; Schreuder, Geziena M Th; Offringa, Rienk; Goulmy, Els; Melief, Cornelis J M; van der Burg, Sjoerd H; Drijfhout, Jan W

    2003-02-01

    We report the development, validation, and application of competition-based peptide binding assays for 13 prevalent human leukocyte antigen (HLA) class I alleles. The assays are based on peptide binding to HLA molecules on living cells carrying the particular allele. Competition for binding between the test peptide of interest and a fluorescein-labeled HLA class I binding peptide is used as read out. The use of cell membrane-bound HLA class I molecules circumvents the need for laborious biochemical purification of these molecules in soluble form. Previously, we have applied this principle for HLA-A2 and HLA-A3. We now describe the assays for HLA-A1, HLA-A11, HLA-A24, HLA-A68, HLA-B7, HLA-B8, HLA-B14, HLA-B35, HLA-B60, HLA-B61, and HLA-B62. Together with HLA-A2 and HLA-A3, these alleles cover more than 95% of the Caucasian population. Several allele-specific parameters were determined for each assay. Using these assays, we identified novel HLA class I high-affinity binding peptides from HIVpol, p53, PRAME, and minor histocompatibility antigen HA-1. Thus these convenient and accurate peptide-binding assays will be useful for the identification of putative cytotoxic T lymphocyte epitopes presented on a diverse array of HLA class I molecules. PMID:12559627

  5. Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

    PubMed Central

    Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

    2015-01-01

    This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic. PMID:26494429

  6. Genetic analyses reveal unusually high diversity of infectious haematopoietic necrosis virus in rainbow trout aquaculture

    USGS Publications Warehouse

    Troyer, Ryan M.; LaPatra, Scott E.; Kurath, Gael

    2000-01-01

    Infectious haematopoietic necrosis virus (IHNV) is the most significant virus pathogen of salmon and trout in North America. Previous studies have shown relatively low genetic diversity of IHNV within large geographical regions. In this study, the genetic heterogeneity of 84 IHNV isolates sampled from rainbow trout (Oncorhynchus mykiss) over a 20 year period at four aquaculture facilities within a 12 mile stretch of the Snake River in Idaho, USA was investigated. The virus isolates were characterized using an RNase protection assay (RPA) and nucleotide sequence analyses. Among the 84 isolates analysed, 46 RPA haplotypes were found and analyses revealed a high level of genetic heterogeneity relative to that detected in other regions. Sequence analyses revealed up to 7·6% nucleotide divergence, which is the highest level of diversity reported for IHNV to date. Phylogenetic analyses identified four distinct monophyletic clades representing four virus lineages. These lineages were distributed across facilities, and individual facilities contained multiple lineages. These results suggest that co-circulating IHNV lineages of relatively high genetic diversity are present in the IHNV populations in this rainbow trout culture study site. Three of the four lineages exhibited temporal trends consistent with rapid evolution.

  7. Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

    NASA Astrophysics Data System (ADS)

    Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

    2015-10-01

    This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic.

  8. Diversity and distribution of unicellular opisthokonts along the European coast analyzed using high-throughput sequencing

    PubMed Central

    del Campo, Javier; Mallo, Diego; Massana, Ramon; de Vargas, Colomban; Richards, Thomas A.; Ruiz-Trillo, Iñaki

    2015-01-01

    Summary The opisthokonts are one of the major super-groups of eukaryotes. It comprises two major clades: 1) the Metazoa and their unicellular relatives and 2) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here we begin to address this gap by analyzing high throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyze the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of choanoflagellates in coastal waters as well as a relevant role of the ichthyosporeans and the uncultured marine opisthokonts (MAOP). Furthermore, we describe a new lineage of marine fonticulids (MAFO) that appears to be abundant in sediments. Therefore, our work points to a greater potential ecological role for unicellular opisthokonts than previously appreciated in marine environments, both in water column and sediments, and also provides evidence of novel opisthokont phylogenetic lineages. This study highlights the importance of high throughput sequencing approaches to unravel the diversity and distribution of both known and novel eukaryotic lineages. PMID:25556908

  9. High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT).

    PubMed

    Howard, E L; Whittock, S P; Jakše, J; Carling, J; Matthews, P D; Probasco, G; Henning, J A; Darby, P; Cerenak, A; Javornik, B; Kilian, A; Koutoulis, A

    2011-05-01

    Implementation of molecular methods in hop (Humulus lupulus L.) breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. However, use of molecular marker technology is limited due to expense, time inefficiency, laborious methodology and dependence on DNA sequence information. Diversity arrays technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of quality polymorphic markers without reliance on DNA sequence information. This study is the first to utilise DArT for hop genotyping, identifying 730 polymorphic markers from 92 hop accessions. The marker quality was high and similar to the quality of DArT markers previously generated for other species; although percentage polymorphism and polymorphism information content (PIC) were lower than in previous studies deploying other marker systems in hop. Genetic relationships in hop illustrated by DArT in this study coincide with knowledge generated using alternate methods. Several statistical analyses separated the hop accessions into genetically differentiated North American and European groupings, with hybrids between the two groups clearly distinguishable. Levels of genetic diversity were similar in the North American and European groups, but higher in the hybrid group. The markers produced from this time and cost-efficient genotyping tool will be a valuable resource for numerous applications in hop breeding and genetics studies, such as mapping, marker-assisted selection, genetic identity testing, guidance in the maintenance of genetic diversity and the directed breeding of superior cultivars. PMID:21243330

  10. Hidden persistence of salinity and productivity gradients shaping pelagic diversity in highly dynamic marine ecosystems.

    PubMed

    Hidalgo, M; Reglero, P; Álvarez-Berastegui, D; Torres, A P; Álvarez, I; Rodriguez, J M; Carbonell, A; Balbín, R; Alemany, F

    2015-03-01

    While large-scale patterns of pelagic marine diversity are generally well described, they remain elusive at regional-scale given the high temporal and spatial dynamics of biological and local oceanographic processes. We here evaluated whether the main drivers of pelagic diversity can be more pervasive than expected at regional scale, using a meroplankton community of a frontal system in the Western Mediterranean. We evidence that regional biodiversity in a highly dynamic ecosystem can be summarized attending to both static (bathymetric) and ephemeral (biological and hydrographical) environmental axes of seascape. This pattern can be observed irrespectively of the regional hydroclimatic scenario with distance to coast, salinity gradient and chlorophyll a concentration being the main and recurrent drivers. By contrast, their effect is overridden in common analyses given that different non-linear effects are buffered between years of contrasting scenarios, emerging the influence of secondary effects on diversity. We conclude that community studies may reveal hidden persistent processes when they take into account different functional effects related to hydroclimatic variability. A better understanding of regional dynamics of the pelagic realm will improve our capability to forecast future responses of plankton communities as well as impacts of climate change on marine biodiversity. PMID:25617678

  11. Importance of Diversity in the Oral Microbiota including Candida Species Revealed by High-Throughput Technologies.

    PubMed

    Cho, Tamaki; Nagao, Jun-Ichi; Imayoshi, Rieko; Tanaka, Yoshihiko

    2014-01-01

    Taking advantage of high-throughput technologies, deep sequencing of the human microbiome has revealed commensal bacteria independent of the ability to culture them. The composition of the commensal microbiome is dependent on bacterial diversity and the state of the host regulated by the immune system. Candida species are well known as components of the commensal oral microbiota. Candida species frequently colonize and develop biofilms on medical devices like dentures and catheters. Therefore, Candida biofilm on dentures leads to a decrease in the bacterial diversity and then to a change in the composition of the oral microbiota. A disturbance in the balance between commensal bacteria and the host immune system results in a switch from a healthy state to a diseased state even in the limited oral niche. PMID:24864144

  12. Importance of Diversity in the Oral Microbiota including Candida Species Revealed by High-Throughput Technologies

    PubMed Central

    Cho, Tamaki; Nagao, Jun-ichi; Tanaka, Yoshihiko

    2014-01-01

    Taking advantage of high-throughput technologies, deep sequencing of the human microbiome has revealed commensal bacteria independent of the ability to culture them. The composition of the commensal microbiome is dependent on bacterial diversity and the state of the host regulated by the immune system. Candida species are well known as components of the commensal oral microbiota. Candida species frequently colonize and develop biofilms on medical devices like dentures and catheters. Therefore, Candida biofilm on dentures leads to a decrease in the bacterial diversity and then to a change in the composition of the oral microbiota. A disturbance in the balance between commensal bacteria and the host immune system results in a switch from a healthy state to a diseased state even in the limited oral niche. PMID:24864144

  13. High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall

    PubMed Central

    Schmitt-Kopplin, Philippe; Gabelica, Zelimir; Gougeon, Régis D.; Fekete, Agnes; Kanawati, Basem; Harir, Mourad; Gebefuegi, Istvan; Eckel, Gerhard; Hertkorn, Norbert

    2010-01-01

    Numerous descriptions of organic molecules present in the Murchison meteorite have improved our understanding of the early interstellar chemistry that operated at or just before the birth of our solar system. However, all molecular analyses were so far targeted toward selected classes of compounds with a particular emphasis on biologically active components in the context of prebiotic chemistry. Here we demonstrate that a nontargeted ultrahigh-resolution molecular analysis of the solvent-accessible organic fraction of Murchison extracted under mild conditions allows one to extend its indigenous chemical diversity to tens of thousands of different molecular compositions and likely millions of diverse structures. This molecular complexity, which provides hints on heteroatoms chronological assembly, suggests that the extraterrestrial chemodiversity is high compared to terrestrial relevant biological- and biogeochemical-driven chemical space. PMID:20160129

  14. A modified PCR protocol for consistent amplification of fatty acid desaturase (FAD) alleles in marker-assisted backcross breeding for high oleic trait in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High oleic acid, such as is found in olive oil, is desirable for the healthy cholesterol-lowering benefits. The oxidative stability of the oil with high oleic acid also gives longer “shelve life” for peanut products. These benefits drive the breeding effort toward developing high oleic peanuts worl...

  15. High Genetic Diversity Detected in Olives beyond the Boundaries of the Mediterranean Sea

    PubMed Central

    Sheikh-Hassani, Massoma; Ataei, Saeedeh; Cultrera, Nicolò G. M.; Pandolfi, Saverio; Baldoni, Luciana

    2014-01-01

    Background Olive trees (Olea europaea subsp. europaea var. europaea) naturally grow in areas spanning the Mediterranean basin and towards the East, including the Middle East. In the Iranian plateau, the presence of olives has been documented since very ancient times, though the early history of the crop in this area is shrouded in uncertainty. Methods The varieties presently cultivated in Iran and trees of an unknown cultivation status, surviving under extreme climate and soil conditions, were sampled from different provinces and compared with a set of Mediterranean cultivars. All samples were analyzed using SSR and chloroplast markers to establish the relationships between Iranian olives and Mediterranean varieties, to shed light on the origins of Iranian olives and to verify their contribution to the development of the current global olive variation. Results Iranian cultivars and ecotypes, when analyzed using SSR markers, clustered separately from Mediterranean cultivars and showed a high number of private alleles, on the contrary, they shared the same single chlorotype with the most widespread varieties cultivated in the Mediterranean. Conclusion We hypothesized that Iranian and Mediterranean olive trees may have had a common origin from a unique center in the Near East region, possibly including the western Iranian area. The present pattern of variation may have derived from different environmental conditions, distinct levels and selection criteria, and divergent breeding opportunities found by Mediterranean and Iranian olives.These unexpected findings emphasize the importance of studying the Iranian olive germplasm as a promising but endangered source of variation. PMID:24709858

  16. Microsatellite allele sizes alone are insufficient to delineate species boundaries in Symbiodinium.

    PubMed

    Howells, E J; Willis, B L; Bay, L K; van Oppen, M J H

    2016-06-01

    Symbiodinium are a diverse group of unicellular dinoflagellates that are important nutritional symbionts of reef-building corals. Symbiodinium putative species ('types') are commonly identified with genetic markers, mostly nuclear and chloroplast encoded ribosomal DNA regions. Population genetic analyses using microsatellite loci have provided insights into Symbiodinium biogeography, connectivity and phenotypic plasticity, but are complicated by: (i) a lack of consensus criteria used to delineate inter- vs. intragenomic variation within species; and (ii) the high density of Symbiodinium in host tissues, which results in single samples comprising thousands of individuals. To address this problem, Wham & LaJeunesse (2016) present a method for identifying cryptic Symbiodinium species from microsatellite data based on correlations between allele size distributions and nongeographic genetic structure. Multilocus genotypes that potentially do not recombine in sympatry are interpreted as secondary 'species' to be discarded from downstream population genetic analyses. However, Symbiodinium species delineations should ideally incorporate multiple physiological, ecological and molecular criteria. This is because recombination tests may be a poor indicator of species boundaries in Symbiodinium due to their predominantly asexual mode of reproduction. Furthermore, discontinuous microsatellite allele sizes in sympatry may be explained by secondary contact between previously isolated populations and by mutations that occur in a nonstepwise manner. Limitations of using microsatellites alone to delineate species are highlighted in earlier studies that demonstrate occasional bimodal distributions of allele sizes within Symbiodinium species and considerable allele size sharing among Symbiodinium species. We outline these issues and discuss the validity of reinterpretations of our previously published microsatellite data from Symbiodinium populations on the Great Barrier Reef

  17. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly.

    PubMed

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Hanski, Ilkka

    2016-03-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction. PMID:26903642

  18. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

    PubMed Central

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Hanski, Ilkka

    2016-01-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction. PMID:26903642

  19. High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

    DOE PAGESBeta

    Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

    2013-08-13

    In this paper we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relativemore » abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Finally, taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.« less

  20. High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

    SciTech Connect

    Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

    2013-08-13

    In this paper we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Finally, taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.

  1. High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

    PubMed Central

    Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

    2013-01-01

    In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost. PMID:23967218

  2. High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

    PubMed

    Steven, Blaire; Lionard, Marie; Kuske, Cheryl R; Vincent, Warwick F

    2013-01-01

    In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost. PMID:23967218

  3. Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits

    PubMed Central

    Dang, Xiaojing; Giang Tran Thi, Thu; Mawuli Edzesi, Wisdom; Liang, Lijun; Liu, Qiangming; Liu, Erbao; Wang, Yang; Qiang, Sheng; Liu, Linglong; Hong, Delin

    2015-01-01

    We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design. PMID:26059752

  4. Examining the Effects of a Highly Rated Science Curriculum Unit on Diverse Students: Results from a Planning Grant

    ERIC Educational Resources Information Center

    Lynch, Sharon; Kuipers, Joel; Pyke, Curtis; Szesze, Michael

    2005-01-01

    This article reports on the results of a planning grant studying the effects of a highly rated curriculum unit on a diverse student population. The treatment was introduced to 1500 eighth grade students in five middle schools selected for their ethnic, linguistic, and socioeconomic diversity. Students were given pre-, post-, and delayed posttests…

  5. Classroom Management Strategies of Highly Effective Teachers in Diverse Middle Schools: Be Strict and Calm, Not Mean

    ERIC Educational Resources Information Center

    McGregor, Katheryne L.

    2012-01-01

    This qualitative research study investigated and identified the classroom management strategies of 12 highly effective middle school teachers who served diverse student populations at two different school sites. In addition, this research explored the beliefs and experiences of 305 diverse middle school students regarding their experiences with…

  6. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

    PubMed

    Diekmann, Onno E; Serrão, Ester A

    2012-04-01

    Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. PMID:22369278

  7. A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity.

    PubMed

    Ren, Yi; Palusiak, Agata; Wang, Wei; Wang, Yi; Li, Xiao; Wei, Huiting; Kong, Qingke; Rozalski, Antoni; Yao, Zhi; Wang, Quan

    2016-01-01

    Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, causing cystitis, pyelonephritis, and renal failure. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTIs. Accurate and rapid discrimination of UPEC lineages is useful for epidemiological surveillance. Fimbriae are necessary for the adherence of UPEC strains to host uroepithelia, and seem to be abundant and diverse in UPEC strains. By analyzing all the possible fimbrial operons in UPEC strains, we found that closely related strains had similar types of chaperone-usher fimbriae, and the diversity of fimbrial genes was higher than that of multilocus sequence typing (MLST) genes. A typing assay based on the polymorphism of four gene sequences (three fimbrial genes and one housekeeping gene) and the diversity of fimbriae present was developed. By comparison with the MLST, whole-genome sequence (WGS) and fumC/fimH typing methods, this was shown to be accurate and have high resolution, and it was also relatively inexpensive and easy to perform. The assay can supply more discriminatory information for UPEC lineages, and have the potential to be applied in epidemiological surveillance of UPEC isolates. PMID:27199951

  8. Novel and highly diverse fungal endophytes in soybean revealed by the consortium of two different techniques.

    PubMed

    de Souza Leite, Tiago; Cnossen-Fassoni, Andréia; Pereira, Olinto Liparini; Mizubuti, Eduardo Seiti Gomide; de Araújo, Elza Fernandes; de Queiroz, Marisa Vieira

    2013-02-01

    Fungal endophytes were isolated from the leaves of soybean cultivars in Brazil using two different isolation techniques - fragment plating and the innovative dilution-to-extinction culturing - to increase the species richness, frequency of isolates and diversity. A total of 241 morphospecies were obtained corresponding to 62 taxa that were identified by analysis of the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). The Phylum Ascomycota predominated, representing 99% and 95.2% of isolates in the Monsoy and Conquista cultivars, respectively, whereas the Phylum Basidiomycota represented 1% and 4.8% of isolates, respectively. The genera Ampelomyces, Annulohypoxylon, Guignardia, Leptospora, Magnaporthe, Ophiognomonia, Paraconiothyrium, Phaeosphaeriopsis, Rhodotorula, Sporobolomyces, and Xylaria for the first time were isolated from soybean; this suggests that soybean harbours novel and highly diverse fungi. The yeasts genera Rhodotorula and Sporobolomyces (subphylum Pucciniomycotina) represent the Phylum Basidiomycota. The species richness was greater when both isolation techniques were used. The diversity of fungal endophytes was similar in both cultivars when the same isolation technique was used except for Hill's index, N1. The use of ITS region sequences allowed the isolates to be grouped according to Order, Class and Phylum. Ampelomyces, Chaetomium, and Phoma glomerata are endophytic species that may play potential roles in the biological control of soybean pathogens. This study is one of the first to apply extinction-culturing to isolate fungal endophytes in plant leaves, thus contributing to the development and improvement of this technique for future studies. PMID:23456713

  9. High levels of Y-chromosome nucleotide diversity in the genus Pan.

    PubMed

    Stone, Anne C; Griffiths, Robert C; Zegura, Stephen L; Hammer, Michael F

    2002-01-01

    Although some mitochondrial, X chromosome, and autosomal sequence diversity data are available for our closest relatives, Pan troglodytes and Pan paniscus, data from the nonrecombining portion of the Y chromosome (NRY) are more limited. We examined approximately 3 kb of NRY DNA from 101 chimpanzees, seven bonobos, and 42 humans to investigate: (i) relative levels of intraspecific diversity; (ii) the degree of paternal lineage sorting among species and subspecies of the genus Pan; and (iii) the date of the chimpanzee/bonobo divergence. We identified 10 informative sequence-tagged sites associated with 23 polymorphisms on the NRY from the genus Pan. Nucleotide diversity was significantly higher on the NRY of chimpanzees and bonobos than on the human NRY. Similar to mtDNA, but unlike X-linked and autosomal loci, lineages defined by mutations on the NRY were not shared among subspecies of P. troglodytes. Comparisons with mtDNA ND2 sequences from some of the same individuals revealed a larger female versus male effective population size for chimpanzees. The NRY-based divergence time between chimpanzees and bonobos was estimated at approximately 1.8 million years ago. In contrast to human populations who appear to have had a low effective size and a recent origin with subsequent population growth, some taxa within the genus Pan may be characterized by large populations of relatively constant size, more ancient origins, and high levels of subdivision. PMID:11756656

  10. A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity

    PubMed Central

    Ren, Yi; Palusiak, Agata; Wang, Wei; Wang, Yi; Li, Xiao; Wei, Huiting; Kong, Qingke; Rozalski, Antoni; Yao, Zhi; Wang, Quan

    2016-01-01

    Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, causing cystitis, pyelonephritis, and renal failure. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTIs. Accurate and rapid discrimination of UPEC lineages is useful for epidemiological surveillance. Fimbriae are necessary for the adherence of UPEC strains to host uroepithelia, and seem to be abundant and diverse in UPEC strains. By analyzing all the possible fimbrial operons in UPEC strains, we found that closely related strains had similar types of chaperone-usher fimbriae, and the diversity of fimbrial genes was higher than that of multilocus sequence typing (MLST) genes. A typing assay based on the polymorphism of four gene sequences (three fimbrial genes and one housekeeping gene) and the diversity of fimbriae present was developed. By comparison with the MLST, whole-genome sequence (WGS) and fumC/fimH typing methods, this was shown to be accurate and have high resolution, and it was also relatively inexpensive and easy to perform. The assay can supply more discriminatory information for UPEC lineages, and have the potential to be applied in epidemiological surveillance of UPEC isolates. PMID:27199951

  11. Dengue virus surveillance in Singapore reveals high viral diversity through multiple introductions and in situ evolution.

    PubMed

    Lee, Kim-Sung; Lo, Sharon; Tan, Sharon Siok-Yin; Chua, Rachel; Tan, Li-Kiang; Xu, Helen; Ng, Lee-Ching

    2012-01-01

    Dengue fever, a vector-borne disease, has caused tremendous burden to countries in the tropics and sub tropics. Over the past 20 years, dengue epidemics have become more widespread, severe and frequent. This study aims to understand the dynamics of dengue viruses in cosmopolitan Singapore. Envelope protein gene sequences of all four dengue serotypes (DENV-1-DENV-4) obtained from human sera in Singapore (2008-2010) revealed that constant viral introductions and in situ evolution contribute to viral diversity in Singapore and play important roles in shaping the epidemiology of dengue in the island state. The diversity of dengue viruses reported here could be a reflection of the on-going dengue situation in the region given Singapore's location in a dengue hyperendemic region and its role as the regional hub for travels and trade. Though cosmopolitan genotype of DENV-2 has remained as the predominant strain circulating in Singapore, we uncovered evidence of in situ evolution which could possibly result in viruses with improved fitness. While we have previously shown that a switch in the predominant dengue serotype could serve as a warning for an impending outbreak, our current data shows that a replacement of a predominant viral clade, even in the absence of a switch in predominant serotype, could signal a possible increase in dengue transmission. The circulating dengue viruses in Singapore are highly diverse, a situation which could offer ample opportunities for selection of strains of higher fitness, thus increasing the risk of outbreaks despite a low Aedes population. PMID:22036707

  12. AfroDb: a select highly potent and diverse natural product library from African medicinal plants.

    PubMed

    Ntie-Kang, Fidele; Zofou, Denis; Babiaka, Smith B; Meudom, Rolande; Scharfe, Michael; Lifongo, Lydia L; Mbah, James A; Mbaze, Luc Meva'a; Sippl, Wolfgang; Efange, Simon M N

    2013-01-01

    Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We assess the bioactivity and "drug-likeness" of a relatively small but structurally diverse dataset (containing >1,000 compounds) from African medicinal plants, which have been tested and proven a wide range of biological activities. The geographical regions of collection of the medicinal plants cover the entire continent of Africa, based on data from literature sources and information from traditional healers. For each isolated compound, the three dimensional (3D) structure has been used to calculate physico-chemical properties used in the prediction of oral bioavailability on the basis of Lipinski's "Rule of Five". A comparative analysis has been carried out with the "drug-like", "lead-like", and "fragment-like" subsets, as well as with the Dictionary of Natural Products. A diversity analysis has been carried out in comparison with the ChemBridge diverse database. Furthermore, descriptors related to absorption, distribution, metabolism, excretion and toxicity (ADMET) have been used to predict the pharmacokinetic profile of the compounds within the dataset. Our results prove that drug discovery, beginning with natural products from the African flora, could be highly promising. The 3D structures are available and could be useful for virtual screening and natural product lead generation programs. PMID:24205103

  13. High diversity of microplankton surrounds deep-water coral reef in the Norwegian Sea.

    PubMed

    Jensen, Sigmund; Bourne, David G; Hovland, Martin; Murrell, J Colin

    2012-10-01

    Coral reefs that exist in the depths of the oceans are surrounded by Eukarya, Archaea and bacterial communities that may play an important role in the nutrition and health of the reef. The first interdomain community structure of planktonic organisms in seawater from a deep-water coral reef is described. Community profiling and analysis of ribosomal RNA gene sequences from a coral reef system at 350 m depth in the Norwegian Sea revealed a rich diversity of Eukarya and Bacteria and a moderate diversity of Archaea. Most sequences affiliated with marine microplankton from deep-sea to cold-surface regions, with many sequences being similar to those described in studies of mesopelagic and oxygen minimum zones. Dominant phylotypes belonged to the Alveolata (group I, II, dinoflagellates), Stramenopiles (silicoflagellates), Alphaproteobacteria (Pelagibacter ubique), Gammaproteobacteria (ARCTIC96BD-19), Bacteroidetes (Flavobacteria) and mesophilic Crenarchaeota (Nitrosopumilus maritimus). Several rare and novel members of the community fell into distinct phylogenetic groups. The inferred function of dominant community members suggested autotrophs that utilise light, ammonium or sulphide, and lifestyles based on host associations. The high diversity reflected a microplankton community structure, which is significantly different from that of microplankton collected at the same depth at a pelagic station away from reefs. PMID:22571287

  14. Invasive Allele Spread under Preemptive Competition

    NASA Astrophysics Data System (ADS)

    Yasi, J. A.; Korniss, G.; Caraco, T.

    We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.

  15. Borrowed alleles and convergence in serpentine adaptation.

    PubMed

    Arnold, Brian J; Lahner, Brett; DaCosta, Jeffrey M; Weisman, Caroline M; Hollister, Jesse D; Salt, David E; Bomblies, Kirsten; Yant, Levi

    2016-07-19

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  16. Borrowed alleles and convergence in serpentine adaptation

    PubMed Central

    Arnold, Brian J.; Lahner, Brett; DaCosta, Jeffrey M.; Weisman, Caroline M.; Hollister, Jesse D.; Salt, David E.; Bomblies, Kirsten; Yant, Levi

    2016-01-01

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata. In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata. This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  17. Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity

    PubMed Central

    Naderi, Saeid; Rezaei, Hamid-Reza; Taberlet, Pierre; Zundel, Stéphanie; Rafat, Seyed-Abbas; Naghash, Hamid-Reza; El-Barody, Mohamed A. A.; Ertugrul, Okan; Pompanon, François

    2007-01-01

    Background From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodology/Principal Findings The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. Conclusions/Significance We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a

  18. The last polar dinosaurs: high diversity of latest Cretaceous arctic dinosaurs in Russia

    NASA Astrophysics Data System (ADS)

    Godefroit, Pascal; Golovneva, Lina; Shchepetov, Sergei; Garcia, Géraldine; Alekseev, Pavel

    2009-04-01

    A latest Cretaceous (68 to 65 million years ago) vertebrate microfossil assemblage discovered at Kakanaut in northeastern Russia reveals that dinosaurs were still highly diversified in Arctic regions just before the Cretaceous-Tertiary mass extinction event. Dinosaur eggshell fragments, belonging to hadrosaurids and non-avian theropods, indicate that at least several latest Cretaceous dinosaur taxa could reproduce in polar region and were probably year-round residents of high latitudes. Palaeobotanical data suggest that these polar dinosaurs lived in a temperate climate (mean annual temperature about 10°C), but the climate was apparently too cold for amphibians and ectothermic reptiles. The high diversity of Late Maastrichtian dinosaurs in high latitudes, where ectotherms are absent, strongly questions hypotheses according to which dinosaur extinction was a result of temperature decline, caused or not by the Chicxulub impact.

  19. Clonal diversity of a lizard malaria parasite, Plasmodium mexicanum, in its vertebrate host, the western fence lizard: role of variation in transmission intensity over time and space.

    PubMed

    Vardo, A M; Schall, J J

    2007-07-01

    Within the vertebrate host, infections of a malaria parasite (Plasmodium) could include a single genotype of cells (single-clone infections) or two to several genotypes (multiclone infections). Clonal diversity of infection plays an important role in the biology of the parasite, including its life history, virulence, and transmission. We determined the clonal diversity of Plasmodium mexicanum, a lizard malaria parasite at a study region in northern California, using variable microsatellite markers, the first such study for any malaria parasite of lizards or birds (the most common hosts for Plasmodium species). Multiclonal infections are common (50-88% of infections among samples), and measures of genetic diversity for the metapopulation (expected heterozygosity, number of alleles per locus, allele length variation, and effective population size) all indicated a substantial overall genetic diversity. Comparing years with high prevalence (1996-1998 = 25-32% lizards infected), and years with low prevalence (2001-2005 = 6-12%) found fewer alleles in samples taken from the low-prevalence years, but no reduction in overall diversity (H = 0.64-0.90 among loci). In most cases, rare alleles appeared to be lost as prevalence declined. For sites chronically experiencing low transmission intensity (prevalence approximately 1%), overall diversity was also high (H = 0.79-0.91), but there were fewer multiclonal infections. Theory predicts an apparent excess in expected heterozygosity follows a genetic bottleneck. Evidence for such a distortion in genetic diversity was observed after the drop in parasite prevalence under the infinite alleles mutation model but not for the stepwise mutation model. The results are similar to those reported for the human malaria parasite, Plasmodium falciparum, worldwide, and support the conclusion that malaria parasites maintain high genetic diversity in host populations despite the potential for loss in alleles during the transmission cycle or

  20. Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting

    PubMed Central

    2009-01-01

    Background Genetic evidence for diversifying selection identified the Merozoite Surface Protein1 block2 (PfMSP1 block2) as a putative target of protective immunity against Plasmodium falciparum. The locus displays three family types and one recombinant type, each with multiple allelic forms differing by single nucleotide polymorphism as well as sequence, copy number and arrangement variation of three amino acid repeats. The family-specific antibody responses observed in endemic settings support immune selection operating at the family level. However, the factors contributing to the large intra-family allelic diversity remain unclear. To address this question, population allelic polymorphism and sequence variant-specific antibody responses were studied in a single Senegalese rural community where malaria transmission is intense and perennial. Results Family distribution showed no significant temporal fluctuation over the 10 y period surveyed. Sequencing of 358 PCR fragments identified 126 distinct alleles, including numerous novel alleles in each family and multiple novel alleles of recombinant types. The parasite population consisted in a large number of low frequency alleles, alongside one high-frequency and three intermediate frequency alleles. Population diversity tests supported positive selection at the family level, but showed no significant departure from neutrality when considering intra-family allelic sequence diversity and all families combined. Seroprevalence, analysed using biotinylated peptides displaying numerous sequence variants, was moderate and increased with age. Reactivity profiles were individual-specific, mapped to the family-specific flanking regions and to repeat sequences shared by numerous allelic forms within a family type. Seroreactivity to K1-, Mad20- and R033 families correlated with the relative family genotype distribution within the village. Antibody specificity remained unchanged with cumulated exposure to an increasingly large

  1. Molecular Evidence For High Levels of Intrapopulation Genetic Diversity in Woodrats (Neotoma Micropus)

    PubMed Central

    Mendez-Harclerode, Francisca M.; Strauss, Richard E.; Fulhorst, Charles F.; Milazzo, Mary L.; Ruthven, Donald C.; Bradley, Robert D.

    2009-01-01

    Nucleotide sequences from the mitochondrial control region and genotypes from 5 nuclear microsatellite loci were used to examine genetic structure and infer recent (within approximately the last 3,000 years) evolutionary history of a population (549 individuals) of the southern plains woodrat (Neotoma micropus). Observed heterozygosity values ranged from 0.61 to 0.89 across microsatellite loci and systematically were lower than expected heterozygosity values (0.66–0.95). Probability of unique identity using microsatellite data was high (1 individual in 66,005,424). Fifty-three mitochondrial haplotypes were obtained from 150 individuals. FST values estimated from sequence and microsatellite data were 0.061 and 0.011, respectively, and the RST for microsatellite data was 0.007. Within-group genetic variation ranged from 93.90% to 99.99% depending on whether sequence or microsatellite data were examined. Analyses of microsatellite data suggested that all sampled individuals belonged to a single population, albeit genetically diverse. However, combined data analyses suggested the presence of low levels of substructure attributable to maternal lineages within the population. Low nucleotide-diversity values (0.007–0.010) in addition to high haplotype-diversity values (0.915–0.933) indicate a high number of closely related haplotypes, and suggest that this population may have undergone a recent expansion. However, Fu's FS statistic did not fully support this finding, because it did not reveal a significant excess of recent mutations. A phylogenetic approach using the haplotype sequence data and a combined set including both haplotype and genotype data was used to test for evolutionary patterns and history. PMID:19890482

  2. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

    PubMed Central

    Brandt, Débora Y. C.; Aguiar, Vitor R. C.; Bitarello, Bárbara D.; Nunes, Kelly; Goudet, Jérôme; Meyer, Diogo

    2015-01-01

    Next-generation sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the human leukocyte antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population genomics analyses, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the single-nucleotide polymorphisms (SNPs) reported by 1000G (phase I) at five HLA genes (HLA-A, -B, -C, -DRB1, and -DQB1). We take advantage of the availability of HLA Sanger sequencing of 930 of the 1092 1000G samples and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls in HLA genes are incorrect and that allele frequencies are estimated with an error greater than ±0.1 at approximately 25% of the SNPs in HLA genes. We found a bias toward overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates and discuss the outcomes of including those sites in different kinds of analyses. Because the HLA region is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity. PMID:25787242

  3. Allelic Spectra of Risk SNPs Are Different for Environment/Lifestyle Dependent versus Independent Diseases

    PubMed Central

    Amos, Christopher I.

    2015-01-01

    Genome-wide association studies (GWAS) have generated sufficient data to assess the role of selection in shaping allelic diversity of disease-associated SNPs. Negative selection against disease risk variants is expected to reduce their frequencies making them overrepresented in the group of minor (<50%) alleles. Indeed, we found that the overall proportion of risk alleles was higher among alleles with frequency <50% (minor alleles) compared to that in the group of major alleles. We hypothesized that negative selection may have different effects on environment (or lifestyle)-dependent versus environment (or lifestyle)-independent diseases. We used an environment/lifestyle index (ELI) to assess influence of environmental/lifestyle factors on disease etiology. ELI was defined as the number of publications mentioning “environment” or “lifestyle” AND disease per 1,000 disease-mentioning publications. We found that the frequency distributions of the risk alleles for the diseases with strong environmental/lifestyle components follow the distribution expected under a selectively neutral model, while frequency distributions of the risk alleles for the diseases with weak environmental/lifestyle influences is shifted to the lower values indicating effects of negative selection. We hypothesized that previously selectively neutral variants become risk alleles when environment changes. The hypothesis of ancestrally neutral, currently disadvantageous risk-associated alleles predicts that the distribution of risk alleles for the environment/lifestyle dependent diseases will follow a neutral model since natural selection has not had enough time to influence allele frequencies. The results of our analysis suggest that prediction of SNP functionality based on the level of evolutionary conservation may not be useful for SNPs associated with environment/lifestyle dependent diseases. PMID:26201053

  4. Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers

    PubMed Central

    Uitdewilligen, Jan G. A. M. L.; Kloosterman, Bjorn A.; Hutten, Ronald C. B.; Visser, Richard G. F.; van Eck, Herman J.

    2010-01-01

    We have investigated the genetics and molecular biology of orange flesh colour in potato (Solanum tuberosum L.). To this end the natural diversity in three genes of the carotenoid pathway was assessed by SNP analyses. Association analysis was performed between SNP haplotypes and flesh colour phenotypes in diploid and tetraploid potato genotypes. We observed that among eleven beta-carotene hydroxylase 2 (Chy2) alleles only one dominant allele has a major effect, changing white into yellow flesh colour. In contrast, none of the lycopene epsilon cyclase (Lcye) alleles seemed to have a large effect on flesh colour. Analysis of zeaxanthin epoxidase (Zep) alleles showed that all (diploid) genotypes with orange tuber flesh were homozygous for one specific Zep allele. This Zep allele showed a reduced level of expression. The complete genomic sequence of the recessive Zep allele, including the promoter, was determined, and compared with the sequence of other Zep alleles. The most striking difference was the presence of a non-LTR retrotransposon sequence in intron 1 of the recessive Zep allele, which was absent in all other Zep alleles investigated. We hypothesise that the presence of this large sequence in intron 1 caused the lower expression level, resulting in reduced Zep activity and accumulation of zeaxanthin. Only genotypes combining presence of the dominant Chy2 allele with homozygosity for the recessive Zep allele produced orange-fleshed tubers that accumulated large amounts of zeaxanthin. Electronic supplementary material The online version of this article (doi:10.1007/s11103-010-9647-y) contains supplementary material, which is available to authorized users. PMID:20490894

  5. High-order myopic coronagraphic phase diversity (COFFEE) for wave-front control in high-contrast imaging systems.

    PubMed

    Paul, B; Mugnier, L M; Sauvage, J-F; Dohlen, K; Ferrari, M

    2013-12-30

    The estimation and compensation of quasi-static aberrations is mandatory to reach the ultimate performance of high-contrast imaging systems. COFFEE is a focal plane wave-front sensing method that consists in the extension of phase diversity to high-contrast imaging systems. Based on a Bayesian approach, it estimates the quasi-static aberrations from two focal plane images recorded from the scientific camera itself. In this paper, we present COFFEE's extension which allows an estimation of low and high order aberrations with nanometric precision for any coronagraphic device. The performance is evaluated by realistic simulations, performed in the SPHERE instrument framework. We develop a myopic estimation that allows us to take into account an imperfect knowledge on the used diversity phase. Lastly, we evaluate COFFEE's performance in a compensation process, to optimize the contrast on the detector, and show it allows one to reach the 10(-6) contrast required by SPHERE at a few resolution elements from the star. Notably, we present a non-linear energy minimization method which can be used to reach very high contrast levels (better than 10(7) in a SPHERE-like context). PMID:24514771

  6. Detection of 549 new HLA alleles in potential stem cell donors from the United States, Poland and Germany.

    PubMed

    Hernández-Frederick, C J; Cereb, N; Giani, A S; Ruppel, J; Maraszek, A; Pingel, J; Sauter, J; Schmidt, A H; Yang, S Y

    2016-01-01

    We characterized 549 new human leukocyte antigen (HLA) class I and class II alleles found in newly registered stem cell donors as a result of high-throughput HLA typing. New alleles include 101 HLA-A, 132 HLA-B, 105 HLA-C, 2 HLA-DRB1, 89 HLA-DQB1 and 120 HLA-DPB1 alleles. Mainly, new alleles comprised single nucleotide variations when compared with homologous sequences. We identified nonsynonymous nucleotide mutations in 70.7% of all new alleles, synonymous variations in 26.4% and nonsense substitutions in 2.9% (null alleles). Some new alleles (55, 10.0%) were found multiple times, HLA-DPB1 alleles being the most frequent among these. Furthermore, as several new alleles were identified in individuals from ethnic minority groups, the relevance of recruiting donors belonging to such groups and the importance of ethnicity data collection in donor centers and registries is highlighted. PMID:26812061

  7. Human oral mucosal epithelial cell sheets imaging with high-resolution phase-diversity homodyne OCT

    NASA Astrophysics Data System (ADS)

    Senda, Naoko; Osawa, Kentaro

    2015-03-01

    There is a need for development of non-invasive technique to evaluate regenerative tissues such as cell sheets for transplantation. We demonstrated non-invasive imaging inside living cell sheets of human oral mucosal epithelial cells by phase-diversity homodyne optical coherence tomography (OCT). The new method OCT developed in Hitachi enables cell imaging because of high resolution (axial resolution; ~2.6 μm, lateral resolution; ~1 μm, in the air). Nuclei inside cell sheets were imaged with sufficient spatial resolution to identify each cell. It suggested that the new method OCT could be useful for non-invasive cell sheet evaluation test.

  8. Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing.

    PubMed

    Sun, Zhihong; Liu, Wenjun; Bao, Qiuhua; Zhang, Jiachao; Hou, Qiangchuan; Kwok, Laiyu; Sun, Tiansong; Zhang, Heping

    2014-10-01

    This is the first study on the bacterial and fungal community diversity in 17 tarag samples (naturally fermented dairy products) through a metagenomic approach involving high-throughput pyrosequencing. Our results revealed the presence of a total of 47 bacterial and 43 fungal genera in all tarag samples, in which Lactobacillus and Galactomyces were the predominant genera of bacteria and fungi, respectively. The number of some microbial genera, such as Lactococcus, Acetobacter, Saccharomyces, Trichosporon, and Kluyveromyces, among others, was found to vary between different samples. Altogether, our results showed that the microbial flora in different samples may be stratified by geographic region. PMID:25129502

  9. Diversion assumptions for high-powered research reactors. ISPO C-50 Phase 1

    SciTech Connect

    Binford, F.T.

    1984-01-01

    This study deals with diversion assumptions for high-powered research reactors -- specifically, MTR fuel; pool- or tank-type research reactors with light-water moderator; and water, beryllium, or graphite reflectors, and which have a power level of 25 MW(t) or more. The objective is to provide assistance to the IAEA in documentation of criteria and inspection observables related to undeclared plutonium production in the reactors described above, including: criteria for undeclared plutonium production, necessary design information for implementation of these criteria, verification guidelines including neutron physics and heat transfer, and safeguards measures to facilitate the detection of undeclared plutonium production at large research reactors.

  10. High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

    PubMed Central

    Wachowiak, W; Salmela, M J; Ennos, R A; Iason, G; Cavers, S

    2011-01-01

    Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=∼0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role. PMID:20823905

  11. Diversity of MHC DQB and DRB Genes in the Endangered Australian Sea Lion (Neophoca cinerea).

    PubMed

    Lau, Quintin; Chow, Natalie; Gray, Rachael; Gongora, Jaime; Higgins, Damien P

    2015-01-01

    Major histocompatibility complex (MHC) class II molecules have an important role in vertebrate adaptive immunity, being responsible for recognizing, binding, and presenting specific antigenic peptides to T lymphocytes. Here, we study the MHC class II DQB and DRB exon 2 genes of the Australian sea lion (Neophoca cinerea), an endangered pinniped species that experiences high pup mortality. Following characterization of N. cinerea DQB and DRB by molecular cloning, and evaluation of diversity in pups across 2 colonies using variant screening (n = 47), 3 DQB alleles and 10 DRB variants (including 1 pseudogene allele) were identified. The higher diversity at DRB relative to DQB is consistent with other studies in marine mammals. Despite overall lower MHC class II allelic diversity relative to some other pinniped species, we observed similar levels of nucleotide diversity and selection in N. cinerea. In addition, we provide support for recent divergence of MHC class II alleles. The characterization of MHC class II diversity in the Australian sea lion establishes a baseline for further investigation of associations with disease, including endemic hookworm infection, and contributes to the conservation management of this species. PMID:25908666

  12. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    PubMed Central

    Seo, Dongwon; Bhuiyan, Md. Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-01-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  13. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    PubMed

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  14. Teaching Thinking to Culturally Diverse, High Ability, High School Students: A Triarchic Approach

    ERIC Educational Resources Information Center

    Coates, Deborah L.; Perkins, Tiffany; Vietze, Peter; Cruz, Mariolga Reyes; Park, Sin-Jae

    2003-01-01

    This final research monograph describes intervention research to improve thinking skills in high ability, high school students attending an urban magnet school for primarily low-income ethnic minority students who come from families that have historically experienced social inequality and various forms of discrimination in the United States. The…

  15. Microsatellite marker diversity in common bean (Phaseolus vulgaris L.).

    PubMed

    Blair, M W; Giraldo, M C; Buendía, H F; Tovar, E; Duque, M C; Beebe, S E

    2006-06-01

    A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity

  16. Genotypic Analysis of Klebsiella pneumoniae Isolates in a Beijing Hospital Reveals High Genetic Diversity and Clonal Population Structure of Drug-Resistant Isolates

    PubMed Central

    Yi, Yong; Woo, Patrick C. Y.; Liu, Cui Hua

    2013-01-01

    Background The genetic diversity and the clinical relevance of the drug-resistant Klebsiella pneumoniae isolates from hospital settings are largely unknown. We thus conducted this prospective study to analyze the molecular epidemiology of K. pneumoniae isolates from patients being treated in the 306 Hospital in Beijing, China for the period of November 1, 2010–October 31, 2011. Methodology/Principal Findings Antibiotic susceptibility testing, PCR amplification and sequencing of the drug resistance-associated genes, and multilocus sequence typing (MLST) were conducted. A total of 163 isolates were analyzed. The percentage of MDR, XDR and PDR isolates were 63.8% (104), 20.9 (34), and 1.8% (3), respectively. MLST results showed that 60 sequence types (STs) were identified, which were further separated by eBURST into 13 clonal complexes and 18 singletons. The most dominant ST was ST15 (10.4%). Seven new alleles and 24 new STs were first identified in this study. Multiple logistic regression analysis revealed that certain clinical characteristics were associated with those prevalent STs such as: from ICU, from medical ward, from community acquired infection, from patients without heart disease, from patients with treatment success, susceptible to extended spectrum cephalosporin, susceptible to cephamycins, susceptible to fluoroquinolones, and with MDR. Conclusions/Significance Our data indicate that certain drug-resistant K. pneumoniae clones are highly prevalent and are associated with certain clinical characteristics in hospital settings. Our study provides evidence demonstrating that intensive nosocomial infection control measures are urgently needed. PMID:23437318

  17. Inference of genetic diversity in popcorn S3 progenies.

    PubMed

    Pena, G F; do Amaral, A T; Ribeiro, R M; Ramos, H C C; Boechat, M S B; Santos, J S; Mafra, G S; Kamphorst, S H; de Lima, V J; Vivas, M; de Souza Filho, G A

    2016-01-01

    Molecular markers are a useful tool for identification of complementary heterotic groups in breeding programs aimed at the production of superior hybrids, particularly for crops such as popcorn in which heterotic groups are not well-defined. The objective of the present study was to analyze the genetic diversity of 47 genotypes of tropical popcorn to identify possible heterotic groups for the development of superior hybrids. Four genotypes of high genetic value were studied: hybrid IAC 125, strain P2, and varieties UENF 14 and BRS Angela. In addition, 43 endogamous S3 progenies obtained from variety UENF 14 were used. Twenty-five polymorphic SSR-EST markers were analyzed. A genetic distance matrix was obtained and the following molecular diversity parameters were estimated: number of alleles, number of effective alleles, polymorphism information content (PIC), observed and expected heterozygosities, Shannon diversity index, and coefficient of inbreeding. We found a moderate PIC and high diversity index, indicating that the studied population presents both good discriminatory ability and high informativeness for the utilized markers. The dendrogram built based on the dissimilarity matrix indicated six distinct groups. Our findings demonstrate the genetic diversity among the evaluated genotypes and provide evidence for heterotic groups in popcorn. Furthermore, the functional genetic diversity indicates that there are informative genetic markers for popcorn. PMID:27173336

  18. Embracing Diversity

    ERIC Educational Resources Information Center

    Roeck, Kathryn T.

    2009-01-01

    The high school art unit "Embracing Diversity" was the author's principal work towards the completion of a Masters thesis. The objective was to learn whether or not teaching an art unit that focused on sexual diversity could have a positive impact on the current culture one finds in high schools. The unit was found to have a positive impact on…

  19. MNSs genotyping by MALDI-TOF MS shows high concordance with serology, allows gene copy number testing and reveals new St(a) alleles.

    PubMed

    Meyer, Stefan; Vollmert, Caren; Trost, Nadine; Sigurdardottir, Sonja; Portmann, Claudia; Gottschalk, Jochen; Ries, Judith; Markovic, Alexander; Infanti, Laura; Buser, Andreas; Amar El Dusouqui, Soraya; Rigal, Emmanuel; Castelli, Damiano; Weingand, Bettina; Maier, Andreas; Mauvais, Simon M; Sarraj, Amira; Braisch, Monica C; Thierbach, Jutta; Hustinx, Hein; Frey, Beat M; Gassner, Christoph

    2016-08-01

    Results of genotyping with true high-throughput capability for MNSs antigens are underrepresented, probably because of technical issues, due to the high level of nucleotide sequence homology of the paralogous genes GYPA, GYPB and GYPE. Eight MNSs-specific single nucleotide polymorphisms (SNP) were detected using matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS) in 5800 serologically M/N and S/s pre-typed Swiss blood donors and 50 individuals of known or presumptive black African ethnicity. Comparison of serotype with genotype delivered concordance rates of 99·70% and 99·90% and accuracy of genotyping alone of 99·88% and 99·95%, for M/N and S/s, respectively. The area under the curve of peak signals was measured in intron 1 of the two highly homologous genes GYPB and GYPE and allowed for gene copy number variation estimates in all individuals investigated. Elevated GYPB:GYPE ratios accumulated in several carriers of two newly observed GYP*401 variants, termed type G and H, both encoding for the low incidence antigen St(a). In black Africans, reduced GYPB gene contents were proven in pre-typed S-s-U- phenotypes and could be reproduced in unknown specimens. Quantitative gene copy number estimates represented a highly attractive supplement to conventional genotyping, solely based on MNSs SNPs. PMID:27072601

  20. Influence of age on reactivity to diverse emotional challenges in low- and high-anxiety rats.

    PubMed

    de Oliveira, Luciana C; Gomes, Margareth Z; Brandão, Marcus L

    2011-02-01

    Studies have revealed that the extent of reactivity of high-anxiety rats to diverse challenges is different than low-anxiety rats and have provided important insights into the psychopathology of anxiety. Various factors intervene to allow defensive mechanisms to react to diverse threatening challenges, including ontogeny and the nature of the emotional challenge (e.g., conditioned vs. unconditioned). The present study investigated the extent to which a particular type of fear extrapolates to other emotional responses to diverse threatening challenges. Groups of 30- and 60-day-old rats were assigned to low freezing behavior (LFB) and high freezing behavior (HFB) groups using the contextual fear conditioning paradigm and subjected to either the fear-potentiated startle (FPS) test, novelty-induced ultrasound vocalizations (USVs) or elevated plus-maze (EPM) tests. At 30 days of age, HFB rats exhibited greater FPS than LFB rats. In contrast, prior selection of HFB and LFB did not affect the performance of 30-day-old animals in the EPM and novelty-induced USVs. Sixty-day-old animals exhibited a performance deficit in all three tests. These data suggest that the performance of young rats in animal models of anxiety parallels their selection as LFB and HFB in the contextual fear conditioning paradigm. However, the increased fear-like behavior exhibited by the 60-day-old HFB rats may elicit performance deficits in conditioned and unconditioned fear tests. These results suggest that the interaction between hyperanxiety and age may cause a performance deficit despite the animals' increased fear-like behavior when facing emotional challenges, thus resembling psychiatric patients in many respects. PMID:20833243

  1. Characterization of alleles in a diversity panel of tomato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Approximately 6,000 accessions of domesticated tomato (Solanum lycopersicum L.), including open-pollinated populations and inbred lines, are conserved at the USDA, ARS Plant Genetic Resources Unit (PGRU). This collection provides a publicly available resource for breeding and experimentation to end-...

  2. Germplasm Enhancement of Maize: Allelic Diversity and Double Haploid Update

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Germplasm Enhancement of Maize (GEM) Project is a collaborative effort of public and private sector researchers to broaden and enhance the germplasm base. To date, 235 germplasm lines have been released to cooperators representing approximately 25 races. These lines were selected based on yiel...

  3. Seed arrival and ecological filters interact to assemble high-diversity plant communities.

    PubMed

    Myers, Jonathan A; Harms, Kyle E

    2011-03-01

    Two prominent mechanisms proposed to structure biodiversity are niche-based ecological filtering and chance arrival of propagules from the species pool. Seed arrival is hypothesized to play a particularly strong role in high-diversity plant communities with large potential species pools and many rare species, but few studies have explored how seed arrival and local ecological filters interactively assemble species-rich communities in space and time. We experimentally manipulated seed arrival and multiple ecological filters in high-diversity, herbaceous-dominated groundcover communities in longleaf pine savannas, which contain the highest small-scale species richness in North America (up to > 40 species/m2). We tested three hypotheses: (1) local communities constitute relatively open-membership assemblages, in which increased seed arrival from the species pool strongly increases species richness; (2) ecological filters imposed by local fire intensity and soil moisture influence recruitment and richness of immigrating species; and (3) ecological filters increase similarity in the composition of immigrating species. In a two-year factorial field experiment, we manipulated local fire intensity by increasing pre-fire fuel loads, soil moisture using rain shelters and irrigation, and seed arrival by adding seeds from the local species pool. Seed arrival increased species richness regardless of fire intensity and soil moisture but interacted with both ecological filters to influence community assembly. High-intensity fire decreased richness of resident species, suggesting an important abiotic filter. In contrast, high-intensity fire increased recruitment and richness of immigrating species, presumably by decreasing effects of other ecological filters (competition and resource limitation) in postfire environments. Drought decreased recruitment and richness of immigrating species, whereas wet soil conditions increased recruitment but decreased or had little effect on

  4. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea.

    PubMed

    Pearman, John K; Irigoien, Xabier; Carvalho, Susana

    2016-04-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore-offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales. PMID:26525270

  5. High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales.

    PubMed

    Healy, R A; Smith, M E; Bonito, G M; Pfister, D H; Ge, Z-W; Guevara, G G; Williams, G; Stafford, K; Kumar, L; Lee, T; Hobart, C; Trappe, J; Vilgalys, R; McLaughlin, D J

    2013-03-01

    Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in Argentina, Chile, China, Mexico and the USA between 2009 and 2012. We collated spore mat ITS sequences with 105 fruit body and 47 EcM root sequences to generate operational taxonomic units (OTUs). Phylogenetic inferences were made through analyses of both molecular data sets. A total of 48 OTUs from spore mats represented six independent EcM Pezizales lineages and included truffles and cup fungi. Three clades of seven OTUs have no known meiospore stage. Mitospores failed to germinate on sterile media, or form ectomycorrhizas on Quercus, Pinus and Populus seedlings, consistent with a hypothesized role of spermatia. The broad geographic range, high frequency and phylogenetic diversity of spore mats produced by EcM Pezizales suggests that a mitospore stage is important for many species in this group in terms of mating, reproduction and/or dispersal. PMID:23205556

  6. Bacterial diversity across a highly stratified ecosystem: A salt-wedge Mediterranean estuary.

    PubMed

    Korlević, M; Šupraha, L; Ljubešić, Z; Henderiks, J; Ciglenečki, I; Dautović, J; Orlić, S

    2016-09-01

    Highly stratified Mediterranean estuaries are unique environments where the tidal range is low and the tidal currents are almost negligible. The main characteristics of these environments are strong salinity gradients and other environmental parameters. In this study, 454 pyrosequencing of the 16S rRNA gene in combination with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to estimate the bacterial diversity across the Krka estuary in February and July 2013. The comparison of the data derived from these two techniques resulted in a significant but weak positive correlation (R=0.28) indicating a substantial difference in the bacterial community structure, depending on the applied method. The phytoplankton bloom observed in February was identified as one of the main factors shaping the bacterial community structure between the two environmentally contrasting sampling months. Roseobacter, Bacteroidetes and Gammaproteobacteria differed substantially between February and July. Typical freshwater bacterial classes (Actinobacteria and Betaproteobacteria) showed strong vertical distribution patterns depending on the salinity gradient. Cyanobacteria decreased in abundance in February due to competition with phytoplankton, while the SAR11 clade increased its abundance in July as a result of a better adaptation toward more oligotrophic conditions. The results provided the first detailed insight into the bacterial diversity in a highly stratified Mediterranean karstic estuary. PMID:27475818

  7. Persistence of high diversity in non-equilibrium ecological communities: implications for modern and fossil ecosystems.

    PubMed

    Olszewski, Thomas D

    2012-01-22

    Explaining the origin and maintenance of biodiversity is critical for understanding the potential consequences of present-day environmental change on ecological communities, as well as the evolutionary history of ecosystems in the Earth's past. Much effort in theoretical ecology has focused on identifying mechanisms that promote stable coexistence of species at equilibrium. However, in a consumer-resource model of competition along an environmental gradient, high-diversity assemblages have the potential to persist in non-equilibrium states for millions of generations with very little species loss. Species' populations in such competitively accommodated communities show slow drift; if disrupted, they rapidly reorganize into alternative persistent states. Fossil examples of prolonged ecological stability lasting 1-5 Myr punctuated by rapid reorganization (e.g. brachiopods from the Permian Reef of west Texas) suggest that some palaeocommunities represent a record of periodically disrupted transient states rather than stable equilibria. The similarity between the theoretical results reported here and palaeontological data suggests that the maintenance of high-diversity communities, both in the past and present, may reflect long-duration, non-equilibrium transient dynamics. If so, this has implications for the response of such communities to present-day environmental change, as well as for the evolution of lineages in such systems. PMID:21653592

  8. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

    PubMed

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

    2016-01-01

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

  9. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

    PubMed Central

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M.; Ramón, Daniel; Porcar, Manuel

    2016-01-01

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

  10. [Diversity and dynamics of a high sub-Andean forest from Northern Andes, Colombia].

    PubMed

    Restrepo, Jesús Oswaldo Velásquez; Maniguaje, Nancy Lorena; Duque, Alvaro Javier

    2012-06-01

    The sub-Andean forests are characterized by a high biodiversity, but little is known about their natural dynamics. In order to generate new information, this study assessed two permanent plots of one hectare each, in the Northern Andean area of the Western Cordillera, Colombia. Methodology included the evaluation of diversity patterns, above ground biomass (AGB) dynamics, and mortality and recruitment rates. Besides, we used the Fisher's Alpha index to calculate species diversity. Forest dynamics and AGB were evaluated in both plots by means of three censuses carried out within a nine years period. In total, we found 1 664 individuals with diameter at breast height (DBH)> or =10cm belonging to 222 species, 113 genera and 60 families. Mean species richness was of 156 species/ha and a mean Fisher's Alpha index of 56.2/ha. The mortality rate was 0.88% and recruitment was 1.16%, which did not allow to lay any external effect of global warming or climate change on individual forest dynamics. However, the mean AGB was 243.44+/-9.82t/ha, with an annual average increase of 2.9t/ha, a higher value than the one reported in other studies of high sub-Andean forests, which suggests that equilibrium in terms of the AGB have not yet been reached. Besides, according to field observations, a recovery process, from a disturbance that occurred in the past, might be on his way. PMID:23894958

  11. Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

    PubMed Central

    Foulongne, Vincent; Sauvage, Virginie; Hebert, Charles; Dereure, Olivier; Cheval, Justine; Gouilh, Meriadeg Ar; Pariente, Kevin; Segondy, Michel; Burguière, Ana; Manuguerra, Jean-Claude; Caro, Valérie; Eloit, Marc

    2012-01-01

    The human skin is a complex ecosystem that hosts a heterogeneous flora. Until recently, the diversity of the cutaneous microbiota was mainly investigated for bacteria through culture based assays subsequently confirmed by molecular techniques. There are now many evidences that viruses represent a significant part of the cutaneous flora as demonstrated by the asymptomatic carriage of beta and gamma-human papillomaviruses on the healthy skin. Furthermore, it has been recently suggested that some representatives of the Polyomavirus genus might share a similar feature. In the present study, the cutaneous virome of the surface of the normal-appearing skin from five healthy individuals and one patient with Merkel cell carcinoma was investigated through a high throughput metagenomic sequencing approach in an attempt to provide a thorough description of the cutaneous flora, with a particular focus on its viral component. The results emphasize the high diversity of the viral cutaneous flora with multiple polyomaviruses, papillomaviruses and circoviruses being detected on normal-appearing skin. Moreover, this approach resulted in the identification of new Papillomavirus and Circovirus genomes and confirmed a very low level of genetic diversity within human polyomavirus species. Although viruses are generally considered as pathogen agents, our findings support the existence of a complex viral flora present at the surface of healthy-appearing human skin in various individuals. The dynamics and anatomical variations of this skin virome and its variations according to pathological conditions remain to be further studied. The potential involvement of these viruses, alone or in combination, in skin proliferative disorders and oncogenesis is another crucial issue to be elucidated. PMID:22723863

  12. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA.

    PubMed

    Bennetzen, J L; Schrick, K; Springer, P S; Brown, W E; SanMiguel, P

    1994-08-01

    We have characterized the copy number, organization, and genomic modification of DNA sequences within and flanking several maize genes. We found that highly repetitive DNA sequences were tightly linked to most of these genes. The highly repetitive sequences were not found within the coding regions but could be found within 6 kb either 3' or 5' to the structural genes. These highly repetitive regions were each composed of unique combinations of different short repetitive sequences. Highly repetitive DNA blocks were not interrupted by any detected single copy DNA. The 13 classes of highly repetitive DNA identified were found to vary little between diverse Zea isolates. The level of DNA methylation in and near these genes was determined by scoring the digestibility of 63 recognition/cleavage sites with restriction enzymes that were sensitive to 5-methylation of cytosines in the sequences 5'-CG-3' and 5'-CNG-3'. All but four of these sites were digestible in chromosomal DNA. The four undigested sites were localized to extragenic DNA within or near highly repetitive DNA, while the other 59 sites were in low copy number DNAs. Pulsed field gel analysis indicated that the majority of cytosine modified tracts range from 20 to 200 kb in size. Single copy sequences hybridized to the unmodified domains, while highly repetitive sequences hybridized to the modified regions. Middle repetitive sequences were found in both domains. PMID:7958822

  13. The Strengths of High-Achieving Black High School Students in a Racially Diverse Setting

    ERIC Educational Resources Information Center

    Marsh, Kris; Chaney, Cassandra; Jones, Derrick

    2012-01-01

    Robert Hill (1972) identified strengths of Black families: strong kinship bonds, strong work orientation, adaptability of family roles, high achievement orientation, and religious orientation. Some suggest these strengths sustain the physical, emotional, social, and spiritual needs of Blacks. This study used narratives and survey data from a…

  14. Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti.

    PubMed

    Godreuil, S; Renaud, F; Choisy, M; Depina, J J; Garnotel, E; Morillon, M; Van de Perre, P; Bañuls, A L

    2010-07-01

    Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases. PMID:19694762

  15. High-Throughput Synthesis of Diverse Compound Collections for Lead Discovery and Optimization.

    PubMed

    Rademacher, C; Seeberger, P H

    2016-01-01

    Small-molecule intervention of protein function is one central dogma of drug discovery. The generation of small-molecule libraries fuels the discovery pipeline at many stages and thereby resembles a key aspect of this endeavor. High-throughput synthesis is a major source for compound libraries utilized in academia and industry, seeking new chemical modulators of pharmacological targets. Here, we discuss the crucial factors of library design strategies from the perspective of synthetic chemistry, giving a brief historic background and a summary of current approaches. Simple measures of success of a high-throughput synthesis such as quantity or diversity have long been discarded and replaced by more integrated measures. Case studies are presented and put into context to highlight the cross-connectivity of the various stages of the drug discovery process. PMID:26330259

  16. Closed loop, DM diversity-based, wavefront correction algorithm for high contrast imaging systems.

    PubMed

    Give'on, Amir; Belikov, Ruslan; Shaklan, Stuart; Kasdin, Jeremy

    2007-09-17

    High contrast imaging from space relies on coronagraphs to limit diffraction and a wavefront control systems to compensate for imperfections in both the telescope optics and the coronagraph. The extreme contrast required (up to 10(-10) for terrestrial planets) puts severe requirements on the wavefront control system, as the achievable contrast is limited by the quality of the wavefront. This paper presents a general closed loop correction algorithm for high contrast imaging coronagraphs by minimizing the energy in a predefined region in the image where terrestrial planets could be found. The estimation part of the algorithm reconstructs the complex field in the image plane using phase diversity caused by the deformable mirror. This method has been shown to achieve faster and better correction than classical speckle nulling. PMID:19547602

  17. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    NASA Astrophysics Data System (ADS)

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-03-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation.

  18. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    PubMed Central

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-01-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation. PMID:27030405

  19. Pyrosequencing revealed highly microbial phylogenetic diversity in ferromanganese nodules from farmland.

    PubMed

    Hu, Min; Li, Fangbai; Lei, Jing; Fang, Yuan; Tong, Hui; Wu, Weijian; Liu, Chengshuai

    2015-01-01

    There is renewed interest in the origin and makeup of ferromanganese nodules (FMNs), long known to soil mineralogists as unusual secondary minerals. However, new evidence suggests that microorganisms play a significant role in the generation of FMNs. The biogenic origin of nodules has remained elusive because until recently, little has been known about the overall microbial community structure in their microbiota. To learn more about the microbial community and to determine the relative abundance, diversity, and composition of the microbial communities present in FMNs and their surrounding soil, we used pyrosequencing to investigate 16S rRNA genes obtained from vertical soil profiles of both paddy fields and sugarcane fields. Using pyrotaq 16S rRNA gene sequencing, we show that the microbial phylogenetic diversity of nodules was higher than those reported in previous studies of this biosphere, and we identified many previously unidentified microorganisms. Here, we show that the microbial community of these nodules is dominated by Burkholderiales, Rhodocyclales, Acidobacteriales, Desulfuromonales, and Clostridiales, and there were no statistically significant differences found when comparing the microbial community structures of FMNs obtained from vertical soil sequences. Although the microbial composition was markedly different between the surrounding soil and the FMNs, the microbes found within the FMNs were very similar to other FMNs from both field types examined here. In addition to their geochemical properties and the microbial community composition of FMNs, we found that the levels of iron (Fe), manganese (Mn), and SiO2 greatly impact the microbial diversity among FMN communities. Our results indicate that the FMN microbial communities from different land-use types are very similar and suggest that natural selection of these microbes is based on the oligotrophic conditions and the high metal content. Researching FMNs in these two land-use patterns, which

  20. Staphylococcus aureus clfB and spa alleles of the repeat regions are segregated into major phylogenetic lineages.

    PubMed

    Basset, Patrick; Hammer, Nevena Basic; Kuhn, Gerrit; Vogel, Valérie; Sakwinska, Olga; Blanc, Dominique S

    2009-09-01

    To reliably differentiate among Staphylococcus aureus isolates we recently developed the Double Locus Sequence Typing (DLST) based on the analysis of partial sequences of clfB and spa genes. This method is highly discriminatory and gives unambiguous definition of types. The highly clonal population structure of S. aureus suggests that isolates with identical clfB or spa alleles belong to the same clonal complex (CC) defined by Multi-Locus Sequence Typing (MLST). To test this hypothesis as well as to investigate putative intra-CC genetic structure, we analyzed a total of 289 isolates (186 MSSA and 103 MRSA) with DLST-, spa- and MLST-typing. Among the 289 strains, 242 were clustered into 7 major MLST CCs, 40 into minor CCs and 7 were not grouped into CCs. A total of 205 DLST- and 129 spa-types were observed. With one exception, all DLST-clfB, DLST-spa and spa-type alleles were segregated into CCs. DLST-types sharing an identical allele (clfB or spa) were clustered using eBURST. Except for one strain, all isolates from each DLST cluster belonged to the same CC. However, using both DLST- and spa-typing we were not able to disclose a clear intra-CC structure. Nevertheless, the high diversity of these loci confirmed that they are good markers for local epidemiological investigations. PMID:19559820

  1. Identification of novel alleles of the rice blast resistance gene Pi54

    NASA Astrophysics Data System (ADS)

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-10-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.

  2. Identification of novel alleles of the rice blast resistance gene Pi54

    PubMed Central

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-01-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs. PMID:26498172

  3. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials

    PubMed Central

    Meyer-Lucht, Yvonne; Otten, Celine; Püttker, Thomas; Sommer, Simone

    2008-01-01

    Background Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. Results G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. Conclusion Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism. PMID:18534008

  4. Character State Reconstruction of Call Diversity in the Neoconocephalus Katydids Reveals High Levels of Convergence.

    PubMed

    Frederick, Katy; Schul, Johannes

    2016-01-01

    The katydid genus Neoconocephalus is characterized by high diversity of the acoustic communication system. Both male signals and female preferences have been thoroughly studied in the past. This study used Bayesian character state reconstruction to elucidate the evolutionary history of diverse call traits, based on an existing, well supported phylogenetic hypothesis. The most common male call pattern consisted of continuous calls comprising one fast pulse rate; this pattern is the likely ancestral state in this genus. Three lines of call divergence existed among the species of the genus. First, four species had significantly slower pulse rates. Second, five species had alternating pulse periods, resulting in a double pulse rhythm. Third, several species had discontinuous calls, when pulses were grouped into rhythmically repeated verses. Bayesian character state reconstruction revealed that the double-pulse pattern likely evolved convergently five times; the slow pulse rate also evolved four times independently. Discontinuous calls have evolved twice and occur in two clades; each of which contains reversals to the ancestral continuous calls. Pairwise phylogenetically independent contrast analyses among the three call traits found no significant correlations among the character states of the different traits, supporting the independent evolution of the three call traits. PMID:27110432

  5. Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae.

    PubMed

    Walterson, Alyssa M; Stavrinides, John

    2015-11-01

    The bacterial genus Pantoea comprises many versatile species that have been isolated from a multitude of environments. Pantoea was delineated as a genus approximately 25 years ago, but since then, approximately 20 species have been identified having a diversity of characteristics. Isolates from water and soil have been harnessed for industrial purposes including bioremediation, and the degradation of herbicides and other toxic products. Other isolates possess nitrogen fixation and plant growth-promoting capabilities, which are currently being explored for agricultural applications. Some isolates are antibiotic producers, and have been developed into biocontrol agents for the management of plant diseases. Pantoea is also known to form host associations with a variety of hosts, including plants, insects and humans. Although often thought of as a plant pathogen, recent evidence suggests that Pantoea is being frequently isolated from the nosocomial environment, with considerable debate as to its role in human disease. This review will explore this highly versatile group and its capabilities, its known associations, and the underlying genetic and genomic determinants that drive its diversity and adaptability. PMID:26109597

  6. Diversity of Bacteroidetes in high-altitude saline evaporitic basins in northern Chile

    NASA Astrophysics Data System (ADS)

    Dorador, Cristina; Meneses, Daniela; Urtuvia, Viviana; Demergasso, Cecilia; Vila, Irma; Witzel, Karl-Paul; Imhoff, Johannes F.

    2009-06-01

    The phylum Bacteroidetes represents one of the most abundant bacterial groups of marine and freshwater bacterioplankton. We investigated the diversity of Bacteroidetes in water and sediment samples from three evaporitic basins located in the highlands of northern Chile. We used both 16S rRNA gene clone libraries created with targeted Bacteroidetes-specific primers and separation of specifically amplified gene fragments by denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed a reduced richness of these organisms in samples from Salar de Huasco (two to four DGGE bands) increasing in Salar de Ascotán (two to seven DGGE bands) and Laguna Tebenquiche at Salar de Atacama (four to eight DGGE bands). Cluster analysis (WPGMA) of DGGE bands showed that bands from Salar de Huasco and Salar de Ascotán grouped together and samples from Salar de Atacama formed separate clusters in water and sediment samples, reflecting different Bacteroidetes communities between sites. Most of the sequences analyzed belonged to the family Flavobacteriaceae and clustered with the genera Psychroflexus, Gillisia, Maribacter, Muricauda, Flavobacterium, and Salegentibacter. The most abundant phylotype was highly related to Psychroflexus spp. and was recovered from all three study sites. The similarity of the analyzed sequences with their closest relatives in GenBank was typically <97% and notably lower when compared with type strains, demonstrating the unique character of these sequences. Culture efforts will be necessary to get a better description of the diversity of this group in saline evaporitic basins of northern Chile.

  7. High-throughput sequencing of microbial diversity in implant-associated infection.

    PubMed

    Wang, Xin; Hu, Xiaoyan; Deng, Kan; Cheng, Xigao; Wei, Junchao; Jiang, Meixiu; Wang, Xiaolei; Chen, Tingtao

    2016-09-01

    Few molecular studies have shown that the number of bacterial species in implant-associated infection may have been underestimated. To determine the actual microbial diversity in implant-associated infection, a high-throughput sequencing method was adopted to sequence the DNAs extracted from the tissues of infected and uninfected patients. Principal component analysis (PCA) and β diversity showed an obvious divergence of infected and uninfected groups, and that the overgrowth of Proteobacteria (80.87%), Firmicutes (13.41%) in the positive deep infection group (P.d, via biopsy) and Proteobacteria (91.68%) in the positive surface infection group (P.s, via swabs) might be the causative factors in implant-associated infection. Moreover, Venn results indicated that a mean of 330 common operational taxonomic units (OTUs) was obtained in all groups, of which 113, 109, 45, 20, 13 and 12 OTUs belonging to Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes and Chloroflexi were identified. In conclusion, many traditional "pathogenic bacteria" were identified as the common bacteria in operation sites, and the disruption of their complex interaction caused infection; therefore, further work is need to illustrate the aetiology of implant-associated infection using in-depth systems-level analyses. PMID:27268150

  8. Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold.

    PubMed

    Beeby, Morgan; Ribardo, Deborah A; Brennan, Caitlin A; Ruby, Edward G; Jensen, Grant J; Hendrixson, David R

    2016-03-29

    Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes. PMID:26976588

  9. Diverse, high-quality test set for the validation of protein-ligand docking performance.

    PubMed

    Hartshorn, Michael J; Verdonk, Marcel L; Chessari, Gianni; Brewerton, Suzanne C; Mooij, Wijnand T M; Mortenson, Paul N; Murray, Christopher W

    2007-02-22

    A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols. PMID:17300160

  10. Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence.

    PubMed

    Liu, Jinbo; Kong, Weidong; Zhang, Guoshuai; Khan, Ajmal; Guo, Guangxia; Zhu, Chunmao; Wei, Xiaojie; Kang, Shichang; Morgan-Kiss, Rachael M

    2016-10-01

    Global warming has resulted in substantial glacier retreats in high-elevation areas, exposing deglaciated soils to harsh environmental conditions. Autotrophic microbes are pioneering colonizers in the deglaciated soils and provide nutrients to the extreme ecosystem devoid of vegetation. However, autotrophic communities remain less studied in deglaciated soils. We explored the diversity and succession of the cbbL gene encoding the large subunit of form I RubisCO, a key CO2-fixing enzyme, using molecular methods in deglaciated soils along a 10-year deglaciation chronosequence on the Tibetan Plateau. Our results demonstrated that the abundance of all types of form I cbbL (IA/B, IC and ID) rapidly increased in young soils (0-2.5 years old) and kept stable in old soils. Soil total organic carbon (TOC) and total nitrogen (TN) gradually increased along the chronosequence and both demonstrated positive correlations with the abundance of bacteria and autotrophs, indicating that soil TOC and TN originated from autotrophs. Form IA/B autotrophs, affiliated with cyanobacteria, exhibited a substantially higher abundance than IC and ID. Cyanobacterial diversity and evenness increased in young soils (<6 years old) and then remained stable. Our findings suggest that cyabobacteria play an important role in accumulating TOC and TN in the deglaciated soils. PMID:27465079

  11. Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold

    PubMed Central

    Ribardo, Deborah A.; Brennan, Caitlin A.; Ruby, Edward G.; Jensen, Grant J.; Hendrixson, David R.

    2016-01-01

    Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes. PMID:26976588

  12. Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya.

    PubMed

    Čapková, Kateřina; Hauer, Tomáš; Řeháková, Klára; Doležal, Jiří

    2016-01-01

    The environment of high-altitudinal cold deserts of Western Himalaya is characterized by extensive development of biological soil crusts, with cyanobacteria as dominant component. The knowledge of their taxonomic composition and dependency on soil chemistry and elevation is still fragmentary. We studied the abundance and the phylogenetic diversity of the culturable cyanobacteria and eukaryotic microalgae in soil crusts along altitudinal gradients (4600-5900 m) at two sites in the dry mountains of Ladakh (SW Tibetan Plateau and Eastern Karakoram), using both microscopic and molecular approaches. The effects of environmental factors (altitude, mountain range, and soil physico-chemical parameters) on the composition and biovolume of phototrophs were tested by multivariate redundancy analysis and variance partitioning. Both phylogenetic diversity and composition of morphotypes were similar between Karakorum and Tibetan Plateau. Phylogenetic analysis of 16S rRNA gene revealed strains belonging to at least five genera. Besides clusters of common soil genera, e.g., Microcoleus, Nodosilinea, or Nostoc, two distinct clades of simple trichal taxa were newly discovered. The most abundant cyanobacterial orders were Oscillatoriales and Nostacales, whose biovolume increased with increasing elevation, while that of Chroococales decreased. Cyanobacterial species richness was low in that only 15 morphotypes were detected. The environmental factors accounted for 52 % of the total variability in microbial data, 38.7 % of which was explained solely by soil chemical properties, 14.5 % by altitude, and 8.4 % by mountain range. The elevation, soil phosphate, and magnesium were the most important predictors of soil phototrophic communities in both mountain ranges despite their different bedrocks and origin. The present investigation represents a first record on phylogenetic diversity of the cyanobacterial community of biological soil crusts from Western Himalayas and first record

  13. Allele-specific disparity in breast cancer

    PubMed Central

    2011-01-01

    Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by

  14. North-South differentiation and a region of high diversity in European wolves (Canis lupus).

    PubMed

    Stronen, Astrid V; Jędrzejewska, Bogumiła; Pertoldi, Cino; Demontis, Ditte; Randi, Ettore; Niedziałkowska, Magdalena; Pilot, Małgorzata; Sidorovich, Vadim E; Dykyy, Ihor; Kusak, Josip; Tsingarska, Elena; Kojola, Ilpo; Karamanlidis, Alexandros A; Ornicans, Aivars; Lobkov, Vladimir A; Dumenko, Vitalii; Czarnomska, Sylwia D

    2013-01-01

    European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part. PMID:24146871

  15. Pseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity

    PubMed Central

    2014-01-01

    Background Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. In addition, genetic variability of all the P. aeruginosa strains whose genomes have been sequenced is extremely low. This low genomic variability might be explained if clinical strains constitute a subpopulation of this bacterial species present in environments that are close to human populations, which preferentially produce virulence associated traits. Results In this work, we sequenced the genomes and performed phenotypic descriptions for four non-human P. aeruginosa isolates collected from a plant, the ocean, a water-spring, and from dolphin stomach. We show that the four strains are phenotypically diverse and that this is not reflected in genomic variability, since their genomes are almost identical. Furthermore, we performed a detailed comparative genomic analysis of the four strains studied in this work with the thirteen previously reported P. aeruginosa genomes by means of describing their core and pan-genomes. Conclusions Contrary to what has been described for other bacteria we have found that the P. aeruginosa core genome is constituted by a high proportion of genes and that its pan-genome is thus relatively small. Considering the high degree of genomic conservation between isolates of P. aeruginosa from diverse environments, including human tissues, some implications for the treatment of infections are discussed. This work also represents a methodological contribution for the genomic study of P. aeruginosa, since we provide a database of the comparison of all the proteins encoded by the seventeen strains analyzed. PMID:24773920

  16. North-South Differentiation and a Region of High Diversity in European Wolves (Canis lupus)

    PubMed Central

    Stronen, Astrid V.; Jędrzejewska, Bogumiła; Pertoldi, Cino; Demontis, Ditte; Randi, Ettore; Niedziałkowska, Magdalena; Pilot, Małgorzata; Sidorovich, Vadim E.; Dykyy, Ihor; Kusak, Josip; Tsingarska, Elena; Kojola, Ilpo; Karamanlidis, Alexandros A.; Ornicans, Aivars; Lobkov, Vladimir A.; Dumenko, Vitalii; Czarnomska, Sylwia D.

    2013-01-01

    European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part. PMID:24146871

  17. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

    PubMed

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

  18. High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin

    PubMed Central

    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

  19. Genetic diversity of high-elevation populations of an endangered medicinal plant

    PubMed Central

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2015-01-01

    Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G′st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks. PMID:25416728

  20. A high-carbohydrate diet enhances the adverse effect of the S2 allele of APOC3 SstI polymorphism on the TG/HDL-C ratio only in young Chinese females.

    PubMed

    Song, Yong Yan; Gong, Ren Rong; Zhang, Zhen; Li, Yuan Hao; Xiao, Li Ying; Zhou, Xue Dong; Fang, Ding Zhi

    2011-06-01

    Both genetic background and diet have profound effects on plasma lipid profiles. We hypothesized that a high-carbohydrate (high-CHO) diet may affect the ratios of serum lipids and apolipoproteins (apo) differently in subjects with different genotypes of the SstI polymorphism in the apoCIII gene (APOC3). Fifty-six healthy university students (27 males and 29 females, 22.89 ± 1.80 years) were given a washout diet of 54% carbohydrate for 7 days, followed by a high-CHO diet of 70% carbohydrate for 6 days without total energy restriction. Serum triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apoB100, apoAI, and the APOC3 SstI polymorphism were analyzed. The ratios of serum lipids and apoB100/apoAI were calculated. At baseline, the TG/HDL-C ratio was significantly higher in females, but not in males, with the S2 allele. The differences in the TG/HDL-C ratio between genotypes remained the same after the washout and the high-CHO diet in females. When compared with those before the high-CHO diet, the TC/HDL-C (male S2 carriers: 3.13 ± 1.00 vs 2.36 ± 0.65, P = 0.000; male subjects with the S1S1 genotype: 2.97 ± 0.74 vs 2.09 ± 0.55, P = 0.000; female S2 carriers: 2.68 ± 0.36 vs 2.24 ± 0.37, P = 0.004; female subjects with the S1S1 genotype: 2.69 ± 0.41 vs 2.09 ± 0.31, P = 0.000) and LDL-C/HDL-C (male S2 carriers: 1.44 ± 0.71 vs 1.06 ± 0.26, P = 0.012; male subjects with the S1S1 genotype: 1.35 ± 0.61 vs 1.01 ± 0.29, P = 0.005; female S2 carriers: 1.18 ± 0.33 vs 1.00 ± 0.18, P = 0.049; female subjects with the S1S1 genotype: 1.18 ± 0.35 vs 1.04 ± 0.19, P = 0.026) ratios were significantly decreased after the high-CHO diet regardless of gender and of genotype of the APOC3 SstI polymorphism. However, in female S2 carriers, the TG/HDL-C (1.38 ± 0.46 vs 1.63 ± 0.70, P = 0.039) ratio was significantly increased after the high-CHO diet. In conclusion, the high-CHO diet has

  1. Race and Academic Achievement in Racially Diverse High Schools: Opportunity and Stratification.

    PubMed

    Muller, Chandra; Riegle-Crumb, Catherine; Schiller, Kathryn S; Wilkinson, Lindsey; Frank, Kenneth A

    2010-04-01

    BACKGROUND/CONTEXT: Brown v Board of Education fundamentally changed our nation's schools, yet we know surprisingly little about how and whether they provide equality of educational opportunity. Although substantial evidence suggests that African American and Latino students who attend these schools face fewer learning opportunities than their White counterparts, until now, it has been impossible to examine this using a representative sample because of lack of data. PURPOSE/OBJECTIVE/RESEARCH QUESTION/FOCUS OF STUDY: This study uses newly available data to investigate whether racially diverse high schools offer equality of educational opportunity to students from different racial and ethnic groups. This is examined by measuring the relative representation of minority students in advanced math classes at the beginning of high school and estimating whether and how this opportunity structure limits the level of achievement attained by African American and Latino students by the end of high school. SETTING: This study uses data from the Adolescent Health and Academic Achievement Study (AHAA) and its partner study, the National Longitudinal Study of Adolescent Health (Add Health), a stratified, nationally representative study of students in U.S. high schools first surveyed in 1994-1995. POPULATION/PARTICIPANTS/SUBJECTS: Two samples of racially diverse high schools were used in the analysis: one with African Americans, Whites, and Asians (26 schools with 3,149 students), and the other with Latinos, Whites, and Asians (22 schools with 2,775 students). RESEARCH DESIGN: Quantitative analyses first assess how high schools vary in the extent to which minority students are underrepresented in advanced sophomore math classes. Hierarchical multilevel modeling is then used to estimate whether racial-ethnic differences in representation in advanced math have an impact on African American and Latino students' achievement by the end of high school, relative to the Whites and Asians

  2. [Screening of peafowl microsatellite primers and analysis of genetic diversity].

    PubMed

    Bao, Wen-Bin; Chen, Guo-Hong; Shu, Jing-Ting; Xu, Qi; Li, Hui-Fang

    2006-10-01

    The applicability of chicken microsatellite primers to peafowl population was analyzed in the present paper, and the results showed 14 of 29 pairs of microsatellite primers from chicken could amplify peafowl DNA and produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, and MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis within and between the green peafowl and the blue peafowl populations demonstrated that the expected heterozygosity of two peafowl populations were 0.2482 and 0.2744, respectively. The inbreeding index (FST), Reynolds' genetic distance and gene flow between the two populations were 0.078, 0.0603 and 3.896 respectively. These results indicate that the heterozygosity and the genetic diversity of these two peafowl populations were very low, and suggest a tendency towards intermixing. PMID:17035182

  3. Tetra-allelic SNPs: Informative forensic markers compiled from public whole-genome sequence data.

    PubMed

    Phillips, C; Amigo, J; Carracedo, Á; Lareu, M V

    2015-11-01

    Multiple-allele single nucleotide polymorphisms (SNPs) are potentially useful for forensic DNA analysis as they can provide more discrimination power than normal binary SNPs. In addition, the presence in a profile of more than two alleles per marker provides a clearer indication of mixed DNA than assessments of imbalanced signals in the peak pairs of binary SNPs. Using the 1000 Genomes Phase III human variant data release of 2014 as the starting point, this study collated 961 tetra-allelic SNPs that pass minimum sequence quality thresholds and where four separate nucleotide substitution alleles were detected. Although most of these loci had three of the four alleles in combined frequencies of 2% or less, 160 had high heterozygosities with 50 exceeding those of 'ideal' 0.5:0.5 binary SNPs. From this set of most polymorphic tetra-allelic SNPs, we identified markers most informative for forensic purposes and explored these loci in detail. Subsets of the most polymorphic tetra-allelic SNPs will make useful additions to current panels of forensic identification SNPs and ancestry-informative SNPs. The 24 most discriminatory tetra-allelic SNPs were estimated to detect more than two alleles in at least one marker per profile in 99.9% of mixtures of African contributors. In European contributor mixtures 99.4% of profiles would show multiple allele patterns, but this drops to 92.6% of East Asian contributor mixtures due to reduced levels of polymorphism for the 24 SNPs in this population group. PMID:26209763

  4. Treatment variable effects on supercritical gasification of high-diversity grassland perennials.

    PubMed

    Zhang, Bo; Zhang, Zhigang; von Keitz, Marc; Valentas, Kenneth

    2009-05-01

    Low-input high-diversity (LIHD) mixtures of native grassland perennials were subjected to a supercritical treatment process with the aim of obtaining hydrogen-rich gases. The process was studied based on the following treatment variables: reaction temperature (374 degrees C to 575 degrees C, corresponding to a pressure range of 22.1 to 40 MPa), residence time (10 to 30 min), biomass content in the feed, and catalysts (0% to 4% NaOH and solid alkali CaO-ZrO(2)). The gaseous phase produced from gasification of LIHD primarily consisted of hydrogen (H(2)), with a mixture of carbon monoxide (CO), methane (CH(4)), and carbon dioxide (CO(2)). The statistical significance of treatment variables was evaluated using analysis of variance (ANOVA). It showed that at the level of P < 0.05, temperature, catalysts, and biomass content in the feed significantly affected gas yields, while residence time was not significant. PMID:19229484

  5. What does impacted look like? High diversity and abundance of epibiota in modified estuaries.

    PubMed

    Clark, Graeme F; Kelaher, Brendan P; Dafforn, Katherine A; Coleman, Melinda A; Knott, Nathan A; Marzinelli, Ezequiel M; Johnston, Emma L

    2015-01-01

    Ecosystems modified by human activities are generally predicted to be biologically impoverished. However, much pollution impact theory stems from laboratory or small-scale field studies, and few studies replicate at the level of estuary. Furthermore, assessments are often based on sediment contamination and infauna, and impacts to epibiota (sessile invertebrates and algae) are seldom considered. We surveyed epibiota in six estuaries in south-east Australia. Half the estuaries were relatively pristine, and half were subject to internationally high levels of contamination, urbanisation, and industrialisation. Contrary to predictions, epibiota in modified estuaries had greater coverage and were similarly diverse as those in unmodified estuaries. Change in epibiota community structure was linearly correlated with sediment-bound copper, and the tubeworm Hydroides elegans showed a strong positive correlation with sediment metals. Stressors such as metal contamination can reduce biodiversity and productivity, but others such as nutrient enrichment and resource provision may obscure signals of impact. PMID:25282127

  6. Mosquito Surveillance for 15 Years Reveals High Genetic Diversity Among West Nile Viruses in Israel.

    PubMed

    Lustig, Yaniv; Hindiyeh, Musa; Orshan, Laor; Weiss, Leah; Koren, Ravit; Katz-Likvornik, Shiri; Zadka, Hila; Glatman-Freedman, Aharona; Mendelson, Ella; Shulman, Lester M

    2016-04-01

    West Nile Virus (WNV) is endemic in Israel and has been the cause of several outbreaks in recent years. In 2000, a countrywide mosquito survey was established to monitor WNV activity and characterize viral genotypes in Israel. We analyzed data from 7135 pools containing 277 186 mosquitoes collected over the past 15 years and, here, report partial sequences of WNV genomes obtained from 102 of the 336 positive mosquito pools. Phylogenetic analysis demonstrated that cluster 4 and the Mediterranean and Eastern European subtypes of cluster 2 within WNV lineage 1 circulated in Israel, as did WNV lineage 2, highlighting a high genetic diversity of WNV genotypes in our region. As a major crossroads for bird migration between Africa and Eurasia and with a long history of human infection, Israel serves as a resource hub for WNV in Africa and Eurasia and provides valuable information on WNV circulation in these regions. PMID:26597260

  7. Detection of Diverse and High Molecular Weight Nesprin-1 and Nesprin-2 Isoforms Using Western Blotting.

    PubMed

    Carthew, James; Karakesisoglou, Iakowos

    2016-01-01

    Heavily utilized in cell and molecular biology, western blotting is considered a crucial technique for the detection and quantification of proteins within complex mixtures. In particular, the detection of members of the nesprin (nuclear envelope spectrin repeat protein) family has proven difficult to analyze due to their substantial isoform diversity, molecular weight variation, and the sheer size of both nesprin-1 and nesprin-2 giant protein variants (>800 kDa). Nesprin isoforms contain distinct domain signatures, perform differential cytoskeletal associations, occupy different subcellular compartments, and vary in their tissue expression profiles. This structural and functional variance highlights the need to distinguish between the full range of proteins within the nesprin protein family, allowing for greater understanding of their specific roles in cell biology and disease. Herein, we describe a western blotting protocol modified for the detection of low to high molecular weight (50-1000 kDa) nesprin proteins. PMID:27147045

  8. New Tools For Understanding Microbial Diversity Using High-throughput Sequence Data

    NASA Astrophysics Data System (ADS)

    Knight, R.; Hamady, M.; Liu, Z.; Lozupone, C.

    2007-12-01

    High-throughput sequencing techniques such as 454 are straining the limits of tools traditionally used to build trees, choose OTUs, and perform other essential sequencing tasks. We have developed a workflow for phylogenetic analysis of large-scale sequence data sets that combines existing tools, such as the Arb phylogeny package and the NAST multiple sequence alignment tool, with new methods for choosing and clustering OTUs and for performing phylogenetic community analysis with UniFrac. This talk discusses the cyberinfrastructure we are developing to support the human microbiome project, and the application of these workflows to analyze very large data sets that contrast the gut microbiota with a range of physical environments. These tools will ultimately help to define core and peripheral microbiomes in a range of environments, and will allow us to understand the physical and biotic factors that contribute most to differences in microbial diversity.

  9. Association of apolipoprotein E allele {epsilon}4 with late-onset sporadic Alzheimer`s disease

    SciTech Connect

    Lucotte, G.; David, F.; Berriche, S.

    1994-09-15

    Apolipoprotein E, type {epsilon}4 allele (ApoE {epsilon}4), is associated with late-onset sporadic Alzheimer`s disease (AD) in French patients. The association is highly significant (0.45 AD versus 0.12 controls for {epsilon}4 allele frequencies). These data support the involvement of ApoE {epsilon}4 allele as a very important risk factor for the clinical expression of AD. 22 refs., 1 fig., 3 tabs.

  10. Demographic history and rare allele sharing among human populations.

    PubMed

    Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D

    2011-07-19

    High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

  11. Demographic history and rare allele sharing among human populations

    PubMed Central

    Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham