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Sample records for human microsatellite variability

  1. Sequence determinants of human microsatellite variability

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    Jakobsson Mattias

    2009-12-01

    Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

  2. Microsatellite marker analysis of the genetic variability in Hanoverian Hounds.

    Science.gov (United States)

    Lüpke, L; Distl, O

    2005-04-01

    Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n=334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy-Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (H(O)) was slightly higher than the expected heterozygosity (H(E)). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average H(O) of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to H(O). We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.

  3. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells

    OpenAIRE

    Baptiste, Beverly A.; Ananda, Guruprasad; Strubczewski, Noelle; Lutzkanin, Andrew; Khoo, Su Jen; Srikanth, Abhinaya; Kim, Nari; Makova, Kateryna D.; Krasilnikova, Maria M.; Eckert, Kristin A.

    2013-01-01

    Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (?10 units) are present within exonic sequences of >350 genes, re...

  4. Evidence for widespread convergent evolution around human microsatellites.

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    Edward J Vowles

    2004-08-01

    Full Text Available Microsatellites are a major component of the human genome, and their evolution has been much studied. However, the evolution of microsatellite flanking sequences has received less attention, with reports of both high and low mutation rates and of a tendency for microsatellites to cluster. From the human genome we generated a database of many thousands of (AC(n flanking sequences within which we searched for common characteristics. Sequences flanking microsatellites of similar length show remarkable levels of convergent evolution, indicating shared mutational biases. These biases extend 25-50 bases either side of the microsatellite and may therefore affect more than 30% of the entire genome. To explore the extent and absolute strength of these effects, we quantified the observed convergence. We also compared homologous human and chimpanzee loci to look for evidence of changes in mutation rate around microsatellites. Most models of DNA sequence evolution assume that mutations are independent and occur randomly. Allowances may be made for sites mutating at different rates and for general mutation biases such as the faster rate of transitions over transversions. Our analysis suggests that these models may be inadequate, in that proximity to even very short microsatellites may alter the rate and distribution of mutations that occur. The elevated local mutation rate combined with sequence convergence, both of which we find evidence for, also provide a possible resolution for the apparently contradictory inferences of mutation rates in microsatellite flanking sequences.

  5. Genetic variability of watermelon accessions based on microsatellite markers.

    Science.gov (United States)

    de S Gama, R N C; Santos, C A F; de C S Dias, R

    2013-03-13

    We analyzed the genetic variability of 40 watermelon accessions collected from 8 regions of Northeastern Brazil using microsatellite markers, in order to suggest strategies of conservation and utilization of genetic variability in this species. These accessions are not commercial cultivars. They were sampled in areas of traditional farmers that usually keep their own seeds for future plantings year after year. An UPGMA dendrogram was generated from a distance matrix of the Jaccard coefficient, based on 41 alleles of 13 microsatellite loci. Analysis of molecular variance was made by partitioning between and within geographical regions. The similarity coefficient between accessions ranged from 37 to 96%; the dendrogram gave a co-phenetic value of 0.80. The among population genetic variability was high ( (^)ϕST = 0.319). Specific clusters of accessions sampled in 3 regions of Maranhão were observed while the other 5 regions did not presented specific clusters by regions. We conclude that watermelon genetic variability is not uniformly dispersed in the regions analyzed, indicating that geographical barriers or edaphoclimatic conditions have limited open mating. We suggest sampling a greater number of populations, so regional species diversity will be better represented and preserved in the germplasm bank.

  6. Genetic variability in local Brazilian horse lines using microsatellite markers.

    Science.gov (United States)

    Silva, A C M; Paiva, S R; Albuquerque, M S M; Egito, A A; Santos, S A; Lima, F C; Castro, S T; Mariante, A S; Correa, P S; McManus, C M

    2012-04-10

    Genetic variability at 11 microsatellite markers was analyzed in five naturalized/local Brazilian horse breeds or genetic groups. Blood samples were collected from 328 animals of the breeds Campeira (Santa Catarina State), Lavradeira (Roraima State), Pantaneira (Pantanal Mato-Grossense), Mangalarga Marchador (Minas Gerais State), as well as the genetic group Baixadeiro (Maranhão State), and the exotic breeds English Thoroughbred and Arab. We found significant genetic variability within evaluated microsatellite loci, with observed heterozygosis varying between 0.426 and 0.768 and polymorphism information content values of 0.751 to 0.914. All breeds showed high inbreeding coefficients and were not in Hardy-Weinberg equilibrium. The smallest genetic distance was seen between the Pantaneira and Arab breeds. The principal component analyzes and Bayesian approach demonstrated that the exotic breeds have had a significant influence on the genetic formation of the local breeds, with introgression of English Throroughbred in Pantaneira and Lavradeira, as well as genetic proximity between the Arab, Pantaneira and Mangalarga Marchador populations. This study shows the need to conserve traits acquired by naturalized horse breeds over centuries of natural selection in Brazil due to the genetic uniqueness of each group, suggesting a reduced gene flow between them. These results reinforce the need to include these herds in animal genetic resource conservation programs to maximize the genetic variability and conserve useful allele combinations.

  7. Genetic variability in Brazilian wheat cultivars assessed by microsatellite markers

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    Ivan Schuster

    2009-01-01

    Full Text Available Wheat (Triticum aestivum is one of the most important food staples in the south of Brazil. Understanding genetic variability among the assortment of Brazilian wheat is important for breeding. The aim of this work was to molecularly characterize the thirty-six wheat cultivars recommended for various regions of Brazil, and to assess mutual genetic distances, through the use of microsatellite markers. Twenty three polymorphic microsatellite markers (PMM delineated all 36 of the samples, revealing a total of 74 simple sequence repeat (SSR alleles, i.e. an average of 3.2 alleles per locus. Polymorphic information content (PIC value calculated to assess the informativeness of each marker ranged from 0.20 to 0.79, with a mean of 0.49. Genetic distances among the 36 cultivars ranged from 0.10 (between cultivars Ocepar 18 and BRS 207 to 0.88 (between cultivars CD 101 and Fudancep 46, the mean distance being 0.48. Twelve groups were obtained by using the unweighted pair-group method with arithmetic means analysis (UPGMA, and thirteen through the Tocher method. Both methods produced similar clusters, with one to thirteen cultivars per group. The results indicate that these tools may be used to protect intellectual property and for breeding and selection programs.

  8. Microsatellite DNA typing for assessment of genetic variability in ...

    Indian Academy of Sciences (India)

    these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. Various .... enced a recent reduction in the effective population size or a genetic ... by using the m p val.exe program (Garza and Williamson.

  9. Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers.

    Science.gov (United States)

    Pajuelo, Mónica J; Eguiluz, María; Roncal, Elisa; Quiñones-García, Stefany; Clipman, Steven J; Calcina, Juan; Gavidia, Cesar M; Sheen, Patricia; Garcia, Hector H; Gilman, Robert H; Gonzalez, Armando E; Zimic, Mirko

    2017-12-01

    The adult Taenia solium, the pork tapeworm, usually lives as a single worm in the small intestine of humans, its only known definitive host. Mechanisms of genetic variation in T. solium are poorly understood. Using three microsatellite markers previously reported [1], this study explored the genetic variability of T. solium from cysts recovered from experimentally infected pigs. It then explored the genetic epidemiology and transmission in naturally infected pigs and adult tapeworms recovered from human carriers from an endemic rural community in Peru. In an initial study on experimental infection, two groups of three piglets were each infected with proglottids from one of two genetically different tapeworms for each of the microsatellites. After 7 weeks, pigs were slaughtered and necropsy performed. Thirty-six (92.3%) out of 39 cysts originated from one tapeworm, and 27 (100%) out of 27 cysts from the other had exactly the same genotype as the parental tapeworm. This suggests that the microsatellite markers may be a useful tool for studying the transmission of T. solium. In the second study, we analyzed the genetic variation of T. solium in cysts recovered from eight naturally infected pigs, and from adult tapeworms recovered from four human carriers; they showed genetic variability. Four pigs had cysts with only one genotype, and four pigs had cysts with two different genotypes, suggesting that multiple infections of genetically distinct parental tapeworms are possible. Six pigs harbored cysts with a genotype corresponding to one of the identified tapeworms from the human carriers. In the dendrogram, cysts appeared to cluster within the corresponding pigs as well as with the geographical origin, but this association was not statistically significant. We conclude that genotyping of microsatellite size polymorphisms is a potentially important tool to trace the spread of infection and pinpoint sources of infection as pigs spread cysts with a shared parental genotype.

  10. Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers.

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    Mónica J Pajuelo

    2017-12-01

    Full Text Available The adult Taenia solium, the pork tapeworm, usually lives as a single worm in the small intestine of humans, its only known definitive host. Mechanisms of genetic variation in T. solium are poorly understood. Using three microsatellite markers previously reported [1], this study explored the genetic variability of T. solium from cysts recovered from experimentally infected pigs. It then explored the genetic epidemiology and transmission in naturally infected pigs and adult tapeworms recovered from human carriers from an endemic rural community in Peru. In an initial study on experimental infection, two groups of three piglets were each infected with proglottids from one of two genetically different tapeworms for each of the microsatellites. After 7 weeks, pigs were slaughtered and necropsy performed. Thirty-six (92.3% out of 39 cysts originated from one tapeworm, and 27 (100% out of 27 cysts from the other had exactly the same genotype as the parental tapeworm. This suggests that the microsatellite markers may be a useful tool for studying the transmission of T. solium. In the second study, we analyzed the genetic variation of T. solium in cysts recovered from eight naturally infected pigs, and from adult tapeworms recovered from four human carriers; they showed genetic variability. Four pigs had cysts with only one genotype, and four pigs had cysts with two different genotypes, suggesting that multiple infections of genetically distinct parental tapeworms are possible. Six pigs harbored cysts with a genotype corresponding to one of the identified tapeworms from the human carriers. In the dendrogram, cysts appeared to cluster within the corresponding pigs as well as with the geographical origin, but this association was not statistically significant. We conclude that genotyping of microsatellite size polymorphisms is a potentially important tool to trace the spread of infection and pinpoint sources of infection as pigs spread cysts with a shared

  11. Analysis of genetic variability in the Czech Dachshund population using microsatellite markers

    Czech Academy of Sciences Publication Activity Database

    Přibáňová, M.; Horák, Pavel; Schröffelová, D.; Urban, T.; Bechyňová, Renata; Musilová, L.

    2009-01-01

    Roč. 126, - (2009), s. 311-318 ISSN 0931-2668 R&D Projects: GA AV ČR 1QS500450578; GA ČR GD523/03/H076 Institutional research plan: CEZ:AV0Z50450515 Keywords : dachshund * dog * genetic variability * microsatellite Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.706, year: 2009

  12. LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability.

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    Marcos R H Estécio

    2007-05-01

    Full Text Available Alterations in DNA methylation in cancer include global hypomethylation and gene-specific hypermethylation. It is not clear whether these two epigenetic errors are mechanistically linked or occur independently. This study was performed to determine the relationship between DNA hypomethylation, hypermethylation and microsatellite instability in cancer.We examined 61 cancer cell lines and 60 colorectal carcinomas and their adjacent tissues using LINE-1 bisulfite-PCR as a surrogate for global demethylation. Colorectal carcinomas with sporadic microsatellite instability (MSI, most of which are due to a CpG island methylation phenotype (CIMP and associated MLH1 promoter methylation, showed in average no difference in LINE-1 methylation between normal adjacent and cancer tissues. Interestingly, some tumor samples in this group showed increase in LINE-1 methylation. In contrast, MSI-showed a significant decrease in LINE-1 methylation between normal adjacent and cancer tissues (P<0.001. Microarray analysis of repetitive element methylation confirmed this observation and showed a high degree of variability in hypomethylation between samples. Additionally, unsupervised hierarchical clustering identified a group of highly hypomethylated tumors, composed mostly of tumors without microsatellite instability. We extended LINE-1 analysis to cancer cell lines from different tissues and found that 50/61 were hypomethylated compared to peripheral blood lymphocytes and normal colon mucosa. Interestingly, these cancer cell lines also exhibited a large variation in demethylation, which was tissue-specific and thus unlikely to be resultant from a stochastic process.Global hypomethylation is partially reversed in cancers with microsatellite instability and also shows high variability in cancer, which may reflect alternative progression pathways in cancer.

  13. Human Postmeiotic Segregation 2 Exhibits Biased Repair at Tetranucleotide Microsatellite Sequences

    OpenAIRE

    Shah, Sandeep N.; Eckert, Kristin A.

    2009-01-01

    The mismatch repair (MMR) system plays a major role in removing DNA polymerization errors, and loss of this pathway results in hereditary cancers characterized by microsatellite instability. We investigated microsatellite stability during DNA replication within human postmeiotic segregation 2 (hPMS2)–deficient and proficient human lymphoblastoid cell lines. Using a shuttle vector assay, we measured mutation rates at reporter cassettes containing defined mononucleotide, dinucleotide, and tetra...

  14. Comparative analysis of microsatellite variability in five macaw species (Psittaciformes, Psittacidae: application for conservation

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    Flavia T. Presti

    2011-01-01

    Full Text Available Cross-amplification was tested and variability in microsatellite primers (designed for Neotropical parrots compared, in five macaw species, viz., three endangered blue macaws (Cyanopsitta spixii [extinct in the wild], Anodorhynchus leari [endangered] and Anodorhynchus hyacinthinus [vulnerable], and two unthreatened red macaws (Ara chloropterus and Ara macao. Among the primers tested, 84.6% successfully amplified products in C. spixii, 83.3% in A. leari, 76.4% in A. hyacinthinus, 78.6% in A. chloropterus and 71.4% in A. macao. The mean expected heterozygosity estimated for each species, and based on loci analyzed in all the five, ranged from 0.33 (A. hyacinthinus to 0.85 (A. macao. As expected, the results revealed lower levels of genetic variability in threatened macaw species than in unthreatened. The low combined probability of genetic identity and the moderate to high potential for paternity exclusion, indicate the utility of the microsatellite loci set selected for each macaw species in kinship and population studies, thus constituting an aid in planning in-situ and ex-situ conservation.

  15. Development of new VNTR markers for pike and assessment of variability at di- and tetranucleotide repeat microsatellite loci

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Taggart, J.B.; Meldrup, Dorte

    1999-01-01

    Levels of variation at six VNTR (variable number of tandem repeats) loci, one minisatellite and five microsatellite loci, isolated from tri- and tetranucleotide enriched DNA libraries for northern pike were generally low in two Danish populations (1-4 alleles; expected heterozygosity 0-0.57), tho......Levels of variation at six VNTR (variable number of tandem repeats) loci, one minisatellite and five microsatellite loci, isolated from tri- and tetranucleotide enriched DNA libraries for northern pike were generally low in two Danish populations (1-4 alleles; expected heterozygosity 0...

  16. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

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    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  17. Germ-line mutations at a mouse ESTR (Pc-3) locus and human microsatellite loci

    International Nuclear Information System (INIS)

    Ryo, Haruko; Nakajima, Hiroo; Nomura, Taisei

    2006-01-01

    We examined the use of the mouse Pc-3 ESTR (expanded simple tandem repeat) locus and 72 human microsatellite loci as potentially sensitive biomarkers for mutagenic exposures to germ cells in mice and humans respectively. In the mouse work, we treated male mice with TCDD (2, 3, 7, 8-tetrachlo-rodibenzo-p-dioxin; a chemical known to induce congenital anomalies in humans and mice) and, analysed the F 1 fetuses for Pc-3 mutations. Although the incidence of anomalies was higher in the TCDD group, there were no induced mutations. However, respiratory distress syndrome (RDS) was observed in 3 of 7 fetuses born to male mice which were treated with TCDD and which showed abnormal length of Pc-3 allele. In the human studies, the children of Chernobyl liquidators were examined for mutations at a total of 72 (31 autosomal, 1 X-linked and 40 Y-linked) microsatellite loci. This study was prompted by earlier findings of increases in microsatellite mutations in barn swallows and wheat in the highly contaminated areas after the Chernobyl accident. We examined 64 liquidator families (70 children) and 66 control families (70 children). However, no increases in mutation rates were found. The estimated mean dose to the liquidators was about 39 mSv and this might be one possible reason why no increases of mutations could be found. (author)

  18. Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers

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    Claudio Brondani

    2006-01-01

    Full Text Available The rice (Oryza sativa breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuária (Embrapa is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.

  19. Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand.

    Science.gov (United States)

    Babaei, Nahid; Abdullah, Nur Ashikin Psyquay; Saleh, Ghizan; Abdullah, Thohirah Lee

    2012-11-01

    Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.

  20. [Microsatellite instability and human papilloma virus genotypes in preneoplastic and neoplastic uterine cervix lesions].

    Science.gov (United States)

    Roa S, Juan Carlos; Martínez S, Ricardo; Montenegro, Sonia; Roa E, Iván; Capurro V, Italo; Ibacache S, Gilda; Melo A, Angélica

    2007-01-01

    The association between some specific human papilloma virus (HPV) types and cervix cancer is well known. However, the genetic conditions that favor the development of cervical cancer are less well known. To determine the presence of satellite instability (MSI) in preneoplastic and neoplastic lesions of the cervix and correlate these findings with HPV genotypes. Biopsy samples of cervical lesions were studied. Sixteen had low grade lesions, 22 had high grade lesions and 28 had an epidermoid cancer. Viral types were identified with polymerase chain reaction, dot-blot hybridization and restriction fragment length polymorphism. MSI was determined using a panel of eight highly informative microsatellites. Microsatellite instability in at least one locus was observed in 91, 56 and 69% of low grade lesions, high grade lesions and epidermoid carcinomas, respectively. MSI-High grade, MSI-Low grade instability and microsatellite stability were observed in 5, 60 and 46% of samples, respectively. Two of three samples with high grade instability had HPV 52 genotype. Other viral subtypes had frequencies that ranged from 78% to 100%, with the exception of HPV16 that was present in only 53% of samples with low grade instability. Two thirds of biopsy samples from cervical lesions had MSI, mechanism that can be involved in the first stages of cervical carcinogenesis. The low frequency of high grade instability, its association with HPV52 and the low frequency of HPV16 in samples with low grade instability, suggest different coadjutant mechanisms in cervical carcinogenesis.

  1. Feasibility study on the FAO chicken microsatellite panel to assess genetic variability in the turkey (Meleagris gallopavo

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    Elena Colombo

    2014-12-01

    Full Text Available The aim of this work was to study the feasibility of the Food and Agriculture Organization (FAO microsatellite panel developed for chickens to assess genetic variability in turkeys. Genomic DNA was extracted from a total of 37 blood samples collected from turkey of different breeds [15 Brianzolo (BR; 12 Colli Euganei (EU; 10 Nero d’Italia (NI], and all 31 chicken microsatellite markers recommended by the FAO were tested. The results show that 22 chicken markers out of 31 suggested by FAO guidelines can be applied to turkey populations. In particular, the multiplex groups confirmed in the turkey were the Multiplex Master Mix 1 (ADL0268, ADL0278, LEI0094, MCW0216, MCW0248 and the Master Mix 2 (MCW0034, MCW0069, MCW0081, MCW0222, MCW0295, whereas 13 microsatellites were amplified only under single polymerase chain reaction (PCR conditions. No PCR products were obtained for 9 markers (LEI0166, MCW0020, MCW0078, MCW0080, MCW0104, MCW0123, MCW0248, MCW0284 and MCW0330, which is 29% of the total markers used. A panel of 22 markers was used to assess genetic diversity in three turkey breeds and a total number of 63 alleles were found. Observed (Ho and expected (He heterozygosity and polymorphism information content (PIC values for each microsatellite and the relative mean values were also calculated. The mean values were 0.210, 0.250, 0.203 for Ho; 0.301, 0.348, 0.228 for He; and 0.265, 0.313, 0.199 for PIC in NI, BR and EU, respectively.

  2. Rapid and inexpensive analysis of genetic variability in Arapaima gigas by PCR multiplex panel of eight microsatellites.

    Science.gov (United States)

    Hamoy, I G; Santos, E J M; Santos, S E B

    2008-01-22

    The aim of the present study was the development of a multiplex genotyping panel of eight microsatellite markers of Arapaima gigas, previously described. Specific primer pairs were developed, each one of them marked with either FAM-6, HEX or NED. The amplification conditions using the new primers were standardized for a single reaction. The results obtained demonstrate high heterozygosity (average of 0.69) in a Lower Amazon population. The multiplex system described can thus be considered a fast, efficient and inexpensive method for the investigation of genetic variability in Arapaima populations.

  3. Microsatellite polymorphisms associated with human behavioural and psychological phenotypes including a gene-environment interaction.

    Science.gov (United States)

    Bagshaw, Andrew T M; Horwood, L John; Fergusson, David M; Gemmell, Neil J; Kennedy, Martin A

    2017-02-03

    The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance. The repeats were a highly conserved poly-AC microsatellite in the upstream promoter region of the T-box brain 1 (TBR1) gene and three previously studied STRs in the activating enhancer-binding protein 2-beta (AP2-β) and androgen receptor (AR) genes. Where significance was found we used multiple regression to assess the influence of confounding factors. Carriers of the shorter, most common, allele of the AR gene's GGN microsatellite polymorphism had fewer anxiety-related symptoms, which was consistent with previous studies, but in our study this was not significant following Bonferroni correction. No associations with two repeats in the AP2-β gene withstood this correction. A novel finding was that carriers of the minor allele of the TBR1 AC microsatellite were at higher risk of conduct problems in childhood at age 7-9 (p = 0.0007, which did pass Bonferroni correction). Including maternal smoking during pregnancy (MSDP) in models controlling for potentially confounding influences showed that an interaction between TBR1 genotype and MSDP was a significant predictor of conduct problems in childhood and adolescence (p behaviour up to age 25 years (p ≤ 0.02). This interaction remained significant after controlling for possible confounders including maternal age at birth, socio-economic status and education, and offspring birth weight. The potential functional importance of the TBR1 gene's promoter microsatellite

  4. Training manual on the analysis of microsatellite repeats in human DNA for diagnostic applications

    International Nuclear Information System (INIS)

    Ioannou, P.

    1998-01-01

    The recent discovery that simple sequence length polymorphisms (SSLPs), or microsatellites, are highly polymorphic has provided a rich source of genetic markers for the development of high-resolution maps. SSLPs are ideal markers because they are widely distributed throughout eukrayotic genomes and can be efficiently analyzed using the polymerase chain reaction (PCR). The recent development of moderate-resolution maps of both human and mouse genomes built entirely with SSLPs reflects the rapid conversion from manual Southern blot-based markers to semi-automated PCR-amplified markers during the last few years. Furthermore, these markers can also be used as 'sequence-tagged sites' (STS) in physical maps and provide a direct connection between the genetic and physical maps of eukaryotic chromosomes

  5. Genetic variability of Herpailurus yagouaroundi, Puma concolor and Panthera onca (Mammalia, Felidae studied using Felis catus microsatellites

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    Vanessa Roma Moreno

    2006-01-01

    Full Text Available We used four microsatellite loci (Fca08, Fca45, Fca77 and Fca96 from the domestic cat, Felis catus, to investigate genetic variability in specimens of Herpailurus yagouaroundi (jaguarundi, otter cat, eyra, Puma concolor (cougar, mountain lion, puma and Panthera onca (jaguar held in various Brazilian zoos. Samples of DNA from the cats were PCR amplified and then sequenced before being analyzed using the CERVUS program. Our results show a mean polymorphic information content (PIC of 0.83 for H. yagouaroundi, 0.66 for P. concolor and 0.69 for P. onca and a mean of 10.3 alleles for the Fca08 locus, 5.3 for Fca 45, 9 for Fca 77 and 14 for Fca 96. These results indicate a relatively high level of genetic diversity for the specimens studied.

  6. Variability in human body size

    Science.gov (United States)

    Annis, J. F.

    1978-01-01

    The range of variability found among homogeneous groups is described and illustrated. Those trends that show significantly marked differences between sexes and among a number of racial/ethnic groups are also presented. Causes of human-body size variability discussed include genetic endowment, aging, nutrition, protective garments, and occupation. The information is presented to aid design engineers of space flight hardware and equipment.

  7. Variability of silver fir (Abies alba Mill. progeny from the Tisovik Reserve expressed in needle traits and chloroplast microsatellite DNA

    Directory of Open Access Journals (Sweden)

    Pawlaczyk Ewa M.

    2017-01-01

    Full Text Available Progeny from nineteen family lines of silver fir (Abies alba Mill. from the Tisovik Reserve growing in an experimental plot were analyzed based on 4 chloroplast microsatellite DNA loci and 12 morphological and anatomical needle traits. The Tisovik Reserve is located in Białowieża Primeval Forest, 120 km north of the natural range limit of this species, and embraces a small and isolated natural population of silver fir. The aim of this study was to determine genetic variation within and between progeny lines. Analysis of phenotypic variation showed that the traits which differed most among individuals were the needle width and the distance from resin canals to vascular bundle. Those traits, which differed most between the progeny lines, were the number of endodermic cells around the vascular bund and the weight of hypodermic cells. In Tisovik progeny, we detected 107 different haplotypes. In progeny lines, we detected more haplotypes than in maternal trees, and most haplotypes did not exist in maternal trees. This may be the result of pollen influx from other silver fir stands. Progeny from Tisovik showed a higher level of variability in comparison with maternal trees.

  8. Polymorphic microsatellites in the human bloodfluke, Schistosoma japonicum, identified using a genomic resource

    Directory of Open Access Journals (Sweden)

    Spear Robert

    2011-02-01

    Full Text Available Abstract Re-emergence of schistosomiasis in regions of China where control programs have ceased requires development of molecular-genetic tools to track gene flow and assess genetic diversity of Schistosoma populations. We identified many microsatellite loci in the draft genome of Schistosoma japonicum using defined search criteria and selected a subset for further analysis. From an initial panel of 50 loci, 20 new microsatellites were selected for eventual optimization and application to a panel of worms from endemic areas. All but one of the selected microsatellites contain simple tri-nucleotide repeats. Moderate to high levels of polymorphism were detected. Numbers of alleles ranged from 6 to 14 and observed heterozygosity was always >0.6. The loci reported here will facilitate high resolution population-genetic studies on schistosomes in re-emergent foci.

  9. Ten polymorphic microsatellite markers characterized for ...

    Indian Academy of Sciences (India)

    MING MING BAO

    development of new microsatellite primers is expensive and time-consuming, whereas ... constructing microsatellite-enriched libraries (Guo et al. 2013). Thirteen markers .... Due to the influence of human activities, stocks of this species have ...

  10. A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes

    Directory of Open Access Journals (Sweden)

    Selvaraj Velu

    2009-12-01

    Full Text Available Abstract Background Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. Results In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles and heterozygosity (0.05-0.79. Combining data on amplification success (including non-invasive samples and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. Conclusion Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to

  11. Loss of genetic variability in a hatchery strain of Senegalese sole (Solea senegalensis revealed by sequence data of the mitochondrial DNA control region and microsatellite markers

    Directory of Open Access Journals (Sweden)

    Pablo Sánchez

    2012-06-01

    Full Text Available Comparisons of the levels of genetic variation within and between a hatchery F1 (FAR, n=116 of Senegalese sole, Solea senegalensis, and its wild donor population (ATL, n = 26, both native to the SW Atlantic coast of the Iberian peninsula, as well as between the wild donor population and a wild western Mediterranean sample (MED, n=18, were carried out by characterizing 412 base pairs of the nucleotide sequence of the mitochondrial DNA control region I, and six polymorphic microsatellite loci. FAR showed a substantial loss of genetic variability (haplotypic diversity, h=0.49±0.066; nucleotide diversity, π=0.006±0.004; private allelic richness, pAg=0.28 to its donor population ATL (h=0.69±0.114; π=0.009±0.006; pAg=1.21. Pairwise FST values of microsatellite data were highly significant (P < 0.0001 between FAR and ATL (0.053 and FAR and MED (0.055. The comparison of wild samples revealed higher values of genetic variability in MED than in ATL, but only with mtDNA CR-I sequence data (h=0.948±0.033; π=0.030±0.016. However, pairwise ΦST and FST values between ATL and MED were highly significant (P < 0.0001 with mtDNA CR-I (0.228 and with microsatellite data (0.095, respectively. While loss of genetic variability in FAR could be associated with the sampling error when the broodstock was established, the results of parental and sibship inference suggest that most of these losses can be attributed to a high variance in reproductive success among members of the broodstock, particularly among females.

  12. Microsatellite characterization of Cimarron Uruguayo dogs

    OpenAIRE

    Gagliardi,Rosa; Silvia,Llambí; García,Cristina; Arruga,María Victoria

    2011-01-01

    Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each micro-satellite, the genetic variability and the consangu...

  13. Variability in Indian bread wheat (Triticum aestivum L.) varieties differing in nitrogen efficiency as assessed by microsatellite markers.

    Science.gov (United States)

    Chandna, Ruby; Gupta, Sarika; Ahmad, Altaf; Iqbal, Muhammad; Prasad, Manoj

    2010-06-01

    Wheat (Triticum aestivum L.) is a staple food for half of the world. Its productivity and agronomical practices, especially for nitrogen supplementation, is governed by the nitrogen efficiency (NE) of the genotypes. We analyzed 16 popular cultivated Indian varieties of wheat for their NE and variability estimates using a set of 21 simple sequence repeat (SSR) markers, derived from each wheat chromosome. These genotypes were categorized into three groups, viz., low, moderate, and high nitrogen efficient. Of these 16 genotypes, we have reported six, eight, and two genotypes in high, moderate, and low NE categories, respectively. The differential NE in these genotypes was supported by nitrogen uptake and assimilation parameters. The values of average polymorphic information content and marker index for these SSR markers were estimated to be 0.32 and 0.59, respectively. The genetic similarity coefficient for all possible pairs of varieties ranged from 0.41 to 0.76, indicating the presence of considerable range of genetic diversity at molecular level. The dendrogram prepared on the basis of unweighted pair-group method of arithmetic average algorithm grouped the 16 wheat varieties into three major clusters. The clustering was strongly supported by high bootstrap values. The distribution of the varieties in different clusters and subclusters appeared to be related to their variability in NE parameter that was scored. Genetically diverse parents were identified that could potentially be used for their desirable characteristics in breeding programs for improvement of NE in wheat.

  14. Eighteen polymorphic microsatellites for domestic pigeon Columba ...

    Indian Academy of Sciences (India)

    certain parasites which cause health problems in humans and domestic animals ... The genomic DNA was isolated using standard protocol as described by ..... panel of polymorphic microsatellite markers in Himalayan monal. Lophophorus ...

  15. The variability problem of normal human walking

    DEFF Research Database (Denmark)

    Simonsen, Erik B; Alkjær, Tine

    2012-01-01

    Previous investigations have suggested considerable inter-individual variability in the time course pattern of net joint moments during normal human walking, although the limited sample sizes precluded statistical analyses. The purpose of the present study was to obtain joint moment patterns from...... a group of normal subjects and to test whether or not the expected differences would prove to be statistically significant. Fifteen healthy male subjects were recorded on video while they walked across two force platforms. Ten kinematic and kinetic parameters were selected and input to a statistical...... cluster analysis to determine whether or not the 15 subjects could be divided into different 'families' (clusters) of walking strategy. The net joint moments showed a variability corroborating earlier reports. The cluster analysis showed that the 15 subjects could be grouped into two clusters of 5 and 10...

  16. Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae

    Science.gov (United States)

    Moyer, G.R.; Sloss, Brian L.; Kreiser, B.R.; Feldheim, K.A.

    2009-01-01

    We report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large-bodied species that has experienced population declines across much of its range. These loci possessed 2-19 alleles and observed heterozygosities of 0-0.974. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management. ?? 2009 Blackwell Publishing Ltd.

  17. Microsatellite Markers for Russian Olive (Elaeagnus angustifolia; Elaeagnaceae

    Directory of Open Access Journals (Sweden)

    John F. Gaskin

    2013-09-01

    Full Text Available Premise of the study: Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. Methods and Results: Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. Conclusions: These microsatellites have sufficient potential variability to define population structure and origins of the Russian olive invasion.

  18. Sources of variability in human communicative skills

    Directory of Open Access Journals (Sweden)

    Inge eVolman

    2012-11-01

    Full Text Available When established communication systems cannot be used, people rapidly create novel systems to modify the mental state of another agent according to their intentions. However, there are dramatic inter-individual differences in the implementation of this human competence for communicative innovation. Here we characterize psychological sources of inter-individual variability in the ability to build a shared communication system from scratch. We consider two potential sources of variability in communicative skills. Cognitive traits of two individuals could independently influence their joint ability to establish a communication system. Another possibility is that the overlap between those individual traits influences the communicative performance of a dyad. We assess these possibilities by quantifying the relationship between cognitive traits and behavior of communicating dyads. Cognitive traits were assessed with psychometric scores quantifying cooperative attitudes and fluid intelligence. Competence for implementing successful communicative innovations was assessed by using a non-verbal communicative task. Individual capacities influence communicative success when communicative innovations are generated. Dyadic similarities and individual traits modulate the type of communicative strategy chosen. The ability to establish novel communicative actions was influenced by a combination of the communicator’s ability to understand intentions and the addressee’s ability to recognize patterns. Communicative pairs with comparable systemizing abilities or behavioral inhibition were more likely to explore the search space of possible communicative strategies by systematically adding new communicative behaviors to those already available. No individual psychometric measure seemed predominantly responsible for communicative success. These findings support the notion that the human ability for fast communicative innovations represents a special type of

  19. Genetic variability and bottleneck analyses of Kanni adu goat population using microsatellite markers [Indian Veterinary Journal, 2015, 92(3): 24-27

    International Nuclear Information System (INIS)

    Thiruvenkadan, R.; Jeyakumar, M.; Saravana, R.; Periasamy, K.

    2016-01-01

    Full text: The genetic characterization and bottleneck analysis in Kodi Adu goat was done using 25 FAO recommended microsatellite markers. The mean observed number of alleles and polymorphism information content (PIC) were estimated to be 11.52±-0.95 and 0.817±0.023 respectively. The mean observed and expected equilibrium hyterozygosities were 0.660±0.045 and 0.846±0.018 respectively. The mean expected equilibrium gene diversity across 21 microsatellite loci under TAM, SMM and TPM were 0.793±0.028, 0.854±0.023 and 0.827±0.026 respectively. All the three statistical tests revealed significant deviation of Kodi Adu goats from mutation-drift equilibrium under the IAM and TPM model. The mode shift analysis supported the results under SMM indicating the absence of genetic bottleneck in the recent past in Kodi Adu goats. (author)

  20. Microsatellite instability in bladder cancer

    DEFF Research Database (Denmark)

    Gonzalez-Zulueta, M; Ruppert, J M; Tokino, K

    1993-01-01

    Somatic instability at microsatellite repeats was detected in 6 of 200 transitional cell carcinomas of the bladder. Instabilities were apparent as changes in (GT)n repeat lengths on human chromosome 9 for four tumors and as alterations in a (CAG)n repeat in the androgen receptor gene on the X...... or larger (> 2 base pairs) alterations in repeat length. All six tumors were low stage (Ta-T1), suggesting that these alterations can occur early in bladder tumorigenesis....

  1. Variables influencing the frictional behaviour of in vivo human skin

    NARCIS (Netherlands)

    Veijgen, N.K.; Masen, Marc Arthur; van der Heide, Emile

    2013-01-01

    In the past decades, skin friction research has focused on determining which variables are important to affect the frictional behaviour of in vivo human skin. Until now, there is still limited knowledge on these variables. This study has used a large dataset to identify the effect of variables on

  2. Variables influencing the frictional behaviour of in vivo human skin

    NARCIS (Netherlands)

    Veijgen, N.K.; Masen, M.A.; Heide, E. van der

    2013-01-01

    In the past decades, skin friction research has focused on determining which variables are important to affect the frictional behaviour of in vivo human skin. Until now, there is still limited knowledge on these variables.This study has used a large dataset to identify the effect of variables on the

  3. Extinction-Induced Variability in Human Behavior

    Science.gov (United States)

    Kinloch, Jennifer M.; Foster, T. Mary; McEwan, James S. A.

    2009-01-01

    Participants earned points by pressing a computer space bar (Experiment 1) or forming rectangles on the screen with the mouse (Experiment 2) under differential-reinforcement-of-low-rate schedules, followed by extinction. Variability in interresponse time (the contingent dimension) increased during extinction, as for Morgan and Lee (1996);…

  4. Polymorphic human (CTAT)n microsatellite provides a conserved linkage marker for mouse mutants causing cleft palate, vestibular defects, obesity and ataxia

    Energy Technology Data Exchange (ETDEWEB)

    Griffith, A.J.; Burgess, D.L.; Kohrman, D. [Univ. of MIchigan, Ann Arbor, MI (United States)] [and others

    1994-09-01

    The Twirler mutation (Tw) causing cleft palate {plus_minus} cleft lip, vestibular defects and obesity is located within 0.5 cM of an ataxia locus (ax) on mouse chromosome 18. We identified a transgene-induced insertional mutation with vestibular and craniofacial defects that appears to be a new allele of Twirler. Mouse DNA flanking the transgene insertion site was isolated from a cosmid library. An evolutionarily conserved, zoo blot positive cosmid subclone was used to probe a human {lambda} genomic library. From the sequence of a highly homologous human {lambda} clone, we designed STS primers and screened a human P1 library. DNA from two positive P1 clones was hybridized with simple sequence probes, and a (CTAT){sub 12} repeat was detected. Analysis of 62 CEPH parents with primers flanking the repeat identified six alleles containing 9 to 14 copies of the repeat, at frequencies of 0.17, 0.17, 0.17, 0.27, 0.15 and 0.07, respectively. The observed heterozygosity was 49/62 with a calculated PIC value of 0.76. This polymorphic microsatellite marker, designated Umi3, was mapped to the predicted conserved human linkage group by analysis of somatic cell hybrid panels. The anticipated short distance between Umi3 and the disease genes will facilitate detection of linkage in small families. We would like to type appropriate human pedigrees with Umi3 in order to identify patients with inherited disorders homologous to the mouse mutations Twirler and ataxia.

  5. Detecting microsatellites within genomes: significant variation among algorithms

    Directory of Open Access Journals (Sweden)

    Rivals Eric

    2007-04-01

    Full Text Available Abstract Background Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker. Results Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp, regardless of motif. Conclusion Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.

  6. Microsatellite Primers for Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen Fredsted, Palle; Gertsch, Pia J.; Boomsma, Jacobus Jan (Koos)

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  7. Microsatellite primers for fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Boomsma, JJ

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  8. Sources of variability in human communicative skills

    NARCIS (Netherlands)

    Volman, Inge; Noordzij, Matthijs Leendert; Toni, Ivan

    2012-01-01

    When established communication systems cannot be used, people rapidly create novel systems to modify the mental state of another agent according to their intentions. However, there are dramatic inter-individual differences in the implementation of this human competence for communicative innovation.

  9. Antigenic and genetic variability of human metapneumoviruses

    NARCIS (Netherlands)

    S. Herfst (Sander); L. Sprong; P.A. Cane; E. Forleo-Neto; A.D.M.E. Osterhaus (Albert); R.A.M. Fouchier (Ron); R.L. de Swart (Rik); B.G. van den Hoogen (Bernadette)

    2004-01-01

    textabstractHuman metapneumovirus (HMPV) is a member of the subfamily Pneumovirinae within the family Paramyxo- viridae. Other members of this subfamily, respiratory syncytial virus and avian pneumovirus, can be divided into subgroups on the basis of genetic or antigenic differences or both. For

  10. Variability in human metabolism of arsenic

    International Nuclear Information System (INIS)

    Loffredo, C.A.; Aposhian, H.V.; Cebrian, M.E.; Yamauchi, Hiroshi; Silbergeld, E.K.

    2003-01-01

    Estimating the nature and extent of human cancer risks due to arsenic (As) in drinking water is currently of great concern, since millions of persons worldwide are exposed to arsenic, primarily through natural enrichment of drinking water drawn from deep wells. Humans metabolize and eliminate As through oxidative methylation and subsequent urinary excretion. While there is debate as to the role of methylation in activation/detoxification, variations in arsenic metabolism may affect individual risks of toxicity and carcinogenesis. Using data from three populations, from Mexico, China, and Chile, we have analyzed the distribution in urine of total arsenic and arsenic species (inorganic arsenic (InAs), monomethyl arsenic (MMA), and dimethyl arsenic (DMA). Data were analyzed in terms of the concentration of each species and by evaluating MMA:DMA and (MMA+DMA):InAs ratios. In all persons most urinary As was present as DMA. Male:female differences were discernible in both high- and low-exposure groups from all three populations, but the gender differences varied by populations. The data also indicated bimodal distributions in the ratios of DMA to InAs and to MMA. While the gene or genes responsible for arsenic methylation are still unknown, the results of our studies among the ethnic groups in this study are consistent with the presence of functional genetic polymorphisms in arsenic methylation leading to measurable differences in toxicity. This analysis highlights the need for continuing research on the health effects of As in humans using molecular epidemiologic methods

  11. Genome-scale multilocus microsatellite typing of Trypanosoma cruzi discrete typing unit I reveals phylogeographic structure and specific genotypes linked to human infection.

    Directory of Open Access Journals (Sweden)

    Martin S Llewellyn

    2009-05-01

    Full Text Available Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is "hidden" at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed.

  12. genetic diversity of microsatellit

    Indian Academy of Sciences (India)

    微软用户

    with inhabit inland dry gypsum soils, coastal cliffs and salt marshes (Palacios .... Twenty microsatellite loci generated a total of 117 alleles in the 102 samples of 6 .... self-incompatibility is thought to take important part in the maintenance of the ...

  13. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea.

    Science.gov (United States)

    Chen, Jing; Xie, Bingbing; Yang, Yaran; Yang, Meng; Liu, Chao; Lv, Yuexin; Chen, Chuguang; Liu, Xu; Fang, Xiangdong; Wu, Huijuan; Yan, Jiangwei

    2017-08-01

    Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10 -38 . The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

  14. Programmed Death-Ligand 1 Expression, Microsatellite Instability, Epstein-Barr Virus, and Human Papillomavirus in Nasopharyngeal Carcinomas of Patients from the Philippines.

    Science.gov (United States)

    Chang, Ann Margaret V; Chiosea, Simion I; Altman, Alexey; Pagdanganan, Hester A; Ma, Changqing

    2017-06-01

    Most nasopharyngeal carcinomas (NPCs) in a high-incidence population are driven by Epstein-Barr virus (EBV) infection. EBV-associated malignancies have increased expression of the programmed death-ligand 1 (PD-L1). Immunotherapy agents targeting the PD-1/PD-L1 pathway have achieved durable treatment effects in patients with various cancer types including EBV-associated malignancies. In this study, we sought to investigate PD-L1 expression in a cohort of patients with NPCs from the Philippines. Fifty-six NPCs were studied for PD-L1, p16, and DNA mismatch repair (MMR) deficiency by immunohistochemistry. One case with MMR deficiency was also assessed for microsatellite instability (MSI) by polymerase chain reaction. EBV and human papillomavirus (HPV) status were tested by in situ hybridization. All NPCs were p16 negative. Three of the 56 NPCs (5%) were EBV negative (EBV-) and HPV negative, while one NPC (1/56, 2%) was EBV positive and showed MSI (EBV+/MSI). Positive PD-L1 expression (PD-L1+), defined as membranous staining in ≥1% tumor cells, was seen in 64% (36/56) of NPCs. All three EBV- NPCs were PD-L1+ as was the EBV+/MSI NPC. PD-L1+ was seen significantly more often in NPCs from non-smokers than those from smokers (23/28, 82% vs 9/18, 50%; P = 0.047). PD-L1+ was not associated with pT, pN, distant metastasis, or clinical stage (P > 0.05). PD-L1+ was not associated with overall survival (P = 0.473). In summary, our results show frequent PD-L1 expression in NPCs regardless of EBV status and a preferential PD-L1 expression in non-smokers. MSI and HPV positivity are exceedingly rare in NPCs.

  15. Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking

    DEFF Research Database (Denmark)

    Ellervik, Christina; Vaught, Jim

    2015-01-01

    BACKGROUND: Most errors in a clinical chemistry laboratory are due to preanalytical errors. Preanalytical variability of biospecimens can have significant effects on downstream analyses, and controlling such variables is therefore fundamental for the future use of biospecimens in personalized...... medicine for diagnostic or prognostic purposes. CONTENT: The focus of this review is to examine the preanalytical variables that affect human biospecimen integrity in biobanking, with a special focus on blood, saliva, and urine. Cost efficiency is discussed in relation to these issues. SUMMARY: The quality...

  16. Genetic variability and bottleneck analyses of Kanni adu goat population using microsatellite markers [Also published in The Indian Journal of Small Ruminants, 2015, 21(2): 216-22

    International Nuclear Information System (INIS)

    Jeyakumar, M.; Thiruvenkadan, R.; Saravana, R.; Periasamy, K.

    2016-01-01

    Full text: Microsatellite data on 25 loci were generated and utilized to evaluate the genetic architecture and mutation drift equilibrium of Kanni Adu goats of southern Tamil Nadu. The genetic diversity analysis of Kanni Adu goats displayed higher level of within breed variability in terms of mean number of alleles per locus (11.24±0.87) and heterozygosity values (Ho= 0.677±0.041, He=0.857±0.016). Within population inbreeding estimate (FIS=0.215±0.040) showed moderate level of inbreeding, which warrant adoption of appropriate breeding strategies under field conditions. The polymorphism information content (PIC) value ranged from 0.531 to 0.915 suggested higher polymorphism in this breed. In general, the sign, standardized differences and Wilcoxon rank tests indicated heterozygosity excess in Kanni Adu goat population in infinite alleles and two-phase model and non-significant in stepwise mutation model. Hence, the mode-shift indicator test was utilized and it indicated the absence of genetic bottleneck in the recent past in Kanni Adu goats. It suggests that any unique alleles present in this breed may not have been lost. The study indicated that Kanni adu goats exhibited substantial amount of genetic variation as reflected from the heterozygosity and number of alleles per locus. (author)

  17. Variabilidad genética de poblaciones en cautiverio de Crocodylus moreletii (Crocodylia: Crocodylidae mediante el uso de marcadores microsatelitales Genetic variability in captive populations of Crocodylus moreletii (Crocodylia: Crocodylidae using microsatellites markers

    Directory of Open Access Journals (Sweden)

    Ricardo Serna-Lagunes

    2012-03-01

    Full Text Available Crocodylus moreletii representa un emblema para los ecosistemas tropicales de México pero actualmente está amenazada por extinción. Sorprendentemente, hay una falta de información de su constitución genética, que debe ser evaluada para un manejo apropiado ex situ y para toma de decisiones en la liberación de cocodrilos a su hábitat natural. El objetivo del estudio fue caracterizar y comparar la variabilidad genética de cuatro grupos poblacionales de C. moreletii (dos silvestres y dos nacidas ex situ. Mediante PCR se amplificaron siete loci de microsatélites polimórficos, sin embargo se encontró déficit de heterocigotos en las poblaciones (promedio H O=0.02 mermado por la presencia de alelos nulos. El AMOVA indicó que la mayor proporción de variabilidad genética se encuentra dentro de las poblaciones y una limitada diferenciación genética entre poblaciones (promedio F ST =0.03, probablemente debida al alto índice de endogamia (promedio F IS=0.97. Al comparar la variabilidad genética inter e intra especies de cocodrilianos, encontramos que en C. moreletii está muy por debajo de los reportados. Se concluye que la limitada variabilidad genética de las poblaciones nacidas ex situ probablemente se debe al efecto fundador derivado de la estructura social de sus progenitores, y de las poblaciones silvestres, por el efecto cuello de botella, inferido por el limitado tamaño efectivo de población que presentó históricamente en su distribución natural.Genetic variability in captive populations of Crocodylus moreletii (Crocodylia: Crocodylidae using microsatellites markers. Crocodylus moreletii, an extinction threatened species, represents an emblem for tropical ecosystems in Mexico. Surprisingly, there is a lack of information about their genetic constitution, which should be evaluated for a proper management ex situ and for making decisions on the release of crocodiles into natural habitats. The aim of this study was to

  18. A new world monkey microsatellite (ap74) highly conserved in primates

    International Nuclear Information System (INIS)

    Oklander, Luciana Ines; Steinberg, Eliana Ruth; Dolores Mudry, Marta

    2012-01-01

    Given their great variability, microsatellites or STRS became the most commonly used genetic markers over the last 15 years. The analysis of these markers requires minimum quantities of DNA, allowing the use of noninvasive samples, such as feces or hair. We amplified the microsatellite ap74 in blood and hair samples in order to analyze the levels of genomic conservation among a wide range of primates including: lemur catta, alouatta caraya, ateles belzebuth, ateles chamek, pan troglodytes, papio sp., and Homo sapiens. in all cases we obtained amplification products that exhibited similar size both in monkeys and human (oscillating between 126 and 176 bp), except in the lemur where the detected fragment presented a size of approximately 1000 bp. the analysis of the nucleotide sequences permitted the evaluation of the molecular modifications experienced during the evolutionary process in primates.

  19. A meta analysis of the variability in firm performance attributable to human resource variables

    Directory of Open Access Journals (Sweden)

    Lloyd Kapondoro

    2015-01-01

    Full Text Available The contribution of Human Resource Management (HRM practices to organisation-wide performance is a critical aspect of the Human Resource (HR value proposition. The purpose of the study was to describe the strength of HRM practices and systems in influencing overall organisational performance. While research has concluded that there is a significant positive relationship between HRM practices or systems and an organisation’s market performance, the strength of this relationship has relatively not received much analysis in order to explain the degree to which HRM practices explain variance in firm performance. The study undertook a meta-analysis of published researches in international journals. The study established that HRM variables accounted for an average of 31% of the variability in firm performance. Cohen’s f2 calculated for this study as a meta effect size calculation yielded an average of 0.681, implying that HRM variables account for 68% of variability in firm performance. A one sample Kolmogorov-Smirnov test showed that the distribution of R2 is not normal. A major managerial implication of this study is that effective HRM practices have a significant business case. The study provides, quantitatively, the average variability in firm success that HRM accounts for.

  20. Human activity and climate variability project: annual report 2001

    International Nuclear Information System (INIS)

    Harle, K.J.; Heijnis, H.; Henderson-Sellers, A.; Sharmeen, S.; Zahorowski, W.

    2002-01-01

    Knowledge of the state of the Australian environment, including natural climate variability, prior to colonial settlement is vital if we are to define and understand the impact of over two hundred years of post-industrial human activity on our landscape. ANSTO, in conjunction with university partners, is leading a major research effort to provide natural archives of human activity and climate variability over the last 500 years in Australia, utilising a variety of techniques, including lead-210 and radiocarbon dating and analyses of proxy indicators (such as microfossils) as well as direct evidence (such as trace elements) of human activity and climate variability. The other major project objectives were to contribute to the understanding of the impact of human induced and natural aerosols in the East Asian region on climate through analysis and sourcing of fine particles and characterisation of air samples using radon concentrations and to contribute to the improvement of land surface parameterisation schemes and investigate the potential to use stable isotopes to improve global climate models and thus improve our understanding of future climate

  1. Human Responses to Climate Variability: The Case of South Africa

    Science.gov (United States)

    Oppenheimer, M.; Licker, R.; Mastrorillo, M.; Bohra-Mishra, P.; Estes, L. D.; Cai, R.

    2014-12-01

    Climate variability has been associated with a range of societal and individual outcomes including migration, violent conflict, changes in labor productivity, and health impacts. Some of these may be direct responses to changes in mean temperature or precipitation or extreme events, such as displacement of human populations by tropical cyclones. Others may be mediated by a variety of biological, social, or ecological factors such as migration in response to long-term changes in crops yields. Research is beginning to elucidate and distinguish the many channels through which climate variability may influence human behavior (ranging from the individual to the collective, societal level) in order to better understand how to improve resilience in the face of current variability as well as future climate change. Using a variety of data sets from South Africa, we show how climate variability has influenced internal (within country) migration in recent history. We focus on South Africa as it is a country with high levels of internal migration and dramatic temperature and precipitation changes projected for the 21st century. High poverty rates and significant levels of rain-fed, smallholder agriculture leave large portions of South Africa's population base vulnerable to future climate change. In this study, we utilize two complementary statistical models - one micro-level model, driven by individual and household level survey data, and one macro-level model, driven by national census statistics. In both models, we consider the effect of climate on migration both directly (with gridded climate reanalysis data) and indirectly (with agricultural production statistics). With our historical analyses of climate variability, we gain insights into how the migration decisions of South Africans may be influenced by future climate change. We also offer perspective on the utility of micro and macro level approaches in the study of climate change and human migration.

  2. Variables associated with human papillomavirus (HPV) vaccine acceptance by men.

    Science.gov (United States)

    Ferris, Daron G; Waller, Jennifer L; Miller, Jeremiah; Patel, Pratik; Price, George A; Jackson, Lanier; Wilson, Courtesia

    2009-01-01

    To determine correlates of human papillomavirus (HPV) vaccine acceptance for men. A convenience sample of men aged 18 to 45 years read a one-page information sheet about HPV and the HPV vaccine, then completed a 29-item questionnaire. chi(2) tests were used to determine whether differences in demographic, sexual, and vaccine-related variables existed between levels of wanting the HPV vaccine. Positive correlates of HPV vaccine acceptance included higher education (P acceptance of the HPV vaccine by men.

  3. The macro-structural variability of the human neocortex.

    Science.gov (United States)

    Kruggel, Frithjof

    2018-05-15

    The human neocortex shows a considerable individual structural variability. While primary gyri and sulci are found in all normally developed brains and bear clear-cut gross structural descriptions, secondary structures are highly variable and not present in all brains. The blend of common and individual structures poses challenges when comparing structural and functional results from quantitative neuroimaging studies across individuals, and sets limits on the precision of location information much above the spatial resolution of current neuroimaging methods. This work aimed at quantifying structural variability on the neocortex, and at assessing the spatial relationship between regions common to all brains and their individual structural variants. Based on structural MRI data provided as the "900 Subjects Release" of the Human Connectome Project, a data-driven analytic approach was employed here from which the definition of seven cortical "communities" emerged. Apparently, these communities comprise common regions of structural features, while the individual variability is confined within a community. Similarities between the community structure and the state of the brain development at gestation week 32 lead suggest that communities are segregated early. Subdividing the neocortex into communities is suggested as anatomically more meaningful than the traditional lobar structure. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. Psychobiological Factors Affecting Cortisol Variability in Human-Dog Dyads.

    Directory of Open Access Journals (Sweden)

    Iris Schöberl

    Full Text Available Stress responses within dyads are modulated by interactions such as mutual emotional support and conflict. We investigated dyadic psychobiological factors influencing intra-individual cortisol variability in response to different challenging situations by testing 132 owners and their dogs in a laboratory setting. Salivary cortisol was measured and questionnaires were used to assess owner and dog personality as well as owners' social attitudes towards the dog and towards other humans. We calculated the individual coefficient of variance of cortisol (iCV = sd/mean*100 over the different test situations as a parameter representing individual variability of cortisol concentration. We hypothesized that high cortisol variability indicates efficient and adaptive coping and a balanced individual and dyadic social performance. Female owners of male dogs had lower iCV than all other owner gender-dog sex combinations (F = 14.194, p<0.001, whereas owner Agreeableness (NEO-FFI scaled positively with owner iCV (F = 4.981, p = 0.028. Dogs of owners high in Neuroticism (NEO-FFI and of owners who were insecure-ambivalently attached to their dogs (FERT, had low iCV (F = 4.290, p = 0.041 and F = 5.948, p = 0.016, as had dogs of owners with human-directed separation anxiety (RSQ or dogs of owners with a strong desire of independence (RSQ (F = 7.661, p = 0.007 and F = 9.192, p = 0.003. We suggest that both owner and dog social characteristics influence dyadic cortisol variability, with the human partner being more influential than the dog. Our results support systemic approaches (i.e. considering the social context in science and in counselling.

  5. General anesthesia suppresses normal heart rate variability in humans

    Science.gov (United States)

    Matchett, Gerald; Wood, Philip

    2014-06-01

    The human heart normally exhibits robust beat-to-beat heart rate variability (HRV). The loss of this variability is associated with pathology, including disease states such as congestive heart failure (CHF). The effect of general anesthesia on intrinsic HRV is unknown. In this prospective, observational study we enrolled 100 human subjects having elective major surgical procedures under general anesthesia. We recorded continuous heart rate data via continuous electrocardiogram before, during, and after anesthesia, and we assessed HRV of the R-R intervals. We assessed HRV using several common metrics including Detrended Fluctuation Analysis (DFA), Multifractal Analysis, and Multiscale Entropy Analysis. Each of these analyses was done in each of the four clinical phases for each study subject over the course of 24 h: Before anesthesia, during anesthesia, early recovery, and late recovery. On average, we observed a loss of variability on the aforementioned metrics that appeared to correspond to the state of general anesthesia. Following the conclusion of anesthesia, most study subjects appeared to regain their normal HRV, although this did not occur immediately. The resumption of normal HRV was especially delayed on DFA. Qualitatively, the reduction in HRV under anesthesia appears similar to the reduction in HRV observed in CHF. These observations will need to be validated in future studies, and the broader clinical implications of these observations, if any, are unknown.

  6. Genetic Variants Contribute to Gene Expression Variability in Humans

    Science.gov (United States)

    Hulse, Amanda M.; Cai, James J.

    2013-01-01

    Expression quantitative trait loci (eQTL) studies have established convincing relationships between genetic variants and gene expression. Most of these studies focused on the mean of gene expression level, but not the variance of gene expression level (i.e., gene expression variability). In the present study, we systematically explore genome-wide association between genetic variants and gene expression variability in humans. We adapt the double generalized linear model (dglm) to simultaneously fit the means and the variances of gene expression among the three possible genotypes of a biallelic SNP. The genomic loci showing significant association between the variances of gene expression and the genotypes are termed expression variability QTL (evQTL). Using a data set of gene expression in lymphoblastoid cell lines (LCLs) derived from 210 HapMap individuals, we identify cis-acting evQTL involving 218 distinct genes, among which 8 genes, ADCY1, CTNNA2, DAAM2, FERMT2, IL6, PLOD2, SNX7, and TNFRSF11B, are cross-validated using an extra expression data set of the same LCLs. We also identify ∼300 trans-acting evQTL between >13,000 common SNPs and 500 randomly selected representative genes. We employ two distinct scenarios, emphasizing single-SNP and multiple-SNP effects on expression variability, to explain the formation of evQTL. We argue that detecting evQTL may represent a novel method for effectively screening for genetic interactions, especially when the multiple-SNP influence on expression variability is implied. The implication of our results for revealing genetic mechanisms of gene expression variability is discussed. PMID:23150607

  7. Country-Specific Effects of Climate Variability on Human Migration

    Science.gov (United States)

    Gray, Clark; Wise, Erika

    2016-01-01

    Involuntary human migration is among the social outcomes of greatest concern in the current era of global climate change. Responding to this concern, a growing number of studies have investigated the consequences of short to medium-term climate variability for human migration using demographic and econometric approaches. These studies have provided important insights, but at the same time have been significantly limited by lack of expertise in the use of climate data, access to cross-national data on migration, and attention to model specification. To address these limitations, we link data on internal and international migration over a 6-year period from 9,812 origin households in Kenya, Uganda, Nigeria, Burkina Faso and Senegal to high-resolution gridded climate data from both station and satellite sources. Analyses of these data using several plausible specifications reveal that climate variability has country-specific effects on migration: Migration tends to increase with temperature anomalies in Uganda, tends to decrease with temperature anomalies in Kenya and Burkina Faso, and shows no consistent relationship with temperature in Nigeria and Senegal. Consistent with previous studies, precipitation shows weak and inconsistent relationships with migration across countries. These results challenge generalizing narratives that foresee a consistent migratory response to climate change across the globe. PMID:27092012

  8. Country-Specific Effects of Climate Variability on Human Migration.

    Science.gov (United States)

    Gray, Clark; Wise, Erika

    2016-04-01

    Involuntary human migration is among the social outcomes of greatest concern in the current era of global climate change. Responding to this concern, a growing number of studies have investigated the consequences of short to medium-term climate variability for human migration using demographic and econometric approaches. These studies have provided important insights, but at the same time have been significantly limited by lack of expertise in the use of climate data, access to cross-national data on migration, and attention to model specification. To address these limitations, we link data on internal and international migration over a 6-year period from 9,812 origin households in Kenya, Uganda, Nigeria, Burkina Faso and Senegal to high-resolution gridded climate data from both station and satellite sources. Analyses of these data using several plausible specifications reveal that climate variability has country-specific effects on migration: Migration tends to increase with temperature anomalies in Uganda, tends to decrease with temperature anomalies in Kenya and Burkina Faso, and shows no consistent relationship with temperature in Nigeria and Senegal. Consistent with previous studies, precipitation shows weak and inconsistent relationships with migration across countries. These results challenge generalizing narratives that foresee a consistent migratory response to climate change across the globe.

  9. Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

    DEFF Research Database (Denmark)

    Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan

    2007-01-01

    the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude...

  10. Microsatellites for the gynogenetic Amazon molly, Poecilia formosa ...

    Indian Academy of Sciences (India)

    of high value for studies on the clonal variability and ori- gin of triploid .... Microsatellites in Poecilia species. Table 1. (contd). Amplification in. Diagnostic for. Locus. P. formosa. P. mexicana. P. latipinna. Species. Ploidy levels. MSD25 m m m n n .... be used to easily determine the species origin of individu- als and ploidy ...

  11. MicroRNA expression variability in human cervical tissues.

    Directory of Open Access Journals (Sweden)

    Patrícia M Pereira

    Full Text Available MicroRNAs (miRNAs are short (approximately 22 nt non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. Cervical cancer is one of the most common cancers in women worldwide and there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform containing probes for mature miRNAs. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL and 9 low-grade squamous intraepithelial lesion (LSIL samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, deregulated miRNAs were identified in malignant and pre-malignant cervical tissues after tackling the high expression variability observed. We were also able to identify putative target genes of relevant candidate miRNAs. Our results show that miRNA expression shows natural variability among human samples, which complicates miRNA data profiling analysis. However, such expression noise can be filtered and does not prevent the identification of deregulated miRNAs that play a role in the malignant transformation of cervical squamous cells. Deregulated miRNAs highlight new candidate gene targets allowing for a better understanding of the molecular mechanism underlying the development of this tumour type.

  12. Human phoneme recognition depending on speech-intrinsic variability.

    Science.gov (United States)

    Meyer, Bernd T; Jürgens, Tim; Wesker, Thorsten; Brand, Thomas; Kollmeier, Birger

    2010-11-01

    The influence of different sources of speech-intrinsic variation (speaking rate, effort, style and dialect or accent) on human speech perception was investigated. In listening experiments with 16 listeners, confusions of consonant-vowel-consonant (CVC) and vowel-consonant-vowel (VCV) sounds in speech-weighted noise were analyzed. Experiments were based on the OLLO logatome speech database, which was designed for a man-machine comparison. It contains utterances spoken by 50 speakers from five dialect/accent regions and covers several intrinsic variations. By comparing results depending on intrinsic and extrinsic variations (i.e., different levels of masking noise), the degradation induced by variabilities can be expressed in terms of the SNR. The spectral level distance between the respective speech segment and the long-term spectrum of the masking noise was found to be a good predictor for recognition rates, while phoneme confusions were influenced by the distance to spectrally close phonemes. An analysis based on transmitted information of articulatory features showed that voicing and manner of articulation are comparatively robust cues in the presence of intrinsic variations, whereas the coding of place is more degraded. The database and detailed results have been made available for comparisons between human speech recognition (HSR) and automatic speech recognizers (ASR).

  13. Microsatellite analysis of Saccharomyces uvarum diversity.

    Science.gov (United States)

    Masneuf-Pomarede, Isabelle; Salin, Franck; Börlin, Marine; Coton, Emmanuel; Coton, Monika; Jeune, Christine Le; Legras, Jean-Luc

    2016-03-01

    Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated. In this study, we report the use of nine microsatellite markers to describe S. uvarum genetic diversity and population structure among 108 isolates from various geographical and substrate origins (wine, cider and natural sources). Our combined microsatellite markers set allowed differentiating 89 genotypes. In contrast to S. cerevisiae genetic diversity, wild and human origin isolates were intertwined. A total of 75% of strains were proven to be homozygotes and estimated heterozygosity suggests a selfing rate above 0.95 for the different population tested here. From this point of view, the S. uvarum life cycle appears to be more closely related to S. paradoxus or S. cerevisiae of natural resources than S. cerevisiae wine isolates. Population structure could not be correlated to distinct geographic or technological origins, suggesting lower differentiation that may result from a large exchange between human and natural populations mediated by insects or human activities. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Microsatellites in the Eukaryotic DNA Mismatch Repair Genes as Modulators of Evolutionary Mutation Rate

    Science.gov (United States)

    Chang, Dong Kyung; Metzgar, David; Wills, Christopher; Boland, C. Richard

    2003-01-01

    All "minor" components of the human DNA mismatch repair (MMR) system-MSH3, MSH6, PMS2, and the recently discovered MLH3-contain mononucleotide microsatellites in their coding sequences. This intriguing finding contrasts with the situation found in the major components of the DNA MMR system-MSH2 and MLH1-and, in fact, most human genes. Although eukaryotic genomes are rich in microsatellites, non-triplet microsatellites are rare in coding regions. The recurring presence of exonal mononucleotide repeat sequences within a single family of human genes would therefore be considered exceptional.

  15. A novel approach for characterizing microsatellite instability in cancer cells.

    Directory of Open Access Journals (Sweden)

    Yuheng Lu

    Full Text Available Microsatellite instability (MSI is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD. Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability.

  16. Microsatellites with Macro-Influence in Ewing Sarcoma

    Directory of Open Access Journals (Sweden)

    Stephen L. Lessnick

    2012-07-01

    Full Text Available Numerous molecular abnormalities contribute to the genetic derangements involved in tumorigenesis. Chromosomal translocations are a frequent source of these derangements, producing unique fusion proteins with novel oncogenic properties. EWS/ETS fusions in Ewing sarcoma are a prime example of this, resulting in potent chimeric oncoproteins with novel biological properties and a unique transcriptional signature essential for oncogenesis. Recent evidence demonstrates that EWS/FLI, the most common EWS/ETS fusion in Ewing sarcoma, upregulates gene expression using a GGAA microsatellite response element dispersed throughout the human genome. These GGAA microsatellites function as enhancer elements, are sites of epigenetic regulation and are necessary for EWS/FLI DNA binding and upregulation of principal oncogenic targets. An increasing number of GGAA motifs appear to substantially enhance EWS/FLI-mediated gene expression, which has compelling biological implications as these GGAA microsatellites are highly polymorphic within and between ethnically distinct populations. Historically regarded as junk DNA, this emerging evidence clearly demonstrates that microsatellite DNA plays an instrumental role in EWS/FLI-mediated transcriptional regulation and oncogenesis in Ewing sarcoma. This unprecedented role of GGAA microsatellite DNA in Ewing sarcoma provides a unique opportunity to expand our mechanistic understanding of how EWS/ETS fusions influence cancer susceptibility, prognosis and transcriptional regulation.

  17. Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates

    DEFF Research Database (Denmark)

    Ziegler, J.O.; Wälther, M.; Linzer, T.R.

    2009-01-01

    Microsatellites are DNA-fragments containing short repetitive motifs with 2-10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during...... on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available....

  18. Clinical Characteristics and Genetic Variability of Human Rhinovirus in Mexico

    Directory of Open Access Journals (Sweden)

    Hilda Montero

    2012-01-01

    Full Text Available Human rhinovirus (HRV is a leading cause of acute respiratory infection (ARI in young children and infants worldwide and has a high impact on morbidity and mortality in this population. Initially, HRV was classified into two species: HRV-A and HRV-B. Recently, a species called HRV-C and possibly another species, HRV-D, were identified. In Mexico, there is little information about the role of HRV as a cause of ARI, and the presence and importance of species such as HRV-C are not known. The aim of this study was to determine the clinical characteristics and genetic variability of HRV in Mexican children. Genetic characterization was carried out by phylogenetic analysis of the 5′-nontranslated region (5′-NTR of the HRV genome. The results show that the newly identified HRV-C is circulating in Mexican children more frequently than HRV-B but not as frequently as HRV-A, which was the most frequent species. Most of the cases of the three species of HRV were in children under 2 years of age, and all species were associated with very mild and moderate ARI.

  19. Conceptual Design of Geophysical Microsatellite

    Directory of Open Access Journals (Sweden)

    Matviyenko, S.A.

    2014-10-01

    Full Text Available The article covers the issue of Earth gravitational field (EGF parameters measurement from space. The radiophysical method of measurement of gravitational frequency shift of electromagnetic radiation using existent GNSS and its two variants are developed by the author. The designlayout drawing of geophysical microsatellite, which implements the radiophysical method of EGF measurement and provides Earth plasmasphere and magnetosphere monitoring, is offered.

  20. Eucalyptus microsatellites mined in silico

    Indian Academy of Sciences (India)

    https://www.ias.ac.in/article/fulltext/jgen/087/01/0021-0025 ... Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. ... In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites ...

  1. Human activity and climate variability project - annual report 2002

    International Nuclear Information System (INIS)

    Chambers, S.; Harle, K.J.; Sharmeen, S.; Zahorowski, W.; Cohen, D.; Heijnis, H.; Henderson-Sellers, A

    2002-01-01

    Work is well underway on identifying the spatial and temporal extent, direction and range of trace element transport across Tasmania through analysis of lake sediments; A follow up investigation of sedimentation and pollution in the Nattai River catchment following the devastating 2001 bushfires in the region has been completed; The project has been extended to include investigations of evidence of human impacts in the highly sensitive and ecologically important Great Lakes of coastal NSW. This has involved the expansion of our collaboration to include Geoscience Australia; Contributions have been made to the IGBP HITE project. Further contributions will be made as the evidence gathered is drawn together and interpreted; Over the coming year, focus will be placed on completion of the investigation of the extent of aerial transport of trace elements across Tasmania over the last 200 years as well as evidence for human activity and impacts on the Great Lakes region of NSW. Further investigation of potential climate signals from sites in northern Australia will also be made. The first 12 months of data for all ACE-Asia radon and fine particle sites is now available with preliminary analyses performed; The seasonal variability of background radon concentration at each of the radon monitoring sites has been characterised for the available data; Major components related to industrial pollution and soil sources in China have been identified and quantified; Regional and seasonal variations and trends in aerosol constituents have been measured and compared across more than 2.8Mk 2 of sampling area; The Hok Tsui and Kosan detectors were visited for general maintenance and recalibration; A grant application to the APN has been submitted in support of regional inventory analyses based on radon time series; Progress on the processing and interpretation of radon data was presented at the Cape Grim Science Meeting (6-7 February 2002) and the 7th Biennial SPERA Conference on

  2. Human activity and climate variability project - annual report 2002

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, S; Harle, K J; Sharmeen, S; Zahorowski, W; Cohen, D; Heijnis, H; Henderson-Sellers, A [Australian Nuclear Science and Technology Organisation, Menai, NSW (Australia)

    2002-07-01

    Work is well underway on identifying the spatial and temporal extent, direction and range of trace element transport across Tasmania through analysis of lake sediments; A follow up investigation of sedimentation and pollution in the Nattai River catchment following the devastating 2001 bushfires in the region has been completed; The project has been extended to include investigations of evidence of human impacts in the highly sensitive and ecologically important Great Lakes of coastal NSW. This has involved the expansion of our collaboration to include Geoscience Australia; Contributions have been made to the IGBP HITE project. Further contributions will be made as the evidence gathered is drawn together and interpreted; Over the coming year, focus will be placed on completion of the investigation of the extent of aerial transport of trace elements across Tasmania over the last 200 years as well as evidence for human activity and impacts on the Great Lakes region of NSW. Further investigation of potential climate signals from sites in northern Australia will also be made. The first 12 months of data for all ACE-Asia radon and fine particle sites is now available with preliminary analyses performed; The seasonal variability of background radon concentration at each of the radon monitoring sites has been characterised for the available data; Major components related to industrial pollution and soil sources in China have been identified and quantified; Regional and seasonal variations and trends in aerosol constituents have been measured and compared across more than 2.8Mk{sup 2} of sampling area; The Hok Tsui and Kosan detectors were visited for general maintenance and recalibration; A grant application to the APN has been submitted in support of regional inventory analyses based on radon time series; Progress on the processing and interpretation of radon data was presented at the Cape Grim Science Meeting (6-7 February 2002) and the 7th Biennial SPERA Conference on

  3. Infrequent widespread microsatellite instability in hepatocellular carcinomas.

    Science.gov (United States)

    Yamamoto, H; Itoh, F; Fukushima, H; Kaneto, H; Sasaki, S; Ohmura, T; Satoh, T; Karino, Y; Endo, T; Toyota, J; Imai, K

    2000-03-01

    Widespread or high-frequency microsatellite instability (MSI) due to the defective DNA mismatch repair (MMR) occurs in the majority of hereditary non-polyposis colorectal cancer and a subset of sporadic malignant tumors. The incidence of MSI and underlying DNA MMR defects have been well characterized in gastrointestinal carcinogenesis, but not in hepatocarcinogenesis. To address the issue, we analyzed 55 Japanese hepatocellular carcinomas using several indicators of DNA MMR defects, such as microsatellite analysis, loss of heterozygosity (LOH) and mutation analysis of MMR genes, methylation of hMLH1 promoter, and frameshift mutations of mononucleotide repeat sequences within possible target genes. Mutation of beta2-microglobulin gene, which is presumably involved in MSI-positive tumor cell escape from immune surveillance was also examined. Some of these analyses were also carried out in 9 human liver cancer cell lines. None of the 3 quasi-monomorphic mononucleotide markers sensitive for MSI, BAT26, BAT25, and BAT34C4 presented shortened unstable alleles in any of the carcinoma, cirrhosis, chronic hepatitis tissues, or cell lines. LOH at MMR genes was infrequent (4.4 approximately 7.1%), and no mutations were detected. Neither hMLH1 hypermethylation nor frameshift mutation in the target genes was detected. No mutations were found in beta2-microglobulin. Widespread MSI due to the defective DNA MMR appears to play little if any part in Japanese hepatocarcinogenesis.

  4. Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis.

    Science.gov (United States)

    Nguyen, Thao T B; Arimatsu, Yuji; Hong, Sung-Jong; Brindley, Paul J; Blair, David; Laha, Thewarach; Sripa, Banchob

    2015-06-01

    Clonorchis sinensis is an important carcinogenic human liver fluke endemic in East and Southeast Asia. There are several conventional molecular markers that have been used for identification and genetic diversity; however, no information about microsatellites of this liver fluke is published so far. We here report microsatellite characterization and marker development for a genetic diversity study in C. sinensis, using a genome-wide bioinformatics approach. Based on our search criteria, a total of 256,990 microsatellites (≥12 base pairs) were identified from a genome database of C. sinensis, with hexanucleotide motif being the most abundant (51%) followed by pentanucleotide (18.3%) and trinucleotide (12.7%). The tetranucleotide, dinucleotide, and mononucleotide motifs accounted for 9.75, 7.63, and 0.14%, respectively. The total length of all microsatellites accounts for 0. 72% of 547 Mb of the whole genome size, and the frequency of microsatellites was found to be one microsatellite in every 2.13 kb of DNA. For the di-, tri-, and tetranucleotide, the repeat numbers redundant are six (28%), four (45%), and three (76%), respectively. The ATC repeat is the most abundant microsatellites followed by AT, AAT, and AC, respectively. Within 40 microsatellite loci developed, 24 microsatellite markers showed potential to differentiate between C. sinensis and Opisthorchis viverrini. Seven out of 24 loci showed to be heterozygous with observed heterozygosity that ranged from 0.467 to 1. Four primer sets could amplify both C. sinensis and O. viverrini DNA with different sizes. This study provides basic information of C. sinensis microsatellites, and the genome-wide markers developed may be a useful tool for the genetic study of C. sinensis.

  5. Statistical validity of using ratio variables in human kinetics research.

    Science.gov (United States)

    Liu, Yuanlong; Schutz, Robert W

    2003-09-01

    The purposes of this study were to investigate the validity of the simple ratio and three alternative deflation models and examine how the variation of the numerator and denominator variables affects the reliability of a ratio variable. A simple ratio and three alternative deflation models were fitted to four empirical data sets, and common criteria were applied to determine the best model for deflation. Intraclass correlation was used to examine the component effect on the reliability of a ratio variable. The results indicate that the validity, of a deflation model depends on the statistical characteristics of the particular component variables used, and an optimal deflation model for all ratio variables may not exist. Therefore, it is recommended that different models be fitted to each empirical data set to determine the best deflation model. It was found that the reliability of a simple ratio is affected by the coefficients of variation and the within- and between-trial correlations between the numerator and denominator variables. It was recommended that researchers should compute the reliability of the derived ratio scores and not assume that strong reliabilities in the numerator and denominator measures automatically lead to high reliability in the ratio measures.

  6. Variability of human hepatic UDP-glucuronosyltransferase activity

    NARCIS (Netherlands)

    Little, JM; Lester, R; Kuipers, F; Vonk, R; Mackenzie, PI; Drake, RR; Frame, L; Radominska-Pandya, A

    1999-01-01

    The availability of a unique series of liver samples from human subjects, both control patients (9) and those with liver disease (6; biliary atresia (2), retransplant, chronic tyrosinemia type I, tyrosinemia, Wilson's disease) allowed us to characterize human hepatic UDP-glucuronosyltransferases

  7. Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites

    Directory of Open Access Journals (Sweden)

    Lelley Tamas

    2008-12-01

    Full Text Available Abstract Background Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner. Results Our in silico survey of microsatellite clustering in genomes of Homo sapiens, Maccaca mulatta, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus, Gallus gallus, Danio rerio and Drosophila melanogaster revealed an unexpected high abundance of compound microsatellites. About 4 – 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90% these motifs differ only by a single mutation (base substitution or indel. We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track. Conclusion Our findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the "death" of microsatellites they might also result in their "birth".

  8. Does the evolutionary conservation of microsatellite loci imply function?

    Energy Technology Data Exchange (ETDEWEB)

    Shriver, M.D.; Deka, R.; Ferrell, R.E. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  9. Variable high pressure processing sensitivities for GII human noroviruses

    Science.gov (United States)

    Human norovirus (HuNoV) is the leading cause of foodborne diseases worldwide. High pressure processing (HPP) is one of the most promising non-thermal technologies for decontamination of viral pathogens in foods. However, the survival of HuNoVs by HPP is poorly understood because these viruses cann...

  10. Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea

    Directory of Open Access Journals (Sweden)

    Palmieri Dario A

    2007-02-01

    Full Text Available Abstract Background The genus Arachis includes Arachis hypogaea (cultivated peanut and wild species that are used in peanut breeding or as forage. Molecular markers have been employed in several studies of this genus, but microsatellite markers have only been used in few investigations. Microsatellites are very informative and are useful to assess genetic variability, analyze mating systems and in genetic mapping. The objectives of this study were to develop A. hypogaea microsatellite loci and to evaluate the transferability of these markers to other Arachis species. Results Thirteen loci were isolated and characterized using 16 accessions of A. hypogaea. The level of variation found in A. hypogaea using microsatellites was higher than with other markers. Cross-transferability of the markers was also high. Sequencing of the fragments amplified using the primer pair Ah11 from 17 wild Arachis species showed that almost all wild species had similar repeated sequence to the one observed in A. hypogaea. Sequence data suggested that there is no correlation between taxonomic relationship of a wild species to A. hypogaea and the number of repeats found in its microsatellite loci. Conclusion These results show that microsatellite primer pairs from A. hypogaea have multiple uses. A higher level of variation among A. hypogaea accessions can be detected using microsatellite markers in comparison to other markers, such as RFLP, RAPD and AFLP. The microsatellite primers of A. hypogaea showed a very high rate of transferability to other species of the genus. These primer pairs provide important tools to evaluate the genetic variability and to assess the mating system in Arachis species.

  11. Microsatellite markers: An important fingerprinting tool for ...

    African Journals Online (AJOL)

    Microsatellites are simple sequence repeats (SSR) of 1-6 nucleotides. They appear to be ubiquitous in higher organisms, both in animal and plant genomes and involving repetitive as well as unique sequences, although the frequency of microsatellites varies between species. They are abundant, dispersed throughout the ...

  12. Microsatellite markers: An important fingerprinting tool for ...

    African Journals Online (AJOL)

    ajl yemi

    2011-08-01

    Aug 1, 2011 ... Microsatellites are simple sequence repeats (SSR) of 1-6 nucleotides. They appear to be ubiquitous in higher organisms, both in animal and plant genomes and involving repetitive as well as unique sequences, although the frequency of microsatellites varies between species. They are abundant,.

  13. Determination of some variables of human dentin for dosimetric purposes

    International Nuclear Information System (INIS)

    Peres, C.

    1990-01-01

    The initial objective of this work is to determine the atomic composition of human dentin, using various techniques of measurements such as X-Ray fluorescence, atomic absorption, spectrophotometry, volumetric analysis, chemistry, colorimetry and thermogravimetry. With the values of the effective atomic number Z bar dependent of the quality of the ionizing radiation, one can find the kind of material that can be used for a phantom equivalent to dentin. (author)

  14. Survey of genetic structure of geese using novel microsatellite markers

    Directory of Open Access Journals (Sweden)

    Fang-Yu Lai

    2018-02-01

    Full Text Available Objective The aim of this study was to create a set of microsatellite markers with high polymorphism for the genetic monitoring and genetic structure analysis of local goose populations. Methods Novel microsatellite markers were isolated from the genomic DNA of white Roman geese using short tandem repeated probes. The DNA segments, including short tandem repeats, were tested for their variability among four populations of geese from the Changhua Animal Propagation Station (CAPS. The selected microsatellite markers could then be used to monitor genetic variability and study the genetic structures of geese from local geese farms. Results 14 novel microsatellite loci were isolated. In addition to seven known loci, two multiplex sets were constructed for the detection of genetic variations in geese populations. The average of allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.09, 5.145, 0.499, 0.745, and 0.705, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting white Roman cluster and a spreading Chinese cluster. In white Roman populations, the CAPS populations were depleted to roughly two clusters when K was set equal to 6 in the Bayesian cluster analysis. The founders of private farm populations had a similar genetic structure. Among the Chinese geese populations, the CAPS populations and private populations represented different clads of the phylogenetic tree and individuals from the private populations had uneven genetic characteristics according to various analyses. Conclusion Based on this study’s analyses, we suggest that the CAPS should institute a proper breeding strategy for white Roman geese to avoid further clustering. In addition, for preservation and stable quality, the Chinese geese in the CAPS and the aforementioned proper breeding scheme should be introduced to

  15. Gene expression variability in human hepatic drug metabolizing enzymes and transporters.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    Full Text Available Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.

  16. Modeling the variability of shapes of a human placenta.

    Science.gov (United States)

    Yampolsky, M; Salafia, C M; Shlakhter, O; Haas, D; Eucker, B; Thorp, J

    2008-09-01

    Placentas are generally round/oval in shape, but "irregular" shapes are common. In the Collaborative Perinatal Project data, irregular shapes were associated with lower birth weight for placental weight, suggesting variably shaped placentas have altered function. (I) Using a 3D one-parameter model of placental vascular growth based on Diffusion Limited Aggregation (an accepted model for generating highly branched fractals), models were run with a branching density growth parameter either fixed or perturbed at either 5-7% or 50% of model growth. (II) In a data set with detailed measures of 1207 placental perimeters, radial standard deviations of placental shapes were calculated from the umbilical cord insertion, and from the centroid of the shape (a biologically arbitrary point). These two were compared to the difference between the observed scaling exponent and the Kleiber scaling exponent (0.75), considered optimal for vascular fractal transport systems. Spearman's rank correlation considered pcentroid) was associated with differences from the Kleiber exponent (p=0.006). A dynamical DLA model recapitulates multilobate and "star" placental shapes via changing fractal branching density. We suggest that (1) irregular placental outlines reflect deformation of the underlying placental fractal vascular network, (2) such irregularities in placental outline indicate sub-optimal branching structure of the vascular tree, and (3) this accounts for the lower birth weight observed in non-round/oval placentas in the Collaborative Perinatal Project.

  17. Microsatellite analysis of Fasciola spp. in Egypt.

    Science.gov (United States)

    Dar, Yasser; Amer, Said; Courtioux, Bertrand; Dreyfuss, Gilles

    2011-12-01

    Recently, the topic of diversity in Fasciola population in Egypt is controversial. The present study was performed to study the genetic diversity of isolated flukes based on microsatellites markers. Fasciola worms were collected from different hosts and geographical locations in Egypt. Control samples of Fasciola hepatica from France as well as Fasciola gigantica from Cameroon were included in the study. Collected flukes were identified morphologically and subjected for analysis using four microsatellite markers. Results of microsatellite profile (FM1 and FM2) proved that both species of Fasciola are distributed in Egypt irrespective of geographical location and host. Nevertheless, the microsatellite profile of some analyzed loci (FM2 and FM3) proved that Egyptian flukes showed more alleles compared to the reference ones. Differences of microsatellite profile in Egyptian isolates than that of corresponding reference samples indicate the remarkable diversity of these isolates. The present results highlighted the utility of microsatellite profile to discriminate between Fasciola species and to elucidate the diversity within the species. To our knowledge, this is the first time to study microsatellite polymorphism in Fasciola populations in Egypt.

  18. Rowing, the ultimate challenge to the human body - implications for physiological variables

    DEFF Research Database (Denmark)

    Volianitis, S.; Secher, Niels H.

    2009-01-01

    Clinical diagnoses depend on a variety of physiological variables but the full range of these variables is seldom known. With the load placed on the human body during competitive rowing, the physiological range for several variables is illustrated. The extreme work produced during rowing...... is explained by the seated position and the associated ability to increase venous return and, thus, cardiac output. This review highlights experimental work on Olympic rowing that presents a unique challenge to the human capacities, including cerebral metabolism, to unprecedented limits, and provides a unique...

  19. Inter-subject variability in human atrial action potential in sinus rhythm versus chronic atrial fibrillation.

    Directory of Open Access Journals (Sweden)

    Carlos Sánchez

    Full Text Available Human atrial electrophysiology exhibits high inter-subject variability in both sinus rhythm (SR and chronic atrial fibrillation (cAF patients. Variability is however rarely investigated in experimental and theoretical electrophysiological studies, thus hampering the understanding of its underlying causes but also its implications in explaining differences in the response to disease and treatment. In our study, we aim at investigating the ability of populations of human atrial cell models to capture the inter-subject variability in action potential (AP recorded in 363 patients both under SR and cAF conditions.Human AP recordings in atrial trabeculae (n = 469 from SR and cAF patients were used to calibrate populations of computational SR and cAF atrial AP models. Three populations of over 2000 sampled models were generated, based on three different human atrial AP models. Experimental calibration selected populations of AP models yielding AP with morphology and duration in range with experimental recordings. Populations using the three original models can mimic variability in experimental AP in both SR and cAF, with median conductance values in SR for most ionic currents deviating less than 30% from their original peak values. All cAF populations show similar variations in G(K1, G(Kur and G(to, consistent with AF-related remodeling as reported in experiments. In all SR and cAF model populations, inter-subject variability in I(K1 and I(NaK underlies variability in APD90, variability in I(Kur, I(CaL and I(NaK modulates variability in APD50 and combined variability in Ito and I(Kur determines variability in APD20. The large variability in human atrial AP triangulation is mostly determined by I(K1 and either I(NaK or I(NaCa depending on the model.Experimentally-calibrated human atrial AP models populations mimic AP variability in SR and cAF patient recordings, and identify potential ionic determinants of inter-subject variability in human atrial AP

  20. Human Performance Technology (HPT): An Examination of Definitions through Dependent and Independent Variables.

    Science.gov (United States)

    Irlbeck, Sonja A.

    2002-01-01

    Provides a chronological perspective of human performance technology (HPT) definitions and an evaluation of them in terms of independent and dependent variables. Discusses human competence and performance technology and compares the definitions with the goals that have been articulated for HPT. (Author/LRW)

  1. Fuzzy variable impedance control based on stiffness identification for human-robot cooperation

    Science.gov (United States)

    Mao, Dachao; Yang, Wenlong; Du, Zhijiang

    2017-06-01

    This paper presents a dynamic fuzzy variable impedance control algorithm for human-robot cooperation. In order to estimate the intention of human for co-manipulation, a fuzzy inference system is set up to adjust the impedance parameter. Aiming at regulating the output fuzzy universe based on the human arm’s stiffness, an online stiffness identification method is developed. A drag interaction task is conducted on a 5-DOF robot with variable impedance control. Experimental results demonstrate that the proposed algorithm is superior.

  2. Identification of variables and their influence on the human resources planning in the territorial level

    Energy Technology Data Exchange (ETDEWEB)

    Martínez Vivar, R.; Sánchez Rodríguez, A.; Pérez Campdesuñer, R.; García Vidal, G.

    2016-07-01

    The purpose of this paper lies in the use of experimental way through empirical tools for identification of the set of variables and their interrelationships and influences on the human resources planning at the territorial level. The methodology used to verify the existence of the variables that affect the planning of human resources at the territorial level consists of two phases: a qualitative study of the variables that influence the planning of human resources, where the explicit variables are measured and / or implied raised in the literature analyzing the main contributions and limitations expressed by each of the authors consulted. Then it proceeds to confirmatory phase (quantitative) to prove the existence of the dimensions of the planning of human resources in the territorial level through the use of multivariate statistics through the combination of expert analysis and techniques of factorial grouping. Identification is achieved by using empirical methods, variables that affect human resources planning at the territorial level, as well as their grouping essential dimensions, while the description of a theoretical model that integrates the dimensions is made essential and relationships that affect human resource planning at the regional level, which is characterized by the existence of systemic and prospective nature. The literature shows two streams that address a wide range of approaches to human resources planning. The first is oriented from the business object and the second part of the management in highlighting a limited territorial level to address this latest theoretical development, an element that has contributed to the fragmented treatment of human resources planning and management in general at this level. The originality of this paper is part of the creation and adaptation, on a scientific basis of a theoretical model developed from the conceptual contribution of this process at the territorial level where the key variables that affect this

  3. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  4. Eguchipsammia fistula Microsatellite Development and Population Analysis

    KAUST Repository

    Mughal, Mehreen

    2012-01-01

    Deep water corals are an understudied yet biologically important and fragile ecosystem under threat from recent increasing temperatures and high carbon dioxide emissions. Using 454 sequencing, we develop 14 new microsatellite markers for the deep

  5. Research Note Development and characterization of microsatellite ...

    Indian Academy of Sciences (India)

    Srirama R

    2School of Biosciences and Technology, VIT University, Vellore 632014, India. 7. 8 ... microsatellite markers developed can be used for studying the population ... characterized by diverse growth forms, including shrubs, trees, and annual or ...

  6. Role of microsatellite instability in colon cancer

    Directory of Open Access Journals (Sweden)

    M. Yu. Fedyanin

    2012-01-01

    Full Text Available Coloncancer is among leading causes of cancer morbidity and mortality both inRussiaand worldwide. Development of molecular biology lead to decoding of carcinogenesis and tumor progression mechanisms. These processes require accumulation of genetic and epigenetic alterations in a tumor cell.Coloncancer carcinogenesis is characterized by mutations cumulation in genes controlling growth and differentiation of epithelial cells, which leads to their genetic instability. Microsatellite instability is a type of genetic instability characterized by deterioration of mismatch DNA repair. This leads to faster accumulation of mutations in DNA. Loss of mismatch repair mechanism can easily be diagnosed by length of DNA microsatellites. These alterations are termed microsatellite instability. They can be found both in hereditary and sporadic colon cancers. This review covers the questions of microsatellite instability, its prognostic and predictive value in colon cancer.

  7. Variable responses of human and non-human primate gut microbiomes to a Western diet.

    Science.gov (United States)

    Amato, Katherine R; Yeoman, Carl J; Cerda, Gabriela; Schmitt, Christopher A; Cramer, Jennifer Danzy; Miller, Margret E Berg; Gomez, Andres; Turner, Trudy R; Wilson, Brenda A; Stumpf, Rebecca M; Nelson, Karen E; White, Bryan A; Knight, Rob; Leigh, Steven R

    2015-11-16

    The human gut microbiota interacts closely with human diet and physiology. To better understand the mechanisms behind this relationship, gut microbiome research relies on complementing human studies with manipulations of animal models, including non-human primates. However, due to unique aspects of human diet and physiology, it is likely that host-gut microbe interactions operate differently in humans and non-human primates. Here, we show that the human microbiome reacts differently to a high-protein, high-fat Western diet than that of a model primate, the African green monkey, or vervet (Chlorocebus aethiops sabaeus). Specifically, humans exhibit increased relative abundance of Firmicutes and reduced relative abundance of Prevotella on a Western diet while vervets show the opposite pattern. Predictive metagenomics demonstrate an increased relative abundance of genes associated with carbohydrate metabolism in the microbiome of only humans consuming a Western diet. These results suggest that the human gut microbiota has unique properties that are a result of changes in human diet and physiology across evolution or that may have contributed to the evolution of human physiology. Therefore, the role of animal models for understanding the relationship between the human gut microbiota and host metabolism must be re-focused.

  8. Clinical and biochemical function of polymorphic NR0B1 GGAA-microsatellites in Ewing sarcoma: a report from the Children's Oncology Group.

    Directory of Open Access Journals (Sweden)

    Michael J Monument

    Full Text Available The genetics involved in Ewing sarcoma susceptibility and prognosis are poorly understood. EWS/FLI and related EWS/ETS chimeras upregulate numerous gene targets via promoter-based GGAA-microsatellite response elements. These microsatellites are highly polymorphic in humans, and preliminary evidence suggests EWS/FLI-mediated gene expression is highly dependent on the number of GGAA motifs within the microsatellite.Here we sought to examine the polymorphic spectrum of a GGAA-microsatellite within the NR0B1 promoter (a critical EWS/FLI target in primary Ewing sarcoma tumors, and characterize how this polymorphism influences gene expression and clinical outcomes.A complex, bimodal pattern of EWS/FLI-mediated gene expression was observed across a wide range of GGAA motifs, with maximal expression observed in constructs containing 20-26 GGAA motifs. Relative to white European and African controls, the NR0B1 GGAA-microsatellite in tumor cells demonstrated a strong bias for haplotypes containing 21-25 GGAA motifs suggesting a relationship between microsatellite function and disease susceptibility. This selection bias was not a product of microsatellite instability in tumor samples, nor was there a correlation between NR0B1 GGAA-microsatellite polymorphisms and survival outcomes.These data suggest that GGAA-microsatellite polymorphisms observed in human populations modulate EWS/FLI-mediated gene expression and may influence disease susceptibility in Ewing sarcoma.

  9. Evidence for a time-invariant phase variable in human ankle control.

    Directory of Open Access Journals (Sweden)

    Robert D Gregg

    Full Text Available Human locomotion is a rhythmic task in which patterns of muscle activity are modulated by state-dependent feedback to accommodate perturbations. Two popular theories have been proposed for the underlying embodiment of phase in the human pattern generator: a time-dependent internal representation or a time-invariant feedback representation (i.e., reflex mechanisms. In either case the neuromuscular system must update or represent the phase of locomotor patterns based on the system state, which can include measurements of hundreds of variables. However, a much simpler representation of phase has emerged in recent designs for legged robots, which control joint patterns as functions of a single monotonic mechanical variable, termed a phase variable. We propose that human joint patterns may similarly depend on a physical phase variable, specifically the heel-to-toe movement of the Center of Pressure under the foot. We found that when the ankle is unexpectedly rotated to a position it would have encountered later in the step, the Center of Pressure also shifts forward to the corresponding later position, and the remaining portion of the gait pattern ensues. This phase shift suggests that the progression of the stance ankle is controlled by a biomechanical phase variable, motivating future investigations of phase variables in human locomotor control.

  10. Contribution of geodiversity, climate and spatial variables for biodiversity across a gradient of human influence

    Science.gov (United States)

    Tukiainen, Helena; Alahuhta, Janne; Ala-Hulkko, Terhi; Field, Richard; Lampinen, Raino; Hjort, Jan

    2016-04-01

    Implementation of geodiversity may provide new perspectives for nature conservation. The relation between geodiversity and biodiversity has been established in recent studies but remains underexplored in environments with high human pressure. In this study, we explored the effect of geodiversity (i.e. geological, hydrological and geomorphological diversity), climate and spatial variables on biodiversity (vascular plant species richness) in environments with different human impact. The study area ranged trough the boreal vegetation zone in Finland and included altogether 1401 1-km2 grid cells from urban, rural and natural environments. The contribution of environmental variable groups for species diversity in different environments was statistically analyzed with variation partitioning method. According to the results, the contribution of geodiversity decreased and the contribution of climate and spatial variables increased as the land use became more human-induced. Hence, the connection between geodiversity and species richness was most pronounced in natural state environments.

  11. Genetic analysis of basmati and non-basmati Pakistani rice (oryza sativa l.) cultivars using microsatellite markers

    International Nuclear Information System (INIS)

    Rabbani, M.A.; Masood, M.A.; Shinwari, Z.K.

    2010-01-01

    Information of genetic variability and relatedness among rice genotypes is essential for future breeding programmes and derivation of superior cultivars. The objective of the present study was to evaluate the genetic relationship among traditional and improved cultivars of Pakistani rice and to determine differences in the patterns of variation between two indica rice groups: basmati and nonbasmati. Forty-one cultivars were evaluated by means of 30 microsatellite markers distributed over the whole rice genome. A total of 104 alleles were detected by 30 markers, all of them (100%) were polymorphic. The number of alleles generated by each marker ranged from 2 to 6 with an average of 3.5 alleles marker-1. Polymorphism information content (PIC) varied from 0.259 to 0.782 with an average of 0.571. A significant positive correlation (r = 0.71) was found between the number of alleles at SSR locus and the PIC values. Pair-wise Nei and Li's similarity coefficients ranged from 0.10 to 0.99. A dendrogram based on cluster analysis by microsatellite polymorphism grouped 41 rice cultivars into 2 major groups effectively differentiating the late maturing, tall and slender-grain basmati and other aromatic rice cultivars from the early, short statured, short bold and long bold grain non-aromatic cultivars. Higher level of genetic diversity between basmati and non-basmati support the concept that former had a long history of independent evolution and diverged from nonbasmati rice a long time ago through human selection and patronage. Present investigation further indicated that genetically basmati rice is different from that of coarse indica and japonica type. The results suggested that microsatellite markers could efficiently be utilized for diversity analysis, and differentiation of basmati and non-basmati rice cultivars. In addition, marker-based identification of traditional basmati rice may help in maintaining the integrity of this high quality product to the benefit of both

  12. A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa

    Science.gov (United States)

    Alonso, Santos; Armour, John A. L.

    2001-01-01

    We have sequenced a highly polymorphic subterminal noncoding region from human chromosome 16p13.3, flanking the 5′ end of the hypervariable minisatellite MS205, in 100 chromosomes sampled from different African and Euroasiatic populations. Coalescence analysis indicates that the time to the most recent common ancestor (approximately 1 million years) predates the appearance of anatomically modern human forms. The root of the network describing this variability lies in Africa. African populations show a greater level of diversity and deeper branches. Most Euroasiatic variability seems to have been generated after a recent out-of-Africa range expansion. A history of population growth is the most likely scenario for the Euroasiatic populations. This pattern of nuclear variability can be reconciled with inferences based on mitochondrial DNA. PMID:11158547

  13. Perspective on sequence evolution of microsatellite locus (CCGn in Rv0050 gene from Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Jin Ruiliang

    2011-08-01

    Full Text Available Abstract Background The mycobacterial genome is inclined to polymerase slippage and a high mutation rate in microsatellite regions due to high GC content and absence of a mismatch repair system. However, the exact molecular mechanisms underlying microsatellite variation have not been fully elucidated. Here, we investigated mutation events in the hyper-variable trinucleotide microsatellite locus MML0050 located in the Rv0050 gene of W-Beijing and non-W-Beijing Mycobacterium tuberculosis strains in order to gain insight into the genomic structure and activity of repeated regions. Results Size analysis indicated the presence of five alleles that differed in length by three base pairs. Moreover, nucleotide gains occurred more frequently than loses in this trinucleotide microsatellite. Mutation frequency was not completely related with the total length, though the relative frequency in the longest allele was remarkably higher than that in the shortest. Sequence analysis was able to detect seven alleles and revealed that point mutations enhanced the level of locus variation. Introduction of an interruptive motif correlated with the total allele length and genetic lineage, rather than the length of the longest stretch of perfect repeats. Finally, the level of locus variation was drastically different between the two genetic lineages. Conclusion The Rv0050 locus encodes the bifunctional penicillin-binding protein ponA1 and is essential to mycobacterial survival. Our investigations of this particularly dynamic genomic region provide insights into the overall mode of microsatellite evolution. Specifically, replication slippage was implicated in the mutational process of this microsatellite and a sequence-based genetic analysis was necessary to determine that point mutation events acted to maintain microsatellite size integrity while providing genomic diversity.

  14. Rangewide Genetic Variation in Coast Redwood Populations at a Chloroplast Microsatellite Locus

    Science.gov (United States)

    Chris Brinegar

    2012-01-01

    Old growth and second growth populations of coast redwood (Sequoia sempervirens) were sampled at 10 locations throughout its range and analyzed at a highly variable chloroplast microsatellite locus. Very low FST values indicated that there was no significant genetic differentiation between adjacent old growth and second growth populations at each location. Genetic...

  15. Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds

    NARCIS (Netherlands)

    Baratti, M.; Alberti, A.; Groenen, M.A.M.; Veenendaal, T.; Fulgheri, F.D.

    2001-01-01

    Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers

  16. Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L.

    NARCIS (Netherlands)

    Schroeder, H.C.; Arens, P.F.P.; Smulders, M.J.M.

    2009-01-01

    Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy¿Weinberg equilibrium. The other two were linked to the

  17. Pathogen prevalence predicts human cross-cultural variability in individualism/collectivism

    OpenAIRE

    Fincher, Corey L; Thornhill, Randy; Murray, Damian R; Schaller, Mark

    2008-01-01

    Pathogenic diseases impose selection pressures on the social behaviour of host populations. In humans (Homo sapiens), many psychological phenomena appear to serve an antipathogen defence function. One broad implication is the existence of cross-cultural differences in human cognition and behaviour contingent upon the relative presence of pathogens in the local ecology. We focus specifically on one fundamental cultural variable: differences in individualistic versus collectivist values. We sug...

  18. Mechanism of blood pressure and R-R variability: insights from ganglion blockade in humans

    Science.gov (United States)

    Zhang, Rong; Iwasaki, Kenichi; Zuckerman, Julie H.; Behbehani, Khosrow; Crandall, Craig G.; Levine, Benjamin D.; Blomqvist, C. G. (Principal Investigator)

    2002-01-01

    Spontaneous blood pressure (BP) and R-R variability are used frequently as 'windows' into cardiovascular control mechanisms. However, the origin of these rhythmic fluctuations is not completely understood. In this study, with ganglion blockade, we evaluated the role of autonomic neural activity versus other 'non-neural' factors in the origin of BP and R-R variability in humans. Beat-to-beat BP, R-R interval and respiratory excursions were recorded in ten healthy subjects (aged 30 +/- 6 years) before and after ganglion blockade with trimethaphan. The spectral power of these variables was calculated in the very low (0.0078-0.05 Hz), low (0.05-0.15 Hz) and high (0.15-0.35 Hz) frequency ranges. The relationship between systolic BP and R-R variability was examined by cross-spectral analysis. After blockade, R-R variability was virtually abolished at all frequencies; however, respiration and high frequency BP variability remained unchanged. Very low and low frequency BP variability was reduced substantially by 84 and 69 %, respectively, but still persisted. Transfer function gain between systolic BP and R-R interval variability decreased by 92 and 88 % at low and high frequencies, respectively, while the phase changed from negative to positive values at the high frequencies. These data suggest that under supine resting conditions with spontaneous breathing: (1) R-R variability at all measured frequencies is predominantly controlled by autonomic neural activity; (2) BP variability at high frequencies (> 0.15 Hz) is mediated largely, if not exclusively, by mechanical effects of respiration on intrathoracic pressure and/or cardiac filling; (3) BP variability at very low and low frequencies (rhythmicity; and (4) the dynamic relationship between BP and R-R variability as quantified by transfer function analysis is determined predominantly by autonomic neural activity rather than other, non-neural factors.

  19. Characterization of ten microsatellite loci in midget faded rattlesnake (Crotalus oreganus concolor)

    Science.gov (United States)

    Oyler-McCance, Sara J.; Parker, Joshua M.

    2010-01-01

    Primers for 10 microsatellite loci were developed for midget faded rattlesnake (Crotalus oreganus concolor), a small bodied subspecies of the Western Rattlesnake, which is found in the Colorado Plateau of eastern Utah, western Colorado and southwestern Wyoming. In a screen of 23 individuals from the most northern portion of the subspecies range in southwestern Wyoming, the 10 loci were found to have levels of variability ranging from 4 to 11 alleles. No loci were found to be linked, although one locus revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci will be applicable for population genetic analyses, which will ultimately aid in management efforts for this rare subspecies of rattlesnake.

  20. Nine microsatellite loci developed from the octocoral, Paragorgia arborea

    Science.gov (United States)

    Coykendall, D. Katharine; Morrison, Cheryl L.

    2015-01-01

    Paragorgia arborea, or bubblegum coral, occurs in continental slope habitats worldwide, which are increasingly threatened by human activities such as energy development and fisheries practices. From 101 putative loci screened, nine microsatellite markers were developed from samples taken from Baltimore canyon in the western North Atlantic Ocean. The number of alleles ranged from two to thirteen per locus and each displayed equilibrium. These nuclear resources will help further research on population connectivity in threatened coral species where mitochondrial markers are known to lack fine-scale genetic diversity.

  1. Development of 12 Chloroplast Microsatellite Markers in Vigna unguiculata (Fabaceae and Amplification in Phaseolus vulgaris

    Directory of Open Access Journals (Sweden)

    Lei Pan

    2014-03-01

    Full Text Available Premise of the study: Vigna unguiculata is an economically important legume, and the complexity of its variability and evolution needs to be further understood. Based on publicly available databases, we developed chloroplast microsatellite primers to investigate genetic diversity within V. unguiculata and its related species Phaseolus vulgaris. Methods and Results: Twelve polymorphic chloroplast microsatellite markers were developed and characterized in 62 V. unguiculata individuals. The number of alleles per locus varied between two and four, the unbiased haploid diversity per locus ranged from 0.123 to 0.497, and the polymorphism information content varied from 0.114 to 0.369. In cross-species amplifications, nine of these markers showed polymorphism in 29 P. vulgaris individuals. Conclusions: The newly developed chloroplast microsatellite markers exhibit variation in V. unguiculata as well as their transferability in P. vulgaris. These markers can be used to investigate genetic diversity and evolution in V. unguiculata and P. vulgaris.

  2. Development of Microsatellites for Verbenoxylum reitzii (Verbenaceae, a Tree Endemic to the Brazilian Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Verônica A. Thode

    2013-07-01

    Full Text Available Premise of the study: Microsatellite markers were developed for Verbenoxylum reitzii (Verbenaceae, a tree endemic to the Brazilian Atlantic Forest, to investigate their usefulness in population genetic studies. The loci were tested for cross-amplification in the related genera Recordia and Duranta. Methods and Results: Eleven polymorphic microsatellite markers were isolated from an enriched library of V. reitzii and characterized. The primers were tested on 60 individuals from three populations of this species. The number of alleles per locus ranged from two to 11, and the observed and expected heterozygosities varied from 0.0 to 1.0 and from 0.088 to 0.758, respectively. Ten loci successfully amplified in R. boliviana and all failed in D. vestita. Conclusions: Our results suggest the usefulness of the microsatellite loci developed here to access genetic variability for phylogeographic and population genetic studies in V. reitzii, which are important for the conservation of this rare species.

  3. Allelic database and accession divergence of a Brazilian mango collection based on microsatellite markers.

    Science.gov (United States)

    Dos Santos Ribeiro, I C N; Lima Neto, F P; Santos, C A F

    2012-12-19

    Allelic patterns and genetic distances were examined in a collection of 103 foreign and Brazilian mango (Mangifera indica) accessions in order to develop a reference database to support cultivar protection and breeding programs. An UPGMA dendrogram was generated using Jaccard's coefficients from a distance matrix based on 50 alleles of 12 microsatellite loci. The base pair number was estimated by the method of inverse mobility. The cophenetic correlation was 0.8. The accessions had a coefficient of similarity from 30 to 100%, which reflects high genetic variability. Three groups were observed in the UPGMA dendrogram; the first group was formed predominantly by foreign accessions, the second group was formed by Brazilian accessions, and the Dashehari accession was isolated from the others. The 50 microsatellite alleles did not separate all 103 accessions, indicating that there are duplicates in this mango collection. These 12 microsatellites need to be validated in order to establish a reliable set to identify mango cultivars.

  4. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  5. Predicting aboveground forest biomass with topographic variables in human-impacted tropical dry forest landscapes

    NARCIS (Netherlands)

    Salinas-Melgoza, Miguel A.; Skutsch, Margaret; Lovett, Jon C.

    2018-01-01

    Topographic variables such as slope and elevation partially explain spatial variations in aboveground biomass (AGB) within landscapes. Human activities that impact vegetation, such as cattle grazing and shifting cultivation, often follow topographic features and also play a key role in determining

  6. A mathematical description of nerve fiber bundle trajectories and their variability in the human retina

    NARCIS (Netherlands)

    Jansonius, N. M.; Nevalainen, J.; Selig, B.; Zangwill, L. M.; Sample, P. A.; Budde, W. M.; Jonas, J. B.; Lagreze, W. A.; Airaksinen, P. J.; Vonthein, R.; Levin, L. A.; Paetzold, J.; Schiefer, U.

    2009-01-01

    We developed a mathematical model wherein retinal nerve fiber trajectories can be described and the corresponding inter-subject variability analyzed. The model was based on traced nerve fiber bundle trajectories extracted from 55 fundus photographs of 55 human subjects. The model resembled the

  7. Inter-Individual Variability in Human Response to Low-Dose Ionizing Radiation, Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Rocke, David [Univ. of California, Davis, CA (United States)

    2016-08-01

    In order to investigate inter-individual variability in response to low-dose ionizing radiation, we are working with three models, 1) in-vivo irradiated human skin, for which we have a realistic model, but with few subjects, all from a previous project, 2) ex-vivo irradiated human skin, for which we also have a realistic model, though with the limitations involved in keeping skin pieces alive in media, and 3) MatTek EpiDermFT skin plugs, which provides a more realistic model than cell lines, which is more controllable than human samples.

  8. Inter-Individual Variability in Human Response to Low-Dose Ionizing Radiation, Final Report

    International Nuclear Information System (INIS)

    Rocke, David

    2016-01-01

    In order to investigate inter-individual variability in response to low-dose ionizing radiation, we are working with three models, 1) in-vivo irradiated human skin, for which we have a realistic model, but with few subjects, all from a previous project, 2) ex-vivo irradiated human skin, for which we also have a realistic model, though with the limitations involved in keeping skin pieces alive in media, and 3) MatTek EpiDermFT skin plugs, which provides a more realistic model than cell lines, which is more controllable than human samples.

  9. Partners in crime: bidirectional transcription in unstable microsatellite disease.

    Science.gov (United States)

    Batra, Ranjan; Charizanis, Konstantinos; Swanson, Maurice S

    2010-04-15

    Nearly two decades have passed since the discovery that the expansion of microsatellite trinucleotide repeats is responsible for a prominent class of neurological disorders, including Huntington disease and fragile X syndrome. These hereditary diseases are characterized by genetic anticipation or the intergenerational increase in disease severity accompanied by a decrease in age-of-onset. The revelation that the variable expansion of simple sequence repeats accounted for anticipation spawned a number of pathogenesis models and a flurry of studies designed to reveal the molecular events affected by these expansions. This work led to our current understanding that expansions in protein-coding regions result in extended homopolymeric amino acid tracts, often polyglutamine or polyQ, and deleterious protein gain-of-function effects. In contrast, expansions in noncoding regions cause RNA-mediated toxicity. However, the realization that the transcriptome is considerably more complex than previously imagined, as well as the emerging regulatory importance of antisense RNAs, has blurred this distinction. In this review, we summarize evidence for bidirectional transcription of microsatellite disease genes and discuss recent suggestions that some repeat expansions produce variable levels of both toxic RNAs and proteins that influence cell viability, disease penetrance and pathological severity.

  10. Nonlinear Synchronization for Automatic Learning of 3D Pose Variability in Human Motion Sequences

    Directory of Open Access Journals (Sweden)

    Mozerov M

    2010-01-01

    Full Text Available A dense matching algorithm that solves the problem of synchronizing prerecorded human motion sequences, which show different speeds and accelerations, is proposed. The approach is based on minimization of MRF energy and solves the problem by using Dynamic Programming. Additionally, an optimal sequence is automatically selected from the input dataset to be a time-scale pattern for all other sequences. The paper utilizes an action specific model which automatically learns the variability of 3D human postures observed in a set of training sequences. The model is trained using the public CMU motion capture dataset for the walking action, and a mean walking performance is automatically learnt. Additionally, statistics about the observed variability of the postures and motion direction are also computed at each time step. The synchronized motion sequences are used to learn a model of human motion for action recognition and full-body tracking purposes.

  11. Eguchipsammia fistula Microsatellite Development and Population Analysis

    KAUST Repository

    Mughal, Mehreen

    2012-12-01

    Deep water corals are an understudied yet biologically important and fragile ecosystem under threat from recent increasing temperatures and high carbon dioxide emissions. Using 454 sequencing, we develop 14 new microsatellite markers for the deep water coral Eguchipsammia fistula, collected from the Red Sea but found in deep water coral ecosystems globally. We tested these microsatellite primers on 26 samples of this coral collected from a single population. Results show that these corals are highly clonal within this population stemming from a high level of asexual reproduction. Mitochondrial studies back up microsatellite findings of high levels of genetic similarity. CO1, ND1 and ATP6 mitochondrial sequences of E. fistula and 11 other coral species were used to build phylogenetic trees which grouped E. fistula with shallow water coral Porites rather than deep sea L. Petusa.

  12. A microsatellite linkage map of Drosophila mojavensis

    Directory of Open Access Journals (Sweden)

    Schully Sheri

    2004-05-01

    Full Text Available Abstract Background Drosophila mojavensis has been a model system for genetic studies of ecological adaptation and speciation. However, despite its use for over half a century, no linkage map has been produced for this species or its close relatives. Results We have developed and mapped 90 microsatellites in D. mojavensis, and we present a detailed recombinational linkage map of 34 of these microsatellites. A slight excess of repetitive sequence was observed on the X-chromosome relative to the autosomes, and the linkage groups have a greater recombinational length than the homologous D. melanogaster chromosome arms. We also confirmed the conservation of Muller's elements in 23 sequences between D. melanogaster and D. mojavensis. Conclusions The microsatellite primer sequences and localizations are presented here and made available to the public. This map will facilitate future quantitative trait locus mapping studies of phenotypes involved in adaptation or reproductive isolation using this species.

  13. Patterns of microsatellite evolution inferred from the Helianthus ...

    Indian Academy of Sciences (India)

    2014-08-21

    Aug 21, 2014 ... selection has favoured the maintenance of microsatellites in these genes over others. This study shows that .... Materials and methods. Data collection ... sequences and different microsatellite motifs should code for specific ...

  14. Functionally relevant microsatellites in sugarcane unigenes

    Directory of Open Access Journals (Sweden)

    Singh Nagendra K

    2010-11-01

    Full Text Available Abstract Background Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane. Results The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome. Conclusion Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6% of which functions were determined in silico. High level of

  15. The pathological phenotype of colon cancer with microsatellite instability

    DEFF Research Database (Denmark)

    Andersen, Helene Schou; Bertelsen, Claus Anders; Henriksen, Rikke

    2016-01-01

    proteins: pMLH1, pMSH2, pMSH6 and pPMS2 for the determination of microsatellite instability. Microsatellite instability was defined as deficient expression of one or more of these proteins. RESULTS: Of the 833 patients, 177 had microsatellite instable tumours (21%). Using multivariable logistic regression...

  16. Microsatellite typing of clinical and environmental Cryptococcus neoformans var. grubii isolates from Cuba shows multiple genetic lineages.

    Directory of Open Access Journals (Sweden)

    Maria-Teresa Illnait-Zaragozi

    Full Text Available BACKGROUND: Human cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of Cryptococcus spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods. METHODOLOGY/PRINCIPAL FINDINGS: We selected nine microsatellite markers for high-resolution fingerprinting from the genome of C. neoformans var. grubii. This panel of markers was applied to a collection of clinical (n = 122 and environmental (n = 68; from pigeon guano C. neoformans var. grubii isolates from Cuba. All markers proved to be polymorphic. The average number of alleles per marker was 9 (range 5-51. A total of 104 genotypes could be distinguished. The discriminatory power of this panel of markers was 0.993. Multiple clusters of related genotypes could be discriminated that differed in only one or two microsatellite markers. These clusters were assigned as microsatellite complexes. The majority of environmental isolates (>70% fell into 1 microsatellite complex containing only few clinical isolates (49 environmental versus 2 clinical. Clinical isolates were segregated over multiple microsatellite complexes. CONCLUSIONS/SIGNIFICANCE: A large genotypic variation exists in C. neoformans var. grubii. The genotypic segregation between clinical and environmental isolates from pigeon guano suggests additional source(s of human cryptococcal infections. The selected panel of microsatellite markers is an excellent tool to study the epidemiology of C. neoformans var. grubii.

  17. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  18. Variable ATP yields and uncoupling of oxygen consumption in human brain

    DEFF Research Database (Denmark)

    Gjedde, Albert; Aanerud, Joel; Peterson, Ericka

    2011-01-01

    normalized the metabolic rate to the population average of that region. Coefficients of variation ranged from 10 to 15% in the different regions of the human brain and the normalized regional metabolic rates ranged from 70% to 140% of the population average for each region, equal to a two-fold variation......The distribution of brain oxidative metabolism values among healthy humans is astoundingly wide for a measure that reflects normal brain function and is known to change very little with most changes of brain function. It is possible that the part of the oxygen consumption rate that is coupled...... to ATP turnover is the same in all healthy human brains, with different degrees of uncoupling explaining the variability of total oxygen consumption among people. To test the hypothesis that about 75% of the average total oxygen consumption of human brains is common to all individuals, we determined...

  19. Genetic variability in the human cannabinoid receptor 1 is associated with resting state EEG theta power in humans.

    Science.gov (United States)

    Heitland, I; Kenemans, J L; Böcker, K B E; Baas, J M P

    2014-11-01

    It has long been postulated that exogenous cannabinoids have a profound effect on human cognitive functioning. These cannabinoid effects are thought to depend, at least in parts, on alterations of phase-locking of local field potential neuronal firing. The latter can be measured as activity in the theta frequency band (4-7Hz) by electroencephalogram. Theta oscillations are supposed to serve as a mechanism in neural representations of behaviorally relevant information. However, it remains unknown whether variability in endogenous cannabinoid activity is involved in theta rhythms and therefore, may serve as an individual differences index of human cognitive functioning. To clarify this issue, we recorded resting state EEG activity in 164 healthy human subjects and extracted EEG power across frequency bands (δ, θ, α, and β). To assess variability in the endocannabinoid system, two genetic polymorphisms (rs1049353, rs2180619) within the cannabinoid receptor 1 (CB1) were determined in all participants. As expected, we observed significant effects of rs1049353 on EEG power in the theta band at frontal, central and parietal electrode regions. Crucially, these effects were specific for the theta band, with no effects on activity in the other frequency bands. Rs2180619 showed no significant associations with theta power after Bonferroni correction. Taken together, we provide novel evidence in humans showing that genetic variability in the cannabinoid receptor 1 is associated with resting state EEG power in the theta frequency band. This extends prior findings of exogenous cannabinoid effects on theta power to the endogenous cannabinoid system. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Development and characterization of microsatellite markers for ...

    Indian Academy of Sciences (India)

    This species is threatened throughout its range in West- ern Ghats as a result of overexploitation and habitat destruc- tion, which have reduced local population sizes and has led many populations to local extinction. In this study, we report the development of microsatellite markers and discuss the utility of these markers in ...

  1. Development of polymorphic microsatellite markers in Sardinella ...

    Indian Academy of Sciences (India)

    differentiation of S. aurita are available, which has limited the proper management and utilization of S. aurita (Kinsey et al. ... 5 -anchored PCR; Sardinella aurita. Journal of Genetics Vol. 93, Online Resources .... 2012 Construction of a high density microsatellite genetic linkage map and mapping of sexual and growthrelated ...

  2. Survey of microsatellite DNA in pine

    Science.gov (United States)

    Craig S. Echt; P. May-Marquardt

    1997-01-01

    A large insert genomic library from eastern white pine (Pinus strobus) was probed for the microsatellite motifs (AC)n and (AG)n, all 10 trinucleotide motifs, and 22 of the 33 possible tetranucleotide motifs. For comparison with a species from a different subgenus, a loblolly pine (Pinus taeda) genomic...

  3. Microsatellite analysis of intracultivar diversity in 'Chinnarasam ...

    African Journals Online (AJOL)

    Their leaves were sampled to study intracultivar diversity following microsatellite analysis. The dendrogram generated based on unweighted pair group mean with arithmetic average, showed three major groups of accessions, which followed geographical separation. Twenty out of 109 mango-specific micro satellites ...

  4. Characterization of microsatellites in white croaker (Pennahia ...

    Indian Academy of Sciences (India)

    [Sun D. Q., Xu T. J. and Wang R. X. 2011 Characterization of microsatellites in ... in northwest Pacific along the coastal seas of China, Japan ... waters (Han et al. ... Cambridge, UK). ..... Taki Y. 2000 Fish: The encyclopedia of fish and seafood.

  5. Microsatellites in wheat and their applications

    International Nuclear Information System (INIS)

    Stephenson, P.; Bryan, G.J.; Kirby, J.; Gale, M.D.

    1998-01-01

    The development of large panels of simply analyzable genetic markers for diversity studies and tagging, agronomically important genes in hexaploid bread wheat is an important goal in applied cereal genetic research. We have isolated and sequenced over two-hundred clones containing microsatellites from the wheat genome, and have tested 150 primer pairs for genetic polymorphism using a panel of ten wheat varieties, including the parents of our main mapping cross. A total of 125 loci were detected by 82 primer pairs, of which 105 loci from 63 primer pairs can be unequivocally allocated to one of the wheat chromosomes. A relatively low frequency of the loci detected are from the D-genome (24%). Generally, the microsatellites show high levels of genetic polymorphism and an average 3.5 alleles per locus with an average polymorphism information content (PIC) value of 0.5. The observed levels of polymorphism are positively correlated with the length of the microsatellite repeats. A high proportion, approximately one half, of primer pairs designed to detect simple sequence repeat (SSR) variation in wheat do not generate the expected amplification products and, more significantly, often generate unresolvable Polymerase Chain Reaction (PCR) products. In general our results agree closely with those obtained from other recent studies using microsatellites in plants. (author)

  6. Isolation and characterization of polymorphic microsatellite markers ...

    African Journals Online (AJOL)

    Flax (Linum usitatissimum L.) is the third largest natural fiber crop and one of the five major oil crops in the world. ... These novel polymorphic microsatellite loci will be useful in genetic linkage map construction, germplasm classification and identification, gene identification and QTL mapping, and marker-assisted selection ...

  7. Supplementary data: Eucalyptus microsatellites mined in silico ...

    Indian Academy of Sciences (India)

    Supplementary data: Eucalyptus microsatellites mined in silico: survey and evaluation. R. Yasodha, R. Sumathi, P. Chezhian, S. Kavitha and M. Ghosh. J. Genet. 87, XX-XX. Tm. CT. 2222. NA. 60 125. 192. Table 1. List of EST-SSR primers developed for E. globulus. No. of. Tm Product. Acc. no. SSR repeats. Forward primer.

  8. Optimization of microsatellite DNA Gelred fluorescence imaging ...

    African Journals Online (AJOL)

    user1

    2012-10-11

    Oct 11, 2012 ... In order to explore the best microsatellite DNA Gelred imaging technology, this ... analysis and character identification breeding practice, because it is ... detection methods are agarose gel electrophoresis (AGE) with ethidium ... method (PG). Gelred 10000X stock reagent was diluted in the 1.5% agarose gel.

  9. Development of microsatellite markers for Helopeltis theivora ...

    African Journals Online (AJOL)

    USER

    2010-07-12

    Jul 12, 2010 ... are highly polymorphic, neutral and show Mendelian inheritance, they therefore represent one of the most powerful tools for population genetic studies (Bruford and. Wayne, 1993). Microsatellites have also been analysed extensively in Drosophila melanogaster (Bachtrog et al.,. 1999), Drosophila simulans ...

  10. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  11. Understanding The Individual Impacts Of Human Interventions And Climate Change On Hydrologic Variables In India

    Science.gov (United States)

    Sharma, T.; Chhabra, S., Jr.; Karmakar, S.; Ghosh, S.

    2015-12-01

    We have quantified the historical climate change and Land Use Land Cover (LULC) change impacts on the hydrologic variables of Indian subcontinent by using Variable Infiltration Capacity (VIC) mesoscale model at 0.5° spatial resolution and daily temporal resolution. The results indicate that the climate change in India has predominating effects on the basic water balance components such as water yield, evapotranspiration and soil moisture. This analysis is with the assumption of naturalised hydrologic cycle, i.e., the impacts of human interventions like construction of controlled (primarily dams, diversions and reservoirs) and water withdrawals structures are not taken into account. The assumption is unrealistic since there are numerous anthropogenic disturbances which result in large changes on vegetation composition and distribution patterns. These activities can directly or indirectly influence the dynamics of water cycle; subsequently affecting the hydrologic processes like plant transpiration, infiltration, evaporation, runoff and sublimation. Here, we have quantified the human interventions by using the reservoir and irrigation module of VIC model which incorporates the irrigation schemes, reservoir characteristics and water withdrawals. The impact of human interventions on hydrologic variables in many grids are found more predominant than climate change and might be detrimental to water resources at regional level. This spatial pattern of impacts will facilitate water manager and planners to design and station hydrologic structures for a sustainable water resources management.

  12. Pathogen prevalence predicts human cross-cultural variability in individualism/collectivism.

    Science.gov (United States)

    Fincher, Corey L; Thornhill, Randy; Murray, Damian R; Schaller, Mark

    2008-06-07

    Pathogenic diseases impose selection pressures on the social behaviour of host populations. In humans (Homo sapiens), many psychological phenomena appear to serve an antipathogen defence function. One broad implication is the existence of cross-cultural differences in human cognition and behaviour contingent upon the relative presence of pathogens in the local ecology. We focus specifically on one fundamental cultural variable: differences in individualistic versus collectivist values. We suggest that specific behavioural manifestations of collectivism (e.g. ethnocentrism, conformity) can inhibit the transmission of pathogens; and so we hypothesize that collectivism (compared with individualism) will more often characterize cultures in regions that have historically had higher prevalence of pathogens. Drawing on epidemiological data and the findings of worldwide cross-national surveys of individualism/collectivism, our results support this hypothesis: the regional prevalence of pathogens has a strong positive correlation with cultural indicators of collectivism and a strong negative correlation with individualism. The correlations remain significant even when controlling for potential confounding variables. These results help to explain the origin of a paradigmatic cross-cultural difference, and reveal previously undocumented consequences of pathogenic diseases on the variable nature of human societies.

  13. An agent-based model of cellular dynamics and circadian variability in human endotoxemia.

    Directory of Open Access Journals (Sweden)

    Tung T Nguyen

    Full Text Available As cellular variability and circadian rhythmicity play critical roles in immune and inflammatory responses, we present in this study an agent-based model of human endotoxemia to examine the interplay between circadian controls, cellular variability and stochastic dynamics of inflammatory cytokines. The model is qualitatively validated by its ability to reproduce circadian dynamics of inflammatory mediators and critical inflammatory responses after endotoxin administration in vivo. Novel computational concepts are proposed to characterize the cellular variability and synchronization of inflammatory cytokines in a population of heterogeneous leukocytes. Our results suggest that there is a decrease in cell-to-cell variability of inflammatory cytokines while their synchronization is increased after endotoxin challenge. Model parameters that are responsible for IκB production stimulated by NFκB activation and for the production of anti-inflammatory cytokines have large impacts on system behaviors. Additionally, examining time-dependent systemic responses revealed that the system is least vulnerable to endotoxin in the early morning and most vulnerable around midnight. Although much remains to be explored, proposed computational concepts and the model we have pioneered will provide important insights for future investigations and extensions, especially for single-cell studies to discover how cellular variability contributes to clinical implications.

  14. An exploration of diffusion tensor eigenvector variability within human calf muscles.

    Science.gov (United States)

    Rockel, Conrad; Noseworthy, Michael D

    2016-01-01

    To explore the effect of diffusion tensor imaging (DTI) acquisition parameters on principal and minor eigenvector stability within human lower leg skeletal muscles. Lower leg muscles were evaluated in seven healthy subjects at 3T using an 8-channel transmit/receive coil. Diffusion-encoding was performed with nine signal averages (NSA) using 6, 15, and 25 directions (NDD). Individual DTI volumes were combined into aggregate volumes of 3, 2, and 1 NSA according to number of directions. Tensor eigenvalues (λ1 , λ2 , λ3 ), eigenvectors (ε1 , ε2 , ε3 ), and DTI metrics (fractional anisotropy [FA] and mean diffusivity [MD]) were calculated for each combination of NSA and NDD. Spatial maps of signal-to-noise ratio (SNR), λ3 :λ2 ratio, and zenith angle were also calculated for region of interest (ROI) analysis of vector orientation consistency. ε1 variability was only moderately related to ε2 variability (r = 0.4045). Variation of ε1 was affected by NDD, not NSA (P < 0.0002), while variation of ε2 was affected by NSA, not NDD (P < 0.0003). In terms of tensor shape, vector variability was weakly related to FA (ε1 :r = -0.1854, ε2 : ns), but had a stronger relation to the λ3 :λ2 ratio (ε1 :r = -0.5221, ε2 :r = -0.1771). Vector variability was also weakly related to SNR (ε1 :r = -0.2873, ε2 :r = -0.3483). Zenith angle was found to be strongly associated with variability of ε1 (r = 0.8048) but only weakly with that of ε2 (r = 0.2135). The second eigenvector (ε2 ) displayed higher directional variability relative to ε1 , and was only marginally affected by experimental conditions that impacted ε1 variability. © 2015 Wiley Periodicals, Inc.

  15. Modelling Inter-relationships among water, governance, human development variables in developing countries with Bayesian networks.

    Science.gov (United States)

    Dondeynaz, C.; Lopez-Puga, J.; Carmona-Moreno, C.

    2012-04-01

    Improving Water and Sanitation Services (WSS), being a complex and interdisciplinary issue, passes through collaboration and coordination of different sectors (environment, health, economic activities, governance, and international cooperation). This inter-dependency has been recognised with the adoption of the "Integrated Water Resources Management" principles that push for the integration of these various dimensions involved in WSS delivery to ensure an efficient and sustainable management. The understanding of these interrelations appears as crucial for decision makers in the water sector in particular in developing countries where WSS still represent an important leverage for livelihood improvement. In this framework, the Joint Research Centre of the European Commission has developed a coherent database (WatSan4Dev database) containing 29 indicators from environmental, socio-economic, governance and financial aid flows data focusing on developing countries (Celine et al, 2011 under publication). The aim of this work is to model the WatSan4Dev dataset using probabilistic models to identify the key variables influencing or being influenced by the water supply and sanitation access levels. Bayesian Network Models are suitable to map the conditional dependencies between variables and also allows ordering variables by level of influence on the dependent variable. Separated models have been built for water supply and for sanitation because of different behaviour. The models are validated if complying with statistical criteria but either with scientific knowledge and literature. A two steps approach has been adopted to build the structure of the model; Bayesian network is first built for each thematic cluster of variables (e.g governance, agricultural pressure, or human development) keeping a detailed level for interpretation later one. A global model is then built based on significant indicators of each cluster being previously modelled. The structure of the

  16. Human Capital Variables and Economic Growth in Nigeria: An Interactive Effect

    Directory of Open Access Journals (Sweden)

    Adenike Mosunmola Osoba

    2017-05-01

    Full Text Available Various studies have focused on the relationship between human capital and economic growth all over the world. However, there is still a missing gap on the joint influence of human capital investment components on economic growth particularly in Nigeria. This study therefore examines the interactive effects of the relationship between human capital investment components and economic growth in Nigeria for the period of 1986 – 2014. The study employed secondary annual data on education expenditure, health expenditure, real gross domestic product and gross capital formation obtained from the Central Bank Statistical bulletin, 2014. The data were analyzed using Fully Modified Ordinary Least Squares (FMOLS technique. The results of the study showed that there was positive and significant relationship between the interactive effects of human capital components and growth in Nigeria. The study concluded that the interactive effect of the human capital variables was also in conformity with the theoretical proposition that increase in human capital will enhance growth as stipulated in the modified Solow growth model by Mankiw, Romer & Weil (1992.

  17. An analytical approach to separate climate and human contributions to basin streamflow variability

    Science.gov (United States)

    Li, Changbin; Wang, Liuming; Wanrui, Wang; Qi, Jiaguo; Linshan, Yang; Zhang, Yuan; Lei, Wu; Cui, Xia; Wang, Peng

    2018-04-01

    Climate variability and anthropogenic regulations are two interwoven factors in the ecohydrologic system across large basins. Understanding the roles that these two factors play under various hydrologic conditions is of great significance for basin hydrology and sustainable water utilization. In this study, we present an analytical approach based on coupling water balance method and Budyko hypothesis to derive effectiveness coefficients (ECs) of climate change, as a way to disentangle contributions of it and human activities to the variability of river discharges under different hydro-transitional situations. The climate dominated streamflow change (ΔQc) by EC approach was compared with those deduced by the elasticity method and sensitivity index. The results suggest that the EC approach is valid and applicable for hydrologic study at large basin scale. Analyses of various scenarios revealed that contributions of climate change and human activities to river discharge variation differed among the regions of the study area. Over the past several decades, climate change dominated hydro-transitions from dry to wet, while human activities played key roles in the reduction of streamflow during wet to dry periods. Remarkable decline of discharge in upstream was mainly due to human interventions, although climate contributed more to runoff increasing during dry periods in the semi-arid downstream. Induced effectiveness on streamflow changes indicated a contribution ratio of 49% for climate and 51% for human activities at the basin scale from 1956 to 2015. The mathematic derivation based simple approach, together with the case example of temporal segmentation and spatial zoning, could help people understand variation of river discharge with more details at a large basin scale under the background of climate change and human regulations.

  18. Evaluation of the genetic variability of 13 microsatellite markers in ...

    Indian Academy of Sciences (India)

    Unknown

    methods. Several DNA-based technologies to type poly- morphic loci have been developed in the last decade. The ... GTGTAGGCCTGGCGGTTGT. CCCTGAAACCTAAAGCAAAG. 55. 2.0. S0225. 8. GCTAATGCCAGAGAAATGCAGA. CAGGTGGAAAGAATGGAATGAA. 55. 4.0. S0226. 2. GCACTTTTAACTTTCATGATACTCC.

  19. Genetic changes of MLH1 and MSH2 genes could explain constant findings on microsatellite instability in intracranial meningioma.

    Science.gov (United States)

    Pećina-Šlaus, Nives; Kafka, Anja; Bukovac, Anja; Vladušić, Tomislav; Tomas, Davor; Hrašćan, Reno

    2017-07-01

    Postreplicative mismatch repair safeguards the stability of our genome. The defects in its functioning will give rise to microsatellite instability. In this study, 50 meningiomas were investigated for microsatellite instability. Two major mismatch repair genes, MLH1 and MSH2, were analyzed using microsatellite markers D1S1611 and BAT26 amplified by polymerase chain reaction and visualized by gel electrophoresis on high-resolution gels. Furthermore, genes DVL3 (D3S1262), AXIN1 (D16S3399), and CDH1 (D16S752) were also investigated for microsatellite instability. Our study revealed constant presence of microsatellite instability in meningioma patients when compared to their autologous blood DNA. Altogether 38% of meningiomas showed microsatellite instability at one microsatellite locus, 16% on two, and 13.3% on three loci. The percent of detected microsatellite instability for MSH2 gene was 14%, and for MLH1, it was 26%, for DVL3 22.9%, for AXIN1 17.8%, and for CDH1 8.3%. Since markers also allowed for the detection of loss of heterozygosity, gross deletions of MLH1 gene were found in 24% of meningiomas. Genetic changes between MLH1 and MSH2 were significantly positively correlated (p = 0.032). We also noted a positive correlation between genetic changes of MSH2 and DVL3 genes (p = 0.034). No significant associations were observed when MLH1 or MSH2 was tested against specific histopathological meningioma subtype or World Health Organization grade. However, genetic changes in DVL3 were strongly associated with anaplastic histology of meningioma (χ 2  = 9.14; p = 0.01). Our study contributes to better understanding of the genetic profile of human intracranial meningiomas and suggests that meningiomas harbor defective cellular DNA mismatch repair mechanisms.

  20. A general auditory bias for handling speaker variability in speech? Evidence in humans and songbirds

    Directory of Open Access Journals (Sweden)

    Buddhamas eKriengwatana

    2015-08-01

    Full Text Available Different speakers produce the same speech sound differently, yet listeners are still able to reliably identify the speech sound. How listeners can adjust their perception to compensate for speaker differences in speech, and whether these compensatory processes are unique only to humans, is still not fully understood. In this study we compare the ability of humans and zebra finches to categorize vowels despite speaker variation in speech in order to test the hypothesis that accommodating speaker and gender differences in isolated vowels can be achieved without prior experience with speaker-related variability. Using a behavioural Go/No-go task and identical stimuli, we compared Australian English adults’ (naïve to Dutch and zebra finches’ (naïve to human speech ability to categorize /ɪ/ and /ɛ/ vowels of an novel Dutch speaker after learning to discriminate those vowels from only one other speaker. Experiment 1 and 2 presented vowels of two speakers interspersed or blocked, respectively. Results demonstrate that categorization of vowels is possible without prior exposure to speaker-related variability in speech for zebra finches, and in non-native vowel categories for humans. Therefore, this study is the first to provide evidence for what might be a species-shared auditory bias that may supersede speaker-related information during vowel categorization. It additionally provides behavioural evidence contradicting a prior hypothesis that accommodation of speaker differences is achieved via the use of formant ratios. Therefore, investigations of alternative accounts of vowel normalization that incorporate the possibility of an auditory bias for disregarding inter-speaker variability are warranted.

  1. Variability of tissue mineral density can determine physiological creep of human vertebral cancellous bone.

    Science.gov (United States)

    Kim, Do-Gyoon; Shertok, Daniel; Ching Tee, Boon; Yeni, Yener N

    2011-06-03

    Creep is a time-dependent viscoelastic deformation observed under a constant prolonged load. It has been indicated that progressive vertebral deformation due to creep may increase the risk of vertebral fracture in the long-term. The objective of this study was to examine the relationships of creep with trabecular architecture and tissue mineral density (TMD) parameters in human vertebral cancellous bone at a physiological static strain level. Architecture and TMD parameters of cancellous bone were analyzed using microcomputerized tomography (micro-CT) in specimens cored out of human vertebrae. Then, creep and residual strains of the specimens were measured after a two-hour physiological compressive constant static loading and unloading cycle. Creep developed (3877 ± 2158 με) resulting in substantial levels of non-recoverable post-creep residual strain (1797 ± 1391 με). A strong positive linear correlation was found between creep and residual strain (r = 0.94, p creep rate. The TMD variability (GL(COV)) was the strongest correlate of creep rate (r = 0.79, p < 0.001). This result suggests that TMD variability may be a useful parameter for estimating the long-term deformation of a whole vertebral body. The results further suggest that the changes in TMD variability resulting from bone remodeling are of importance and may provide an insight into the understanding of the mechanisms underlying progressive failure of vertebral bodies and development of a clinical fracture. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Quasi-supervised scoring of human sleep in polysomnograms using augmented input variables.

    Science.gov (United States)

    Yaghouby, Farid; Sunderam, Sridhar

    2015-04-01

    The limitations of manual sleep scoring make computerized methods highly desirable. Scoring errors can arise from human rater uncertainty or inter-rater variability. Sleep scoring algorithms either come as supervised classifiers that need scored samples of each state to be trained, or as unsupervised classifiers that use heuristics or structural clues in unscored data to define states. We propose a quasi-supervised classifier that models observations in an unsupervised manner but mimics a human rater wherever training scores are available. EEG, EMG, and EOG features were extracted in 30s epochs from human-scored polysomnograms recorded from 42 healthy human subjects (18-79 years) and archived in an anonymized, publicly accessible database. Hypnograms were modified so that: 1. Some states are scored but not others; 2. Samples of all states are scored but not for transitional epochs; and 3. Two raters with 67% agreement are simulated. A framework for quasi-supervised classification was devised in which unsupervised statistical models-specifically Gaussian mixtures and hidden Markov models--are estimated from unlabeled training data, but the training samples are augmented with variables whose values depend on available scores. Classifiers were fitted to signal features incorporating partial scores, and used to predict scores for complete recordings. Performance was assessed using Cohen's Κ statistic. The quasi-supervised classifier performed significantly better than an unsupervised model and sometimes as well as a completely supervised model despite receiving only partial scores. The quasi-supervised algorithm addresses the need for classifiers that mimic scoring patterns of human raters while compensating for their limitations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Variable postpartum responsiveness among humans and other primates with "cooperative breeding": A comparative and evolutionary perspective.

    Science.gov (United States)

    Hrdy, Sarah B

    2016-01-01

    This article is part of a Special Issue "Parental Care".Until recently, evolutionists reconstructing mother-infant bonding among human ancestors relied on nonhuman primate models characterized by exclusively maternal care, overlooking the highly variable responsiveness exhibited by mothers in species with obligate reliance on allomaternal care and provisioning. It is now increasingly recognized that apes as large-brained, slow maturing, and nutritionally dependent for so long as early humans were, could not have evolved unless "alloparents" (group members other than genetic parents), in addition to parents, had helped mothers to care for and provision offspring, a rearing system known as "cooperative breeding." Here I review situation-dependent maternal responses ranging from highly possessive to permissive, temporarily distancing, rejecting, or infanticidal, documented for a small subset of cooperatively breeding primates. As in many mammals, primate maternal responsiveness is influenced by physical condition, endocrinological priming, prior experience and local environments (especially related to security). But mothers among primates who evolved as cooperative breeders also appear unusually sensitive to cues of social support. In addition to more "sapient" or rational decision-making, humankind's deep history of cooperative breeding must be considered when trying to understand the extremely variable responsiveness of human mothers. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Human θ burst stimulation enhances subsequent motor learning and increases performance variability.

    Science.gov (United States)

    Teo, James T H; Swayne, Orlando B C; Cheeran, Binith; Greenwood, Richard J; Rothwell, John C

    2011-07-01

    Intermittent theta burst stimulation (iTBS) transiently increases motor cortex excitability in healthy humans by a process thought to involve synaptic long-term potentiation (LTP), and this is enhanced by nicotine. Acquisition of a ballistic motor task is likewise accompanied by increased excitability and presumed intracortical LTP. Here, we test how iTBS and nicotine influences subsequent motor learning. Ten healthy subjects participated in a double-blinded placebo-controlled trial testing the effects of iTBS and nicotine. iTBS alone increased the rate of learning but this increase was blocked by nicotine. We then investigated factors other than synaptic strengthening that may play a role. Behavioral analysis and modeling suggested that iTBS increased performance variability, which correlated with learning outcome. A control experiment confirmed the increase in motor output variability by showing that iTBS increased the dispersion of involuntary transcranial magnetic stimulation-evoked thumb movements. We suggest that in addition to the effect on synaptic plasticity, iTBS may have facilitated performance by increasing motor output variability; nicotine negated this effect on variability perhaps via increasing the signal-to-noise ratio in cerebral cortex.

  5. A probabilistic model of human variability in physiology for future application to dose reconstruction and QIVIVE.

    Science.gov (United States)

    McNally, Kevin; Loizou, George D

    2015-01-01

    The risk assessment of environmental chemicals and drugs is undergoing a paradigm shift in approach which seeks the full replacement of animal testing with high throughput, mechanistic, in vitro systems. This new approach will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated by in vitro, in silico, and in chemico systems can be integrated and utilized for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited to this and are needed to translate in vitro concentration- response relationships to an exposure or dose, route and duration regime in human populations. Thus, a realistic description of the variation in the physiology of the human population being modeled is critical. Whilst various studies in the past decade have made progress in describing human variability, the algorithms are typically coded in computer programs and as such are unsuitable for reverse dosimetry. In this report we overcome this limitation by developing a hierarchical statistical model using standard probability distributions for the specification of a virtual US and UK human population. The work draws on information from both population databases and cadaver studies.

  6. A probabilistic model of human variability in physiology for future application to dose reconstruction and QIVIVE

    Directory of Open Access Journals (Sweden)

    Kevin eMcNally

    2015-10-01

    Full Text Available The risk assessment of environmental chemicals and drugs is undergoing a paradigm shift in approach which seeks the full replacement of animal testing with high throughput, mechanistic, in vitro systems. This new approach will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated by in vitro, in silico and in chemico systems can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE, ultimately to the human population level. Physiologically based pharmacokinetic (PBPK models are ideally suited to this and are needed to translate in vitro concentration- response relationships to an exposure or dose, route and duration regime in human populations. Thus a realistic description of the variation in the physiology of the human population being modelled is critical. Whilst various studies in the past decade have made progress in describing human variability, the algorithms are typically coded in computer programs and as such are unsuitable for reverse dosimetry. In this report we overcome this limitation by developing a hierarchical statistical model using standard probability distributions for the specification of a virtual US and UK human population. The work draws on information from both population databases and cadaver studies.

  7. Modeling impacts of human footprint and soil variability on the potential distribution of invasive plant species in different biomes

    Science.gov (United States)

    Wan, Ji-Zhong; Wang, Chun-Jing; Yu, Fei-Hai

    2017-11-01

    Human footprint and soil variability may be important in shaping the spread of invasive plant species (IPS). However, until now, there is little knowledge on how human footprint and soil variability affect the potential distribution of IPS in different biomes. We used Maxent modeling to project the potential distribution of 29 IPS with wide distributions and long introduction histories in China based on various combinations of climatic correlates, soil characteristics and human footprint. Then, we evaluated the relative importance of each type of environmental variables (climate, soil and human footprint) as well as the difference in range and similarity of the potential distribution of IPS between different biomes. Human footprint and soil variables contributed to the prediction of the potential distribution of IPS, and different types of biomes had varying responses and degrees of impacts from the tested variables. Human footprint and soil variability had the highest tendency to increase the potential distribution of IPS in Montane Grasslands and Shrublands. We propose to integrate the assessment in impacts of human footprint and soil variability on the potential distribution of IPS in different biomes into the prevention and control of plant invasion.

  8. Finite element analysis to investigate variability of MR elastography in the human thigh.

    Science.gov (United States)

    Hollis, L; Barnhill, E; Perrins, M; Kennedy, P; Conlisk, N; Brown, C; Hoskins, P R; Pankaj, P; Roberts, N

    2017-11-01

    To develop finite element analysis (FEA) of magnetic resonance elastography (MRE) in the human thigh and investigate inter-individual variability of measurement of muscle mechanical properties. Segmentation was performed on MRI datasets of the human thigh from 5 individuals and FEA models consisting of 12 muscles and surrounding tissue created. The same material properties were applied to each tissue type and a previously developed transient FEA method of simulating MRE using Abaqus was performed at 4 frequencies. Synthetic noise was applied to the simulated data at various levels before inversion was performed using the Elastography Software Pipeline. Maps of material properties were created and visually assessed to determine key features. The coefficient of variation (CoV) was used to assess the variability of measurements in each individual muscle and in the groups of muscles across the subjects. Mean measurements for the set of muscles were ranked in size order and compared with the expected ranking. At noise levels of 2% the CoV in measurements of |G * | ranged from 5.3 to 21.9% and from 7.1 to 36.1% for measurements of ϕ in the individual muscles. A positive correlation (R 2 value 0.80) was attained when the expected and measured |G * | ranking were compared, whilst a negative correlation (R 2 value 0.43) was found for ϕ. Created elastograms demonstrated good definition of muscle structure and were robust to noise. Variability of measurements across the 5 subjects was dramatically lower for |G * | than it was for ϕ. This large variability in ϕ measurements was attributed to artefacts. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. The FLP microsatellite platform flight operations manual

    CERN Document Server

    2016-01-01

    This book represents the Flight Operations Manual for a reusable microsatellite platform – the “Future Low-cost Platform” (FLP), developed at the University of Stuttgart, Germany. It provides a basic insight on the onboard software functions, the core data handling system and on the power, communications, attitude control and thermal subsystem of the platform. Onboard failure detection, isolation and recovery functions are treated in detail. The platform is suited for satellites in the 50-150 kg class and is baseline of the microsatellite “Flying Laptop” from the University. The book covers the essential information for ground operators to controls an FLP-based satellite applying international command and control standards (CCSDS and ECSS PUS). Furthermore it provides an overview on the Flight Control Center in Stuttgart and on the link to the German Space Agency DLR Ground Station which is used for early mission phases. Flight procedure and mission planning chapters complement the book. .

  10. A standardized approach to study human variability in isometric thermogenesis during low-intensity physical activity

    Directory of Open Access Journals (Sweden)

    Delphine eSarafian

    2013-07-01

    Full Text Available Limitations of current methods: The assessment of human variability in various compartments of daily energy expenditure (EE under standardized conditions is well defined at rest (as basal metabolic rate and thermic effect of feeding, and currently under validation for assessing the energy cost of low-intensity dynamic work. However, because physical activities of daily life consist of a combination of both dynamic and isometric work, there is also a need to develop standardized tests for assessing human variability in the energy cost of low-intensity isometric work.Experimental objectives: Development of an approach to study human variability in isometric thermogenesis by incorporating a protocol of intermittent leg press exercise of varying low-intensity isometric loads with measurements of EE by indirect calorimetry. Results: EE was measured in the seated position with the subject at rest or while intermittently pressing both legs against a press-platform at 5 low-intensity isometric loads (+5, +10, + 15, +20 and +25 kg force, each consisting of a succession of 8 cycles of press (30 s and rest (30 s. EE, integrated over each 8-min period of the intermittent leg press exercise, was found to increase linearly across the 5 isometric loads with a correlation coefficient (r > 0.9 for each individual. The slope of this EE-Load relationship, which provides the energy cost of this standardized isometric exercise expressed per kg force applied intermittently (30 s in every min, was found to show good repeatability when assessed in subjects who repeated the same experimental protocol on 3 separate days: its low intra-individual coefficient of variation (CV of ~ 10% contrasted with its much higher inter-individual CV of 35%; the latter being mass-independent but partly explained by height. Conclusion: This standardized approach to study isometric thermogenesis opens up a new avenue for research in EE phenotyping and metabolic predisposition to obesity

  11. Effects of supine, prone, and lateral positions on cardiovascular and renal variables in humans

    DEFF Research Database (Denmark)

    Pump, Bettina; Talleruphuus, Ulrik; Christensen, Niels Juel

    2002-01-01

    The hypothesis was tested that changing the direction of the transverse gravitational stress in horizontal humans modulates cardiovascular and renal variables. On different study days, 14 healthy males were placed for 6 h in either the horizontal supine or prone position following 3 h of being...... supine. Eight of the subjects were in addition investigated in the horizontal left lateral position. Compared with supine, the prone position slightly increased free water clearance (349 +/- 38 vs. 447 +/- 39 ml/6 h, P = 0.05) and urine output (1,387 +/- 55 vs. 1,533 +/- 52 ml/6 h, P = 0...

  12. 2 D gel based analysis of biological variability of the human plasma proteome

    DEFF Research Database (Denmark)

    Rentsch, Maria Louise; Jessen, Flemming

    individuals and within an individual changes will also happen over time (e.g. after meal intake). Thus, the aim of the present study was to examine the inter-individual variability of plasma protein levels in humans after meal intake. Five subjects consumed three single meals in a randomised order separated...... by one-week interval. Blood samples were drawn before the meal intake and five times during 24 hours for proteome analysis. Plasma was fractionated by use of IgY-12 spin column depleting the 12 highly abundant proteins and further processed for two-dimensional gel electrophoresis. The plasma proteome...

  13. MYRIADE: CNES Micro-Satellite Program

    OpenAIRE

    Thoby, Michel

    2001-01-01

    CNES is currently leading the development of a program of micro-satellites, which has been now blessed with a name in line with the ambition: MYRIADE. The intention is to primarily fulfill the needs of the national scientific research in small space missions. Technology experiments as well as demonstration flights for new mission concepts shall however not be forgotten. The main objective is to make access to space much easier and affordable. The first five scientific and technological mixed ...

  14. An Inclusive Design Method for Addressing Human Variability and Work Performance Issues

    Directory of Open Access Journals (Sweden)

    Amjad Hussain

    2013-07-01

    Full Text Available Humans play vital roles in manufacturing systems, but work performance is strongly influenced by factors such as experience, age, level of skill, physical and cognitive abilities and attitude towards work. Current manufacturing system design processes need to consider these human variability issues and their impact on work performance. An ‘inclusive design’ approach is proposed to consider the increasing diversity of the global workforce in terms of age, gender, cultural background, skill and experience. The decline in physical capabilities of older workers creates a mismatch between job demands and working capabilities which can be seen in manufacturing assembly that typically requires high physical demands for repetitive and accurate motions. The inclusive design approach leads to a reduction of this mismatch that results in a more productive, safe and healthy working environment giving benefits to the organization and individuals in terms of workforce satisfaction, reduced turnover, higher productivity and improved product quality.

  15. Microsatellites in varied arenas of research

    Directory of Open Access Journals (Sweden)

    K S Remya

    2010-01-01

    Full Text Available Microsatellites known as simple-sequence repeats (SSRs or short-tandem repeats (STRs, represent specific sequences of DNA consisting of tandemly repeated units of one to six nucleotides. The repetitive nature of microsatellites makes them particularly prone to grow or shrink in length and these changes can have both good and bad consequences for the organisms that possess them. They are responsible for various neurological diseases and hence the same cause is now utilized for the early detection of various diseases, such as, Schizophrenia and Bipolar Disorder, Congenital generalized Hypertrichosis, Asthma, and Bronchial Hyperresponsiveness. These agents are widely used for forensic identification and relatedness testing, and are predominant genetic markers in this area of application. The application of microsatellites is an extending web and covers the varied scenarios of science, such as, conservation biology, plant genetics, and population studies. At present, researches are progressing round the globe to extend the use of these genetic repeaters to unmask the hidden genetic secrets behind the creation of the world.

  16. Genetic diversity analysis in the section Caulorrhizae (genus Arachis using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Darío A. Palmieri

    2010-01-01

    Full Text Available Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  17. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers.

    Science.gov (United States)

    Palmieri, Darío A; Bechara, Marcelo D; Curi, Rogério A; Monteiro, Jomar P; Valente, Sérgio E S; Gimenes, Marcos A; Lopes, Catalina R

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  18. Microsatellite Polymorphisms Adjacent to the Oxytocin Receptor Gene in Domestic Cats: Association with Personality?

    Directory of Open Access Journals (Sweden)

    Minori Arahori

    2017-12-01

    Full Text Available A growing number of studies have explored the oxytocin system in humans and non-human animals, and some have found important genetic polymorphisms in the oxytocin receptor gene (OXTR associated with the bonding system, social behaviors, and personality in several species. Although single nucleotide polymorphisms in OXTR have been well-examined in various species, microsatellites (or short tandem repeats adjacent to OXTR have rarely been studied, despite some suggestions that microsatellite polymorphisms near genes might play a role in genetic transcription and translation. In this study, we surveyed microsatellites in the upstream, intron, and downstream regions of OXTR in domestic cats (Felis catus. We succeeded in amplifying 5 out of 10 regions, and recognized these five regions as polymorphic. We compared allele frequencies in these five regions between mongrel cats in Japan (n = 100 and cats of 10 pure breeds (n = 40. There were significant differences in allele frequencies between the two populations in all microsatellite regions. Additionally, the owners of mongrel cats answered a comprehensive personality questionnaire, and factor analysis extracted four factors (Openness, Friendliness, Roughness, and Neuroticism. We examined the association between the microsatellite genotypes, age, sex, neutering status, and personality scores. Compared to their counterparts, younger cats tended to score higher on Openness, male cats scored higher on Friendliness, and female and neutered cats scored higher on Roughness. When we divided the sample into three groups depending on the length of alleles, we found a marginally significant association between Friendliness and MS3. Additionally, we found a sex-mediated effect of genotypes in MS4 on Friendliness, resulting in different effects on females and males. Our findings that mongrel cats had longer alleles in MS3 and MS4 than purebred cats, and that those cats tended to score higher on Friendliness

  19. The Genetic Relationship between Leishmania aethiopica and Leishmania tropica Revealed by Comparing Microsatellite Profiles.

    Science.gov (United States)

    Krayter, Lena; Schnur, Lionel F; Schönian, Gabriele

    2015-01-01

    Leishmania (Leishmania) aethiopica and L. (L.) tropica cause cutaneous leishmaniases and appear to be related. L. aethiopica is geographically restricted to Ethiopia and Kenya; L. tropica is widely dispersed from the Eastern Mediterranean, through the Middle East into eastern India and in north, east and south Africa. Their phylogenetic inter-relationship is only partially revealed. Some studies indicate a close relationship. Here, eight strains of L. aethiopica were characterized genetically and compared with 156 strains of L. tropica from most of the latter species' geographical range to discern the closeness. Twelve unlinked microsatellite markers previously used to genotype strains of L. tropica were successfully applied to the eight strains of L. aethiopica and their microsatellite profiles were compared to those of 156 strains of L. tropica from various geographical locations that were isolated from human cases of cutaneous and visceral leishmaniasis, hyraxes and sand fly vectors. All the microsatellite profiles were subjected to various analytical algorithms: Bayesian statistics, distance-based and factorial correspondence analysis, revealing: (i) the species L. aethiopica, though geographically restricted, is genetically very heterogeneous; (ii) the strains of L. aethiopica formed a distinct genetic cluster; and (iii) strains of L. aethiopica are closely related to strains of L. tropica and more so to the African ones, although, by factorial correspondence analysis, clearly separate from them. The successful application of the 12 microsatellite markers, originally considered species-specific for the species L. tropica, to strains of L. aethiopica confirmed the close relationship between these two species. The Bayesian and distance-based methods clustered the strains of L. aethiopica among African strains of L. tropica, while the factorial correspondence analysis indicated a clear separation between the two species. There was no correlation between

  20. Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

    Science.gov (United States)

    King, Timothy L.; Eackles, Michael S.; Reshetnikov, Andrey N.

    2015-01-01

    Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated

  1. Isolation and Characterization of Microsatellite Markers in Beilschmiedia roxburghiana (Lauraceae

    Directory of Open Access Journals (Sweden)

    Lu Liu

    2013-07-01

    Full Text Available Premise of the study: Although there are as many as 250 species in the genus Beilschmiedia, their genetic diversity has been poorly investigated. Our objective was to develop microsatellite markers for B. roxburghiana to study its genetic diversity for the sustainable management of this species. Methods and Results: Using the microsatellite-enriched library and PCR-based screening method, 22 microsatellite markers were developed and 10 showed high polymorphism in a population. The number of alleles per locus for these 10 microsatellites ranged from five to 19. The observed and expected heterozygosities ranged from 0.298 to 1.000 and from 0.314 to 0.878, respectively. Conclusions: Our results from the 10 highly polymorphic microsatellites indicate that the principal reproductive mode of B. roxburghiana is clonal in the studied population. These microsatellites will facilitate further studies on genetic diversity and structure in B. roxburghiana.

  2. Toward Microsatellite Based Space Situational Awareness

    Science.gov (United States)

    Scott, L.; Wallace, B.; Sale, M.; Thorsteinson, S.

    2013-09-01

    The NEOSSat microsatellite is a dual mission space telescope which will perform asteroid detection and Space Situational Awareness (SSA) observation experiments on deep space, earth orbiting objects. NEOSSat was launched on 25 February 2013 into a 800 dawn-dusk sun synchronous orbit and is currently undergoing satellite commissioning. The microsatellite consists of a small aperture optical telescope, GPS receiver, high performance attitude control system, and stray light rejection baffle designed to reject stray light from the Sun while searching for asteroids with elongations 45 degrees along the ecliptic. The SSA experimental mission, referred to as HEOSS (High Earth Orbit Space Surveillance), will focus on objects in deep space orbits. The HEOSS mission objective is to evaluate the utility of microsatellites to perform catalog maintenance observations of resident space objects in a manner consistent with the needs of the Canadian Forces. The advantages of placing a space surveillance sensor in low Earth orbit are that the observer can conduct observations without the day-night interruption cycle experienced by ground based telescopes, the telescope is insensitive to adverse weather and the system has visibility to deep space resident space objects which are not normally visible from ground based sensors. Also, from a photometric standpoint, the microsatellite is able to conduct observations on objects with a rapidly changing observer position. The possibility of spin axis estimation on geostationary satellites may be possible and an experiment characterize spin axis of distant resident space objects is being planned. Also, HEOSS offers the ability to conduct observations of satellites at high phase angles which can potentially extend the trackable portion of space in which deep space objects' orbits can be monitored. In this paper we describe the HEOSS SSA experimental data processing system and the preliminary findings of the catalog maintenance experiments

  3. Identification and characterization of microsatellites from calafate (Berberis microphylla, Berberidaceae).

    Science.gov (United States)

    Varas, Benjamín; Castro, María H; Rodriguez, Roberto; von Baer, Dietrich; Mardones, Claudia; Hinrichsen, Patricio

    2013-07-01

    Southern barberry or calafate (Berberis microphylla) is a shrub species endemic to the Patagonian region of South America that is used for human consumption. The fruit is very rich in vitamin C and anthocyanins and has a very high antioxidant capacity. There have been only a few genetic studies of this and other closely related species. • Here we present the first 18 microsatellite markers of B. microphylla that were characterized using 66 accessions of calafate from Patagonia. On average, they had 7.6 alleles per marker, with an expected heterozygosity of 0.688. The informativeness of these markers was also evaluated in another 15 Berberis species, including most of the native and endemic Chilean species. • The results confirm that these new simple sequence repeat markers are very polymorphic and potentially useful in genetic studies in any species of the genus Berberis.

  4. Identification and Characterization of Microsatellites from Calafate (Berberis microphylla, Berberidaceae

    Directory of Open Access Journals (Sweden)

    Benjamín Varas

    2013-07-01

    Full Text Available Premise of the study: Southern barberry or calafate (Berberis microphylla is a shrub species endemic to the Patagonian region of South America that is used for human consumption. The fruit is very rich in vitamin C and anthocyanins and has a very high antioxidant capacity. There have been only a few genetic studies of this and other closely related species. Methods and Results: Here we present the first 18 microsatellite markers of B. microphylla that were characterized using 66 accessions of calafate from Patagonia. On average, they had 7.6 alleles per marker, with an expected heterozygosity of 0.688. The informativeness of these markers was also evaluated in another 15 Berberis species, including most of the native and endemic Chilean species. Conclusions: The results confirm that these new simple sequence repeat markers are very polymorphic and potentially useful in genetic studies in any species of the genus Berberis.

  5. Imprecision in estimates of dose from ingested 137Cs due to variability in human biological characteristics

    International Nuclear Information System (INIS)

    Schwarz, G.; Dunning, D.E. Jr.

    1982-01-01

    An attempt has been made to quantify the variability in human biological parameters determining dose to man from ingestion of a unit activity of soluble 137 Cs and the resulting imprecision in the predicted total-body dose commitment. The analysis is based on an extensive review of the literature along with the application of statistical methods to determine parameter variability, correlations between parameters, and predictive imprecision. The variability in the principal biological parameters (biological half-time and total-body mass) involved can be described by a geometric standard deviation of 1.2-1.5 for adults and 1.6-1.9 for children/ adolescents of age 0.1-18 yr. The estimated predictive imprecision (using a Monte Carlo technique) in the total-body dose commitment from ingested 137 Cs can be described by a geometric standard deviation on the order of 1.3-1.4, meaning that the 99th percentile of the predicted distribution of dose is within approximately 2.1 times the mean value. The mean dose estimate is 0.009 Sv/MBq (34 mrem/μ Ci) for children/adolescents and 0.01 Sv/MBq (38 mrem/μ Ci) for adults. Little evidence of age dependence in the total-body dose from ingested 137 Cs is observed. (author)

  6. Cloning and characterization of 29 tetranucleotide and two dinucleotide polymorphic microsatellite loci from the endangered marbled murrelet (Brachyramphus marmoratus)

    NARCIS (Netherlands)

    Rew, MB; Peery, MZ; Beissinger, Steven R.; Berube, M; Lozier, JD; Rubidge, EM; Palsboll, PJ

    We developed 31 novel, polymorphic microsatellite loci in the marbled murrelet (Brachyramphus marmoratus), a critically endangered seabird. Variability was tested on 15 individuals from the Santa Cruz, California population, with each locus characterized by two to 12 alleles. Observed levels of

  7. Contouring variability of human- and deformable-generated contours in radiotherapy for prostate cancer

    International Nuclear Information System (INIS)

    Gardner, Stephen J; Wen, Ning; Kim, Jinkoo; Liu, Chang; Pradhan, Deepak; Aref, Ibrahim; Cattaneo, Richard II; Vance, Sean; Movsas, Benjamin; Chetty, Indrin J; Elshaikh, Mohamed A

    2015-01-01

    This study was designed to evaluate contouring variability of human-and deformable-generated contours on planning CT (PCT) and CBCT for ten patients with low-or intermediate-risk prostate cancer. For each patient in this study, five radiation oncologists contoured the prostate, bladder, and rectum, on one PCT dataset and five CBCT datasets. Consensus contours were generated using the STAPLE method in the CERR software package. Observer contours were compared to consensus contour, and contour metrics (Dice coefficient, Hausdorff distance, Contour Distance, Center-of-Mass [COM] Deviation) were calculated. In addition, the first day CBCT was registered to subsequent CBCT fractions (CBCTn: CBCT2–CBCT5) via B-spline Deformable Image Registration (DIR). Contours were transferred from CBCT1 to CBCTn via the deformation field, and contour metrics were calculated through comparison with consensus contours generated from human contour set. The average contour metrics for prostate contours on PCT and CBCT were as follows: Dice coefficient—0.892 (PCT), 0.872 (CBCT-Human), 0.824 (CBCT-Deformed); Hausdorff distance—4.75 mm (PCT), 5.22 mm (CBCT-Human), 5.94 mm (CBCT-Deformed); Contour Distance (overall contour)—1.41 mm (PCT), 1.66 mm (CBCT-Human), 2.30 mm (CBCT-Deformed); COM Deviation—2.01 mm (PCT), 2.78 mm (CBCT-Human), 3.45 mm (CBCT-Deformed). For human contours on PCT and CBCT, the difference in average Dice coefficient between PCT and CBCT (approx. 2%) and Hausdorff distance (approx. 0.5 mm) was small compared to the variation between observers for each patient (standard deviation in Dice coefficient of 5% and Hausdorff distance of 2.0 mm). However, additional contouring variation was found for the deformable-generated contours (approximately 5.0% decrease in Dice coefficient and 0.7 mm increase in Hausdorff distance relative to human-generated contours on CBCT). Though deformable contours provide a reasonable starting point for contouring

  8. Statistical Learning and Adaptive Decision-Making Underlie Human Response Time Variability in Inhibitory Control

    Directory of Open Access Journals (Sweden)

    Ning eMa

    2015-08-01

    Full Text Available Response time (RT is an oft-reported behavioral measure in psychological and neurocognitive experiments, but the high level of observed trial-to-trial variability in this measure has often limited its usefulness. Here, we combine computational modeling and psychophysics to examine the hypothesis that fluctuations in this noisy measure reflect dynamic computations in human statistical learning and corresponding cognitive adjustments. We present data from the stop-signal task, in which subjects respond to a go stimulus on each trial, unless instructed not to by a subsequent, infrequently presented stop signal. We model across-trial learning of stop signal frequency, P(stop, and stop-signal onset time, SSD (stop-signal delay, with a Bayesian hidden Markov model, and within-trial decision-making with an optimal stochastic control model. The combined model predicts that RT should increase with both expected P(stop and SSD. The human behavioral data (n=20 bear out this prediction, showing P(stop and SSD both to be significant, independent predictors of RT, with P(stop being a more prominent predictor in 75% of the subjects, and SSD being more prominent in the remaining 25%. The results demonstrate that humans indeed readily internalize environmental statistics and adjust their cognitive/behavioral strategy accordingly, and that subtle patterns in RT variability can serve as a valuable tool for validating models of statistical learning and decision-making. More broadly, the modeling tools presented in this work can be generalized to a large body of behavioral paradigms, in order to extract insights about cognitive and neural processing from apparently quite noisy behavioral measures. We also discuss how this behaviorally validated model can then be used to conduct model-based analysis of neural data, in order to help identify specific brain areas for representing and encoding key computational quantities in learning and decision-making.

  9. Human platelet lysate supplementation of mesenchymal stromal cell delivery: issues of xenogenicity and species variability.

    Science.gov (United States)

    Allen, Ashley B; Butts, Emily B; Copland, Ian B; Stevens, Hazel Y; Guldberg, Robert E

    2017-10-01

    Immunogenicity of fetal bovine serum (FBS) poses a problem for its use in the propagation of autologous mesenchymal stromal cells (MSCs) for cell therapy. Human platelet lysate (hPL), an enriched growth factor solution containing mitogenic and angiogenic cues, has potential utility in replacing FBS for human MSC (hMSC) delivery strategies. Despite its potentiation of hMSC number in vitro, little is known concerning its capacity to supplement implanted hMSC-seeded constructs and promote tissue regeneration in vivo. In this study, we tested the effects of incorporating hPL in cell-seeded constructs implanted subcutaneously into immunocompromised rats, investigated in vitro interactions between hPL and rat MSCs (rMSCs) and determined interspecies variability in the PL product [hPL vs rat PL (rPL)] and its effect on cultured MSCs (hPL/hMSCs vs rPL/rMSCs). The overarching aim was to determine the utility of hPL to foster MSC survival in preclinical rodent models. Exposure to hPL-supplemented media resulted in rMSC death, by a process attributable to heat-labile proteins, but not membrane attack complex formation. In the in vitro syngeneic model, the rodent product proved fundamentally distinct from the human product, with rPL having substantially lower growth factor content than hPL. Moreover, contrary to the positive effects of hPL on hMSC expansion, rPL did not reduce rMSC doubling time for the serum concentrations examined. When tested in vivo, hPL did not improve cell survival within hydrogel constructs through 2 weeks postimplantation. In summary, this study highlights the many facets of xenogenicity and interspecies variability that must be considered in the preclinical evaluation of hPL. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  10. Statistical learning and adaptive decision-making underlie human response time variability in inhibitory control.

    Science.gov (United States)

    Ma, Ning; Yu, Angela J

    2015-01-01

    Response time (RT) is an oft-reported behavioral measure in psychological and neurocognitive experiments, but the high level of observed trial-to-trial variability in this measure has often limited its usefulness. Here, we combine computational modeling and psychophysics to examine the hypothesis that fluctuations in this noisy measure reflect dynamic computations in human statistical learning and corresponding cognitive adjustments. We present data from the stop-signal task (SST), in which subjects respond to a go stimulus on each trial, unless instructed not to by a subsequent, infrequently presented stop signal. We model across-trial learning of stop signal frequency, P(stop), and stop-signal onset time, SSD (stop-signal delay), with a Bayesian hidden Markov model, and within-trial decision-making with an optimal stochastic control model. The combined model predicts that RT should increase with both expected P(stop) and SSD. The human behavioral data (n = 20) bear out this prediction, showing P(stop) and SSD both to be significant, independent predictors of RT, with P(stop) being a more prominent predictor in 75% of the subjects, and SSD being more prominent in the remaining 25%. The results demonstrate that humans indeed readily internalize environmental statistics and adjust their cognitive/behavioral strategy accordingly, and that subtle patterns in RT variability can serve as a valuable tool for validating models of statistical learning and decision-making. More broadly, the modeling tools presented in this work can be generalized to a large body of behavioral paradigms, in order to extract insights about cognitive and neural processing from apparently quite noisy behavioral measures. We also discuss how this behaviorally validated model can then be used to conduct model-based analysis of neural data, in order to help identify specific brain areas for representing and encoding key computational quantities in learning and decision-making.

  11. The postglacial recolonization of Northern Europe by Rana arvalis as revealed by microsatellite and mitochondrial DNA analyses.

    Science.gov (United States)

    Knopp, T; Merilä, J

    2009-02-01

    The postglacial history of the moor frog (Rana arvalis) in Northern Europe was investigated with the aid of eight variable microsatellite loci and a 661 bp sequence of the mitochondrial cytochrome b gene. A division between eastern and western mitochondrial lineages was discovered, supporting two recolonization routes to Fennoscandia since the last glacial maximum. This result was corroborated by the microsatellite data, which revealed a contact zone between the two lineages in Northern Sweden. These findings add to the increasing evidence that an intraspecific genetic biodiversity founded on the existence of eastern and western clades is a common element in Fennoscandian fauna and flora.

  12. Characterization of small microsatellite loci isolated in endangered Indiana bat (Myotis sodalis) for use in non-invasive sampling

    Science.gov (United States)

    Oyler-McCance, Sara J.; Fike, Jennifer A.

    2011-01-01

    Primers for 10 microsatellite loci were developed specifically to amplify low quantity and quality DNA in the endangered Indiana Bat (Myotis sodalis). In a screen of 20 individuals from a population in Missouri, the 10 loci were found to have levels of variability ranging from seven to 18 alleles. No loci were found to be linked, although two loci revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci will be applicable for population genetic analyses and for use in mark-recapture studies that utilize DNA collected non-invasively from fecal pellets, which will ultimately aid in management efforts.

  13. Early variability in the conceptualisation of "sustainable development and human factors".

    Science.gov (United States)

    Thatcher, Andrew

    2012-01-01

    The sub-discipline of "sustainable development and human factors" is relatively new, first being used in 2006 with a Technical Committee of the IEA being established only in 2009 and a similar special interest group on "green ergonomics" at the Institute of Ergonomics and Human Factors being established in 2010. In general though, the definitions and practice of "sustainable development" is highly contentious and ambiguous across a range of disciplines. This paper examines the diversity of definitions and approaches to sustainable development and human factors in the early papers in this sub-discipline. An examination of 45 chapters and papers (from 2008 to 2011) reveals a surprising consistency in the definitions used for sustainable development but also a large proportion of the papers where no definitions are given at all. The majority of papers were, however, biased towards an economic capital and social capital emphasis, which is to be expected of work traditionally in the ergonomics paradigm. Further, most papers were theoretical in nature demonstrating a great opportunity for empirical work. The variability in definitions is discussed in relation to the future challenges facing the growth of this emergent sub-discipline and opportunities for further theoretical and empirical work.

  14. THE SEAFARERS’ HUMAN CAPITAL VARIABLES AND THE CREW PROFILE DYNAMIC ADJUSTMENT

    Directory of Open Access Journals (Sweden)

    Catalin POPA

    2016-06-01

    Full Text Available The human capital is one of the most relevant functional dimensions of the maritime transportation business, considering the seaborne particularities in the crossing countries, cultures and heterogeneous environment as onboard the maritime vessels. The nowadays great competitiveness in this area of transportation services has encouraged many companies to pursue new ways to maintain a competitive advantage, valuing its human capital. Thus, in spite of the propensity for standardisation in field of human resources profile, the seafaring crews’ management is still facing lots of issues in operational tasks’ fulfilment onboard to maritime ships, due to individual misalignment within the collective framework of the on-board teams. As is presented in the article, the individual profile of a seafarer has to be precisely defined to be efficiently integrated in the crew, but not only in professional matters, but also into a comprehensive manner, in order to support a proper adjustment of the individual seafarer behaviour to the group profile requirement, onboard to maritime vessels. STCW provisions are very welcomed in establishing common standards for professional variable of the seafarers’ individual profile, but is still missing to approach the organizational dimensions, apart to the leadership skills or risk behaviour. As shown in the article below, for a recruitment agent and further, for the ship Master is important to find the suitable employee, not only in terms of professional knowledge, skills and abilities, but also in cultural or psycho-sociological individual dimensions, as to adjust the individual to the group profile, accordingly and effectively.

  15. Analysing inter-relationships among water, governance, human development variables in developing countries

    Science.gov (United States)

    Dondeynaz, C.; Carmona Moreno, C.; Céspedes Lorente, J. J.

    2012-10-01

    The "Integrated Water Resources Management" principle was formally laid down at the International Conference on Water and Sustainable development in Dublin 1992. One of the main results of this conference is that improving Water and Sanitation Services (WSS), being a complex and interdisciplinary issue, passes through collaboration and coordination of different sectors (environment, health, economic activities, governance, and international cooperation). These sectors influence or are influenced by the access to WSS. The understanding of these interrelations appears as crucial for decision makers in the water sector. In this framework, the Joint Research Centre (JRC) of the European Commission (EC) has developed a new database (WatSan4Dev database) containing 42 indicators (called variables in this paper) from environmental, socio-economic, governance and financial aid flows data in developing countries. This paper describes the development of the WatSan4Dev dataset, the statistical processes needed to improve the data quality, and finally, the analysis to verify the database coherence is presented. Based on 25 relevant variables, the relationships between variables are described and organised into five factors (HDP - Human Development against Poverty, AP - Human Activity Pressure on water resources, WR - Water Resources, ODA - Official Development Aid, CEC - Country Environmental Concern). Linear regression methods are used to identify key variables having influence on water supply and sanitation. First analysis indicates that the informal urbanisation development is an important factor negatively influencing the percentage of the population having access to WSS. Health, and in particular children's health, benefits from the improvement of WSS. Irrigation is also enhancing Water Supply service thanks to multi-purpose infrastructure. Five country profiles are also created to deeper understand and synthetize the amount of information gathered. This new

  16. Analysing inter-relationships among water, governance, human development variables in developing countries

    Directory of Open Access Journals (Sweden)

    C. Dondeynaz

    2012-10-01

    Full Text Available The "Integrated Water Resources Management" principle was formally laid down at the International Conference on Water and Sustainable development in Dublin 1992. One of the main results of this conference is that improving Water and Sanitation Services (WSS, being a complex and interdisciplinary issue, passes through collaboration and coordination of different sectors (environment, health, economic activities, governance, and international cooperation. These sectors influence or are influenced by the access to WSS. The understanding of these interrelations appears as crucial for decision makers in the water sector. In this framework, the Joint Research Centre (JRC of the European Commission (EC has developed a new database (WatSan4Dev database containing 42 indicators (called variables in this paper from environmental, socio-economic, governance and financial aid flows data in developing countries. This paper describes the development of the WatSan4Dev dataset, the statistical processes needed to improve the data quality, and finally, the analysis to verify the database coherence is presented. Based on 25 relevant variables, the relationships between variables are described and organised into five factors (HDP – Human Development against Poverty, AP – Human Activity Pressure on water resources, WR – Water Resources, ODA – Official Development Aid, CEC – Country Environmental Concern. Linear regression methods are used to identify key variables having influence on water supply and sanitation. First analysis indicates that the informal urbanisation development is an important factor negatively influencing the percentage of the population having access to WSS. Health, and in particular children's health, benefits from the improvement of WSS. Irrigation is also enhancing Water Supply service thanks to multi-purpose infrastructure. Five country profiles are also created to deeper understand and synthetize the amount of information gathered

  17. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758

    Directory of Open Access Journals (Sweden)

    Christine Ewers-Saucedo

    2016-05-01

    Full Text Available Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758. Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria.

  18. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

    Science.gov (United States)

    Zardus, John D.; Wares, John P.

    2016-01-01

    Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria. PMID:27231653

  19. In Silico Mining of Microsatellites in Coding Sequences of the Date Palm (Arecaceae Genome, Characterization, and Transferability

    Directory of Open Access Journals (Sweden)

    Frédérique Aberlenc-Bertossi

    2014-01-01

    Full Text Available Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

  20. Functionality of promoter microsatellites of arginine vasopressin receptor 1A (AVPR1A): implications for autism

    LENUS (Irish Health Repository)

    Tansey, Katherine E

    2011-03-31

    Abstract Background Arginine vasopressin (AVP) has been hypothesized to play a role in aetiology of autism based on a demonstrated involvement in the regulation of social behaviours. The arginine vasopressin receptor 1A gene (AVPR1A) is widely expressed in the brain and is considered to be a key receptor for regulation of social behaviour. Moreover, genetic variation at AVPR1A has been reported to be associated with autism. Evidence from non-human mammals implicates variation in the 5\\'-flanking region of AVPR1A in variable gene expression and social behaviour. Methods We examined four tagging single nucleotide polymorphisms (SNPs) (rs3803107, rs1042615, rs3741865, rs11174815) and three microsatellites (RS3, RS1 and AVR) at the AVPR1A gene for association in an autism cohort from Ireland. Two 5\\'-flanking region polymorphisms in the human AVPR1A, RS3 and RS1, were also tested for their effect on relative promoter activity. Results The short alleles of RS1 and the SNP rs11174815 show weak association with autism in the Irish population (P = 0.036 and P = 0.008, respectively). Both RS1 and RS3 showed differences in relative promoter activity by length. Shorter repeat alleles of RS1 and RS3 decreased relative promoter activity in the human neuroblastoma cell line SH-SY5Y. Conclusions These aligning results can be interpreted as a functional route for this association, namely that shorter alleles of RS1 lead to decreased AVPR1A transcription, which may proffer increased susceptibility to the autism phenotype.

  1. Variability in anatomical features of human clavicle: Its forensic anthropological and clinical significance

    Directory of Open Access Journals (Sweden)

    Jagmahender Singh Sehrawat

    2016-06-01

    Full Text Available Bones can reflect the basic framework of human body and may provide valuable information about the biological identity of the deceased. They, often, survive the morphological alterations, taphonomic destructions, decay/mutilation and decomposition insults. In-depth knowledge of variations in clavicular shape, size and its dimensions is very important from both clinical (fixation of clavicular fractures using external or inter-medullary devices, designing orthopedic fixation devices as well as forensic anthropological perspectives. Human clavicle is the most frequently fractured bone of human skeleton, possessing high degree of variability in its anatomical, biomechanical and morphological features. Extended period of skeletal growth (up to third decade in clavicle imparts it an additional advantage for forensic identification purposes. In present study, five categories of clavicular features like lengths, diameters, angles, indices and robustness were examined to explore the suitability of collarbone for forensic and clinical purposes. For this purpose, 263 pairs of adult clavicles (195 Males and 68 Females were collected from autopsied cadavers and were studied for 13 anatomical features. Gender and occupational affiliations of cadavers were found to have significant influences on anatomical dimensions of their clavicles. Product index, weight and circumference of collarbone were found the best univariate variables, discriminating sex of more than 80% individuals. The best multivariate Function-I (DF: -17.315 + 0.054 CL-L+0.196 CC-R+0.184 DM-L could identify sex and occupation of 89.4% (89.2% Male and 89.7% Female and 65.4% individuals, respectively. All clavicular variables were found bilaterally asymmetric; left clavicles being significantly longer in length, lighter in weight, smooth in texture and less curved than the right side bones. Among non-metric traits, sub-clavian groove, nutrient foramina and ‘type’ of clavicle exhibited

  2. Genetic characterization of the Bardigiano horse using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Claudio Lisa

    2010-01-01

    Full Text Available The study was aimed at investigating the genetic structure of the Bardigiano horse and its relationships with the Haflinger, Maremmano and Arabian breeds using 11 microsatellite markers. A total of 94 alleles were detected across the breeds, with a mean of 8.5 alleles per locus and a mean observed heterozygosity of 0.69. Compared to the other breeds, the Bardigiano horse showed quite a high genetic variability, as indicated by the mean number of alleles (7.0 vs 6.1÷7.6 and by the observed heterozygosity (0.72 vs 0.66÷0.71. Moreover, the genotype distributions in the Bardigiano groups of different sex and age were not significantly different. The overall FST value showed that the genetic differences among breeds accounted for 7.8% (P=0.001 of the total variation, and the pairwise FST values were all significant. The assignment test allocated between 96.8 and 98.9% of the individuals to the population they were collected from, with a mean probability of assignment of about 97% for all breeds, except for the Arabian, where it approached 100%. The results have highlighted that the Bardigiano breed has a high within and between breed variability, which is considerably more than could be expected by looking at its evolution history. This justifies the need for the development of additional breeding strategies to preserve the existing genetic variability.

  3. Multilocus microsatellite typing (MLMT of strains from Turkey and Cyprus reveals a novel monophyletic L. donovani sensu lato group.

    Directory of Open Access Journals (Sweden)

    Evi Gouzelou

    Full Text Available BACKGROUND: New foci of human CL caused by strains of the Leishmania donovani (L. donovani complex have been recently described in Cyprus and the Çukurova region in Turkey (L. infantum situated 150 km north of Cyprus. Cypriot strains were typed by Multilocus Enzyme Electrophoresis (MLEE using the Montpellier (MON system as L. donovani zymodeme MON-37. However, multilocus microsatellite typing (MLMT has shown that this zymodeme is paraphyletic; composed of distantly related genetic subgroups of different geographical origin. Consequently the origin of the Cypriot strains remained enigmatic. METHODOLOGY/PRINCIPAL FINDINGS: The Cypriot strains were compared with a set of Turkish isolates obtained from a CL patient and sand fly vectors in south-east Turkey (Çukurova region; CUK strains and from a VL patient in the south-west (Kuşadasi; EP59 strain. These Turkish strains were initially analyzed using the K26-PCR assay that discriminates MON-1 strains by their amplicon size. In line with previous DNA-based data, the strains were inferred to the L. donovani complex and characterized as non MON-1. For these strains MLEE typing revealed two novel zymodemes; L. donovani MON-309 (CUK strains and MON-308 (EP59. A population genetic analysis of the Turkish isolates was performed using 14 hyper-variable microsatellite loci. The genotypic profiles of 68 previously analyzed L. donovani complex strains from major endemic regions were included for comparison. Population structures were inferred by combination of bayesian model-based and distance-based approaches. MLMT placed the Turkish and Cypriot strains in a subclade of a newly discovered, genetically distinct L. infantum monophyletic group, suggesting that the Cypriot strains may originate from Turkey. CONCLUSION: The discovery of a genetically distinct L. infantum monophyletic group in the south-eastern Mediterranean stresses the importance of species genetic characterization towards better understanding

  4. Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

    Science.gov (United States)

    Wordley, Claire; Slate, Jon; Stapley, Jessica

    2011-01-01

    Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage. © 2010 Blackwell Publishing Ltd.

  5. Searching for the variables that control human rule-governed "insensitivity".

    Science.gov (United States)

    Fox, Adam E; Kyonka, Elizabeth G E

    2017-09-01

    Verbal rules or instructions often exert obvious and meaningful control over human behavior. Sometimes instructions benefit the individual by enabling faster acquisition of a skill or by obviating an aversive consequence. However, research has also suggested a clear disadvantage: "insensitivity" to changing underlying contingencies. The two experiments described here investigated the variables that control initial rule-following behavior and rule-following insensitivity. When the initial rule was inaccurate, behavior was consistent with the rule for approximately half of participants and all participants' behavior was mostly insensitive to changing contingencies. When the initial rule was accurate, behavior of all participants was consistent with it and behavior for nearly all participants was insensitive to changes in underlying contingencies. These findings have implications for how best to establish and maintain rule-following behavior in applied settings when deviant behavior would be more reinforcing to the individual. © 2017 Society for the Experimental Analysis of Behavior.

  6. Androgen responsiveness to competition in humans: the role of cognitive variables

    Directory of Open Access Journals (Sweden)

    Oliveira GA

    2014-02-01

    Full Text Available Gonçalo A Oliveira,1 Rui F Oliveira1,2 1Unidade de Investigação em Eco-Etologia, ISPA – Instituto Universitário, Lisbon, Portugal; 2Champalimaud Neuroscience Program, Instituto Gulbenkian de Ciência, Oeiras, Portugal Abstract: Although androgens are commonly seen as male sex hormones, it has been established over the years that in both sexes, androgens also respond to social challenges. To explain the socially driven changes in androgens, two theoretical models have been proposed: the biosocial model and the challenge hypothesis. These models are typically seen as partly overlapping; however, they generate different predictions that are clarified here. In humans, sports competition and nonmetabolic competitive tasks have been used in the laboratory setting, as a proxy for agonistic interactions in animals. The results reviewed here show that the testosterone (T response to competition in humans is highly variable – the studies present postcompetition T levels and changes in T that depend on the contest outcome and that cannot be predicted by the current theoretical models. These conflicting results bring to the foreground the importance of considering cognitive factors that could moderate the androgen response to competition. Among these variables, we elect cognitive appraisal and its components as a key candidate modulating factor. It is known that T also modulates the cognitive processes that are relevant to performance in competition. In this article, we reviewed the evidence arising from studies investigating the effect of administering exogenous T and compare those results with the findings from studies that measured endogenous T levels. Finally, we summarized the importance of also considering the interaction between androgens and other hormones, such as cortisol, when investigating the social modulation of T, as proposed by the dual-hormone hypothesis. Keywords: testosterone, challenge hypothesis, biosocial model, cognitive

  7. Climate Variability and Human Migration in the Netherlands, 1865–1937

    Science.gov (United States)

    Jennings, Julia A.; Gray, Clark L.

    2014-01-01

    Human migration is frequently cited as a potential social outcome of climate change and variability, and these effects are often assumed to be stronger in the past when economies were less developed and markets more localized. Yet, few studies have used historical data to test the relationship between climate and migration directly. In addition, the results of recent studies that link demographic and climate data are not consistent with conventional narratives of displacement responses. Using longitudinal individual-level demographic data from the Historical Sample of the Netherlands (HSN) and climate data that cover the same period, we examine the effects of climate variability on migration using event history models. Only internal moves in the later period and for certain social groups are associated with negative climate conditions, and the strength and direction of the observed effects change over time. International moves decrease with extreme rainfall, suggesting that the complex relationships between climate and migration that have been observed for contemporary populations extend into the nineteenth century. PMID:25937689

  8. Dynamic Network Communication in the Human Functional Connectome Predicts Perceptual Variability in Visual Illusion.

    Science.gov (United States)

    Wang, Zhiwei; Zeljic, Kristina; Jiang, Qinying; Gu, Yong; Wang, Wei; Wang, Zheng

    2018-01-01

    Ubiquitous variability between individuals in visual perception is difficult to standardize and has thus essentially been ignored. Here we construct a quantitative psychophysical measure of illusory rotary motion based on the Pinna-Brelstaff figure (PBF) in 73 healthy volunteers and investigate the neural circuit mechanisms underlying perceptual variation using functional magnetic resonance imaging (fMRI). We acquired fMRI data from a subset of 42 subjects during spontaneous and 3 stimulus conditions: expanding PBF, expanding modified-PBF (illusion-free) and expanding modified-PBF with physical rotation. Brain-wide graph analysis of stimulus-evoked functional connectivity patterns yielded a functionally segregated architecture containing 3 discrete hierarchical networks, commonly shared between rest and stimulation conditions. Strikingly, communication efficiency and strength between 2 networks predominantly located in visual areas robustly predicted individual perceptual differences solely in the illusory stimulus condition. These unprecedented findings demonstrate that stimulus-dependent, not spontaneous, dynamic functional integration between distributed brain networks contributes to perceptual variability in humans. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. UL146 variability among clinical isolates of Human Cytomegalovirus from Japan

    Directory of Open Access Journals (Sweden)

    Francisco Aguayo

    2010-01-01

    Full Text Available Human Cytomegalovirus (HCMV is a herpesvirus associated with serious diseases in immunocompromised subjects. The region between ORF UL133 and UL151 from HCMV, named ULb' is frequently deleted in attenuated AD169 and in highly passaged laboratory strains. However, this region is conserved in low-passaged and more virulent HCMV, like the Toledo strain. The UL146 gene, which is located in the ULb' region, encodes a CXC-chemokine analogue. The diversity of UL146 gene was evaluated among fifty-six clinical isolates of HCMV from Japan. Results show that UL146 gene was successfully amplified by the polymerase chain reaction (PCR in only 17/56 strains (30%, while the success rate for UL145/UL147 gene was 18/56 strains (32%. After DNA sequencing, the 35 amplified strains were classified into 8 groups. When compared, variability of UL146 ranged from 25.1% to 52.9% at the DNA level and from 34.5% to 67% at the amino acid level. Seven groups had the interleukin-8 (IL-8 motif ERL (Glu-Leu-Arg CXC and one group had only the CXC motif, suggesting the absence of the IL-8 function of UL146. In conclusion, we found that UL146 gene of HCMV is hyper-variable in clinical strains from Japan suggesting the possibility of a different function in each sequence group.

  10. Exploring the impact of climate variability during the Last Glacial Maximum on the pattern of human occupation of Iberia.

    Science.gov (United States)

    Burke, Ariane; Levavasseur, Guillaume; James, Patrick M A; Guiducci, Dario; Izquierdo, Manuel Arturo; Bourgeon, Lauriane; Kageyama, Masa; Ramstein, Gilles; Vrac, Mathieu

    2014-08-01

    The Last Glacial Maximum (LGM) was a global climate event, which had significant repercussions for the spatial distribution and demographic history of prehistoric populations. In Eurasia, the LGM coincides with a potential bottleneck for modern humans and may mark the divergence date for Asian and European populations (Keinan et al., 2007). In this research, the impact of climate variability on human populations in the Iberian Peninsula during the Last Glacial Maximum (LGM) is examined with the aid of downscaled high-resolution (16 × 16 km) numerical climate experiments. Human sensitivity to short time-scale (inter-annual) climate variability during this key time period, which follows the initial modern human colonisation of Eurasia and the extinction of the Neanderthals, is tested using the spatial distribution of archaeological sites. Results indicate that anatomically modern human populations responded to small-scale spatial patterning in climate variability, specifically inter-annual variability in precipitation levels as measured by the standard precipitation index. Climate variability at less than millennial scale, therefore, is shown to be an important component of ecological risk, one that played a role in regulating the spatial behaviour of prehistoric human populations and consequently affected their social networks. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret.

    Science.gov (United States)

    Santos, K L; Santos, M O; Laborda, P R; Souza, A P; Peroni, N; Nodari, R O

    2008-11-01

    Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding. Journal compilation © 2008 Blackwell Publishing Ltd. No claim to original US government works.

  12. Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

    Science.gov (United States)

    Agha, S H; Pilla, F; Galal, S; Shaat, I; D'Andrea, M; Reale, S; Abdelsalam, A Z A; Li, M H

    2008-06-01

    Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.

  13. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.

    Science.gov (United States)

    Kijas, J M; Fowler, J C; Thomas, M R

    1995-04-01

    Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.

  14. Development and characterization of thirteen microsatellite loci in Clark's nutcracker (Nucifraga columbiana)

    Science.gov (United States)

    Oyler-McCance, Sara J.; Fike, Jennifer A.; Castoe, Todd A.; Tomback, Diana F.; Wunder, Michael B.; Schaming, Taza D.

    2013-01-01

    Clark’s nutcrackers are important seed dispersers for two widely-distributed western North American conifers, whitebark pine and limber pine, which are declining due to outbreaks of mountain pine beetle and white pine blister rust. Because nutcracker seed dispersal services are key to maintaining viable populations of these imperiled pines, knowledge of movement patterns of Clark’s nutcrackers helps managers understand local extinction risks for these trees. To investigate population structure within Clark’s nutcracker, we developed primers for and characterized 13 polymorphic microsatellite loci. In a screen of 22 individuals from one population, levels of variability ranged from 6 to 15 alleles. No loci were found to be linked, although 4 loci revealed significant departures from Hardy–Weinberg equilibrium and evidence of null alleles. These microsatellite loci will enable population genetic analyses of Clark’s nutcrackers, which could provide insights into the spatial relationships between nutcrackers and the trees they help disperse.

  15. Characterization of ten microsatellite loci in the Broad-tailed hummingbird (Selasphorus platycercus)

    Science.gov (United States)

    Oyler-McCance, Sara J.; Fike, Jennifer A.; Talley-Farnham, Tiffany; Engelman, Tena; Engelman, Fred

    2011-01-01

    The Broad-tailed Hummingbird (Selaphorus platycercus) breeds at higher elevations in the central and southern Rockies, eastern California, and Mexico and has been studied for 8 years in Rocky Mountain National Park, Colorado. Questions regarding the relatedness of Broad-tailed Hummingbirds banded together and then recaptured in close time proximity in later years led us to isolate and develop primers for 10 polymorphic microsatellite loci. In a screen of 25 individuals from a population in Rocky Mountain National Park, the 10 loci were found to have levels of variability ranging from two to 16 alleles. No loci were found to depart from linkage disequilibrium, although two loci revealed significant departures from Hardy–Weinberg equilibrium. These 10 microsatellite loci will be applicable for population genetic analyses, investigation of mating systems and relatedness, and may help gain insight into the migration timing and routes for this species.

  16. Isolation and characterization of novel microsatellite markers in pomegranate (Punica granatum L.).

    Science.gov (United States)

    Pirseyedi, Seyed Mostafa; Valizadehghan, Sahar; Mardi, Mohsen; Ghaffari, Mohammad Reza; Mahmoodi, Parvaneh; Zahravi, Mehdi; Zeinalabedini, Mehrshad; Nekoui, Seyed Mojtaba Khayam

    2010-05-03

    Pomegranate (Punica granatum L.) has been cultivated from ancient times for its economic, ornamental and medicinal properties globally. Here, we report the isolation and characterization of 12 polymorphic microsatellite markers from a repeat-enriched genomic library of Punica granatum L. The genetic diversity of these loci was assessed in 60 genotypes of Punica granatum L. All loci were variable: the number of polymorphic alleles per locus ranged from two to five (average 2.9). The observed and expected heterozygosities ranged from 0.15 to 0.87 and 0.29 to 0.65, respectively. The polymorphic information content ranged from 0.26 to 0.61 (average: 0.43). To the best of our knowledge, this is the first time that polymorphic microsatellite markers have been reported for P. granatum L. These new markers should allow studies of the population structure and genetic diversity of pomegranate to be performed in the future.

  17. Sinai and Norfa chicken diversity revealed by microsatellite markers ...

    African Journals Online (AJOL)

    The present study aimed to outline the population differentiation of Sinai and Norfa chicken, native to Egypt, with microsatellite markers. Twenty microsatellite loci recommended by the Food and Agriculture Organization (FAO) were used. Fifty eight birds were sampled (29 for each strain: 12 males + 17 females). Data were ...

  18. Screening of seven microsatellite markers for litter size in Xinong ...

    African Journals Online (AJOL)

    Jane

    2011-08-08

    Aug 8, 2011 ... microsatellite loci. The number of effective alleles (Ne), polymorphism information content (PIC) and average heterozygosity (He) were the highest at OarFCB11 and the lowest at OarAE129 in Xinong. Saanen dairy goat. The analysis of the effect of the six polymorphisms microsatellite loci on the litter size of ...

  19. Candidate driver genes in microsatellite-unstable colorectal cancer

    DEFF Research Database (Denmark)

    Alhopuro, Pia; Sammalkorpi, Heli; Niittymäki, Iina

    2012-01-01

    Defects in the mismatch repair system lead to microsatellite instability (MSI), a feature observed in ∼ 15% of all colorectal cancers (CRCs). Microsatellite mutations that drive tumourigenesis, typically inactivation of tumour suppressors, are selected for and are frequently detected in MSI cancers...

  20. Development of polymorphic microsatellite loci for Iranian river buffalo

    African Journals Online (AJOL)

    STORAGESEVER

    2009-12-15

    Dec 15, 2009 ... defining the functional composition of their genome. Microsatellites have been .... species such as fishes (Hsu et al., 2004; Sanches and. JR, 2006; Chung-Jian ... Phylogenetic study of the Iranian buffalo by microsatellite ... Molecular Ecology Laboratory, Department of Biological Sciences,. University of Hull ...

  1. Trinucleotide repeat microsatellite markers for Black Poplar (Populus nigra L.)

    NARCIS (Netherlands)

    Smulders, M.J.M.; Schoot, van der J.; Arens, P.; Vosman, B.

    2001-01-01

    Using an enrichment procedure, we have cloned microsatellite repeats from black poplar (Populus nigra L.) and developed primers for microsatellite marker analysis. Ten primer pairs, mostly for trinucleotide repeats, produced polymorphic fragments in P. nigra. Some of them also showed amplification

  2. Microsatellite analysis of the genetic relationships between wild

    Indian Academy of Sciences (India)

    In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different ...

  3. Polymorphism and association of microsatellite SJ01 with birth ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-12-15

    Dec 15, 2009 ... 2College of Life Science, Linyi Normal University, Linyi 276005, China. Accepted 9 November, 2009. Myostatin is a negative regulator of animal skeletal muscle development and SJ01 is a microsatellite locus flanking porcine myostatin gene. In the present study, the polymorphism of microsatellite SJ01 in.

  4. Human and bovine viruses in the Milwaukee River Watershed: hydrologically relevant representation and relations with environmental variables

    Science.gov (United States)

    Corsi, Steven R.; Borchardt, M. A.; Spencer, S. K.; Hughes, Peter E.; Baldwin, Austin K.

    2014-01-01

    To examine the occurrence, hydrologic variability, and seasonal variability of human and bovine viruses in surface water, three stream locations were monitored in the Milwaukee River watershed in Wisconsin, USA, from February 2007 through June 2008. Monitoring sites included an urban subwatershed, a rural subwatershed, and the Milwaukee River at the mouth. To collect samples that characterize variability throughout changing hydrologic periods, a process control system was developed for unattended, large-volume (56–2800 L) filtration over extended durations. This system provided flow-weighted mean concentrations during runoff and extended (24-h) low-flow periods. Human viruses and bovine viruses were detected by real-time qPCR in 49% and 41% of samples (n = 63), respectively. All human viruses analyzed were detected at least once including adenovirus (40% of samples), GI norovirus (10%), enterovirus (8%), rotavirus (6%), GII norovirus (1.6%) and hepatitis A virus (1.6%). Three of seven bovine viruses analyzed were detected including bovine polyomavirus (32%), bovine rotavirus (19%), and bovine viral diarrhea virus type 1 (5%). Human viruses were present in 63% of runoff samples resulting from precipitation and snowmelt, and 20% of low-flow samples. Maximum human virus concentrations exceeded 300 genomic copies/L. Bovine viruses were present in 46% of runoff samples resulting from precipitation and snowmelt and 14% of low-flow samples. The maximum bovine virus concentration was 11 genomic copies/L. Statistical modeling indicated that stream flow, precipitation, and season explained the variability of human viruses in the watershed, and hydrologic condition (runoff event or low-flow) and season explained the variability of the sum of human and bovine viruses; however, no model was identified that could explain the variability of bovine viruses alone. Understanding the factors that affect virus fate and transport in rivers will aid watershed management for minimizing

  5. Expression profiling of interindividual variability following xenobiotic exposures in primary human hepatocyte cultures

    International Nuclear Information System (INIS)

    Goyak, Katy M.O.; Johnson, Mary C.; Strom, Stephen C.; Omiecinski, Curtis J.

    2008-01-01

    To examine the magnitude of human variability across the entire transcriptome after chemical challenge, we profiled gene expression responses to three different prototypic chemical inducers in primary human hepatocyte cultures from ten independent donors. Correlation between basal expression in any two hepatocyte donors ranged from r 2 values of 0.967 to 0.857, and chemical treatment tended to negatively impact correlation between donors. Including anticipated target genes, 10,812, 8373, and 7847 genes were changed in at least one donor by Aroclor 1254 (A1254), di(2-ethylhexyl) phthalate (DEHP), and phenobarbital (PB), respectively. A subset of these gene targets (n = 41) were altered with a high level of reproducibility in at least 9 donors, gene responses that correlated well with literature-reported mechanism of action. Filtering responses to the level of gene subsets clarified the biological impact associated with the respective chemical effectors, in lieu of substantial interindividual variation among donor responses. In these respects, the use of hierarchical clustering methods successfully grouped seven of the ten donors into chemical-specific rather than donor-specific clusters. However, at the whole-genome level, the magnitude of conserved gene expression changes among donors was surprisingly small, with fewer than 50% of the gene responses altered by a single chemical conserved in more than one donor. The use of higher level descriptors, such as those defined by the PANTHER classification system, may enable more consistent categorization of gene expression changes across individuals, as increased reproducibility was identified using this method

  6. On the Climate Variability and Energy Demands for Indoor Human Comfort Levels in Tropical Urban Environment

    Science.gov (United States)

    Pokhrel, R.; Ortiz, L. E.; González, J. E.; Ramírez-Beltran, N. D.

    2017-12-01

    The main objective of this study is to identify how climate variability influences human comfort levels in tropical urban environments. San Juan Metropolitan Area (SJMA) of the island of Puerto Rico was chosen as a reference point. A new human discomfort index (HDI) based on environmental enthalpy is defined. This index is expanded to determine the energy required to maintain indoor human comfort levels and was compared to Total Electricity consumption for the Island of Puerto Rico. Regression analysis shows that both Temperature and HDI are good indictor to predict total electrical energy consumption. Results showed that over the past 35 years the average enthalpy have increased and have mostly been above thresholds for human comfort for SJMA. The weather stations data further shows a clear indication of urbanization biases ramping up the index considered. From the trend analysis local scale (weather station) data shows a decreasing rate of maximum cooling at -11.41 kW-h/years, and minimum is increasing at 10.64 kW-h/years. To compare human comfort levels under extreme heat wave events conditions, an event of 2014 in the San Juan area was identified. The analysis for this extreme heat event is complemented by data from the National Center for environmental Prediction (NCEP) at 250km spatial resolution, North American Re-Analysis (NARR) at 32 km spatial resolution, by simulations of the Weather Forecasting System (WRF) at a resolution of 2 km, and by weather station data for San Juan. WRF simulation's results showed an improvement for both temperature and relative humidity from the input NCEP data. It also shows that difference in Energy per Capita (EPC) in urban area during a heat wave event can increase to 16% over a non-urban area. Sensitivity analysis was done by modifying the urban land cover to the most common rural references of evergreen broadleaf forest and cropland to investigate the Urban Heat Island (UHI) effect on HDI. UHI is seen to be maximum during

  7. Elasticity in ecosystem services: exploring the variable relationship between ecosystems and human well-being

    Directory of Open Access Journals (Sweden)

    Tim M. Daw

    2016-06-01

    Full Text Available Although ecosystem services are increasingly recognized as benefits people obtain from nature, we still have a poor understanding of how they actually enhance multidimensional human well-being, and how well-being is affected by ecosystem change. We develop a concept of "ecosystem service elasticity" (ES elasticity that describes the sensitivity of human well-being to changes in ecosystems. ES Elasticity is a result of complex social and ecological dynamics and is context dependent, individually variable, and likely to demonstrate nonlinear dynamics such as thresholds and hysteresis. We present a conceptual framework that unpacks the chain of causality from ecosystem stocks through flows, goods, value, and shares to contribute to the well-being of different people. This framework builds on previous conceptualizations, but places multidimensional well-being of different people as the final element. This ultimately disaggregated approach emphasizes how different people access benefits and how benefits match their needs or aspirations. Applying this framework to case studies of individual coastal ecosystem services in East Africa illustrates a wide range of social and ecological factors that can affect ES elasticity. For example, food web and habitat dynamics affect the sensitivity of different fisheries ecosystem services to ecological change. Meanwhile high cultural significance, or lack of alternatives enhance ES elasticity, while social mechanisms that prevent access can reduce elasticity. Mapping out how chains are interlinked illustrates how different types of value and the well-being of different people are linked to each other and to common ecological stocks. We suggest that examining chains for individual ecosystem services can suggest potential interventions aimed at poverty alleviation and sustainable ecosystems while mapping out of interlinkages between chains can help to identify possible ecosystem service trade-offs and winners and

  8. Isolation and characterization of eight novel microsatellite loci in the double-crested cormorant (Phalacrocorax auritus)

    Science.gov (United States)

    Mercer, Dacey; Haig, Susan; Mullins, Thomas

    2010-01-01

    We describe the isolation and characterization of eight microsatellite loci from the double-crested cormorant (Phalacrocorax auritus). Genetic variability was assessed using 60 individuals from three populations. All loci were variable with the number of alleles ranging from two to 17 per locus, and observed heterozygosity varying from 0.05 to 0.89. No loci showed signs of linkage disequilibrium and all loci conformed to Hardy–Weinberg equilibrium frequencies. Further, all loci amplified and were polymorphic in two related Phalacrocorax species. These loci should prove useful for population genetic studies of the double-crested cormorant and other pelecaniform species.

  9. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  10. Relating Linear and Volumetric Variables Through Body Scanning to Improve Human Interfaces in Space

    Science.gov (United States)

    Margerum, Sarah E.; Ferrer, Mike A.; Young, Karen S.; Rajulu, Sudhakar

    2010-01-01

    Designing space suits and vehicles for the diverse human population present unique challenges for the methods of traditional anthropometry. Space suits are bulky and allow the operator to shift position within the suit and inhibit the ability to identify body landmarks. Limited suit sizing options also cause variability in fit and performance between similarly sized individuals. Space vehicles are restrictive in volume in both the fit and the ability to collect data. NASA's Anthropometric and Biomechanics Facility (ABF) has utilized 3D scanning to shift from traditional linear anthropometry to explore and examine volumetric capabilities to provide anthropometric solutions for design. Overall, the key goals are to improve the human-system performance and develop new processes to aid in the design and evaluation of space systems. Four case studies are presented that illustrate the shift from purely linear analyses to an augmented volumetric toolset to predict and analyze the human within the space suit and vehicle. The first case study involves the calculation of maximal head volume to estimate total free volume in the helmet for proper air exchange. Traditional linear measurements resulted in an inaccurate representation of the head shape, yet limited data exists for the determination of a large head volume. Steps were first taken to identify and classify a maximum head volume and the resulting comparisons to the estimate are presented in this paper. This study illustrates the gap between linear components of anthropometry and the need for overall volume metrics in order to provide solutions. A second case study examines the overlay of the space suit scans and components onto scanned individuals to quantify fit and clearance to aid in sizing the suit to the individual. Restrictions in space suit size availability present unique challenges to optimally fit the individual within a limited sizing range while maintaining performance. Quantification of the clearance and

  11. SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).

    Science.gov (United States)

    Muñoz, Irene; Henriques, Dora; Jara, Laura; Johnston, J Spencer; Chávez-Galarza, Julio; De La Rúa, Pilar; Pinto, M Alice

    2017-07-01

    The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content. © 2016 John Wiley & Sons Ltd.

  12. Identification of geographically distributed sub-populations of Leishmania (Leishmania major by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Schwenkenbecher Jan

    2008-06-01

    Full Text Available Abstract Background Leishmania (Leishmania major, one of the agents causing cutaneous leishmaniasis (CL in humans, is widely distributed in the Old World where different species of wild rodent and phlebotomine sand fly serve as animal reservoir hosts and vectors, respectively. Despite this, strains of L. (L. major isolated from many different sources over many years have proved to be relatively uniform. To investigate the population structure of the species highly polymorphic microsatellite markers were employed for greater discrimination among it's otherwise closely related strains, an approach applied successfully to other species of Leishmania. Results Multilocus Microsatellite Typing (MLMT based on 10 different microsatellite markers was applied to 106 strains of L. (L. major from different regions where it is endemic. On applying a Bayesian model-based approach, three main populations were identified, corresponding to three separate geographical regions: Central Asia (CA; the Middle East (ME; and Africa (AF. This was congruent with phylogenetic reconstructions based on genetic distances. Re-analysis separated each of the populations into two sub-populations. The two African sub-populations did not correlate well with strains' geographical origin. Strains falling into the sub-populations CA and ME did mostly group according to their place of isolation although some anomalies were seen, probably, owing to human migration. Conclusion The model- and distance-based analyses of the microsatellite data exposed three main populations of L. (L. major, Central Asia, the Middle East and Africa, each of which separated into two sub-populations. This probably correlates with the different species of rodent host.

  13. Impacts of climate variability and future climate change on harmful algal blooms and human health

    Science.gov (United States)

    Moore, Stephanie K; Trainer, Vera L; Mantua, Nathan J; Parker, Micaela S; Laws, Edward A; Backer, Lorraine C; Fleming, Lora E

    2008-01-01

    Anthropogenically-derived increases in atmospheric greenhouse gas concentrations have been implicated in recent climate change, and are projected to substantially impact the climate on a global scale in the future. For marine and freshwater systems, increasing concentrations of greenhouse gases are expected to increase surface temperatures, lower pH, and cause changes to vertical mixing, upwelling, precipitation, and evaporation patterns. The potential consequences of these changes for harmful algal blooms (HABs) have received relatively little attention and are not well understood. Given the apparent increase in HABs around the world and the potential for greater problems as a result of climate change and ocean acidification, substantial research is needed to evaluate the direct and indirect associations between HABs, climate change, ocean acidification, and human health. This research will require a multidisciplinary approach utilizing expertise in climatology, oceanography, biology, epidemiology, and other disciplines. We review the interactions between selected patterns of large-scale climate variability and climate change, oceanic conditions, and harmful algae. PMID:19025675

  14. Neuronal Substrates Underlying Performance Variability in Well-Trained Skillful Motor Task in Humans.

    Science.gov (United States)

    Mizuguchi, Nobuaki; Uehara, Shintaro; Hirose, Satoshi; Yamamoto, Shinji; Naito, Eiichi

    2016-01-01

    Motor performance fluctuates trial by trial even in a well-trained motor skill. Here we show neural substrates underlying such behavioral fluctuation in humans. We first scanned brain activity with functional magnetic resonance imaging while healthy participants repeatedly performed a 10 s skillful sequential finger-tapping task. Before starting the experiment, the participants had completed intensive training. We evaluated task performance per trial (number of correct sequences in 10 s) and depicted brain regions where the activity changes in association with the fluctuation of the task performance across trials. We found that the activity in a broader range of frontoparietocerebellar network, including the bilateral dorsolateral prefrontal cortex (DLPFC), anterior cingulate and anterior insular cortices, and left cerebellar hemisphere, was negatively correlated with the task performance. We further showed in another transcranial direct current stimulation (tDCS) experiment that task performance deteriorated, when we applied anodal tDCS to the right DLPFC. These results indicate that fluctuation of brain activity in the nonmotor frontoparietocerebellar network may underlie trial-by-trial performance variability even in a well-trained motor skill, and its neuromodulation with tDCS may affect the task performance.

  15. Climate Variability and the Occurrence of Human Puumala Hantavirus Infections in Europe: A Systematic Review.

    Science.gov (United States)

    Roda Gracia, J; Schumann, B; Seidler, A

    2015-09-01

    Hantaviruses are distributed worldwide and are transmitted by rodents. In Europe, the infection usually manifests as a mild form of haemorrhagic fever with renal syndrome (HFRS) known as nephropathia epidemica (NE), which is triggered by the virus species Puumala. Its host is the bank vole (Myodes glareolus). In the context of climate change, interest in the role of climatic factors for the disease has increased. A systematic review was conducted to investigate the association between climate variability and the occurrence of human Puumala hantavirus infections in Europe. We performed a literature search in the databases MEDLINE, EMBASE and Web of Science. Studies that investigated Puumala virus infection and climatic factors in any European country with a minimum collection period of 2 years were included. The selection of abstracts and the evaluation of included studies were performed by two independent reviewers. A total of 434 titles were identified in the databases, of which nine studies fulfilled the inclusion criteria. The majority of studies were conducted in central Europe (Belgium, France and Germany), while only two came from the north (Sweden) and one from the south (Bosnia). Strong evidence was found for a positive association between temperature and NE incidence in central Europe, while the evidence for northern Europe so far appears insufficient. Results regarding precipitation were contradictory. Overall, the complex relationships between climate and hantavirus infections need further exploration to identify specific health risks and initiate appropriate intervention measures in the context of climate change. © 2014 Blackwell Verlag GmbH.

  16. Impacts of climate variability and future climate change on harmful algal blooms and human health.

    Science.gov (United States)

    Moore, Stephanie K; Trainer, Vera L; Mantua, Nathan J; Parker, Micaela S; Laws, Edward A; Backer, Lorraine C; Fleming, Lora E

    2008-11-07

    Anthropogenically-derived increases in atmospheric greenhouse gas concentrations have been implicated in recent climate change, and are projected to substantially impact the climate on a global scale in the future. For marine and freshwater systems, increasing concentrations of greenhouse gases are expected to increase surface temperatures, lower pH, and cause changes to vertical mixing, upwelling, precipitation, and evaporation patterns. The potential consequences of these changes for harmful algal blooms (HABs) have received relatively little attention and are not well understood. Given the apparent increase in HABs around the world and the potential for greater problems as a result of climate change and ocean acidification, substantial research is needed to evaluate the direct and indirect associations between HABs, climate change, ocean acidification, and human health. This research will require a multidisciplinary approach utilizing expertise in climatology, oceanography, biology, epidemiology, and other disciplines. We review the interactions between selected patterns of large-scale climate variability and climate change, oceanic conditions, and harmful algae.

  17. Human and bovine viruses in the Milwaukee River watershed: Hydrologically relevant representation and relations with environmental variables

    Energy Technology Data Exchange (ETDEWEB)

    Corsi, S.R., E-mail: srcorsi@usgs.gov [U.S. Geological Survey, Wisconsin Water Science Center, Middleton, WI 53562 (United States); Borchardt, M.A.; Spencer, S.K. [U.S. Department of Agriculture, Agricultural Research Service, 2615 Yellowstone Dr., Marshfield, WI 54449 (United States); Hughes, P.E.; Baldwin, A.K. [U.S. Geological Survey, Wisconsin Water Science Center, Middleton, WI 53562 (United States)

    2014-08-15

    To examine the occurrence, hydrologic variability, and seasonal variability of human and bovine viruses in surface water, three stream locations were monitored in the Milwaukee River watershed in Wisconsin, USA, from February 2007 through June 2008. Monitoring sites included an urban subwatershed, a rural subwatershed, and the Milwaukee River at the mouth. To collect samples that characterize variability throughout changing hydrologic periods, a process control system was developed for unattended, large-volume (56–2800 L) filtration over extended durations. This system provided flow-weighted mean concentrations during runoff and extended (24-h) low-flow periods. Human viruses and bovine viruses were detected by real-time qPCR in 49% and 41% of samples (n = 63), respectively. All human viruses analyzed were detected at least once including adenovirus (40% of samples), GI norovirus (10%), enterovirus (8%), rotavirus (6%), GII norovirus (1.6%) and hepatitis A virus (1.6%). Three of seven bovine viruses analyzed were detected including bovine polyomavirus (32%), bovine rotavirus (19%), and bovine viral diarrhea virus type 1 (5%). Human viruses were present in 63% of runoff samples resulting from precipitation and snowmelt, and 20% of low-flow samples. Maximum human virus concentrations exceeded 300 genomic copies/L. Bovine viruses were present in 46% of runoff samples resulting from precipitation and snowmelt and 14% of low-flow samples. The maximum bovine virus concentration was 11 genomic copies/L. Statistical modeling indicated that stream flow, precipitation, and season explained the variability of human viruses in the watershed, and hydrologic condition (runoff event or low-flow) and season explained the variability of the sum of human and bovine viruses; however, no model was identified that could explain the variability of bovine viruses alone. Understanding the factors that affect virus fate and transport in rivers will aid watershed management for minimizing

  18. Human and bovine viruses in the Milwaukee River watershed: Hydrologically relevant representation and relations with environmental variables

    International Nuclear Information System (INIS)

    Corsi, S.R.; Borchardt, M.A.; Spencer, S.K.; Hughes, P.E.; Baldwin, A.K.

    2014-01-01

    To examine the occurrence, hydrologic variability, and seasonal variability of human and bovine viruses in surface water, three stream locations were monitored in the Milwaukee River watershed in Wisconsin, USA, from February 2007 through June 2008. Monitoring sites included an urban subwatershed, a rural subwatershed, and the Milwaukee River at the mouth. To collect samples that characterize variability throughout changing hydrologic periods, a process control system was developed for unattended, large-volume (56–2800 L) filtration over extended durations. This system provided flow-weighted mean concentrations during runoff and extended (24-h) low-flow periods. Human viruses and bovine viruses were detected by real-time qPCR in 49% and 41% of samples (n = 63), respectively. All human viruses analyzed were detected at least once including adenovirus (40% of samples), GI norovirus (10%), enterovirus (8%), rotavirus (6%), GII norovirus (1.6%) and hepatitis A virus (1.6%). Three of seven bovine viruses analyzed were detected including bovine polyomavirus (32%), bovine rotavirus (19%), and bovine viral diarrhea virus type 1 (5%). Human viruses were present in 63% of runoff samples resulting from precipitation and snowmelt, and 20% of low-flow samples. Maximum human virus concentrations exceeded 300 genomic copies/L. Bovine viruses were present in 46% of runoff samples resulting from precipitation and snowmelt and 14% of low-flow samples. The maximum bovine virus concentration was 11 genomic copies/L. Statistical modeling indicated that stream flow, precipitation, and season explained the variability of human viruses in the watershed, and hydrologic condition (runoff event or low-flow) and season explained the variability of the sum of human and bovine viruses; however, no model was identified that could explain the variability of bovine viruses alone. Understanding the factors that affect virus fate and transport in rivers will aid watershed management for minimizing

  19. Development of 16 Microsatellite Markers within the Camassia (Agavaceae Species Complex and Amplification in Related Taxa

    Directory of Open Access Journals (Sweden)

    Theresa M. Culley

    2013-07-01

    Full Text Available Premise of the study: The North American genus Camassia is an ecologically important group whose variability and evolution are little understood, being influenced by hybridization and geographic isolation. We developed microsatellite markers to investigate patterns of gene flow, population structure, and taxonomic relationships within this group. Methods and Results: Using a traditional approach with biotin-labeled probes, we developed 16 microsatellite primers in three species of Camassia: C. howellii, C. leichtlinii, and C. quamash. The number of alleles per locus averaged 3.94 per species, and levels of heterozygosity ranged from 0.000 to 1.00 and 0.033 to 0.917 for observed and expected heterozygosities, respectively. All primers amplified to varying extents in additional species (C. angusta, C. cusickii, C. scilloides and in putative species in a related genus (Hastingsia alba, H. atropurpurea, H. bracteosa, H. serpentinicola. Conclusions: These microsatellite markers exhibit variation and are useful for ongoing studies of integrative taxonomy and population differentiation within this species complex.

  20. Distinguishing the impacts of human activities and climate variability on runoff and sediment load change based on paired periods with similar weather conditions

    NARCIS (Netherlands)

    Wang, Fei; Hessel, Rudi; Mu, Xingmin; Maroulis, Jerry; Zhao, Guangju; Geissen, Violette; Ritsema, Coen

    2015-01-01

    Runoff and sediment loads from river basin are largely affected by the interplay of climate variability and human activities within the basin. However, distinguishing the impacts of climate variability and human activities would vastly improve our knowledge of water resources, climate variability

  1. Long-term variability and impact on human health of biologically active UV radiation in Moscow

    Science.gov (United States)

    Zhdanova, Ekaterina; Chubarova, Natalia

    2014-05-01

    the developed classification for Moscow. Booth, C.R. and S. Madronich, 1994: Radiation amplification factors: improved formulation accounts for large increases in ultraviolet radiation associated with Antarctic ozone depletion. In: Ultraviolet Radiation in Antarctica: Measurements and Biological Research [Weiler, C.S. and P.A. Penhale (eds.)]. AGU Antarctic Research Series, 62, Washington, DC, USA, 39-42. Chubarova N.Y., 2008: UV variability in Moscow according to long-term UV measurements and reconstruction model. Atmos.Chem.Phys., 8, 3025-3031 Oriowo, M. et al., 2001:, Action spectrum for in vitro UV-induced cataract using whole lenses. Invest.Ophthalmol.&Vis.Sci, 42, 2596-2602. CIE, 1993: Reference Action Spectra for Ultraviolet Induced Erythema and Pigmentation of Different Human skin Types. CIE Research Note, CIE Technical Collection., N.3 CIE, 2006: Action spectrum for the production of previtamin D3 in human skin, Technical report 174, International commission on illumination

  2. Microsatellite Primers in the Lichen Symbiotic Alga Trebouxia decolorans (Trebouxiophyceae

    Directory of Open Access Journals (Sweden)

    Francesco Dal Grande

    2013-03-01

    Full Text Available Premise of the study: Polymorphic microsatellite markers were developed for the symbiotic green alga Trebouxia decolorans to study fine-scale population structure and clonal diversity. Methods and Results: Using Illumina pyrosequencing, 20 microsatellite primer sets were developed for T. decolorans. The primer sets were tested on 43 individuals sampled from four subpopulations in Germany. The primers amplified di-, tri-, and tetranucleotide repeats with three to 15 alleles per locus, and the unbiased haploid diversity per locus ranged from 0.636 to 0.821. Conclusions: The identified microsatellite markers will be useful to study the genetic diversity, dispersal, and reproductive mode of this common lichen photobiont.

  3. European climate variability and human susceptibility over the past 2500 years

    Science.gov (United States)

    Buentgen, U.

    2010-09-01

    Climate variations including droughts in the western US and African Sahel, landfalls of Atlantic hurricanes, and shifts in the Asian monsoon have affected human societies throughout history mainly by modulating water supply and agricultural productivity, health risk and civil conflict. Yet, discriminations of environmental impacts from political, economical and technological drivers of societal shifts are may be hampered by the indirect effects of climate on society, but certainly by the paucity of high-resolution palaeoclimatic evidence. Here we present a tree-ring network of 7284 precipitation sensitive oak series from lower elevations in France and Germany, and a compilation of 1546 temperature responsive conifers from higher elevations in the Austrian Alps, both covering the past 2500 years. Temporal distribution of historical felling dates of construction timber refers to changes in settlement activity that mirror different stages of economic wealth. Variations in Central European summer precipitation and temperature are contrasted with societal benchmarks. Prolonged periods of generally wet and warm summers, favourable for cultural prosperity, appeared during the Roman epoch between ~200 BC and 200 AD and from ~700-1000 AD, with the latter facilitating the rapid economic, cultural and political growth of medieval Europe. Unprecedented climate variability from ~200-500 AD coincides with the demise of the Western Roman Empire and the subsequent Barbarian Migrations. This period was characterized by continental-scale political turmoil, cultural stagnation and socio-economic instability including settlement abandonment, population migration, and societal collapse. Driest and coldest summers of the Late Holocene concurred in the 6th century, during which regional consolidation began. The recent political, cultural and fiscal reluctance to adapt to and mitigate projected climate change reflects the common belief of societal insusceptibility to environmental

  4. Analysis of Intra- and Intersubject Variability in Oral Drug Absorption in Human Bioequivalence Studies of 113 Generic Products.

    Science.gov (United States)

    Sugihara, Masahisa; Takeuchi, Susumu; Sugita, Masaru; Higaki, Kazutaka; Kataoka, Makoto; Yamashita, Shinji

    2015-12-07

    In this study, the data of 113 human bioequivalence (BE) studies of immediate release (IR) formulations of 74 active pharmaceutical ingredients (APIs) conducted at Sawai Pharmaceutical Co., Ltd., was analyzed to understand the factors affecting intra- and intersubject variabilities in oral drug absorption. The ANOVA CV (%) calculated from area under the time-concentration curve (AUC) in each BE study was used as an index of intrasubject variability (Vintra), and the relative standard deviation (%) in AUC was used as that of intersubject variability (Vinter). Although no significant correlation was observed between Vintra and Vinter of all drugs, Vintra of class 3 drugs was found to increase in association with a decrease in drug permeability (P(eff)). Since the absorption of class 3 drugs was rate-limited by the permeability, it was suggested that, for such drugs, the low P(eff) might be a risk factor to cause a large intrasubject variability. To consider the impact of poor water solubility on the variability in BE study, a parameter of P(eff)/Do (Do; dose number) was defined to discriminate the solubility-limited and dissolution-rate-limited absorption of class 2 drugs. It was found that the class 2 drugs with a solubility-limited absorption (P(eff)/Do high intrasubject variability. Furthermore, as a reason for high intra- or intersubject variability in AUC for class 1 drugs, effects of drug metabolizing enzymes were investigated. It was demonstrated that intrasubject variability was high for drugs metabolized by CYP3A4 while intersubject variability was high for drugs metabolized by CYP2D6. For CYP3A4 substrate drugs, the Km value showed the significant relation with Vintra, indicating that the affinity to the enzyme can be a parameter to predict the risk of high intrasubject variability. In conclusion, by analyzing the in house data of human BE study, low permeability, solubility-limited absorption, and high affinity to CYP3A4 are identified as risk factors for

  5. The sequence of cortical activity inferred by response latency variability in the human ventral pathway of face processing.

    Science.gov (United States)

    Lin, Jo-Fu Lotus; Silva-Pereyra, Juan; Chou, Chih-Che; Lin, Fa-Hsuan

    2018-04-11

    Variability in neuronal response latency has been typically considered caused by random noise. Previous studies of single cells and large neuronal populations have shown that the temporal variability tends to increase along the visual pathway. Inspired by these previous studies, we hypothesized that functional areas at later stages in the visual pathway of face processing would have larger variability in the response latency. To test this hypothesis, we used magnetoencephalographic data collected when subjects were presented with images of human faces. Faces are known to elicit a sequence of activity from the primary visual cortex to the fusiform gyrus. Our results revealed that the fusiform gyrus showed larger variability in the response latency compared to the calcarine fissure. Dynamic and spectral analyses of the latency variability indicated that the response latency in the fusiform gyrus was more variable than in the calcarine fissure between 70 ms and 200 ms after the stimulus onset and between 4 Hz and 40 Hz, respectively. The sequential processing of face information from the calcarine sulcus to the fusiform sulcus was more reliably detected based on sizes of the response variability than instants of the maximal response peaks. With two areas in the ventral visual pathway, we show that the variability in response latency across brain areas can be used to infer the sequence of cortical activity.

  6. Physical-mathematical model for cybernetic description of the human organs with trace element concentrations as input variables

    International Nuclear Information System (INIS)

    Mihai, Maria; Popescu, I.V.

    2003-01-01

    In this paper we report a physical-mathematical model for studying the organs and humans fluids by cybernetic principle. The input variables represent the trace elements which are determined by atomic and nuclear methods of elemental analysis. We have determined the health limits between which the organs might function. (authors)

  7. Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes

    Directory of Open Access Journals (Sweden)

    HUAN GAO

    2009-01-01

    Full Text Available To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia, rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

  8. Dose uncertainties for large solar particle events: Input spectra variability and human geometry approximations

    International Nuclear Information System (INIS)

    Townsend, Lawrence W.; Zapp, E. Neal

    1999-01-01

    The true uncertainties in estimates of body organ absorbed dose and dose equivalent, from exposures of interplanetary astronauts to large solar particle events (SPEs), are essentially unknown. Variations in models used to parameterize SPE proton spectra for input into space radiation transport and shielding computer codes can result in uncertainty about the reliability of dose predictions for these events. Also, different radiation transport codes and their input databases can yield significant differences in dose predictions, even for the same input spectra. Different results may also be obtained for the same input spectra and transport codes if different spacecraft and body self-shielding distributions are assumed. Heretofore there have been no systematic investigations of the variations in dose and dose equivalent resulting from these assumptions and models. In this work we present a study of the variability in predictions of organ dose and dose equivalent arising from the use of different parameters to represent the same incident SPE proton data and from the use of equivalent sphere approximations to represent human body geometry. The study uses the BRYNTRN space radiation transport code to calculate dose and dose equivalent for the skin, ocular lens and bone marrow using the October 1989 SPE as a model event. Comparisons of organ dose and dose equivalent, obtained with a realistic human geometry model and with the oft-used equivalent sphere approximation, are also made. It is demonstrated that variations of 30-40% in organ dose and dose equivalent are obtained for slight variations in spectral fitting parameters obtained when various data points are included or excluded from the fitting procedure. It is further demonstrated that extrapolating spectra from low energy (≤30 MeV) proton fluence measurements, rather than using fluence data extending out to 100 MeV results in dose and dose equivalent predictions that are underestimated by factors as large as 2

  9. Agricultural, socioeconomic and environmental variables as risks for human verotoxigenic Escherichia coli (VTEC) infection in Finland.

    Science.gov (United States)

    Jalava, Katri; Ollgren, Jukka; Eklund, Marjut; Siitonen, Anja; Kuusi, Markku

    2011-10-18

    Verotoxigenic E. coli (VTEC) is the cause of severe gastrointestinal infection especially among infants. Between 10 and 20 cases are reported annually to the National Infectious Disease Register (NIDR) in Finland. The aim of this study was to identify explanatory variables for VTEC infections reported to the NIDR in Finland between 1997 and 2006. We applied a hurdle model, applicable for a dataset with an excess of zeros. We enrolled 131 domestically acquired primary cases of VTEC between 1997 and 2006 from routine surveillance data. The isolated strains were characterized by virulence type, serogroup, phage type and pulsed-field gel electrophoresis. By applying a two-part Bayesian hurdle model to infectious disease surveillance data, we were able to create a model in which the covariates were associated with the probability for occurrence of the cases in the logistic regression part and the magnitude of covariate changes in the Poisson regression part if cases do occur. The model also included spatial correlations between neighbouring municipalities. The average annual incidence rate was 4.8 cases per million inhabitants based on the cases as reported to the NIDR. Of the 131 cases, 74 VTEC O157 and 58 non-O157 strains were isolated (one person had dual infections). The number of bulls per human population and the proportion of the population with a higher education were associated with an increased occurrence and incidence of human VTEC infections in 70 (17%) of 416 of Finnish municipalities. In addition, the proportion of fresh water per area, the proportion of cultivated land per area and the proportion of low income households with children were associated with increased incidence of VTEC infections. With hurdle models we were able to distinguish between risk factors for the occurrence of the disease and the incidence of the disease for data characterised by an excess of zeros. The density of bulls and the proportion of the population with higher education were

  10. Microchemical and structural regular variability of apatites in 'overbuilt' enamel and dentin of human molar teeth

    International Nuclear Information System (INIS)

    Kuczumow, A.; Nowak, J.; ChaLas, R.

    2011-01-01

    The aim of a recent paper was to recognize the chemical and structural changes in apatites, which form both the enamel and the dentin of the human tooth. The aim was achieved by scrutinizing the linear elemental profiles along the cross-sections of human molar teeth. Essentially, the task was accomplished with the application of the Electron Probe Microanalysis method and with some additional studies by Micro-Raman spectrometry. All the trends in linear profiles were strictly determined. In the enamel zone they were either increasing or decreasing curves of exponential character. The direction of the investigations was to start with the tooth surface and move towards the dentin-enamel junction (DEJ). The results of the elemental studies were more visible when the detected material was divided, in an arbitrary way, into the prevailing 'core' enamel (∼93.5% of the total mass) and the remaining 'overbuilt' enamel. The material in the 'core' enamel was fully stable, with clearly determined chemical and mechanical features. However, the case was totally different in the 'overbuilt enamel', with dynamic changes in the composition. In the 'overbuilt' layer Ca, P, Cl and F profiles present the decaying distribution curves, whereas Mg, Na, K and CO 3 2- present the growing ones. Close to the surface of the tooth the mixture of hydroxy-, chlor- and fluor-apatite is formed, which is much more resistant than the rest of the enamel. On passing towards the DEJ, the apatite is enriched with Na, Mg and CO 3 2- . In this location, three of six phosphate groups were substituted with carbonate groups. Simultaneously, Mg is associated with the hydroxyl groups around the hexad axis. In this way, the mechanisms of exchange reactions were established. The crystallographic structures were proposed for new phases located close to DEJ. In the dentin zone, the variability of elemental profiles looks different, with the most characteristic changes occurring in Mg and Na concentrations. Mg

  11. Human heavy-chain variable region gene family nonrandomly rearranged in familial chronic lymphocytic leukemia

    International Nuclear Information System (INIS)

    Shen, A.; Humphries, C.; Tucker, P.; Blattner, F.

    1987-01-01

    The authors have identified a family of human immunoglobulin heavy-chain variable-region (V/sub H/) genes, one member of which is rearranged in two affected members of a family in which the father and four of five siblings developed chronic lymphocytic leukemia. Cloning and sequencing of the rearranged V/sub H/ genes from leukemic lymphocytes of three affected siblings showed that two siblings had rearranged V/sub H/ genes (V/sub H/TS1 and V/sub H/WS1) that were 90% homologous. The corresponding germ-line gene, V/sub H/251, was found to part of a small (four gene) V/sub H/ gene family, which they term V/sub H/V. The DNA sequence homology to V/sub H/WS1 (95%) and V/sub H/TS1 (88%) and identical restriction sites on the 5' side of V/sub H/ confirm that rearrangement of V/sub H/251 followed by somatic mutation produced the identical V/sub H/ gene rearrangements in the two siblings. V/sub H/TS1 is not a functional V/sub H/ gene; a functional V/sub H/ rearrangement was found on the other chromosome of this patient. The other two siblings had different V/sub H/ gene rearrangements. All used different diversity genes. Mechanisms proposed for nonrandom selection of a single V/sub H/ gene include developmental regulation of this V/sub H/ gene rearrangement or selection of a subpopulation of B cells in which this V/sub H/ has been rearranged

  12. A new electrophoresis technique to separate microsatellite alleles ...

    African Journals Online (AJOL)

    A new electrophoresis technique to separate microsatellite alleles* ... African Journal of Biotechnology ... with the CEQTM 8000 Genetic Analysis System and ABI 3130xl DNA Sequencer easily separated products and determined allelic size, ...

  13. Microsatellite loci and peroxidase alleles correlation in somaclonal ...

    African Journals Online (AJOL)

    A dimer locus, a tetramer locus and two epigenetic bands were observed. Genome variation among somaclonal plantlets were investigated using microsatellite markers. SSR (Simple Sequence Repeat) markers revealed polymorphism among the studied population. Nonparametric statistical analysis showed significant ...

  14. Development of twenty-nine polymorphic microsatellite loci from ...

    Indian Academy of Sciences (India)

    genetic management decisions for artificial propagation populations. ... Genomic DNA for genomic library construction was ..... the research of population dynamics and genetic structure of Cor- ... genotyping errors in microsatellite data. Mol.

  15. Eucalyptus microsatellites mined in silico: survey and evaluation

    Indian Academy of Sciences (India)

    2008-04-01

    Apr 1, 2008 ... Eucalyptus microsatellites mined in silico: survey and evaluation ... cific regions of the genome of different species (Marques et ..... Received 21 June 2007, in revised form 11 September 2007; accepted 12 September 2007.

  16. Genetic Variation of 28 microsatellite markers in Australian merino ...

    African Journals Online (AJOL)

    ratiyat

    2016-02-26

    Feb 26, 2016 ... Microsatellite-based estimation of inbreeding level in sheep populations .... progeny testing system used in sheep lineage analysis at McMaster Laboratory- ..... are less related than one might expect under a model of random.

  17. Cross-genus amplification and characterisation of microsatellite loci ...

    African Journals Online (AJOL)

    Cross-genus amplification and characterisation of microsatellite loci in the little free tailed bat, Chaerephon pumilus s. l. (Molossidae) from South Eastern Africa. Theshnie Naidoo, Angus Macdonald, Jennifer M Lamb ...

  18. Isolation and characterization of ten microsatellite loci from Korean ...

    Indian Academy of Sciences (India)

    Leguminosae) and its cytotaxonomic signifi- cance. Cathaya 2, 139–150. Estoup A., Garnery L., Solignac M. and Cornuet J. M. 1995. Microsatellite variation in honey bee (Apis mellifera L.) popula- tions: hierarchical genetic structure and test of ...

  19. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane.

    Science.gov (United States)

    Parida, Swarup K; Kalia, Sanjay K; Kaul, Sunita; Dalal, Vivek; Hemaprabha, G; Selvi, Athiappan; Pandit, Awadhesh; Singh, Archana; Gaikwad, Kishor; Sharma, Tilak R; Srivastava, Prem Shankar; Singh, Nagendra K; Mohapatra, Trilochan

    2009-01-01

    Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

  20. Development of Pedigree Classification Using Microsatellite and Mitochondrial Markers for Giant Grouper Broodstock (Epinephelus lanceolatus Management in Taiwan

    Directory of Open Access Journals (Sweden)

    Hsiao-Che Kuo

    2014-04-01

    Full Text Available Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals’ fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as genetic markers to analyze the genetic relationships among giant grouper broodstocks. The 776-bp fragment of high polymorphic mitochondrial D-loop sequence was selected for measuring sibling relatedness. In a sample of 118 giant groupers, 42 haplotypes were categorized, with nucleotide diversity (π of 0.00773 and haplotype diversity (HD of 0.983. Furthermore, microsatellites were used for investigation of parentage. Six out of 33 microsatellite loci were selected as markers based on having a high number of alleles and compliance with Hardy-Weinberg equilibrium. Microsatellite profiles based on these loci provide high variability with low combined non-exclusion probability, permitting practical use in aquaculture. The method described here could be used to improve grouper broodstock management and lower the chances of inbreeding. This approach is expected to lead to production of higher quality groupers with higher disease resistance, thereby reducing the need for drug application.

  1. Development of Pedigree Classification Using Microsatellite and Mitochondrial Markers for Giant Grouper Broodstock (Epinephelus lanceolatus) Management in Taiwan

    Science.gov (United States)

    Kuo, Hsiao-Che; Hsu, Hao-Hsuan; Chua, Chee Shin; Wang, Ting-Yu; Chen, Young-Mao; Chen, Tzong-Yueh

    2014-01-01

    Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals’ fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as genetic markers to analyze the genetic relationships among giant grouper broodstocks. The 776-bp fragment of high polymorphic mitochondrial D-loop sequence was selected for measuring sibling relatedness. In a sample of 118 giant groupers, 42 haplotypes were categorized, with nucleotide diversity (π) of 0.00773 and haplotype diversity (HD) of 0.983. Furthermore, microsatellites were used for investigation of parentage. Six out of 33 microsatellite loci were selected as markers based on having a high number of alleles and compliance with Hardy-Weinberg equilibrium. Microsatellite profiles based on these loci provide high variability with low combined non-exclusion probability, permitting practical use in aquaculture. The method described here could be used to improve grouper broodstock management and lower the chances of inbreeding. This approach is expected to lead to production of higher quality groupers with higher disease resistance, thereby reducing the need for drug application. PMID:24796300

  2. Relative roles of weather variables and change in human population in malaria: comparison over different states of India.

    Directory of Open Access Journals (Sweden)

    Prashant Goswami

    Full Text Available Pro-active and effective control as well as quantitative assessment of impact of climate change on malaria requires identification of the major drivers of the epidemic. Malaria depends on vector abundance which, in turn, depends on a combination of weather variables. However, there remain several gaps in our understanding and assessment of malaria in a changing climate. Most of the studies have considered weekly or even monthly mean values of weather variables, while the malaria vector is sensitive to daily variations. Secondly, rarely all the relevant meteorological variables have been considered together. An important question is the relative roles of weather variables (vector abundance and change in host (human population, in the change in disease load.We consider the 28 states of India, characterized by diverse climatic zones and changing population as well as complex variability in malaria, as a natural test bed. An annual vector load for each of the 28 states is defined based on the number of vector genesis days computed using daily values of temperature, rainfall and humidity from NCEP daily Reanalysis; a prediction of potential malaria load is defined by taking into consideration changes in the human population and compared with the reported number of malaria cases.For most states, the number of malaria cases is very well correlated with the vector load calculated with the combined conditions of daily values of temperature, rainfall and humidity; no single weather variable has any significant association with the observed disease prevalence.The association between vector-load and daily values of weather variables is robust and holds for different climatic regions (states of India. Thus use of all the three weather variables provides a reliable means of pro-active and efficient vector sanitation and control as well as assessment of impact of climate change on malaria.

  3. Novel Polymorphic Multilocus Microsatellite Markers to Distinguish Candida tropicalis Isolates.

    Directory of Open Access Journals (Sweden)

    Xin Fan

    Full Text Available Candida tropicalis is an important pathogen. Here we developed and evaluated a polymorphic multilocus microsatellite scheme employing novel genetic markers for genotyping of C. tropicalis. Using 10 isolates from 10 unique (separate patients to screen over 4000 tandem repeats from the C. tropicalis genome (strain MYA-3404, six new candidate microsatellite loci (ctm1, ctm3, ctm8, ctm18, ctm24 and ctm26 were selected according to amplification success, observed polymorphisms and stability of flanking regions by preliminary testing. Two known microsatellite loci CT14 and URA3 were also studied. The 6-locus scheme was then tested against a set of 82 different isolates from 32 patients. Microsatellite genotypes of isolates from the same patient (two to five isolates per patient were identical. The six loci produced eight to 17 allele types and identified 11 to 24 genotypes amongst 32 patients' isolates, achieving a discriminatory power (DP of 0.76 to 0.97 (versus 0.78 for both CT14 and URA3 loci, respectively. Testing of a combination of only three loci, ctm1, ctm3 and ctm24, also achieved maximum typing efficiency (DP = 0.99, 29 genotypes. The microsatellite typing scheme had good correlation compared with pulsed-field gel electrophoresis, although was slightly less discriminatory. The new six-locus microsatellite typing scheme is a potentially valuable tool for genotyping and investigating microevolution of C. tropicalis.

  4. DNA Fingerprinting of Olive Varieties by Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dunja Bandelj

    2002-01-01

    Full Text Available Microsatellites combine several features of an ultimate molecular marker and they are used increasingly in various plant genetic studies and applications. In this work we report on the utilisation of fourteen previously developed olive microsatellite markers for the identification and differentiation of a set of nineteen olive varieties. All analysed microsatellite markers revealed a high level of polymorphism that allowed unique genotyping of the examined varieties. Ninety-six alleles were detected at all 14 loci, which multiplied into a large number of observed genotypes, giving high discrimination value for varietal identification. A minimum number of three microsatellite markers was chosen for the rapid and unambiguous varietal identification of nineteen olive varieties and only two markers were sufficient for differentiation of five local varieties. DNA fingerprints of olive cultivars by means of microsatellites provided meaningful data, which can be extended by additional olive varieties or new microsatellites and used for accurate inter-laboratory comparison. The data obtained can be used for the varietal survey and construction of a database of all olive varieties grown in Slovenia providing also additional genetic information on the agronomic and quality characteristics of the olive varieties.

  5. Evaluation of the Effects of Variable Helmet Weight on Human Response During Lateral +Gy Impact

    National Research Council Canada - National Science Library

    Perry, Chris

    2003-01-01

    .... A series of tests was conducted by AFRL/HEPA on a horizontal impulse accelerator using human subjects to investigate the effects of helmet inertial properties on human response to short duration...

  6. Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris)

    Science.gov (United States)

    Pause, K.C.; Nourisson, C.; Clark, A.; Kellogg, M.E.; Bonde, R.K.; McGuire, P.M.

    2007-01-01

    Florida manatees (Trichechus manatus latirostris) are marine mammals that inhabit the coastal waters and rivers of the southeastern USA, primarily Florida. Previous studies have shown that Florida manatees have low mitochondrial DNA variability, suggesting that nuclear DNA loci are necessary for discriminatory analyses. Here we report 10 polymorphic microsatellite loci with an average of 4.2 alleles per locus, and average heterozygosity of 50.1%. These loci have been developed for use in population studies, parentage assignment, and individual identification. ?? 2007 Blackwell Publishing Ltd.

  7. Genetic diversity assessed by microsatellite markers in sweet corn cultivars

    Directory of Open Access Journals (Sweden)

    Ana Daniela Lopes

    2015-12-01

    Full Text Available Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity of sweet corn cultivars. We detected a total of 86 alleles using 30 microsatellite primers. The mean polymorphism was 82 %. The highest heterozygosity values (Ho = 0.20 were found in the PR030-Doce Flor da Serra and BR427 III OPVs, whereas the lowest values (0.14 were recorded in the MG161-Branco Doce and Doce Cubano OPVs. The polymorphism information content ranged from 0.19 (Umc2319 to 0.71 (Umc2205. The analysis of molecular variance revealed that most of the genetic variability was concentrated within the cultivars of sweet corn (75 %, with less variability between them (25 %. The consensus tree derived from the neighbor-joining (NJ algorithm using 1,000 bootstrapping replicates revealed seven genetically different groups. Nei’s diversity values varied between 0.103 (Doce do Hawai × CNPH-1 cultivars and 0.645 (Amarelo Doce × Lili cultivars, indicating a narrow genetic basis. The Lili hybrid was the most distant cultivar, as revealed by Principal Coordinates Analysis and the NJ tree. This study on genetic diversity will be useful for planning future studies on sweet corn genetic resources and can complement the breeding programs for this crop.

  8. Effects of human activities and climate variability on water resources in the Saveh plain, Iran.

    Science.gov (United States)

    Mohammadi Ghaleni, M; Ebrahimi, K

    2015-02-01

    Quantity and quality distribution of surface water and groundwater are changing under the impacts of both climate variability and human activities. The main goal of this paper is to evaluate the abovementioned impacts on the water resources in the Saveh plain, central Iran. To achieve this aim, spatial and temporal changes of the surface and groundwater quality and quantity have been analyzed, using hydrometric and meteorological data. The nonparametric Mann-Kendall test was used to identify trends and change points in the annual rainfall and runoff for the period of 1946 to 2011. In order to analyze the impacts of the Saveh Dam on runoff, the dam operation year, 1994, was considered as a change point. Mann-Kendall test results show that rainfall time series was divided into two parts, namely, 1966-1989 and 1990-2007, and averages of annual rainfall in five stations increase from 10 to 21 %. Also, runoff time series was divided into two parts, namely, 1946-1995 and 1996-2007 and averages of annual runoff in four stations decrease from 8 to 83 %. Results show that rainfall changes in Shahabasi, Razin, Jalayer, Emamabad, and Ahmadabad stations increased from 9 to 33 % before and after 1994. Nevertheless, runoff decreased from 24 to 81 %. The results indicate that the greatest lack of runoff between stations is at Shahabasi station and one important reason for the severe lack is operation of the Saveh Dam in 1994. Highest groundwater level decline, about 168.67 cm, occurred in 1994 that is the operation year of the Saveh Dam. Trend analysis of surface water quality show that electrical conductivity increased 957.34 μmho/cm before and after 1994. Also, the Wilcox water quality classification method has been reduced from C3-S1 to C4-S2. Average groundwater electrical conductivity (EC) during 1999-2003 and 2004-2009 increased to 89.6 μmho/cm. Also, the groundwater quality indices for agricultural usages are classified in four classes including, C4-S2 16, C4-S1 46, C3-S

  9. Microsatellites grant more stable flanking genes

    Directory of Open Access Journals (Sweden)

    Joukhadar Reem

    2012-10-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are DNA sequences that include tandem copies of specific sequences no longer than six bases. SSRs are ubiquitous in all genomes and highly mutable. Presentation of the hypothesis Results from previous studies suggest that flanking regions of SSR are exhibit high stability in a wide range of organisms. We hypothesized that the SSRs ability to discard weak DNA polymerases could be responsible for this unusual stability. . When the weak polymerases are being decayed over SSRs, the flanking sequences would have higher opportunity to be replicated by more stable DNA polymerases. We present evidence of the molecular basis of our hypothesis. Testing the hypothesis The hypothesis could be tested by examining the activity of DNA polymerase during and after a number of PCRs. The PCR reactions should be run with the same SSR locus possessing differences in the SSR length. The hypothesis could also be tested by comparing the mutational rate of a transferred gene between two transformations. The first one has a naked T-DNA (transferred DNA, while the second one has the same T-DNA flanked with two SSRs. Implications of the hypothesis In any transformation experiment, flanking the T-DNA fragment with SSR sequences would result in more stably transferred genes. This process would decrease the unpredictable risks that may occur because of the mutational pressure on this foreign segment.

  10. Microsatellite analysis of medfly bioinfestations in California.

    Science.gov (United States)

    Bonizzoni, M; Zheng, L; Guglielmino, C R; Haymer, D S; Gasperi, G; Gomulski, L M; Malacrida, A R

    2001-10-01

    The Mediterranean fruit fly, Ceratitis capitata, is a destructive agricultural pest with a long history of invasion success. This pest has been affecting different regions of the United States for the past 30 years, but a number of studies of medfly bioinfestations has focused on the situation in California. Although some progress has been made in terms of establishing the origin of infestations, the overall status of this pest in this area remains controversial. Specifically, do flies captured over the years represent independent infestations or the persistence of a resident population? We present an effort to answer this question based on the use of multilocus genotyping. Ten microsatellite loci were used to analyse 109 medflies captured in several infestations within California between 1992 and 1998. Using these same markers, 242 medflies from regions of the world having 'established' populations of this pest including Hawaii, Guatemala, El Salvador, Ecuador, Brazil, Argentina and Peru, were also analysed. Although phylogenetic analysis, amova analysis, the IMMANC assignment test and geneclass exclusion test analysis suggest that some of the medflies captured in California are derived from independent invasion events, analysis of specimens from the Los Angeles basin provides support for the hypothesis that an endemic population, probably derived from Guatemala, has been established.

  11. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

    OpenAIRE

    Ewers-Saucedo, Christine; Zardus, John D.; Wares, John P.

    2016-01-01

    Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, su...

  12. Quantification of collateral flow in humans: a comparison of angiographic, electrocardiographic and hemodynamic variables

    NARCIS (Netherlands)

    van Liebergen, R. A.; Piek, J. J.; Koch, K. T.; de Winter, R. J.; Schotborgh, C. E.; Lie, K. I.

    1999-01-01

    Evaluation of collateral vascular circulation according to hemodynamic variables and its relation to myocardial ischemia. There is limited information regarding the hemodynamic quantification of recruitable collateral vessels. Angiography of the donor coronary artery was performed before and during

  13. Increased heart rate variability but normal resting metabolic rate in hypocretin/orexin-deficient human narcolepsy.

    NARCIS (Netherlands)

    Fronczek, R.; Overeem, S.; Reijntjes, R.; Lammers, G.J.; Dijk, J.G.M.; Pijl, H.

    2008-01-01

    STUDY OBJECTIVES: We investigated autonomic balance and resting metabolic rate to explore their possible involvement in obesity in hypocretin/orexin-deficient narcoleptic subjects. METHODS: Resting metabolic rate (using indirect calorimetry) and variability in heart rate and blood pressure were

  14. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

    DEFF Research Database (Denmark)

    Ecker, Simone; Chen, Lu; Pancaldi, Vera

    2017-01-01

    Background: A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results: We apply a novel analytical approach to measure and compare transcriptional and epigenetic v...

  15. A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence.

    Science.gov (United States)

    Grattapaglia, Dario; Mamani, Eva M C; Silva-Junior, Orzenil B; Faria, Danielle A

    2015-03-01

    Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus. © 2014 John Wiley & Sons Ltd.

  16. Shape of the orbital opening: individual characterization and analysis of variability in modern humans, Gorilla gorilla, and Pan troglodytes.

    Science.gov (United States)

    Schmittbuhl, M; Le Minor, J M; Allenbach, B; Schaaf, A

    1999-05-01

    The description of the human orbital shape is principally qualitative in the classical literature, and characterised by adjectives such as circular, rectangular or quadrangular. In order to provide a precise quantification and interpretation of this shape, a study based on automatic image analysis and Fourier analysis was carried out on 45 human skulls (30 males, 15 females), and for comparison on 61 skulls of Gorilla gorilla (40 males, 21 females), and 34 skulls of Pan troglodytes (20 males, 14 females). Sexual dimorphism in the shape of the orbital opening was not demonstrated. Its dominant morphological features could be characterized by Fourier analysis; elliptical elongation and quadrangularity were dominant morphological features of the shape of the orbital opening in the three species. Elliptical elongation was more marked in humans and Pan, whereas quadrangularity was particularly emphasized in Gorilla. An intraspecific variability of the shape of the orbital opening existed in humans, Gorilla and Pan, and seemed close in the three species. Interspecific partition between humans, Gorilla and Pan was demonstrated despite the variability observed in the three species studied. Interspecific differences between Gorilla and the Pan-humans group were principally explained by the differences in quadrangularity, and by differences in orientation of triangularity and pentagonality. Differences in the shape of the orbital opening between humans and Pan were principally explained by differences in hexagonality, and by differences in orientation of quadrangularity. A closeness of shape between some humans and some individuals in Pan and, to a lesser degree, with some individuals in Gorilla was observed, demonstrating the existence of a morphological continuum of the shape of the orbital opening in hominoids.

  17. Fault trees and the impact of human variability on probabilistic risk analysis

    International Nuclear Information System (INIS)

    1983-01-01

    It has long been recognized that human reliability is an important factor in probabilistic risk analysis. In the field, this is true in a direct operational sense as well as in the areas of installation and maintenance. The interest in quantification arises from the desire to achieve optimum design in the human factors sense (operability-maintainability) and from the need to include human reliability considerations in probabilistic risk analysis to achieve complete and valid risk evaluation. In order to integrate human reliability into the system analysis, it is necessary to consider two questions. These relate to the way that human functions fit into the existing analytical models and methods as well as the nature of human failure mechanisms, modes and failure (error) rates

  18. A new set of microsatellite markers for the peach palm (Bactris gasipaes Kunth): characterization and across-taxa utility within the tribe Cocoeae.

    NARCIS (Netherlands)

    Billotte, N.; Couvreur, T.L.P.; Marseillac, P.; Brottier, P.; Perthuis, B.; Vallejo, M.; Noyer, J.L.; Jacquemoud, J.P.; Risterucci, A.M.; Pintaud, J.C.

    2004-01-01

    A (GA)n microsatellite-enriched library was constructed and a new set of 18 nuclear simple sequence repeat loci was isolated in Bactris gasipaes var. gasipaes. The loci were found to be highly variable in the target species and readily transferable to related Bactris species as well as to the

  19. Probabilistic tractography recovers a rostrocaudal trajectory of connectivity variability in the human insular cortex

    NARCIS (Netherlands)

    Cerliani, Leonardo; Thomas, Rajat M.; Jbabdi, Saad; Siero, Jeroen C. W.; Nanetti, Luca; Crippa, Alessandro; Gazzola, Valeria; D'Arceuil, Helen; Keysers, Christian

    The insular cortex of macaques has a wide spectrum of anatomical connections whose distribution is related to its heterogeneous cytoarchitecture. Although there is evidence of a similar cytoarchitectural arrangement in humans, the anatomical connectivity of the insula in the human brain has not yet

  20. Accounting for human variability and sensitivity in setting standards for electromagnetic fields.

    Science.gov (United States)

    Bailey, William H; Erdreich, Linda S

    2007-06-01

    Biological sensitivity and variability are key issues for risk assessment and standard setting. Variability encompasses general inter-individual variations in population responses, while sensitivity relates to unusual or extreme responses based on genetic, congenital, medical, or environmental conditions. For risk assessment and standard setting, these factors affect estimates of thresholds for effects and dose-response relationships and inform efforts to protect the more sensitive members of the population, not just the typical or average person. While issues of variability and sensitivity can be addressed by experimental and clinical studies of electromagnetic fields, investigators have paid little attention to these important issues. This paper provides examples that illustrate how default assumptions regarding variability can be incorporated into estimates of 60-Hz magnetic field exposures with no risk of cardiac stimulation and how population thresholds and variability of peripheral nerve stimulation responses at 60-Hz can be estimated from studies of pulsed gradient magnetic fields in magnetic resonance imaging studies. In the setting of standards for radiofrequency exposures, the International Commission for Non-Ionizing Radiation Protection uses inter-individual differences in thermal sensitivity as one of the considerations in the development of "safety factors." However, neither the range of sensitivity nor the sufficiency or excess of the 10-fold and the additional 5-fold safety factors have been assessed quantitatively. Data on the range of responses between median and sensitive individuals regarding heat stress and cognitive function should be evaluated to inform a reassessment of these safety factors and to identify data gaps.

  1. A universal system for highly efficient cardiac differentiation of human induced pluripotent stem cells that eliminates interline variability.

    Directory of Open Access Journals (Sweden)

    Paul W Burridge

    2011-04-01

    Full Text Available The production of cardiomyocytes from human induced pluripotent stem cells (hiPSC holds great promise for patient-specific cardiotoxicity drug testing, disease modeling, and cardiac regeneration. However, existing protocols for the differentiation of hiPSC to the cardiac lineage are inefficient and highly variable. We describe a highly efficient system for differentiation of human embryonic stem cells (hESC and hiPSC to the cardiac lineage. This system eliminated the variability in cardiac differentiation capacity of a variety of human pluripotent stem cells (hPSC, including hiPSC generated from CD34(+ cord blood using non-viral, non-integrating methods.We systematically and rigorously optimized >45 experimental variables to develop a universal cardiac differentiation system that produced contracting human embryoid bodies (hEB with an improved efficiency of 94.7±2.4% in an accelerated nine days from four hESC and seven hiPSC lines tested, including hiPSC derived from neonatal CD34(+ cord blood and adult fibroblasts using non-integrating episomal plasmids. This cost-effective differentiation method employed forced aggregation hEB formation in a chemically defined medium, along with staged exposure to physiological (5% oxygen, and optimized concentrations of mesodermal morphogens BMP4 and FGF2, polyvinyl alcohol, serum, and insulin. The contracting hEB derived using these methods were composed of high percentages (64-89% of cardiac troponin I(+ cells that displayed ultrastructural properties of functional cardiomyocytes and uniform electrophysiological profiles responsive to cardioactive drugs.This efficient and cost-effective universal system for cardiac differentiation of hiPSC allows a potentially unlimited production of functional cardiomyocytes suitable for application to hPSC-based drug development, cardiac disease modeling, and the future generation of clinically-safe nonviral human cardiac cells for regenerative medicine.

  2. EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

    Directory of Open Access Journals (Sweden)

    Grover Atul

    2007-07-01

    Full Text Available Abstract Background Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database http://ipu.ac.in/usbt/EuMicroSatdb.htm is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes. Description A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP. The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect, repeat unit length (mono- to hexa-nucleotide, repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided. Conclusion The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.

  3. The strv 1 microsatellite semes: Exploiting the geosynchronous transfer orbit

    Science.gov (United States)

    Blott, R. J.; Wells, N. S.; Eves, J.

    Following 3 successful years in orbit, the UK Defence Evaluation and Research Agency's two Space Technology Research Vehicle microsatellites (STRV) 1 a&b will be followed by a second mission. STRV 1 c&d are now in construction for a planned launch in 1999. The new mission, which includes 22 experimental payloads and developmental spacecraft bus technologies from European, US and Canadian military, civil and commercial sponsors, exploits the Geosynchronous Transfer Orbit (GTO) to offer an affordable, working space research tool for both government and industry. The STRV 1 programme objective is to promote the enhancement of military and civil space communications, remote sensing and navigation capabilities at reduced cost and risk. Additional aims are to help industry to achieve commercial benefit from investment in emerging technologies and to develop the synergy between government, commercial and civilian space applications. The paper explains how STRV 1 exploits the variable altitude and high radiation environment of GTO to investigate the performance of emerging technologies and techniques. This includes the accelerated life testing of components and materials, such as infra-red detectors, advanced microprocessors and solar cell technologies, and the prototyping of new techniques to improve communications and spacecraft autonomy. Experiments include implementing a secure version of the Consultative Committee for Space Data Systems (CCSDS) packet telecommand and telemetry standards, further development of the Internet-based Space Communication Protocol Standards (SCPS) and evaluating the exploitation of the Global Positioning System (GPS) in geosynchronous orbit. The new mission also builds on and extends the comprehensive environmental monitoring achieved by STRV 1 a&b.

  4. Analysis of the in vivo confocal Raman spectral variability in human skin

    Science.gov (United States)

    Mogilevych, Borys; dos Santos, Laurita; Rangel, Joao L.; Grancianinov, Karen J. S.; Sousa, Mariane P.; Martin, Airton A.

    2015-06-01

    Biochemical composition of the skin changes in each layer and, therefore, the skin spectral profile vary with the depth. In this work, in vivo Confocal Raman spectroscopy studies were performed at different skin regions and depth profile (from the surface down to 10 μm) of the stratum corneum, to verify the variability and reproducibility of the intra- and interindividual Raman data. The Raman spectra were collected from seven healthy female study participants using a confocal Raman system from Rivers Diagnostic, with 785 nm excitation line and a CCD detector. Measurements were performed in the volar forearm region, at three different points at different depth, with the step of 2 μm. For each depth point, three spectra were acquired. Data analysis included the descriptive statistics (mean, standard deviation and residual) and Pearson's correlation coefficient calculation. Our results show that inter-individual variability is higher than intraindividual variability, and variability inside the SC is higher than on the skin surface. In all these cases we obtained r values, higher than 0.94, which correspond to high correlation between Raman spectra. It reinforces the possibility of the data reproducibility and direct comparison of in vivo results obtained with different study participants of the same age group and phototype.

  5. [Variability of the sensitivity of human lymphocytes to the antiproliferative action of alkylating agents].

    Science.gov (United States)

    Veremko, L N; Telegin, L Iu; Pevnitskii, L A

    1983-05-01

    A study was made of variability of the sensitivity of peripheral blood lymphocytes from different donors to an antiproliferative action of cyclophosphamide and thiophosphamide. A similar degree of the sensitivity was revealed to alkylating agents differing in the action mode, with this degree being independent of the "stimulation index" magnitude.

  6. Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

    Directory of Open Access Journals (Sweden)

    Lígia Regina Lima Gouvêa

    2010-01-01

    Full Text Available Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC, Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (H T' = 0.58 and high gene differentiation (Gst' = 0.61 were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

  7. Variability in the Geographic Distribution of Fires in Interior Alaska Considering Cause, Human Proximity, and Level of Suppression

    Science.gov (United States)

    Calef, M. P.; Varvak, A.; McGuire, A. D.; Chapin, T.

    2015-12-01

    The boreal forest of Interior Alaska is characterized by frequent extensive wildfires that have been mapped for the past 70 years. Simple predictions based on this record indicate that area burned will increase as a response to climate warming in Alaska. However, two additional factors have affected the area burned in this time record: the Pacific Decadal Oscillation (PDO) switched from cool and moist to warm and dry in the late 1970s and the Alaska Fire Service instituted a fire suppression policy in the late 1980s. Using Geographic Information Systems (GIS) and statistics, this presentation evaluates the variability in area burned and fire ignitions in Interior Alaska in space and time with particular emphasis on the human influence via ignition and suppression. Our analysis shows that while area burned has been increasing by 2.4% per year, the number of lightning ignitions has decreased by 1.9 ignitions per year. Human ignitions account for 50% of all fire ignitions in Interior Alaska and are clearly influenced by human proximity: human fires mostly occur close to settlements, highways and in intense fire suppression zones (which are in turn close to human settlements and roads); fires close to settlements, highways and in intense fire suppression zones burn much shorter than fires further away from this sphere of human influence; and 60% of all human fire ignitions in Interior Alaska are concentrated in the Fairbanks area and thereby strongly influence regional analyses. Fire suppression has effectively reduced area burned since it was implemented but the PDO change has also had some influence. Finally, we found that human fires start earlier in the year and burn for a shorter duration than lightning fires. This study provides insights into the importance of human behavior as well as regional climate patterns as large-scale controls on fires over time and across the Alaskan boreal forest.

  8. Differential Responding by Rhesus Monkeys (Macaca mulatta and Humans (Homo sapiens to Variable Outcomes in the Assurance Game

    Directory of Open Access Journals (Sweden)

    Audrey E. Parrish

    2014-08-01

    Full Text Available Behavioral flexibility in how one responds to variable partner play can be examined using economic coordination games in which subjects play against a variety of partners and therefore may need to alter their behavior to produce the highest payoff. But how do we study this behavioral flexibility once players have settled on a response? Here, we investigated how responding by rhesus monkeys (Macaca mulatta and humans (Homo sapiens playing a computerized single-player version of a coordination game, the Assurance game, changed as a function of the variable responses (Stag/Hare generated by multiple simulations (SIMs. We were interested in whether individuals could track and differentially respond to changing frequencies of Stag and Hare play by the SIMs, especially with regard to the payoff dominant (Stag-Stag outcome, something that could not be done with real partners as they quickly settled on the Stag response. For both monkeys and humans, there was a linear relationship between proportion of Stag play by the subject and the likelihood of the Stag choice by the SIM such that both species increased their use of Stag as the SIM increased its use of the Stag response. However, humans more closely matched their proportion of Stag responses to that of the SIM, whereas monkeys adopted a different, but equally effective, strategy of exploiting the higher-paying Stag alternative. These results suggest that monkeys and humans demonstrate sensitivity to a dynamic game environment in which they encounter variable contingencies for the same response options, although they may employ different strategies to maximize reward.

  9. Do climate variables and human density affect Achatina fulica (Bowditch) (Gastropoda: Pulmonata) shell length, total weight and condition factor?

    Science.gov (United States)

    Albuquerque, F S; Peso-Aguiar, M C; Assunção-Albuquerque, M J T; Gálvez, L

    2009-08-01

    The length-weight relationship and condition factor have been broadly investigated in snails to obtain the index of physical condition of populations and evaluate habitat quality. Herein, our goal was to describe the best predictors that explain Achatina fulica biometrical parameters and well being in a recently introduced population. From November 2001 to November 2002, monthly snail samples were collected in Lauro de Freitas City, Bahia, Brazil. Shell length and total weight were measured in the laboratory and the potential curve and condition factor were calculated. Five environmental variables were considered: temperature range, mean temperature, humidity, precipitation and human density. Multiple regressions were used to generate models including multiple predictors, via model selection approach, and then ranked with AIC criteria. Partial regressions were used to obtain the separated coefficients of determination of climate and human density models. A total of 1.460 individuals were collected, presenting a shell length range between 4.8 to 102.5 mm (mean: 42.18 mm). The relationship between total length and total weight revealed that Achatina fulica presented a negative allometric growth. Simple regression indicated that humidity has a significant influence on A. fulica total length and weight. Temperature range was the main variable that influenced the condition factor. Multiple regressions showed that climatic and human variables explain a small proportion of the variance in shell length and total weight, but may explain up to 55.7% of the condition factor variance. Consequently, we believe that the well being and biometric parameters of A. fulica can be influenced by climatic and human density factors.

  10. Do climate variables and human density affect Achatina fulica (Bowditch (Gastropoda: Pulmonata shell length, total weight and condition factor?

    Directory of Open Access Journals (Sweden)

    FS. Albuquerque

    Full Text Available The length-weight relationship and condition factor have been broadly investigated in snails to obtain the index of physical condition of populations and evaluate habitat quality. Herein, our goal was to describe the best predictors that explain Achatina fulica biometrical parameters and well being in a recently introduced population. From November 2001 to November 2002, monthly snail samples were collected in Lauro de Freitas City, Bahia, Brazil. Shell length and total weight were measured in the laboratory and the potential curve and condition factor were calculated. Five environmental variables were considered: temperature range, mean temperature, humidity, precipitation and human density. Multiple regressions were used to generate models including multiple predictors, via model selection approach, and then ranked with AIC criteria. Partial regressions were used to obtain the separated coefficients of determination of climate and human density models. A total of 1.460 individuals were collected, presenting a shell length range between 4.8 to 102.5 mm (mean: 42.18 mm. The relationship between total length and total weight revealed that Achatina fulica presented a negative allometric growth. Simple regression indicated that humidity has a significant influence on A. fulica total length and weight. Temperature range was the main variable that influenced the condition factor. Multiple regressions showed that climatic and human variables explain a small proportion of the variance in shell length and total weight, but may explain up to 55.7% of the condition factor variance. Consequently, we believe that the well being and biometric parameters of A. fulica can be influenced by climatic and human density factors.

  11. Gene expression signatures for colorectal cancer microsatellite status and HNPCC

    DEFF Research Database (Denmark)

    Kruhøffer, M; Jensen, J L; Laiho, P

    2005-01-01

    The majority of microsatellite instable (MSI) colorectal cancers are sporadic, but a subset belongs to the syndrome hereditary non-polyposis colorectal cancer (HNPCC). Microsatellite instability is caused by dysfunction of the mismatch repair (MMR) system that leads to a mutator phenotype, and MSI...... of 101 stage II and III colorectal cancers (34 MSI, 67 microsatellite stable (MSS)) using high-density oligonucleotide microarrays. From these data, we constructed a nine-gene signature capable of separating the mismatch repair proficient and deficient tumours. Subsequently, we demonstrated...... is correlated to prognosis and response to chemotherapy. Gene expression signatures as predictive markers are being developed for many cancers, and the identification of a signature for MMR deficiency would be of interest both clinically and biologically. To address this issue, we profiled the gene expression...

  12. The Ventasso Horse: genetic characterization by microsatellites markers

    Directory of Open Access Journals (Sweden)

    M. Blasi

    2010-04-01

    Full Text Available The genetic structure of Ventasso Horse (VH was investigated using 12 microsatellites. The analyses were carried out on 117 VH individuals and the results were compared with those obtained analysing 11 other breeds reared in Italy. All microsatellites were polymorphic in VH and in the other breeds. A total of 124 alleles (from 6 to 19 alleles per microsatellite were detected. Average heterozygosity was 0.743 in VH and ranged from 0.613 to 0.759 in the other breeds. The mean FST value had an average value of 0.0932. Genetic distances were calculated using Nei’s standard genetic distance (Ds. The smallest Ds values were found between VH and Anglo-Arab, Thoroughbred, Maremmano and Lipizzan horse breeds. Phylogenetic trees constructed using neighbour-joining method showed two clear separate clusters: the first includes Bardigiano, Haflinger and Italian Heavy Draught Horse, the second contains the other 9 breeds.

  13. Tracing Asian seabass individuals to single fish farms using microsatellites.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    Full Text Available Traceability through physical labels is well established, but it is not highly reliable as physical labels can be easily changed or lost. Application of DNA markers to the traceability of food plays an increasingly important role for consumer protection and confidence building. In this study, we tested the efficiency of 16 polymorphic microsatellites and their combinations for tracing 368 fish to four populations where they originated. Using the maximum likelihood and Bayesian methods, three most efficient microsatellites were required to assign over 95% of fish to the correct populations. Selection of markers based on the assignment score estimated with the software WHICHLOCI was most effective in choosing markers for individual assignment, followed by the selection based on the allele number of individual markers. By combining rapid DNA extraction, and high-throughput genotyping of selected microsatellites, it is possible to conduct routine genetic traceability with high accuracy in Asian seabass.

  14. Tracing Asian Seabass Individuals to Single Fish Farms Using Microsatellites

    Science.gov (United States)

    Yue, Gen Hua; Xia, Jun Hong; Liu, Peng; Liu, Feng; Sun, Fei; Lin, Grace

    2012-01-01

    Traceability through physical labels is well established, but it is not highly reliable as physical labels can be easily changed or lost. Application of DNA markers to the traceability of food plays an increasingly important role for consumer protection and confidence building. In this study, we tested the efficiency of 16 polymorphic microsatellites and their combinations for tracing 368 fish to four populations where they originated. Using the maximum likelihood and Bayesian methods, three most efficient microsatellites were required to assign over 95% of fish to the correct populations. Selection of markers based on the assignment score estimated with the software WHICHLOCI was most effective in choosing markers for individual assignment, followed by the selection based on the allele number of individual markers. By combining rapid DNA extraction, and high-throughput genotyping of selected microsatellites, it is possible to conduct routine genetic traceability with high accuracy in Asian seabass. PMID:23285169

  15. Detection of Sequence Polymorphism in Rubus Occidentalis L. Monomorphic Microsatellite Markers by High Resolution Melting

    Science.gov (United States)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. Development of microsatellite primers through the identification of appropriate repeate...

  16. Rainfall erosivity and sediment load over the Poyang Lake Basin under variable climate and human activities since the 1960s

    Science.gov (United States)

    Gu, Chaojun; Mu, Xingmin; Gao, Peng; Zhao, Guangju; Sun, Wenyi; Yu, Qiang

    2018-03-01

    Accelerated soil erosion exerts adverse effects on water and soil resources. Rainfall erosivity reflects soil erosion potential driven by rainfall, which is essential for soil erosive risk assessment. This study investigated the spatiotemporal variation of rainfall erosivity and its impacts on sediment load over the largest freshwater lake basin of China (the Poyang Lake Basin, abbreviate to PYLB). The spatiotemporal variations of rainfall erosivity from 1961 to 2014 based on 57 meteorological stations were detected using the Mann-Kendall test, linear regression, and kriging interpolation method. The sequential t test analysis of regime shift (STARS) was employed to identify the abrupt changes of sediment load, and the modified double mass curve was used to assess the impacts of rainfall erosivity variability on sediment load. It was found that there was significant increase (P change-points were identified in both 1985 and 2003. It was found that take annual rainfall erosivity as the explanatory variables of the double mass curves is more reasonable than annual rainfall and erosive rainfall. The estimation via the modified double mass curve demonstrated that compared with the period before change-point (1961-1984), the changes of rainfall erosivity increased 8.0 and 2.1% of sediment load during 1985-2002 and 2003-2014, respectively. Human activities decreased 50.2 and 69.7% of sediment load during the last two periods, which indicated effects of human activities on sediment load change was much larger than that of rainfall erosivity variability in the PYLB.

  17. Use of a variable tracer infusion method to determine glucose turnover in humans

    International Nuclear Information System (INIS)

    Molina, J.M.; Baron, A.D.; Edelman, S.V.; Brechtel, G.; Wallace, P.; Olefsky, J.M.

    1990-01-01

    The single-compartment pool fraction model, when used with the hyperinsulinemic glucose clamp technique to measure rates of glucose turnover, sometimes underestimates true rates of glucose appearance (Ra) resulting in negative values for hepatic glucose output (HGO). We focused our attention on isotope discrimination and model error as possible explanations for this underestimation. We found no difference in [3-3H] glucose specific activity in samples obtained simultaneously from the femoral artery and vein (2,400 +/- 455 vs. 2,454 +/- 522 dpm/mg) in 6 men during a hyperinsulinemic euglycemic clamp study where insulin was infused at 40 mU.m-2.min-1 for 3 h; therefore, isotope discrimination did not occur. We compared the ability of a constant (0.6 microCi/min) vs. variable tracer infusion method (tracer added to the glucose infusate) to measure non-steady-state Ra during hyperinsulinemic clamp studies. Plasma specific activity fell during the constant tracer infusion studies but did not change from base line during the variable tracer infusion studies. By maintaining a constant plasma specific activity the variable tracer infusion method eliminates uncertainty about changes in glucose pool size. This overcame modeling error and more accurately measures non-steady-state Ra (P less than 0.001 by analysis of variance vs. constant infusion method). In conclusion, underestimation of Ra determined isotopically during hyperinsulinemic clamp studies is largely due to modeling error that can be overcome by use of the variable tracer infusion method. This method allows more accurate determination of Ra and HGO under non-steady-state conditions

  18. Human Vulnerability to Climate Variability in the Sahel: Farmers' Adaptation Strategies in Northern Burkina Faso

    Science.gov (United States)

    Barbier, Bruno; Yacouba, Hamma; Karambiri, Harouna; Zoromé, Malick; Somé, Blaise

    2009-05-01

    In this study, the authors investigate farmers’ vulnerability to climate variability and evaluate local adoption of technology and farmers’ perceptions of adaptation strategies to rainfall variability and policies. A survey was conducted in a community in northern Burkina Faso following the crop failure of 2004. In 2006, following a better harvest, another survey was conducted to compare farmers’ actions and reactions during two contrasted rainy seasons. The results confirm that farmers from this community have substantially changed their practices during the last few decades. They have adopted a wide range of techniques that are intended to simultaneously increase crop yield and reduce yield variability. Micro water harvesting (Zaï) techniques have been widely adopted (41%), and a majority of fields have been improved with stone lines (60%). Hay (48%) and sorghum residues are increasingly stored to feed animals during the dry season, making bull and sheep fattening now a common practice. Dry season vegetable production also involves a majority of the population (60%). According to farmers, most of the new techniques have been adopted because of growing land scarcity and new market opportunities, rather than because of climate variability. Population pressure has reached a critical threshold, while land scarcity, declining soil fertility and reduced animal mobility have pushed farmers to intensify agricultural production. These techniques reduce farmers’ dependency on rainfall but are still insufficient to reduce poverty and vulnerability. Thirty-nine percent of the population remains vulnerable after a good rainy season. Despite farmers’ desire to remain in their own communities, migrations are likely to remain a major source of regular income and form of recourse in the event of droughts.

  19. Variability of excretion rates of 210Pb and 210Po of humans at environmental levels

    International Nuclear Information System (INIS)

    Spencer, H.; Holtzman, R.B.; Ilcewicz, F.H.; Kramer, L.

    1977-01-01

    Variability of the excretion rates of the nuclides 210 Pb and 210 Po at natural levels was studied in a group of samples collected from men maintained under the carefully controlled conditions of a metabolic ward. They consumed only the standard diet of the ward in which they had been resident for at least several months prior to this study. The mean urinary rates were about 0.1 to 0.5 pCi/day for both 210 Pb and 210 Po, while fecal rates ranged from 1 to 2.7 pCi/day for the two nuclides. For urinary 210 Pb the coefficients of variation (ratio of standard deviation to mean) for three subjects ranged from 19 to 45 percent for eight continuous 24-hr samples compared to 11 to 13 percent for subsequently collected multiday samples (4 to 9 days each) for each subject. However, the standard errors of the means for the one day collections were about equal to the standard deviations of the pooled samples. Similar variability was noted for the 210 Po data. Six day fecal collections from these time periods exhibited higher variabilities than did the urine, from about 12 percent to 50 percent for each of the nuclides. Multiday collections for 12 subjects showed mean coefficients of variation of about 16 percent for 210 Pb and 13 percent for the 210 Po for urine and 21 and 25 percent, respectively, in fecal collections. Since dietary intake was maintained fairly constant, excreta collections were carefully controlled, and the analytical precision was about 5 percent, these variabilities appear to be due to biological variations and are characteristic of the individuals studied. Some possible causes of these effects are discussed

  20. [Cognitive complaints in people with human immunodeficiency virus in Spain: prevalence and related variables].

    Science.gov (United States)

    Muñoz-Moreno, José A; Fuster-Ruiz de Apodaca, Maria J; Fumaz, Carmina R; Ferrer, Maria J; Molero, Fernando; Jaen, Àngels; Clotet, Bonaventura; Dalmau, David

    2014-05-20

    Cognitive complaints have been scarcely studied in people with HIV in Spain. The aim of this research was to know the prevalence of cognitive complaints in HIV-infected people, as well as its potential relationships with demographic, clinical and psychological variables, in the era of combination antiretroviral therapies. Observational multicenter study developed in 4 hospitals and 10 NGOs, in which 791 people with HIV in Spain participated. A self-reported questionnaire was used to evaluate demographic and clinical variables, and an assessment of cognitive complaints, emotional status and quality of life variables was also included. Descriptive and inferential tests were used for statistical analyses. Almost half of the sample (49.8%) referred cognitive complaints, in 72.1% of them an association with interference on daily living activities was found. Memory and attention were the areas most prevalently perceived as affected. The existence of cognitive complaints correlated with a longer HIV infection, lower CD4+ cell count, undetectable viral load and worse quality of life. A discriminant analysis determined that depression, anxiety, older age, living with no partner and low education level allowed to classify optimally HIV-infected people with cognitive complaints. Self-reported cognitive complaints are frequent in people infected with HIV in the current era of combination antiretroviral therapies. This fact is related to emotional disturbances and poor quality of life, but also to impaired immunological and virological status. Copyright © 2012 Elsevier España, S.L. All rights reserved.

  1. Characterization of small microsatellite loci for use in non invasive sampling studies of Gunnison Sage-grouse (Centrocercus minimus)

    Science.gov (United States)

    Oyler-McCance, Sara J.; St. John, Judy

    2010-01-01

    Primers for 10 microsatellite loci were developed specifically to amplify low quantity and quality DNA for Gunnison Sage-grouse (Centrocercus minimus), a species that has been petitioned for listing under the US Endangered Species Act. In a screen of 20 individuals from the largest population in the Gunnison Basin, Colorado, the 10 loci were found to have levels of variability ranging from two to seven alleles. No loci were found to be linked, although one locus revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci will be applicable for population genetic analyses and for use in mark recapture studies that utilize DNA collected non invasively from feathers and fecal pellets, which will ultimately aid in management efforts.

  2. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

  3. Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

    Science.gov (United States)

    Rout, P. K.; Thangraj, K.; Mandal, A.; Roy, R.

    2012-01-01

    Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation

  4. Polyploidy in the Olive Complex (Olea europaea): Evidence from Flow Cytometry and Nuclear Microsatellite Analyses

    Science.gov (United States)

    Besnard, G.; Garcia-Verdugo, C.; Rubio De Casas, R.; Treier, U. A.; Galland, N.; Vargas, P.

    2008-01-01

    Background Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites to assess the presence of multiple alleles at co-dominant loci. In addition, nine individuals from a controlled cross between two individuals of O. europaea subsp. maroccana were characterized with microsatellites to check for chromosome inheritance. Key Results Based on flow cytometry and genetic analyses, strong evidence for polyploidy was obtained in subspp. cerasiformis (tetraploid) and maroccana (hexaploid), whereas the other subspecies appeared to be diploids. Agreement between flow cytometry and genetic analyses gives an alternative approach to chromosome counting to determine ploidy level of trees. Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation of tetraploids and hexaploids may have played a major role in the diversification of the olive complex in north-west Africa. The fact that polyploidy is found in narrow endemic subspecies from Madeira (subsp. cerasiformis) and the Agadir Mountains (subsp. maroccana) suggests that polyploidization has been favoured to overcome inbreeding depression. Lastly, based on previous phylogenetic analyses, we hypothesize that subsp. cerasiformis resulted from hybridization between ancestors

  5. Polymorphic microsatellite markers in the invasive shrub Buddleja davidii (Scrophulariaceae).

    Science.gov (United States)

    Schreiter, Susanne; Ebeling, Susan K; Durka, Walter

    2011-02-01

    Microsatellite primers were developed for the invasive plant Buddleja davidii, a Chinese shrub that is an invader in most other continents. An invasive population was analyzed using eight di- and tetranucleotide microsatellite loci. The number of alleles per locus ranged from 5 to 14. Due to polyploidy, exact genotypes could not be determined. Progeny arrays were used to study the outcrossing rate using presence/absence data of alleles resulting in an estimate of multilocus outcrossing rate of 93%. The markers were successfully tested in five congeneric species. The results indicate the utility of these loci in future studies of population genetics and breeding systems in B. davidii and in congeneric species.

  6. Microsatellite loci isolated from the scleractinian coral, Acropora nobilis.

    Science.gov (United States)

    Isomura, Naoko; Hidaka, Michio

    2008-05-01

    We report the isolation and characterization of eight microsatellite loci from the scleractinian coral, Acropora nobilis. The microsatellite loci were obtained using compound SSR primers or an enrichment protocol. All the loci were polymorphic with four to eight alleles per locus and observed heterozygosities ranging from 0.22 to 0.76. Some of the primers developed for the two congeners, Acropora palmata and Acropora millepora were applicable to A. nobilis. These loci are useful for studying the connectivity among A. nobilis populations in Okinawa, southern Japan. © 2007 The Authors.

  7. Accounting for pH heterogeneity and variability in modelling human health risks from cadmium in contaminated land

    International Nuclear Information System (INIS)

    Gay, J. Rebecca; Korre, Anna

    2009-01-01

    The authors have previously published a methodology which combines quantitative probabilistic human health risk assessment and spatial statistical methods (geostatistics) to produce an assessment, incorporating uncertainty, of risks to human health from exposure to contaminated land. The model assumes a constant soil to plant concentration factor (CF veg ) when calculating intake of contaminants. This model is modified here to enhance its use in a situation where CF veg varies according to soil pH, as is the case for cadmium. The original methodology uses sequential indicator simulation (SIS) to map soil concentration estimates for one contaminant across a site. A real, age-stratified population is mapped across the contaminated area, and intake of soil contaminants by individuals is calculated probabilistically using an adaptation of the Contaminated Land Exposure Assessment (CLEA) model. The proposed improvement involves not only the geostatistical estimation of the contaminant concentration, but also that of soil pH, which in turn leads to a variable CF veg estimate which influences the human intake results. The results presented demonstrate that taking pH into account can influence the outcome of the risk assessment greatly. It is proposed that a similar adaptation could be used for other combinations of soil variables which influence CF veg .

  8. An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.

    Science.gov (United States)

    Burel, Julie G; Qian, Yu; Lindestam Arlehamn, Cecilia; Weiskopf, Daniela; Zapardiel-Gonzalo, Jose; Taplitz, Randy; Gilman, Robert H; Saito, Mayuko; de Silva, Aruna D; Vijayanand, Pandurangan; Scheuermann, Richard H; Sette, Alessandro; Peters, Bjoern

    2017-02-15

    In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. In this study, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed the technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intraindividual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high interindividual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naive T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these covariates in immune profiling studies. We also exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies. Copyright © 2017 by The American Association of Immunologists, Inc.

  9. Variable epitope libraries: new vaccine immunogens capable of inducing broad human immunodeficiency virus type 1-neutralizing antibody response.

    Science.gov (United States)

    Charles-Niño, Claudia; Pedroza-Roldan, Cesar; Viveros, Monica; Gevorkian, Goar; Manoutcharian, Karen

    2011-07-18

    The extreme antigenic variability of human immunodeficiency virus (HIV) leads to immune escape of the virus, representing a major challenge in the design of effective vaccine. We have developed a novel concept for immunogen construction based on introduction of massive mutations within the epitopes targeting antigenically variable pathogens and diseases. Previously, we showed that these immunogens carrying large combinatorial libraries of mutated epitope variants, termed as variable epitope libraries (VELs), induce potent, broad and long lasting CD8+IFN-γ+ T-cell response. Moreover, we demonstrated that these T cells recognize more than 50% of heavily mutated variants (5 out of 10 amino acid positions were mutated in each epitope variant) of HIV-1 gp120 V3 loop-derived cytotoxic T lymphocyte epitope (RGPGRAFVTI) in mice. The constructed VELs had complexities of 10000 and 12500 individual members, generated as plasmid DNA or as M13 phage display combinatorial libraries, respectively, and with structural composition RGPGXAXXXX or XGXGXAXVXI, where X is any of 20 natural amino acids. Here, we demonstrated that sera from mice immunized with these VELs are capable of neutralizing 5 out of 10 viral isolates from Tier 2 reference panel of subtype B envelope clones, including HIV-1 isolates which are known to be resistant to neutralization by several potent monoclonal antibodies, described previously. These data indicate the feasibility of the application of immunogens based on VEL concept as an alternative approach for the development of molecular vaccines against antigenically variable pathogens. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Analysis of beta-catenin, Ki-ras, and microsatellite stability in azoxymethane-induced colon tumors of BDIX/Orl Ico rats

    DEFF Research Database (Denmark)

    Sørensen, Nanna Møller; Kobaek-Larsen, Morten; Bonne, Anita

    2003-01-01

    The aim of the study reported here was to investigate whether the azoxymethane (AOM)-induced colon cancer rat model mimics the human situation with regard to microsatellite stability, changes in expression of beta-catenin, and/or changes in the sequence of the proto-oncogene Ki-ras. Colon cancer ...

  11. Natural and human-induced variability in the composition of fish assemblages in the Northwestern Cuban shelf.

    Science.gov (United States)

    González-Sansón, Gaspar; Aguilar, Consuelo; Hernández, Ivet; Cabrera, Yureidy; Suarez-Montes, Noelis; Bretos, Fernando; Guggenheim, David

    2009-09-01

    The main goal of the study was to obtain field data to build a baseline of fish assemblage composition that can be used comparatively for future analyses of the impact of human actions in the region. A basic network of 68 sampling stations was defined for the entire region (4,050 km2). Fish assemblage species and size composition was estimated using visual census methods at three different spatial scales: a) entire region, b) inside the main reef area and c) along a human impact coastal gradient. Multivariate numerical analyses revealed habitat type as the main factor inducing spatial variability of fish community composition, while the level of human impact appears to play the main role in fish assemblage composition changes along the coast. A trend of decreasing fish size toward the east supports the theory of more severe human impact due to overfishing and higher urban pollution in that direction. This is the first detailed study along the northwest coast of Cuba that focuses on fish community structure and the natural and human-induced variations at different spatial scales for the entire NW shelf. This research also provides input for a more comprehensive understanding of coastal marine fish communities' status in the Gulf of Mexico basin.

  12. Characterization of Common Measures of Heart Period Variability in Healthy Human Subjects: Implications for Patient Monitoring

    Science.gov (United States)

    2010-01-01

    sports medicine and science. Sports Med 2000; 30: 1–15. 41. Eckberg DL. The human respiratory gate. J Physiol 2003; 548: 339–352. 42. Kamen PW, Krum H...in short-term HRV analysis. Biomed Tech 2006; 51: 190–193. 45. Hayano J, Taylor JA, Yamada A, et al. Continuous assessment of hemodynamic control by

  13. A general auditory bias for handling speaker variability in speech? Evidence in humans and songbirds

    NARCIS (Netherlands)

    Kriengwatana, B.; Escudero, P.; Kerkhoven, A.H.; ten Cate, C.

    2015-01-01

    Different speakers produce the same speech sound differently, yet listeners are still able to reliably identify the speech sound. How listeners can adjust their perception to compensate for speaker differences in speech, and whether these compensatory processes are unique only to humans, is still

  14. Cross-species amplification of human microsatellite markers in pig ...

    Indian Academy of Sciences (India)

    Author Affiliations. Sapna Godavarthi1 Archana Jayaraman1 Ajay Gaur1. Laboratory for the Conservation of Endangered Species (LaCONES), Centre for Cellular and Molecular Biology Annexe 1, Attapur, Hyderabad 500 048, India ...

  15. Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon

    NARCIS (Netherlands)

    Alvarez, A.; Wiel, van de C.; Smulders, M.J.M.; Vosman, B.

    2001-01-01

    In order to determine how informative a set of microsatellites from tomato is across the genus Lycopersicon, 17 microsatellite loci, derived from regions in and around genes, were tested on 31 accessions comprising the nine species of the genus. The microsatellite polymorphisms were used to estimate

  16. Microsatellite instability and the association with plasma homocysteine and thymidylate synthase in colorectal cancer

    DEFF Research Database (Denmark)

    Jensen, Lars Henrik; Lindebjerg, Jan; Crüger, Dorthe G.

    2008-01-01

    , carcinoembryonic antigen, vitamin B12, and folate. Microsatellite instability of tumors was associated with higher levels of plasma homocysteine (p = 0.008) and higher protein expression of thymidylate synthase (p ... factors. CEA was not associated with neither homocysteine nor microsatellite instability. The data suggests that there is a more pronounced methyl unit deficiency in microsatellite instable tumors....

  17. Human activities and climate variability drive fast-paced change across the world's estuarine-coastal ecosystems

    Science.gov (United States)

    Cloern, James E.; Abreu, Paulo C.; Carstensen, Jacob; Chauvaud, Laurent; Elmgren, Ragnar; Grall, Jacques; Greening, Holly; Johansson, John O.R.; Kahru, Mati; Sherwood, Edward T.; Xu, Jie; Yin, Kedong

    2016-01-01

    Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2–5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to develop a global view of changes occurring in marine systems influenced by connectivity to land. Our review is organized around four themes: (i) human activities as drivers of change; (ii) variability of the climate system as a driver of change; (iii) successes, disappointments and challenges of managing change at the sea-land interface; and (iv) discoveries made from observations over time. Multidecadal time series reveal that many of the world's estuarine–coastal ecosystems are in a continuing state of change, and the pace of change is faster than we could have imagined a decade ago. Some have been transformed into novel ecosystems with habitats, biogeochemistry and biological communities outside the natural range of variability. Change takes many forms including linear and nonlinear trends, abrupt state changes and oscillations. The challenge of managing change is daunting in the coastal zone where diverse human pressures are concentrated and intersect with different responses to climate variability over land and over ocean basins. The pace of change in estuarine–coastal ecosystems will likely accelerate as the human population and economies continue to grow and as global climate change accelerates. Wise stewardship of the resources upon which we depend is critically dependent upon a continuing flow of information from observations to measure, understand and anticipate future changes along the world's coastlines.

  18. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed...... and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability...

  19. Uncertainty versus variability in Monte Carlo simulations of human exposure through food pathways

    International Nuclear Information System (INIS)

    McKone, T.E.

    1994-01-01

    An important issue in both the risk characterization and subsequent risk management of contaminated soil is how precisely we can characterize the distribution among individuals of potential doses associated with chemical contaminants in soil and whether this level of precision favors the use of population distributions of exposure over the use of single scenario representations. For lipophilic contaminants, such as dioxins, furans, polychlorinated biphenyls, pesticides, and for metals such as lead and mercury, exposures through food have been demonstrated to be dominant contributors to total dose within non-occupationally exposed populations. However, overall uncertainties in estimating potential doses through food chains are much larger than uncertainties associated with other exposure pathways. A general model is described here for estimating the ratio of potential dose to contaminant concentration in soil for homegrown foods contaminated by lipophilic, nonionic organic chemicals. This model includes parameters describing homegrown food consumption rates, exposure duration, biotransfer factors, and partition factors. For the parameters needed in this model, the mean and variance are often the only moments of the parameter distribution available. Parameters are divided into three categories, uncertain parameters, variable parameters, and mixed uncertain/variable parameters. Using soils contaminated by hexachlorbenzene (HCB) and benzo(a)pyrene (BaP) as cases studies, a stepwise Monte Carlo analysis is used to develop a histogram that apportions variance in the outcome (ratio of potential dose by food pathways to soil concentration) to variance in each of the three input categories. The results represent potential doses in households consuming homegrown foods

  20. Scaling prediction errors to reward variability benefits error-driven learning in humans.

    Science.gov (United States)

    Diederen, Kelly M J; Schultz, Wolfram

    2015-09-01

    Effective error-driven learning requires individuals to adapt learning to environmental reward variability. The adaptive mechanism may involve decays in learning rate across subsequent trials, as shown previously, and rescaling of reward prediction errors. The present study investigated the influence of prediction error scaling and, in particular, the consequences for learning performance. Participants explicitly predicted reward magnitudes that were drawn from different probability distributions with specific standard deviations. By fitting the data with reinforcement learning models, we found scaling of prediction errors, in addition to the learning rate decay shown previously. Importantly, the prediction error scaling was closely related to learning performance, defined as accuracy in predicting the mean of reward distributions, across individual participants. In addition, participants who scaled prediction errors relative to standard deviation also presented with more similar performance for different standard deviations, indicating that increases in standard deviation did not substantially decrease "adapters'" accuracy in predicting the means of reward distributions. However, exaggerated scaling beyond the standard deviation resulted in impaired performance. Thus efficient adaptation makes learning more robust to changing variability. Copyright © 2015 the American Physiological Society.

  1. Hydrocortisone at stress-associated concentrations helps maintain human heart rate variability during subsequent endotoxin challenge.

    Science.gov (United States)

    Rassias, Athos J; Guyre, Paul M; Yeager, Mark P

    2011-12-01

    We evaluated the differential impact of stress-associated vs high pharmacologic concentrations of hydrocortisone pretreatment on heart rate variability (HRV) during a subsequent systemic inflammatory stimulus. Healthy volunteers were randomized to receive placebo (Control) and hydrocortisone at 1.5 μg/kg per minute (STRESS) or at 3.0 μg/kg per minute (PHARM) as a 6-hour infusion. The STRESS dose was chosen to replicate the condition of physiologic adrenal cortical output during acute systemic stress. The PHARM dose was chosen to induce a supraphysiologic concentration of cortisol. The next day, all subjects received 2 ng/kg Escherichia coli endotoxin (lipopolysaccharide). Heart rate variability was analyzed with the statistic approximate entropy (ApEn). A lower ApEn correlates with decreased HRV. At the 3-hour nadir, the decrease in ApEn in the STRESS group was significantly less compared to placebo (P statistically different. We also found that the maximal decrease in ApEn preceded maximal increase in heart rate in all groups. The decrease in R-R interval was maximal at 4 hours, whereas the ApEn nadir was 1 hour earlier at 3 hours. Pretreatment with a stress dose of hydrocortisone but not a higher pharmacologic dose maintained a significantly higher ApEn after endotoxin exposure when compared to a placebo. In addition, decreases in ApEn preceded increases in heart rate. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Probabilistic Tractography Recovers a Rostrocaudal Trajectory of Connectivity Variability in the Human Insular Cortex

    Science.gov (United States)

    Cerliani, Leonardo; Thomas, Rajat M; Jbabdi, Saad; Siero, Jeroen CW; Nanetti, Luca; Crippa, Alessandro; Gazzola, Valeria; D'Arceuil, Helen; Keysers, Christian

    2012-01-01

    The insular cortex of macaques has a wide spectrum of anatomical connections whose distribution is related to its heterogeneous cytoarchitecture. Although there is evidence of a similar cytoarchitectural arrangement in humans, the anatomical connectivity of the insula in the human brain has not yet been investigated in vivo. In the present work, we used in vivo probabilistic white-matter tractography and Laplacian eigenmaps (LE) to study the variation of connectivity patterns across insular territories in humans. In each subject and hemisphere, we recovered a rostrocaudal trajectory of connectivity variation ranging from the anterior dorsal and ventral insula to the dorsal caudal part of the long insular gyri. LE suggested that regional transitions among tractography patterns in the insula occur more gradually than in other brain regions. In particular, the change in tractography patterns was more gradual in the insula than in the medial premotor region, where a sharp transition between different tractography patterns was found. The recovered trajectory of connectivity variation in the insula suggests a relation between connectivity and cytoarchitecture in humans resembling that previously found in macaques: tractography seeds from the anterior insula were mainly found in limbic and paralimbic regions and in anterior parts of the inferior frontal gyrus, while seeds from caudal insular territories mostly reached parietal and posterior temporal cortices. Regions in the putative dysgranular insula displayed more heterogeneous connectivity patterns, with regional differences related to the proximity with either putative granular or agranular regions. Hum Brain Mapp 33:2005–2034, 2012. © 2011 Wiley Periodicals, Inc. PMID:21761507

  3. Climate variability, human wildlife conflict and population dynamics of lions Panthera leo

    Science.gov (United States)

    Trinkel, Martina

    2013-04-01

    Large carnivores are threatened by habitat loss, declining prey populations and direct persecution. Pride dynamics of eight lion prides in the centre of the Etosha National Park, Namibia are described during a 16-year study. Since the beginning of the 1980s, the number of adult and subadult lions declined continuously to two third of its initial population size, and reached a new equilibrium in the 1990s. Pride sizes decreased from 6.3 adult females in 1989 to 2.8 lionesses in 1997. While the number of adult females declined continuously, the number of adult males, subadult females and subadult males remained constant over the years. A severe drought period, lasting for more than 20 years, led to declining prey populations inside the lions' territory. Besides declining prey populations, conflict with humans at the border of Etosha puts substantial pressure onto the lion population: 82 % of all known lion mortalities were caused by humans, and most of these consisted of adult females (28 %) and subadult males (29 %). I postulate that the considerable decline in the lion population is a response to declining prey populations, and although the human predator conflict is severe, it does not seem to limit the size of Etosha's lion population.

  4. Human genetic basis of interindividual variability in the course of infection

    Science.gov (United States)

    Casanova, Jean-Laurent

    2015-01-01

    The key problem in human infectious diseases was posed at the turn of the 20th century: their pathogenesis. For almost any given virus, bacterium, fungus, or parasite, life-threatening clinical disease develops in only a small minority of infected individuals. Solving this infection enigma is important clinically, for diagnosis, prognosis, prevention, and treatment. Some microbes will inevitably remain refractory to, or escape vaccination, or chemotherapy, or both. The solution also is important biologically, because the emergence and evolution of eukaryotes alongside more rapidly evolving prokaryotes, archaea, and viruses posed immunological challenges of an ecological and evolutionary nature. We need to study these challenges in natural, as opposed to experimental, conditions, and also at the molecular and cellular levels. According to the human genetic theory of infectious diseases, inborn variants underlie life-threatening infectious diseases. Here I review the history of the field of human genetics of infectious diseases from the turn of the 19th century to the second half of the 20th century. This paper thus sets the scene, providing the background information required to understand and appreciate the more recently described monogenic forms of resistance or predisposition to specific infections discussed in a second paper in this issue. PMID:26621739

  5. Single genome retrieval of context-dependent variability in mutation rates for human germline.

    Science.gov (United States)

    Sahakyan, Aleksandr B; Balasubramanian, Shankar

    2017-01-13

    Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database. Due to the nature of the method design and the imposed stringency criteria, we expect our rate constants to be good estimates for the rates of spontaneous mutations. Benefiting from such data, we study the short-range nucleotide (up to 7-mer) organisation and the germline basal substitution propensity (BSP) profile of the human genome; characterise novel, CpG-independent, substitution prone and resistant motifs; confirm a decreased tendency of moieties with low BSP to undergo somatic mutations in a number of cancer types; and, produce a Trek-based estimate of the overall mutation rate in human. The extended set of rate constants we report may enrich our resources and help advance our understanding of genome dynamics and evolution, with possible implications for the role of spontaneous mutations in the emergence of pathological genotypes and neutral evolution of proteomes.

  6. Morphological and microsatellite diversity associated with ecological ...

    Indian Academy of Sciences (India)

    Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits .... closely related to model organisms present the opportunity .... the Rogers and Bendish (1988) protocol, modified by Gher-.

  7. Physical linkage of a human immunoglobulin heavy chain variable region gene segment to diversity and joining region elements

    International Nuclear Information System (INIS)

    Schroeder, H.W. Jr.; Walter, M.A.; Hofker, M.H.; Ebens, A.; Van Dijk, K.W.; Liao, L.C.; Cox, D.W.; Milner, E.C.B.; Perlmutter, R.M.

    1988-01-01

    Antibody genes are assembled from a series of germ-line gene segments that are juxtaposed during the maturation of B lymphocytes. Although diversification of the adult antibody repertoire results in large part from the combinatorial joining of these gene segments, a restricted set of antibody heavy chain variable (V H ), diversity (D H ), and joining (J H ) region gene segments appears preferentially in the human fetal repertoire. The authors report here that one of these early-expressed V H elements (termed V H 6) is the most 3' V H gene segment, positioned 77 kilobases on the 5' side of the J H locus and immediately adjacent to a set of previously described D H sequences. In addition to providing a physical map linking human V H , D H , and J H elements, these results support the view that the programmed development of the antibody V H repertoire is determined in part by the chromosomal position of these gene segments

  8. BALANCE CAPACITY WITH VARIABILITY CAUSED BY HUMAN FACTOR: AN APPLICATION IN A LINE WITH MONTE CARLO SIMULATION

    Directory of Open Access Journals (Sweden)

    Augusto Sandes Mendes

    2016-07-01

    Full Text Available The variation in processing times due to the human factor between the working stations of a production line can generate queues resulting in a higher cost to the productive process. The objective of this study was to apply Monte Carlo simulation to balance the capacity of a production line with stations suffering variability in processing time due to the human factor. Simulations of the current situation of the production line were performed by comparing it with a proposal to align capacity with the production restriction in order to reduce inventories process while maintaining full capacity of the line. To develop the study, the selection involves the case of a company’s production line in the metal industry that produces machinery and products for metalworking area. The results allowed pointing suggestions for the company to reduce in-process inventory, keeping then total capacity of the line.

  9. Natural and Human-Induced Variability in Barrier-Island Response to Sea Level Rise

    Science.gov (United States)

    Miselis, Jennifer L.; Lorenzo-Trueba, Jorge

    2017-12-01

    Storm-driven sediment fluxes onto and behind barrier islands help coastal barrier systems keep pace with sea level rise (SLR). Understanding what controls cross-shore sediment flux magnitudes is critical for making accurate forecasts of barrier response to increased SLR rates. Here, using an existing morphodynamic model for barrier island evolution, observations are used to constrain model parameters and explore potential variability in future barrier behavior. Using modeled drowning outcomes as a proxy for vulnerability to SLR, 0%, 28%, and 100% of the barrier is vulnerable to SLR rates of 4, 7, and 10 mm/yr, respectively. When only overwash fluxes are increased in the model, drowning vulnerability increases for the same rates of SLR, suggesting that future increases in storminess may increase island vulnerability particularly where sediment resources are limited. Developed sites are more vulnerable to SLR, indicating that anthropogenic changes to overwash fluxes and estuary depths could profoundly affect future barrier response to SLR.

  10. Source of variability in localized P-31 spectroscopy in human liver

    International Nuclear Information System (INIS)

    Wear, K.A.; Rajan, S.; Myers, K.J.; Grossman, L.W.; Garra, B.S.

    1990-01-01

    This paper reports on chemical shift imaging which is an emerging clinical tool. Variability in measurements potentially can arise from variations in diet and coil geometry. Factors with significant effects must be identified and controlled to reduce variance of measurements and hence enhance discrimination among disease classes. One-dimensional P-31 chemical shift images of seven healthy volunteers were generated. A 1.5-T Siemens Magnetom and a custom-built double-tuned surface coil were used. Volunteers were imaged once after 7 hours of fasting and again 2 hours following a meal containing abundant quantities of complex carbohydrates and sugar. Data were processed with a 100-Hz convolution difference filter and a 15-Hz exponential filter

  11. Wide Variability in Caloric Density of Expressed Human Milk Can Lead to Major Underestimation or Overestimation of Nutrient Content.

    Science.gov (United States)

    Sauer, Charles W; Boutin, Mallory A; Kim, Jae H

    2017-05-01

    Very-low-birth-weight infants continue to face significant difficulties with postnatal growth. Human milk is the optimal form of nutrition for infants but may exhibit variation in nutrient content. This study aimed to perform macronutrient analysis on expressed human milk from mothers whose babies are hospitalized in the neonatal intensive care unit. Up to five human milk samples per participant were analyzed for protein, carbohydrate, and fat content using reference chemical analyses (Kjeldahl for protein, high pressure liquid chromatography for carbohydrates, and Mojonnier for fat). Calorie content was calculated. A total of 64 samples from 24 participants was analyzed. Wide variability was found in calorie, protein, carbohydrate, and fat composition. The authors found an average of 17.9 kcal/ounce, with only 34% of samples falling within 10% of the expected caloric density. The assumption that human milk contains 20 kcal/ounce is no longer supported based on this study. This supports promoting an individualized nutrition strategy as a crucial aspect to optimal nutrition.

  12. Cross-species applicability of chicken microsatellite markers for ...

    African Journals Online (AJOL)

    We obtained blood samples of 57 Indian ducks (Anas platyrhynchos) belonging to three indigenous duck populations of geographically distinct locations of the country and genotyped them using chicken microsatellite markers. Twenty three of the 30 loci were amplified and 17 loci yielded high success rate (> 91%).

  13. Isolation and characterization of polymorphic microsatellite loci from ...

    African Journals Online (AJOL)

    Administrator

    2011-09-19

    Sep 19, 2011 ... Page 1 ... information for the studies on genetic diversity and structure, construction of genetic linkage maps and the effectively management of S. paramamosain. Key words: Scylla paramamosain, microsatellite markers ... landing center in Hainan, China. Genomic DNA was extracted from the muscle tissue ...

  14. Novel polymorphic microsatellites from Florida red tilapia and cross ...

    Indian Academy of Sciences (India)

    tems, Foster City, USA), M13 and M13R primers with the sequencer AB13730xl. Sequences were aligned using. Sequencher (GeneCodes, Ann Arbor, USA). Primers were designed for each microsatellite. One primer of each pair was labelled with either a 6FAM or a HEX fluorescent dye. Twenty Nile tilapia, 20 Mozambique ...

  15. Cross-genus amplification and characterisation of microsatellite loci ...

    African Journals Online (AJOL)

    Taryn

    School of Life Sciences, New Biology Building, University of KwaZulu-Natal, University Road, Westville, KwaZulu-Natal. 3630, South ... Afro-tropical members of the Old World genus Otomops, ..... Population genetic software for teaching and research – an update. ... guide to using and evaluating microsatellite markers. Ecol.

  16. Identification of novel microsatellite markers for Saraca asoca, a ...

    Indian Academy of Sciences (India)

    [Sumangala R. C., Shaanker R. U., Dayanandan S., Vasudeva R. and Ravikanth G. 2013 Identification of novel microsatellite mark- ers for Saraca ..... Biometrics 48, 361–. 372. Hattori M., Nakabayashi T., Lim Y. A., Miyashio H., Kurokawa M.,. Gupta M. P. et al. 1995 Inhibitory effects of various Ayurvedic and Panamanian ...

  17. Characterization of microsatellite markers in eastern white pine

    Science.gov (United States)

    Craig S. Echt; P. May-Marquardt; M. Hseih; R. Zahorchak

    1996-01-01

    An enrichment cloning method was evaluated for the isolation of microsatellite loci from eastern white pine and the resulting markers were examined for polymorphisms. A 200-fold enrichment was achieved for highly abundant (AC), repeats, but for much less abundant (ACAG), repeats an enrichment of only 20-fold was obtained. Using a single set of PCR conditions, 19...

  18. Dietary factors and microsatellite instability in sporadic colon carcinomas

    NARCIS (Netherlands)

    Diergaarde, B.; Braam, H.; Muijen, van G.N.P.; Ligtenberg, M.J.L.; Kok, F.J.; Kampman, E.

    2003-01-01

    Microsatellite instability (MSI) occurs in 10-20% of the sporadic colon carcinomas and appears to be primarily due to alterations in hMLH1 and hMSH2. Little is known about the role of diet in MSI-related colon carcinogenesis. We used data from a Dutch population-based case-control study on sporadic

  19. Dietary factors and microsatellite instability in sporadic colon carcinomas.

    NARCIS (Netherlands)

    Diergaarde, B.; Braam, H.; Muijen, G.N.P. van; Ligtenberg, M.J.L.; Kok, F.J.; Kampman, E.

    2003-01-01

    Microsatellite instability (MSI) occurs in 10-20% of the sporadic colon carcinomas and appears to be primarily due to alterations in hMLH1 and hMSH2. Little is known about the role of diet in MSI-related colon carcinogenesis. We used data from a Dutch population-based case-control study on sporadic

  20. Transferability of Rubus Microsatellite Markers for use in Black Raspberry

    Science.gov (United States)

    Microsatellites or simple sequence repeats (SSRs) are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. To date, SSR marker development in Rubus has focused on red raspberry (Rubus idaeus L., subgenu...

  1. Eleven novel polymorphic microsatellite loci in the ornate spiny ...

    Indian Academy of Sciences (India)

    Southeast Asia, Australia and the West Pacific. Because of their high market value, lobsters are under severe fishing pressure and this ... help to evaluate ornate spiny lobster resources condi- tion and develop its artificial propagation techniques in future. A microsatellite-enriched genomic library of ornate spiny lobster was ...

  2. Evolutionary process of a tetranucleotide microsatellite locus in ...

    Indian Academy of Sciences (India)

    2011-08-19

    Aug 19, 2011 ... 1Institute of Hydroecology, Ministry of Water Resources, Chinese Academy of Sciences, ... The MS-Align phylogenetic method, newly applied to microsatellite sequences, ..... vidual (given by an anonymous small fish farm, see table 1), ..... I. 2001 Genome duplication events and functional reduction of.

  3. Isolation and characterization of microsatellites in Rattus rattus

    Czech Academy of Sciences Publication Activity Database

    Loiseau, A.; Rahelinirina, S.; Rahalison, L.; Konečný, Adam; Duplantier, J.-M.; Brouat, C.

    2008-01-01

    Roč. 8, č. 4 (2008), s. 916-918 ISSN 1755-098X R&D Projects: GA AV ČR IAA6093404 Institutional research plan: CEZ:AV0Z60930519 Keywords : genetic diversity * microsatellite * Rattus rattus * Rodentia Subject RIV: EB - Genetics ; Molecular Biology

  4. Characterization of microsatellites in Fusicladium effusum, cause of pecan scab

    Science.gov (United States)

    Pecan scab, caused by the plant pathogenic fungus Fusicladium effusum, is the most destructive disease of pecan. Little is known of the population genetic diversity of this pathogen. In this study, microsatellites were mined from the F. effusum genome, and flanking primers were subsequently designed...

  5. Microsatellites for the gynogenetic Amazon molly, Poecilia formosa

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 85; Issue 1. Microsatellites for the gynogenetic Amazon molly, Poecilia formosa: useful tools for detection of mutation rate, ploidy determination and overall genetic diversity. Kathrin P. Lampert Dunja K. Lamatsch Susanne Schories Armin Hopf Francisco J. García De León ...

  6. Development of a microsatellite primer set to investigate the genetic ...

    Indian Academy of Sciences (India)

    Development of a microsatellite primer set to investigate the genetic population structure of Armadillidium nasatum (Crustacea, Oniscidea). Séverine Masson, Cédric Faivre, Isabelle Giraud, Catherine Souty-Grosset, Richard Cordaux, Carine Delaunay,. Didier Bouchon and Nicolas Bech. J. Genet. 93, 545-549. Table 1.

  7. The use of microsatellite markers for genetic diversity assessment of ...

    African Journals Online (AJOL)

    In this study, gene diversity and genetic relationships among 30 genotypes of genus Hordeum from Kerman province (Iran) were assessed using 10 simple sequence repeat (SSR) primers. Seven of these markers were highly polymorphic. A total of 96 alleles were detected. The number of alleles per microsatellite marker ...

  8. DNA marker mining of ILSTS035 microsatellite locus on ...

    Indian Academy of Sciences (India)

    Unknown

    We describe tests for detecting and locating quantitative trait loci (QTL) for traits in Hanwoo cattle. From results of a permutation test to detect QTL for marbling, we selected the microsatellite locus ILSTS035 on chromosome 6 for further analysis. K-means clustering analysis applied to five traits and nine DNA markers in ...

  9. Genetic diversity of Najdi sheep based on microsatellite analysis ...

    African Journals Online (AJOL)

    The prime objective of this research was to measure the genetic polymorphism of main sheep breed of Saudi Arabia, Najdi. Randomly selected 49 blood samples were used to extract the DNA followed by polymerase chain reaction (PCR), using 19 microsatellite markers, which were used to investigate the genetic ...

  10. Microsatellite markers associated with body and carcass weights in ...

    African Journals Online (AJOL)

    Microsatellite markers are presently used in selection to facilitate the genetic improvement of growth and carcass traits in chickens. The genetic improvement of six weeks live body and carcass weights of Cairo B-2 line, after six generation of selection, was compared with the control line (C line). Cairo B-2 line had higher ...

  11. Thirty novel microsatellite markers for the coastal pelagic fish ...

    Indian Academy of Sciences (India)

    Scomber japonicus (Scombridae: Scomber) is a wide-spread pelagic fish in the warm and temperate transition coastal areas and adjacent seas of Atlantic, Pacific and northwest. Indian oceans (Collette and Nauen 1983). Although there are few studies on development of microsatellite markers that provide useful tool to ...

  12. Spatial and population genetic structure of microsatellites in white pine

    Science.gov (United States)

    Paula E. Marquardt; Bryan K. Epperson

    2004-01-01

    We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

  13. Genetic variation among pelt sheep population using microsatellite ...

    African Journals Online (AJOL)

    Genetic variation in three Iranian pelt sheep breeds namely: Gray Shiraz, Zandi and Karakul were investigated using fifteen microsatellite loci. Genomic DNA was extracted from 360 blood samples by extraction kits and salting-out procedure with some modifications. The total number of alleles ranged from 6 to12 in loci.

  14. Identification of oligoclonal agamospermous microspecies: taxonomic specialists versus microsatellites

    Czech Academy of Sciences Publication Activity Database

    Kirschner, Jan; Oplaat, C.; Verhoeven, K. J. F.; Zeisek, Vojtěch; Uhlemann, I.; Trávníček, B.; Räsänen, J.; Wilschut, R. A.; Štěpánek, Jan

    2016-01-01

    Roč. 88, č. 1 (2016), s. 1-17 ISSN 0032-7786 R&D Projects: GA ČR GA13-13368S EU Projects: European Commission(XE) 613697 - DRIVE4EU Institutional support: RVO:67985939 Keywords : agamospermy * clonality * microsatellites Subject RIV: EF - Botanics Impact factor: 3.000, year: 2016

  15. Characterization of nine new microsatellite loci for the marbled newt ...

    Indian Academy of Sciences (India)

    on a GsFLX PTP (Roche, Basel, Switzerland) following the manufacturer's instructions. One hundred and seventy- three microsatellite sequences were identified. From these, all sequences with an important number of repeats (as they have better chances to be polymorphic) and a size greater than 100 bp were selected.

  16. Isolation and characterization of fourteen novel microsatellite loci ...

    Indian Academy of Sciences (India)

    [Liu Q., Li Y., Liang H. and Liu X. 2014 Isolation and characterization of fourteen ... management and conservation, little information is available on the genetic structure and genetic variation of B. lenok tsin- lingensis. Microsatellites are currently the markers of choice ... sue according to the simplified method of Laird et al.

  17. Mining microsatellite markers from public expressed sequence tag

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 91; Issue 3. Mining microsatellite markers from public expressed sequence tag sequences for genetic diversity analysis in pomegranate. Zai-Hai Jian Xin-She Liu Jian-Bin Hu Yan-Hui Chen Jian-Can Feng. Research Note Volume 91 Issue 3 December 2012 pp 353-358 ...

  18. Development of microsatellite markers for identifying Brazilian coffee arabica varieties

    NARCIS (Netherlands)

    Vieira, E.S.N.; Pinho, Von E.V.R.; Carvalho, M.G.G.; Esselink, G.; Vosman, B.

    2010-01-01

    Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of

  19. Development and use of microsatellite markers in Marama bean ...

    African Journals Online (AJOL)

    Recently, the development of SSR enrichment techniques has increased the efficiency of SSR characterisation in new species. The aim of the study was to develop SSR's for detection of polymorphisms in Marama bean. The microsatellite regions of the genome were the main focus for potential to be used in Marama bean ...

  20. Development of polymorphic microsatellite loci for the tomato leaf ...

    Indian Academy of Sciences (India)

    lite loci for the tomato leaf miner, Tuta absoluta (Lepidoptera: Gelechiidae). J. Genet. 92, e110–e112. Online only ... idae) is a devastating pest of tomato originating from South. America (García and Espul 1982). .... ture of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in. China identified using microsatellites.

  1. Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers.

    Science.gov (United States)

    Moncada, Ximena; Pelsy, Frédérique; Merdinoglu, Didier; Hinrichsen, Patricio

    2006-11-01

    Intravarietal genetic diversification associated with geographical dispersal of a vegetatively propagated species was studied using grapevine Vitis vinifera L. 'Cabernet Sauvignon' as a model. Fifty-nine clonal samples obtained from 7 countries (France, Chile, Spain, Australia, Hungary, USA, and Italy) were analyzed using 84 microsatellite markers. Eighteen polymorphic microsatellite loci (21.4%) were detected, finding 22 different genotypes in the population analyzed with a genetic similarity of over 97%. The presence of chimeric clones was evidenced at locus VMC5g7 by means of a segregation analysis of descendants by self-pollination of a triallelic Chilean clone and by somatic embryogenesis analysis, showing a mutation in L2 cell layer. Only 2 clones (obtained from France and Australia) presented the ancestral genotype, and the most divergent genotype was exhibited by another French clone, which had accumulated 5 somatic mutations. The 2 largest populations considered (from France and Chile) showed a clear divergency in the polymorphisms detected. These antecedents enabled the tracing of geographical dispersal with a phylogenetic hypothesis supporting France as the center of origin of diversification of Cabernet Sauvignon. The results obtained could help to explain diversification processes in other grapevine cultivars. The possibility that this kind of genetic variability occurs in other vegetatively propagated species is discussed, focusing on possible fingerprinting applications.

  2. Investigating Intergenerational Differences in Human PCB Exposure due to Variable Emissions and Reproductive Behaviors

    Science.gov (United States)

    Quinn, Cristina L.; Wania, Frank; Czub, Gertje; Breivik, Knut

    2011-01-01

    Background Reproductive behaviors—such as age of childbearing, parity, and breast-feeding prevalence—have changed over the same historical time period as emissions of polychlorinated biphenyls (PCB) and may produce intergenerational differences in human PCB exposure. Objectives Our goal in this study was to estimate prenatal, postnatal, and lifetime PCB exposures for women at different ages according to year of birth, and to evaluate the impact of reproductive characteristics on intergenerational differences in exposure. Methods We used the time-variant mechanistic model CoZMoMAN to calculate human bioaccumulation of PCBs, assuming both hypothetical constant and realistic time-variant emissions. Results Although exposure primarily depends on when an individual was born relative to the emission history of PCBs, reproductive behaviors can have a significant impact. Our model suggests that a mother’s reproductive history has a greater influence on the prenatal and postnatal exposures of her children than it does on her own cumulative lifetime exposure. In particular, a child’s birth order appears to have a strong influence on their prenatal exposure, whereas postnatal exposure is determined by the type of milk (formula or breast milk) fed to the infant. Conclusions Prenatal PCB exposure appears to be delayed relative to the time of PCB emissions, particularly among those born after the PCB production phaseout. Consequently, the health repercussions of environmental PCBs can be expected to persist for several decades, despite bans on their production for > 40 years. PMID:21156396

  3. Development of microsatellite loci in Scrophularia incisa (Scrophulariaceae) and cross-amplification in congeneric species.

    Science.gov (United States)

    Wang, Rui-Hong; Chen, Chuan; Ma, Qing; Li, Pan; Fu, Cheng-Xin

    2014-02-01

    To elucidate the population genetics and phylogeography of Scrophularia incisa, microsatellite primers were developed. We also applied these microsatellite markers to its closely related species S. dentata and S. kiriloviana. • Using the compound microsatellite marker technique, 12 microsatellite primers were identified in S. incisa. The number of alleles ranged from 14 to 26 when assessed in 78 individuals from four populations. With high cross-species transferability, these primers also amplified in S. dentata and S. kiriloviana. • These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure in the Chinese species of sect. Tomiophyllum at fine and range-wide geographical scales.

  4. Culture of human dental pulp cells at variable times post-tooth extraction

    Directory of Open Access Journals (Sweden)

    BENÍCIO Daniela Ferreira Araújo

    2018-02-01

    Full Text Available Abstract The aim of this study was to investigate the viability of human dental pulp cells from extracted teeth kept at standard room temperature and atmospheric pressure for different periods of time. Twenty-one healthy permanent teeth were used. They were divided into five groups according to the expected time from extraction to processing. One group was tested immediately after extraction; the other groups were each tested at one of the following time points: 30 minutes, 1 hour, 2 hours, and 5 hours post-extraction. Cell morphology was analysed by light microscopy; cell proliferation was analysed using MTT assay and by counting the viable cells in a haemocytometer. Similar results were observed in all groups (p < 0.05. A delay of up to five hours for tooth processing and tissue collection does not preclude the establishment of dental pulp cell cultures, affect the morphology of these cells, or reduce their proliferative potential.

  5. The role of protozoa-driven selection in shaping human genetic variability.

    Science.gov (United States)

    Pozzoli, Uberto; Fumagalli, Matteo; Cagliani, Rachele; Comi, Giacomo P; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2010-03-01

    Protozoa exert a strong selective pressure in humans. The selection signatures left by these pathogens can be exploited to identify genetic modulators of infection susceptibility. We show that protozoa diversity in different geographic locations is a good measure of protozoa-driven selective pressure; protozoa diversity captured selection signatures at known malaria resistance loci and identified several selected single nucleotide polymorphisms in immune and hemolytic anemia genes. A genome-wide search enabled us to identify 5180 variants mapping to 1145 genes that are subjected to protozoa-driven selective pressure. We provide a genome-wide estimate of protozoa-driven selective pressure and identify candidate susceptibility genes for protozoa-borne diseases. Copyright 2010 Elsevier Ltd. All rights reserved.

  6. Primer sets for cloning the human repertoire of T cell Receptor Variable regions

    Directory of Open Access Journals (Sweden)

    Santoro Claudio

    2008-08-01

    Full Text Available Abstract Background Amplification and cloning of naïve T cell Receptor (TR repertoires or antigen-specific TR is crucial to shape immune response and to develop immuno-based therapies. TR variable (V regions are encoded by several genes that recombine during T cell development. The cloning of expressed genes as large diverse libraries from natural sources relies upon the availability of primers able to amplify as many V genes as possible. Results Here, we present a list of primers computationally designed on all functional TR V and J genes listed in the IMGT®, the ImMunoGeneTics information system®. The list consists of unambiguous or degenerate primers suitable to theoretically amplify and clone the entire TR repertoire. We show that it is possible to selectively amplify and clone expressed TR V genes in one single RT-PCR step and from as little as 1000 cells. Conclusion This new primer set will facilitate the creation of more diverse TR libraries than has been possible using currently available primer sets.

  7. Primer sets for cloning the human repertoire of T cell Receptor Variable regions.

    Science.gov (United States)

    Boria, Ilenia; Cotella, Diego; Dianzani, Irma; Santoro, Claudio; Sblattero, Daniele

    2008-08-29

    Amplification and cloning of naïve T cell Receptor (TR) repertoires or antigen-specific TR is crucial to shape immune response and to develop immuno-based therapies. TR variable (V) regions are encoded by several genes that recombine during T cell development. The cloning of expressed genes as large diverse libraries from natural sources relies upon the availability of primers able to amplify as many V genes as possible. Here, we present a list of primers computationally designed on all functional TR V and J genes listed in the IMGT, the ImMunoGeneTics information system. The list consists of unambiguous or degenerate primers suitable to theoretically amplify and clone the entire TR repertoire. We show that it is possible to selectively amplify and clone expressed TR V genes in one single RT-PCR step and from as little as 1000 cells. This new primer set will facilitate the creation of more diverse TR libraries than has been possible using currently available primer sets.

  8. Morphometric variability of precuneus in relation to gender and the hemisphere of human brain

    Directory of Open Access Journals (Sweden)

    Spasojević Goran

    2004-01-01

    Full Text Available Precuneus, a quadrangular gyrus of the medial surface of the human parietal lobe, is bound by three primary brain sulci and by superior hemispheric border. Precise encephalometric data about precuneus are important in the studies of brain lateralization, sex dimorphism, and brain functions in general. In this study, total and visible (exstrasulcal surface area of the precuneus were measured on 50 brains of the adult persons (31 male, and 29 female, together with the investigation of its relationship to the side (left/right and gender (sex dimorphism. The average total surface area of the precuneus was 16.07 cm2 on the right (males 16.44 cm2, females 15.27 cm2, and 15.44 cm2 on the left (males 15.67 cm2, females 14.62 cm2. The average visible (extrasulcal surface area of cortex of precuneus was 9.97 cm2 on the left (males 10.75 cm2, females 8.91 cm2, and 9.38 cm2 on the right (males 10.25 cm2, females 8.19 cm2. Exstrasulcal surface area of the left precuneus was larger, by 0.59 cm on the average, which was not statistically significant. Total surface area of precuneus of males was significantly larger on the right (16.44 cm2 (p<0.01 than on the left (15.67 cm2. In females it was also larger on the right (15.27 cm2 than on the left (14.62 cm2, but with no statistical significance. Visible (exstrasulcal surface area of both, (left and right precuneus of males was highly significantly larger in comparison with the females (p<0.001. The obtained results and other facts suggested that sex dimorphism of human brain, including precuneus, was present, but not always easily observable studied or proven in all the details.

  9. Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago.

    Science.gov (United States)

    Legrand, Delphine; Vautrin, Dominique; Lachaise, Daniel; Cariou, Marie-Louise

    2011-07-01

    Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

  10. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae

    Directory of Open Access Journals (Sweden)

    Catherine Jan

    2016-09-01

    Full Text Available The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni. From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  11. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae).

    Science.gov (United States)

    Jan, Catherine; Fumagalli, Luca

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  12. MICROSATELLITE ANALYSIS OF INTRA CULTIVAR DIVERSITY IN ...

    African Journals Online (AJOL)

    ACSS

    d'Andhra Pradesh, dont la production et la qualité sont variables à travers la région. ... dendrogramme généré sur base de la moyenne du groupe paire non ..... The pair-wise genetic dissimilarities ..... gene pool registration by seed proteins in.

  13. Allelic database and divergence among Psidium accessions by using microsatellite markers.

    Science.gov (United States)

    da Costa, S R; Santos, C A F

    2013-12-16

    This study aimed to investigate the genetic variability among guava accessions and wild Psidium species of the Embrapa Semiárido germplasm collection by using microsatellite loci to guide genetic resources and breeding programs, emphasizing crosses between guava and other Psidium species. DNA was extracted using the 2X CTAB method, and polymerase chain reaction products were analyzed on 6% denatured polyacrylamide gels stained with silver nitrate. The unweighted pair-group method using arithmetic average dendrogram generated from the distance matrix of the Jaccard coefficient for 183 alleles of 13 microsatellite loci was used for visualization of genetic similarity. The number of base pairs was estimated using inverse mobility method based on the regression of known-size products. Analysis of molecular variance was performed using total decomposition between and within guava accessions. The accessions showed similarity from 0.75 to 1.00, with the dendrogram presenting cophenetic value of 0.85. Five groups were observed: the first included guava accessions; the second, P. guineense accessions; the third, one accession of P. friedrichsthalianum; and the last 2 groups, P. cattleianum. The genetic similarity among P. guineense and some guava accessions were above 80%, suggesting greater possibility to obtain interspecies hybrids between these 2 species. The genetic variability between the accessions was considered to be high (ΦST = 0.238), indicating that guava genetic variability is not uniformly distributed among the 9 Brazilian states from where the accession were obtained. Obtaining a greater number of accessions by Brazilian states is recommended in order to have greater diversity among the species.

  14. Variability of in vivo linear microcrack accumulation in the cortex of elderly human ribs

    Directory of Open Access Journals (Sweden)

    Amanda M. Agnew

    2017-06-01

    Full Text Available Excessive accumulation of microdamage in the skeleton in vivo is believed to contribute to fragility and risk of fracture, particularly in the elderly. Current knowledge of how much in vivo damage accrual varies between individuals, if at all, is lacking. In this study, paired sixth ribs from five male and five female elderly individuals (76–92 years, mean age = 84.7 years were examined using en bloc staining and fluorescent microcopy to quantify linear microcracks present at the time of death (i.e. in vivo microdamage. Crack number, crack length, crack density, and crack surface density were measured for each complete cross-section, with densities calculated using the variable of bone area (which accounts for the influence of porosity on the cortex, unlike the more frequently used cortical area, and analyzed using a two-way mixed model analysis of variance. Results indicate that while microcracks between individuals differ significantly, differences between the left and right corresponding pairs within individuals and the pleural and cutaneous cortices within each rib did not. These results suggest that systemic influences, such as differential metabolic activity, affect the accumulation of linear microcracks. Furthermore, variation in remodeling rates between individuals may be a major factor contributing to differential fracture risk in the elderly. Future work should expand to include a wider age range to examine differences in in vivo microdamage accumulation across the lifespan, as well as considering the influence of bisphosphonates on microdamage accumulation in the context of compromised remodeling rates in the elderly.

  15. Radial Pressure Pulse and Heart Rate Variability in Heat- and Cold-Stressed Humans

    Directory of Open Access Journals (Sweden)

    Chin-Ming Huang

    2011-01-01

    Full Text Available This study aims to explore the effects of heat and cold stress on the radial pressure pulse (RPP and heart rate variability (HRV. The subjects immersed their left hand into 45°C and 7°C water for 2 minutes. Sixty healthy subjects (age 25±4 yr; 29 men and 31 women were enrolled in this study. All subjects underwent the supine temperature measurements of the bilateral forearms, brachial arterial blood pressure, HRV and RPP with a pulse analyzer in normothermic conditions, and thermal stresses. The power spectral low-frequency (LF and high-frequency (HF components of HRV decreased in the heat test and increased in the cold test. The heat stress significantly reduced radial augmentation index (AIr (P<.05, but the cold stress significantly increased AIr (P<.01. The spectral energy of RPP did not show any statistical difference in 0∼10 Hz region under both conditions, but in the region of 10∼50 Hz, there was a significant increase (P<.01 in the heat test and a significant decrease in the cold test (P<.01. The changes in AIr induced by heat and cold stress were significantly negatively correlated with the spectral energy in the region of 10∼50 Hz (SE10−50 Hz but not in the region of 0∼10 Hz (SE0−10 Hz. The results demonstrated that the SE10−50 Hz, which only possessed a small percentage in total pulse energy, presented more physiological characteristics than the SE0−10 Hz under the thermal stresses.

  16. Radial Pressure Pulse and Heart Rate Variability in Heat- and Cold-Stressed Humans

    Science.gov (United States)

    Huang, Chin-Ming; Chang, Hsien-Cheh; Kao, Shung-Te; Li, Tsai-Chung; Wei, Ching-Chuan; Chen, Chiachung; Liao, Yin-Tzu; Chen, Fun-Jou

    2011-01-01

    This study aims to explore the effects of heat and cold stress on the radial pressure pulse (RPP) and heart rate variability (HRV). The subjects immersed their left hand into 45°C and 7°C water for 2 minutes. Sixty healthy subjects (age 25 ± 4 yr; 29 men and 31 women) were enrolled in this study. All subjects underwent the supine temperature measurements of the bilateral forearms, brachial arterial blood pressure, HRV and RPP with a pulse analyzer in normothermic conditions, and thermal stresses. The power spectral low-frequency (LF) and high-frequency (HF) components of HRV decreased in the heat test and increased in the cold test. The heat stress significantly reduced radial augmentation index (AIr) (P < .05), but the cold stress significantly increased AIr (P < .01). The spectral energy of RPP did not show any statistical difference in 0 ~ 10 Hz region under both conditions, but in the region of 10 ~ 50 Hz, there was a significant increase (P < .01) in the heat test and a significant decrease in the cold test (P < .01). The changes in AIr induced by heat and cold stress were significantly negatively correlated with the spectral energy in the region of 10 ~ 50 Hz (SE10−50 Hz) but not in the region of 0 ~ 10 Hz (SE0−10 Hz). The results demonstrated that the SE10−50 Hz, which only possessed a small percentage in total pulse energy, presented more physiological characteristics than the SE0−10 Hz under the thermal stresses. PMID:21113292

  17. Platelet-rich plasma differs according to preparation method and human variability.

    Science.gov (United States)

    Mazzocca, Augustus D; McCarthy, Mary Beth R; Chowaniec, David M; Cote, Mark P; Romeo, Anthony A; Bradley, James P; Arciero, Robert A; Beitzel, Knut

    2012-02-15

    Varying concentrations of blood components in platelet-rich plasma preparations may contribute to the variable results seen in recently published clinical studies. The purposes of this investigation were (1) to quantify the level of platelets, growth factors, red blood cells, and white blood cells in so-called one-step (clinically used commercial devices) and two-step separation systems and (2) to determine the influence of three separate blood draws on the resulting components of platelet-rich plasma. Three different platelet-rich plasma (PRP) separation methods (on blood samples from eight subjects with a mean age [and standard deviation] of 31.6 ± 10.9 years) were used: two single-spin processes (PRPLP and PRPHP) and a double-spin process (PRPDS) were evaluated for concentrations of platelets, red and white blood cells, and growth factors. Additionally, the effect of three repetitive blood draws on platelet-rich plasma components was evaluated. The content and concentrations of platelets, white blood cells, and growth factors for each method of separation differed significantly. All separation techniques resulted in a significant increase in platelet concentration compared with native blood. Platelet and white blood-cell concentrations of the PRPHP procedure were significantly higher than platelet and white blood-cell concentrations produced by the so-called single-step PRPLP and the so-called two-step PRPDS procedures, although significant differences between PRPLP and PRPDS were not observed. Comparing the results of the three blood draws with regard to the reliability of platelet number and cell counts, wide variations of intra-individual numbers were observed. Single-step procedures are capable of producing sufficient amounts of platelets for clinical usage. Within the evaluated procedures, platelet numbers and numbers of white blood cells differ significantly. The intra-individual results of platelet-rich plasma separations showed wide variations in

  18. Blood pressure and heart rate variability analysis of orthostatic challenge in normal human pregnancies.

    Science.gov (United States)

    Heiskanen, Nonna; Saarelainen, Heli; Valtonen, Pirjo; Lyyra-Laitinen, Tiina; Laitinen, Tomi; Vanninen, Esko; Heinonen, Seppo

    2008-11-01

    The aim of the present study was to evaluate pregnancy-related changes in autonomic regulatory functions in healthy subjects. We studied cardiovascular autonomic responses to head-up tilt (HUT) in 28 pregnant women during the third trimester of pregnancy and 3 months after parturition. The maternal ECG and non-invasive beat-to-beat blood pressure were recorded in the horizontal position (left-lateral position) and during HUT in the upright position. Stroke volume was assessed from blood pressure signal by using the arterial pulse contour method. Heart rate variability (HRV) was analysed in frequency domain, and baroreflex sensitivity by the cross-spectral and the sequence methods. In the horizontal position, all frequency components of HRV were lower during pregnancy than 3 months after parturition (P pregnancy had no influence on normalized low frequency and high frequency powers. During pregnancy haemodynamics was well balanced with only minor changes in response to postural change while haemodynamic responses to HUT were more remarkable after parturition. In pregnant women HRV and especially its very low frequency component increased in response to HUT, whereas at 3 months after parturition the direction of these changes was opposite. Parasympathetic deactivation towards term is likely to contribute to increased heart rate and cardiac output at rest, whereas restored sympathetic modulation with modest responses may contribute stable peripheral resistance and sufficient placental blood supply under stimulated conditions. It is important to understand cardiovascular autonomic nervous system and haemodynamic control in normal pregnancy before being able to judge whether they are dysregulated in complicated pregnancies.

  19. Nonrandom variability in respiratory cycle parameters of humans during stage 2 sleep.

    Science.gov (United States)

    Modarreszadeh, M; Bruce, E N; Gothe, B

    1990-08-01

    We analyzed breath-to-breath inspiratory time (TI), expiratory time (TE), inspiratory volume (VI), and minute ventilation (Vm) from 11 normal subjects during stage 2 sleep. The analysis consisted of 1) fitting first- and second-order autoregressive models (AR1 and AR2) and 2) obtaining the power spectra of the data by fast-Fourier transform. For the AR2 model, the only coefficients that were statistically different from zero were the average alpha 1 (a1) for TI, VI, and Vm (a1 = 0.19, 0.29, and 0.15, respectively). However, the power spectra of all parameters often exhibited peaks at low frequency (less than 0.2 cycles/breath) and/or at high frequency (greater than 0.2 cycles/breath), indicative of periodic oscillations. After accounting for the corrupting effects of added oscillations on the a1 estimates, we conclude that 1) breath-to-breath fluctuations of VI, and to a lesser extent TI and Vm, exhibit a first-order autoregressive structure such that fluctuations of each breath are positively correlated with those of immediately preceding breaths and 2) the correlated components of variability in TE are mostly due to discrete high- and/or low-frequency oscillations with no underlying autoregressive structure. We propose that the autoregressive structure of VI, TI, and Vm during spontaneous breathing in stage 2 sleep may reflect either a central neural mechanism or the effects of noise in respiratory chemical feedback loops; the presence of low-frequency oscillations, seen more often in Vm, suggests possible instability in the chemical feedback loops. Mechanisms of high-frequency periodicities, seen more often in TE, are unknown.

  20. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae uncovered by microsatellite loci.

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    Chris D Lowe

    2010-12-01

    Full Text Available Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST values indicated weak to moderate population sub-division (0.01-0.12, but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.

  1. A study of genetic variability of human parainfluenza virus type 1 in Croatia, 2011-2014.

    Science.gov (United States)

    Košutić-Gulija, Tanja; Slovic, Anamarija; Ljubin-Sternak, Sunčanica; Mlinarić-Galinović, Gordana; Forčić, Dubravko

    2016-08-01

    Molecular epidemiology of human parainfluenza viruses type 1 (HPIV1) was investigated. Samples were collected from patients hospitalized in Croatia during the three consecutive epidemic seasons (2011-2014). Results indicated co-circulation of two major genetic clusters of HPIV1. Samples from the current study refer to clades II and III in a phylogenetic tree of haemagglutinin-neuraminidase (HN) gene. Additional phylogenetic trees of fusion (F) and phosphoprotein (P) genes confirmed the topology. Analysis of nucleotide diversity of entire P, F and HN genes demonstrated similar values: 0.0255, 0.0236 and 0.0237, respectively. However, amino acid diversity showed F protein to be the most conserved, while P protein was the most tolerant to mutations. Potential N- and O-glycosylation sites suggested that HPIV1 HN protein is abundantly glycosylated, and a specific N-glycosylation pattern could distinguish between clades II and III. Analysis of potential O-glycosylation sites in F protein indicated that samples from this study have two potential O-glycosylation sites, while publicly available sequences have five potential sites. This study provides data on the molecular characterization and epidemic pattern of HPIV1 in Croatia.

  2. Human movement stochastic variability leads to diagnostic biomarkers In Autism Spectrum Disorders (ASD)

    Science.gov (United States)

    Wu, Di; Torres, Elizabeth B.; Jose, Jorge V.

    2015-03-01

    ASD is a spectrum of neurodevelopmental disorders. The high heterogeneity of the symptoms associated with the disorder impedes efficient diagnoses based on human observations. Recent advances with high-resolution MEM wearable sensors enable accurate movement measurements that may escape the naked eye. It calls for objective metrics to extract physiological relevant information from the rapidly accumulating data. In this talk we'll discuss the statistical analysis of movement data continuously collected with high-resolution sensors at 240Hz. We calculated statistical properties of speed fluctuations within the millisecond time range that closely correlate with the subjects' cognitive abilities. We computed the periodicity and synchronicity of the speed fluctuations' from their power spectrum and ensemble averaged two-point cross-correlation function. We built a two-parameter phase space from the temporal statistical analyses of the nearest neighbor fluctuations that provided a quantitative biomarker for ASD and adult normal subjects and further classified ASD severity. We also found age related developmental statistical signatures and potential ASD parental links in our movement dynamical studies. Our results may have direct clinical applications.

  3. Variability in DNA repair capacity in the human population and its relationship to carcinogenic risk

    International Nuclear Information System (INIS)

    Nuzzo, F.; Stefanini, M.; Giulotto, E.; Falaschi, A.

    1980-01-01

    Several inherited diseases, all characterized by a high incidence of tumours in the homozygous patients, show pronounced defects in DNA repair mechanisms, thus confirming the relationship between the repair process and mutation induction, and indicating clearly that a fraction of the population is certainly much more exposed to cancer that the bulk of the human population. The basic molecular defects in such diseases are summarized. The estimated heterozygote frequency in tumour predisposing syndromes is considered and possible identification of heterozygotes discussed. A procedure to reveal DNA repair capacity at the cellular level would perhaps identify the cancer-prone fraction of the population. A simple assay for measuring repair synthesis is outlined which can be used to determine whether a given substance or treatment elicits repair synthesis and is hence harmful to DNA and potentially mutagenic and/or carcinogenic. It can also be used to assess the capacity of an individual to respond to a known DNA damaging agent. (Auth./C.F.)

  4. Human and bovine viruses and bacteria at three Great Lakes beaches: Environmental variable associations and health risk

    Science.gov (United States)

    Corsi, Steven R.; Borchardt, Mark A.; Carvin, Rebecca B.; Burch, Tucker R; Spencer, Susan K.; Lutz, Michelle A.; McDermott, Colleen M.; Busse, Kimberly M.; Kleinheinz, Gregory; Feng, Xiaoping; Zhu, Jun

    2016-01-01

    Waterborne pathogens were measured at three beaches in Lake Michigan, environmental factors for predicting pathogen concentrations were identified, and the risk of swimmer infection and illness was estimated. Waterborne pathogens were detected in 96% of samples collected at three Lake Michigan beaches in summer, 2010. Samples were quantified for 22 pathogens in four microbial categories (human viruses, bovine viruses, protozoa, and pathogenic bacteria). All beaches had detections of human and bovine viruses and pathogenic bacteria indicating influence of multiple contamination sources at these beaches. Occurrence ranged from 40 to 87% for human viruses, 65–87% for pathogenic bacteria, and 13–35% for bovine viruses. Enterovirus, adenovirus A, Salmonella spp., Campylobacter jejuni, bovine polyomavirus, and bovine rotavirus A were present most frequently. Variables selected in multiple regression models used to explore environmental factors that influence pathogens included wave direction, cloud cover, currents, and water temperature. Quantitative Microbial Risk Assessment was done for C. jejuni, Salmonella spp., and enteroviruses to estimate risk of infection and illness. Median infection risks for one-time swimming events were approximately 3 × 10–5, 7 × 10–9, and 3 × 10–7 for C. jejuni, Salmonella spp., and enteroviruses, respectively. Results highlight the importance of investigating multiple pathogens within multiple categories to avoid underestimating the prevalence and risk of waterborne pathogens.

  5. mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer

    Directory of Open Access Journals (Sweden)

    Calin George A

    2007-08-01

    Full Text Available Abstract Background Colorectal cancer develops through two main genetic instability pathways characterized by distinct pathologic features and clinical outcome. Results We investigated colon cancer samples (23 characterized by microsatellite stability, MSS, and 16 by high microsatellite instability, MSI-H for genome-wide expression of microRNA (miRNA and mRNA. Based on combined miRNA and mRNA gene expression, a molecular signature consisting of twenty seven differentially expressed genes, inclusive of 8 miRNAs, could correctly distinguish MSI-H versus MSS colon cancer samples. Among the differentially expressed miRNAs, various members of the oncogenic miR-17-92 family were significantly up-regulated in MSS cancers. The majority of protein coding genes were also up-regulated in MSS cancers. Their functional classification revealed that they were most frequently associated with cell cycle, DNA replication, recombination, repair, gastrointestinal disease and immune response. Conclusion This is the first report that indicates the existence of differences in miRNA expression between MSS versus MSI-H colorectal cancers. In addition, the work suggests that the combination of mRNA/miRNA expression signatures may represent a general approach for improving bio-molecular classification of human cancer.

  6. FANCJ suppresses microsatellite instability and lymphomagenesis independent of the Fanconi anemia pathway.

    Science.gov (United States)

    Matsuzaki, Kenichiro; Borel, Valerie; Adelman, Carrie A; Schindler, Detlev; Boulton, Simon J

    2015-12-15

    Microsatellites are short tandem repeat sequences that are highly prone to expansion/contraction due to their propensity to form non-B-form DNA structures, which hinder DNA polymerases and provoke template slippage. Although error correction by mismatch repair plays a key role in preventing microsatellite instability (MSI), which is a hallmark of Lynch syndrome, activities must also exist that unwind secondary structures to facilitate replication fidelity. Here, we report that Fancj helicase-deficient mice, while phenotypically resembling Fanconi anemia (FA), are also hypersensitive to replication inhibitors and predisposed to lymphoma. Whereas metabolism of G4-DNA structures is largely unaffected in Fancj(-/-) mice, high levels of spontaneous MSI occur, which is exacerbated by replication inhibition. In contrast, MSI is not observed in Fancd2(-/-) mice but is prevalent in human FA-J patients. Together, these data implicate FANCJ as a key factor required to counteract MSI, which is functionally distinct from its role in the FA pathway. © 2015 Matsuzaki et al.; Published by Cold Spring Harbor Laboratory Press.

  7. Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue

    Directory of Open Access Journals (Sweden)

    Dourisboure Ricardo J

    2006-01-01

    Full Text Available Abstract Background Hereditary non-polyposis colon cancer (HNPCC is an autosomal dominant syndrome predisposing to the early development of various cancers including those of colon, rectum, endometrium, ovarium, small bowel, stomach and urinary tract. HNPCC is caused by germline mutations in the DNA mismatch repair genes, mostly hMSH2 or hMLH1. In this study, we report the analysis for genetic counseling of three first-degree relatives (the mother and two sisters of a male who died of colorectal adenocarcinoma at the age of 23. The family fulfilled strict Amsterdam-I criteria (AC-I with the presence of extracolonic tumors in the extended pedigree. We overcame the difficulty of having a proband post-mortem non-tumor tissue sample for MSI testing by studying the alleles carried by his progenitors. Methods Tumor MSI testing is described as initial screening in both primary and metastasis tumor tissue blocks, using the reference panel of 5 microsatellite markers standardized by the National Cancer Institute (NCI for the screening of HNPCC (BAT-25, BAT-26, D2S123, D5S346 and D17S250. Subsequent mutation analysis of the hMLH1 and hMSH2 genes was performed. Results Three of five microsatellite markers (BAT-25, BAT-26 and D5S346 presented different alleles in the proband's tumor as compared to those inherited from his parents. The tumor was classified as high frequency microsatellite instability (MSI-H. We identified in the HNPCC family a novel germline missense (c.1864C>A mutation in exon 12 of hMSH2 gene, leading to a proline 622 to threonine (p.Pro622Thr amino acid substitution. Conclusion This approach allowed us to establish the tumor MSI status using the NCI recommended panel in the absence of proband's non-tumor tissue and before sequencing the obligate carrier. According to the Human Gene Mutation Database (HGMD and the International Society for Gastrointestinal Hereditary Tumors (InSiGHT Database this is the first report of this mutation.

  8. Quantifying the effects of climate variability and human activities on runoff for Kaidu River Basin in arid region of northwest China

    Science.gov (United States)

    Chen, Zhongsheng; Chen, Yaning; Li, Baofu

    2013-02-01

    Much attention has recently been focused on the effects that climate variability and human activities have had on runoff. In this study, data from the Kaidu River Basin in the arid region of northwest China were analyzed to investigate changes in annual runoff during the period of 1960-2009. The nonparametric Mann-Kendall test and the Mann-Kendall-Sneyers test were used to identify trend and step change point in the annual runoff. It was found that the basin had a significant increasing trend in annual runoff. Step change point in annual runoff was identified in the basin, which occurred in the year around 1993 dividing the long-term runoff series into a natural period (1960-1993) and a human-induced period (1994-2009). Then, the hydrologic sensitivity analysis method was employed to evaluate the effects of climate variability and human activities on mean annual runoff for the human-induced period based on precipitation and potential evapotranspiration. In 1994-2009, climate variability was the main factor that increased runoff with contribution of 90.5 %, while the increasing percentage due to human activities only accounted for 9.5 %, showing that runoff in the Kaidu River Basin is more sensitive to climate variability than human activities. This study quantitatively distinguishes the effects between climate variability and human activities on runoff, which can do duty for a reference for regional water resources assessment and management.

  9. Variable effects of cinder-cone eruptions on prehistoric agrarian human populations in the American southwest

    Science.gov (United States)

    Ort, Michael H.; Elson, Mark D.; Anderson, Kirk C.; Duffield, Wendell A.; Samples, Terry L.

    2008-10-01

    Two ˜ 900 BP cinder-cone eruptions in the American Southwest affected prehistoric human populations in different ways, mostly because of differences in the eruption styles and area affected. Primary pre-eruption cultural factors that may have led to successful adaptation to the eruptions include decision-making at the family or household level, low investment in site structures, dispersion of agricultural sites in varied environments, and settlement spread over a large area so that those who were less affected could shelter and feed evacuees. Sunset Crater, near Flagstaff, Arizona, produced about 8 km 2 lava flow fields and a ˜ 2300-km 2 tephra blanket in an area that had been settled by prehistoric groups for at least 1000 years. Local subsistence relied on agriculture, primarily maize, and > 30 cm tephra cover rendered 265 km 2 of prime land unfarmable. This area was apparently abandoned for at least several generations. A > 500-km 2 area was probably marked by collapsed roofs and other structural damage from the fallout. If the eruption occurred during the agricultural season, the fallout would also have significantly damaged crops. The eruption did have some benefits to local groups because lower elevation land, which had previously been too dry to farm, became agriculturally productive due to 3-8 cm of tephra 'mulch' and some temporary soil nutrient improvements. This previously uninhabited land became the site of significant year-round settlement and farming, eventually containing some of the largest pueblo structures ever built in the region. New agricultural techniques were developed to manage the fallout mulch. The eruption also affected ceramic production and trading patterns, and volcano-related ritual behavior - the production of maize-impressed lava-spatter agglutinate - was initiated. Little Springs Volcano, about 200 km northwest of Sunset Crater, is a small spatter rampart around a series of vents that produced about 5 km 2 of lava flow fields

  10. Hydrological Responses of Andean Lakes and Tropical Floodplains to Climate Variability and Human Intervention: an Integrative Modelling Framework

    Science.gov (United States)

    Hoyos, I. C.; González Morales, C.; Serna López, J. P.; Duque, C. L.; Canon Barriga, J. E.; Dominguez, F.

    2013-12-01

    Andean water bodies in tropical regions are significantly influenced by fluctuations associated with climatic and anthropogenic drivers, which implies long term changes in mountain snow peaks, land covers and ecosystems, among others. Our work aims at providing an integrative framework to realistically assess the possible future of natural water bodies with different degrees of human intervention. We are studying in particular the evolution of three water bodies in Colombia: two Andean lakes and a floodplain wetland. These natural reservoirs represent the accumulated effect of hydrological processes in their respective basins, which exhibit different patterns of climate variability and distinct human intervention and environmental histories. Modelling the hydrological responses of these local water bodies to climate variability and human intervention require an understanding of the strong linkage between geophysical and social factors. From the geophysical perspective, the challenge is how to downscale global climate projections in the local context: complex orography and relative lack of data. To overcome this challenge we combine the correlational and physically based analysis of several sources of spatially distributed biophysical and meteorological information to accurately determine aspects such as moisture sources and sinks and past, present and future local precipitation and temperature regimes. From the social perspective, the challenge is how to adequately represent and incorporate into the models the likely response of social agents whose water-related interests are diverse and usually conflictive. To deal with the complexity of these systems we develop interaction matrices, which are useful tools to holistically discuss and represent each environment as a complex system. Our goal is to assess partially the uncertainties of the hydrological balances in these intervened water bodies we establish climate/social scenarios, using hybrid models that combine

  11. Population genetic structure of the major malaria vector Anopheles darlingi (Diptera: Culicidae from the Brazilian Amazon, using microsatellite markers

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    Vera Margarete Scarpassa

    2007-06-01

    Full Text Available The population genetic structure of Anopheles darlingi, the major human malaria vector in the Neotropics, was examined using seven microsatellite loci from nine localities in central and western Amazonian Brazil. High levels of genetic variability were detected (5-25 alleles per locus; H E = 0.519-0.949. There was deviation from Hardy-Weinberg Equilibrium for 59.79% of the tests due to heterozygote deficits, while the analysis of linkage disequilibrium was significant for only two of 189 (1.05% tests, most likely caused by null alleles. Genetic differentiation (F ST = 0.001-0.095; Nm = 4.7-363.8 indicates that gene flow is extensive among locations < 152 km apart (with two exceptions and reduced, but not absent, at a larger geographic scale. Genetic and geographic distances were significantly correlated (R² = 0.893, P < 0.0002, supporting the isolation by distance (IBD model. The overall estimate of Ne was 202.4 individuals under the linkage disequilibrium model, and 8 under the heterozygote excess model. Analysis of molecular variance showed that nearly all variation (~ 94% was within sample locations. The UPGMA phenogram clustered the samples geographically, with one branch including 5/6 of the state of Amazonas localities and the other branch the Acre, Rondônia, and remaining Amazonas localities. Taken together, these data suggest little genetic structure for An. darlingi from central and western Amazonian Brazil. These findings also imply that the IBD model explains nearly all of the differentiation detected. In practical terms, populations of An. darlingi at distances < 152 km should respond similarly to vector control measures, because of high gene flow.

  12. A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus populations

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    Li Meng-Hua

    2010-08-01

    Full Text Available Abstract Background Microsatellites surrounding functionally important candidate genes or quantitative trait loci have received attention as proxy measures of polymorphism level at the candidate loci themselves. In cattle, selection for economically important traits is a long-term strategy and it has been reported that microsatellites are linked to these important loci. Methods We have investigated the variation of seven microsatellites on BTA1 (Bos taurus autosome 1 and 16 on BTA20, using bovine populations of typical production types and horn status in northern Eurasia. Genetic variability of these loci and linkage disequilibrium among these loci were compared with those of 28 microsatellites on other bovine chromosomes. Four different tests were applied to detect molecular signatures of selection. Results No marked difference in locus variability was found between microsatellites on BTA1, BTA20 and the other chromosomes in terms of different diversity indices. Average D' values of pairwise syntenic markers (0.32 and 0.28 across BTA 1 and BTA20 respectively were significantly (P FST-test indicated elevated or decreased genetic differentiation, at SOD1 and AGLA17 markers respectively, deviating significantly (P SOD1 and AGLA17. Our data also indicate significant intergenic linkage disequilibrium around the candidate loci and suggest that hitchhiking selection has played a role in shaping the pattern of observed linkage disequilibrium. Conclusion Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations.

  13. Association between the human herpesvirus 8 and the diffuse nodular lymphoid hyperplasia of the small intestine in common variable immunodeficiency

    International Nuclear Information System (INIS)

    Kokuina, Elena; Dominguez Alvarez, Carlos; Noa Pedroso, Guillermo; Martinez Rodriguez Pedro Ariel

    2009-01-01

    The common variable immunodeficiency (CVID) is the more frequent primary immunodeficiency in clinical field and its presentation forms are very variable. We describe the case of a women presenting with adult CVID with chronic diarrhea syndrome, weight loss and diffuse lymphadenopathies, where the more marked immunologic features were a deep hypogammaglobulinemia of the three major kinds of immunoglobulins and numerical decrease of B cells (CD19 +) and NK cells (CD3 -C D56 +) in peripheral blood. Biopsy of small intestine obtained by video-assisted panendoscope, showed the presence of a multinodular lymphoid hyperplasia with partial atrophy of hairinesses. Immunohistochemistry showed that nodules were high germinal centers with distribution of B cells (CD20 +) and T cells (CD3 +) , similar to that of normal follicle. There was not differential expression of the K and λ light chains. The real time polymerase chain reaction (QRT-PCR) method detected many copies from the genome of type 8 human herpesvirus (VHH-8) (133 copies/μL of DNA) in biopsy of intestinal nodule DNA. VHH-8 infection may to be a significant factor in pathogenesis of lymphoproliferative disorders in patients presenting with CVID

  14. MONITORING OF GENETIC DIVERSITY IN FARMED DEER POPULATIONS USING MICROSATELLITE MARKERS

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    Pavol Bajzík

    2011-12-01

    Full Text Available Deer (Cervidaei belong to the most important species used as farmed animals. We focused on assesing the genetic diversity among five deer populations. Analysis has been performed on a total of 183 animals originating from Czech Republic, Hungary, New Zealand, Poland and Slovak Republic. Genetic variability were investigated using 8 microsatellite markers used in deer. Statistical data of all populations we obtained on the basis of Nei statistics, using by POWERMARKER 3.23 programme. Graphical view of relationships among populations and individuals in the populations was obtained using the Dendroscope software. Molecular genetic data combinated with evaluation in statistical programmes could lead to a complex view of populations and diffrences among them.doi:10.5219/172

  15. Molecular diversity of Pakistani mango (Mangifera indica L.) varieties based on microsatellite markers.

    Science.gov (United States)

    Nazish, T; Shabbir, G; Ali, A; Sami-Ul-Allah, S; Naeem, M; Javed, M; Batool, S; Arshad, H; Hussain, S B; Aslam, K; Seher, R; Tahir, M; Baber, M

    2017-04-05

    Understanding the genetic diversity of different Pakistani mango varieties is important for germplasm management and varietal characterization. Microsatellites are efficient and highly polymorphic markers for comparative genome mapping, and were used in the present study to determine the genetic relatedness and variability among 15 indigenous mango cultivars (Mangifera indica L.). Overall, 181 bands were produced using 12 simple sequence repeat (SSR) primers. Out of the 12 primers used, 10 were polymorphic and two were monomorphic. Genetic relatedness among cultivars was assessed by constructing a dendrogram using the unweighted pair group method of arithmetic means. The accessions exhibited coefficients of similarity ranging from 75 to 100%, indicating the frequent use of only a few parent cultivars and the presence of inbreeding. The primers used in the present study were found to be valuable for identifying genetic relationships among mango cultivars.

  16. Development and characterization of 16 polymorphic microsatellite loci for the Alaska blackfish (Esociformes: Dallia pectoralis)

    Science.gov (United States)

    Campbell, Matthew A.; Sage, George K.; DeWilde, Rachel L.; López, J. Andres; Talbot, Sandra L.

    2014-01-01

    Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is debated, disjunct populations and distinct mitochondrial divisions that predate the end of the last glacial maximum are apparent. We developed sixteen polymorphic microsatellites from the Alaska blackfish (Dallia pectoralis) to study genetic diversity in Dallia. Genotypes from two populations, Denali (n = 31) and Bethel (n = 35), demonstrated the usefulness of the loci for population-level investigation. Observed and expected heterozygosity averaged 18.6 and 19.8 % in Denali and 61.1 and 63.7 % in Bethel. Number of alleles at each locus averaged 3.50 in Denali and 9.63 in Bethel. The observed signature of variability and structuring between populations is consistent with mitochondrial data.

  17. Undermethylated DNA as a source of microsatellites from a conifer genome.

    Science.gov (United States)

    Zhou, Y; Bui, T; Auckland, L D; Williams, C G

    2002-02-01

    Developing microsatellites from the large, highly duplicated conifer genome requires special tools. To improve the efficiency of developing Pinus taeda L. microsatellites, undermethylated (UM) DNA fragments were used to construct a microsatellite-enriched copy library. A methylation-sensitive restriction enzyme, McrBC, was used to enrich for UM DNA before library construction. Digested DNA fragments larger than 9 kb were then excised and digested with RsaI and used to construct nine dinucleotide and trinucleotide libraries. A total of 1016 microsatellite-positive clones were detected among 11 904 clones and 620 of these were unique. Of 245 primer sets that produced a PCR product, 113 could be developed as UM microsatellite markers and 70 were polymorphic. Inheritance and marker informativeness were tested for a random sample of 36 polymorphic markers using a three-generation outbred pedigree. Thirty-one microsatellites (86%) had single-locus inheritance despite the highly duplicated nature of the P. taeda genome. Nineteen UM microsatellites had highly informative intercross mating type configurations. Allele number and frequency were estimated for eleven UM microsatellites using a population survey. Allele numbers for these UM microsatellites ranged from 3 to 12 with an average of 5.7 alleles/locus. Frequencies for the 63 alleles were mostly in the low-common range; only 14 of the 63 were in the rare allele (q < 0.05) class. Enriching for UM DNA was an efficient method for developing polymorphic microsatellites from a large plant genome.

  18. Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping Various Plant Pathogenic Fungi with Special Emphasis on Fusaria and Mycospherella graminicola

    Directory of Open Access Journals (Sweden)

    Joseph-Alexander Verreet

    2012-03-01

    Full Text Available The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG4, (TCC5 and (CA7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based on morphology and other methods of phylogenetic analysis. The current research demonstrates that the newly designed microsatellite primers are reliable, sensitive and technically simple tools for assaying genetic variability in plant pathogenic fungi.

  19. Development of Microsatellite Markers for Isodon longitubus (Lamiaceae

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    Tadashi Yamashiro

    2013-10-01

    Full Text Available Premise of the study: Microsatellite markers were developed for Isodon longitubus to study the natural hybridization of the species and its congeners. Methods and Results: A total of 10 primer sets were developed for I. longitubus. From the initial screening, all of 10 loci were polymorphic with five to 19 alleles per locus in the Mt. Ishizuchi population, whereas nine loci were polymorphic with two to 12 alleles per loci in the Toon population. Although one locus was monomorphic at one population, the observed and expected heterozygosity values estimated from 34 I. longitubus samples ranged from 0.273 to 1.000 and from 0.483 to 0.918, respectively. Six primer sets could amplify all three species examined in this study (I. inflexus, I. japonicus, and I. shikokianus. Conclusions: The 10 microsatellite markers developed here will be useful in analyzing the population genetic structure of I. longitubus and in studying the natural hybridization between Isodon species.

  20. Ancient conservation of trinucleotide microsatellite loci in polistine wasps

    DEFF Research Database (Denmark)

    Ezenwa, V O; Peters, J M; Zhu, Y

    1998-01-01

    Microsatellites have proven to be very useful genetic markers for studies of kinship, parentage, and gene mapping. If microsatellites are conserved among species, then those developed for one species can be used on related species, which would save the time and effort of developing new loci. We...... evaluated conservation of 27 trinucleotide loci that were derived from 2 species of Polistes wasps in cross-species applications on 27 species chosen from the major lineages of the Vespidae, which diverged as much as 144 million years ago. We further investigated cross-species polymorphism levels for 18...... of the loci. There was a clear relationship between cladistic distance and both conservation of the priming sites and heterozygosity. However the loci derived from P. bellicosus were much more widely conserved and polymorphic than were those derived from P. annularis. The disparity in cross-species utility...

  1. A test of mink microsatellite markers in the ferret

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Christensen, Knud

    2006-01-01

    Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variations at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite mar...... that were identical in size to those from mink displayed a high degree of conservation, with some differences at the repeat motif sites. These results could aid cross-utilization of markers between these two species.......Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variations at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite...

  2. Microsatellite-based phylogeny of Indian domestic goats

    Science.gov (United States)

    Rout, Pramod K; Joshi, Manjunath B; Mandal, Ajoy; Laloe, D; Singh, Lalji; Thangaraj, Kumarasamy

    2008-01-01

    Background The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones. Results The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution. Conclusion Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information. PMID:18226239

  3. Isolation and Characterization of Microsatellite Markers for Shorea platyclados (Dipterocarpaceae

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    Chin Hong Ng

    2013-06-01

    Full Text Available Premise of the study: Microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae for DNA profiling and genetic diversity assessment of this tropical timber species. Methods and Results: Fifteen polymorphic microsatellite loci were developed and characterized in S. platyclados using a genomic library enriched for dinucleotide (CT repeats. The primers amplified dinucleotide repeats with 3–14 alleles per locus across four natural populations. The observed and expected heterozygosities ranged from 0.292 to 1.000 and from 0.301 to 0.894, respectively. No significant deviation from Hardy–Weinberg equilibrium was detected in the 15 loci. Four loci pairs displayed linkage disequilibrium. Conclusions: These highly polymorphic markers are adequate for DNA profiling and studies of population genetics in S. platyclados.

  4. Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers.

    Science.gov (United States)

    Revidatti, M A; Delgado Bermejo, J V; Gama, L T; Landi Periati, V; Ginja, C; Alvarez, L A; Vega-Pla, J L; Martínez, A M

    2014-11-01

    Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.

  5. Effects of seasonal meteorological variables on E. coli persistence in livestock faeces and implications for environmental and human health.

    Science.gov (United States)

    Oliver, David M; Page, Trevor

    2016-11-15

    Agriculture contributes significant volumes of livestock faeces to land. Understanding how faecal microbes respond to shifts in meteorological patterns of contrasting seasons is important in order to gauge how environmental (and human health) risks may alter under a changing climate. The aim of this study was to: (i) quantify the temporal pattern of E. coli growth within dairy faeces post defecation; and (ii) derive E. coli seasonal population change profiles associated with contrasting environmental drivers. Evaluation of the die-off dynamics of E. coli revealed that a treatment mimicking drought and warming conditions significantly enhanced persistence relative to E. coli in faeces that were exposed to field conditions, and that this pattern was consistent across consecutive years. The internal temperature of faeces was important in driving the rate of change in the E. coli population in the immediate period post defecation, with most E. coli activity (as either die-off or growth) occurring at low dry matter content. This study highlighted that the use of seasonal E. coli persistence profiles should be approached with caution when modelling environmental and human health risks given the increased likelihood of atypical seasonal meteorological variables impacting on E. coli growth and die-off.

  6. Specific proliferation rates of human osteoblasts on calcium phosphate surfaces with variable concentrations of α-TCP

    International Nuclear Information System (INIS)

    Santos, Euler A. dos; Farina, Marcos; Soares, Gloria A.

    2007-01-01

    Ideally, ceramics used in the repair of bone defects need to be resorbed and replaced by newly formed bone in vivo. Tricalcium phosphate (TCP) has been widely used in association with hydroxyapatite (HA) due to its higher resorption kinetics when compared with HA alone. The aim of our study was to quantitatively investigate the effect of α-tricalcium phosphate (α-TCP) on human osteoblasts' adhesion and proliferation. Ceramic samples with variable concentrations of α-TCP and HA were produced by the calcination of calcium-deficient and stoichiometric HA. Human osteoblasts were cultured on the materials in three distinct experiments with different concentrations of cells. Numerical evaluation of cellular growth along time in culture was performed for each condition. The quantity of cells seeded onto the ceramics seems to influence the osteoblast behavior once proliferation was lower when more cells were seeded onto the samples. However, a smaller content of α-TCP in relation to that of HA did not significantly modify the specific proliferation rates of the osteoblasts. Only after a long time in culture, the increasing of the α-TCP content seems to change the cells' behavior

  7. Chemical variability of water and sediment over time and along a mountain river subjected to natural and human impact

    Directory of Open Access Journals (Sweden)

    Szarek-Gwiazda Ewa

    2018-01-01

    Full Text Available We studied the variability of physico-chemical parameters in water, and heavy metal contents in water and sediment over time and along the Carpathian Biała Tarnowska River (southern Poland and related them to catchment geology, human impact and the effect of barriers as a side aspect. The river water was well oxygenated, had pH 7.7–9.5 and was characterised by low and average flow. Temperature, pH and dissolved oxygen did not change significantly, while the contents of major ions, NO3−, NH4+, Mn and Fe increased gradually along the river. The major ion contents were negatively, and nitrate, Mn, and Fe positively, correlated with the flow. We recognise correlations between nitrate, Fe and Mn to be good indicators of soil erosion processes in the catchment. River sediment was unpolluted by most of the studied metals (slightly polluted by Ni and Cd. The differences in the values of some parameters (pH and NH4+, PO43−, HCO3−, Mn, Cd and Pb concentrations in the water, and heavy metals in the sediment upstream and downstream of some of the barriers were determined. Spatiotemporal changes in the values of studied parameters and the results of statistical calculation indicate the impact of human activity in the catchment basin (land use, wastewater on the water chemistry.

  8. SINGLE CHAIN VARIABLE FRAGMENTS OF ANTIBODIES AGAINST DIPHTHERIA TOXIN B-SUBUNIT ISOLATED FROM PHAGE DISPLAY HUMAN ANTIBODY LIBRARY

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    Oliinyk O. S.

    2014-02-01

    Full Text Available Diphtheria toxin is an exoantigen of Corynebacterium diphtheriae that inhibits protein synthesis and kills sensitive cells. The aim of this study was to obtain human recombinant single-chain variable fragment (scFv antibodies against receptor-binding B subunit of diphtheria toxin. 12 specific clones were selected after three rounds of a phage display naїve (unimmunized human antibody library against recombinant B-subunit. scFv DNA inserts from these 12 clones were digested with MvaI, and 6 unique restriction patterns were found. Single-chain antibodies were expressed in Escherichia coli XL1-blue. The recombinant proteins were characterized by immunoblotting of bacterial extracts and detection with an anti-E-tag antibody. The toxin B-subunit-binding function of the single-chain antibody was shown by ELISA. The affinity constants for different clones were found to be from 106 to 108 М–1. Due to the fact, that these antibody fragments recognized epitopes in the receptor-binding Bsubunit of diphtheria toxin, further studies are interesting to evaluate their toxin neutralization properties and potential for therapeutic applications. Obtained scFv-antibodies can also be used for detection and investigation of biological properties of diphtheria toxin.

  9. Molecular characterization of Doom pigs using microsatellite markers

    African Journals Online (AJOL)

    SAM

    2014-07-23

    Jul 23, 2014 ... 3020. Afr. J. Biotechnol. Table 1. Microsatellite analysis in Doom pig population. Panel. Locus. Size range. (bp). Parameter. Na. Ne. PIC. Ho. He. I. FIS. HWE ... 145-161. 4. 2.5641. 0.6422. 0.7000. 0.6100. 1.1097. -0.1475. 3.3NS. Panel 3. SO218. 193-201. 5. 2.0769. 0.4850. 0.5556. 0.5185. 1.0507. -0.0714.

  10. Microsatellite analyses of the trout of northwest Mexico

    Science.gov (United States)

    Nielsen, J.L.; Sage, G.K.

    2001-01-01

    The trout of northwest Mexico represent an undescribed group of fish considered part of the Oncorhynchus mykiss (Pacific trout) complex of species and subspecies. Recent genetic studies have shown these fish to have important genetic diversity and a unique evolutionary history when compared to coastal rainbow trout. Increased levels of allelic diversity have been found in this species at the southern extent of its range. In this study we describe the trout in the Sierra Madre Occidental from the rios Yaqui, Mayo, Casas Grandes and de Bavispe, and their relationship to the more southern distribution of Mexican golden trout (O. chrysogaster) using 11 microsatellite loci. Microsatellite allelic diversity in Mexican trout was high with a mean of 6.6 alleles/locus, average heterozygosity = 0.35, and a mean Fst = 0.43 for all loci combined. Microsatellite data were congruent with previously published mtDNA results showing unique panmictic population structure in the Rio Yaqui trout that differs from Pacific coastal trout and Mexican golden trout. These data also add support for the theory of headwaters transfer of trout across the Continental Divide from tributaries of the Rio de Bavispe into the Rio Casas Grandes. Rio Mayo trout share a close genetic relationship to trout in Rio Yaqui, but sample sizes from the Rio Mayo prevent significant comparisons in this study. Microsatellite analyses show significant allelic frequency differences between Rio Yaqui trout and O. chrysogaster in Sinaloa and Durango Mexico, adding further support for a unique evolutionary status for this group of northwestern Mexican trout.

  11. Isolation of primary microglia from the human post-mortem brain: effects of ante- and post-mortem variables.

    Science.gov (United States)

    Mizee, Mark R; Miedema, Suzanne S M; van der Poel, Marlijn; Adelia; Schuurman, Karianne G; van Strien, Miriam E; Melief, Jeroen; Smolders, Joost; Hendrickx, Debbie A; Heutinck, Kirstin M; Hamann, Jörg; Huitinga, Inge

    2017-02-17

    Microglia are key players in the central nervous system in health and disease. Much pioneering research on microglia function has been carried out in vivo with the use of genetic animal models. However, to fully understand the role of microglia in neurological and psychiatric disorders, it is crucial to study primary human microglia from brain donors. We have developed a rapid procedure for the isolation of pure human microglia from autopsy tissue using density gradient centrifugation followed by CD11b-specific cell selection. The protocol can be completed in 4 h, with an average yield of 450,000 and 145,000 viable cells per gram of white and grey matter tissue respectively. This method allows for the immediate phenotyping of microglia in relation to brain donor clinical variables, and shows the microglia population to be distinguishable from autologous choroid plexus macrophages. This protocol has been applied to samples from over 100 brain donors from the Netherlands Brain Bank, providing a robust dataset to analyze the effects of age, post-mortem delay, brain acidity, and neurological diagnosis on microglia yield and phenotype. Our data show that cerebrospinal fluid pH is positively correlated to microglial cell yield, but donor age and post-mortem delay do not negatively affect viable microglia yield. Analysis of CD45 and CD11b expression showed that changes in microglia phenotype can be attributed to a neurological diagnosis, and are not influenced by variation in ante- and post-mortem parameters. Cryogenic storage of primary microglia was shown to be possible, albeit with variable levels of recovery and effects on phenotype and RNA quality. Microglial gene expression substantially changed due to culture, including the loss of the microglia-specific markers, showing the importance of immediate microglia phenotyping. We conclude that primary microglia can be isolated effectively and rapidly from human post-mortem brain tissue, allowing for the study of the

  12. A Microsatellite Genetic Map of the Turbot (Scophthalmus maximus)

    Science.gov (United States)

    Bouza, Carmen; Hermida, Miguel; Pardo, Belén G.; Fernández, Carlos; Fortes, Gloria G.; Castro, Jaime; Sánchez, Laura; Presa, Pablo; Pérez, Montse; Sanjuán, Andrés; de Carlos, Alejandro; Álvarez-Dios, José Antonio; Ezcurra, Susana; Cal, Rosa M.; Piferrer, Francesc; Martínez, Paulino

    2007-01-01

    A consensus microsatellite-based linkage map of the turbot (Scophthalmus maximus) was constructed from two unrelated families. The mapping panel was derived from a gynogenetic family of 96 haploid embryos and a biparental diploid family of 85 full-sib progeny with known linkage phase. A total of 242 microsatellites were mapped in 26 linkage groups, six markers remaining unlinked. The consensus map length was 1343.2 cM, with an average distance between markers of 6.5 ± 0.5 cM. Similar length of female and male maps was evidenced. However, the mean recombination at common intervals throughout the genome revealed significant differences between sexes, ∼1.6 times higher in the female than in the male. The comparison of turbot microsatellite flanking sequences against the Tetraodon nigroviridis genome revealed 55 significant matches, with a mean length of 102 bp and high sequence similarity (81–100%). The comparative mapping revealed significant syntenic regions among fish species. This study represents the first linkage map in the turbot, one of the most important flatfish in European aquaculture. This map will be suitable for QTL identification of productive traits in this species and for further evolutionary studies in fish and vertebrate species. PMID:18073440

  13. Research on formation of microsatellite communication with genetic algorithm.

    Science.gov (United States)

    Wu, Guoqiang; Bai, Yuguang; Sun, Zhaowei

    2013-01-01

    For the formation of three microsatellites which fly in the same orbit and perform three-dimensional solid mapping for terra, this paper proposes an optimizing design method of space circular formation order based on improved generic algorithm and provides an intersatellite direct spread spectrum communication system. The calculating equation of LEO formation flying satellite intersatellite links is guided by the special requirements of formation-flying microsatellite intersatellite links, and the transmitter power is also confirmed throughout the simulation. The method of space circular formation order optimizing design based on improved generic algorithm is given, and it can keep formation order steady for a long time under various absorb impetus. The intersatellite direct spread spectrum communication system is also provided. It can be found that, when the distance is 1 km and the data rate is 1 Mbps, the input wave matches preferably with the output wave. And LDPC code can improve the communication performance. The correct capability of (512, 256) LDPC code is better than (2, 1, 7) convolution code, distinctively. The design system can satisfy the communication requirements of microsatellites. So, the presented method provides a significant theory foundation for formation-flying and intersatellite communication.

  14. Breed traceability of buffalo meat using microsatellite genotyping technique.

    Science.gov (United States)

    Kannur, Bheemashankar H; Fairoze, Md Nadeem; Girish, P S; Karabasanavar, Nagappa; Rudresh, B H

    2017-02-01

    Although buffalo has emerged as a major meat producing animal in Asia, major research on breed traceability has so far been focused on cattle (beef). This research gap on buffalo breed traceability has impelled development and validation of buffalo breed traceability using a set of eight microsatellite (STR) markers in seven Indian buffalo breeds (Bhadawari, Jaffaarabadi, Murrah, Mehsana, Nagpuri, Pandharpuri and Surti). Probability of sharing same profile by two individuals at a specific locus was computed considering different STR numbers, allele pooling in breed and population. Match probabilities per breed were considered and six most polymorphic loci were genotyped. Out of eight microsatellite markers studied, markers CSSMO47, DRB3 and CSSM060 were found most polymorphic. Developed technique was validated with known and unknown, blood and meat samples; wherein, samples were genetically traced in 24 out of 25 samples tested. Results of this study showed potential applications of the methodology and encourage other researchers to address the problem of buffalo traceability so as to create a world-wide archive of breed specific genotypes. This work is the first report of breed traceability of buffalo meat utilizing microsatellite genotyping technique.

  15. Chromosomal localization of microsatellite loci in Drosophila mediopunctata

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    Renato Cavasini

    2015-03-01

    Full Text Available Drosophila mediopunctata has been used as a model organism for genetics and evolutionary studies in the last three decades. A linkage map with 48 microsatellite loci recently published for this species showed five syntenic groups, which had their homology determined to Drosophila melanogaster chromosomes. Then, by inference, each of the groups was associated with one of the five major chromosomes of D. mediopunctata. Our objective was to carry out a genetic (chromosomal analysis to increase the number of available loci with known chromosomal location. We made a simultaneous analysis of visible mutant phenotypes and microsatellite genotypes in a backcross of a standard strain and a mutant strain, which had each major autosome marked. Hence, we could establish the chromosomal location of seventeen loci; including one from each of the five major linkage groups previously published, and twelve new loci. Our results were congruent with the previous location and they open new possibilities to future work integrating microsatellites, chromosomal inversions, and genetic determinants of physiological and morphological variation.

  16. Microsatellite Primer Development for Post Oak, Quercus stellata (Fagaceae

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    Warren B. Chatwin

    2014-10-01

    Full Text Available Premise of the study: The American Cross Timbers forest ecosystem runs from southeastern Kansas to Central Texas and is primarily composed of post oak (Quercus stellata. This old-growth forest currently occupies only about 2% of its ancestral range. To facilitate genetic research on this species, we developed microsatellite primers specific to post oak from reduced genomic libraries. Methods and Results: Two Q. stellata individuals, sampled from the northern and southern range of the post oak forest, were subject to genomic reduction and 454 pyrosequencing. Bioinformatic analysis identified putative microsatellites from which 12 polymorphic primer sets were screened on three populations. The number of alleles observed ranged from five to 20 across all populations, while observed and expected heterozygosity values ranged from 0.05 to 0.833 and 0.236 to 0.893, respectively, within individual populations. Conclusions: We report the development of microsatellite markers, specific to post oak, to aid the study of genetic diversity and population structure of extant forest remnants.

  17. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Jordana Jordi

    2001-07-01

    Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

  18. Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.

    Science.gov (United States)

    Huang, Jie; Li, Yu-Zhi; Du, Lian-Ming; Yang, Bo; Shen, Fu-Jun; Zhang, He-Min; Zhang, Zhi-He; Zhang, Xiu-Yue; Yue, Bi-Song

    2015-02-07

    The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda. By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What's more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system. The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual

  19. Isolation and Characterization of Polymorphic Microsatellite Loci from Metapenaeopsis barbata Using PCR-Based Isolation of Microsatellite Arrays (PIMA)

    Science.gov (United States)

    Chiang, Tzen-Yuh; Tzeng, Tzong-Der; Lin, Hung-Du; Cho, Ching-Ju; Lin, Feng-Jiau

    2012-01-01

    The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species. PMID:22489123

  20. Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies

    Directory of Open Access Journals (Sweden)

    Vaidhegi R

    2009-10-01

    Full Text Available Abstract Background Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. Results In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P Conclusion The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.

  1. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.

    Science.gov (United States)

    Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

    2015-01-01

    A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10(-7) in peach to 9.48 × 10(-10) in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.

  2. Identification and characterization of microsatellites from calafate (Berberis microphylla, Berberidaceae)1

    Science.gov (United States)

    Varas, Benjamín; Castro, María H.; Rodriguez, Roberto; von Baer, Dietrich; Mardones, Claudia; Hinrichsen, Patricio

    2013-01-01

    • Premise of the study: Southern barberry or calafate (Berberis microphylla) is a shrub species endemic to the Patagonian region of South America that is used for human consumption. The fruit is very rich in vitamin C and anthocyanins and has a very high antioxidant capacity. There have been only a few genetic studies of this and other closely related species. • Methods and Results: Here we present the first 18 microsatellite markers of B. microphylla that were characterized using 66 accessions of calafate from Patagonia. On average, they had 7.6 alleles per marker, with an expected heterozygosity of 0.688. The informativeness of these markers was also evaluated in another 15 Berberis species, including most of the native and endemic Chilean species. • Conclusions: The results confirm that these new simple sequence repeat markers are very polymorphic and potentially useful in genetic studies in any species of the genus Berberis. PMID:25202561

  3. Development of twelve microsatellite loci in the red tree corals Primnoa resedaeformis and Primnoa pacifica

    Science.gov (United States)

    Morrison, Cheryl L.; Springmann, Marcus J.; Shroades, Kelsey; Stone, Robert P.

    2015-01-01

    A suite of tetra-, penta-, and hexa-nucleotide microsatellite loci were developed from Roche 454 pyrosequencing data for the cold-water octocorals Primnoa resedaeformis and P. pacifica. Twelve of 98 primer sets tested consistently amplified in 30 P. resedaeformis samples from Baltimore Canyon (western North Atlantic Ocean) and in 24 P. pacifica samples (Shutter Ridge, eastern Gulf of Alaska). The loci displayed moderate levels of allelic diversity (average 7.5 alleles/locus) and heterozygosity (average 47 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and to distinguish species. These common species are long-lived (hundreds of years) and provide essential fish habitat (P. pacifica), yet populations are provided little protection from human activities. These loci will be used to determine regional patterns of population connectivity to inform effective marine spatial planning and ecosystem-based fisheries management.

  4. Studying variability in human brain aging in a population-based German cohort – Rationale and design of 1000BRAINS

    Directory of Open Access Journals (Sweden)

    Svenja eCaspers

    2014-07-01

    Full Text Available The ongoing 1000 brains study (1000BRAINS is an epidemiological and neuroscientific investigation of structural and functional variability in the human brain during aging. The two recruitment sources are the 10-year follow-up cohort of the German Heinz Nixdorf Recall (HNR Study, and the HNR MultiGeneration Study cohort, which comprises spouses and offspring of HNR subjects. The HNR is a longitudinal epidemiological investigation of cardiovascular risk factors, with a comprehensive collection of clinical, laboratory, socioeconomic, and environmental data from population-based subjects aged 45-75 years on inclusion. HNR subjects underwent detailed assessments in 2000, 2006, and 2011, and completed annual postal questionnaires on health status. 1000BRAINS accesses these HNR data and applies a separate protocol comprising: neuropsychological tests of attention, memory, executive functions & language; examination of motor skills; ratings of personality, life quality, mood & daily activities; analysis of laboratory and genetic data; and state-of-the-art magnetic resonance imaging (MRI, 3 Tesla of the brain. The latter includes (i 3D-T1- and 3D-T2-weighted scans for structural analyses and myelin mapping; (ii three diffusion imaging sequences optimized for diffusion tensor imaging, high-angular resolution diffusion imaging for detailed fibre tracking and for diffusion kurtosis imaging; (iii resting-state and task-based functional MRI; and (iv fluid-attenuated inversion recovery and MR angiography for the detection of vascular lesions and the mapping of white matter lesions. The unique design of 1000BRAINS allows: (i comprehensive investigation of various influences including genetics, environment and health status on variability in brain structure and function during aging; and (ii identification of the impact of selected influencing factors on specific cognitive subsystems and their anatomical correlates.

  5. Orbit Determination for a Microsatellite Rendezvous with a Non-Cooperative Target

    National Research Council Canada - National Science Library

    Foster, Brian

    2003-01-01

    This study investigated the minimum requirements to establish a satellite tracking system architecture for a hostile "parasitic microsatellite" to rendezvous with a larger, non-cooperative target satellite...

  6. Development and characterization of polymorphic microsatellite markers in Dysosma pleiantha (Berberidaceae).

    Science.gov (United States)

    Guan, Bi-Cai; Gong, Xi; Zhou, Shi-Liang

    2011-08-01

    The development of compound microsatellite markers was conducted in Dysosma pleiantha to investigate genetic diversity and population genetic structure of this threatened medicinal plant. Using the compound microsatellite marker technique, 14 microsatellite markers that were successfully amplified showed polymorphism when tested on 38 individuals from three populations in eastern China. Overall, the number of alleles per locus ranged from 2 to 14, with an average of 7.71 alleles per locus. These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure and genetic diversity in Dysosma pleiantha.

  7. Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

    Science.gov (United States)

    Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

    2009-01-01

    Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

  8. Human activity and climate variability impacts on sediment discharge and runoff in the Yellow River of China

    Science.gov (United States)

    He, Yi; Wang, Fei; Mu, Xingmin; Guo, Lanqin; Gao, Peng; Zhao, Guangju

    2017-07-01

    We analyze the variability of sediment discharge and runoff in the Hekou-Longmen segment in the middle reaches of the Yellow River, China. Our analysis is based on Normalized Difference Vegetation Index (NDVI), sediment discharge, runoff, and monthly meteorological data (1961-2010). The climate conditions are controlled via monthly regional average precipitation and potential evapotranspiration (ET0) that are calculated with the Penman-Monteith method. Data regarding water and soil conservation infrastructure and their effects were investigated as causal factors of runoff and sediment discharge changes. The results indicated the following conclusions: (1) The sediment concentration, sediment discharge, and annual runoff, varied considerably during the study period and all of these factors exhibited larger coefficients of variation than ET0 and precipitation. (2) Sediment discharge, annual runoff, and sediment concentration significantly declined over the study period in a linear fashion. This was accompanied by an increase in ET0 and decline in precipitation that were not significant. (3) Within paired years with similar precipitation and potential evapotranspiration conditions (SPEC), all pairs showed a decline in runoff, sediment discharge, and sediment concentration. (4) Human impacts in this region were markedly high as indicated by NDVI, and soil and water measurements, and especially the soil and water conservation infrastructure resulting in an approximately 312 Mt year-1 of sediment deposition during 1960-1999.

  9. The impact of the matrix of red beet products and interindividual variability on betacyanins bioavailability in humans.

    Science.gov (United States)

    Wiczkowski, Wieslaw; Romaszko, Ewa; Szawara-Nowak, Dorota; Piskula, Mariusz K

    2018-06-01

    The influence of the matrix of red beetroot products and interindividual variability on betacyanins bioavailability in humans was studied. In a randomized crossover study 12 volunteers consumed red beet juice and crunchy slices containing betanin and isobetanin. Betalains were analyzed by the HPLC-DAD-MS. Urine samples examined after the consumption of both products contained not only native betacyanins but also their aglycones. In case of juice, the highest betacyanins urine excretion rate was observed within the first 2 h (64 nmol/h), while in case of crunchy slices within the period of 2-4 h (66 nmol/h). Among volunteers, the average total betacyanins excretion rate ranged from 18.54 to 67.96 nmol/h and, 13.15 to 63.58 nmol/h for red beet juice and crunchy slices, respectively. In total, approximately 0.3% of betacyanins (ranging from 0.12 to 0.58%) ingested from both products was excreted. The study showed that betacyanins bioavailability from juice and crunchy slices is similar, with the matrix of products consumed having an impact on betacyanins excretion profile, and the phenotype of volunteers affecting betacyanins excretion rate. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Association of CLEC16A with human common variable immunodeficiency disorder and role in murine B cells.

    Science.gov (United States)

    Li, Jin; Jørgensen, Silje F; Maggadottir, S Melkorka; Bakay, Marina; Warnatz, Klaus; Glessner, Joseph; Pandey, Rahul; Salzer, Ulrich; Schmidt, Reinhold E; Perez, Elena; Resnick, Elena; Goldacker, Sigune; Buchta, Mary; Witte, Torsten; Padyukov, Leonid; Videm, Vibeke; Folseraas, Trine; Atschekzei, Faranaz; Elder, James T; Nair, Rajan P; Winkelmann, Juliane; Gieger, Christian; Nöthen, Markus M; Büning, Carsten; Brand, Stephan; Sullivan, Kathleen E; Orange, Jordan S; Fevang, Børre; Schreiber, Stefan; Lieb, Wolfgang; Aukrust, Pål; Chapel, Helen; Cunningham-Rundles, Charlotte; Franke, Andre; Karlsen, Tom H; Grimbacher, Bodo; Hakonarson, Hakon; Hammarström, Lennart; Ellinghaus, Eva

    2015-04-20

    Common variable immunodeficiency disorder (CVID) is the most common symptomatic primary immunodeficiency in adults, characterized by B-cell abnormalities and inadequate antibody response. CVID patients have considerable autoimmune comorbidity and we therefore hypothesized that genetic susceptibility to CVID may overlap with autoimmune disorders. Here, in the largest genetic study performed in CVID to date, we compare 778 CVID cases with 10,999 controls across 123,127 single-nucleotide polymorphisms (SNPs) on the Immunochip. We identify the first non-HLA genome-wide significant risk locus at CLEC16A (rs17806056, P=2.0 × 10(-9)) and confirm the previously reported human leukocyte antigen (HLA) associations on chromosome 6p21 (rs1049225, P=4.8 × 10(-16)). Clec16a knockdown (KD) mice showed reduced number of B cells and elevated IgM levels compared with controls, suggesting that CLEC16A may be involved in immune regulatory pathways of relevance to CVID. In conclusion, the CLEC16A associations in CVID represent the first robust evidence of non-HLA associations in this immunodeficiency condition.

  11. Microsatellites variation in sterlet sturgeon, Acipenser ruthenus from the Lower Danube

    Directory of Open Access Journals (Sweden)

    Andreea Dudu

    2013-05-01

    Full Text Available Sturgeons represent an ancient group of fish with an important scientific and commercial value. The economical significance of these species is due to their meat and roes that are considered to be a gastronomic delicacy. Unfortunately, precisely due to their economical value the sturgeons have been overexploited by fishing and poaching and nowadays are facing extinction. Currently, in the Ponto-Caspian region is found the greatest diversity of acipenserid species and the Lower Danube is the last refuge for the sturgeons from the Black Sea. Acipenser ruthenus (sterlet is a fresh water sturgeon species which has undergone a large population decline, but local populations are still surviving in most parts of the rivers draining to Black, Azov and Caspian Seas. In order to have successful conservation programs of this species is essential to evaluate its genetic diversity. Microsatellites represent valuable markers for genetic analyses aiming the assessment of genetic variability of population. In our study we analyzed the cross-amplification and the polymorphism in A. ruthenus population from the Lower Danube of seven microsatellite loci (LS-19, LS-34, LS-54, LS-57, LS-68, Aox23 and Aox45, originally isolated in North-American sturgeon species. Among the seven loci, three (LS57, Aox23 and Aox45 have showed a tetrasomic profile. The most polymorphic loci were LS-57 with 12 alleles in population, followed by Aox23 and Aox45 with 11 alleles and LS-68 with 10 alleles. Four loci (LS-19, LS-34 and LS-54 presented a lower level of polymorphism, only three alleles being identified for the analyzed individuals.

  12. In silico characterization of microsatellites in Eucalyptus spp.: abundance, length variation and transposon associations

    Directory of Open Access Journals (Sweden)

    Edenilson Rabello

    2005-01-01

    Full Text Available This study assessed the abundance of microsatellites, or simple sequence repeats (SSR, in 19 Eucalyptus EST libraries from FORESTs, containing cDNA sequences from five species: E. grandis, E. globulus, E. saligna, E. urophylla and E. camaldulensis. Overall, a total of 11,534 SSRs and 8,447 SSR-containing sequences (25.5% of total ESTs were identified, with an average of 1 SSR/2.5 kb when considering all motifs and 1 SSR/3.1 kb when mononucleotides were not included. Dimeric repeats were the most abundant (41.03%, followed by trimerics (36.11% and monomerics (19.59%. The most frequent motifs were A/T (87.24% for monomerics, AG/CT (94.44% for dimerics, CCG/CGG (37.87% for trimerics, AAGG/CCTT (18.75% for tetramerics, AGAGG/CCTCT (14.04% for pentamerics and ACGGCG/CGCCGT (6.30% for hexamerics. According to sequence length, Class II or potentially variable markers were the most commonly found, followed by Class III. Two sequences presented high similarity to previously published Eucalyptus sequences from the NCBI database, EMBRA_72 and EMBRA_122. Local blastn search for transposons did not reveal the presence of any transposable elements with a cut-off value of 10-50. The large number of microsatellites identified will contribute to the refinement of marker-assisted mapping and to the discovery of novel markers for virtually all genes of economic interest.

  13. Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

    Directory of Open Access Journals (Sweden)

    M. T. Vajed Ebrahimi

    2017-07-01

    Full Text Available Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35 and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05. The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively, while the highest value for polymorphic information content was observed for the Arabi breed (0.88. A UPGMA (unweighted pair group method with arithmetic mean dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0 for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

  14. MICROSATELLITE GENETIC VARIATION IN CULTURED POPULATIONS OF AFRICAN CATFISH (Clarias gariepinus IN INDONESIA

    Directory of Open Access Journals (Sweden)

    Imron Imron

    2011-06-01

    Full Text Available African catfish, Clarias gariepinus, is one of economically important farmed species in Indonesia. To support the development of aquaculture industry, high genetic quality of both broodstock and seeds is required and breeding program is considered as viable option. Information on genetic variation of the populations being considered to form a base population may give insight toward the appropriate strategy to be implemented in breeding program. This study was aimed to assess genetic variation in farmed populations of catfish in Indonesia using microsatellite markers with special emphasis on their use to develop breeding program. Three populations of farmed catfish, namely Dumbo, Paiton, and Sangkuriang were collected. Fifteen individuals representing each population were screened for microsatellite variability using seven primer sets (cga01, cga02, cga03, cga05, cga06, cga09, cga10. Results found that with exception of two loci (cga01 and cg02 which had a slight increase, the other four loci showed reduction in the number of alleles ranging from 35% to 80% depending on loci. Farmed populations also showed heterozygote deficient and inbreeding level, being the highest was found in Sangkuriang and the least was observed in Dumbo population. Individuals within populations contributed most (95% while interpopulation variation accounted for only 5% of the total genetic variation. Populations of Dumbo and Sangkuriang were genetically similar while populations of Paiton were genetically different from both Dumbo and Sangkuriang. Viewed from genetic perspective, by combining all information emerging from this study, the best possible strategy to establish a base population with broad genetic base and less inbreeding would be to combine all the populations into a synthetic base population.

  15. TGFBR2 and BAX mononucleotide tract mutations, microsatellite instability, and prognosis in 1072 colorectal cancers.

    Directory of Open Access Journals (Sweden)

    Kaori Shima

    Full Text Available Mononucleotide tracts in the coding regions of the TGFBR2 and BAX genes are commonly mutated in microsatellite instability-high (MSI-high colon cancers. The receptor TGFBR2 plays an important role in the TGFB1 (transforming growth factor-β, TGF-β signaling pathway, and BAX plays a key role in apoptosis. However, a role of TGFBR2 or BAX mononucleotide mutation in colorectal cancer as a prognostic biomarker remains uncertain.We utilized a database of 1072 rectal and colon cancers in two prospective cohort studies (the Nurses' Health Study and the Health Professionals Follow-up Study. Cox proportional hazards model was used to compute mortality hazard ratio (HR, adjusted for clinical, pathological and molecular features including the CpG island methylator phenotype (CIMP, LINE-1 methylation, and KRAS, BRAF and PIK3CA mutations. MSI-high was observed in 15% (162/1072 of all colorectal cancers. TGFBR2 and BAX mononucleotide mutations were detected in 74% (117/159 and 30% (48/158 of MSI-high tumors, respectively. In Kaplan-Meier analysis as well as univariate and multivariate Cox regression analyses, compared to microsatellite stable (MSS/MSI-low cases, MSI-high cases were associated with superior colorectal cancer-specific survival [adjusted HR, 0.34; 95% confidence interval (CI, 0.20-0.57] regardless of TGFBR2 or BAX mutation status. Among MSI-high tumors, TGFBR2 mononucleotide mutation was associated with CIMP-high independent of other variables [multivariate odds ratio, 3.57; 95% CI, 1.66-7.66; p = 0.0011].TGFBR2 or BAX mononucleotide mutations are not associated with the patient survival outcome in MSI-high colorectal cancer. Our data do not support those mutations as prognostic biomarkers (beyond MSI in colorectal carcinoma.

  16. Genetic structure and gene flow among Komodo dragon populations inferred by microsatellite loci analysis.

    Science.gov (United States)

    Ciofi, C; Bruford, M W

    1999-12-01

    A general concern for the conservation of endangered species is the maintenance of genetic variation within populations, particularly when they become isolated and reduced in size. Estimates of gene flow and effective population size are therefore important for any conservation initiative directed to the long-term persistence of a species in its natural habitat. In the present study, 10 microsatellite loci were used to assess the level of genetic variability among populations of the Komodo dragon Varanus komodoensis. Effective population size was calculated and gene flow estimates were compared with palaeogeographic data in order to assess the degree of vulnerability of four island populations. Rinca and Flores, currently separated by an isthmus of about 200 m, retained a high level of genetic diversity and showed a high degree of genetic similarity, with gene flow values close to one migrant per generation. The island of Komodo showed by far the highest levels of genetic divergence, and its allelic distinctiveness was considered of great importance in the maintenance of genetic variability within the species. A lack of distinct alleles and low levels of gene flow and genetic variability were found for the small population of Gili Motang island, which was identified as vulnerable to stochastic threats. Our results are potentially important for both the short- and long-term management of the Komodo dragon, and are critical in view of future re-introduction or augmentation in areas where the species is now extinct or depleted.

  17. Determinants in the Ig Variable Domain of Human HAVCR1 (TIM-1) Are Required To Enhance Hepatitis C Virus Entry.

    Science.gov (United States)

    Kachko, Alla; Costafreda, Maria Isabel; Zubkova, Iryna; Jacques, Jerome; Takeda, Kazuyo; Wells, Frances; Kaplan, Gerardo; Major, Marian E

    2018-03-15

    Hepatitis C virus (HCV) is the leading cause of chronic hepatitis in humans. Several host molecules participate in HCV cell entry, but this process remains unclear. The complete unraveling of the HCV entry process is important to further understand viral pathogenesis and develop therapeutics. Human hepatitis A virus (HAV) cellular receptor 1 (HAVCR1), CD365, also known as TIM-1, functions as a phospholipid receptor involved in cell entry of several enveloped viruses. Here, we studied the role of HAVCR1 in HCV infection. HAVCR1 antibody inhibited entry in a dose-dependent manner. HAVCR1 soluble constructs neutralized HCV, which did not require the HAVCR1 mucinlike region and was abrogated by a mutation of N to A at position 94 (N94A) in the Ig variable (IgV) domain phospholipid-binding pocket, indicating a direct interaction of the HAVCR1 IgV domain with HCV virions. However, knockout of HAVCR1 in Huh7 cells reduced but did not prevent HCV growth. Interestingly, the mouse HAVCR1 ortholog, also a phospholipid receptor, did not enhance infection and a soluble form failed to neutralize HCV, although replacement of the mouse IgV domain with the human HAVCR1 IgV domain restored the enhancement of HCV infection. Mutations in the cytoplasmic tail revealed that direct HAVCR1 signaling is not required to enhance HCV infection. Our data show that the phospholipid-binding function and other determinant(s) in the IgV domain of human HAVCR1 enhance HCV infection. Although the exact mechanism is not known, it is possible that HAVCR1 facilitates entry by stabilizing or enhancing attachment, leading to direct interactions with specific receptors, such as CD81. IMPORTANCE Hepatitis C virus (HCV) enters cells through a multifaceted process. We identified the human hepatitis A virus cellular receptor 1 (HAVCR1), CD365, also known as TIM-1, as a facilitator of HCV entry. Antibody blocking and silencing or knockout of HAVCR1 in hepatoma cells reduced HCV entry. Our findings that the

  18. Natural and human-induced variability in the composition of fish assemblages in the Northwestern Cuban shelf

    Directory of Open Access Journals (Sweden)

    Gaspar González-Sansón

    2009-09-01

    Full Text Available The main goal of the study was to obtain field data to build a baseline of fish assemblage composition that can be used comparatively for future analyses of the impact of human actions in the region. A basic network of 68 sampling stations was defined for the entire region (4 050 km2. Fish assemblage species and size composition was estimated using visual census methods at three different spatial scales: a entire region, b inside the main reef area and c along a human impact coastal gradient. Multivariate numerical analyses revealed habitat type as the main factor inducing spatial variability of fish community composition, while the level of human impact appears to play the main role in fish assemblage composition changes along the coast. A trend of decreasing fish size toward the east supports the theory of more severe human impact due to overfishing and higher urban pollution in that direction. This is the first detailed study along the northwest coast of Cuba that focuses on fish community structure and the natural and human-induced variations at different spatial scales for the entire NW shelf. This research also provides input for a more comprehensive understanding of coastal marine fish communities’ status in the Gulf of Mexico basin. Rev. Biol. Trop. 57 (3: 721-740. Epub 2009 September 30.Se obtuvieron datos de campo para una línea base de la composición de la ictiofauna que pueda ser usada comparativamente para el análisis de impactos humanos futuros en la región. Se estableció una red básica de 68 estaciones de muestreo para la región completa (4 050 km2. La composición por especies y por tallas de la ictiofauna fue estimada utilizando métodos de censo visual en tres escalas espaciales diferentes: a La región completa, b dentro del área principal de arrecifes y c a lo largo de un gradiente costero de impacto humano. El tipo de hábitat es el factor principal que induce la variación espacial en la composición de la

  19. Genetic variability in Melipona scutellaris from Recôncavo, Bahia, Brazil.

    Science.gov (United States)

    Viana, J L; Francisco, A K; Carvalho, C A L; Waldschmidt, A M

    2013-09-10

    Bees play a key role in pollination and thereby help maintain plant diversity. The stingless bee Melipona scutellaris is an important pollinator in northeastern Brazil because it is endemic to this region. Both deforestation and timber harvesting have reduced the nesting sites for this species, thus reducing its population and range. Genetic studies may help reverse this process by providing important tools for their proper management with a view to conservation of this species. Microsatellite markers have proven to be ideal for mapping genes and population genetic studies. Our aim was to study, using microsatellite markers, the interpopulation genetic variability of M. scutellaris in different parts of the Recôncavo region in Bahia State, Brazil. In all, 95 adult workers from 11 localities in Recôncavo Baiano (Amargosa, Cabaceiras do Paraguaçu, Conceição da Feira, Conceição do Almeida, Domingos Macedo Costa, Governador Mangabeira, Jaguaripe, Jiquiriça, Maragojipe, São Felipe, and Vera Cruz) were analyzed using 10 pairs of microsatellite primers developed for different Meliponini species. The total number of alleles, allele richness, and genetic diversity ranged from 2 to 7 per locus (average = 4.4), 1.00 to 4.88, and 0.0 to 0.850, respectively. The expected and observed heterozygosities varied from 0.0 to 0.76 and 0.0 to 0.84, respectively. No locus showed deviation from the expected frequencies in the chi-square test or linkage disequilibrium. The fixation index, analysis of molecular variance, and unweighted pair-group method using the arithmetic average revealed the effects of human activities on the populations of M. scutellaris, as little genetic structure was detected.

  20. Transference of microsatellite markers from Eucalyptus spp to Acca sellowiana and the successful use of this technique in genetic characterization

    Directory of Open Access Journals (Sweden)

    Karine Louise dos Santos

    2007-01-01

    Full Text Available The pineapple guava (Acca sellowiana, known in portuguese as the goiabeira-serrana or "Feijoa", is a native fruit tree from southern Brazil and northern Uruguay that has commercial potential due to the quality and unique flavor of its fruits. Knowledge of genetic variability is an important tool in various steps of a breeding program, which can be facilitated by the use of molecular markers. The conservation of repeated sequences among related species permits the transferability of microsatellite markers from Eucalyptus spp. to A. sellowiana for testing. We used primers developed for Eucalyptus to characterize A. sellowiana accessions. Out of 404 primers tested, 180 amplified visible products and 38 were polymorphic. A total of 48 alleles were detected with ten Eucalyptus primer pairs against DNA from 119 A. sellowiana accessions. The mean expected heterozygosity among accessions was 0.64 and the mean observed heterozygosity 0.55. A high level of genetic diversity was also observed in the dendrogram, where the degree of genetic dissimilarity ranged from 0 to 65% among the 119 genotypes tested. This study demonstrates the possibility of transferring microsatellite markers between species of different genera in addition to evaluating the extent of genetic variability among plant accessions.

  1. Micro-satellite for space debris observation by optical sensors

    Science.gov (United States)

    Thillot, Marc; Brenière, Xavier; Midavaine, Thierry

    2017-11-01

    The purpose of this theoretical study carried out under CNES contract is to analyze the feasibility of small space debris detection and classification with an optical sensor on-board micro-satellite. Technical solutions based on active and passive sensors are analyzed and compared. For the most appropriated concept an optimization was made and theoretical performances in terms of number of detection versus class of diameter were calculated. Finally we give some preliminary physical sensor features to illustrate the concept (weight, volume, consumption,…).

  2. Microsatellite markers for the silver arowana (Osteoglossum bicirrhosum, Osteoglossidae, Osteoglossiformes).

    Science.gov (United States)

    DE Jesus DA Silva, Themis; Hrbek, Tomas; Farias, Izeni P

    2009-05-01

    Osteoglossum bicirrhosum (silver arowana) is an important fish for the economy of the Amazon region, both as an ornamental fish and as a food fish. To provide tools for addressing ecological and genetic questions, we developed 19 polymorphic microsatellite markers that had between 2 and 7 alleles per locus in the 24 tested individuals. The transferability of many of the loci was confirmed for Osteoglossum ferreirai (black arowana) and Arapaima gigas, and for three African osteoglossiform species. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

  3. Thirteen nuclear microsatellite loci for butternut (Juglans cinerea L.).

    Science.gov (United States)

    Hoban, Sean; Anderson, Robert; McCleary, Tim; Schlarbaum, Scott; Romero-Severson, Jeanne

    2008-05-01

    Butternut (Juglans cinerea L.) is an eastern North American forest tree severely threatened by an exotic fungal pathogen, Sirococcus clavigignenti-juglandacearum. We report here 13 nuclear microsatellites for genetic evaluation of the remaining natural populations. Summary statistics are reported for individuals from a population of butternuts in central Kentucky (N = 63). All markers were polymorphic, with an average of 13.7 alleles per locus observed. Four loci exhibited significantly fewer heterozygotes than expected under Hardy-Weinberg equilibrium (P < 0.05). © 2007 The Authors.

  4. Quantifying human disturbance in watersheds: Variable selection and performance of a GIS-based disturbance index for predicting the biological condition of perennial streams

    Science.gov (United States)

    Falcone, James A.; Carlisle, Daren M.; Weber, Lisa C.

    2010-01-01

    Characterizing the relative severity of human disturbance in watersheds is often part of stream assessments and is frequently done with the aid of Geographic Information System (GIS)-derived data. However, the choice of variables and how they are used to quantify disturbance are often subjective. In this study, we developed a number of disturbance indices by testing sets of variables, scoring methods, and weightings of 33 potential disturbance factors derived from readily available GIS data. The indices were calibrated using 770 watersheds located in the western United States for which the severity of disturbance had previously been classified from detailed local data by the United States Environmental Protection Agency (USEPA) Environmental Monitoring and Assessment Program (EMAP). The indices were calibrated by determining which variable or variable combinations and aggregation method best differentiated between least- and most-disturbed sites. Indices composed of several variables performed better than any individual variable, and best results came from a threshold method of scoring using six uncorrelated variables: housing unit density, road density, pesticide application, dam storage, land cover along a mainstem buffer, and distance to nearest canal/pipeline. The final index was validated with 192 withheld watersheds and correctly classified about two-thirds (68%) of least- and most-disturbed sites. These results provide information about the potential for using a disturbance index as a screening tool for a priori ranking of watersheds at a regional/national scale, and which landscape variables and methods of combination may be most helpful in doing so.

  5. Microchemical and structural regular variability of apatites in 'overbuilt' enamel and dentin of human molar teeth

    Energy Technology Data Exchange (ETDEWEB)

    Kuczumow, A., E-mail: kuczon@kul.lublin.pl [Department of Chemistry, Lublin Catholic University, 20-718 Lublin (Poland); Nowak, J. [Department of Chemistry, Lublin Catholic University, 20-718 Lublin (Poland); ChaLas, R. [Department of Conservative Medicine, Lublin Medical University, 20-081 Lublin (Poland)

    2011-10-15

    The aim of a recent paper was to recognize the chemical and structural changes in apatites, which form both the enamel and the dentin of the human tooth. The aim was achieved by scrutinizing the linear elemental profiles along the cross-sections of human molar teeth. Essentially, the task was accomplished with the application of the Electron Probe Microanalysis method and with some additional studies by Micro-Raman spectrometry. All the trends in linear profiles were strictly determined. In the enamel zone they were either increasing or decreasing curves of exponential character. The direction of the investigations was to start with the tooth surface and move towards the dentin-enamel junction (DEJ). The results of the elemental studies were more visible when the detected material was divided, in an arbitrary way, into the prevailing 'core' enamel ({approx}93.5% of the total mass) and the remaining 'overbuilt' enamel. The material in the 'core' enamel was fully stable, with clearly determined chemical and mechanical features. However, the case was totally different in the 'overbuilt enamel', with dynamic changes in the composition. In the 'overbuilt' layer Ca, P, Cl and F profiles present the decaying distribution curves, whereas Mg, Na, K and CO{sub 3}{sup 2-} present the growing ones. Close to the surface of the tooth the mixture of hydroxy-, chlor- and fluor-apatite is formed, which is much more resistant than the rest of the enamel. On passing towards the DEJ, the apatite is enriched with Na, Mg and CO{sub 3}{sup 2-}. In this location, three of six phosphate groups were substituted with carbonate groups. Simultaneously, Mg is associated with the hydroxyl groups around the hexad axis. In this way, the mechanisms of exchange reactions were established. The crystallographic structures were proposed for new phases located close to DEJ. In the dentin zone, the variability of elemental profiles looks different, with

  6. A pilot investigation of the effect of extremely low frequency pulsed electromagnetic fields on humans' heart rate variability.

    Science.gov (United States)

    Baldi, Emilio; Baldi, Claudio; Lithgow, Brian J

    2007-01-01

    The question whether pulsed electromagnetic field (PEMF) can affect the heart rhythm is still controversial. This study investigates the effects on the cardiocirculatory system of ELF-PEMFs. It is a follow-up to an investigation made of the possible therapeutic effect ELF-PEMFs, using a commercially available magneto therapeutic unit, had on soft tissue injury repair in humans. Modulation of heart rate (HR) or heart rate variability (HRV) can be detected from changes in periodicity of the R-R interval and/or from changes in the numbers of heart-beat/min (bpm), however, R-R interval analysis gives only a quantitative insight into HRV. A qualitative understanding of HRV can be obtained considering the power spectral density (PSD) of the R-R intervals Fourier transform. In this study PSD is the investigative tool used, more specifically the low frequency (LF) PSD and high frequency (HF) PSD ratio (LF/HF) which is an indicator of sympatho-vagal balance. To obtain the PSD value, variations of the R-R time intervals were evaluated from a continuously recorded ECG. The results show a HR variation in all the subjects when they are exposed to the same ELF-PEMF. This variation can be detected by observing the change in the sympatho-vagal equilibrium, which is an indicator of modulation of heart activity. Variation of the LF/HF PSD ratio mainly occurs at transition times from exposure to nonexposure, or vice versa. Also of interest are the results obtained during the exposure of one subject to a range of different ELF-PEMFs. This pilot study suggests that a full investigation into the effect of ELF-PEMFs on the cardiovascular system is justified.

  7. Microsatellite loci development in mycoheterotrophic Corallorhiza maculata with amplification in C. mertensiana

    Science.gov (United States)

    Sarah E. Hopkins; D. Lee. Taylor

    2011-01-01

    Microsatellite primers were developed for the first time in the species Corallorhiza maculata, a nonphotosynthetic orchid that is becoming a model for studying mycorrhizal specificity. Eight polymorphic microsatellite markers were developed using an enrichment and cloning protocol. The number of alleles for each locus ranged from two to seven. The...

  8. Microsatellite profiles as a basis for intellectual property protection in grape

    NARCIS (Netherlands)

    Ibanez, J.; Eeuwijk, van F.A.

    2003-01-01

    The use of microsatellite analysis in a forensic procedure for establishing infringement on plant breeders¿ rights in vegetatively propagated crops was evaluated. A reference collection of 45 seedless grape varieties was chosen as reference collection. Matching probabilities of grape microsatellite

  9. Constraints on Allele size at microsatellite loci : Implications for genetic differentiation

    NARCIS (Netherlands)

    Nauta, M.J.; Weissing, F.J.

    Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small

  10. Novel and cross-species microsatellite markers for parentage analysis in Sanderling

    NARCIS (Netherlands)

    Luttikhuizen, P.C.; Bol, A.; Witte, H.; van Bleijswijk, J.; Haddrath, O.; Baker, A.J.; Piersma, T.; Reneerkens, J.; Piersma, T.

    2011-01-01

    We isolated and tested six novel microsatellite loci in Sanderling (Calidris alba) from Greenland for paternity analyses. In addition, we tested 11 already published microsatellite markers which were originally developed for the congeneric species, the Pectoral Sandpiper (C. melanotos). All loci

  11. Novel and cross-species microsatellite markers for parentage analysis in Sanderling Calidris alba

    NARCIS (Netherlands)

    Luttikhuizen, Pieternella C.; Bol, Anneke; Witte, Harry; van Bleijswijk, Judith; Haddrath, Oliver; Baker, Allan J.; Piersma, Theunis; Reneerkens, Jeroen

    We isolated and tested six novel microsatellite loci in Sanderling (Calidris alba) from Greenland for paternity analyses. In addition, we tested 11 already published microsatellite markers which were originally developed for the congeneric species, the Pectoral Sandpiper (C. melanotos). All loci

  12. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae.

    Directory of Open Access Journals (Sweden)

    Isabel A S Bonatelli

    Full Text Available Microsatellite markers (also known as SSRs, Simple Sequence Repeats are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  13. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    Science.gov (United States)

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  14. Use of microsatellite markers in an American beech (Fagus grandifolia) population and paternity testing

    Science.gov (United States)

    Jennifer Koch; Dave Carey; M.E. Mason

    2010-01-01

    Cross-species amplification of six microsatellite markers from European beech (Fagus sylvatica Linn) and nine markers from Japanese beech (Fagus crenata Blume) was tested in American beech (Fagus grandifolia Ehrh.). Three microsatellites from each species were successfully adapted for use in American beech...

  15. Development of Microsatellite Markers for the Korean Mussel, Mytilus coruscus (Mytilidae Using Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Hye Suck An

    2012-08-01

    Full Text Available Mytilus coruscus (family Mytilidae is one of the most important marine shellfish species in Korea. During the past few decades, this species has become endangered due to the loss of habitats and overfishing. Despite this species’ importance, information on its genetic background is scarce. In this study, we developed microsatellite markers for M. coruscus using next-generation sequencing. A total of 263,900 raw reads were obtained from a quarter-plate run on the 454 GS-FLX titanium platform, and 176,327 unique sequences were generated with an average length of 381 bp; 2569 (1.45% sequences contained a minimum of five di- to tetra-nucleotide repeat motifs. Of the 51 loci screened, 46 were amplified successfully, and 22 were polymorphic among 30 individuals, with seven of trinucleotide repeats and three of tetranucleotide repeats. All loci exhibited high genetic variability, with an average of 17.32 alleles per locus, and the mean observed and expected heterozygosities were 0.67 and 0.90, respectively. In addition, cross-amplification was tested for all 22 loci in another congener species, M. galloprovincialis. None of the primer pairs resulted in effective amplification, which might be due to their high mutation rates. Our work demonstrated the utility of next-generation 454 sequencing as a method for the rapid and cost-effective identification of microsatellites. The high degree of polymorphism exhibited by the 22 newly developed microsatellites will be useful in future conservation genetic studies of this species.

  16. Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum.

    Science.gov (United States)

    Mallick, Prashant K; Sutton, Patrick L; Singh, Ruchi; Singh, Om P; Dash, Aditya P; Singh, Ashok K; Carlton, Jane M; Bhasin, Virendra K

    2013-10-01

    Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite's acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST=0.253, Pstructure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation at both neutral and adaptive loci across India. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

    Science.gov (United States)

    Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

    2012-11-01

    Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to

  18. Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum

    Science.gov (United States)

    Mallick, Prashant K.; Sutton, Patrick L.; Singh, Ruchi; Singh, Om P.; Dash, Aditya P.; Singh, Ashok K.; Carlton, Jane M.; Bhasin, Virendra K.

    2013-01-01

    Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite’s acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST = 0.253, P<0.001) suggests a long period of isolation or a possibility of different origin between them. A pattern of significant isolation by distance was observed in low transmission areas (r = 0.49, P=0.003, N = 83, Mantel test). An unanticipated pattern of spread of hitchhiking suggests genetic structure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation

  19. Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites

    KAUST Repository

    Pamidimarri, D. V N N Sudheer

    2010-03-11

    Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J

  20. GENETIC DIVERSITY OF SOME IRANIAN SWEET CHERRY (PRUNUS AVIUM) CULTIVARS USING MICROSATELLITE MARKERS AND MORPHOLOGICAL TRAITS.

    Science.gov (United States)

    Farsad, A; Esna-Ashari, M

    2016-01-01

    The aim of this study was to characterize 23 important Iranian sweet cherry (Prunus avium) cultivars collected from different provinces of Iran and 1 foreign cultivar, which was used as control, considered for breeding programs by using 21 microsatellite markers and 27 morphological traits. In sweet cherry (Prunus avium) accessions, leaf, fruit, and stone morphological characters were evaluated during two consecutive years. The study revealed a high variability in the set of evaluated sweet cherry accessions. The majority of important correlations were determined among variables representing fruit and leaf size and variables related to color. Cluster analysis distinguished sweet cherry accessions into two distinct groups. Principal component analysis (PCA) of qualitative and quantitative morphological parameters explained over 86.59% of total variability in the first seven axes. In PCA, leaf traits such as leaf length and width, and fruit traits such as length, width, and weight, and fruit flesh and juice color were predominant in the first two components, indicating that they were useful for the assessment of sweet cherry germplasm characterization. Out of 21 SSR markers, 16 were polymorphic, producing 177 alleles that varied from 4 to 16 alleles (9.35 on average) with a mean heterozygosity value of 0.82 that produced successful amplifications and revealed DNA polymorphisms. Allele size varied from 95 to 290 bp. Cluster analyses showed that the studied sweet cherry genotypes were classified intofive main groups based mainly on their species characteristics and SSR data. In general, our results did not show a clear structuring of genetic variability within the Iranian diffusion area of sweet cherry, so it was not possible to draw any indications on regions of provenance delimitation. The results of this study contribute to a better understanding of sweet cherry genetic variations in Iran, thus making for more efficient programs aimed at preserving biodiversity and

  1. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species.

    Science.gov (United States)

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M Iqbal; Zerega, Nyree J C

    2013-07-01

    Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

  2. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species1

    Science.gov (United States)

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M. Iqbal; Zerega, Nyree J. C.

    2013-01-01

    • Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit. PMID:25202565

  3. Development of Microsatellite Loci in Artocarpus altilis (Moraceae and Cross-Amplification in Congeneric Species

    Directory of Open Access Journals (Sweden)

    Colby Witherup

    2013-07-01

    Full Text Available Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241, A. camansi (34, A. mariannensis (15, and A. altilis × mariannensis (64 samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426 samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

  4. Development of Microsatellite Loci in Scrophularia incisa (Scrophulariaceae and Cross-Amplification in Congeneric Species

    Directory of Open Access Journals (Sweden)

    Rui-Hong Wang

    2014-02-01

    Full Text Available Premise of the study: To elucidate the population genetics and phylogeography of Scrophularia incisa, microsatellite primers were developed. We also applied these microsatellite markers to its closely related species S. dentata and S. kiriloviana. Methods and Results: Using the compound microsatellite marker technique, 12 microsatellite primers were identified in S. incisa. The number of alleles ranged from 14 to 26 when assessed in 78 individuals from four populations. With high cross-species transferability, these primers also amplified in S. dentata and S. kiriloviana. Conclusions: These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure in the Chinese species of sect. Tomiophyllum at fine and range-wide geographical scales.

  5. Microsatellites for Oenothera gayleana and O. hartwegii subsp. filifolia (Onagraceae), and their utility in section Calylophus.

    Science.gov (United States)

    Lewis, Emily M; Fant, Jeremie B; Moore, Michael J; Hastings, Amy P; Larson, Erica L; Agrawal, Anurag A; Skogen, Krissa A

    2016-02-01

    Eleven nuclear and four plastid microsatellite markers were screened for two gypsum endemic species, Oenothera gayleana and O. hartwegii subsp. filifolia, and tested for cross-amplification in the remaining 11 taxa within Oenothera sect. Calylophus (Onagraceae). Microsatellite markers were tested in two to three populations spanning the ranges of both O. gayleana and O. hartwegii subsp. filifolia. The nuclear microsatellite loci consisted of both di- and trinucleotide repeats with one to 17 alleles per population. Several loci showed significant deviation from Hardy-Weinberg equilibrium, which may be evidence of chromosomal rings. The plastid microsatellite markers identified one to seven haplotypes per population. The transferability of these markers was confirmed in all 11 taxa within Oenothera sect. Calylophus. The microsatellite loci characterized here are the first developed and tested in Oenothera sect. Calylophus. These markers will be used to assess whether pollinator foraging distance influences population genetic parameters in predictable ways.

  6. FullSSR: Microsatellite Finder and Primer Designer

    Directory of Open Access Journals (Sweden)

    Sebastián Metz

    2016-01-01

    Full Text Available Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

  7. Evolution of Microsatellite Loci of Tropical and Temperate Anguilla Eels

    Directory of Open Access Journals (Sweden)

    Mei-Chen Tseng

    2012-04-01

    Full Text Available Anguilla eels are divided into temperate and tropical eels, based on their major distributions. The present study collected two temperate eels, Anguilla japonica and Anguilla anguilla, and two tropical eels, Anguilla marmorata and Anguilla bicolor pacifica, to examine two questions: do temperate and tropical Anguilla eels have different genetic polymorphic patterns?; and do temperate Anguilla japonica and Anguilla anguilla have a closer relationship to each other than to tropical eels? In total, 274 sequences were cloned and sequenced from six conserved microsatellite loci to examine polymorphic patterns of these four catadromous eels. Different mutational events, including substitutions, and repeat-unit deletions and insertions, appeared in major regions, while different point mutations were observed in flanking regions. The results implied that parallel patterns of microsatellite sequences occurred within both tropical and temperate freshwater eels. Consensus flanking sequences of six homologous loci from each of the four species were constructed. Genetic distances ranged from 0.044 (Anguilla bicolor pacifica vs. Anguilla marmorata to 0.061 (Anguilla marmorata vs. Anguilla anguilla. The tree topology suggests the hypothesis of Anguilla japonica and Anguilla anguilla being a sister group must be rejected.

  8. Phylogeography of haplotypes of five microsatellites located in a low-recombination region of the X chromosome: studies worldwide and in Brazilian populations.

    Science.gov (United States)

    Pereira, Rinaldo Wellerson; Pena, Sérgio D J

    2006-01-01

    We studied five microsatellites (DXS995, DXS8076, DXS8114, DXS1002 and DXS1050) located in a region of very low recombination rate in the long arm of the human X chromosome (Xq13.3-Xq21.3). No recombination was seen in 291 meioses in CEPH families. To test whether haplotypes composed of the five microsatellites could differentiate among distinct human continental populations, we studied an international panel containing 72 males from Africa, Europe, Asia and the America. Haplotypic diversity was very high within these groups and no haplotypes were shared among them. This led to the hope that we might be able to identify continent-specific lineages. However, in a median joining network there was no clear discrimination of the different continental groups. We then tested whether we could identify X chromosomal lineages from different continental origins in Brazilians. We typed 180 white Brazilians from four different geographical regions and examined their proportions of haplotype sharing with Africans, Asians, Europeans and Amerindians. No phylogeographical patterns emerged from the data. Moreover, there were several instances of the same haplotype being shared by many (and in one instance all) groups, suggesting that recombination might be occurring. We thus studied pairwise the level of linkage disequilibrium (LD) between the microsatellites. No detectable linkage disequilibrium between the most external loci DXS995 and DXS1050 was observed. Thus, even though recombination may be absent on short time spans, as seen in the CEPH pedigrees, on a long term basis it occurs often enough to dissipate all linkage disequilibrium. On the other hand, we observed very strong linkage disequilibrium between the pairs DXS995/DXS8076 and DXS1002/DXS8114, raising the possibility of resequencing the segment between them to identify single nucleotide polymorphisms (SNPs) in their intervals. The combination of X-linked microsatellites and SNPs in strong linkage disequilibrium might

  9. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.

    Science.gov (United States)

    López-Giráldez, Francesc; Andrés, Olga; Domingo-Roura, Xavier; Bosch, Montserrat

    2006-10-23

    The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding

  10. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

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    Bosch Montserrat

    2006-10-01

    Full Text Available Abstract Background The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. Results We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Conclusion Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes. Finally, due to their higher complexity and lower potential informative content of microsatellites

  11. RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

    Science.gov (United States)

    Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

    2017-02-08

    Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of F ST and R ST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

  12. Food Fingerprinting: Characterization of the Ecuadorean Type CCN-51 of Theobroma cacao L. Using Microsatellite Markers.

    Science.gov (United States)

    Herrmann, Luise; Felbinger, Christine; Haase, Ilka; Rudolph, Barbara; Biermann, Bernhard; Fischer, Markus

    2015-05-13

    The cocoa type "Colección Castro Naranjal 51" (CCN-51) is known for its resistance to specific climate conditions and its high yield, but it shows a weaker flavor profile and therefore is marketed as bulk cocoa. In a previous study, the two cocoa types Arriba and CCN-51 could easily be distinguished, but differences among the CCN-51 samples were observed. This was unexpected, as CCN-51 is reported to be a clone. To confirm whether CCN-51 is a pure clone, 10 simple sequence repeats (SSR) located on the nuclear genome were used to analyze various CCN-51 samples in comparison to the cocoa varieties Arriba and Criollo. As expected, there are differences in the SSR pattern among CCN-51, Arriba, and Criollo, but a variability within the CCN-51 sample set was detected as well. The previously described sequence variation in the chloroplast genome was confirmed by a variability in the microsatellite loci of the nuclear genome for a comprehensive cultivar collection of CCN-51 of both bean and leaf samples. In summary, beneath somaclonal variation, misidentification of plant collections and also sexual reproduction of CCN-51 can be suggested.

  13. Human and methodological sources of variability in the measurement of urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine

    DEFF Research Database (Denmark)

    Barregard, Lars; Møller, Peter; Henriksen, Trine

    2013-01-01

    Urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) is a widely used biomarker of oxidative stress. However, variability between chromatographic and ELISA methods hampers interpretation of data, and this variability may increase should urine composition differ between individuals, leading to as...

  14. Application of plant DNA markers in forensic botany: genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites.

    Science.gov (United States)

    Craft, Kathleen J; Owens, Jeffrey D; Ashley, Mary V

    2007-01-05

    As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

  15. Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

    Science.gov (United States)

    Shi, Jiaqin; Huang, Shunmou; Fu, Donghui; Yu, Jinyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2013-01-01

    Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with

  16. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

    Directory of Open Access Journals (Sweden)

    Jiaqin Shi

    Full Text Available Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences. The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type the angiosperm species (aside from a few species all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite

  17. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826.

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    Magally Torres-Leguizamon

    Full Text Available Despite the fundamental role that soil invertebrates (e.g. earthworms play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci and mitochondrial markers (COI. Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

  18. Population Genetics of European Anchovy (Engraulis encrasicolus L. in the Seas of Turkey Based on Microsatellite DNA

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    Fevzi Bardakci

    2014-06-01

    Results: In this study, 13 microsatellite loci in 541 samples were analysed for determination of genetic structure of anchovy along Turkish coasts. The genetic variability was high among population, the average alleles numbers per locus per population ranged from 11.0 to 22.8. Observed heterozygosity per population was ranged from 0.612 (Mersin to 0.733 (İstanbul while expected heterozygosity was ranged from 0.774 (Mersin to 0.823 (Perşembe. The highest genetic distance was found between Antalya and Trabzon populations (FST=0.06949, the lowest between Antalya and İskenderun populations (0,00010. Analyses of 13 microsatellite loci were showed that there was low population structuring among all anchovy population (Fst: 0,024; SE 0,005. Although high genetic diversities was detected, for most loci with most populations were showed Hardy-Weinberg disequilibrium. Genetic distance analyses showed up Mediterranean specimens were highly distinct from Aegean and Black sea populations. Aegean populations were closer to Black sea populations because of higher gene flow between them rather than Mediterranean. A STRUCTURE computer program was indicated the presence of four possible genetic groups in Turkish territorial waters. Conclusions: Data to obtained from this study has found useful for the identification of genetic structuring of European anchovy distributed along the coasts of Turkish Seas. Results are also useful for planning of fishery management of anchovies in Turkey.

  19. Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

    Science.gov (United States)

    Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

    2015-09-25

    In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

  20. Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability

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    Ranbir Singh Fougat

    2014-06-01

    Full Text Available Isabgol (Plantago ovata Forsk. is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™ to obtain simple sequence repeats (SSRs for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata.

  1. Cardiac parasympathetic outflow during dynamic exercise in humans estimated from power spectral analysis of P-P interval variability.

    Science.gov (United States)

    Takahashi, Makoto; Nakamoto, Tomoko; Matsukawa, Kanji; Ishii, Kei; Watanabe, Tae; Sekikawa, Kiyokazu; Hamada, Hironobu

    2016-03-01

    What is the central question of this study? Should we use the high-frequency (HF) component of P-P interval as an index of cardiac parasympathetic nerve activity during moderate exercise? What is the main finding and its importance? The HF component of P-P interval variability remained even at a heart rate of 120-140 beats min(-1) and was further reduced by atropine, indicating incomplete cardiac vagal withdrawal during moderate exercise. The HF component of R-R interval is invalid as an estimate of cardiac parasympathetic outflow during moderate exercise; instead, the HF component of P-P interval variability should be used. The high-frequency (HF) component of R-R interval variability has been widely used as an indirect estimate of cardiac parasympathetic (vagal) outflow to the sino-atrial node of the heart. However, we have recently found that the variability of the R-R interval becomes much smaller during dynamic exercise than that of the P-P interval above a heart rate (HR) of ∼100 beats min(-1). We hypothesized that cardiac parasympathetic outflow during dynamic exercise with a higher intensity may be better estimated using the HF component of P-P interval variability. To test this hypothesis, the HF components of both P-P and R-R interval variability were analysed using a Wavelet transform during dynamic exercise. Twelve subjects performed ergometer exercise to increase HR from the baseline of 69 ± 3 beats min(-1) to three different levels of 100, 120 and 140 beats min(-1). We also examined the effect of atropine sulfate on the HF components in eight of the 12 subjects during exercise at an HR of 140 beats min(-1) . The HF component of P-P interval variability was significantly greater than that of R-R interval variability during exercise, especially at the HRs of 120 and 140 beats min(-1). The HF component of P-P interval variability was more reduced by atropine than that of R-R interval variability. We conclude that cardiac parasympathetic outflow to the

  2. Successful development of microsatellite markers in a challenging species: the horizontal borer Austroplatypus incompertus (Coleoptera: Curculionidae).

    Science.gov (United States)

    Smith, S; Joss, T; Stow, A

    2011-10-01

    The analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.

  3. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  4. FISH mapping of microsatellite loci from Drosophila subobscura and its comparison to related species.

    Science.gov (United States)

    Santos, Josiane; Serra, Lluis; Solé, Elisabet; Pascual, Marta

    2010-02-01

    Microsatellites are highly polymorphic markers that are distributed through all the genome being more abundant in non-coding regions. Whether they are neutral or under selection, these markers if localized can be used as co-dominant molecular markers to explore the dynamics of the evolutionary processes. Their cytological localization can allow identifying genes under selection, inferring recombination from a genomic point of view, or screening for the genomic reorganizations occurring during the evolution of a lineage, among others. In this paper, we report for the first time the localization of microsatellite loci by fluorescent in situ hybridization on Drosophila polytene chromosomes. In Drosophila subobscura, 72 dinucleotide microsatellite loci were localized by fluorescent in situ hybridization yielding unique hybridization signals. In the sex chromosome, microsatellite distribution was not uniform and its density was higher than in autosomes. We identified homologous segments to the sequence flanking the microsatellite loci by browsing the genome sequence of Drosophila pseudoobscura and Drosophila melanogaster. Their localization supports the conservation of Muller's chromosomal elements among Drosophila species and the existence of multiple intrachromosomal rearrangements within each evolutionary lineage. Finally, the lack of microsatellite repeats in the homologous D. melanogaster sequences suggests convergent evolution for high microsatellite density in the distal part of the X chromosome.

  5. In Silico Retrieving of Opium Poppy (Papaver Somniferum L. Microsatellites

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    Masárová Veronika

    2015-12-01

    Full Text Available Repetitive tandem sequences were retrieved within nucleotide sequences of opium poppy (Papaver somniferum L. genomic DNA available in the GenBank® database. Altogether 538 different microsatellites with the desired length characteristics of tandem repeats have been identified within 450 sequences of opium poppy DNA available in the database. The most frequented were mononucleotide repeats (246; nevertheless, 44 dinucleotide, 148 trinucleotide, 62 tetranucleotide, 28 pentanucleotide and 5 hexanucleotide tandem repeats have also been found. The most abundant were trinucleotide motifs (27.50%, and the most abundant motifs within each group of tandem repeats were TA/AT, TTC/GAA, GGTT/AACC and TTTTA/ TAAAA. Five hexanucleotide repeats contained four different motifs.

  6. Microsatellite loci for the stingless bee Melipona rufiventris (Hymenoptera: Apidae).

    Science.gov (United States)

    Lopes, Denilce Meneses; D Silva, Filipe Oliveira; Fernandes Salomão, Tânia Maria; Campos, Lúcio Antônio D Oliveira; Tavares, Mara Garcia

    2009-05-01

    Eight microsatellite primers were developed from ISSR (intersimple sequence repeats) markers for the stingless bee Melipona rufiventris. These primers were tested in 20 M. rufiventris workers, representing a single population from Minas Gerais state. The number of alleles per locus ranged from 2 to 5 (mean = 2.63) and the observed and expected heterozygosity values ranged from 0.00 to 0.44 (mean = 0.20) and from 0.05 to 0.68 (mean = 0.31), respectively. Several loci were also polymorphic in M. quadrifasciata, M. bicolor, M. mandacaia and Partamona helleri and should prove useful in population studies of other stingless bees. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

  7. Tetranucleotide microsatellite loci from the black bear (Ursus americanus)

    Science.gov (United States)

    Sanderlin, J.S.; Faircloth, B.C.; Shamblin, B.; Conroy, M.J.

    2009-01-01

    We describe primers and polymerase chain reaction conditions to amplify 21 tetranucleotide microsatellite DNA loci in black bears (Ursus americanus). We tested primers using individuals from two populations, one each in Georgia and Florida. Among individuals from Georgia (n = 29), primer pairs yielded an average of 2.9 alleles (range, one to four) and an average observed heterozygosity (HO) of 0.50 (range, 0.00 to 0.79). Among individuals from Florida (n = 19), primer pairs yielded an average of 5.7 alleles (range, one to 14) and an HO of 0.55 (range, 0.00 to 1.00). A comparison of previously developed markers with individuals from Georgia suggests that bear populations in Georgia and Florida have reduced allelic diversity relative to other populations. ?? 2008 The Authors.

  8. New Microsatellite Loci for Prosopis alba and P. chilensis (Fabaceae

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    Cecilia F. Bessega

    2013-05-01

    Full Text Available Premise of the study: As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis. Methods and Results: Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida. Conclusions: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.

  9. New microsatellite loci for Prosopis alba and P. chilensis (Fabaceae).

    Science.gov (United States)

    Bessega, Cecilia F; Pometti, Carolina L; Miller, Joe T; Watts, Richard; Saidman, Beatriz O; Vilardi, Juan C

    2013-05-01

    As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR) markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis. • Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida. • These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.

  10. Spherical gyroscopic moment stabilizer for attitude control of microsatellites

    Science.gov (United States)

    Keshtkar, Sajjad; Moreno, Jaime A.; Kojima, Hirohisa; Uchiyama, Kenji; Nohmi, Masahiro; Takaya, Keisuke

    2018-02-01

    This paper presents a new and improved concept of recently proposed two-degrees of freedom spherical stabilizer for triaxial orientation of microsatellites. The analytical analysis of the advantages of the proposed mechanism over the existing inertial attitude control devices are introduced. The extended equations of motion of the stabilizing satellite including the spherical gyroscope, for control law design and numerical simulations, are studied in detail. A new control algorithm based on continuous high-order sliding mode algorithms, for managing the torque produced by the stabilizer and therefore the attitude control of the satellite in the presence of perturbations/uncertainties, is presented. Some numerical simulations are carried out to prove the performance of the proposed mechanism and control laws.

  11. Microsatellite analysis in two populations of Kunming mice

    DEFF Research Database (Denmark)

    Shang, Haitao; Wei, Hong; Yue, Bingfei

    2009-01-01

    populations are unclear. Fifteen microsatellite markers were screened by a fluorescence-based semi-automated genotyping method for the two main populations of Kunming mice from Beijing (BJ) and Shanghai (SH) in China. The observed number of alleles, effective number of alleles, observed heterozygosity......Kunming mice are the most widely used outbred colony in China. Differences in biological characters and drug reactions among different populations have been observed when using Kunming mice. But the molecular genetic profiles of Kunming mice and the extent of genetic differentiation among...... that there is abundant genetic variation in the populations of Kunming mice. Population differentiation was shown by shared alleles, F-statistics, Nei genetic distance and Nei genetic identity. In population BJ and population SH, respectively, only 35 of 61 and 35 of 63 alleles were shared by both. The Fst per locus...

  12. Development and characterization of microsatellite markers for Berberis thunbergii (Berberidaceae).

    Science.gov (United States)

    Allen, Jenica M; Obae, Samuel G; Brand, Mark H; Silander, John A; Jones, Kenneth L; Nunziata, Schyler O; Lance, Stacey L

    2012-05-01

    Microsatellite markers were isolated and characterized in Berberis thunbergii, an invasive and ornamental shrub in the eastern United States, to assess genetic diversity among populations and potentially identify horticultural cultivars. A total of 12 loci were identified for the species. Eight of the loci were polymorphic and were screened in 24 individuals from two native (Tochigi and Ibaraki prefectures, Japan) and one invasive (Connecticut, USA) population and 21 horticultural cultivars. The number of alleles per locus ranged from three to seven, and observed heterozygosity ranged from 0.048 to 0.636. These new markers will provide tools for examining genetic relatedness of B. thunbergii plants in the native and invasive range, including phylogeographic studies and assessment of rapid evolution in the invasive range. These markers may also provide tools for examining hybridization with other related species in the invasive range.

  13. Development of microsatellite markers from loquat, Eriobotrya japonica (Thunb.) Lindl.

    Science.gov (United States)

    Gisbert, A D; Lopez-Capuz, I; Soriano, J M; Llacer, G; Romero, C; Badenes, M L

    2009-05-01

    Loquat (Eriobotrya japonica) is a minor fruit which has become an interesting alternative into the European fruit industry. This interest resulted in a loquat germplasm collection established at the Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain. Currently, it is the main reservoir of this species outside Asia. We developed and characterized the first 21 polymorphic microsatellite loci from a CT/AG-enriched loquat genomic library. The observed heterozygosity ranged between 0.20 and 1.00, expected heterozygosity ranged between 0.17 and 0.81, three markers were multilocus and eight loci departed significantly from Hardy-Weinberg equilibrium. These markers will facilitate diversity and genetic studies into the species. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

  14. Microsatellite Instability Use in Mismatch Repair Gene Sequence Variant Classification

    Directory of Open Access Journals (Sweden)

    Bryony A. Thompson

    2015-03-01

    Full Text Available Inherited mutations in the DNA mismatch repair genes (MMR can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review.

  15. Colon and rectal cancer survival by tumor location and microsatellite instability: the Colon Cancer Family Registry.

    Science.gov (United States)

    Phipps, Amanda I; Lindor, Noralane M; Jenkins, Mark A; Baron, John A; Win, Aung Ko; Gallinger, Steven; Gryfe, Robert; Newcomb, Polly A

    2013-08-01

    Cancers in the proximal colon, distal colon, and rectum are frequently studied together; however, there are biological differences in cancers across these sites, particularly in the prevalence of microsatellite instability. We assessed the differences in survival by colon or rectal cancer site, considering the contribution of microsatellite instability to such differences. This is a population-based prospective cohort study for cancer survival. This study was conducted within the Colon Cancer Family Registry, an international consortium. Participants were identified from population-based cancer registries in the United States, Canada, and Australia. Information on tumor site, microsatellite instability, and survival after diagnosis was available for 3284 men and women diagnosed with incident invasive colon or rectal cancer between 1997 and 2002, with ages at diagnosis ranging from 18 to 74. Cox regression was used to calculate hazard ratios for the association between all-cause mortality and tumor location, overall and by microsatellite instability status. Distal colon (HR, 0.59; 95% CI, 0.49-0.71) and rectal cancers (HR, 0.68; 95% CI, 0.57-0.81) were associated with lower mortality than proximal colon cancer overall. Compared specifically with patients with proximal colon cancer exhibiting no/low microsatellite instability, patients with distal colon and rectal cancers experienced lower mortality, regardless of microsatellite instability status; patients with proximal colon cancer exhibiting high microsatellite instability had the lowest mortality. Study limitations include the absence of stage at diagnosis and cause-of-death information for all but a subset of study participants. Some patient groups defined jointly by tumor site and microsatellite instability status are subject to small numbers. Proximal colon cancer survival differs from survival for distal colon and rectal cancer in a manner apparently dependent on microsatellite instability status. These

  16. Automatic maintenance payload on board of a Mexican LEO microsatellite

    Science.gov (United States)

    Vicente-Vivas, Esaú; García-Nocetti, Fabián; Mendieta-Jiménez, Francisco

    2006-02-01

    Few research institutions from Mexico work together to finalize the integration of a technological demonstration microsatellite called Satex, aiming the launching of the first ever fully designed and manufactured domestic space vehicle. The project is based on technical knowledge gained in previous space experiences, particularly in developing GASCAN automatic experiments for NASA's space shuttle, and in some support obtained from the local team which assembled the México-OSCAR-30 microsatellites. Satex includes three autonomous payloads and a power subsystem, each one with a local microcomputer to provide intelligent and dedicated control. It also contains a flight computer (FC) with a pair of full redundancies. This enables the remote maintenance of processing boards from the ground station. A fourth communications payload depends on the flight computer for control purposes. A fifth payload was decided to be developed for the satellite. It adds value to the available on-board computers and extends the opportunity for a developing country to learn and to generate domestic space technology. Its aim is to provide automatic maintenance capabilities for the most critical on-board computer in order to achieve continuous satellite operations. This paper presents the virtual computer architecture specially developed to provide maintenance capabilities to the flight computer. The architecture is periodically implemented by software with a small amount of physical processors (FC processors) and virtual redundancies (payload processors) to emulate a hybrid redundancy computer. Communications among processors are accomplished over a fault-tolerant LAN. This allows a versatile operating behavior in terms of data communication as well as in terms of distributed fault tolerance. Obtained results, payload validation and reliability results are also presented.

  17. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2013-01-01

    Full Text Available Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8% of the 94 Simple Sequence Repeat (SSR loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp., and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus. Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

  18. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    Science.gov (United States)

    Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

    2013-01-01

    Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

  19. Population genetics of Leishmania infantum in Israel and the Palestinian Authority through microsatellite analysis.

    Science.gov (United States)

    Amro, Ahmad; Schönian, Gabriele; Al-Sharabati, Mohamed Barakat; Azmi, Kifaya; Nasereddin, Abedelmajeed; Abdeen, Ziad; Schnur, Lionel F; Baneth, Gad; Jaffe, Charles L; Kuhls, Katrin

    2009-04-01

    Multilocus microsatellite typing (MLMT) was used to investigate the genetic variation among 44 Israeli and Palestinian strains of L. infantum isolated from infected dogs and human cases to determine their population structure and to compare them with strains isolated from different European countries. Most of the Israeli and Palestinian strains had their own individual MLMT profiles; a few shared the same profile. A Bayesian model-based approach and phylogenetic reconstructions based on genetic distances inferred two main populations that were significantly different from the European strains: population A, containing 16 strains from places in the West Bank and 11 strains from central Israel;and population B, containing 7 strains from northern Israel, 9 from central Israel, and one Palestinian strain from the Jenin District.Geographically distributed sub-populations were detected within population B. These results demonstrate similar disease dynamics in Israel and the Palestinian Authority. The re-emergence of VL in the case of population A is more likely owing to increased dog and human contact with sylvatic cycles of parasitic infection rather than to recent introduction from the older foci of northern Israel. The latter scenario could be true for population B found in few foci of Central Israel. (c) 2009 Elsevier Masson SAS. All rights reserved.

  20. Microsatellite Analysis of the Population Genetic Structure of Anolis carolinensis Introduced to the Ogasawara Islands.

    Science.gov (United States)

    Sugawara, Hirotaka; Takahashi, Hiroo; Hayashi, Fumio

    2015-01-01

    DNA analysis can reveal the origins and dispersal patterns of invasive species. The green anole Anolis carolinensis is one such alien animal, which has been dispersed widely by humans from its native North America to many Pacific Ocean islands. In the Ogasawara (Bonin) Islands, this anole was recorded from Chichi-jima at the end of the 1960s, and then from Haha-jima in the early 1980s. These two islands are inhabited. In 2013, it was also found on the uninhabited Ani-jima, close to Chichi-jima. Humans are thought to have introduced the anole to Haha-jima, while the mode of introduction to Ani-jima is unknown. To clarify its dispersal patterns within and among these three islands, we assessed the fine-scale population genetic structure using five microsatellite loci. The results show a homogeneous genetic structure within islands, but different genetic structures among islands, suggesting that limited gene flow occurs between islands. The recently established Ani-jima population may have originated from several individuals simultaneously, or by repeated immigration from Chichi-jima. We must consider frequent incursions among these islands to control these invasive lizard populations and prevent their negative impact on native biodiversity.