Locus-specific mutational events in a multilocus variable-number tandem repeat analysis of Escherichia coli O157:H7.

PubMed

Noller, Anna C; McEllistrem, M Catherine; Shutt, Kathleen A; Harrison, Lee H

2006-02-01

Multilocus variable-number tandem repeat analysis (MLVA) is a validated molecular subtyping method for detecting and evaluating Escherichia coli O157:H7 outbreaks. In a previous study, five outbreaks with a total of 21 isolates were examined by MLVA. Nearly 20% of the epidemiologically linked strains were single-locus variants (SLV) of their respective predominant outbreak clone. This result prompted an investigation into the mutation rates of the seven MLVA loci (TR1 to TR7). With an outbreak strain that was an SLV at the TR1 locus of the predominant clone, parallel and serial batch culture experiments were performed. In a parallel experiment, none (0/384) of the strains analyzed had mutations at the seven MLVA loci. In contrast, in the two 5-day serial experiments, 4.3% (41/960) of the strains analyzed had a significant variation in at least one of these loci (P < 0.001). The TR2 locus accounted for 85.3% (35/41) of the mutations, with an average mutation rate of 3.5 x 10(-3); the mutations rates for TR1 and TR5 were 10-fold lower. Single additions accounted for 77.1% (27/35) of the mutation events in TR2 and all (6/6) of the additions in TR1 and TR5. The remaining four loci had no slippage events detected. The mutation rates were locus specific and may impact the interpretation of MLVA data for epidemiologic investigations.

Clostridium botulinum Group I Strain Genotyping by 15-Locus Multilocus Variable-Number Tandem-Repeat Analysis ▿ †

PubMed Central

Fillo, Silvia; Giordani, Francesco; Anniballi, Fabrizio; Gorgé, Olivier; Ramisse, Vincent; Vergnaud, Gilles; Riehm, Julia M.; Scholz, Holger C.; Splettstoesser, Wolf D.; Kieboom, Jasper; Olsen, Jaran-Strand; Fenicia, Lucia; Lista, Florigio

2011-01-01

Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse. PMID:22012011

Clostridium botulinum group I strain genotyping by 15-locus multilocus variable-number tandem-repeat analysis.

PubMed

Fillo, Silvia; Giordani, Francesco; Anniballi, Fabrizio; Gorgé, Olivier; Ramisse, Vincent; Vergnaud, Gilles; Riehm, Julia M; Scholz, Holger C; Splettstoesser, Wolf D; Kieboom, Jasper; Olsen, Jaran-Strand; Fenicia, Lucia; Lista, Florigio

2011-12-01

Clostridium botulinum is a taxonomic designation that encompasses a broad variety of spore-forming, Gram-positive bacteria producing the botulinum neurotoxin (BoNT). C. botulinum is the etiologic agent of botulism, a rare but severe neuroparalytic disease. Fine-resolution genetic characterization of C. botulinum isolates of any BoNT type is relevant for both epidemiological studies and forensic microbiology. A 10-locus multiple-locus variable-number tandem-repeat analysis (MLVA) was previously applied to isolates of C. botulinum type A. The present study includes five additional loci designed to better address proteolytic B and F serotypes. We investigated 79 C. botulinum group I strains isolated from human and food samples in several European countries, including types A (28), B (36), AB (4), and F (11) strains, and 5 nontoxic Clostridium sporogenes. Additional data were deduced from in silico analysis of 10 available fully sequenced genomes. This 15-locus MLVA (MLVA-15) scheme identified 86 distinct genotypes that clustered consistently with the results of amplified fragment length polymorphism (AFLP) and MLVA genotyping in previous reports. An MLVA-7 scheme, a subset of the MLVA-15, performed on a lab-on-a-chip device using a nonfluorescent subset of primers, is also proposed as a first-line assay. The phylogenetic grouping obtained with the MLVA-7 does not differ significantly from that generated by the MLVA-15. To our knowledge, this report is the first to analyze genetic variability among all of the C. botulinum group I serotypes by MLVA. Our data provide new insights into the genetic variability of group I C. botulinum isolates worldwide and demonstrate that this group is genetically highly diverse.

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

PubMed Central

Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

2011-01-01

Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

Characterization of Escherichia coli O157:H7 in New Zealand using multiple-locus variable-number tandem-repeat analysis.

PubMed

Dyet, K H; Robertson, I; Turbitt, E; Carter, P E

2011-03-01

Recently, multiple-locus variable-number tandem-repeat analysis (MLVA) has been proposed as an alternative to pulsed-field gel electrophoresis (PFGE) for characterization of Escherichia coli O157:H7. In this study we characterized 118 E. coli O157:H7 isolates from cases of gastrointestinal disease in New Zealand using XbaI PFGE profiles and a MLVA scheme that assessed variability in eight polymorphic loci. The 118 isolates characterized included all 80 E. coli O157:H7 referred to New Zealand's Enteric Reference Laboratory in 2006 and 29 phage-type 2 isolates from 2005. When applied to these isolates the discriminatory power of PFGE and MLVA was not significantly different. However, MLVA data may be more epidemiologically relevant as isolates from family clusters of disease had identical MLVA profiles, even when the XbaI PFGE profiles differed slightly. Furthermore, most isolates with indistinguishable XbaI PFGE profiles that did not appear to be epidemiologically related had distinct MLVA profiles.

spa typing for epidemiological surveillance of Staphylococcus aureus.

PubMed

Hallin, Marie; Friedrich, Alexander W; Struelens, Marc J

2009-01-01

The spa typing method is based on sequencing of the polymorphic X region of the protein A gene (spa), present in all strains of Staphylococcus aureus. The X region is constituted of a variable number of 24-bp repeats flanked by well-conserved regions. This single-locus sequence-based typing method combines a number of technical advantages, such as rapidity, reproducibility, and portability. Moreover, due to its repeat structure, the spa locus simultaneously indexes micro- and macrovariations, enabling the use of spa typing in both local and global epidemiological studies. These studies are facilitated by the establishment of standardized spa type nomenclature and Internet shared databases.

Allele frequency distribution for the variable number of tandem repeat locus D10S28 in Tamil Nadu (south India) population.

PubMed

Pandian, S K; Kumar, S; Krishnan, M; Dharmalingam, K; Damodaran, C

1995-09-01

Allele frequencies were determined in unrelated individuals of Tamil speaking population from the Madras City (Tamil Nadu, South India) area for the polymorphic DNA locus D10S28 using the probe TBQ7. Membranes hybridized with the probe YNH24 were subjected to deprobing and were subsequently hybridized with random priming - labeled, purified inserts of TBQ7. The sizes of the fragments were grouped to 100 bp as well as to arbitrary fixed bins (Federal Bureau of Investigation / Royal Canadian Mounted Police). There were 14 bins in the latter with the most common bin being 11 (1789-1924 bp) with a frequency of 9.8%. We observed a heterozygosity of 92% comparable to Caucasian populations. The data presented here can be used as the basis for utilizing this variable number of tandem repeats (TNTR) DNA marker for paternity determinations and forensic investigations.

Resolving the Conflict Between Associative Overdominance and Background Selection

PubMed Central

Zhao, Lei; Charlesworth, Brian

2016-01-01

In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance) and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical, and simulation studies that shed light on the conditions under which retardation vs. acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection. With mutation and selection, retardation occurs only when S, the product of twice the effective population size and the selection coefficient, is of order 1. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, loss of variability is nearly always retarded. The results shed light on experiments on the loss of variability at marker loci in laboratory populations and on the results of computer simulations of the effects of multiple selected loci on neutral variability. PMID:27182952

Work stress and emotional exhaustion in nurses: the mediating role of internal locus of control.

PubMed

Partlak Günüşen, Neslihan; Ustün, Besti; Erdem, Sabri

2014-01-01

Burnout is a major problem for nursing. There is a strong relationship between work stress and emotional exhaustion. Although studies report a negative correlation between the internal locus of control and emotional exhaustion and work stress, the number of studies available on the subject is limited. This study intends to examine the extent to which the relationship between work stress and emotional exhaustion is mediated by nurses' internal locus of control. The study adopted a cross-sectional survey design. The data were analyzed using structural equation modeling techniques. The study sample consisted of 347 nurses who worked in a university hospital in Izmir, Turkey and who agreed to participate in the study. The Work-Related Strain Inventory was used to evaluate the nurses' work stress level, Maslach Burnout Inventory was used to evaluate their emotional exhaustion levels, and the Locus of Control Scale was used to evaluate the internal locus of control. The variables of the study were based on the Neuman Systems Model. Work stress was positively related to internal locus of control (β3 = .21, p < .001), which was, in turn, negatively associated with emotional exhaustion (β = -.03, p > 0.1). Internal locus of control was negatively related to emotional exhaustion (β = -.14, p < .001). Work stress is directly (β = .87, p < .001) and indirectly related to emotional exhaustion (mediated by internal locus of control β = .84, p < .001). Work stress is directly (β = .87, p < .001) and indirectly related to emotional exhaustion (mediated by internal locus of control, β = .84, p < .001). Although the relationship between emotional exhaustion and work stress was mediated, the impact of internal locus of control was limited. It is recommended that different variables be included in future studies so that they can mediate the relationship between work stress and emotional exhaustion.

Molecular typing of Argentinian Mycobacterium avium subsp. paratuberculosis isolates by multiple-locus variable number-tandem repeat analysis

PubMed Central

Gioffré, Andrea; Correa Muñoz, Magnolia; Alvarado Pinedo, María F.; Vaca, Roberto; Morsella, Claudia; Fiorentino, María Andrea; Paolicchi, Fernando; Ruybal, Paula; Zumárraga, Martín; Travería, Gabriel E.; Romano, María Isabel

2015-01-01

Multiple-locus variable number-tandem repeat analysis (MLVA) of Mycobacterium avium subspecies paratuberculosis (MAP) isolates may contribute to the knowledge of strain diversity in Argentina. Although the diversity of MAP has been previously investigated in Argentina using IS900-RFLP, a small number of isolates were employed, and a low discriminative power was reached. The aim of the present study was to test the genetic diversity among MAP isolates using an MLVA approach based on 8 repetitive loci. We studied 97 isolates from cattle, goat and sheep and could describe 7 different patterns: INMV1, INMV2, INMV11, INMV13, INMV16, INMV33 and one incomplete pattern. INMV1 and INMV2 were the most frequent patterns, grouping 76.3% of the isolates. We were also able to demonstrate the coexistence of genotypes in herds and co-infection at the organism level. This study shows that all the patterns described are common to those described in Europe, suggesting an epidemiological link between the continents. PMID:26273274

MULTIPLE-LOCUS VARIABLE-NUMBER TANDEM REPEAT ANALYSIS OF BRUCELLA ISOLATES FROM THAILAND.

PubMed

Kumkrong, Khurawan; Chankate, Phanita; Tonyoung, Wittawat; Intarapuk, Apiradee; Kerdsin, Anusak; Kalambaheti, Thareerat

2017-01-01

Brucellosis-induced abortion can result in significant economic loss to farm animals. Brucellosis can be transmitted to humans during slaughter of infected animals or via consumption of contaminated food products. Strain identification of Brucella isolates can reveal the route of transmission. Brucella strains were isolated from vaginal swabs of farm animal, cow milk and from human blood cultures. Multiplex PCR was used to identify Brucella species, and owing to high DNA homology among Brucella isolates, multiple-locus variable-number tandem repeat analysis (MLVA) based on the number of tandem repeats at 16 different genomic loci was used for strain identification. Multiplex PCR categorized the isolates into B. abortus (n = 7), B. melitensis (n = 37), B. suis (n = 3), and 5 of unknown Brucella spp. MLVA-16 clustering analysis differentiated the strains into various genotypes, with Brucella isolates from the same geographic region being closely related, and revealed that the Thai isolates were phylogenetically distinct from those in other countries, including within the Southeast Asian region. Thus, MLVA-16 typing has utility in epidemiological studies.

Resurgence of Pertussis and Emergence of the Ptxp3 Toxin Promoter Allele in South Italy.

PubMed

Loconsole, Daniela; De Robertis, Anna Lisa; Morea, Anna; Metallo, Angela; Lopalco, Pier Luigi; Chironna, Maria

2018-05-01

Despite universal immunization programs, pertussis remains a major public health concern. This study aimed to describe the pertussis epidemiology in the Puglia region in 2006-2015 and to identify recent polymorphisms in Bordetella pertussis virulence-associated genes. The pertussis cases in 2006-2015 were identified from the National Hospital Discharge Database and the Information System of Infectious Diseases. Samples of pertussis cases in 2014-2016 that were confirmed by the Regional Reference Laboratory were subjected to ptxA, ptxP and prn gene sequencing and, in 10 cases, multiple-locus variable-number tandem repeat analysis. In Puglia in 2006-2015, the pertussis incidence rose from an average of 1.39/100,000 inhabitants in 2006-2013 to 2.56-2.54/100,000 in 2014-2015. In infants <1 year of age, the incidence rose from an average of 60.4/100,000 infants in 2006-2013 to 149.9/100,000 in 2015. Of the 661 cases recorded in 2006-2015, 80.3% required hospitalization; of these, 45.4% were <1 year of age. Of the 80 sequenced samples, the allelic profile ptxA1-ptxP3-prn2 was detected in 74. This variant was detected in both vaccinated and unvaccinated people. Six Bordetella pertussis samples were prn deficient. The multiple-locus variable-number tandem repeat analysis cases exhibited multiple-locus variable-number tandem repeat analysis-type 27. The pertussis incidence in Puglia has risen. The hypervirulent strain was also found in vaccinated people. This suggests bacterial adaptation to the vaccine and raises questions about acellular vaccine effectiveness. Prevention of infant pertussis cases is best achieved by immunizing the pregnant mother. Enhanced surveillance and systematic laboratory confirmation of pertussis should be improved in Italy.

Multiple-locus variable number of tandem repeat analysis (MLVA) of Irish verocytotoxigenic Escherichia coli O157 from feedlot cattle: uncovering strain dissemination routes.

PubMed

Murphy, Mary; Minihan, Donal; Buckley, James F; O'Mahony, Micheál; Whyte, Paul; Fanning, Séamus

2008-01-24

The identification of the routes of dissemination of Escherichia coli (E. coli) O157 through a cohort of cattle is a critical step to control this pathogen at farm level. The aim of this study was to identify potential routes of dissemination of E. coli O157 using Multiple-Locus Variable number of tandem repeat Analysis (MLVA). Thirty-eight environmental and sixteen cattle faecal isolates, which were detected in four adjacent pens over a four-month period were sub-typed. MLVA could separate these isolates into broadly defined clusters consisting of twelve MLVA types. Strain diversity was observed within pens, individual cattle and the environment. Application of MLVA is a broadly useful and convenient tool when applied to uncover the dissemination of E. coli O157 in the environment and in supporting improved on-farm management of this important pathogen. These data identified diverse strain types based on amplification of VNTR markers in each case.

A multiple-locus variable-number tandem repeat analysis (MLVA) of Listeria monocytogenes isolated from Norwegian salmon-processing factories and from listeriosis patients.

PubMed

Lunestad, B T; Truong, T T T; Lindstedt, B-A

2013-10-01

The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

PubMed Central

Lee, Tong Geon; Kumar, Indrajit; Diers, Brian W; Hudson, Matthew E

2015-01-01

The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1. PMID:25735447

Multivariate analysis of molecular and morphological diversity in fig (Ficus carica L.)

USDA-ARS?s Scientific Manuscript database

Genetic polymorphism across 15 microsatellite loci among 194 fig accessions including Common, Smyrna, San Pedro, and Caprifig were analyzed using a cluster analysis (CA) and the principal components analysis (PCA). The collection was moderately variable with observed number of alleles per locus rang...

Correlates of Eating Disorders in College Students.

ERIC Educational Resources Information Center

McCanne, Lynn P. Fisher

Recent research indicates that a significant number of college-age women suffer from bulimarexia (also called the gorging-purging syndrome, the binge-purge cycle, bulimia or bulimia nervosa). To examine the relationship of three personality variables (anxiety, assertiveness, and locus of control) to eating disorders, 46 college students…

Determination of Sources of Escherichia coli on Beef by Multiple-Locus Variable-Number Tandem Repeat Analysis.

PubMed

Yang, Xianqin; Tran, Frances; Youssef, Mohamed K; Gill, Colin O

2015-07-01

The possible origin of Escherichia coli found on cuts and trimmings in the breaking facility of a beef packing plant was examined using multiple-locus variable-number tandem repeat analysis. Coliforms and E. coli were enumerated in samples obtained from 160 carcasses that would enter the breaking facility when work commenced and after each of the three production breaks throughout the day, from the conveyor belt before work and after each break, and from cuts and trimmings when work commenced and after each break. Most samples yielded no E. coli, irrespective of the surface types. E. coli was recovered from 7 (<5%) carcasses, at numbers mostly ≤1.0 log CFU/160,000 cm(2). The log total numbers of E. coli recovered from the conveyor belt, cuts, and trimmings were mostly between 1 and 2 log CFU/80,000 cm(2). A total of 554 E. coli isolates were recovered. Multiple-locus variable-number tandem repeat analysis of 327 selected isolates identified 80 distinct genotypes, with 37 (46%) each containing one isolate. However, 28% of the isolates were of genotypes that were recovered from more than one sampling day. Of the 80 genotypes, 65 and 2% were found in one or all four sampling periods throughout the day. However, they represented 23 and 14% of the isolates, respectively. Of the genotypes identified for each surface type, at least one contained ≥9 isolates. No unique genotypes were associated with carcasses, but 10, 17, and 19 were uniquely associated with cuts, trimmings, and the belt, respectively. Of the isolates recovered from cuts, 49, 3, and 19% were of genotypes that were found among isolates recovered from the belt, carcasses, or both the belt and carcasses, respectively. A similar composition was found for isolates recovered from trimmings. These findings show that the E. coli found on cuts and trimmings at this beef packing plant mainly originated from the conveyor belt and that small number of E. coli strains survived the daily cleaning and sanitation process, thus persisting in the plant.

A Trio of Human Molecular Genetics PCR Assays

ERIC Educational Resources Information Center

Reinking, Jeffrey L.; Waldo, Jennifer T.; Dinsmore, Jannett

2013-01-01

This laboratory exercise demonstrates three different analytical forms of the polymerase chain reaction (PCR) that allow students to genotype themselves at four different loci. Here, we present protocols to allow students to a) genotype a non-coding polymorphic Variable Number of Tandem Repeat (VNTR) locus on human chromosome 5 using conventional…

Investigation of Salmonella Enteritidis outbreaks in South Africa using multi-locus variable-number tandem-repeats analysis, 2013-2015.

PubMed

Muvhali, Munyadziwa; Smith, Anthony Marius; Rakgantso, Andronica Moipone; Keddy, Karen Helena

2017-10-02

Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) has become a significant pathogen in South Africa, and the need for improved molecular surveillance of this pathogen has become important. Over the years, multi-locus variable-number tandem-repeats analysis (MLVA) has become a valuable molecular subtyping technique for Salmonella, particularly for highly homogenic serotypes such as Salmonella Enteritidis. This study describes the use of MLVA in the molecular epidemiological investigation of outbreak isolates in South Africa. Between the years 2013 and 2015, the Centre for Enteric Diseases (CED) received 39 Salmonella Enteritidis isolates from seven foodborne illness outbreaks, which occurred in six provinces. MLVA was performed on all isolates. Three MLVA profiles (MLVA profiles 21, 22 and 28) were identified among the 39 isolates. MLVA profile 28 accounted for 77% (30/39) of the isolates. Isolates from a single outbreak were grouped into a single MLVA profile. A minimum spanning tree (MST) created from the MLVA data showed a close relationship between MLVA profiles 21, 22 and 28, with a single VNTR locus difference between them. MLVA has proven to be a reliable method for the molecular epidemiological investigation of Salmonella Enteritidis outbreaks in South Africa. These foodborne outbreaks emphasize the importance of the One Health approach as an essential component for combating the spread of zoonotic pathogens such as Salmonella Enteritidis.

Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers.

PubMed

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.

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

PubMed Central

Laukkanen-Ninios, R.; Ortiz Martínez, P.; Siitonen, A.; Fredriksson-Ahomaa, M.; Korkeala, H.

2013-01-01

Sporadic and epidemiologically linked Yersinia enterocolitica strains (n = 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared. PMID:23637293

Poverty, Psychological Resources and Subjective Well-Being

ERIC Educational Resources Information Center

Lever, Joaquina Palomar; Pinol, Nuria Lanzagorta; Uralde, Jorge Hernandez

2005-01-01

This study was carried out for the purpose of explaining the mediating effects of a number of psychological variables (strategies for coping with stress, competitiveness, mastery, locus of control, depression and self-esteem) in the relationship between poverty and the well-being of individuals. To carry out the study, a non-probabilistic,…

Molecular characterization of Shiga-toxigenic Escherichia coli isolated from diverse sources from India by multi-locus variable number tandem repeat analysis (MLVA).

PubMed

Kumar, A; Taneja, N; Sharma, R K; Sharma, H; Ramamurthy, T; Sharma, M

2014-12-01

In a first study from India, a diverse collection of 140 environmental and clinical non-O157 Shiga-toxigenic Escherichia coli strains from a large geographical area in north India was typed by multi-locus variable number tandem repeat analysis (MLVA). The distribution of major virulence genes stx1, stx2 and eae was found to be 78%, 70% and 10%, respectively; 15 isolates were enterohaemorrhagic E. coli (stx1 +/stx2 + and eae +). By MLVA analysis, 44 different alleles were obtained. Dendrogram analysis revealed 104 different genotypes and 19 MLVA-type complexes divided into two main lineages, i.e. mutton and animal stool. Human isolates presented a statistically significant greater odds ratio for clustering with mutton samples compared to animal stool isolates. Five human isolates clustered with animal stool strains suggesting that some of the human infections may be from cattle, perhaps through milk, contact or the environment. Further epidemiological studies are required to explore these sources in context with occurrence of human cases.

Perceptions of Blended Learning Competencies and Obstacles among Educational Technology Students in Light of Different Anxiety Levels and Locus of Control

ERIC Educational Resources Information Center

Aldalalah, Osamah Ahmad; Gasaymeh, Al-Mothana M.

2014-01-01

The purpose of this study was to investigate the effects of locus of control and anxiety level on the Jordanian educational technology students' perceived blended learning competencies and obstacles. The independent variables were the locus of control (Internal, External) and anxiety level (Low, Moderate, High). The dependent variables were the…

Investigation of Teachers' Self-Efficacy Beliefs, Locus of Control and Intercultural Sensitivities from the Perspective of Individual Differences

ERIC Educational Resources Information Center

Akca, Figen; Ulutas, Emrah; Yabanci, Cemile

2018-01-01

The purpose of this study is to examine the correlation between Teachers' Self-efficacy beliefs, locus of control and intercultural sensitivities and to analyze these variables based on various demographic variables. The data of the study were collected through teachers' locus of control scale developed by Sadowski, Taylor, Woodward, Peacher,…

Discrete interference modeling via boolean algebra.

PubMed

Beckhoff, Gerhard

2011-01-01

Two types of boolean functions are considered, the locus function of n variables, and the interval function of ν = n - 1 variables. A 1-1 mapping is given that takes elements (cells) of the interval function to antidual pairs of elements in the locus function, and vice versa. A set of ν binary codewords representing the intervals are defined and used to generate the codewords of all genomic regions. Next a diallelic three-point system is reviewed in the light of boolean functions, which leads to redefining complete interference by a logic function. Together with the upper bound of noninterference already defined by a boolean function, it confines the region of interference. Extensions of these two functions to any finite number of ν are straightforward, but have been also made in terms of variables taken from the inclusion-exclusion principle (expressing "at least" and "exactly equal to" a decimal integer). Two coefficients of coincidence for systems with more than three loci are defined and discussed, one using the average of several individual coefficients and the other taking as coefficient a real number between zero and one. Finally, by way of a malfunction of the mod-2 addition, it is shown that a four-point system may produce two different functions, one of which exhibiting loss of a class of odd recombinants.

Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark.

PubMed

de Knegt, Leonardo V; Pires, Sara M; Löfström, Charlotta; Sørensen, Gitte; Pedersen, Karl; Torpdahl, Mia; Nielsen, Eva M; Hald, Tine

2016-03-01

Salmonella is an important cause of bacterial foodborne infections in Denmark. To identify the main animal-food sources of human salmonellosis, risk managers have relied on a routine application of a microbial subtyping-based source attribution model since 1995. In 2013, multiple locus variable number tandem repeat analysis (MLVA) substituted phage typing as the subtyping method for surveillance of S. Enteritidis and S. Typhimurium isolated from animals, food, and humans in Denmark. The purpose of this study was to develop a modeling approach applying a combination of serovars, MLVA types, and antibiotic resistance profiles for the Salmonella source attribution, and assess the utility of the results for the food safety decisionmakers. Full and simplified MLVA schemes from surveillance data were tested, and model fit and consistency of results were assessed using statistical measures. We conclude that loci schemes STTR5/STTR10/STTR3 for S. Typhimurium and SE9/SE5/SE2/SE1/SE3 for S. Enteritidis can be used in microbial subtyping-based source attribution models. Based on the results, we discuss that an adjustment of the discriminatory level of the subtyping method applied often will be required to fit the purpose of the study and the available data. The issues discussed are also considered highly relevant when applying, e.g., extended multi-locus sequence typing or next-generation sequencing techniques. © 2015 Society for Risk Analysis.

Psychosocial and behavioural factors in the regulation of weight: Self-regulation, self-efficacy and locus control.

PubMed

Menéndez-González, Lara; Orts-Cortés, María Isabel

To identify the relationship and behaviour of the variables of self-control, self-efficacy and locus control in weight regulation of obese, overweight and normal weight adults. Transversal study undertaken in the Health Centre of El Coto (Gijón) from 1st April to 30th July 2015. Subjects between 18-65 years of age with a body mass index recording within the last two years. serious medical illness, eating disorders or pregnant women. Behavioural variables: self-regulation of body weight (Inventory of self-control of body weight), perceived self-efficacy in weight regulation (Inventory of perceived self-efficacy in weight regulation) and locus control in weight regulation (Inventory of locus control in weight regulation). Anthropometric variables: weight (kg) and height (m), body mass index. One hundred and six participants were included: 32 were obese, 28 overweight and 46 normal weight. Significant differences were found between the 3 study groups for total scale of self-efficacy (F=61.77; p<.01), total scale of self-regulation (F=45.97; p<.01), internal locus control (F=13.92; p=.019), other weighty influences of locus control (F=9.21; p<.01) and random locus control (F=3.50; p=.011). The relationship between body mass index and behavioural variables of self-efficacy, self-regulation and locus control, suggests the need for healthcare professionals to include psychological factors of behaviour in any preventive action and intervention directed at weight control. Copyright © 2018 Elsevier España, S.L.U. All rights reserved.

Development of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) for Leptospira interrogans and its application to Leptospira interrogans serovar Australis isolates from Far North Queensland, Australia

PubMed Central

Slack, Andrew T; Dohnt, Michael F; Symonds, Meegan L; Smythe, Lee D

2005-01-01

Background Leptospirosis is a zoonotic disease caused by the genus, Leptospira. Leptospira interrogans is the most common genomospecies implicated in the disease. Epidemiological investigations are needed to distinguish outbreak situations or to trace reservoirs of the organisms. Current methodologies used for typing Leptospira have significant drawbacks. The development of an easy to perform yet high resolution method is needed for this organism. Methods In this study we have searched the available genomic sequence of L. interrogans serovar Copenhageni strain Fiocruz L1-130 for the presence of tandem repeats [1]. These repeats were evaluated against reference strains for diversity. Six loci were selected to create a Multiple Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) to explore the genetic diversity within L. interrogans serovar Australis clinical isolates from Far North Queensland. Results The 39 reference strains used for the development of the method displayed 39 distinct patterns. Diversity Indexes for the loci varied between 0.80 and 0.93 and the number of repeat units at each locus varied between less than one to 52 repeats. When the MLVA was applied to serovar Australis isolates three large clusters were distinguishable, each comprising various hosts including Rattus species, human and canines. Conclusion The MLVA described in this report, was easy to perform, analyse and was reproducible. The loci selected had high diversity allowing discrimination between serovars and also between strains within a serovar. This method provides a starting point on which improvements to the method and comparisons to other techniques can be made. PMID:15987533

Genetic characterization of non-O157 verocytotoxigenic Escherichia coli isolated from raw beef products using multiple-locus variable-number tandem repeat analysis.

PubMed

Franci, Tomás; Sanso, A Mariel; Bustamante, Ana V; Lucchesi, Paula M A; Parma, Alberto E

2011-09-01

Verocytotoxigenic Escherichia coli (VTEC) can produce serious human illness linked to the consumption of contaminated food, mainly of bovine origin. There is growing concern about non-O157 VTEC serotypes, which in some countries cause severe infections in a proportion similar to O157:H7 strains. As several epidemiological studies indicated the important role of meat as the major vehicle in the transmission of this pathogen to human consumers, our aim was to investigate the genetic diversity among non-O157:H7 VTEC isolated from raw beef products. We performed a multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA), and to our knowledge, this is the first time that VTEC serotypes O8:H19, O112:H2, O113:NM, O171:NM, ONT:H7, ONT:H19, and ONT:H21 were typed by this method. MLVA typing grouped the total number of strains from this study (51) into 21 distinct genotypes, and 11 of them were unique. Several MLVA profiles were found in different serotypes, O178:H19 being the most variable. The isolates could be principally discriminated by alleles of three of seven loci studied (CVN001, CVN004, and CVN014), and on the other hand, CVN003 rendered null alleles in all the isolates. As some VNTR markers might be serotype specific, it is possible that the implementation of new VNTR loci will increase intraserotype discrimination.

Antibiotic Susceptibility and Molecular Diversity of Bacillus anthracis Strains in Chad: Detection of a New Phylogenetic Subgroup

PubMed Central

Maho, Angaya; Rossano, Alexandra; Hächler, Herbert; Holzer, Anita; Schelling, Esther; Zinsstag, Jakob; Hassane, Mahamat H.; Toguebaye, Bhen S.; Akakpo, Ayayi J.; Van Ert, Matthew; Keim, Paul; Kenefic, Leo; Frey, Joachim; Perreten, Vincent

2006-01-01

We genotyped 15 Bacillus anthracis isolates from Chad, Africa, using multiple-locus variable-number tandem repeat analysis and three additional direct-repeat markers. We identified two unique genotypes that represent a novel genetic lineage in the A cluster. Chadian isolates were susceptible to 11 antibiotics and free of 94 antibiotic resistance genes. PMID:16954291

Population structure of Heterobasidion annosum from North America and Europe

Treesearch

W.J. Otrosina; T.E. Chase; F.W. Cobb; K. Korhonen

1993-01-01

Isolates of Heterobasidion annosum (Fr.) Bref. representing North American S and P and European S, P, and F intersterility groups were subjected to isozyme analysis.European S, P, and F groups had more variability than the North American S and P groups in expected heterozygosity, number of alleles per locus, and percent polymorphic loci.In contrast with the North...

Allozyme variation of Port-Orford-Cedar (Chamaecyparis lawsoniana): implications for genetic conservation

Treesearch

Constance I. Millar; Kimberly A. Marshall

1991-01-01

Variation at 32 allozyme loci in nine disjunct populations of Part-Orford-cedar (POC) from the California floristic region was measured to estimate the amount and pattern of genetic variability in natural stands. Variation in electrophoretically detectable loci was moderately high, with mean number of alleles per locus = 1.9, 64.9% polymorphic loci, and observed...

Multiple-locus variable-number tandem-repeats analysis of Listeria monocytogenes using multicolour capillary electrophoresis and comparison with pulsed-field gel electrophoresis typing.

PubMed

Lindstedt, Bjørn-Arne; Tham, Wilhelm; Danielsson-Tham, Marie-Louise; Vardund, Traute; Helmersson, Seved; Kapperud, Georg

2008-02-01

The multiple-locus variable-number tandem-repeats analysis (MLVA) method for genotyping has proven to be a fast and reliable typing tool in several bacterial species. MLVA is in our laboratory the routine typing method for Salmonella enterica subsp. enterica serovar Typhimurium and Escherichia coli O157. The gram-positive bacteria Listeria monocytogenes, while not isolated as frequent as S. Typhimurium and E. coli, causes severe illness with an overall mortality rate of 30%. Thus, it is important that any outbreak of this pathogen is detected early and a fast trace to the source can be performed. In view of this, we have used the information provided by two fully sequenced L. monocytogenes strains to develop a MLVA assay coupled with high-resolution capillary electrophoresis and compared it to pulsed-field gel electrophoresis (PFGE) in two sets of isolates, one Norwegian (79 isolates) and one Swedish (61 isolates) set. The MLVA assay could resolve all of the L. monocytogenes serotypes tested, and was slightly more discriminatory than PFGE for the Norwegian isolates (28 MLVA profiles and 24 PFGE profiles) and opposite for the Swedish isolates (42 MLVA profiles and 43 PFGE profiles).

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2005-07-01

AD Award Number: DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia M. MacCollin, M.D...NUMBER Molecular Identification of the Schwannomatosis Locus 5b. GRANT NUMBER DAMD17-03-1-0445 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...can be found on next page. 15. SUBJECT TERMS schwannomatosis , tumor suppressor gene, NF2, molecular genetics 16. SECURITY CLASSIFICATION OF: 17

Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157).

PubMed

Hyytiä-Trees, Eija; Smole, Sandra C; Fields, Patricia A; Swaminathan, Bala; Ribot, Efrain M

2006-01-01

Most bacterial genomes contain tandem duplications of short DNA sequences, termed "variable-number tandem repeats" (VNTR). A subtyping method targeting these repeats, multiple-locus VNTR analysis (MLVA), has emerged as a powerful tool for characterization of clonal organisms such as Shiga toxin-producing Escherichia coli O157 (STEC O157). We modified and optimized a recently published MLVA scheme targeting 29 polymorphic VNTR regions of STEC O157 to render it suitable for routine use by public health laboratories that participate in PulseNet, the national and international molecular subtyping network for foodborne disease surveillance. Nine VNTR loci were included in the final protocol. They were amplified in three PCR reactions, after which the PCR products were sized using capillary electrophoresis. Two hundred geographically diverse, sporadic and outbreak- related STEC O157 isolates were characterized by MLVA and the results were compared with data obtained by pulsed-field gel electrophoresis (PFGE) using XbaI macrorestriction of genomic DNA. A total of 139 unique XbaI PFGE patterns and 162 MLVA types were identified. A subset of 100 isolates characterized by both XbaI and BlnI macrorestriction had 62 unique PFGE and MLVA types. Although the clustering of isolates by the two subtyping systems was generally in agreement, some discrepancies were observed. Importantly, MLVA was able to discriminate among some epidemiologically unrelated isolates which were indistinguishable by PFGE. However, among strains from three of the eight outbreaks included in the study, two single locus MLVA variants and one double locus variant were detected among epidemiologically implicated isolates that were indistinguishable by PFGE. Conversely, in three other outbreaks, isolates that were indistinguishable by MLVA displayed multiple PFGE types. An additional more extensive multi-laboratory validation of the MLVA protocol is in progress in order to address critical issues such as establishing epidemiologically relevant interpretation guidelines for the MLVA data.

Arousal and Expression of Anger: A Function of Locus of Control?

ERIC Educational Resources Information Center

Stockin, Bruce C.

Although psychologists have been investigating locus of control for more than two decades, few studies have examined how locus of control interacts with affective variables. To investigate the function of locus of control on arousal patterns and expressions of anger, 120 college students (60 internals, 60 externals, as measured by Rotter's (1966)…

Sub-typing of extended-spectrum-β-lactamase-producing isolates from a nosocomial outbreak: application of a 10-loci generic Escherichia coli multi-locus variable number tandem repeat analysis.

PubMed

Karami, Nahid; Helldal, Lisa; Welinder-Olsson, Christina; Ahrén, Christina; Moore, Edward R B

2013-01-01

Extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) were isolated from infants hospitalized in a neonatal, post-surgery ward during a four-month-long nosocomial outbreak and six-month follow-up period. A multi-locus variable number tandem repeat analysis (MLVA), using 10 loci (GECM-10), for 'generic' (i.e., non-STEC) E. coli was applied for sub-species-level (i.e., sub-typing) delineation and characterization of the bacterial isolates. Ten distinct GECM-10 types were detected among 50 isolates, correlating with the types defined by pulsed-field gel electrophoresis (PFGE), which is recognized to be the 'gold-standard' method for clinical epidemiological analyses. Multi-locus sequence typing (MLST), multiplex PCR genotyping of bla CTX-M, bla TEM, bla OXA and bla SHV genes and antibiotic resistance profiling, as well as a PCR assay specific for detecting isolates of the pandemic O25b-ST131 strain, further characterized the outbreak isolates. Two clusters of isolates with distinct GECM-10 types (G06-04 and G07-02), corresponding to two major PFGE types and the MLST-based sequence types (STs) 131 and 1444, respectively, were confirmed to be responsible for the outbreak. The application of GECM-10 sub-typing provided reliable, rapid and cost-effective epidemiological characterizations of the ESBL-producing isolates from a nosocomial outbreak that correlated with and may be used to replace the laborious PFGE protocol for analyzing generic E. coli.

Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli.

PubMed

Timmons, Chris; Trees, Eija; Ribot, Efrain M; Gerner-Smidt, Peter; LaFon, Patti; Im, Sung; Ma, Li Maria

2016-06-01

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of growing concern worldwide that have been associated with several recent multistate and multinational outbreaks of foodborne illness. Rapid and sensitive molecular-based bacterial strain discrimination methods are critical for timely outbreak identification and contaminated food source traceback. One such method, multiple-locus variable-number tandem repeat analysis (MLVA), is being used with increasing frequency in foodborne illness outbreak investigations to augment the current gold standard bacterial subtyping technique, pulsed-field gel electrophoresis (PFGE). The objective of this study was to develop a MLVA assay for intra- and inter-serogroup discrimination of six major non-O157 STEC serogroups-O26, O111, O103, O121, O45, and O145-and perform a preliminary internal validation of the method on a limited number of clinical isolates. The resultant MLVA scheme consists of ten variable number tandem repeat (VNTR) loci amplified in three multiplex PCR reactions. Sixty-five unique MLVA types were obtained among 84 clinical non-O157 STEC strains comprised of geographically diverse sporadic and outbreak related isolates. Compared to PFGE, the developed MLVA scheme allowed similar discrimination among serogroups O26, O111, O103, and O121 but not among O145 and O45. To more fully compare the discriminatory power of this preliminary MLVA method to PFGE and to determine its epidemiological congruence, a thorough internal and external validation needs to be performed on a carefully selected large panel of strains, including multiple isolates from single outbreaks. Copyright © 2016. Published by Elsevier B.V.

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2007-07-01

Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia MacCollin, M.D. CONTRACTING ORGANIZATION: Massachusetts General Hospital...Identification of the Schwannomatosis Locus 5b. GRANT NUMBER DAMD17-03-1-0445 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Mia...Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Schwannomatosis is a recently recognized third major type of neurofibromatosis. Our

Simple Sequence Repeat and S-locus Genotyping to Explore Genetic Variability in Polyploid Prunus spinosa and P. insititia.

PubMed

Halász, Júlia; Makovics-Zsohár, Noémi; Szőke, Ferenc; Ercisli, Sezai; Hegedűs, Attila

2017-02-01

Polyploid Prunus spinosa (2n = 4×) and P. insititia (2n = 6×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programmes. In Hungary, 17 cultivar candidates were selected from wild-growing populations including 10 P. spinosa, 4 P. insititia and three P. spinosa × P. domestica hybrids (2n = 5×). Their taxonomic classification was based on their phenotypic characteristics. Six simple sequence repeats (SSRs) and the multiallelic S-locus genotyping were used to characterize genetic variability and reliable identification of the tested accessions. A total of 98 SSR alleles were identified, which presents 19.5 average allele number per locus, and each of the 17 genotypes could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified. The complete and partial S-genotype was determined for 8 and 9 accessions, respectively. The identification of a cross-incompatible pair of cultivar candidates and several semi-compatible combinations help maximize fruit set in commercial orchards. Our results indicate that the S-allele pools of wild-growing P. spinosa and P. insititia are overlapping in Hungary. A phylogenetic and principal component analysis confirmed the high level of diversity and genetic differentiation present within the analysed genotypes and helped clarify doubtful taxonomic identities. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species. The analysed accessions represent huge genetic potential that can be exploited in commercial cultivation.

The Ties that Bind (the Igh Locus).

PubMed

Krangel, Michael S

2016-05-01

Immunoglobulin heavy-chain locus V(D)J recombination requires a 3D chromatin organization which permits widely distributed variable (V) gene segments to contact distant diversity (D) and joining (J) gene segments. A recent study has identified key nodes in the locus interactome, paving the way for new molecular insights into how the locus is configured for recombination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of Locus of Control, Academic Self-Efficacy, and Tutoring on Academic Performance

ERIC Educational Resources Information Center

Drago, Anthony; Rheinheimer, David C.; Detweiler, Thomas N.

2018-01-01

This study investigated the connection between locus of control (LOC), academic self-efficacy (ASE), and academic performance, and whether these variables are affected by tutoring. Additional variables of interest, including gender, students' Pell Grant status, ethnicity, and class size, were also considered for the research models. The population…

Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest.

PubMed

Castilho, Camila S; Marins-Sá, Luiz G; Benedet, Rodrigo C; Freitas, Thales R O

2012-01-01

The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, F(IS), effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software), we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software) that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk.

Methane Seeps in the Gulf of Mexico: repeat acoustic surveying shows highly temporally and spatially variable venting

NASA Astrophysics Data System (ADS)

Beaumont, B. C.; Raineault, N.

2016-02-01

Scientists have recognized that natural seeps account for a large amount of methane emissions. Despite their widespread occurrence in areas like the Gulf of Mexico, little is known about the temporal variability and site-scale spatial variability of venting over time. We used repeat acoustic surveys to compare multiple days of seep activity and determine the changes in the locus of methane emission and plume height. The Sleeping Dragon site was surveyed with an EM302 multibeam sonar on three consecutive days in 2014 and 4 days within one week in 2015. The data revealed three distinctive plume regions. The locus of venting varied by 10-60 meters at each site. The plume that exhibited the least spatial variability in venting, was also the most temporally variable. This seep was present in one-third of survey dates in 2014 and three quarters of survey dates in 2015, showing high day-to-day variability. The plume height was very consistent for this plume, whereas the other plumes were more consistent temporally, but varied in maximum plume height detection by 25-85 m. The single locus of emission at the site that had high day-to-day variability may be due to a single conduit for methane release, which is sometimes closed off by carbonate or clathrate hydrate formation. In addition to day-to-day temporal variability, the locus of emission at one site was observed to shift from a point-source in 2014 to a diffuse source in 2015 at a nearby location. ROV observations showed that one of the seep sites that closed off temporarily, experienced an explosive breakthrough of gas, releasing confined methane and blowing out rock. The mechanism that causes on/off behavior of certain plumes, combined with the spatial variability of the locus of methane release shown in this study may point to carbonate or hydrate formation in the seep plumbing system and should be further investigated.

Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

PubMed Central

Schouls, Leo M.; van der Heide, Han G. J.; Vauterin, Luc; Vauterin, Paul; Mooi, Frits R.

2004-01-01

Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected. PMID:15292152

Molecular characterization of enterohemorrhagic Escherichia coli O157:H7 isolates dispersed across Japan by pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analysis.

PubMed

Pei, Yingxin; Terajima, Jun; Saito, Yasunori; Suzuki, Reiko; Takai, Nobuko; Izumiya, Hidemasa; Morita-Ishihara, Tomoko; Ohnishi, Makoto; Miura, Masashi; Iyoda, Sunao; Mitobe, Jiro; Wang, Binyou; Watanabe, Haruo

2008-01-01

We identified seven distinct subtypes of enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates that were derived from sporadic cases and outbreaks from multiple prefectures in Japan in 2005. A surveillance system utilizing pulsed-field gel electrophoresis (PFGE), PulseNet Japan, was used. Some strains showed indistinguishable PFGE patterns using another restriction enzyme (BlnI or SpeI) in each subtype of EHEC O157:H7 isolates that were routinely subtyped by the XbaI PFGE pattern. In order to examine the genotypic relatedness of these strains, we carried out a multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA). By using the MLVA system, we found that three of seven subtypes of EHEC O157:H7 strains that were isolated from sporadic cases dispersed across multiple prefectures within a few months showed indistinguishable PFGE patterns and identical MLVA types. Strains belonging to the other four subtypes of EHEC O157:H7 in the PFGE analysis were further classified into different clusters of EHEC O157:H7. Therefore, compared to PFGE, MLVA showed greater discriminatory power with respect to analysis of the isolates in this study.

Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae

PubMed Central

2012-01-01

Background Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs) analysis (MLVA) to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae. Results MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP) typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus. Conclusions MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing. PMID:22624829

Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

PubMed Central

Techaruvichit, Punnida; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2015-01-01

Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni. PMID:26025899

Relationships among Reading Performance, Locus of Control and Achievement for Marginal Admission Students.

ERIC Educational Resources Information Center

Pepper, Roger S.; Drexler, John A., Jr.

The first phase of the study was a 2 x 2 factorial design, with locus of control and instructional method (lecture and demonstration) as independent variables and honor point average (HPA) as the dependent variable. The second phase used correlational techniques to test the extent to which reading performance and traditional predictors of…

Estimation of selection intensity under overdominance by Bayesian methods.

PubMed

Buzbas, Erkan Ozge; Joyce, Paul; Abdo, Zaid

2009-01-01

A balanced pattern in the allele frequencies of polymorphic loci is a potential sign of selection, particularly of overdominance. Although this type of selection is of some interest in population genetics, there exists no likelihood based approaches specifically tailored to make inference on selection intensity. To fill this gap, we present Bayesian methods to estimate selection intensity under k-allele models with overdominance. Our model allows for an arbitrary number of loci and alleles within a locus. The neutral and selected variability within each locus are modeled with corresponding k-allele models. To estimate the posterior distribution of the mean selection intensity in a multilocus region, a hierarchical setup between loci is used. The methods are demonstrated with data at the Human Leukocyte Antigen loci from world-wide populations.

Locus of control and contraceptive knowledge, attitude and practice among university students.

PubMed

Alves, Aline Salheb; Lopes, Maria Helena Baena de Moraes

2010-02-01

To assess the relationship between locus of control and knowledge, attitude and practice regarding pill and condom use among university students. The inquiry was developed in Campinas, a city in Southeastern Brazil, in 2006. A total of 295 adolescent newcomers to a public university answered a structured questionnaire and Levenson's multidimensional locus of control scale. The scores of the dimensions of locus of control were calculated and Spearman's correlation coefficient was used to assess their correlation with knowledge and practice concerning pill and condom use. In order to assess the relationship between the dimensions of locus of control and sociodemographic variables and variables related to the individuals' sex life, Kruskal-Wallis and Mann-Whitney tests were used. Male adolescents had higher scores of powerful others externality when compared to female adolescents (p=0.01). Students living alone had lower internality (p=0.01). When locus of control was compared to condom use in the first intercourse, considering only the 102 students who informed the age of the beginning of sexual activity, greater internality was found among male adolescents who did not use condoms (p<0.05). When the locus of control scores were correlated with contraceptive knowledge and practice, it was found that the higher the powerful others externality locus, the lower the adequate use of contraceptive methods (r = -0.22, p=0.03). The powerful others externality locus influences the practice of contraceptive use in this group of adolescents.

The immunoglobulin heavy chain locus of the duck. Genomic organization and expression of D, J, and C region genes.

PubMed

Lundqvist, M L; Middleton, D L; Hazard, S; Warr, G W

2001-12-14

The region of the duck IgH locus extending from upstream of the proximal diversity (D) segment to downstream of the constant gene cluster has been cloned and mapped. A sequence contig of 48,796 base pairs established that the organization of the genes is D-J(H)-mu-alpha-upsilon. No evidence for a functional homologue (or remnant) of a delta gene was found. The alpha gene is in inverted transcriptional orientation; class switch to IgA expression thus requires inversion of the approximately 27-kilobase pair region that includes both mu and alpha genes. The secreted forms of duck alpha and mu are each encoded by 4 constant region exons, and the hydrophobic C-terminal regions of the membrane receptor forms of alpha and mu are encoded by one and two transmembrane exons, respectively. Putative switch (S) regions were identified for duck mu and upsilon by comparison with chicken Smu and Supsilon sequences and for duck alpha by comparison with mouse Salpha. The duck IgH locus is rich in complex variable number tandem repeats, which occupy approximately 60% of the sequenced region, and occur at a much higher frequency in the IgH locus than in other sequenced regions of the duck genome.

An Examination of Locus of Control, Epistemological Beliefs and Metacognitive Awareness in Preservice Early Childhood Teachers

ERIC Educational Resources Information Center

Bedel, Emine Ferda

2012-01-01

This study aims to explore the locus of control, epistemological beliefs and metacognitive awareness levels of preservice early childhood education teachers and to determine the interrelations among these variables. 206 teacher candidates have been asked to fill out Rotter's Internal-External Locus of Control Scale, Central Epistemological Beliefs…

Sequence and Characterization of the Ig Heavy Chain Constant and Partial Variable Region of the Mouse Strain 129S11

PubMed Central

Retter, Ida; Chevillard, Christophe; Scharfe, Maren; Conrad, Ansgar; Hafner, Martin; Im, Tschong-Hun; Ludewig, Monika; Nordsiek, Gabriele; Severitt, Simone; Thies, Stephanie; Mauhar, America; Blöcker, Helmut; Müller, Werner; Riblet, Roy

2009-01-01

Although the entire mouse genome has been sequenced, there remain challenges concerning the elucidation of particular complex and polymorphic genomic loci. In the murine Igh locus, different haplotypes exist in different inbred mouse strains. For example, the Ighb haplotype sequence of the Mouse Genome Project strain C57BL/6 differs considerably from the Igha haplotype of BALB/c, which has been widely used in the analyses of Ab responses. We have sequenced and annotated the 3′ half of the Igha locus of 129S1/SvImJ, covering the CH region and approximately half of the VH region. This sequence comprises 128 VH genes, of which 49 are judged to be functional. The comparison of the Igha sequence with the homologous Ighb region from C57BL/6 revealed two major expansions in the germline repertoire of Igha. In addition, we found smaller haplotype-specific differences like the duplication of five VH genes in the Igha locus. We generated a VH allele table by comparing the individual VH genes of both haplotypes. Surprisingly, the number and position of DH genes in the 129S1 strain differs not only from the sequence of C57BL/6 but also from the map published for BALB/c. Taken together, the contiguous genomic sequence of the 3′ part of the Igha locus allows a detailed view of the recent evolution of this highly dynamic locus in the mouse. PMID:17675503

Subcultural Determinants of Locus of Control (IE) Development. A Locus of Control (IE) Measure for Preschool-Age Children: Model, Method, and Validity.

ERIC Educational Resources Information Center

Stephens, Mark; Delys, Pamela

Both papers are concerned with locus of control (of reinforcement) expectancies among young children, especially preschoolers. The first reviews a number of studies which examined the relationship between locus of control, socioeconomic status, and ethnicity. The results indicate that (1) economic status is consistently related to locus of…

An evaluation of new and established methods to determine T‐DNA copy number and homozygosity in transgenic plants.

PubMed Central

Głowacka, Katarzyna; Kromdijk, Johannes; Leonelli, Lauriebeth; Niyogi, Krishna K.; Clemente, Tom E.

2016-01-01

Abstract Stable transformation of plants is a powerful tool for hypothesis testing. A rapid and reliable evaluation method of the transgenic allele for copy number and homozygosity is vital in analysing these transformations. Here the suitability of Southern blot analysis, thermal asymmetric interlaced (TAIL‐)PCR, quantitative (q)PCR and digital droplet (dd)PCR to estimate T‐DNA copy number, locus complexity and homozygosity were compared in transgenic tobacco. Southern blot analysis and ddPCR on three generations of transgenic offspring with contrasting zygosity and copy number were entirely consistent, whereas TAIL‐PCR often underestimated copy number. qPCR deviated considerably from the Southern blot results and had lower precision and higher variability than ddPCR. Comparison of segregation analyses and ddPCR of T1 progeny from 26 T0 plants showed that at least 19% of the lines carried multiple T‐DNA insertions per locus, which can lead to unstable transgene expression. Segregation analyses failed to detect these multiple copies, presumably because of their close linkage. This shows the importance of routine T‐DNA copy number estimation. Based on our results, ddPCR is the most suitable method, because it is as reliable as Southern blot analysis yet much faster. A protocol for this application of ddPCR to large plant genomes is provided. PMID:26670088

Self Esteem, Locus of Control and Multidimensional Perfectionism as the Predictors of Subjective Well Being

ERIC Educational Resources Information Center

Karatas, Zeynep; Tagay, Ozlem

2012-01-01

The purpose of this study is to determine whether there is a relationship between self-esteem, locus of control and multidimensional perfectionism, and the extent to which the variables of self-esteem, locus of control and multidimensional perfectionism contribute to the prediction of subjective well-being. The study was carried out with 318 final…

Prolonged and mixed non-O157 Escherichia coli infection in an Australian household.

PubMed

Staples, M; Graham, R M A; Doyle, C J; Smith, H V; Jennison, A V

2012-05-01

An Australian family was identified through a Public Health follow up on a Shiga-toxigenic Escherichia coli (STEC) positive bloody diarrhoea case, with three of the four family members experiencing either symptomatic or asymptomatic STEC shedding. Bacterial isolates were submitted to stx sequence sub-typing, multi-locus variable number tandem repeat analysis (MLVA), multi-locus sequence typing (MLST) and binary typing. The analysis revealed that there were multiple strains of STEC being shed by the family members, with similar virulence gene profiles and the same serogroup but differing in their MLVA and MLST profiles. This study illustrates the potentially complicated nature of non-O157 STEC infections and the importance of molecular epidemiology in understanding disease clusters. © 2012 QUEENSLAND HEALTH. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.

Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest

PubMed Central

Castilho, Camila S.; Marins-Sá, Luiz G.; Benedet, Rodrigo C.; Freitas, Thales R.O.

2012-01-01

The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, FIS, effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software), we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software) that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk. PMID:22481876

Genetic diversity of O157:H7 and non-O157 verocytotoxigenic Escherichia coli from Argentina inferred from multiple-locus variable-number tandem repeat analysis (MLVA).

PubMed

Bustamante, Ana V; Sanso, A Mariel; Lucchesi, Paula M A; Parma, Alberto E

2010-04-01

Although serotype O157:H7 has been implicated in most cases of haemolytic-uraemic syndrome (HUS), there is growing concern about non-O157 serotypes of verocytotoxigenic Escherichia coli (VTEC). Multiple-locus variable-number tandem repeat analysis (MLVA) has been focused on the specific typing of O157:H7 isolates, but recently, a generic MLVA assay for E. coli and Shigella has been developed. We performed a study of the polymorphism in 7 generic VNTR loci both in VTEC O157:H7 and non-O157 isolates from Argentina, in order to asses the ability of the method to type this group of isolates and to get insight into their genetic diversity. Sixty-four isolates from cattle, patients with diarrhoea, and contaminated food belonging to 8 different serotypes were studied. All of them could be typed by this method and revealed 41 different MLVA genotypes. The MLVA dendrogram showed 2 main clusters which corresponded to O157:H7 and non-O157, respectively. Our results confirm the suitability of this MLVA method for analyzing VTEC isolates belonging to several serotypes, both O157:H7 as well as non-O157, highlight the genetic variability of the O157:H7 serotype and the need of additional research in order to find more VNTR loci that could allow a higher discrimination among non-O157 VTEC. (c) 2009 Elsevier GmbH. All rights reserved.

A conceptual model of factors contributing to the development of muscle dysmorphia.

PubMed

Grieve, Frederick G

2007-01-01

Muscle dysmorphia is a recently described subcategory of Body Dysmorphic Disorder. It is most prevalent in males and has a number of cognitive, behavioral, socioenviornmental, emotional, and psychological factors that influence its expression. An etiological model describing these influences is presented for evaluation. Nine variables (body mass, media influences, ideal body internalization, low self-esteem, body dissatisfaction, health locus of control, negative affect, perfectionism, and body distortion) were identified through the use of extant literature on muscle dysmorphia and through extrapolation from literature involving women and eating disorders. The functional relationships among these variables are described and implications of the model are discussed.

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

USGS Publications Warehouse

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.

Diversity among French Bacillus anthracis isolates.

PubMed

Fouet, Agnès; Smith, Kimothy L; Keys, Chris; Vaissaire, Josée; Le Doujet, Claudine; Lévy, Martine; Mock, Michèle; Keim, Paul

2002-12-01

While outbreaks of animal anthrax zoonoses still regularly occur in France, little is known about the epidemiology links between them. We have used the eight-locus multilocus variable-number tandem repeat analysis typing technique against a collection of 50 Bacillus anthracis isolates from France. There were eight distinct genotypes belonging to two dissimilar genetic clusters. Regional strain patterns were observed, with the B2 genotypes prevalent in southern France and the A1a genotypes found only in northern France.

[The significance of the relationship between external/internal locus of control and adolescent substance use in behavioral medicine].

PubMed

Pikó, Bettina; Kovács, Eszter; Kriston, Pálma

2011-02-27

Prevention and treatment of the addictions are key public health priorities in modern society. In medical practice, in relation to the biochemical processes, mapping the addiction-prone personality traits, like external/internal locus of control are getting more and more attention. Individuals with high level on internal locus of control, for example, tend to take care of their health behavior; the lack of it, on the other hand, may worsen the effectiveness of stress release which may increase the likelihood of turning to substance use. The main goal of the present study was to investigate the relationship between adolescent substance use (both lifetime prevalence and the actual substance user status) and external/internal locus of control). The data collection of the questionnaire survey was going on among 656 high school students in Szeged (age range between 14-21 years, mean = 16.5 years, S.D. = 1.5 years of age, 49.1% of the sample was female). Associations between indicators of substance use (as dependent variables) and scale points of external/internal locus of control (as independent variables) were assessed using odds ratios calculated by logistic regression analyses, whereas gender was used as a controlling variable. Among boys, scale points of external, among girls, those of internal locus of control showed higher values. External locus of control increased, whereas internal locus of control decreased the risk of substance use, however, the relative role of external/internal locus of control was different according to the type of substance use and the prevalence values. In terms of smoking, lifetime prevalence, whereas in terms of marijuana use, the actual user status was influenced. In addition, while the latter one was also affected by gender, it did not play a role at all in the previous one. All these findings suggest that behavioral control may play a particularly important role in prevention of adolescent substance use. For developing this, methods of cognitive therapy would be effective to be completed with autogenic relaxation training as well.

Use of multiple-locus variable-number tandem repeat analysis to evaluate Escherichia coli O157 subtype distribution and transmission dynamics following natural exposure on a closed beef feedlot facility.

PubMed

Williams, Michele L; Pearl, David L; Bishop, Katherine E; Lejeune, Jeffrey T

2013-10-01

To better understand the epizootiology of Escherichia coli O157:H7 among cattle, all E. coli O157 isolates recovered on a research feedlot during a single feeding period were characterized by multiple-locus variable-number tandem repeat analysis (MLVA). Three distinct MLVA subtypes (A, B, C), accounting for 24%, 15%, and 64% of total isolates, respectively, were identified. Subtypes A and B were isolated at the initiation of sampling, but their prevalence waned and subtype C, first isolated on the third sampling date, became the predominant subtype on the feedlot. Supershedding events, however, occurred with equal frequency for all three MLVA-types. Using a multilevel logistic regression model, we investigated whether the odds of shedding subtype C relative to subtypes A or B were associated with time, diet, or the presence of a penmate shedding high numbers of subtype C. Only time and exposure to an animal shedding MLVA-type C at 10³ colony-forming units or greater in the pen at the time of sampling were significantly associated with increased shedding of subtype C. High-level shedding of those E. coli O157 subtypes better suited for survival in the environment and/or in the host appear to play a significant role in the development of predominant E. coli O157 subtypes. Supershedding events alone are neither required nor sufficient to drive the epidemiology of specific E. coli O157 subtypes. Additional factors are necessary to direct successful on-farm transmission of E. coli O157.

The efficacy of a modified Theory of Reasoned Action to explain gambling behavior in college students.

PubMed

Thrasher, Robert G; Andrew, Damon P S; Mahony, Daniel F

2011-09-01

Recently, Thrasher et al. (College Student Affairs Journal 27(1): 57-75, 2007) explored the efficacy of the Theory of Reasoned Action (TRA; Ajzen and Fishbein, Attitudes, personality, and behavior, 1980) in explaining gambling behavior of college students. However, their study found the TRA only predicted small amounts of variance in gambling intentions. Heeding their call to enhance the efficacy of the TRA through the addition of explanatory variables to the model, the present study incorporated gambling motivations and locus of control as moderating variables within the TRA to test the potential of a modified TRA in explaining gambling behavior of college students. A total of 345 students at a major metropolitan research university in the Midwest volunteered to participate in the study. A series of hierarchical linear regressions indicated intrinsic motivation to accomplish (p = .002) significantly moderated the relationship between gambling attitudes and gambling intentions. Further, internal locus of control (p < .001), chance locus of control (p < .001), and powerful others locus of control (p < .001) also significantly moderated the relationship between gambling attitudes and gambling intentions. The significant impact of the moderating variables on the relationship between gambling attitudes and intentions suggests intrinsic motivation and locus of control can alter the impact of the relationship between gambling attitudes and gambling intentions.

CRISPR: A Useful Genetic Feature to Follow Vaginal Carriage of Group B Streptococcus

PubMed Central

Beauruelle, Clémence; Pastuszka, Adeline; Horvath, Philippe; Perrotin, Franck; Mereghetti, Laurent; Lanotte, Philippe

2017-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) and Cas (CRISPR-associated proteins) play a critical role in adaptive immunity against mobile genetic elements, especially phages, through their ability to acquire novel spacer sequences. Polarized spacer acquisition results in spacer polymorphism and temporal organization of CRISPR loci, making them attractive epidemiological markers. Group B Streptococcus (GBS), a genital commensal for 10 to 30% of healthy women and a major neonatal pathogen, possesses a ubiquitous and functional CRISPR1 locus. Our aim was to assess the CRISPR1 locus as an epidemiological marker to follow vaginal carriage of GBS in women. This study also allowed us to observe the evolution of the CRISPR1 locus in response to probable phage infection occurring in vivo. We followed carriage of GBS among 100 women over an 11-year period, with a median duration of approximately 2 years. The CRISPR1 locus was highly conserved over time. The isolates that show the same CRISPR1 genotype were collected from 83% of women. There was an agreement between CRISPR genotyping and other typing methods [MLVA (multilocus variable number of tandem repeat Analysis) and MLST (multilocus sequence typing)] for 94% of the cases. The CRISPR1 locus of the isolates from 18 women showed modifications, four of which acquired polarized spacer, highlighting the in vivo functionality of the system. The novel spacer of one isolate had sequence similarity with phage, suggesting that phage infection occurred during carriage. These findings improve our understanding of CRISPR-Cas evolution in GBS and provide a glimpse of host-phage dynamics in vivo. PMID:29075246

Application of multilocus variable number tandem repeat analysis to monitor Verocytotoxin-producing Escherichia coli O157 phage type 8 in England and Wales: emergence of a profile associated with a national outbreak.

PubMed

Perry, N; Cheasty, T; Dallman, T; Launders, N; Willshaw, G

2013-10-01

Evaluation of multilocus variable number tandem repeat analysis (MLVA) to subtype all isolates of Vero cytotoxin-producing Escherichia coli O157 phage type 8 in England and Wales. Over a 13 month period from December 2010, 483 isolates of VTEC O157 PT8 were tested by MLVA; 39% were received in the first 4 months of 2011, when infections are generally low. One profile, or single locus variants of it, was present in 249 (52%) isolates but was not common previously. These cases represented a national increase in PT8, associated epidemiologically with soil-contaminated vegetables. Most of the 177 other MLVA profiles were unique to a single isolate. Profiles shared by >1 isolate included cases from two small community, food-borne outbreaks and 11 households. Several shared profiles were found among 23 isolates without known links. Apart from one group, isolates linked to travel abroad had very diverse profiles. Multilocus variable number tandem repeat analysis discriminated apparent sporadic isolates of the same PT and assisted in detection of cases in an emerging national outbreak. Multilocus variable number tandem repeat analysis is an epidemiologically valid complement to surveillance and applicable as a rapid, practical test for large numbers of isolates. © 2013 The Society for Applied Microbiology.

Multidimensional profiles of health locus of control in Hispanic Americans

PubMed Central

Champagne, Brian R; Fox, Rina S; Mills, Sarah D; Sadler, Georgia Robins; Malcarne, Vanessa L

2016-01-01

Latent profile analysis identified health locus of control profiles among 436 Hispanic Americans who completed the Multidimensional Health Locus of Control scales. Results revealed four profiles: Internally Oriented-Weak, -Moderate, -Strong, and Externally Oriented. The profile groups were compared on sociocultural and demographic characteristics, health beliefs and behaviors, and physical and mental health outcomes. The Internally Oriented-Strong group had less cancer fatalism, religiosity, and equity health attributions, and more alcohol consumption than the other three groups; the Externally Oriented group had stronger equity health attributions and less alcohol consumption. Deriving multidimensional health locus of control profiles through latent profile analysis allows examination of the relationships of health locus of control subtypes to health variables. PMID:25855212

Systematic cloning of human minisatellites from ordered array charomid libraries.

PubMed

Armour, J A; Povey, S; Jeremiah, S; Jeffreys, A J

1990-11-01

We present a rapid and efficient method for the isolation of minisatellite loci from human DNA. The method combines cloning a size-selected fraction of human MboI DNA fragments in a charomid vector with hybridization screening of the library in ordered array. Size-selection of large MboI fragments enriches for the longer, more variable minisatellites and reduces the size of the library required. The library was screened with a series of multi-locus probes known to detect a large number of hypervariable loci in human DNA. The gridded library allowed both the rapid processing of positive clones and the comparative evaluation of the different multi-locus probes used, in terms of both the relative success in detecting hypervariable loci and the degree of overlap between the sets of loci detected. We report 23 new human minisatellite loci isolated by this method, which map to 14 autosomes and the sex chromosomes.

Genetic variability among populations of Lutzomyia (Psathyromyia) shannoni (Dyar 1929) (Diptera: Psychodidae: Phlebotominae) in Colombia.

PubMed

Cárdenas, E; Munstermann, L E; Martínez, O; Corredor, D; Ferro, C

2001-02-01

Polyacrylamide gel electrophoresis was used to elucidate genetic variation at 13 isozyme loci among forest populations of Lutzomyia shannoni from three widely separated locations in Colombia: Palambí (Nariño Department), Cimitarra (Santander Department) and Chinácota (Norte de Santander Department). These samples were compared with a laboratory colony originating from the Magdalena Valley in Central Colombia. The mean heterozygosity ranged from 16 to 22%, with 2.1 to 2.6 alleles detected per locus. Nei's genetic distances among populations were low, ranging from 0.011 to 0.049. The estimated number of migrants (Nm=3.8) based on Wright's F-Statistic, F ST, indicated low levels of gene flow among Lu. shannoni forest populations. This low level of migration indicates that the spread of stomatitis virus occurs via infected host, not by infected insect. In the colony sample of 79 individuals, the Gpi locus was homozygotic (0.62/0.62) in all females and heterozygotic (0.62/0.72) in all males. Although this phenomenon is probably a consequence of colonization, it indicates that Gpi is linked to a sex determining locus.

Human minisatellite alleles detectable only after PCR amplification.

PubMed

Armour, J A; Crosier, M; Jeffreys, A J

1992-01-01

We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

Transition to academic nurse educator: a survey exploring readiness, confidence, and locus of control.

PubMed

Goodrich, Robin S

2014-01-01

The purpose of this study was to describe nurse transition to the role of academic nurse educator and to investigate the resources and barriers that nurses experience during this career transition, specifically the relationships among levels of readiness, confidence, personal control, support, decision independence, general self-esteem, and work locus of control. A convenience sample of registered nurses in the United States (N = 541) who hold current full-time employment at an accredited nursing program granting baccalaureate or higher degrees was utilized. Subjects were recruited via electronic mail and answered an on-line survey. Pearson product-moment correlation and multivariate analysis of variance were used for statistical calculations. Results indicated significant, positive relationships among all the variables except readiness and personal control (p = .01). Significant differences were found in amount of time that nurses were in the role of academic nurse educator and the demographic variables of number of children, marital status, and highest degree held. The results of this study provide evidence to support and enhance processes to develop and retain nurse academicians, to promote excellence in the academic nurse educator role, and to advance the science and practice of the profession. © 2014.

Cognitive mechanisms of sleep outcomes in a randomized clinical trial of internet-based cognitive behavioral therapy for insomnia.

PubMed

Chow, Philip I; Ingersoll, Karen S; Thorndike, Frances P; Lord, Holly R; Gonder-Frederick, Linda; Morin, Charles M; Ritterband, Lee M

2018-07-01

The aim of this study was to investigate in a randomized clinical trial the role of sleep-related cognitive variables in the long-term efficacy of an online, fully automated cognitive behavioral therapy intervention for insomnia (CBT-I) (Sleep Healthy Using the Internet [SHUTi]). Three hundred and three participants (M age  = 43.3 years; SD = 11.6) were randomly assigned to SHUTi or an online patient education condition and assessed at baseline, postintervention (nine weeks after baseline), and six and 12 months after the intervention period. Cognitive variables were self-reported internal and chance sleep locus of control, dysfunctional beliefs and attitudes about sleep (DBAS), sleep specific self-efficacy, and insomnia knowledge. Primary outcomes were self-reported online ratings of insomnia severity (Insomnia Severity Index), and sleep onset latency and wake after sleep onset from online sleep diaries, collected 12 months after the intervention period. Those who received SHUTi had, at postassessment, higher levels of insomnia knowledge (95% confidence interval [CI] = 0.10-0.16) and internal sleep locus of control (95% CI = 0.04-0.55) as well as lower DBAS (95% CI = 1.52-2.39) and sleep locus of control attributed to chance (95% CI = 0.15-0.71). Insomnia knowledge, chance sleep locus of control, and DBAS mediated the relationship between condition and at least one 12-month postassessment sleep outcome. Within the SHUTi condition, changes in each cognitive variable (with the exception of internal sleep locus of control) predicted improvement in at least one sleep outcome one year later. Online CBT-I may reduce the enormous public health burden of insomnia by changing underlying cognitive variables that lead to long-term changes in sleep outcomes. Published by Elsevier B.V.

Individualism and collectivism: cultural orientation in locus of control and moral attribution under conditions of social change.

PubMed

Santiago, Jose H; Tarantino, Santo J

2002-12-01

This study examined the validity of the view that the constructs of individualism and collectivism are coherent cultural manifestations necessarily reflected in an individual's attribution patterns. It was hypothesized that the attribution patterns of locus of control and moral accountability would show divergent individualistic and collectivistic influences in a culture during change from a collectivist culture to an individualist culture. 98 university students from the United States and Puerto Rico were administered the Singelis Individualism-Collectivism Scale, Rotter's Locus of Control Scale, and Miller and Luthar's justice-related moral accountability vignettes. Contrary to expectation, the Puerto Rican sample scored less external in locus of control than the United States sample. No cultural differences in moral accountability were found. No strong correlations were found among the variables at the individual level of analysis. Accounting for these results included the lack of representativeness of the samples, the independence of relation between variables at different levels of analysis, and social change.

Genome complexity in the coelacanth is reflected in its adaptive immune system

USGS Publications Warehouse

Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W.; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T.

2014-01-01

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

Multidimensional profiles of health locus of control in Hispanic Americans.

PubMed

Champagne, Brian R; Fox, Rina S; Mills, Sarah D; Sadler, Georgia Robins; Malcarne, Vanessa L

2016-10-01

Latent profile analysis identified health locus of control profiles among 436 Hispanic Americans who completed the Multidimensional Health Locus of Control scales. Results revealed four profiles: Internally Oriented-Weak, -Moderate, -Strong, and Externally Oriented. The profile groups were compared on sociocultural and demographic characteristics, health beliefs and behaviors, and physical and mental health outcomes. The Internally Oriented-Strong group had less cancer fatalism, religiosity, and equity health attributions, and more alcohol consumption than the other three groups; the Externally Oriented group had stronger equity health attributions and less alcohol consumption. Deriving multidimensional health locus of control profiles through latent profile analysis allows examination of the relationships of health locus of control subtypes to health variables. © The Author(s) 2015.

Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database.

PubMed

Garcia, Sònia; Kovařík, Ales; Leitch, Andrew R; Garnatje, Teresa

2017-03-01

The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco

PubMed Central

Bouklata, Nada; Supply, Philip; Jaouhari, Sanae; Charof, Reda; Seghrouchni, Fouad; Sadki, Khalid; El Achhab, Youness; Nejjari, Chakib; Filali-Maltouf, Abdelkarim

2015-01-01

Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context. PMID:26285026

High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

PubMed

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

[Use of multiple locus variable number tandem repeats analysis for the Brucella systematization].

PubMed

Kulakov, Iu K; Kovalev, D A; Misetova, E N; Golovneva, S I; Liapustina, L V; Zheludkov, M M

2012-01-01

The methods of molecular-genetic differentiation to strain level acquire increasing significance in the current system of struggle with brucellosis. MLVA (multiple locus variable number tandem repeats analysis) was selected for molecular-genetic differentiation to strain level and simultaneous establishment of the genetic relationship of investigated Brucella strains. The goal of this work was MLVA typing of three pathogenic Brucella species strains with the analysis of stability of chosen loci, discrimination power and concordance to conventional phenotypic methods of the Brucella differentiation for use in systematization of brucellosis causing agents. Twenty six Brucella strains representing reference (n = 15), vaccine (n = 2) and field strains of three pathogenic Brucella species were tested: B. melitensis (n = 3), B. abortus (n = 2), B. suis (n = 2), and isolates (n = 2) with unidentified taxonomic position using MLVA with 9 pairs primers on known variable loci of Brucella genome. The analysis of the stability of chosen loci, discrimination power on Hunter-Gaston discrimination index (HGDI) and consistency to phenotypic methods of identification was performed. MLVA was confirmed for the results of phenotypic methods of identification, stability of the chosen loci in majority reference, and vaccine strains with a high index of variability HGDI 0.9969 for all loci. A dendrogram was plotted on the basis of MLVA data on distributed Brucella strains in related clusters according to its taxonomic species and biovar positions and construction of 25 genotypes. B. melitensis strains formed cluster related to the reference strain of B. melitensis 63/9 biovar 2. Australian isolates of Brucella 83-4 and Brucella 83-6 isolated from rodents formed a cluster distant from other strains of Brucella. MLVA is a promising method for differentiation of Brucella strains with known and unresolved taxonomic status for their systematization and creation of MLVA genotype catalogue that will promote qualitative improvement of brucellosis surveillance system in Russia.

Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis.

PubMed

Gyuranecz, Miklós; Wernery, Ulli; Kreizinger, Zsuzsa; Juhász, Judit; Felde, Orsolya; Nagy, Péter

2016-04-15

Camel brucellosis is a widespread zoonotic disease in camel-rearing countries caused by Brucella melitensis and Brucella abortus. The aim of this study was the first genetic analysis of B. melitensis strains isolated from dromedary camels (Camelus dromedarius) using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA 16 and its MLVA 8 and MLVA11 subsets were used to determine the genotypes of 15 B. melitensis isolates from dromedary camels (11 strains) and other host species (4 strains) from the United Arab Emirates and the results were then compared to B. melitensis MLVA genotypes from other parts of the world. Five, including two novel genotypes were identified with MLVA 8. MLVA 16 further discriminated these five genotypes to ten variants. The eleven camel isolates clustered into four main genetic groups within the East-Mediterranean and African clades and this clustering correlated with the geographic origin of the hosts (United Arab Emirates, Kingdom of Saudi Arabia and Sudan) and the date of their isolation. The camel strains were also genetically related to strains isolated from wild and domestic ruminants from their close habitat or from other parts of the world. Although limited number of strains were analysed, based on our data imported animals from foreign countries, local small ruminants and wildlife species are hypothesized to be the main sources of camel brucellosis in the United Arab Emirates. MLVA was successfully applied to determine the epidemiological links between the different camel B. melitensis infections in the United Arab Emirates and it can be a beneficial tool in future disease control programs. Copyright © 2016 Elsevier B.V. All rights reserved.

Preliminary Investigation on Multiple-Locus Variable Number Tandem Repeat Analysis Profiles of Listeria Monocytogenes Isolates from Pork Meat Tested from Packaging to Fork

PubMed Central

Parisi, Antonio; Caruso, Marta; Pasquali, Frédérique; Manfreda, Gerardo

2014-01-01

Listeria monocytogenes is recognised as a public health issue and a serious challenge for the food industry. L. monocytogenes strain characterisation on the basis of serotyping and molecular typing methods is used for surveillance, epidemiological tracking and outbreak investigation purposes. Genetic variants of L. monocytogenes have diversified into four major phylogenetic lineages, with lineages 1 and 2 each containing multiple clonal groups of public health importance. Standardised tools for easy identification of clonal groups are needed to trace such groups and determine their presence in a large variety of sources. Given the current limitations of available methods for L. monocytogenes strain typing, a potentially useful approach is multiple locus variable number of tandem repeats (VNTR) analysis (MLVA). In this study, MLVA has been applied to a random group of 82 L. monocytogenes strains isolated from 8 different batches of loin chops obtained from the same facility and tested between packaging and consumption time. The strains typed were classified into 10 MLVA profiles containing a number of isolates ranging between 1 to 20. According to the identified MLVA profiles, 75.6% of the pork isolates belonged to the phylogenetic lineage 2 and serotype 1/2c, frequently associated to food isolates. However, 3 pork strains belonged to the phylogenetic lineage 1 and serotype 4b. Moreover, 17 isolates were classified in the phylogenetic lineages 2 and serotype 1/2a. Both serotypes 4b and 1/2a are frequently associated to human isolates of L. monocytogenes. These preliminary results show how the MLVA profiles can support the assessment of the risk profile of food products based on the contaminating L. monocytogenes strain types. PMID:27800312

Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis.

PubMed

Armas, Federica; Camperio, Cristina; Coltella, Luana; Selvaggini, Serena; Boniotti, Maria Beatrice; Pacciarini, Maria Lodovica; Di Marco Lo Presti, Vincenzo; Marianelli, Cinzia

2017-08-04

Highly discriminatory genotyping strategies are essential in molecular epidemiological studies of tuberculosis. In this study we evaluated, for the first time, the efficacy of the repetitive sequence-based PCR (rep-PCR) DiversiLab Mycobacterium typing kit over spoligotyping, 12-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and embB single nucleotide polymorphism (SNP) analysis for Mycobacterium bovis typing. A total of 49 M. bovis animal isolates were used. DNA was extracted and genomic DNA was amplified using the DiversiLab Mycobacterium typing kit. The amplified fragments were separated and detected using a microfluidics chip with Agilent 2100. The resulting rep-PCR-based DNA fingerprints were uploaded to and analysed using web-based DiversiLab software through Pearson's correlation coefficient. Rep-PCR DiversiLab grouped M. bovis isolates into ten different clusters. Most isolates sharing identical spoligotype, MIRU-VNTR profile or embB gene polymorphism were grouped into different rep-PCR clusters. Rep-PCR DiversiLab displayed greater discriminatory power than spoligotyping and embB SNP analysis but a lower resolution power than the 12-locus MIRU-VNTR analysis. MIRU-VNTR confirmed that it is superior to the other PCR-based methods tested here. In combination with spoligotyping and 12-locus MIRU-VNTR analysis, rep-PCR improved the discriminatory power for M. bovis typing.

Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.).

PubMed

Finkers-Tomczak, Anna; Bakker, Erin; de Boer, Jan; van der Vossen, Edwin; Achenbach, Ute; Golas, Tomasz; Suryaningrat, Suwardi; Smant, Geert; Bakker, Jaap; Goverse, Aska

2011-02-01

The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146-152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.

Locus of Control, Self-esteem, Stimulus Appraisal, and Depressive Symptoms in Children

ERIC Educational Resources Information Center

Moyal, Barbara R.

1977-01-01

Variables of self-esteem, locus of control, stimulus appraisal, and depressive symptoms, which are related to depression in adults, were investigated in a sample of nonreferred Grade 5 and Grade 6 children. Grade and sex effects were not significant. All other intervariable correlations were significant. (Author)

Locus of Control and Neuropsychological Performance in Chronic Alcoholics.

ERIC Educational Resources Information Center

Shelton, M. D.; And Others

1982-01-01

Examined correlated neuropsychological performance in male chronic alcoholics and non-alcoholic controls. Results showed external locus of control (LOC-E) scores to predict performance on neuropsychological tests in alcoholics but not in controls. Suggests the LOC-E variables cannot account for the widespread differences between the groups on…

Multifactor Determinants of Visual Accommodation as a Critical Intervening Variable in the Perception of Size and Distance: Phase I Report

DTIC Science & Technology

1997-11-01

Expanded subset of the illustration to clarify the locus of the off-axis end point of retinal stimulation for correct accommodation. 55 Figure...12c. Expanded illustration to clarify the locus of the off -axis end point of retinal stimulation for myopic accommodation. 55 Figure 12d...Expanded illustration to clarify the locus of the off -axis end point of retinal stimulation for hyperopic accommodation. 56 Figure 13. Simplified

Escherichia coli O157:H7 in Ecuador: animal reservoirs, yet no human disease.

PubMed

Trueba, Gabriel; Garcés, Verónica; V, Verónica Barragan; Colman, Rebecca E; Seymour, Meagan; Vogler, Amy J; Keim, Paul

2013-05-01

Escherichia coli O157:H7 is frequently isolated from cases of diarrhea in many industrialized countries; however, it is seldom found in developing countries. The present manuscript reports the presence of E. coli O157:H7 in Ecuadorian livestock, a country where enterohemorrhagic E. coli disease in humans has never been reported. The Ecuadorian isolates were genetically related to some strains linked to clinical cases in the United States as assessed by multiple-locus variable number tandem repeat (VNTR) analysis.

Shiftwork in the Norwegian petroleum industry: overcoming difficulties with family and social life – a cross sectional study

PubMed Central

Ljoså, Cathrine Haugene; Lau, Bjørn

2009-01-01

Background Continuous shift schedules are required in the petroleum industry because of its dependency on uninterrupted production. Although shiftwork affects health, less is known about its effects on social and domestic life. Methods Consequently, we studied these relationships in a sample of 1697 (response rate 55.9%) petroleum workers who worked onshore and offshore for a Norwegian oil and gas company. We also examined the roles of coping strategies and locus of control for handling self-reported problems with social and domestic life. A questionnaire containing scales from the Standard Shiftwork Index and Shiftwork Locus of Control was answered electronically. Results In general, only a few participants reported that their shift schedule affected their social and domestic/family life, and several participants had enough time to spend by themselves and with their partner, close family, friends, and children. Despite this general positive trend, differences were found for shift type and individual factors such as locus of control and coping strategies. Internal locus of control was associated positively with all the dependent variables. However, engaging problem-focused coping strategies were associated only slightly with the dependent variables, while disengaging emotion-focused coping strategies were negatively associated with the dependent variables. Conclusion Since most participants reported few problems with social and domestic/family life, the availability of more leisure time may be a positive feature of shiftwork in the Norwegian petroleum industry. Locus of control and the use of coping strategies were important for shiftworkers' social and domestic/family life. PMID:19650903

Cognitive functioning correlates of self-esteem and health locus of control in schizophrenia

PubMed Central

Wang, Chien-Shu; Wu, Jo Yung-Wei; Chang, Wei-Chung; Chuang, Shu-Ping

2013-01-01

Aim The study aimed to investigate the relationship among sociodemographic factors, neurocognitive factors, self-esteem, and health locus of control in patients diagnosed with schizophrenia. We examined the self-esteem, internal health locus of control, and external health locus of control through sociodemographic and neurocognitive factors. Methods Forty-six schizophrenic patients and 31 healthy residents from the community or hospital were recruited as the control group. All subjects participated in the self-esteem questionnaire, health locus of control questionnaire, and a series of neuropychological measures. Results Multiple regression analysis revealed that inhibition of attention and external health locus of control were predictors for self-esteem (r=−0.30, P<0.05; r=0.41, P<0.01); inhibition of attention and external health locus of control were contributors for internal health locus of control (r=−0.43, P<0.01; r=0.61, P<0.001); and education was related to external health locus of control (r=−0.31, P<0.05). Conclusion The current study integrated background characteristics and cognitive function to better understand the impact of self-esteem and health locus of control in schizophrenia. The findings indicated that inhibition of attention, external health locus of control, and education contributed to self-esteem, internal health locus of control and external health locus of control. However, the overall predicted variance accounted for by these predictors was small; thus, further research is necessary to examine imperative variables related with self-esteem and health locus of control in schizophrenia. PMID:24194641

Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli

PubMed Central

Del Canto, Felipe; O'Ryan, Miguel; Pardo, Mirka; Torres, Alexia; Gutiérrez, Daniela; Cádiz, Leandro; Valdés, Raul; Mansilla, Aquiles; Martínez, Rodrigo; Hernández, Daniela; Caro, Benjamin; Levine, Myron M.; Rasko, David A.; Hill, Christopher M.; Pop, Mihai; Stine, O. Colin; Vidal, Roberto

2017-01-01

Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of diarrhea worldwide. Among the 25 different ETEC adhesins, 22 are known as “colonization factors” (CFs), of which 17 are assembled by the chaperone-usher (CU) mechanism. Currently, there is no preventive therapy against ETEC, and CFs have been proposed as components for vaccine development. However, studies of diarrhea-causing ETEC strains worldwide indicate that between 15 and 50% of these are negative for known CFs, hindering the selection of the most widespread structures and suggesting that unknown adhesins remain to be identified. Here, we report the result of a comprehensive analysis of 35 draft genomes of ETEC strains which do not carry known adhesin genes; our goal was to find new CU pili loci. The phylogenetic profiles and serogroups of these strains were highly diverse, a majority of which produced only the heat-labile toxin. We identified 10 pili loci belonging to CU families β (1 locus), γ2 (7 loci), κ (1 locus), and π (1 locus), all of which contained the required number of open reading frames (ORFs) to encode functional structures. Three loci were variants of previously-known clusters, three had been only-partially described, and four are novel loci. Intra-loci genetic variability identified would allow the synthesis of up to 14 different structures. Clusters of putative γ2-CU pili were most common (23 strains), followed by putative β-CU pili (12 strains), which have not yet been fully characterized. Overall, our findings significantly increase the number of ETEC adhesion genes associated with human infections. PMID:28111618

MHC ANTIGEN-BINDING LOCUS SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETEROCLITUS POPULATIONS

EPA Science Inventory

The major histocompatibility system provides a unique genetic locus in vertebrates to assess genetic diversity and to look for the effects of selecti.on on the immune system. Fish population studies using MHC are fairly new, and thus far they have focused on endangered population...

Relationship between Locus of Control and Health-Related Variables

ERIC Educational Resources Information Center

Graffeo, Lisa Cotlar; Silvestri, Lynette

2006-01-01

Locus of Control (LOC) deals with an individual's personal attribution of successful or failure. Those with internal LOC believe that events in their lives are under their personal control while individuals with external LOC feel that their lives are dominated by the environment. The theory has been applied to achievement and health-related issues…

Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination

PubMed Central

Nicolas, Laura; Cols, Montserrat; Choi, Jee Eun; Chaudhuri, Jayanta; Vuong, Bao

2018-01-01

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity. PMID:29744038

Does the perception that God controls health outcomes matter for health behaviors?

PubMed

Karvinen, Kristina H; Carr, Lucas J

2014-04-01

The purpose of this study was to examine the associations between God Locus of Health Control, health behaviors, and beliefs utilizing a cross-sectional online survey (N = 549). Results indicated that God Locus of Health Control was correlated with alcohol use, physical activity, perceived risk of chronic disease, and beliefs that poor health behaviors contribute to chronic disease (all p values < .05). Multiple regression analyses including covariates and other locus of control variables revealed that God Locus of Health Control was only an independent correlate of the belief that physical inactivity contributed to chronic disease. Insights from this study may be important for future faith-based health behavior change interventions.

Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

PubMed

Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

2012-06-01

The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Validation of a pXO2-A PCR Assay To Explore Diversity among Italian Isolates of Bacillus anthracis Strains Closely Related to the Live, Attenuated Carbosap Vaccine

PubMed Central

Muscillo, M.; La Rosa, G.; Sali, M.; De Carolis, E.; Adone, R.; Ciuchini, F.; Fasanella, A.

2005-01-01

Several circulating Bacillus anthracis strains isolated in Italy and belonging to the A1.a cluster, genotype 3 (A1.a-3) are genotypically indistinguishable from Carbosap, a live attenuated vaccine strain, containing both pXO1 and pXO2 plasmids. The genotype was assessed by using eight-locus multilocus variable-number tandem repeat analysis. We describe here the use of a ninth locus able to explore variability among strains that have the same genotype. It is important to be able to genotype the wild isolate of B. anthracis strains from outbreaks of anthrax in areas where Carbosap vaccination of cattle and sheep is common practice. A total of 27 representative field strains isolated in Italy and four vaccinal strains, namely, Carbosap, Sterne, Pasteur I, and Pasteur II, were characterized by a ninth marker, called pXO2-A. Twenty-three field strains were genotype 3 and therefore identical to Carbosap. The marker was in the pXO2 plasmid and is based on the polymorphism of the already-known VX2-3 locus. Detection was obtained by PCR with fluorescence-labeled forward primers in order to produce appropriate fragments for capillary electrophoresis with an ABI 310 genetic analyzer. Genetic relationships showed heterogeneity in all of the examined samples. Interestingly, with respect to genotype 3, samples grouped into eight different subtypes, A to H, and the subtype G, had only two samples indistinguishable from Carbosap. The results of the present study confirm the validity of a hierarchical progressive protocol for discrimination among closely related isolates. PMID:16145138

Genetic Relatedness of Clostridium difficile Isolates from Various Origins Determined by Triple-Locus Sequence Analysis Based on Toxin Regulatory Genes tcdC, tcdR, and cdtR▿

PubMed Central

Bouvet, Philippe J. M.; Popoff, Michel R.

2008-01-01

A triple-locus nucleotide sequence analysis based on toxin regulatory genes tcdC, tcdR and cdtR was initiated to assess the sequence variability of these genes among Clostridium difficile isolates and to study the genetic relatedness between isolates. A preliminary investigation of the variability of the tcdC gene was done with 57 clinical and veterinary isolates. Twenty-three isolates representing nine main clusters were selected for tcdC, tcdR, and cdtR analysis. The numbers of alleles found for tcdC, tcdR and cdtR were nine, six, and five, respectively. All strains possessed the cdtR gene except toxin A-negative toxin B-positive variants. All but one binary toxin CDT-positive isolate harbored a deletion (>1 bp) in the tcdC gene. The combined analyses of the three genes allowed us to distinguish five lineages correlated with the different types of deletion in tcdC, i.e., 18 bp (associated or not with a deletion at position 117), 36 bp, 39 bp, and 54 bp, and with the wild-type tcdC (no deletion). The tcdR and tcdC genes, though located within the same pathogenicity locus, were found to have evolved separately. Coevolution of the three genes was noted only with strains harboring a 39-bp or a 54-bp deletion in tcdC that formed two homogeneous, separate divergent clusters. Our study supported the existence of the known clones (PCR ribotype 027 isolates and toxin A-negative toxin B-positive C. difficile variants) and evidence for clonality of isolates with a 39-bp deletion (toxinotype V, PCR ribotype 078) that are frequently isolated worldwide from human infections and from food animals. PMID:18832125

Two different secondary metabolism gene clusters occupied the same ancestral locus in fungal dermatophytes of the arthrodermataceae.

PubMed

Zhang, Han; Rokas, Antonis; Slot, Jason C

2012-01-01

Dermatophyte fungi of the family Arthrodermataceae (Eurotiomycetes) colonize keratinized tissue, such as skin, frequently causing superficial mycoses in humans and other mammals, reptiles, and birds. Competition with native microflora likely underlies the propensity of these dermatophytes to produce a diversity of antibiotics and compounds for scavenging iron, which is extremely scarce, as well as the presence of an unusually large number of putative secondary metabolism gene clusters, most of which contain non-ribosomal peptide synthetases (NRPS), in their genomes. To better understand the historical origins and diversification of NRPS-containing gene clusters we examined the evolution of a variable locus (VL) that exists in one of three alternative conformations among the genomes of seven dermatophyte species. The first conformation of the VL (termed VLA) contains only 539 base pairs of sequence and lacks protein-coding genes, whereas the other two conformations (termed VLB and VLC) span 36 Kb and 27 Kb and contain 12 and 10 genes, respectively. Interestingly, both VLB and VLC appear to contain distinct secondary metabolism gene clusters; VLB contains a NRPS gene as well as four porphyrin metabolism genes never found to be physically linked in the genomes of 128 other fungal species, whereas VLC also contains a NRPS gene as well as several others typically found associated with secondary metabolism gene clusters. Phylogenetic evidence suggests that the VL locus was present in the ancestor of all seven species achieving its present distribution through subsequent differential losses or retentions of specific conformations. We propose that the existence of variable loci, similar to the one we studied, in fungal genomes could potentially explain the dramatic differences in secondary metabolic diversity between closely related species of filamentous fungi, and contribute to host adaptation and the generation of metabolic diversity.

Orosomucoid typing of apes (family Pongidae) by isoelectric focusing: Among primates do only humans have two functional orosomucoid loci

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuasa, I.; Umetsu, K.; Udono, T.

1991-12-01

It has been demonstrated that human orosomucoid (ORM) is controlled by more than one functional loci, while Macaca ORM is controlled by one locus. To examine the time when the ORM gene was duplicated in the evolution of primates, plasma samples from 118 apes (family Pongidae) belonging to 4 genera and 12 species were investigated for ORM polymorphism using isoelectric focusing followed by immunoprinting. The band patterns of ORM in the subfamily Ponginae showed quantitatively different products as in humans. A pedigree study of common chimpanzees supported the two-locus model for ORM. Gibbons (subfamily Hylobatinae) displayed highly variable band patterns,more » but the number of loci was not determined unequivocally. Thus, this study shows that duplication of the ORM gene in primates occurred either before or after the divergence of hylobatinae and Ponginae, consistent with a previous prediction from the molecular evolutionary rate of ORM.« less

Isolation and characterization of ten novel microsatellite loci in the red-winged tinamou (Rhynchotus rufescens, Tinamiformes, Aves) and cross-amplification in other tinamous.

PubMed

Santos, Dimas O; Moreira, Lucas R; Tonhati, Humberto; Caparroz, Renato

2012-04-01

We describe the isolation and characterization of ten microsatellite loci from the red-winged tinamou (Rhynchotus rufescens) and also evaluated the cross-amplification of these loci and other ten loci previously developed for the great tinamou (Tinamus major) in other tinamous. Genetic variability was assessed using 24 individuals. Six loci were polymorphic with moderate to high number of alleles per locus (2-12 alleles) and showed expected heterozygosity (HE) ranging from 0.267 to 0.860. All loci conformed to the Hardy-Weinberg expectation and linkage disequilibrium was not significant for any pair of loci. This battery of polymorphic loci showed high paternity exclusion probability (0.986) and low genetic identity probability (4.95 × 10(-5)), proving to be helpful for parentage tests and population analyses in the red-winged tinamou. The cross-amplification was moderate where of the 160 locus/taxon combinations, 46 (28.75%) successfully amplified.

Anxiety, locus of control and appraisal of air pollution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Navarro, P.L.; Simpson-Housley, P.; de Man, A.F.

1987-06-01

100 residents of Santiago de Chile took part in a study of the relationship among locus of control, trait-anxiety, and perception of air pollution. Concern over the problem of atmospheric pollution and number of antipollution measures taken was related to trait-anxiety. Locus of control was associated with variation in awareness of pollution hazard.

Multiple-locus variable-number tandem-repeat analysis of the swine dysentery pathogen, Brachyspira hyodysenteriae.

PubMed

Hidalgo, Alvaro; Carvajal, Ana; La, Tom; Naharro, Germán; Rubio, Pedro; Phillips, Nyree D; Hampson, David J

2010-08-01

The spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe colonic infection of pigs that has a considerable economic impact in many swine-producing countries. In spite of its importance, knowledge about the global epidemiology and population structure of B. hyodysenteriae is limited. Progress in this area has been hampered by the lack of a low-cost, portable, and discriminatory method for strain typing. The aim of the current study was to develop and test a multiple-locus variable-number tandem-repeat analysis (MLVA) method that could be used in basic veterinary diagnostic microbiology laboratories equipped with PCR technology or in more advanced laboratories with access to capillary electrophoresis. Based on eight loci, and when performed on isolates from different farms in different countries, as well as type and reference strains, the MLVA technique developed was highly discriminatory (Hunter and Gaston discriminatory index, 0.938 [95% confidence interval, 0.9175 to 0.9584]) while retaining a high phylogenetic value. Using the technique, the species was shown to be diverse (44 MLVA types from 172 isolates and strains), although isolates were stable in herds over time. The population structure appeared to be clonal. The finding of B. hyodysenteriae MLVA type 3 in piggeries in three European countries, as well as other, related, strains in different countries, suggests that spreading of the pathogen via carrier pigs is likely. MLVA overcame drawbacks associated with previous typing techniques for B. hyodysenteriae and was a powerful method for epidemiologic and population structure studies on this important pathogenic spirochete.

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

PubMed Central

Jhunjhunwala, Suchit; van Zelm, Menno C.; Peak, Mandy M.; Cutchin, Steve; Riblet, Roy; van Dongen, Jacques J.M.; Grosveld, Frank G.; Knoch, Tobias A.; Murre, Cornelis

2009-01-01

SUMMARY The immunoglobulin heavy-chain (Igh) locus is organized into distinct regions that contain multiple variable (VH), diversity (DH), joining (JH) and constant (CH) coding elements. How the Igh locus is structured in 3D space is unknown. To probe the topography of the Igh locus, spatial distance distributions were determined between 12 genomic markers that span the entire Igh locus. Comparison of the distance distributions to computer simulations of alternative chromatin arrangements predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. Trilateration and triple-point angle measurements indicated the mean relative 3D positions of the VH, DH, JH, and CH elements, showed compartmentalization and striking conformational changes involving VH and DH-JH elements during early B cell development. In pro-B cells, the entire repertoire of VH regions (2 Mbp) appeared to have merged and juxtaposed to the DH elements, mechanistically permitting long-range genomic interactions to occur with relatively high frequency. PMID:18423198

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

Treesearch

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...

Should Farmers' Locus of Control Be Used in Extension?

ERIC Educational Resources Information Center

Nuthall, Peter L.

2010-01-01

To explore whether Farmers' Locus of Control (LOC) could be useful in agricultural extension programmes to improve managerial ability. This test records a farmer's belief in her/his control over production outcomes. A mail survey of 2300 New Zealand farmers was used to obtain a range of variables, and to measure their LOC using a question set…

The Effect of Locus of Control, Self-Efficacy, and Gender-Role Identity on Academic Performance Outcomes of Female College Students

ERIC Educational Resources Information Center

Sierra, Jade Simone

2013-01-01

This quantitative study investigated the predictive worthiness of the predictor variable indices--locus of control, self-efficacy, and gender identity--to ascertain if elevated levels of the predictors influence academic performance outcomes (individually as well as interactionally). The study theorized that students with increased levels of locus…

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2006-07-01

DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia MacCollin, M.D...COVERED (From - To) 1 Jul 2005 – 30 Jun 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Molecular Identification of the Schwannomatosis Locus 5b...Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Background: Schwannomatosis is a recently recognized third major type of

VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation

USGS Publications Warehouse

Vogler, Amy J.; Nottingham, Roxanne; Busch, Joseph D.; Sahl, Jason W.; Shuey, Megan M.; Foster, Jeffrey T.; Schupp, James M.; Smith, Susan; Rocke, Tonie E.; Klein, Paul; Wagner, David M.

2016-01-01

Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used.

An Outbreak of Food-Borne Typhoid Fever Due to Salmonella enterica Serotype Typhi in Japan Reported for the First Time in 16 Years

PubMed Central

Kobayashi, Tetsuro; Kutsuna, Satoshi; Hayakawa, Kayoko; Kato, Yasuyuki; Ohmagari, Norio; Uryu, Hideko; Yamada, Ritsuko; Kashiwa, Naoyuki; Nei, Takahito; Ehara, Akihito; Takei, Reiko; Mori, Nobuaki; Yamada, Yasuhiro; Hayasaka, Tomomi; Kagawa, Narito; Sugawara, Momoko; Suzaki, Ai; Takahashi, Yuno; Nishiyama, Hiroyuki; Morita, Masatomo; Izumiya, Hidemasa; Ohnishi, Makoto

2016-01-01

For the first time in 16 years, a food-borne outbreak of typhoid fever due to Salmonella enterica serotype Typhi was reported in Japan. Seven patients consumed food in an Indian buffet at a restaurant in the center of Tokyo, while one was a Nepali chef in the restaurant, an asymptomatic carrier and the implicated source of this outbreak. The multiple-locus variable-number tandem repeat analysis showed 100% consistency in the genomic sequence for five of the eight cases. PMID:26621565

Generalized Beliefs and Attitudes: Locus of Control and Science Attitudes in High School and College Students.

ERIC Educational Resources Information Center

Stuessy, Carol L.; Rowland, Paul McD.

Locus of control, a generalized belief about causality in one's personal life, was identified as a potential variable impinging upon the acquisition of science-related attitudes in classes of high school students from 10th grade biology, and 11th and 12th grade chemistry, and of college elementary education majors. Correlations of the…

The Ecology of Older Adult Locus of Control, Mindlessness, and Self-Esteem: A Review of Research and Educational Implications.

ERIC Educational Resources Information Center

Schiamberg, Lawrence B.; And Others

A review of research literature pertaining to locus of control in older adults and its application to social and educational settings indicates that reliable generalizations about the self-concept of older adults require a careful consideration of both personal and situational variables. Four separate processes are useful in understanding the…

Locus of Control and Self-Efficacy: Potential Mediators of Stress, Illness, and Utilization of Health Services in College Students

ERIC Educational Resources Information Center

Roddenberry, Angela; Renk, Kimberly

2010-01-01

Although many studies examine the biological phenomena that mediate the relationship between stress and illness, more research is needed regarding psychological variables that may mediate this relationship. Thus, the current study investigates the mediating effects of locus of control and self-efficacy in the relationships among stress, illness,…

Locus of Control and Values of Adult Learners in Schools of Business, Dentistry, and Education.

ERIC Educational Resources Information Center

Linder, Fredric; And Others

The locus of control orientation and value priorities of graduate students in business, dentistry, and education were studied, along with the relationship between these variables. Students in the study were attending Virginia Commonwealth University during the 1983-86 academic years and ranged in age from 18 to over 40 years old. There were 212…

Parenting Styles Influence on Locus of Control, Self-Efficacy and Academic Adjustment in College Students

ERIC Educational Resources Information Center

Mills, Kimberly Tracey

2010-01-01

The purpose of this study was to investigate the relationship between perceived parenting style, locus of control, self-efficacy, and student outcome (i.e. academic performance, GPA) in a sample of college students. The relationship among gender and ethnicity were also examined across these variables. There were 100 participants in this study,…

An Investigation into the Self-Handicapping Behaviors of Undergraduates in Terms of Academic Procrastination, the Locus of Control and Academic Success

ERIC Educational Resources Information Center

Akça, Figen

2012-01-01

The aim of this study was to investigate the relationship between self-handicapping, academic procrastination, the locus of control and academic success. The aim was also to determine whether these variables predicted self-handicapping behavior. The population of the study consisted of 263 undergraduates studying in different departments of the…

Gender Differences in Self-Concept, Locus of Control, and Goal Orientation in Mexican High-Achieving Students

ERIC Educational Resources Information Center

Valdés-Cuervo, Angel Alberto; Sánchez Escobedo, Pedro Antonio; Valadez-Sierra, María Dolores

2015-01-01

The study compares self-concept, locus of control, and goal orientation characteristics of male and female Mexican high school high-achieving students. Three scales were administered to 220 students; 106 (49%) were males and 114 (51%) females. By means of a discriminant analysis, both groups were compared in relation to the variables such as…

SE33 locus as a reliable genetic marker for forensic DNA analysis systems

PubMed

Bhinder, Munir Ahmad; Zahoor, Muhammad Yasir; Sadia, Haleema; Qasim, Muhammad; Perveen, Rukhsana; Anjum, Ghulam Murtaza; Iqbal, Muhammad; Ullah, Najeeb; Shehzad, Wasim; Tariq, Muhammad; Waryah, Ali Muhammad

2018-06-14

Background/aim: Genetic variation, an authentic tool of individual discrimination, is being used for forensic investigations worldwide. A missing result for even one out of 13-17 markers leads to an inconclusive report. Additional reliable markers are required to compensate such deficiencies. The SE33 locus has high genetic variability in different populations and is being used in forensic investigation systems in some countries. The purpose of the study was to assess the viability of use of the SE33 locus as a supportive marker for forensic DNA profiling. Materials and methods: Amplification of the SE33 locus was performed using the PowerPlex ES Monoplex System SE33 (Promega). After genotyping 204 Pakistani individuals, different genetic and forensic parameters for the SE33 locus were studied. Results: Genotyping of the SE33 locus revealed a total of 43 alleles including 3 novel alleles. Significant values of different forensic and genetic parameters including power of discrimination, power of exclusion, and polymorphism information content were observed. Conclusions: Addition of the SE33 locus in forensic DNA profiling may help to produce conclusive reports where results are inconclusive due to degraded evidence samples. The SE33 locus can confidently be used for Pakistani and neighboring populations having common ancestors from Iran to Central Asia, the Middle East, India and Turkey.

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2008-07-01

Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia MacCollin Scott R. Plotkin, M.D., Ph.D...DATES COVERED 1 July 2003 – 30 June 2008 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Molecular Identification of the Schwannomatosis Locus 5b...In 2007, mutations in the SMARCB1 tumor suppressor (also known as INI1 and hSNF5), which lies in the familial schwannomatosis candidate region, were

Social and cultural influences among Mexican border entrepreneurs.

PubMed

Díaz Bretones, Francisco; Cappello, Héctor M; Garcia, Pedro A

2009-06-01

Social and cultural conditions (including U.S. border and inland influence, role models within the family, and educational background) which affect locus of control and achievement motivation among Mexican entrepreneurs were explored among 64 selected entrepreneurs in two Mexican towns, one on the Mexico-U.S. border, the other located inland. Analyses showed that the border subsample scored higher on External locus of control; however, in both subsamples the father was an important element in the locus of control variable and the entrepreneur status. No statistically significant mean difference was noted for achievement motivation. Practical applications and limitations are discussed.

Internal predictors of burnout in psychiatric nurses: An Indian study

PubMed Central

Chakraborty, Rudraprosad; Chatterjee, Arunima; Chaudhury, Suprakash

2012-01-01

Background: Research has not adequately focused on the issue of burnout in Psychiatric nurses, despite the fact that they suffer considerable stress in their work. Till date no study has been conducted on burnout among psychiatric nurses in India. Further, there is a particular lack of research in internal variables predicting burnout in them. Aims: To determine whether there are any internal psychological factors relevant to burnout in psychiatric nurses in India. Materials and Methods: We recruited 101 psychiatric nurses scoring less than two in General Health Questionnaire, version 12 (GHQ-12) from two psychiatric hospitals after obtaining informed consent. All subjects filled up a sociodemographic data sheet along with global adjustment scale, emotional maturity scale, PGI general well-being scale, locus of control scale, and Copenhagen burnout inventory (CBI). Correlations between burnout and sociodemographic/clinical variables were done by Pearson's r or Spearman's rho. Signi ficant variables were entered in a stepwise multiple linear regression analysis with total burnout score as dependent variable. Results: Age, duration of total period of nursing, prior military training, locus of control, sense of general well-being, adjustment capabilities, and emotional maturity had significant relation with burnout. Of them, emotional maturity was the most significant protective factors against burnout along with adjustment capabilities, sense of physical well-being, and military training in decreasing significance. Together they explained 41% variation in total burnout score which is significant at <0.001 level. An internal locus of control was inversely correlated with burnout, but failed to predict it in regression analysis. Conclusion: Emotional maturity, adjustability, sense of general physical well-being as well as prior military training significantly predicted lower burnout. Of them, emotional maturity was the most important predictor. Internal locus of control was also correlated with lower burnout. PMID:24250044

Internal predictors of burnout in psychiatric nurses: An Indian study.

PubMed

Chakraborty, Rudraprosad; Chatterjee, Arunima; Chaudhury, Suprakash

2012-07-01

Research has not adequately focused on the issue of burnout in Psychiatric nurses, despite the fact that they suffer considerable stress in their work. Till date no study has been conducted on burnout among psychiatric nurses in India. Further, there is a particular lack of research in internal variables predicting burnout in them. To determine whether there are any internal psychological factors relevant to burnout in psychiatric nurses in India. We recruited 101 psychiatric nurses scoring less than two in General Health Questionnaire, version 12 (GHQ-12) from two psychiatric hospitals after obtaining informed consent. All subjects filled up a sociodemographic data sheet along with global adjustment scale, emotional maturity scale, PGI general well-being scale, locus of control scale, and Copenhagen burnout inventory (CBI). Correlations between burnout and sociodemographic/clinical variables were done by Pearson's r or Spearman's rho. Signi ficant variables were entered in a stepwise multiple linear regression analysis with total burnout score as dependent variable. Age, duration of total period of nursing, prior military training, locus of control, sense of general well-being, adjustment capabilities, and emotional maturity had significant relation with burnout. Of them, emotional maturity was the most significant protective factors against burnout along with adjustment capabilities, sense of physical well-being, and military training in decreasing significance. Together they explained 41% variation in total burnout score which is significant at <0.001 level. An internal locus of control was inversely correlated with burnout, but failed to predict it in regression analysis. Emotional maturity, adjustability, sense of general physical well-being as well as prior military training significantly predicted lower burnout. Of them, emotional maturity was the most important predictor. Internal locus of control was also correlated with lower burnout.

Content and organization of the human Ig VH locus: definition of three new VH families and linkage to the Ig CH locus.

PubMed Central

Berman, J E; Mellis, S J; Pollock, R; Smith, C L; Suh, H; Heinke, B; Kowal, C; Surti, U; Chess, L; Cantor, C R

1988-01-01

We present a detailed analysis of the content and organization of the human immunoglobulin VH locus. Human VH genes representing five distinct families were isolated, including novel members belonging to two out of three of the known VH gene families (VH1 and VH3) as well as members of three new families (VH4, VH5, and VH6). We report the nucleotide sequence of 21 novel human VH genes, many of which belong to the three new VH gene families. In addition, we provide a preliminary analysis of the organization of these gene segments over the full extent of the locus. We find that the five multi-segment families (VH1-5) have members interspersed over nearly the full 1500-2000 kb of the VH locus, and estimate that the entire heavy chain locus covers 2500 kb or less. Finally, we provide the first report of the physical linkage of the variable and constant loci of a human Ig gene family by demonstrating that the most proximal known human VH segments lie within 100 kb of the constant region locus. Images PMID:3396540

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2004-07-01

AD Award Number: DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia M. MacCollin, M.D...COVERED (Leave blank) July 2004 Annual (1 Jul 2003 - 30 Jun 2004) 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Molecular Identification of the Schwannomatosis ...DISTRIBUTION CODE Approved for Public Release; Distribution Unlimited 13. ABSTRACT (Maximum 200 Words) Background: Schwannomatosis is a recently recognized

Characterization of 23 polymorphic SSR markers in Salix humboldtiana (Salicaceae) using next-generation sequencing and cross-amplification from related species1

PubMed Central

Bozzi, Jorge A.; Liepelt, Sascha; Ohneiser, Sebastian; Gallo, Leonardo A.; Marchelli, Paula; Leyer, Ilona; Ziegenhagen, Birgit; Mengel, Christina

2015-01-01

Premise of the study: We present a set of 23 polymorphic nuclear microsatellite loci, 18 of which are identified for the first time within the riparian species Salix humboldtiana (Salicaceae) using next-generation sequencing. Methods and Results To characterize the 23 loci, up to 60 individuals were sampled and genotyped at each locus. The number of alleles ranged from two to eight, with an average of 4.43 alleles per locus. The effective number of alleles ranged from 1.15 to 3.09 per locus, and allelic richness ranged from 2.00 to 7.73 alleles per locus. Conclusions The new marker set will be used for future studies of genetic diversity and differentiation as well as for unraveling spatial genetic structures in S. humboldtiana populations in northern Patagonia, Argentina. PMID:25909042

Linkage analysis with chromosome 9 markers in hereditary essential tremor.

PubMed

Conway, D; Bain, P G; Warner, T T; Davis, M B; Findley, L J; Thompson, P D; Marsden, C D; Harding, A E

1993-07-01

Hereditary essential tremor (ET) is an autosomal dominant disorder with variable expression and reduced penetrance. A tremor indistinguishable from ET may be observed in patients with autosomal dominant idiopathic torsion dystonia (ITD), in which the disease locus has been mapped to 9q32-34 in some kindreds, tightly linked to the argininosuccinate synthetase (ASS) locus. We performed linkage analysis in 15 families with ET containing 60 definitely affected individuals, using dinucleotide repeat polymorphisms at the ASS locus and the Abelson locus (ABL). Cumulative lod scores were -19.5 for ASS and -10.8 for ABL at a recombination fraction of 0.01, and tight linkage to ASS was excluded individually in 11 of the families. These data indicate that the ET gene is not allelic to that causing ITD.

Investigating a tuberculosis cluster among Filipino health care workers in a low-incidence country.

PubMed

Davidson, J A; Fulton, N; Thomas, H L; Lalor, M K; Zenner, D; Brown, T; Murphy, S; Anderson, L F

2018-03-01

Nearly 8% of adult tuberculosis (TB) cases in England, Wales and Northern Ireland (EW&NI) occur among health care workers (HCWs), the majority of whom are from high TB incidence countries. To determine if a TB cluster containing multiple HCWs was due to nosocomial transmission. A cluster of TB cases notified in EW&NI from 2009 to 2014, with indistinguishable 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) profiles, was identified through routine national cluster review. Cases were investigated to identify epidemiological links, and occupational health (OH) information was collected for HCW cases. To further discriminate strains, typing of eight additional loci was conducted. Of the 53 cases identified, 22 were HCWs. The majority (n = 43), including 21 HCWs, were born in the Philippines. Additional typing split the cluster into three subclusters and seven unique strains. No epidemiological links were identified beyond one household and a common residential area. HCWs in this cluster received no or inadequate OH assessment. The MIRU-VNTR profile of this cluster probably reflects common endemic strains circulating in the Philippines, with reactivation occurring in the UK. Furthermore, 32-locus typing showed that 24-locus MIRU-VNTR failed to distinguish strain diversity. The lack of OH assessment indicates that latent tuberculous infection could have been identified and treated, thereby preventing active cases from occurring.

Variability and genetics of spacer DNA sequences between the ribosomal-RNA genes of hexaploid wheat (Triticum aestivum).

PubMed

May, C E; Appels, R

1987-09-01

Using restriction enzyme digests of genomic DNA extracted from the leaves of 25 hexaploid wheat (Triticum aestivum L. em. Thell.) cultivars and their hybrids, restriction fragment length polymorphisms of the spacer DNA which separates the ribosomal-RNA genes have been examined. (From one to three thousand of these genes are borne on chromosomes 1B and 6B of hexaploid wheat). The data show that there are three distinct alleles of the 1B locus, designated Nor-B1a, Nor-B1b, and Nor-B1c, and at least five allelic variants of the 6B locus, designated Nor-B2a, Nor-B2b, Nor-B2c, Nor-B2d, and Nor-B2e. A further, previously reported allele on 6B has been named Nor-B2f. Chromosome 5D has only one allelic variant, Nor-D3. Whereas the major spacer variants of the 1B alleles apparently differ by the loss or gain of one or two of the 133 bp sub-repeat units within the spacer DNA, the 6B allelic variants show major differences in their compositions and lengths. This may be related to the greater number of rDNA repeat units at this locus. The practical implications of these differences and their application to wheat breeding are discussed.

Variability in CNR1 locus influences protein intake and smoking status in the Central-European population.

PubMed

Bienertova-Vasku, Julie; Bienert, Petr; Slovackova, Lenka; Sablikova, Lenka; Piskackova, Zlata; Forejt, Martin; Splichal, Zbynek; Zlamal, Filip; Vasku, Anna

2012-07-01

The endocannabinoid receptor 1 (CB1) is encoded by the CNR1 gene and has been recently recognized to play an important role in the regulation of satiety and feeding behaviour with a huge potential of modulating metabolic response and feeding control. The aim of the study was to investigate the potential of three selected single nucleotide polymorphisms (SNPs) in the CNR1 locus on native dietary composition in the Central-European Caucasian population. A total of 258 unrelated individuals originating from the Central-European Caucasian population were enrolled into the study and rs1049353, rs12720071, and rs806368 polymorphisms in CNR1 locus were examined in these individuals using PCR-based methodology. Body composition was assessed using a bioimpedance method, various anthropometric parameters were investigated (waist and hip circumference, skin folds), and native dietary composition was analysed using 7-day food records as well as a food frequency questionnaire. Allelic variations and common haplotypes in the CNR1 gene were associated with the daily intake of proteins, fluids, and fibre, regardless of the physical activity of the individuals. The common haplotype in the CNR1 gene was associated with self-reported smoking (number of cigarettes per day, smoking years). Our results indicate that specific genetic variations in the CNR1 gene may act as susceptibility markers for specific dietary composition in the Central-European population.

Lambda Red recombinase-mediated integration of the high molecular weight DNA into the Escherichia coli chromosome.

PubMed

Juhas, Mario; Ajioka, James W

2016-10-05

Escherichia coli K-12 is a frequently used host for a number of synthetic biology and biotechnology applications and chassis for the development of the minimal cell factories. Novel approaches for integrating high molecular weight DNA into the E. coli chromosome would therefore greatly facilitate engineering efforts in this bacterium. We developed a reliable and flexible lambda Red recombinase-based system, which utilizes overlapping DNA fragments for integration of the high molecular weight DNA into the E. coli chromosome. Our chromosomal integration strategy can be used to integrate high molecular weight DNA of variable length into any non-essential locus in the E. coli chromosome. Using this approach we integrated 15 kb DNA encoding sucrose catabolism and lactose metabolism and transport operons into the fliK locus of the flagellar region 3b in the E. coli K12 MG1655 chromosome. Furthermore, with this system we integrated 50 kb of Bacillus subtilis 168 DNA into two target sites in the E. coli K12 MG1655 chromosome. The chromosomal integrations into the fliK locus occurred with high efficiency, inhibited motility, and did not have a negative effect on the growth of E. coli. In addition to the rational design of synthetic biology devices, our high molecular weight DNA chromosomal integration system will facilitate metabolic and genome-scale engineering of E. coli.

[Forensic hematology genetics--paternity testing].

PubMed

Kratzer, A; Bär, W

1997-05-01

In Switzerland paternity investigations are carried out using DNA analysis only since 1991. DNA patterns are inherited and only with the exception of genetically identical twins they are different in everyone and therefore unique to an individual. Hence DNA-systems are an excellent tool to resolve paternity disputes. DNA polymorphisms used for paternity diagnosis are length polymorphisms of the highly polymorphic VNTR loci [variable number of tandem repeats]. The most frequently applied systems are the DNA single locus systems. In addition to the DNA single locus systems the application of PCR (PCR = polymerase chain reaction) based DNA systems has increased particularly in difficult deficiency cases or in cases where only small evidential samples or partially degraded DNA are available. Normally four independent DNA single probes are used to produce a DNA profile from the mother, the child and the alleged father. A child inherits half the DNA patterns from its mother and the other half from its true biological father. If an alleged father doesn't possess the paternal specific DNA pattern in his DNA profile he is excluded from the paternity. In case of non-exclusion the probability for paternity is calculated according to Essen-Möller. When applying four highly polymorphic DNA single locus systems the biostatistical evaluation leads always to W-values exceeding 99.8% [= required value for positive proof of paternity]. DNA analysis is currently the best available method to achieve such effective conclusions in paternity investigations.

Sylvatic plague reduces genetic variability in black-tailed prairie dogs.

PubMed

Trudeau, Kristie M; Britten, Hugh B; Restani, Marco

2004-04-01

Small, isolated populations are vulnerable to loss of genetic diversity through in-breeding and genetic drift. Sylvatic plague due to infection by the bacterium Yersinia pestis caused an epizootic in the early 1990s resullting in declines and extirpations of many black-tailed prairie dog (Cynomys ludovicianus) colonies in north-central Montana, USA. Plague-induced population bottlenecks may contribute to significant reductions in genetic variability. In contrast, gene flow maintains genetic variability within colonies. We investigated the impacts of the plague epizootic and distance to nearest colony on levels of genetic variability in six prairie dog colonies sampled between June 1999 and July 2001 using 24 variable randomly amplified polymorphic DNA (RAPD) markers. Number of effective alleles per locus (n(e)) and gene diversity (h) were significantly decreased in the three colonies affected by plague that were recovering from the resulting bottlenecks compared with the three colonies that did not experience plague. Genetic variability was not significantly affected by geographic distance between colonies. The majority of variance in gene fieqnencies was found within prairie clog colonies. Conservation of genetic variability in black-tailed prairie dogs will require the preservation of both large and small colony complexes and the gene flow amonog them.

Effects of Social Reinforcement, Locus of Control, and Cognitive Style on Concept Learning among Retarded Children.

ERIC Educational Resources Information Center

Panda, Kailas C.

To examine the effects of locus of control (the extent to which an individual feels he has control over his own behavior) and cognitive style variables on learning deficits among mentally handicapped children, 80 mentally retarded boys (IQ 50 to 83, age 160 to 196 months) were administered a battery of tests. Analyses of student performance…

The Interrelationship of Social Anxiety with Anxiety, Depression, Locus of Control, Ways of Coping and Ego Strength amongst University Students

ERIC Educational Resources Information Center

Shepherd, Robin-Marie; Edelman, Robert J.

2009-01-01

This is the first study to investigate the interrelationship of social anxiety with the variables anxiety, depression, locus of control, ego strength and ways of coping in a sample of university students. There were high scores of social anxiety which were related to high scores on measures of anxiety and depression, low ego strength, external…

Resilience of Greek Youth at an Educational Transition Point: The Role of Locus of Control and Coping Strategies as Resources

ERIC Educational Resources Information Center

Leontopoulou, Sophia

2006-01-01

Variable--and person--focused approaches were applied to study the resilient outcomes of 326 Greek male and female 1st year university students at a major educational transition point. Results indicated that resilience was related to both cognitive and behavioural psychosocial resources in late adolescence. Locus of control emerged as an important…

An Examination of Meaning in Life, Satisfaction with Life, Self-Concept and Locus of Control among Teachers

ERIC Educational Resources Information Center

Tas, Ibrahim; Iskender, Murat

2018-01-01

The aim of this study is to examine meaning in life, satisfaction with life, self-concept and locus of control among teachers by several variables. The research group was composed of 363 teachers (114 [40%] women, 219 [60%] men) working in several districts of Istanbul. The data were collected with Meaning in Life Scale (MLS), Satisfaction with…

Multi-locus variable-number tandem repeat analysis of Bordetella pertussis isolates circulating in Poland in the period 1959-2013.

PubMed

Mosiej, Ewa; Krysztopa-Grzybowska, Katarzyna; Polak, Maciej; Prygiel, Marta; Lutyńska, Anna

2017-06-01

Despite the long history of pertussis vaccination and high vaccination coverage in Poland and many other developed countries, pertussis incidence rates have increased substantially, making whooping cough one of the most prevalent vaccine-preventable diseases. Among the factors potentially involved in pertussis resurgence, the adaptation of the Bordetella pertussis population to country-specific vaccine-induced immunity through selection of non-vaccine-type strains still needs detailed studies. Multi-locus variable-number tandem repeat analysis (MLVA), also linked to MLST and PFGE profiling, was applied to trace the genetic changes in the B. pertussis population circulating in Poland in the period 1959-2013 versus country-specific vaccine strains. Generally, among 174 B. pertussis isolates, 31 MLVA types were detected, of which 11 were not described previously. The predominant MLVA types of recent isolates in Poland were different from those of the typical isolates circulating in other European countries. The MT27 type, currently predominant in Europe, was rarely seen and detected in only five isolates among all studied. The features of the vaccine strains used for production of the pertussis component of a national whole-cell diphtheria-tetanus-pertussis (DTP) vaccine, as studied by MLVA and MLST tools, were found to not match those observed in the currently circulating B. pertussis isolates in Poland. Differences traced by MLVA in relation to the MLST and PFGE profiling confirmed that the B. pertussis strain types currently observed elsewhere in Europe, even if appearing in Poland, were not able to successfully disseminate within a human population in Poland that has been vaccinated with a whole-cell pertussis vaccine not used in other countries.

Multiple-locus variable number of tandem repeats fingerprinting (MLVF) and virulence factor analysis of methicillin resistant Staphylococcus aureus SCCmec type III.

PubMed

Emaneini, Mohammad; Jabalameli, Leila; Iman-Eini, Hossein; Aligholi, Marzieh; Ghasemi, Amir; Nakhjavani, Farrokh Akbari; Taherikalani, Morovat; Khoramian, Babak; Asadollahi, Parisa; Jabalameli, Fereshteh

2011-01-01

Methicillin resistant Staphylococcus aureus (MRSA), particularly strains with type III staphylococcal cassette chromosome mec (SCCmec), represent a serious human pathogen in Tehran, Iran. The disease-causing capability depends on their ability to produce a wide variety of virulent factors. The prevalence of exotoxin genes and multiple-locus variable number of tandem repeats fingerprinting (MLVF) profile among MRSA isolates, from patients in Tehran, was evaluated by PCR and Multiplex-PCR. The MLVF typing of 144 MRSA isolates with type III SCCmec produced 5 different MLVF types. Generally, 97.2% (140/144) of all the isolates were positive for at least one of the tested exotoxin genes. The most prevalent genes were hld, found in 87.5% (126/144) of the isolates followed by lukE-lukD and hla found in 72.9% (105/144) and 70.1% (101/144) of the isolates, respectively. The tst gene, belonging to MLVF types I, IV and V, was found among three of the isolates from blood and wound samples. The sea gene was detected in 58.3% (84/144) of the isolates and the sed and see genes were found in one isolate with MLVF type V. The coexistence of genes was observed in the 87.5% (126/144) of the isolates. The rate of coexistence of hld with lukE-lukD, hla with lukE-lukD and sea with lukE-lukD were 66.7% (96/144), 44.4% (64/144) and 44.4% (64/144), respectively. The present study demonstrated that MRSA strains with type III SCCmec show different MLVF patterns and exotoxin profiles.

Leptospira interrogans serovars Bratislava and Muenchen animal infections: Implications for epidemiology and control.

PubMed

Arent, Z; Frizzell, C; Gilmore, C; Allen, A; Ellis, W A

2016-07-15

Strains of Leptospira interrogans belonging to two very closely related serovars - Bratislava and Muenchen - have been associated with disease in domestic animals, in particular pigs, but also in horses and dogs. Similar strains have also been recovered from various wildlife species. Their epidemiology is poorly understood. Two hundred and forty seven such isolates, from UK domestic animal and wildlife species, were examined by restriction endonuclease analysis in an attempt to elucidate their epidemiology. A representative sub-sample of 65 of these isolates was further examined by multiple-locus variable-number tandem repeat analysis and 22 by secY sequencing. Ten restriction pattern types were identified. The majority of isolates fell into one of three restriction endonuclease analysis pattern types designated B2a, B2b and M2a. B2a was ubiquitous and was isolated from 10 species and represented the majority of the horse and all dog isolates. B2b was very different, being isolated only from pigs, indicating that this type was maintained by pigs. The pattern M2a was reported for the majority of isolates from pigs but also was common in small rodents isolates. Five restriction pattern types were found only in wildlife suggesting that they are unlikely to pose a disease threat to domestic animals. Multiple-locus variable-number tandem repeat analysis identified six clusters. The REA types B2a and B2b were all found in one MLVA cluster while the majority of the M2a strains examined occurred in another cluster. The secY sequencing detected only one sequence type, clustered with other serovars of Leptospira interrogans. Copyright © 2016 Elsevier B.V. All rights reserved.

Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013.

PubMed

Tian, Guo-Zhong; Cui, Bu-Yun; Piao, Dong-Ri; Zhao, Hong-Yan; Li, Lan-Yu; Liu, Xi; Xiao, Pei; Zhao, Zhong-Zhi; Xu, Li-Qing; Jiang, Hai; Li, Zhen-Jun

2017-05-02

Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. IDOP-D-16-00101.

Recent transmission of drug-resistant Mycobacterium tuberculosis in a prison population in southern Brazil.

PubMed

Reis, Ana Julia; David, Simone Maria Martini de; Nunes, Luciana de Souza; Valim, Andreia Rosane de Moura; Possuelo, Lia Gonçalves

2016-01-01

We conducted a cross-sectional, retrospective study, characterized by classical and molecular epidemiology, involving M. tuberculosis isolates from a regional prison in southern Brazil. Between January of 2011 and August of 2014, 379 prisoners underwent sputum smear microscopy and culture; 53 (13.9%) were diagnosed with active tuberculosis. Of those, 8 (22.9%) presented with isoniazid-resistant tuberculosis. Strain genotyping was carried out by 15-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat analysis; 68.6% of the patients were distributed into five clusters, and 87.5% of the resistant cases were in the same cluster. The frequency of drug-resistant tuberculosis cases and the rate of recent transmission were high. Our data suggest the need to implement an effective tuberculosis control program within the prison system. RESUMO Estudo transversal, retrospectivo, com isolados de M. tuberculosis de pacientes de um presídio regional no sul do Brasil, caracterizado através de epidemiologia clássica e molecular. Entre janeiro de 2011 e agosto de 2014, 379 detentos foram submetidos a baciloscopia e cultura, sendo 53 (13,9%) diagnosticados com tuberculose ativa. Desses, 8 (22,9%) apresentavam tuberculose resistente a isoniazida. A genotipagem das cepas foi realizada por 15-locus mycobacterial interspersed repetitive units-variable number of tandem repeat analysis; 68,6% dos pacientes estavam distribuídos em cinco clusters, e 87,5% dos casos resistentes estavam em um mesmo cluster. Verificou-se uma frequência elevada de casos de resistência e alta taxa de transmissão recente. Estes dados sugerem a necessidade da implantação de um programa efetivo de controle da tuberculose no sistema prisional.

Longitudinal prevalence and molecular typing of Escherichia coli O157:H7 by use of multiple-locus variable-number tandem-repeat analysis and pulsed-field gel electrophoresis in fecal samples collected from a range-based herd of beef cattle in California.

PubMed

Kondo, Sonoko; Hoar, Bruce R; Villanueva, Veronica; Mandrell, Robert E; Atwill, Edward R

2010-11-01

To evaluate seasonal patterns and risk factors for Escherichia coli O157:H7 in feces in a beef cattle herd and determine strain diversity and transition in E coli over time by use of multiple-locus variable-number tandem-repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE). 456 samples of freshly passed feces collected over a 1-year period from cattle in a range-based cow-calf operation located in the foothills of the Sierra Nevada Mountains in California. E coli O157:H7 was recovered from feces by use of immunomagnetic separation and 2 selective media. Virulence factors were detected via reverse transcriptase-PCR assay. Escherichia coli O157:H7 isolates were subtyped with MLVA and PFGE. Prevalence estimates were calculated and significant risk factors determined. A dendrogram was constructed on the basis of results of MLVA typing. Overall prevalence estimate for E coli O157:H7 was 10.5%, with the prevalence lowest during the winter. Mean temperature during the 30 days before collection of samples was significantly associated with prevalence of E coli O157:H7 in feces. Nineteen MLVA and 12 PFGE types were identified. A seasonal pattern was detected for prevalence of E coli O157:H7 in feces collected from beef cattle in California. Subtyping via MLVA and PFGE revealed a diversity of E coli O157:H7 strains in a cow-calf operation and noteworthy turnover of predominant types. Given the importance of accurately determining sources of contamination in investigations of disease outbreaks in humans, MLVA combined with PFGE should be powerful tools for epidemiologists.

Verocytotoxigenic Escherichia coli O157 in beef and sheep abattoirs in Ireland and characterisation of isolates by Pulsed-Field Gel Electrophoresis and Multi-Locus Variable Number of Tandem Repeat Analysis.

PubMed

Prendergast, Deirdre M; Lendrum, Lynsey; Pearce, Rachel; Ball, Caroline; McLernon, Joanne; O'Grady, Don; Scott, Lourda; Fanning, Seamus; Egan, John; Gutierrez, Montserrat

2011-01-05

This study aimed to investigate verocytotoxigenic Escherichia coli O157 in the largest beef and sheep slaughter plants in Ireland over a one-year period. Samples consisted of pooled rectal swabs (n=407) and pooled carcass swabs (n=407) from 5 animals belonging to the same herd or flock and minced meat (n=91) from the same sampling date. E. coli O157 isolates were characterised using PCR for a range of genes, i.e. 16S, rfbE, fliC, vtx1, vtx2, eaeA and confirmed VTEC O157 isolates were tested for antimicrobial susceptibility and typed using Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA). VTEC O157 was isolated from 7.6% and 3.9% of bovine rectal and carcass swab samples and from 5.8% and 2.9% of ovine rectal and carcass swab samples respectively. None of the bovine minced meat samples (n=77) and only one of the 14 ovine minced meat samples was positive for VTEC O157. Following PFGE and MLVA, cross contamination from faeces to carcasses was identified. While PFGE and MLVA identified the same clusters for highly related strains, MLVA discriminated better than PFGE in addition to being more rapid and less labour intensive. Results showed that cattle and sheep presented for slaughter in Ireland harbour VTEC O157, and although the levels entering the food chain are low, this should not be overlooked as possible sources of zoonotic infection; molecular typing was able to demonstrate relationships among strains and could be used to elucidate the sources of human infection. Copyright © 2010 Elsevier B.V. All rights reserved.

The complexity of selection at the major primate beta-defensin locus.

PubMed

Semple, Colin A M; Maxwell, Alison; Gautier, Philippe; Kilanowski, Fiona M; Eastwood, Hayden; Barran, Perdita E; Dorin, Julia R

2005-05-18

We have examined the evolution of the genes at the major human beta-defensin locus and the orthologous loci in a range of other primates and mouse. For the first time these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as the ancient past. We have used a combination of maximum likelihood based tests and a maximum parsimony based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. Consequently variable selective pressures have acted on beta-defensin genes in different evolutionary lineages, with episodes both of negative, and more rarely positive selection, during the divergence of primates. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel, rodent-specific beta-defensin genes. These observations allow a fuller understanding of the evolution of mammalian innate immunity. In both the rodent and primate lineages, sites in the second exon have been subject to positive selection and by implication are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions predicted to be important for the specificity of the antimicrobial or chemoattractant properties of beta-defensins. Surprisingly, sites within the prepropeptide region were also implicated as being subject to significant positive selection, suggesting previously unappreciated functional significance for this region. Identification of these putatively functional sites has important implications for our understanding of beta-defensin function and for novel antibiotic design.

Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.)

PubMed Central

Bakker, Erin; de Boer, Jan; van der Vossen, Edwin; Achenbach, Ute; Golas, Tomasz; Suryaningrat, Suwardi; Smant, Geert; Bakker, Jaap; Goverse, Aska

2010-01-01

The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1472-9) contains supplementary material, which is available to authorized users. PMID:21049265

Study of mathematical models of mutation and selection in multi-locus systems. Annual progress report, October 1, 1980-September 30, 1981

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewontin, R C

1981-01-01

During the past year, research has been devoted to two related studies of two-locus systems under natural selection and one on selection in haplo-diploid organisms. The principal results are: (1) Numerical studies were made of 2 locus selection models with asymmetric fitnesses. These were created by perturbing the fitness matrices of symmetric models whose results are known analytically. A complete classification of solved models has been made and all perturbations of these have been undertaken. The result is that all models lead to three classes of equilibrium structure. All are characterized by multiple equilbria with small linkage disequilibria under loosemore » linkage and high complementarity equilibria under tight linkage. In some cases there is gene fixation at intermediate linkage. (2) It has been shown that selection may favor more recombination, contrary to the usual expectation, if multiple locus polymorphisms are maintained by a mechanism other than marginal overdominance. This may be the result of mutation-selection balance or frequency-dependent selection. (3) In a haplo-diploid system in which diploid males are lethal (as in bees and braconid wasps) the number of sex alleles that can be maintained depends both on breeding size and the number of colonies. Simulations show that the steady number is sensitive to the number of colonies but insensitive to the number of matings. Thirty-five to fifty colonies are sufficient to maintain very large numbers of sex alleles.« less

Genetic heterogeneity in psoriasis vulgaris based on linkage analyses of a large family material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wahlstroem, J.; Swanbeck, G.; Inerot, A.

1994-09-01

Information on psoriasis among parents and siblings in 14,008 families has been collected. On the basis of this material, evidence for monogenetic autosomal recessive inheritance of psoriasis has recently been presented. Indications from more than one type of non-pustular psoriasis has been obtained from the population genetic data. Molecular genetic linkage analysis of psoriasis to a number of polymorphic genetic markers for a large number of families has been made. It is apparent that there is genetic heterogeneity in a psoriasis population with regard to psoriasis genes. Using the computer program Linkage 5.0 and a formula for heterogeneity, a lodscoremore » over 3.0 for one locus has been obtained. This locus has further been confirmed by several other markers in the vicinity. The locus found is linked to slightly over half of the families, indicating that there are more genetically independent types of psoriasis. The age at onset of those families that are apparently linked to this locus have a slightly higher age at onset than those not linked to that locus but with a considerable overlap. In spite of close coverage of the whole chromosomes number 6 and 17, no linkage has been found in this regions. This indicates that neither the HLA region nor the region earlier found to be involved in one family with psoriasis are primarily involved in our families.« less

Beta-defensin genomic copy number is not a modifier locus for cystic fibrosis

PubMed Central

Hollox, Edward J; Davies, Jane; Griesenbach, Uta; Burgess, Juliana; Alton, Eric WFW; Armour, John AL

2005-01-01

Human beta-defensin 2 (DEFB4, also known as DEFB2 or hBD-2) is a salt-sensitive antimicrobial protein that is expressed in lung epithelia. Previous work has shown that it is encoded in a cluster of beta-defensin genes at 8p23.1, which varies in copy number between 2 and 12 in different individuals. We determined the copy number of this locus in 355 patients with cystic fibrosis (CF), and tested for correlation between beta-defensin cluster genomic copy number and lung disease associated with CF. No significant association was found. PMID:16336654

Factors influencing adherence to psychopharmacological medications in psychiatric patients: a structural equation modeling approach.

PubMed

De Las Cuevas, Carlos; de Leon, Jose; Peñate, Wenceslao; Betancort, Moisés

2017-01-01

To evaluate pathways through which sociodemographic, clinical, attitudinal, and perceived health control variables impact psychiatric patients' adherence to psychopharmacological medications. A sample of 966 consecutive psychiatric outpatients was studied. The variables were sociodemographic (age, gender, and education), clinical (diagnoses, drug treatment, and treatment duration), attitudinal (attitudes toward psychopharmacological medication and preferences regarding participation in decision-making), perception of control over health (health locus of control, self-efficacy, and psychological reactance), and level of adherence to psychopharmacological medications. Structural equation modeling was applied to examine the nonstraightforward relationships and the interactive effects among the analyzed variables. Structural equation modeling demonstrated that psychiatric patients' treatment adherence was associated: 1) negatively with cognitive psychological reactance (adherence decreased as cognitive psychological reactance increased), 2) positively with patients' trust in their psychiatrists (doctors' subscale), 3) negatively with patients' belief that they are in control of their mental health and that their mental health depends on their own actions (internal subscale), and 4) positively (although weakly) with age. Self-efficacy indirectly influenced treatment adherence through internal health locus of control. This study provides support for the hypothesis that perceived health control variables play a relevant role in psychiatric patients' adherence to psychopharmacological medications. The findings highlight the importance of considering prospective studies of patients' psychological reactance and health locus of control as they may be clinically relevant factors contributing to adherence to psychopharmacological medications.

Mutation affecting the expression of immunoglobulin variable regions in the rabbit.

PubMed

Kelus, A S; Weiss, S

1986-07-01

We have found a variant of the allotype allele a2 in the rabbit, which presumably arose by mutation, that segregates as expected for an allele at the a locus. This allele is called "ali" and the corresponding rabbit strain is called "Alicia." In heterozygous animals (ali/a1 and ali/a3) the concentration of a2 molecules is lower by a factor of 1000 than in standard a2/a2 homozygotes. In homozygous ali/ali individuals the a2 concentration varies with age--i.e., very low in young rabbits and higher in older ones--but it never reaches normal levels. The low level of a2 is compensated by increased amounts of a-negative molecules. Southern blot analysis did not reveal any gross changes in the intron between JH and C mu (joining region of immunoglobulin heavy chain and constant region of immunoglobulin mu chain) or in the number of VH gene segments encoding a locus specificities. We suggest that the ali phenotype is due to a mutation in a control element.

Mutation affecting the expression of immunoglobulin variable regions in the rabbit.

PubMed Central

Kelus, A S; Weiss, S

1986-01-01

We have found a variant of the allotype allele a2 in the rabbit, which presumably arose by mutation, that segregates as expected for an allele at the a locus. This allele is called "ali" and the corresponding rabbit strain is called "Alicia." In heterozygous animals (ali/a1 and ali/a3) the concentration of a2 molecules is lower by a factor of 1000 than in standard a2/a2 homozygotes. In homozygous ali/ali individuals the a2 concentration varies with age--i.e., very low in young rabbits and higher in older ones--but it never reaches normal levels. The low level of a2 is compensated by increased amounts of a-negative molecules. Southern blot analysis did not reveal any gross changes in the intron between JH and C mu (joining region of immunoglobulin heavy chain and constant region of immunoglobulin mu chain) or in the number of VH gene segments encoding a locus specificities. We suggest that the ali phenotype is due to a mutation in a control element. Images PMID:3014517

The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain suggests the importance of clan III variable segments in repertoire diversity

USGS Publications Warehouse

Breaux, Breanna; Deiss, Thaddeus C.; Chen, Patricia L.; Cruz-Schneider, Maria Paula; Sena, Leonardo; Hunter, Margaret E.; Bonde, Robert K.; Criscitiello, Michael F.

2017-01-01

Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis. The Florida manatee has low V(D)J combinatorial diversity (3744 potential combinations) and few constant region isotypes. They also lack clan III V segments, which may have caused reduced VH segment numbers. However, we found productive somatic hypermutation concentrated in the complementarity determining regions. In conclusion, manatees have limited IGHV clan and combinatorial diversity. This suggests that clan III V segments are essential for maintaining IgH locus diversity.

Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone ( Haliotis discus hannai)

NASA Astrophysics Data System (ADS)

Li, Qi; Shu, Jing; Zhao, Cui; Liu, Shikai; Kong, Lingfeng; Zheng, Xiaodong

2010-01-01

Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone ( Haliotis discus hannai). Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences, after redundancy elimination. Seventeen polymorphic EST-SSRs were developed. The number of alleles per locus varied from 2-17, with an average of 6.8 alleles per locus. The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922, respectively. Twelve of the 17 loci (70.6%) were successfully amplified in H. diversicolor. Seventeen loci segregated in three families, with three showing the presence of null alleles (17.6%). The adequate level of variability and low frequency of null alleles observed in H. discus hannai, together with the high rate of transportability across Haliotis species, make this set of EST-SSR markers an important tool for comparative mapping, marker-assisted selection, and evolutionary studies, not only in the Pacific abalone, but also in related species.

The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

PubMed

Diaz, Maureen H; Winchell, Jonas M

2016-01-01

Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii).

PubMed

Cai, Ruibo; Shafer, Aaron B A; Laguardia, Alice; Lin, Zhenzhen; Liu, Shuqiang; Hu, Defu

2015-11-25

The forest musk deer (Moschus berezovskii) is a high elevation species distributed across western China and northern Vietnam. Once abundant, habitat loss and poaching has led to a dramatic decrease in population numbers prompting the IUCN to list the species as endangered. Here, we characterized the genetic diversity of a Major Histocompatibility Complex (MHC) locus and teased apart driving factors shaping its variation. Seven DRB exon 2 alleles were identified among a group of randomly sampled forest musk deer from a captive population in the Sichuan province of China. Compared to other endangered or captive ungulates, forest musk deer have relatively low levels of MHC genetic diversity. Non-synonymous substitutions primarily occurred in the putative peptide-binding region (PBR), with analyses suggesting that recombination and selection has shaped the genetic diversity across the locus. Specifically, inter-allelic recombination generated novel allelic combinations, with evidence for both positive selection acting on the PBR and negative selection on the non-PBR. An improved understanding of functional genetic variability of the MHC will facilitate better design and management of captive breeding programs for this endangered species.

The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain suggests the importance of clan III variable segments in repertoire diversity.

PubMed

Breaux, Breanna; Deiss, Thaddeus C; Chen, Patricia L; Cruz-Schneider, Maria Paula; Sena, Leonardo; Hunter, Margaret E; Bonde, Robert K; Criscitiello, Michael F

2017-07-01

Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis. The Florida manatee has low V(D)J combinatorial diversity (3744 potential combinations) and few constant region isotypes. They also lack clan III V segments, which may have caused reduced VH segment numbers. However, we found productive somatic hypermutation concentrated in the complementarity determining regions. In conclusion, manatees have limited IGHV clan and combinatorial diversity. This suggests that clan III V segments are essential for maintaining IgH locus diversity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Psychological and Organizational Variables Associated with Workplace Learning in Small and Medium Manufacturing Businesses in Korea

ERIC Educational Resources Information Center

Moon, Se-Yeon; Na, Seung-Il

2009-01-01

The purpose of this study was to determine the relationship between workplace learning and psychological variables, such as learning competency, motivation, curiosity, self-esteem and locus of control, and organizational variables, such as centralization of power, formality, merit system and communication. The studied population consisted entirely…

Personality and Demographic Variables Related to Career Development and Career Concerns.

ERIC Educational Resources Information Center

Ralph, Joan; And Others

Following a literature search of the theories of personal maturation and career development, a study was conducted to identify personality and demographic variables related to career development and career concerns. Specifically investigated was the relationship between two sets of variables with self-concept, locus of control, and age in one set…

The locus control region is required for association of the murine β-globin locus with engaged transcription factories during erythroid maturation

PubMed Central

Ragoczy, Tobias; Bender, M.A.; Telling, Agnes; Byron, Rachel; Groudine, Mark

2006-01-01

We have examined the relationship between nuclear localization and transcriptional activity of the endogenous murine β-globin locus during erythroid differentiation. Murine fetal liver cells were separated into distinct erythroid maturation stages by fluorescence-activated cell sorting, and the nuclear position of the locus was determined at each stage. We find that the β-globin locus progressively moves away from the nuclear periphery with increasing maturation. Contrary to the prevailing notion that the nuclear periphery is a repressive compartment in mammalian cells, βmajor-globin expression begins at the nuclear periphery prior to relocalization. However, relocation of the locus to the nuclear interior with maturation is accompanied by an increase in βmajor-globin transcription. The distribution of nuclear polymerase II (Pol II) foci also changes with erythroid differentiation: Transcription factories decrease in number and contract toward the nuclear interior. Moreover, both efficient relocalization of the β-globin locus from the periphery and its association with hyperphosphorylated Pol II transcription factories require the locus control region (LCR). These results suggest that the LCR-dependent association of the β-globin locus with transcriptionally engaged Pol II foci provides the driving force for relocalization of the locus toward the nuclear interior during erythroid maturation. PMID:16705039

The Complete Nucleotide Sequence of the Human Immunoglobulin Heavy Chain Variable Region Locus

PubMed Central

Matsuda, Fumihiko; Ishii, Kazuo; Bourvagnet, Patrice; Kuma, Kei-ichi; Hayashida, Hidenori; Miyata, Takashi; Honjo, Tasuku

1998-01-01

The complete nucleotide sequence of the 957-kb DNA of the human immunoglobulin heavy chain variable (VH) region locus was determined and 43 novel VH segments were identified. The region contains 123 VH segments classifiable into seven different families, of which 79 are pseudogenes. Of the 44 VH segments with an open reading frame, 39 are expressed as heavy chain proteins and 1 as mRNA, while the remaining 4 are not found in immunoglobulin cDNAs. Combinatorial diversity of VH region was calculated to be ∼6,000. Conservation of the promoter and recombination signal sequences was observed to be higher in functional VH segments than in pseudogenes. Phylogenetic analysis of 114 VH segments clearly showed clustering of the VH segments of each family. However, an independent branch in the tree contained a single VH, V4-44.1P, sharing similar levels of homology to human VH families and to those of other vertebrates. Comparison between different copies of homologous units that appear repeatedly across the locus clearly demonstrates that dynamic DNA reorganization of the locus took place at least eight times between 133 and 10 million years ago. One nonimmunoglobulin gene of unknown function was identified in the intergenic region. PMID:9841928

Dynamic modulation of decision biases by brainstem arousal systems.

PubMed

de Gee, Jan Willem; Colizoli, Olympia; Kloosterman, Niels A; Knapen, Tomas; Nieuwenhuis, Sander; Donner, Tobias H

2017-04-11

Decision-makers often arrive at different choices when faced with repeated presentations of the same evidence. Variability of behavior is commonly attributed to noise in the brain's decision-making machinery. We hypothesized that phasic responses of brainstem arousal systems are a significant source of this variability. We tracked pupil responses (a proxy of phasic arousal) during sensory-motor decisions in humans, across different sensory modalities and task protocols. Large pupil responses generally predicted a reduction in decision bias. Using fMRI, we showed that the pupil-linked bias reduction was (i) accompanied by a modulation of choice-encoding pattern signals in parietal and prefrontal cortex and (ii) predicted by phasic, pupil-linked responses of a number of neuromodulatory brainstem centers involved in the control of cortical arousal state, including the noradrenergic locus coeruleus. We conclude that phasic arousal suppresses decision bias on a trial-by-trial basis, thus accounting for a significant component of the variability of choice behavior.

Dynamic modulation of decision biases by brainstem arousal systems

PubMed Central

de Gee, Jan Willem; Colizoli, Olympia; Kloosterman, Niels A; Knapen, Tomas; Nieuwenhuis, Sander; Donner, Tobias H

2017-01-01

Decision-makers often arrive at different choices when faced with repeated presentations of the same evidence. Variability of behavior is commonly attributed to noise in the brain’s decision-making machinery. We hypothesized that phasic responses of brainstem arousal systems are a significant source of this variability. We tracked pupil responses (a proxy of phasic arousal) during sensory-motor decisions in humans, across different sensory modalities and task protocols. Large pupil responses generally predicted a reduction in decision bias. Using fMRI, we showed that the pupil-linked bias reduction was (i) accompanied by a modulation of choice-encoding pattern signals in parietal and prefrontal cortex and (ii) predicted by phasic, pupil-linked responses of a number of neuromodulatory brainstem centers involved in the control of cortical arousal state, including the noradrenergic locus coeruleus. We conclude that phasic arousal suppresses decision bias on a trial-by-trial basis, thus accounting for a significant component of the variability of choice behavior. DOI: http://dx.doi.org/10.7554/eLife.23232.001 PMID:28383284

Management Styles, Mediating Variables, and Stress among HRD Professionals.

ERIC Educational Resources Information Center

Lind, Susan L.; Otte, Fred L.

1994-01-01

Data from 355 valid responses from 1,000 human resource professionals showed that specific variables predicted stress according to the management style of respondents' managers (authoritative, benevolent, consultative, participative). Self-esteem, locus of control, and Type A behavior were consistent predictors. (SK)

Predictors of Parental Locus of Control in Mothers of Pre- and Early-Adolescents

PubMed Central

Freed, Rachel D.; Tompson, Martha C.

2016-01-01

Parental locus of control refers to parents’ perceived power and efficacy in child-rearing situations. This study explored parental locus of control and its correlates in 160 mothers of children ages 8–14 cross-sectionally and 1 year later. Maternal depression, maternal expressed emotion, and child internalizing and externalizing behavior were examined, along with a number of sociodemographic factors. Cross-sectional analyses indicated that external parental locus of control was associated with child externalizing behavior, maternal depression, less maternal education, lower income, and older maternal age. Longitudinal analyses showed that child age and externalizing behavior also predicted increases in external parental locus of control 1 year later. Finally, lower income and less parental perceived control predicted increases in child externalizing behavior over time. PMID:21229447

Gene amplification of the Hps locus in Glycine max

PubMed Central

Gijzen, Mark; Kuflu, Kuflom; Moy, Pat

2006-01-01

Background Hydrophobic protein from soybean (HPS) is an 8 kD cysteine-rich polypeptide that causes asthma in persons allergic to soybean dust. HPS is synthesized in the pod endocarp and deposited on the seed surface during development. Past evidence suggests that the protein may mediate the adherence or dehiscence of endocarp tissues during maturation and affect the lustre, or glossiness of the seed surface. Results A comparison of soybean germplasm by genomic DNA blot hybridization shows that the copy number and structure of the Hps locus is polymorphic among soybean cultivars and related species. Changes in Hps gene copy number were also detected by comparative genomic DNA hybridization using cDNA microarrays. The Hps copy number polymorphisms co-segregated with seed lustre phenotype and HPS surface protein in a cross between dull- and shiny-seeded soybeans. In soybean cultivar Harosoy 63, a minimum of 27 ± 5 copies of the Hps gene were estimated to be present in each haploid genome. The isolation and analysis of genomic clones indicates that the core Hps locus is comprised of a tandem array of reiterated units, with each 8.6 kb unit containing a single HPS open reading frame. Conclusion This study shows that polymorphisms at the Hps locus arise from changes in the gene copy number via gene amplification. We present a model whereby Hps copy number modulates protein expression levels and seed lustre, and we suggest that gene amplification may result from selection pressures imposed on crop plants. PMID:16536872

Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae

PubMed Central

Zhang, Han; Rokas, Antonis; Slot, Jason C.

2012-01-01

Background Dermatophyte fungi of the family Arthrodermataceae (Eurotiomycetes) colonize keratinized tissue, such as skin, frequently causing superficial mycoses in humans and other mammals, reptiles, and birds. Competition with native microflora likely underlies the propensity of these dermatophytes to produce a diversity of antibiotics and compounds for scavenging iron, which is extremely scarce, as well as the presence of an unusually large number of putative secondary metabolism gene clusters, most of which contain non-ribosomal peptide synthetases (NRPS), in their genomes. To better understand the historical origins and diversification of NRPS-containing gene clusters we examined the evolution of a variable locus (VL) that exists in one of three alternative conformations among the genomes of seven dermatophyte species. Results The first conformation of the VL (termed VLA) contains only 539 base pairs of sequence and lacks protein-coding genes, whereas the other two conformations (termed VLB and VLC) span 36 Kb and 27 Kb and contain 12 and 10 genes, respectively. Interestingly, both VLB and VLC appear to contain distinct secondary metabolism gene clusters; VLB contains a NRPS gene as well as four porphyrin metabolism genes never found to be physically linked in the genomes of 128 other fungal species, whereas VLC also contains a NRPS gene as well as several others typically found associated with secondary metabolism gene clusters. Phylogenetic evidence suggests that the VL locus was present in the ancestor of all seven species achieving its present distribution through subsequent differential losses or retentions of specific conformations. Conclusions We propose that the existence of variable loci, similar to the one we studied, in fungal genomes could potentially explain the dramatic differences in secondary metabolic diversity between closely related species of filamentous fungi, and contribute to host adaptation and the generation of metabolic diversity. PMID:22860027

Evaluation of a highly discriminating multiplex multi-locus variable-number of tandem-repeats (MLVA) analysis for Vibrio cholerae.

PubMed

Olsen, Jaran S; Aarskaug, Tone; Skogan, Gunnar; Fykse, Else Marie; Ellingsen, Anette Bauer; Blatny, Janet M

2009-09-01

Vibrio cholerae is the etiological agent of cholera and may be used in bioterror actions due to the easiness of its dissemination, and the public fear for acquiring the cholera disease. A simple and highly discriminating method for connecting clinical and environmental isolates of V. cholerae is needed in microbial forensics. Twelve different loci containing variable numbers of tandem-repeats (VNTRs) were evaluated in which six loci were polymorphic. Two multiplex reactions containing PCR primers targeting these six VNTRs resulted in successful DNA amplification of 142 various environmental and clinical V. cholerae isolates. The genetic distribution inside the V. cholerae strain collection was used to evaluate the discriminating power (Simpsons Diversity Index=0.99) of this new MLVA analysis, showing that the assay have a potential to differentiate between various strains, but also to identify those isolates which are collected from a common V. cholerae outbreak. This work has established a rapid and highly discriminating MLVA assay useful for track back analyses and/or forensic studies of V. cholerae infections.

Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

PubMed

Mouton, L; Ebert, D

2008-05-01

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rass-Rothchild, A.: Abeliovitch, D.; Kornstein, A.

The acronym LEOPARD stands for a syndromic association of Lentigines, Eletrocardiographic changes, Ocular hypertelorism, Pulmonic stenosis, Abnormal genitalia, Retardation of growth and sensorineural Deafness. Inheritance is autosomal dominant with high penetrance and variable expressivity. In 1990 Torok et al. reported on the association of LEOPARD and Marfan syndrome. In addition a clinical similarity (cardiac and cutaneous involvement) exists with the Watson syndrome (neurofibromatosis and pulmonic stenosis) which is linked to the marker D17S33 on chromosome 17. We studied possible linkage of LEOPARD syndrome to the Marfan syndrome locus on chromosome 15 (D15S1, MF13, and (TAAAA)n repeats) and to the NF-1more » locus on chromosome 17 in a family with 9 cases of LEOPARD syndrome. Close linkage between LEOPARD syndrome and both the Marfan locus on chromosome 15 and the NF-1 locus on chromosome 17 was excluded (lod score <-2.0 through {theta} = 0.1).« less

USH1H, a novel locus for type I Usher syndrome, maps to chromosome 15q22-23.

PubMed

Ahmed, Z M; Riazuddin, S; Khan, S N; Friedman, P L; Riazuddin, S; Friedman, T B

2009-01-01

Usher syndrome (USH) is a hereditary disorder associated with sensorineural hearing impairment, progressive loss of vision attributable to retinitis pigmentosa (RP) and variable vestibular function. Three clinical types have been described with type I (USH1) being the most severe. To date, six USH1 loci have been reported. We ascertained two large Pakistani consanguineous families segregating profound hearing loss, vestibular dysfunction, and RP, the defining features of USH1. In these families, we excluded linkage of USH to the 11 known USH loci and subsequently performed a genome-wide linkage screen. We found a novel USH1 locus designated USH1H that mapped to chromosome 15q22-23 in a 4.92-cM interval. This locus overlaps the non-syndromic deafness locus DFNB48 raising the possibility that the two disorders may be caused by allelic mutations.

Note on guilt appeals in advertising: covariate effects of self-esteem and locus of control.

PubMed

Pinto, M B; Worobetz, N D

1992-02-01

A 1991 study by Pinto and Priest demonstrated the effectiveness of advertisements employing moderate levels of guilt in inducing guilt responses in subjects. Because individuals' responses to guilt are often influenced by their specific personality characteristics, researchers have pointed to the potential moderating effects of individual difference variables such as level of self-esteem and locus of control on individuals' susceptibility to guilt appeals. A study was conducted to evaluate the possibility that self-esteem and locus of control can act as covariates across three treatment levels of guilt advertising. From a sample of 57 working mothers, advertisements stimulating medium and high levels of guilt elicited significantly greater feelings of guilt in subjects than the control advertisement stimulating low guilt. However, the relationship between susceptibility to guilt appeals and self-esteem and locus of control was not observed to covary.

Locus ceruleus neurons in people with autism contain no histochemically-detectable mercury.

PubMed

Pamphlett, Roger; Kum Jew, Stephen

2016-02-01

Exposure to environmental mercury has been proposed to play a part in autism. Mercury is selectively taken up by the human locus ceruleus, a region of the brain that has been implicated in autism. We therefore looked for the presence of mercury in the locus ceruleus of people who had autism, using the histochemical technique of autometallography which can detect nanogram amounts of mercury in tissues. In addition, we sought evidence of damage to locus ceruleus neurons in autism by immunostaining for hyperphosphorylated tau. No mercury was found in any neurons of the locus ceruleus of 6 individuals with autism (5 male, 1 female, age range 16-48 years). Mercury was present in locus ceruleus neurons in 7 of 11 (64%) age-matched control individuals who did not have autism, which is significantly more than in individuals with autism. No increase in numbers of locus ceruleus neurons containing hyperphosphorylated tau was detected in people with autism. In conclusion, most people with autism have not been exposed early in life to quantities of mercury large enough to be found later in adult locus ceruleus neurons. Human locus ceruleus neurons are sensitive indicators of mercury exposure, and mercury appears to remain in these neurons indefinitely, so these findings do not support the hypothesis that mercury neurotoxicity plays a role in autism.

On measures of association among genetic variables

PubMed Central

Gianola, Daniel; Manfredi, Eduardo; Simianer, Henner

2012-01-01

Summary Systems involving many variables are important in population and quantitative genetics, for example, in multi-trait prediction of breeding values and in exploration of multi-locus associations. We studied departures of the joint distribution of sets of genetic variables from independence. New measures of association based on notions of statistical distance between distributions are presented. These are more general than correlations, which are pairwise measures, and lack a clear interpretation beyond the bivariate normal distribution. Our measures are based on logarithmic (Kullback-Leibler) and on relative ‘distances’ between distributions. Indexes of association are developed and illustrated for quantitative genetics settings in which the joint distribution of the variables is either multivariate normal or multivariate-t, and we show how the indexes can be used to study linkage disequilibrium in a two-locus system with multiple alleles and present applications to systems of correlated beta distributions. Two multivariate beta and multivariate beta-binomial processes are examined, and new distributions are introduced: the GMS-Sarmanov multivariate beta and its beta-binomial counterpart. PMID:22742500

The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces.

PubMed

League, Garrett P; Slot, Jason C; Rokas, Antonis

2012-11-01

The asparagine degradation pathway in the S288c laboratory strain of Saccharomyces cerevisiae is comprised of genes located at two separate loci. ASP1 is located on chromosome IV and encodes for cytosolic l-asparaginase I, whereas ASP3 contains a gene cluster located on chromosome XII comprised of four identical genes, ASP3-1, ASP3-2, ASP3-3, and ASP3-4, which encode for cell wall-associated l-asparaginase II. Interestingly, the ASP3 locus appears to be only present, in variable copy number, in S. cerevisiae strains isolated from laboratory or industrial environments and is completely absent from the genomes of 128 diverse fungal species. Investigation of the evolutionary history of ASP3 across these 128 genomes as well as across the genomes of 43 S. cerevisiae strains shows that ASP3 likely arose in a S. cerevisiae strain via horizontal gene transfer (HGT) from, or a close relative of, the wine yeast Wickerhamomyces anomalus, which co-occurs with S. cerevisiae in several biotechnological processes. Thus, because the ASP3 present in the S288c laboratory strain of S. cerevisiae is induced in response to nitrogen starvation, its acquisition may have aided yeast adaptation to artificial environments. Our finding that the ASP3 locus in S. cerevisiae originated via HGT further highlights the importance of gene sharing between yeasts in the evolution of their remarkable metabolic diversity. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Diversifying Selection Underlies the Origin of Allozyme Polymorphism at the Phosphoglucose Isomerase Locus in Tigriopus californicus

PubMed Central

Schoville, Sean D.; Flowers, Jonathan M.; Burton, Ronald S.

2012-01-01

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations. PMID:22768211

Rapid Birth-and-Death Evolution of Imprinted snoRNAs in the Prader-Willi Syndrome Locus: Implications for Neural Development in Euarchontoglires

PubMed Central

Zhang, Yi-Jun; Yang, Jian-Hua; Shi, Qiao-Su; Zheng, Ling-Ling; Liu, Jun; Zhou, Hui; Zhang, Hui; Qu, Liang-Hu

2014-01-01

Imprinted small nucleolar RNAs (snoRNAs) are only found in eutherian genomes and closely related to brain functions. A complex human neurological disease, Prader-Willi syndrome (PWS), is primarily attributed to the deletion of imprinted snoRNAs in chromosome 15q11-q13. Here we investigated the snoRNA repertoires in the PWS locus of 12 mammalian genomes and their evolution processes. A total of 613 imprinted snoRNAs were identified in the PWS homologous loci and the gene number was highly variable across lineages, with a peak in Euarchontoglires. Lineage-specific gene gain and loss events account for most extant genes of the HBII-52 (SNORD115) and the HBII-85 (SNORD116) gene family, and remarkable high gene-birth rates were observed in the primates and the rodents. Meanwhile, rapid sequence substitution occurred only in imprinted snoRNA genes, rather than their flanking sequences or the protein-coding genes located in the same imprinted locus. Strong selective constraints on the functional elements of these imprinted snoRNAs further suggest that they are subjected to birth-and-death evolution. Our data suggest that the regulatory role of HBII-52 on 5-HT2CR pre-mRNA might originate in the Euarchontoglires through adaptive process. We propose that the rapid evolution of PWS-related imprinted snoRNAs has contributed to the neural development of Euarchontoglires. PMID:24945811

Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern

USGS Publications Warehouse

Landguth, Erin L.; Gedy, Bradley C.; Oyler-McCance, Sara J.; Garey, Andrew L.; Emel, Sarah L.; Mumma, Matthew; Wagner, Helene H.; Fortin, Marie-Josée; Cushman, Samuel A.

2012-01-01

The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially-explicit, individual-based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation-by-distance, isolation-by-barrier, and isolation-by-landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non-equilibrium conditions after introduction of isolation-by-landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals.

Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern

USGS Publications Warehouse

Landguth, E.L.; Fedy, B.C.; Oyler-McCance, S.J.; Garey, A.L.; Emel, S.L.; Mumma, M.; Wagner, H.H.; Fortin, M.-J.; Cushman, S.A.

2012-01-01

The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially-explicit, individual-based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation-by-distance, isolation-by-barrier, and isolation-by-landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non-equilibrium conditions after introduction of isolation-by-landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals. ?? 2011 Blackwell Publishing Ltd.

Development and characterization of 16 polymorphic microsatellite loci for the Alaska blackfish (Esociformes: Dallia pectoralis)

USGS Publications Warehouse

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.

Psychosocial and cognitive factors associated with adherence to dietary and fluid restriction regimens by people on chronic haemodialysis.

PubMed

Sensky, T; Leger, C; Gilmour, S

1996-01-01

Failure by people on chronic haemodialysis to adhere adequately to dietary and fluid restrictions can have serious medical consequences. Numerous psychosocial factors possibly associated with adherence have been investigated in previous research. However, most previous studies have examined one or a few variables in isolation, and have tended to focus on sociodemographic variables not easily amenable to intervention. Much previous work has tended to ignore potential differences in adherence between male and female dialysands. Sociodemographic and psychosocial factors associated with adherence to dietary and fluid restrictions were investigated in 45 people on haemodialysis attending one renal unit, excluding those with a residual urine volume > 500 ml/day. Multiple regression analyses were used to estimate the contribution to adherence of a range of variables, including gender, age, duration of dialysis, affective disturbance, past psychiatric history, health locus of control, social adjustment and social supports. Adherence to diet (measured by predialysis serum potassium) and to fluid restriction (interdialysis weight gain) were not linked, and had different psychosocial correlates. Regression models of four different aspects of adherence revealed very distinct psychosocial correlates, with contributions to adherence from complex interactions between psychosocial and cognitive variables, notably gender, age, social adjustment, health locus of control, and depression. The findings cast doubt on the results of many previous studies which have used simple models of adherence. Adherence is likely to be influenced in a complex manner by multiple factors including age, gender, locus of control, social adjustment, and past psychiatric history.

Atlas-Independent, Electrophysiological Mapping of the Optimal Locus of Subthalamic Deep Brain Stimulation for the Motor Symptoms of Parkinson Disease.

PubMed

Conrad, Erin C; Mossner, James M; Chou, Kelvin L; Patil, Parag G

2018-05-23

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) improves motor symptoms of Parkinson disease (PD). However, motor outcomes can be variable, perhaps due to inconsistent positioning of the active contact relative to an unknown optimal locus of stimulation. Here, we determine the optimal locus of STN stimulation in a geometrically unconstrained, mathematically precise, and atlas-independent manner, using Unified Parkinson Disease Rating Scale (UPDRS) motor outcomes and an electrophysiological neuronal stimulation model. In 20 patients with PD, we mapped motor improvement to active electrode location, relative to the individual, directly MRI-visualized STN. Our analysis included a novel, unconstrained and computational electrical-field model of neuronal activation to estimate the optimal locus of DBS. We mapped the optimal locus to a tightly defined ovoid region 0.49 mm lateral, 0.88 mm posterior, and 2.63 mm dorsal to the anatomical midpoint of the STN. On average, this locus is 11.75 lateral, 1.84 mm posterior, and 1.08 mm ventral to the mid-commissural point. Our novel, atlas-independent method reveals a single, ovoid optimal locus of stimulation in STN DBS for PD. The methodology, here applied to UPDRS and PD, is generalizable to atlas-independent mapping of other motor and non-motor effects of DBS. © 2018 S. Karger AG, Basel.

Higher locus coeruleus MRI contrast is associated with lower parasympathetic influence over heart rate variability

PubMed Central

Mather, Mara; Yoo, Hyun Joo; Clewett, David V.; Lee, Tae-Ho; Greening, Steven G.; Ponzio, Allison; Min, Jungwon; Thayer, Julian F.

2017-01-01

The locus coeruleus (LC) is a key node of the sympathetic nervous system and suppresses parasympathetic activity that would otherwise increase heart rate variability. In the current study, we examined whether LC-MRI contrast reflecting neuromelanin accumulation in the LC was associated with high-frequency heart rate variability (HF-HRV), a measure reflecting parasympathetic influences on the heart. Recent evidence indicates that neuromelanin, a byproduct of catecholamine metabolism, accumulates in the LC through young and mid adulthood, suggesting that LC-MRI contrast may be a useful biomarker of individual differences in habitual LC activation. We found that, across younger and older adults, greater LC-MRI contrast was negatively associated with HF-HRV during fear conditioning and spatial detection tasks. This correlation was not accounted for by individual differences in age or anxiety. These findings indicate that individual differences in LC structure relate to key cardiovascular parameters. PMID:28215623

A Survey on Turkish Elementary School Students' Environmental Friendly Behaviours and Associated Variables

ERIC Educational Resources Information Center

Alp, Elvan; Ertepinar, Hamide; Tekkaya, Ceren; Yilmaz, Ayhan

2008-01-01

This study investigated elementary school students' environmental knowledge and attitudes, the effects of sociodemographic variables on environmental knowledge and attitudes, and how self-reported environmentally friendly behaviour is related to environmental knowledge, behavioural intentions, environmental affects, and the students' locus of…

Recalling Experiences of Teen Dating Violence: An Examination of Its Relationship to Family Violence and Locus of Control amongst African Americans and How These Variables Impact Relationships in Adulthood

ERIC Educational Resources Information Center

McCain, Stephanie D.

2015-01-01

The purpose of this study was two-fold: 1) to identify the relationship between witnessing violence at home and the effects it has on teen dating violence and future experiences with violence; and 2) to assess how perceived locus of control may reduce or exacerbate the relationship between each of the risk factors and perpetration of dating…

Dealing with extreme environmental degradation: stress and marginalization of Sahel dwellers.

PubMed

Van Haaften, E H; Van de Vijver, F J

1999-07-01

Psychological aspects of environmental degradation are hardly investigated. In the present study these aspects were examined among Sahel dwellers, who live in environments with different states of degradation. The degradation was assessed in terms of vegetation cover, erosion, and loss of organic matter. Subjects came from three cultural groups: Dogon (agriculturalists, n = 225), Mossi (agriculturalists, n = 914), and Fulani (pastoralists, n = 844). Questionnaires addressing marginalization, locus of control, and coping were administered. Environmental degradation was associated with higher levels of stress, marginalization, passive coping (avoidance), a more external locus of control, and lower levels of active coping (problem solving and support seeking). Compared to agriculturalists, pastoralists showed a stronger variation in all psychological variables across all regions, from the least to the most environmentally degraded. Women showed higher scores of stress, (external) locus of control, problem solving, and support seeking than men. The interaction of gender and region was significant for several variables. It was concluded that environmental degradation has various psychological correlates: people are likely to display an active approach to environmental degradation as long as the level of degradation is not beyond their control.

Identifying environmental correlates of intraspecific genetic variation.

PubMed

Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

2016-09-01

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Interpersonal problem-solving deficits in self-poisoning patients.

PubMed

McLeavey, B C; Daly, R J; Murray, C M; O'Riordan, J; Taylor, M

1987-01-01

Self-poisoning patients (n = 40) were compared with psychiatric patients (n = 40) and nonpatient controls (n = 20) on measures of interpersonal problem-solving skills and locus of control in an effort to determine the importance of these cognitive and personality variables in self-poisoning behavior. The psychiatric and self-poisoning groups showed deficits on measures assessing interpersonal problem solving when compared with nonpatient controls. The self-poisoning group performed below the level of the psychiatric patients on all except one test, on which they performed at the level of the psychiatric group. Locus of control did not differentiate self-poisoning patients from nonpatient controls, and it was concluded that this variable is not an important factor in self-poisoning behavior.

Transcriptome and Allele Specificity Associated with a 3BL Locus for Fusarium Crown Rot Resistance in Bread Wheat

PubMed Central

Ma, Jian; Stiller, Jiri; Zhao, Qiang; Feng, Qi; Cavanagh, Colin; Wang, Penghao; Gardiner, Donald; Choulet, Frédéric; Feuillet, Catherine; Zheng, You-Liang; Wei, Yuming; Yan, Guijun; Han, Bin; Manners, John M.; Liu, Chunji

2014-01-01

Fusarium pathogens cause two major diseases in cereals, Fusarium crown rot (FCR) and head blight (FHB). A large-effect locus conferring resistance to FCR disease was previously located to chromosome arm 3BL (designated as Qcrs-3B) and several independent sets of near isogenic lines (NILs) have been developed for this locus. In this study, five sets of the NILs were used to examine transcriptional changes associated with the Qcrs-3B locus and to identify genes linked to the resistance locus as a step towards the isolation of the causative gene(s). Of the differentially expressed genes (DEGs) detected between the NILs, 12.7% was located on the single chromosome 3B. Of the expressed genes containing SNP (SNP-EGs) detected, 23.5% was mapped to this chromosome. Several of the DEGs and SNP-EGs are known to be involved in host-pathogen interactions, and a large number of the DEGs were among those detected for FHB in previous studies. Of the DEGs detected, 22 were mapped in the Qcrs-3B interval and they included eight which were detected in the resistant isolines only. The enrichment of DEG, and not necessarily those containing SNPs between the resistant and susceptible isolines, around the Qcrs-3B locus is suggestive of local regulation of this region by the resistance allele. Functions for 13 of these DEGs are known. Of the SNP-EGs, 28 were mapped in the Qcrs-3B interval and biological functions for 16 of them are known. These results provide insights into responses regulated by the 3BL locus and identify a tractable number of target genes for fine mapping and functional testing to identify the causative gene(s) at this QTL. PMID:25405461

Distinct Genetic Signatures for Variability in Total and Free Serum Thyroxine Levels in Four Sets of Recombinant Inbred Mice

PubMed Central

Lu, Lu; Aliesky, Holly A.; Williams, Robert W.; Rapoport, Basil

2011-01-01

C3H/He and BALB/c mice have elevated serum thyroxine levels associated with low deiodinase type-1 activity whereas C57BL/6 (B6) mice have low thyroxine levels and elevated deiodinase type-1 activity. High-resolution genetic maps are available for four sets of recombinant inbred (RI) mice derived from B6 parents bred to C3H/He, BALB/c, DBA/2, or A strains. Total and free T4 (T-T4 and F-T4) levels in females from these RI sets (BXH, CXB, BXD, and AXBXA) were analyzed to test two hypotheses: first, serum T4 variability is linked to the deiodinase type-1 gene; second, because of their shared B6 parent, the RI sets will share linkages responsible for T-T4 or F-T4 variability. A number of chromosomes (Chr) and loci were linked to T-T4 (Chr 1, 4, 13, 11) or F-T4 (Chr 1, 6, 13, 18, 19). Linkage between T-T4 and Chr 4 was limited to CXB and BXH strains, but the locus was distinct from the deiodinase type-1 gene. Surprisingly, many linkages were unique providing “genetic signatures” for T-T4 or F-T4 in each set of RI mice. Indeed, the strongest linkage between T-T4 (or F-T4) and a Chr 2 locus (logarithm of the odds scores >4.4) was only observed in AXBXA strains. Some loci corresponded to genes/Chr associated in humans with variable TSH or T-T4 levels. Unlike inbred mice, human populations are extremely diverse. Consequently, our data suggest that the contributions of unique chromosomes/loci controlling T-T4 and F-T4 in distinct human subgroups are likely to be “buried” in genetic analyses of heterogeneous human populations. PMID:21209025

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient

PubMed Central

2011-01-01

Background Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. Methods We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. Results In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. Conclusions This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus. PMID:22044463

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient.

PubMed

Thonberg, Håkan; Fallström, Marie; Björkström, Jenny; Schoumans, Jacqueline; Nennesmo, Inger; Graff, Caroline

2011-11-01

Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus.

Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.

PubMed

Leushkin, Evgeny V; Logacheva, Maria D; Penin, Aleksey A; Sutormin, Roman A; Gerasimov, Evgeny S; Kochkina, Galina A; Ivanushkina, Natalia E; Vasilenko, Oleg V; Kondrashov, Alexey S; Ozerskaya, Svetlana M

2015-05-21

Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50 Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100-10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.

Detection of linkage between a quantitative trait and a marker locus by the lod score method: sample size and sampling considerations.

PubMed

Demenais, F; Lathrop, G M; Lalouel, J M

1988-07-01

A simulation study is here conducted to measure the power of the lod score method to detect linkage between a quantitative trait and a marker locus in various situations. The number of families necessary to detect such linkage with 80% power is assessed for different sets of parameters at the trait locus and different values of the recombination fraction. The effects of varying the mode of sampling families and the sibship size are also evaluated.

Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.

PubMed

Phillips, Anastasia; Sotomayor, Cristina; Wang, Qinning; Holmes, Nadine; Furlong, Catriona; Ward, Kate; Howard, Peter; Octavia, Sophie; Lan, Ruiting; Sintchenko, Vitali

2016-09-15

Salmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance. We performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, food-borne outbreaks along with sporadic cases in New South Wales, Australia, during 2014. Genomes of case and environmental isolates were sequenced using HiSeq (Illumina) and the genetic distance between them was assessed by single nucleotide polymorphism (SNP) analysis. SNP analysis was compared to the epidemiological context. The WGS analysis supported epidemiological evidence and genomes of within-outbreak isolates were nearly identical. Sporadic cases differed from outbreak cases by a small number of SNPs, although their close relationship to outbreak cases may represent an unidentified common food source that may warrant further public health follow up. Previously unrecognised mini-clusters were detected. WGS of STM can discriminate foodborne community outbreaks within a single endemic MLVA clone. Our findings support the translation of WGS into public health laboratory surveillance of salmonellosis.

[Family-based association study of a variable number of tandem repeat polymorphism of DAT1 gene with Tourette syndrome in a Chinese Han population].

PubMed

Zheng, Lanlan; Han, Zhen-liang; Zhang, Xin-hua; Wang, Xue-qin; Jiang, Wei-hua; Yi, Ming-ji; Liu, Shi-guo

2013-10-01

To assess the association of a 40 bp variable number of tandem repeat (VNTR) polymorphism within 3 untranslated region of dopamine transporter gene (DAT1) with Tourette syndrome (TS) in a Chinese Han population. A total of 160 TS patients and their parents were recruited. The VNTR polymorphism was detected with polymerase chain reaction-VNTR analysis, and its association with TS and its subtypes were assessed through a family-based association study comprising transmission disequilibrium test (TDT) and haplotype relative risk (HRR) analysis. The repeat numbers at the DAT1 40 bp locus were 11, 10, 9, 7.5 and 7 among the patients and their parents, with the most common type being a 10-repeat allele. No significant association was detected between the polymorphism and TS (TDT: X ² = 0.472, df = 1, P = 0.583; HRR: X ² = 0.313, P = 0.576, OR = 0.855, 95%CI: 0.493-1.481). Our data suggested that the VNTR polymorphism of DAT1 gene is not associated with susceptibility to TS in Chinese Han population. However, our results are to be validated in larger sets of patients collected from other populations.

Julia Sets in Parameter Spaces

NASA Astrophysics Data System (ADS)

Buff, X.; Henriksen, C.

Given a complex number λ of modulus 1, we show that the bifurcation locus of the one parameter family {fb(z)=λz+bz2+z3}b∈ contains quasi-conformal copies of the quadratic Julia set J(λz+z2). As a corollary, we show that when the Julia set J(λz+z2) is not locally connected (for example when z|-->λz+z2 has a Cremer point at 0), the bifurcation locus is not locally connected. To our knowledge, this is the first example of complex analytic parameter space of dimension 1, with connected but non-locally connected bifurcation locus. We also show that the set of complex numbers λ of modulus 1, for which at least one of the parameter rays has a non-trivial accumulation set, contains a dense Gδ subset of S1.

Prospective Genotyping of Mycobacterium tuberculosis from Fresh Clinical Samples

PubMed Central

Bidovec-Stojkovič, Urška; Seme, Katja; Žolnir-Dovč, Manca; Supply, Philip

2014-01-01

Shorter time-to-result is key for improving molecular-guided epidemiological investigation of tuberculosis (TB) cases. We performed a prospective study to evaluate the use of standardized MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing of Mycobacterium tuberculosis directly on 79 fresh clinical samples from 26 TB patients consecutively enrolled over a 17-month period. Overall, complete 24-locus types were obtained for 18 out of the 26 (69.2%) patients and 14 of the 16 grade 3+ and grade 2+ samples (87.5%). The degree of completion of the genotypes obtained significantly correlated with smear microscopy grade both for 26 first samples (p = 0.0003) and for 53 follow-up samples (p = 0.002). For 20 of the 26 patients for whom complete or even incomplete M. tuberculosis isolate genotypes were obtained, typing applied to the clinical samples allowed the same unambiguous conclusions regarding case clustering or uniqueness as those that could have been drawn based on the corresponding cultured isolates. Standard 24 locus MIRU-VNTR typing of M. tuberculosis can be applied directly to fresh clinical samples, with typeability depending on the bacterial load in the sample. PMID:25313883

Gender differences in the roles of religion and locus of control on alcohol use and smoking among African Americans.

PubMed

Holt, Cheryl L; Roth, David L; Huang, Jin; Clark, Eddie M

2015-05-01

Spiritual health locus of control reflects a person's beliefs about the role of a higher power in one's health and can take an active or a passive perspective. The purpose of this study was to examine the moderating role of active and passive spiritual health locus of control beliefs on select health risk behaviors--alcohol use and smoking--in a national sample of African Americans. A national U.S. probability sample of study participants (N = 2,370; 906 men; 1,464 women) completed a telephone survey assessing religious involvement, active and passive spiritual health locus of control beliefs, and alcohol consumption and smoking status. Because of previous research suggesting gender-specific associations among these variables, moderation analyses were conducted separately for men and women. For women, higher religious behaviors were associated with less alcohol use, and this effect was more pronounced among those high in active spiritual health locus of control. For men, the combination of lower religious beliefs and higher passive spiritual health locus of control was associated with more alcohol consumption and more days of consuming five or more alcoholic drinks. No moderation effects were found for smoking. This study identified unique patterns of religious involvement and spiritual health locus of control beliefs that are associated with alcohol use, including heavy drinking, among African Americans. These findings have implications for pastoral counseling and other faith-based approaches for addressing heavy drinking in African Americans.

Geophysical variables and behavior: XXIII. Relations between UFO reports within the Uinta Basin and local seismicity.

PubMed

Persinger, M A; Derr, J S

1985-02-01

A strong temporal correlation was found between the numbers of reports of UFOs (unidentified flying objects) and nearby seismic activity within the Uinta Basin for the year 1967. The numbers of UFO reports per month during this classic UFO flap were correlated 0.80 with the sum of the earthquake magnitudes per month for events within 150 km of the report area. Numbers of UFO reports were not correlated significantly with earthquake activity at distances greater than 150 km but less than 250 km away. The strongest correlation occurred between UFO reports and nearby seismic activity within the same month but not for previous or consequent months. Close scrutiny of daily shifts in epicenters and reports of UFOs indicate that they occurred when the locus of successive epicenters shifted across the area. These analyses were interpreted as support for the existence of strain fields whose movements generate natural phenomena that are reported as UFOs.

Comparison of 2 proposed MLVA protocols for subtyping non-O157:H7 verotoxigenic Escherichia coli.

PubMed

González, Juliana; Sanso, Andrea Mariel; Lucchesi, Paula María Alejandra; Bustamante, Ana Victoria

2014-04-01

Multiple locus variable number tandem repeats (VNTRs) analysis (MLVA) has become a reliable tool, able to establish genetic relationships for epidemiological surveillance and molecular subtyping of pathogens such as verotoxigenic Escherichia coli (VTEC). This emerging pathogen whose primary reservoir is the cattle causes severe disease in humans, such as hemorrhagic colitis and hemolytic uremic syndrome. With the aim of comparing a recently proposed MLVA assay with that used routinely in our laboratory, we analyzed a set of VTEC isolates (n = 72) obtained from meat using both assays. All samples could be typed by the new MLVA assay, and an increase in the number of distinct profiles (31-43) was observed. However, intraserotype resolution was not significantly enhanced; thus, the incorporation of more VNTR loci is still needed to achieve a greater discrimination among non-O157:H7 serotypes. Copyright © 2014 Elsevier Inc. All rights reserved.

Locus of control and utilization of social support among mothers of young children with physical disabilities.

PubMed

Rimmerman, A; Stanger, V

1992-01-01

Sixty mothers of young children with physical disabilities were studied with respect to the effect of the mothers' locus of control on the utilization of social support. The initial findings failed to support the thesis that mothers with an 'internally' focused locus of control would demonstrate greater utilization of their support system, both in terms of descriptive and functional measures. A secondary analysis showed that the mothers' age, the children's level of functioning, and the existence of additional members of the family with a disability served as intervening variables. Only among older mothers, who perceived their children's functioning as severe, was there significant association between the locus of control ('internal') and greater use of their social support system. 'Internal' mothers who had no additional extended family members with a disability reported higher levels of functional social support, as compared to 'external' mothers. Findings are interpreted with respect to social support theory and its implications to applied research.

The complexity of selection at the major primate β-defensin locus

PubMed Central

Semple, Colin AM; Maxwell, Alison; Gautier, Philippe; Kilanowski, Fiona M; Eastwood, Hayden; Barran, Perdita E; Dorin, Julia R

2005-01-01

Background We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mouse. For the first time these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as the ancient past. We have used a combination of maximum likelihood based tests and a maximum parsimony based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. Results We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. Consequently variable selective pressures have acted on β-defensin genes in different evolutionary lineages, with episodes both of negative, and more rarely positive selection, during the divergence of primates. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel, rodent-specific β-defensin genes. These observations allow a fuller understanding of the evolution of mammalian innate immunity. In both the rodent and primate lineages, sites in the second exon have been subject to positive selection and by implication are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions predicted to be important for the specificity of the antimicrobial or chemoattractant properties of β-defensins. Surprisingly, sites within the prepropeptide region were also implicated as being subject to significant positive selection, suggesting previously unappreciated functional significance for this region. Conclusions Identification of these putatively functional sites has important implications for our understanding of β-defensin function and for novel antibiotic design. PMID:15904491

Cognitive and Life Event Correlates of Depressive Symptoms in Children.

ERIC Educational Resources Information Center

Mullins, Larry L.; And Others

The present study examines the relationship of various cognitive and life event variables to depressive symptoms in children. The variables studied are locus of control, interpersonal and impersonal problem-solving ability, and objective and subjective life stress. Subjects were 47 students in the fourth grade, 58 students in the fifth grade, and…

Associations between Procrastination, Personality, Perfectionism, Self-Esteem and Locus of Control

ERIC Educational Resources Information Center

Boysan, Murat; Kiral, Erkan

2017-01-01

To date, many variables but particularly trait-like psychological constructs have been found to strongly contribute to procrastination but the complex relations among these variables collectively have received almost no attention. The purpose of the study was to provide a more profound understanding of the relations between procrastination,…

Situational and Intrapersonal Predictors of School and Life Satisfaction of Elementary School Students

ERIC Educational Resources Information Center

Drost, Amy Linden

2012-01-01

This study examined predictors of school and life satisfaction of fifth-grade students. Two situational predictor variables (school climate and school stress) and two intrapersonal predictor variables (locus of control and academic self-concept) were examined. It was hypothesized that positive school climate, low levels of school stress, internal…

The Role of Chance Events in the School-to-Work Transition: The Influence of Demographic, Personality and Career Development Variables

ERIC Educational Resources Information Center

Hirschi, Andreas

2010-01-01

Chance events are considered important in career development, yet little empirical research is available on their predictors and consequences. The present study investigated socio-demographic (gender, nationality, school-type), personality (openness, locus of control) and career development variables (career decidedness, career planning) in…

Screening large-scale association study data: exploiting interactions using random forests.

PubMed

Lunetta, Kathryn L; Hayward, L Brooke; Segal, Jonathan; Van Eerdewegh, Paul

2004-12-10

Genome-wide association studies for complex diseases will produce genotypes on hundreds of thousands of single nucleotide polymorphisms (SNPs). A logical first approach to dealing with massive numbers of SNPs is to use some test to screen the SNPs, retaining only those that meet some criterion for further study. For example, SNPs can be ranked by p-value, and those with the lowest p-values retained. When SNPs have large interaction effects but small marginal effects in a population, they are unlikely to be retained when univariate tests are used for screening. However, model-based screens that pre-specify interactions are impractical for data sets with thousands of SNPs. Random forest analysis is an alternative method that produces a single measure of importance for each predictor variable that takes into account interactions among variables without requiring model specification. Interactions increase the importance for the individual interacting variables, making them more likely to be given high importance relative to other variables. We test the performance of random forests as a screening procedure to identify small numbers of risk-associated SNPs from among large numbers of unassociated SNPs using complex disease models with up to 32 loci, incorporating both genetic heterogeneity and multi-locus interaction. Keeping other factors constant, if risk SNPs interact, the random forest importance measure significantly outperforms the Fisher Exact test as a screening tool. As the number of interacting SNPs increases, the improvement in performance of random forest analysis relative to Fisher Exact test for screening also increases. Random forests perform similarly to the univariate Fisher Exact test as a screening tool when SNPs in the analysis do not interact. In the context of large-scale genetic association studies where unknown interactions exist among true risk-associated SNPs or SNPs and environmental covariates, screening SNPs using random forest analyses can significantly reduce the number of SNPs that need to be retained for further study compared to standard univariate screening methods.

How visualization layout relates to locus of control and other personality factors.

PubMed

Ziemkiewicz, Caroline; Ottley, Alvitta; Crouser, R Jordan; Yauilla, Ashley Rye; Su, Sara L; Ribarsky, William; Chang, Remco

2013-07-01

Existing research suggests that individual personality differences are correlated with a user's speed and accuracy in solving problems with different types of complex visualization systems. We extend this research by isolating factors in personality traits as well as in the visualizations that could have contributed to the observed correlation. We focus on a personality trait known as "locus of control” (LOC), which represents a person's tendency to see themselves as controlled by or in control of external events. To isolate variables of the visualization design, we control extraneous factors such as color, interaction, and labeling. We conduct a user study with four visualizations that gradually shift from a list metaphor to a containment metaphor and compare the participants' speed, accuracy, and preference with their locus of control and other personality factors. Our findings demonstrate that there is indeed a correlation between the two: participants with an internal locus of control perform more poorly with visualizations that employ a containment metaphor, while those with an external locus of control perform well with such visualizations. These results provide evidence for the externalization theory of visualization. Finally, we propose applications of these findings to adaptive visual analytics and visualization evaluation.

Genetic and Molecular Characterization of the I Locus of Phaseolus vulgaris

PubMed Central

Vallejos, C. Eduardo; Astua-Monge, Gustavo; Jones, Valerie; Plyler, Tammy R.; Sakiyama, Ney S.; Mackenzie, Sally A.

2006-01-01

The I locus of the common bean, Phaseolus vulgaris, controls the development of four different phenotypes in response to inoculation with Bean common mosaic virus, Bean common mosaic necrosis virus, several other related potyviruses, and one comovirus. We have generated a high-resolution linkage map around this locus and have aligned it with a physical map constructed with BAC clones. These clones were obtained from a library of the cultivar “Sprite,” which carries the dominant allele at the I locus. We have identified a large cluster of TIR–NBS–LRR sequences associated within this locus, which extends over a distance >425 kb. Bean cultivars from the Andean or Mesoamerican gene pool that contain the dominant allele share the same haplotypes as revealed by gel blot hybridizations with a TIR probe. In contrast, beans with a recessive allele display simpler and variable haplotypes. A survey of wild accessions from Argentina to Mexico showed that this multigene family has expanded significantly during evolution and domestication. RNA gel blot analysis indicated that the TIR family of genes plays a role in the response to inoculations with BCMV or BCMNV. PMID:16322513

Social and psychological theories and their use for dental practice.

PubMed

Reisine, S; Litt, M

1993-06-01

This paper discusses four major theoretical constructs that have helped broaden our understanding of oral hygiene behaviours and dental health risks, including: social class, life stress, self-efficacy and locus of control. The potential of these constructs to enhance the treatment of dental diseases is illustrated using data from a study based on a biopsychosocial model of caries risk. In two cities in Connecticut, 481 children aged 3 years were recruited from the Head Start programme. Two dentists examined the children with a mirror and explorer and collected data on dmfs. A parent or guardian of 369 of these children completed an interview with a research assistant which provided data on each child's brushing habits, dietary intake of sugar, social class indicators, stressful life events, dental health locus of control and perceived dental self efficacy. The effects of psychosocial variables on two clinical measures were assessed, the levels of S. mutans and the prevalence of decay. Analysis indicated that S. mutans was the most important predictor of caries risk. Mothers who had more external locus of control beliefs, lower income, more knowledge about tooth decay and higher stress levels had children with greater risk of having caries. Further, use of a baby bottle at night was a significant factor in caries risk. Analyses of S. mutans risk showed that socioeconomic status and ethnicity significantly differentiated those with no colonies from those with one or more colonies while attitudinal and behaviour factors predicted who would be in the group with the highest number of S. mutans colonies.

Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins.

PubMed

Szafranski, Przemyslaw; Gambin, Tomasz; Dharmadhikari, Avinash V; Akdemir, Kadir Caner; Jhangiani, Shalini N; Schuette, Jennifer; Godiwala, Nihal; Yatsenko, Svetlana A; Sebastian, Jessica; Madan-Khetarpal, Suneeta; Surti, Urvashi; Abellar, Rosanna G; Bateman, David A; Wilson, Ashley L; Markham, Melinda H; Slamon, Jill; Santos-Simarro, Fernando; Palomares, María; Nevado, Julián; Lapunzina, Pablo; Chung, Brian Hon-Yin; Wong, Wai-Lap; Chu, Yoyo Wing Yiu; Mok, Gary Tsz Kin; Kerem, Eitan; Reiter, Joel; Ambalavanan, Namasivayam; Anderson, Scott A; Kelly, David R; Shieh, Joseph; Rosenthal, Taryn C; Scheible, Kristin; Steiner, Laurie; Iqbal, M Anwar; McKinnon, Margaret L; Hamilton, Sara Jane; Schlade-Bartusiak, Kamilla; English, Dawn; Hendson, Glenda; Roeder, Elizabeth R; DeNapoli, Thomas S; Littlejohn, Rebecca Okashah; Wolff, Daynna J; Wagner, Carol L; Yeung, Alison; Francis, David; Fiorino, Elizabeth K; Edelman, Morris; Fox, Joyce; Hayes, Denise A; Janssens, Sandra; De Baere, Elfride; Menten, Björn; Loccufier, Anne; Vanwalleghem, Lieve; Moerman, Philippe; Sznajer, Yves; Lay, Amy S; Kussmann, Jennifer L; Chawla, Jasneek; Payton, Diane J; Phillips, Gael E; Brosens, Erwin; Tibboel, Dick; de Klein, Annelies; Maystadt, Isabelle; Fisher, Richard; Sebire, Neil; Male, Alison; Chopra, Maya; Pinner, Jason; Malcolm, Girvan; Peters, Gregory; Arbuckle, Susan; Lees, Melissa; Mead, Zoe; Quarrell, Oliver; Sayers, Richard; Owens, Martina; Shaw-Smith, Charles; Lioy, Janet; McKay, Eileen; de Leeuw, Nicole; Feenstra, Ilse; Spruijt, Liesbeth; Elmslie, Frances; Thiruchelvam, Timothy; Bacino, Carlos A; Langston, Claire; Lupski, James R; Sen, Partha; Popek, Edwina; Stankiewicz, Paweł

2016-05-01

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in the etiology of ACDMPV.

Pathogenetics of Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins

PubMed Central

Szafranski, Przemyslaw; Gambin, Tomasz; Dharmadhikari, Avinash V.; Akdemir, Kadir Caner; Jhangiani, Shalini N.; Schuette, Jennifer; Godiwala, Nihal; Yatsenko, Svetlana A.; Sebastian, Jessica; Madan-Khetarpal, Suneeta; Surti, Urvashi; Abellar, Rosanna G.; Bateman, David A.; Wilson, Ashley L.; Markham, Melinda H.; Slamon, Jill; Santos-Simarro, Fernando; Palomares, María; Nevado, Julián; Lapunzina, Pablo; Hon-Yin, Brian Chung; Wai-Lap, Wong; Chu, Yoyo Wing Yiu; Mok, Gary Tsz Kin; Eitan, Kerem; Reiter, Joel; Ambalavanan, Namasivayam; Anderson, Scott A.; Kelly, David R.; Shieh, Joseph; Rosenthal, Taryn C.; Scheible, Kristin; Steiner, Laurie; Iqbal, M. Anwar; McKinnon, Margaret; Hamilton, Sara Jane; Schlade-Bartusiak, Kamilla; English, Dawn; Hendson, Glenda; Roeder, Elizabeth R.; DeNapoli, Thomas S.; Littlejohn, Rebecca Okashah; Wolff, Daynna J.; Wagner, Carol L.; Yeung, Alison; Francis, David; Fiorino, Elizabeth K.; Edelman, Morris; Fox, Joyce; Hayes, Denise A.; Janssens, Sandra; De Baere, Elfride; Menten, Bjorn; Loccufier, Anne; Van Walleghem, Lieve; Moerman, Philippe; Sznajer, Yves; Lay, Amy S.; Kussmann, Jennifer L.; Chawla, Jasneek; Payton, Diane J.; Phillips, Gael E.; Brosens, Erwin; Tibboel, Dick; de Klein, Annelies; Maystadt, Isabelle; Fisher, Richard; Sebire, Neil; Male, Alison; Chopra, Maya; Pinner, Jason; Malcolm, Girvan; Peters, Gregory; Arbuckle, Susan; Lees, Melissa; Mead, Zoe; Quarrell, Oliver; Sayers, Richard; Owens, Martina; Shaw-Smith, Charles; Lioy, Janet; McKay, Eileen; de Leeuw, Nicole; Feenstra, Ilse; Spruijt, Liesbeth; Elmslie, Frances; Thiruchelvam, Timothy; Bacino, Carlos A.; Langston, Claire; Lupski, James R.; Sen, Partha; Popek, Edwina; Stankiewicz, Paweł

2017-01-01

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in etiology of ACDMPV. PMID:27071622

Genetic characterization of the partial mitochondrial cytochrome oxidase c subunit I (cox 1) gene of the zoonotic parasitic nematode, Ancylostoma ceylanicum from humans, dogs and cats.

PubMed

Ngui, Romano; Mahdy, Mohammed A K; Chua, Kek Heng; Traub, Rebecca; Lim, Yvonne A L

2013-10-01

Ancylostoma ceylanicum is the only zoonotic hookworm species that is able to produce patent infections in humans with the majority of cases reported in South East Asia. Over the past few years, there have been an increasing number of studies investigating the prevalence of this parasitic zoonosis using molecular diagnostic tools and a single genetic locus as marker for species identification. As there can be limitations in using a single genetic locus for epidemiological studies and genetic discrimination, the complementary use of a more variable locus will provide additional evidence to support the zoonotic exchange of hookworm species between humans and animals. In the present study, the cytochrome c oxidase subunit 1 (cox 1) sequence of A. ceylanicum from positive human and animal fecal samples were determined and compared with published reference sequences. Phylogenetic analysis demonstrated that isolates of A. ceylanicum were divided into two clusters, one consisting 3 human isolates and the other comprising 19 isolates of human and animal origin from different geographical locations within Malaysia. The two groups of A. ceylanicum could be distinguished from one another through five fixed nucleotide differences at locations 891, 966, 1008, 1077 and 1083. The detection of genetically distinct groups and considerable level of genetic variation within the cox 1 sequence of A. ceylanicum might suggest potential haplotype-linked differences in zoonotic, epidemiological and pathobiological characteristics, a hypothesis that still needs further investigation. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluation of genetic variability in a small, insular population of spruce grouse

USGS Publications Warehouse

O'Connell, A.F.; Rhymer, Judith; Keppie, D.M.; Svenson, K.L.; Paigan, B.J.

2002-01-01

Using microsatellite markers we determined genetic variability for two populations of spruce grouse in eastern North America, one on a coastal Maine island where breeding habitat is limited and highly fragmented, the other in central New Brunswick (NB), where suitable breeding habitat is generally contiguous across the region. We examined six markers for both populations and all were polymorphic. Although the number of alleles per locus and the proportion of unique alleles were lower in the island population, and probably a result of small sample.size, heterozygosity and a breeding coefficient (Fis) indicated slightly more variability in the island population. Deviation from Hardy-Weinberg equilibrium also was more evident in loci for the mainland population. Several traits previously documented in the island population: relatively long natal dispersal distances, reproductive success, territoriality, adult survival, and longevity support the maintenance of hetrerzygosity, at least in the short-term. Sample collection from two small (500 ha), separate areas in NB, and the predicted importance of immigration density to supplement this population demonstrate the need for behavioral and ecological information when interpreting genetic variation. We discuss the relevance of these issues with respect to genetic variability and viability.

Diversity among strains of Pseudomonas aeruginosa from manure and soil, evaluated by multiple locus variable number tandem repeat analysis and antibiotic resistance profiles.

PubMed

Youenou, Benjamin; Brothier, Elisabeth; Nazaret, Sylvie

2014-01-01

The results of a multiple locus variable number of tandem repeat (VNTR) analysis (MLVA)-based study designed to understand the genetic diversity of soil and manure-borne Pseudomonas aeruginosa isolates, and the relationship between these isolates and a set of clinical and environmental isolates, are hereby reported. Fifteen described VNTR markers were first selected, and 62 isolates recovered from agricultural and industrial soils in France and Burkina Faso, and from cattle and horse manure, along with 26 snake-related isolates and 17 environmental and clinical isolates from international collections, were genotyped. Following a comparison with previously published 9-marker MLVA schemes, an optimal 13-marker MLVA scheme (MLVA13-Lyon) was identified that was found to be the most efficient, as it showed high typability (90%) and high discriminatory power (0.987). A comparison of MLVA with PFGE for typing of the snake-related isolates confirmed the MLVA13-Lyon scheme to be a robust method for quickly discriminating and inferring genetic relatedness among environmental isolates. The 62 isolates displayed wide diversity, since 41 MLVA types (i.e. MTs) were observed, with 26 MTs clustered in 10 MLVA clonal complexes (MCs). Three and eight MCs were found among soil and manure isolates, respectively. Only one MC contained both soil and manure-borne isolates. No common MC was observed between soil and manure-borne isolates and the snake-related or environmental and clinical isolates. Antibiotic resistance profiles were performed to determine a potential link between resistance properties and the selective pressure that might be present in the various habitats. Except for four soil and manure isolates resistant to ticarcillin and ticarcillin/clavulanic acid and one isolate from a hydrocarbon-contaminated soil resistant to imipenem, all environmental isolates showed wild-type antibiotic profiles. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Genetic stability of Brucella abortus isolates from an outbreak by multiple-locus variable-number tandem repeat analysis (MLVA16)

PubMed Central

2014-01-01

Background Brucellosis caused by Brucella abortus is one of the most important zoonoses in the world. Multiple-locus variable-number tandem repeat analysis (MLVA16) has been shown be a useful tool to epidemiological traceback studies in B. abortus infection. Thus, the present study aimed (i) to evaluate the genetic diversity of B. abortus isolates from a brucellosis outbreak, and (ii) to investigate the in vivo stability of the MLVA16 markers. Results Three-hundred and seventy-five clinical samples, including 275 vaginal swabs and 100 milk samples, were cultured from a brucellosis outbreak in a cattle herd, which adopted RB51 vaccination and test-and-slaughter policies. Thirty-seven B. abortus isolates were obtained, eight from milk and twenty-nine from post-partum/abortion vaginal swabs, which were submitted to biotyping and genotyping by MLVA16. Twelve B. abortus isolates obtained from vaginal swabs were identified as RB51. Twenty four isolates, seven obtained from milk samples and seventeen from vaginal swabs, were identified as B. abortus biovar 3, while one isolate from vaginal swabs was identified as B. abortus biovar 1. Three distinct genotypes were observed during the brucellosis outbreak: RB observed in all isolates identified as RB51; W observed in all B. abortus biovar 3 isolates; and Z observed in the single B. abortus biovar 1 isolate. Epidemiological and molecular data show that the B. abortus biovar 1 genotype Z strain is not related to the B. abortus biovar 3 genotype W isolates, and represents a new introduction B. abortus during the outbreak. Conclusions The results of the present study on typing of multiple clinical B. abortus isolates from the same outbreak over a sixteen month period indicate the in vivo stability of MLVA16 markers, a low genetic diversity among B. abortus isolates and the usefulness of MLVA16 for epidemiological studies of bovine brucellosis. PMID:25015840

Subtyping of Canadian isolates of Salmonella Enteritidis using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) alone and in combination with Pulsed-Field Gel Electrophoresis (PFGE) and phage typing.

PubMed

Ziebell, Kim; Chui, Linda; King, Robin; Johnson, Suzanne; Boerlin, Patrick; Johnson, Roger P

2017-08-01

Salmonella enterica subspecies enterica serovar Enteritidis (SE) is one of the most common causes of human salmonellosis and in Canada currently accounts for over 40% of human cases. Reliable subtyping of isolates is required for outbreak detection and source attribution. However, Pulsed-Field Gel Electrophoresis (PFGE), the current standard subtyping method for Salmonella spp., is compromised by the high genetic homogeneity of SE. Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) was introduced to supplement PFGE, although there is a lack of data on the ability of MLVA to subtype Canadian isolates of SE. Three subtyping methods, PFGE, MLVA and phage typing were compared for their discriminatory power when applied to three panels of Canadian SE isolates: Panel 1: 70 isolates representing the diversity of phage types (PTs) and PFGE subtypes within these PTs; Panel 2: 214 apparently unrelated SE isolates of the most common PTs; and Panel 3: 27 isolates from 10 groups of epidemiologically related strains. For Panel 2 isolates, four MLVA subtypes were shared among 74% of unrelated isolates and in Panel 3 isolates, one MLVA subtype accounted for 62% of the isolates. For all panels, combining results from PFGE, MLVA and PT gave the best discrimination, except in Panel 1, where the combination of PT and PFGE was equally as high, due to the selection criteria for this panel. However, none of these methods is sufficiently discriminatory alone for reliable outbreak detection or source attribution, and must be applied together to achieve sufficient discrimination for practical purposes. Even then, some large clusters were not differentiated adequately. More discriminatory methods are required for reliable subtyping of this genetically highly homogeneous serovar. This need will likely be met by whole genome sequence analysis given the recent promising reports and as more laboratories implement this tool for outbreak response and surveillance. Copyright © 2017 Elsevier B.V. All rights reserved.

Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis

PubMed Central

Malorny, Burkhard; Junker, Ernst; Helmuth, Reiner

2008-01-01

Background Salmonella enterica subsp. enterica serotype Enteritidis is known as an important and pathogenic clonal group which continues to cause worldwide sporadic cases and outbreaks in humans. Here a new multiple-locus variable-number tandem repeat analysis (MLVA) method is reported for highly-discriminative subtyping of Salmonella Enteritidis. Emphasis was given on the most predominant phage types PT4 and PT8. The method comprises multiplex PCR specifically amplifying repeated sequences from nine different loci followed by an automatic fragment size analysis using a multicolor capillary electrophoresis instrument. A total of 240 human, animal, food and environmental isolates of S. Enteritidis including 23 definite phage types were used for development and validation. Furthermore, the MLVA types were compared to the phage types of several isolates from two recent outbreaks to determine the concordance between both methods and to estimate their in vivo stability. The in vitro stability of the two MLVA types specifically for PT4 and PT8 strains were determined by multiple freeze-thaw cycles. Results Seventy-nine different MLVA types were identified in 240 S. Enteritidis strains. The Simpson's diversity index for the MLVA method was 0.919 and Nei diversity values for the nine VNTR loci ranged from 0.07 to 0.65. Twenty-four MLVA types could be assigned to 62 PT4 strains and 21 types to 81 PT8 strains. All outbreak isolates had an indistinguishable outbreak specific MLVA type. The in vitro stability experiments showed no changes of the MLVA type compared to the original isolate. Conclusion This MLVA method is useful to discriminate S. Enteritidis strains even within a single phage type. It is easy in use, fast, and cheap compared to other high-resolution molecular methods and therefore an important tool for surveillance and outbreak studies for S. Enteritidis. PMID:18513386

Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

PubMed Central

2010-01-01

Background Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts. PMID:21143842

Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.

PubMed

Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

2007-06-20

The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.

Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

PubMed Central

2012-01-01

Background Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition. PMID:22369244

Nuclear-Cytoplasmic Conflict in Pea (Pisum sativum L.) Is Associated with Nuclear and Plastidic Candidate Genes Encoding Acetyl-CoA Carboxylase Subunits

PubMed Central

Bogdanova, Vera S.; Zaytseva, Olga O.; Mglinets, Anatoliy V.; Shatskaya, Natalia V.; Kosterin, Oleg E.; Vasiliev, Gennadiy V.

2015-01-01

In crosses of wild and cultivated peas (Pisum sativum L.), nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized. PMID:25789472

Locus coeruleus activation accelerates perceptual learning.

PubMed

Glennon, Erin; Carcea, Ioana; Martins, Ana Raquel O; Multani, Jasmin; Shehu, Ina; Svirsky, Mario A; Froemke, Robert C

2018-05-31

Neural representations of the external world are constructed and updated in a manner that depends on behavioral context. For neocortical networks, this contextual information is relayed by a diverse range of neuromodulatory systems, which govern attention and signal the value of internal state variables such as arousal, motivation, and stress. Neuromodulators enable cortical circuits to differentially process specific stimuli and modify synaptic strengths in order to maintain short- or long-term memory traces of significant perceptual events and behavioral episodes. One of the most important subcortical neuromodulatory systems for attention and arousal is the noradrenergic locus coeruleus. Here we report that the noradrenergic system can enhance behavior in rats performing a self-initiated auditory recognition task, and optogenetic stimulation of noradrenergic locus coeruleus neurons accelerated the rate at which trained rats began correctly responding to a change in reward contingency. Animals successively progressed through distinct behavioral epochs, including periods of perseverance and exploration that occurred much more rapidly when animals received locus coeruleus stimulation. In parallel, we made recordings from primary auditory cortex and found that pairing tones with locus coeruleus stimulation led to a similar set of changes to cortical tuning profiles. Thus both behavioral and neural responses go through phases of adjustment for exploring and exploiting environmental reward contingencies. Furthermore, behavioral engagement does not necessarily recruit optimal locus coeruleus activity. Copyright © 2018. Published by Elsevier B.V.

Higher locus coeruleus MRI contrast is associated with lower parasympathetic influence over heart rate variability.

PubMed

Mather, Mara; Joo Yoo, Hyun; Clewett, David V; Lee, Tae-Ho; Greening, Steven G; Ponzio, Allison; Min, Jungwon; Thayer, Julian F

2017-04-15

The locus coeruleus (LC) is a key node of the sympathetic nervous system and suppresses parasympathetic activity that would otherwise increase heart rate variability. In the current study, we examined whether LC-MRI contrast reflecting neuromelanin accumulation in the LC was associated with high-frequency heart rate variability (HF-HRV), a measure reflecting parasympathetic influences on the heart. Recent evidence indicates that neuromelanin, a byproduct of catecholamine metabolism, accumulates in the LC through young and mid adulthood, suggesting that LC-MRI contrast may be a useful biomarker of individual differences in habitual LC activation. We found that, across younger and older adults, greater LC-MRI contrast was negatively associated with HF-HRV during fear conditioning and spatial detection tasks. This correlation was not accounted for by individual differences in age or anxiety. These findings indicate that individual differences in LC structure relate to key cardiovascular parameters. Copyright © 2017 Elsevier Inc. All rights reserved.

Rapid and high resolution genotyping of all Escherichia coli serotypes using 10 genomic repeat-containing loci.

PubMed

Løbersli, Inger; Haugum, Kjersti; Lindstedt, Bjørn-Arne

2012-01-01

Our laboratory has previously published two multiple-locus variable-number tandem-repeats analysis (MLVA) methods for rapid genotyping of Escherichia coli (E. coli), which are now in routine use for surveillance and outbreak detection. The first assay developed was specific for E. coli O157:H7; however this assay was not suitable for genotyping other E. coli serotypes. A new generic MLVA-assay was then developed with the capability of genotyping all E. coli serotypes. This generic E. coli MLVA (GECM7) was based on polymorphism in seven variable number of tandem repeats (VNTR) loci. GECM7 worked well with the majority of E. coli serotypes; however we wanted to increase the resolution for this method based in part of comparison with PFGE typing of E. coli O26:H11, where PFGE appeared to display higher resolution. The GECM7 method was improved by adding three new repeat-loci to a total of ten (GECM10), and a considerable increase in resolution was observed (from 296 to 507 genotypes on the same set of strains). Copyright © 2011 Elsevier B.V. All rights reserved.

The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander.

PubMed

Hime, Paul M; Hotaling, Scott; Grewelle, Richard E; O'Neill, Eric M; Voss, S Randal; Shaffer, H Bradley; Weisrock, David W

2016-12-01

Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence data sets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large data sets is time-consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions. Here, we investigated how locus number and information content affect species delimitation results for an endangered Mexican salamander species, Ambystoma ordinarium. We compared results for an eight-locus, 137-individual data set and an 89-locus, seven-individual data set. For both data sets, we used species discovery methods to define delimitation models and species validation methods to rigorously test these hypotheses. We also used integrated demographic model selection tools to choose among delimitation models, while accounting for gene flow. Our results indicate that while cryptic lineages may be delimited with relatively few loci, sampling larger numbers of loci may be required to ensure that enough informative loci are available to accurately identify and validate shallow-scale divergences. These analyses highlight the importance of striking a balance between dense sampling of loci and individuals, particularly in shallowly diverged lineages. They also suggest the presence of a currently unrecognized, endangered species in the western part of A. ordinarium's range. © 2016 John Wiley & Sons Ltd.

The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications

PubMed Central

Djogbénou, Luc S.; Berthomieu, Arnaud; Makoundou, Patrick; Baba-Moussa, Lamine S.; Fiston-Lavier, Anna-Sophie; Belkhir, Khalid; Labbé, Pierrick; Weill, Mylène

2016-01-01

Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides’ target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype level, to investigate the influence of duplication architecture and gene-dosage on mosquito fitness. We found that both heterogeneous (i.e., one susceptible and one resistant ace-1 copy) and homogeneous (i.e., identical resistant copies) duplications segregated in field populations. The number of copies in homogeneous duplications was variable and positively correlated with acetylcholinesterase activity and resistance level. Determining the genomic structure of the duplicated region revealed that, in both types of duplication, ace-1 and 11 other genes formed tandem 203kb amplicons. We developed a diagnostic test for duplications, which showed that ace-1 was amplified in all 173 resistant mosquitoes analyzed (field-collected in several African countries), in heterogeneous or homogeneous duplications. Each type was associated with different fitness trade-offs: heterogeneous duplications conferred an intermediate phenotype (lower resistance and fitness costs), whereas homogeneous duplications tended to increase both resistance and fitness cost, in a complex manner. The type of duplication selected seemed thus to depend on the intensity and distribution of selection pressures. This versatility of trade-offs available through gene duplication highlights the importance of large mutation events in adaptation to environmental variation. This impressive adaptability could have a major impact on vector control in Africa. PMID:27918584

Molecular characteristics of "Mycobacterium canettii" the smooth Mycobacterium tuberculosis bacilli.

PubMed

Fabre, Michel; Hauck, Yolande; Soler, Charles; Koeck, Jean-Louis; van Ingen, Jakko; van Soolingen, Dick; Vergnaud, Gilles; Pourcel, Christine

2010-12-01

Since the first discovery of the smooth tubercle (SmTB) bacilli "Mycobacterium canettii" less than 60 isolates have been reported, all but one originating from a limited geographical location, the Horn of Africa. In spite of its rarity, the SmTB lineage deserves special attention. Previous investigations suggested that SmTB isolates represent an ancestral lineage of the Mycobacterium tuberculosis complex (MTBC) and that consequently they might provide essential clues on the origin and evolution of the MTBC. There is evidence that unlike the rest of the MTBC, SmTB strains recombine chromosomal sequences with a yet unknown Mycobacterium species. This behavior contributes to the much larger genetic heterogeneity observed in the SmTB isolates compared to the other members of the MTBC. We have collected 59 SmTB isolates of which 14 were newly recovered since previous reports, and performed extensive phenotypical and genotypical characterization. We take advantage of these investigations to review the current knowledge of "M. canettii". Their characteristics and the apparent lack of human to human transmission are consistent with the previously proposed existence of non-human sources of infection. SmTB strains show remarkably common features together with secondary and taxonomically minor genetic differences such as the presence or absence of the CRISPR (Clustered Regularly Interspersed Palindromic Repeat) locus (usually called Direct Repeat or DR region) or number of IS sequences. Multiple Locus Variable number of tandem repeat Analysis (MLVA) and DR region analyses reveal one predominant clone, one minor clone and a number of more distantly related strains. This suggests that the two most frequent clones may represent successfully emerging lineages. Copyright © 2010 Elsevier B.V. All rights reserved.

Structural forms of the human amylase locus and their relationships to SNPs, haplotypes, and obesity

PubMed Central

Usher, Christina L; Handsaker, Robert E; Esko, Tõnu; Tuke, Marcus A; Weedon, Michael N; Hastie, Alex R; Cao, Han; Moon, Jennifer E; Kashin, Seva; Fuchsberger, Christian; Metspalu, Andres; Pato, Carlos N; Pato, Michele T; McCarthy, Mark I; Boehnke, Michael; Altshuler, David M; Frayling, Timothy M; Hirschhorn, Joel N; McCarroll, Steven A

2016-01-01

Hundreds of genes reside in structurally complex, poorly understood regions of the human genome1-3. One such region contains the three amylase genes (AMY2B, AMY2A, and AMY1) responsible for digesting starch into sugar. The copy number of AMY1 is reported to be the genome’s largest influence on obesity4, though genome-wide association studies for obesity have found this locus unremarkable. Using whole genome sequence analysis3,5, droplet digital PCR6, and genome mapping7, we identified eight common structural haplotypes of the amylase locus that suggest its mutational history. We found that AMY1 copy number in individuals’ genomes is generally even (rather than odd) and partially correlates to nearby SNPs, which do not associate with BMI. We measured amylase gene copy number in 1,000 obese or lean Estonians and in two other cohorts totaling ~3,500 individuals. We had 99% power to detect the lower bound of the reported effects on BMI4, yet found no association. PMID:26098870

The unusual S locus of Leavenworthia is composed of two sets of paralogous loci.

PubMed

Chantha, Sier-Ching; Herman, Adam C; Castric, Vincent; Vekemans, Xavier; Marande, William; Schoen, Daniel J

2017-12-01

The Leavenworthia self-incompatibility locus (S locus) consists of paralogs (Lal2, SCRL) of the canonical Brassicaceae S locus genes (SRK, SCR), and is situated in a genomic position that differs from the ancestral one in the Brassicaceae. Unexpectedly, in a small number of Leavenworthia alabamica plants examined, sequences closely resembling exon 1 of SRK have been found, but the function of these has remained unclear. BAC cloning and expression analyses were employed to characterize these SRK-like sequences. An SRK-positive Bacterial Artificial Chromosome clone was found to contain complete SRK and SCR sequences located close by one another in the derived genomic position of the Leavenworthia S locus, and in place of the more typical Lal2 and SCRL sequences. These sequences are expressed in stigmas and anthers, respectively, and crossing data show that the SRK/SCR haplotype is functional in self-incompatibility. Population surveys indicate that < 5% of Leavenworthia S loci possess such alleles. An ancestral translocation or recombination event involving SRK/SCR and Lal2/SCRL likely occurred, together with neofunctionalization of Lal2/SCRL, and both haplotype groups now function as Leavenworthia S locus alleles. These findings suggest that S locus alleles can have distinctly different evolutionary origins. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Dynamic of mutational events in variable number tandem repeats of Escherichia coli O157:H7.

PubMed

Bustamante, A V; Sanso, A M; Segura, D O; Parma, A E; Lucchesi, P M A

2013-01-01

VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenic E. coli O157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10(-05) to 1.8 × 10(-03) mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10(-03) mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.

Tracing Staphylococcus aureus in small and medium-sized food-processing factories on the basis of molecular sub-species typing.

PubMed

Koreňová, Janka; Rešková, Zuzana; Véghová, Adriana; Kuchta, Tomáš

2015-01-01

Contamination by Staphylococcus aureus of the production environment of three small or medium-sized food-processing factories in Slovakia was investigated on the basis of sub-species molecular identification by multiple locus variable number of tandem repeats analysis (MLVA). On the basis of MLVA profiling, bacterial isolates were assigned to 31 groups. Data from repeated samplings over a period of 3 years facilitated to draw spatial and temporal maps of the contamination routes for individual factories, as well as identification of potential persistent strains. Information obtained by MLVA typing allowed to identify sources and routes of contamination and, subsequently, will allow to optimize the technical and sanitation measures to ensure hygiene.

What is white?

PubMed Central

Bosten, J. M.; Beer, R. D.; MacLeod, D. I. A.

2015-01-01

To shed light on the perceptual basis of the color white, we measured settings of unique white in a dark surround. We find that settings reliably show more variability in an oblique (blue-yellow) direction in color space than along the cardinal axes of the cone-opponent mechanisms. This is against the idea that white perception arises at the null point of the cone-opponent mechanisms, but one alternative possibility is that it occurs through calibration to the visual environment. We found that the locus of maximum variability in settings lies close to the locus of natural daylights, suggesting that variability may result from uncertainty about the color of the illuminant. We tested this by manipulating uncertainty. First, we altered the extent to which the task was absolute (requiring knowledge of the illumination) or relative. We found no clear effect of this factor on the reduction in sensitivity in the blue-yellow direction. Second, we provided a white surround as a cue to the illumination or left the surround dark. Sensitivity was selectively worse in the blue-yellow direction when the surround was black than when it was white. Our results can be functionally related to the statistics of natural images, where a greater blue-yellow dispersion is characteristic of both reflectances (where anisotropy is weak) and illuminants (where it is very pronounced). Mechanistically, the results could suggest a neural signal responsive to deviations from the blue-yellow locus or an adaptively matched range of contrast response functions for signals that encode different directions in color space. PMID:26641948

Identification of a Major Locus Contributing to Erythrocyte 2,3-Diphosphoglycerate Variability in Hooded (Long-Evans) Rats

PubMed Central

Noble, N. A.; Brewer, G. J.

1977-01-01

The erythrocyte glycolytic intermediate 2,3-diphosphoglycerate (DPG) and adenosine triphosphate (ATP) play an important role in oxygen transport and delivery by binding to hemoglobin (Hb) and reducing its affinity for oxygen. Considerable quantitative variability in the levels of DPG and ATP exists in human populations and in a population of hooded (Long-Evans) rats we have studied. This paper presents the results of studies on the genetic component of DPG-level variation in an outbred population of hooded rats. Beginning with about 100 rats, a two-way selection experiment was initiated. Pairs of rats with the highest DPG levels were mated to produce a High-DPG rat strain and animals with the lowest DPG levels were mated to produce a Low-DPG strain. Mean DPG levels responded rapidly to selection and, from generation 3 on, the differences between strain means were highly significant. Ten High-DPG strain rats were intercrossed with 10 Low-DPG strain rats of generation 10 to produce an F1 generation in which the DPG levels were almost as high as those of High-DPG animals. This indicates partial dominance of High-DPG alleles. The F2 DPG-level distribution showed two distinct subpopulations. The high DPG subpopulation contained three times as many animals as the low DPG subpopulation. From these results and the statistical analyses performed, it was concluded that the DPG differences between strains were due to an allelic difference at one major locus, the allele carried by the High-DPG strain showing partial dominance over the allele carried by the Low-DPG strain. It appears that this locus may also effect ATP levels to a large extent and is polymorphic in hooded rat populations. Identification of this locus gives us a useful tool for studies of the physiological effects of DPG variability, as well as providing an example of a major gene effect in a quantitatively varying trait. PMID:863239

Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus.

PubMed

Takahata, Satoshi; Yago, Takumi; Iwabuchi, Keisuke; Hirakawa, Hideki; Suzuki, Yutaka; Onodera, Yasuyuki

2016-01-01

Spinach (Spinacia oleracea, 2n = 12) and sugar beet (Beta vulgaris, 2n = 18) are important crop members of the family Chenopodiaceae ss Sugar beet has a basic chromosome number of 9 and a cosexual breeding system, as do most members of the Chenopodiaceae ss. family. By contrast, spinach has a basic chromosome number of 6 and, although certain cultivars and genotypes produce monoecious plants, is considered to be a dioecious species. The loci determining male and monoecious sexual expression were mapped to different loci on the spinach sex chromosomes. In this study, a linkage map with 46 mapped protein-coding sequences was constructed for the spinach sex chromosomes. Comparison of the linkage map with a reference genome sequence of sugar beet revealed that the spinach sex chromosomes exhibited extensive synteny with sugar beet chromosomes 4 and 9. Tightly linked protein-coding genes linked to the male-determining locus in spinach corresponded to genes located in or around the putative pericentromeric and centromeric regions of sugar beet chromosomes 4 and 9, supporting the observation that recombination rates were low in the vicinity of the male-determining locus. The locus for monoecism was confined to a chromosomal segment corresponding to a region of approximately 1.7Mb on sugar beet chromosome 9, which may facilitate future positional cloning of the locus. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.).

PubMed

Blair, Matthew W; Prieto, Sergio; Díaz, Lucy M; Buendía, Héctor F; Cardona, César

2010-04-29

An interesting seed protein family with a role in preventing insect herbivory is the multi-gene, APA family encoding the alpha-amylase inhibitor, phytohemagglutinin and arcelin proteins of common bean (Phaseolus vulgaris). Variability for this gene family exists and has been exploited to breed for insect resistance. For example, the arcelin locus has been successfully transferred from wild to cultivated common bean genotypes to provide resistance against the bruchid species Zabrotes subfasciatus although the process has been hampered by a lack of genetic tools for and understanding about the locus. In this study, we analyzed linkage disequilibrium (LD) between microsatellite markers at the APA locus and bruchid resistance in a germplasm survey of 105 resistant and susceptible genotypes and compared this with LD in other parts of the genome. Microsatellite allele diversity was found to vary with each of the eight APA-linked markers analyzed, and two markers within the APA locus were found to be diagnostic for bruchid resistance or susceptibility and for the different arcelin alleles inherited from the wild accessions. Arc1 was found to provide higher levels of resistance than Arc5 and the markers in the APA locus were highly associated with resistance showing that introgression of this gene-family from wild beans provides resistance in cultivated beans. LD around the APA locus was found to be intermediate compared to other regions of the genome and the highest LD was found within the APA locus itself for example between the markers PV-atct001 and PV-ag004. We found the APA locus to be an important genetic determinant of bruchid resistance and also found that LD existed mostly within the APA locus but not beyond it. Moderate LD was also found for some other regions of the genome perhaps related to domestication genes. The LD pattern may reflect the introgression of arcelin from the wild into the cultivated background through breeding. LD and association studies for the arcelin gene, linked genes and other members of the APA family are essential for breaking linkage drag while maintaining high levels of bruchid resistance in common bean.

Investigating the population structure and genetic differentiation of livestock guard dog breeds.

PubMed

Bigi, D; Marelli, S P; Liotta, L; Frattini, S; Talenti, A; Pagnacco, G; Polli, M; Crepaldi, P

2018-01-14

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

From mild ataxia to huntington disease phenocopy: the multiple faces of spinocerebellar ataxia 17.

PubMed

Koutsis, Georgios; Panas, Marios; Paraskevas, George P; Bougea, Anastasia M; Kladi, Athina; Karadima, Georgia; Kapaki, Elisabeth

2014-01-01

Introduction. Spinocerebellar ataxia 17 (SCA 17) is a rare autosomal dominant cerebellar ataxia (ADCA) caused by a CAG/CAA expansion in the TBP gene, reported from a limited number of countries. It is a very heterogeneous ADCA characterized by ataxia, cognitive decline, psychiatric symptoms, and involuntary movements, with some patients presenting with Huntington disease (HD) phenocopies. The SCA 17 expansion is stable during parent-child transmission and intrafamilial phenotypic homogeneity has been reported. However, significant phenotypic variability within families has also been observed. Report of the Family. We presently report a Greek family with a pathological expansion of 54 repeats at the SCA 17 locus that displayed remarkable phenotypic variability. Among 3 affected members, one presented with HD phenocopy; one with progressive ataxia, dementia, chorea, dystonia, and seizures, and one with mild slowly progressive ataxia with minor cognitive and affective symptoms. Conclusions. This is the first family with SCA 17 identified in Greece and highlights the multiple faces of this rare disorder, even within the same family.

From Mild Ataxia to Huntington Disease Phenocopy: The Multiple Faces of Spinocerebellar Ataxia 17

PubMed Central

Panas, Marios; Paraskevas, George P.; Bougea, Anastasia M.; Karadima, Georgia; Kapaki, Elisabeth

2014-01-01

Introduction. Spinocerebellar ataxia 17 (SCA 17) is a rare autosomal dominant cerebellar ataxia (ADCA) caused by a CAG/CAA expansion in the TBP gene, reported from a limited number of countries. It is a very heterogeneous ADCA characterized by ataxia, cognitive decline, psychiatric symptoms, and involuntary movements, with some patients presenting with Huntington disease (HD) phenocopies. The SCA 17 expansion is stable during parent-child transmission and intrafamilial phenotypic homogeneity has been reported. However, significant phenotypic variability within families has also been observed. Report of the Family. We presently report a Greek family with a pathological expansion of 54 repeats at the SCA 17 locus that displayed remarkable phenotypic variability. Among 3 affected members, one presented with HD phenocopy; one with progressive ataxia, dementia, chorea, dystonia, and seizures, and one with mild slowly progressive ataxia with minor cognitive and affective symptoms. Conclusions. This is the first family with SCA 17 identified in Greece and highlights the multiple faces of this rare disorder, even within the same family. PMID:25349749

[Observation and analysis on mutation of routine STR locus].

PubMed

Li, Qiu-yang; Feng, Wei-jun; Yang, Qin-gen

2005-05-01

To observe and analyze the characteristic of mutation at STR locus. 27 mutant genes observed in 1211 paternity testing cases were checked by PAGE-silver stained and PowerPlex 16 System Kit and validated by sequencing. Mutant genes locate on 15 loci. The pattern of mutation was accord with stepwise mutation model. The mutation ratio of male-to-female was 8:1 and correlated to the age of father. Mutation rate is correlated to the geometric mean of the number of homogeneous repeats of locus. The higher the mean, the higher the mutation rate. These loci are not so appropriate for use in paternity testing.

Predictors of outcome of an Internet-based cognitive-behavioural therapy for post-traumatic stress disorder in older adults.

PubMed

Böttche, Maria; Kuwert, Philipp; Pietrzak, Robert H; Knaevelsrud, Christine

2016-03-01

The aim of this study was to evaluate the role of resource-oriented variables such as self-efficacy, locus of control (LOC) and post-traumatic growth (PTG) in predicting treatment response in older adults with post-traumatic stress. Fifty-eight older adults with subsyndromal or greater severity of war-associated post-traumatic stress disorder (PTSD) symptoms completed a randomized controlled Internet-based cognitive-behavioural therapy (CBT) with immediate and delayed treatment groups. Assessments of PTSD severity and resource-oriented variables of self-efficacy, LOC and PTG were conducted at baseline, post-treatment and at a 6-month follow-up. Results revealed that pre-treatment scores on measures of internal LOC and PTG predicted PTSD symptom severity at post-treatment, even after controlling for initial PTSD. At a 6-month follow-up, internal LOC continued to predict PTSD symptom severity. In addition, repeated-measures analyses of variance revealed that, relative to older adults with low internal LOC and PTG, older adults with high internal LOC and PTG, respectively, did not differ with respect to initial PTSD severity, but they showed a more pronounced response to treatment. These findings suggest that greater locus of control and post-traumatic growth is associated with greater improvement in PTSD symptoms following Internet-based CBT. Assessment of these constructs may be useful in identifying trauma survivors who are most likely to respond to CBT. Greater internal locus of control and post-traumatic growth is associated with greater improvement in PTSD symptoms following Internet-based CBT. Older adults with initial high internal locus of control and post-traumatic growth, respectively, did not differ with respect to initial PTSD severity, but they showed a more pronounced response to treatment. It could be assumed that patients with initial functional appraisals could benefit easier and faster from a trauma-focused cognitive-behavioural therapy compared to individuals with lower internal locus of control and post-traumatic growth. © 2015 The British Psychological Society.

Identification and genetic effect of a variable duplication in the promoter region of the cattle ADIPOQ gene

USDA-ARS?s Scientific Manuscript database

The ADIPOQ gene of cattle, is located in the vicinity of the quantitative trait locus (QTL) wich effects marbling, the rib eye muscle area and fat thickness on BTA1. In our study, a novel variable duplication (NW_003103812.1:g.9232067_9232133 dup) in the bovine ADIPOQ promoter region was identified ...

Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability

PubMed Central

Fehrmann, Steffen; Bottin-Duplus, Hélène; Leonidou, Andri; Mollereau, Esther; Barthelaix, Audrey; Wei, Wu; Steinmetz, Lars M; Yvert, Gaël

2013-01-01

Living systems may have evolved probabilistic bet hedging strategies that generate cell-to-cell phenotypic diversity in anticipation of environmental catastrophes, as opposed to adaptation via a deterministic response to environmental changes. Evolution of bet hedging assumes that genotypes segregating in natural populations modulate the level of intraclonal diversity, which so far has largely remained hypothetical. Using a fluorescent Pmet17-GFP reporter, we mapped four genetic loci conferring to a wild yeast strain an elevated cell-to-cell variability in the expression of MET17, a gene regulated by the methionine pathway. A frameshift mutation in the Erc1p transmembrane transporter, probably resulting from a release of laboratory strains from negative selection, reduced Pmet17-GFP expression variability. At a second locus, cis-regulatory polymorphisms increased mean expression of the Mup1p methionine permease, causing increased expression variability in trans. These results demonstrate that an expression quantitative trait locus (eQTL) can simultaneously have a deterministic effect in cis and a probabilistic effect in trans. Our observations indicate that the evolution of transmembrane transporter genes can tune intraclonal variation and may therefore be implicated in both reactive and anticipatory strategies of adaptation. PMID:24104478

Maintenance of Genetic Variability under Strong Stabilizing Selection: A Two-Locus Model

PubMed Central

Gavrilets, S.; Hastings, A.

1993-01-01

We study a two locus model with additive contributions to the phenotype to explore the relationship between stabilizing selection and recombination. We show that if the double heterozygote has the optimum phenotype and the contributions of the loci to the trait are different, then any symmetric stabilizing selection fitness function can maintain genetic variability provided selection is sufficiently strong relative to linkage. We present results of a detailed analysis of the quadratic fitness function which show that selection need not be extremely strong relative to recombination for the polymorphic equilibria to be stable. At these polymorphic equilibria the mean value of the trait, in general, is not equal to the optimum phenotype, there exists a large level of negative linkage disequilibrium which ``hides'' additive genetic variance, and different equilibria can be stable simultaneously. We analyze dependence of different characteristics of these equilibria on the location of optimum phenotype, on the difference in allelic effect, and on the strength of selection relative to recombination. Our overall result that stabilizing selection does not necessarily eliminate genetic variability is compatible with some experimental results where the lines subject to strong stabilizing selection did not have significant reductions in genetic variability. PMID:8514145

[Genetic diversity of microsatellite loci in captive Amur tigers].

PubMed

Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

2004-09-01

The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species.

Health locus of control in patients undergoing coronary artery surgery - changes and associated outcomes: a seven-year cohort study.

PubMed

Rideout, Andrew; Tolmie, Elizabeth; Lindsay, Grace

2017-01-01

Health locus of control is a measure of an individual's beliefs in factors that are thought to determine health experiences. Scores are generated and form a graduated linear scale from external to internal control, with respect to their views on health causality. Health locus of control has been considered to be a relatively stable entity. However, it is not clear if this status changes in the advent of serious health challenges, such as coronary artery bypass graft surgery. The aim of this study is to explore the variability of health locus of control and its association with postoperative health in this context. In a longitudinal cohort study of patients undergoing coronary artery bypass graft surgery, a purposive sample ( n=215) were recruited from the waiting list and followed up postoperatively, at approximately one year and seven years later. Patients undergoing coronary artery bypass graft surgery demonstrated marked fluctuations in health locus of control in their peri-operative and rehabilitative phases. Mean health locus of control became more external (often associated with poorer outcomes) peri-operatively, and more internal (generally associated with better health outcomes) in the rehabilitative period. Health locus of control scores were shown to be changeable during a major health care intervention, with possible consequences for patient outcomes and care needs. The significant health belief upheaval demonstrated in this cohort should be considered in assessing patients preoperatively, and managed as part of the patients' clinical journey by both acute and rehabilitation staff. It is likely to have particular importance in individualised assessment and management of future prevention advice for patients.

Diversity at the Locus Associated with Transcription of a Variable Surface Antigen of Pneumocystis carinii as an Index of Population Structure and Dynamics in Infected Rats

PubMed Central

Keely, Scott P.; Cushion, Melanie T.; Stringer, James R.

2003-01-01

Pneumocystis carinii expresses a surface glycoprotein called MSG. Different isoforms of MSG are encoded by a gene family spread over at least 15 telomeric sites. Only one locus, called UCS, supports the production of MSG mRNA. Previous studies showed that P. carinii populations from individual rats exhibited high degrees of diversity with respect to the MSG genes attached to the UCS locus. This diversity could have been generated primarily in the rats studied. Alternatively, the rats may have been infected by P. carinii organisms that were already different at the UCS locus. To investigate this issue, we examined the UCS locus in P. carinii from rats that had been exposed to few of the microbes at a specified time, which produced a bottleneck in the microbial population. Some of the rats with bottlenecks produced P. carinii populations in which a single MSG sequence resided at the UCS locus in 80 to 90% of the organisms, showing that P. carinii can proliferate within a rat without generating the very high levels of UCS diversity previously seen. From the degree of diversity observed in the bottlenecked populations, the maximum rate of switching appeared to be 0.01 event per generation. These data also suggest that the infectious dose is as low as one organism, that rats that share a cage readily infect each other, and that the doubling time of P. carinii in vivo is ∼3 days. In addition, we found that inoculation with 107 P. carinii organisms from a population highly heterogeneous at the UCS locus reproduced this heterogeneity. By contrast, shifts in population structure occurred in rats given 104 P. carinii organisms, suggesting that a small fraction of these proliferated. PMID:12496148

Statistical correction of the Winner’s Curse explains replication variability in quantitative trait genome-wide association studies

PubMed Central

Pe’er, Itsik

2017-01-01

Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10−14), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner’s Curse (p < 10−16). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium. PMID:28715421

Molecular epidemiological characteristics of Salmonella enterica serovars Enteritidis, Typhimurium and Livingstone strains isolated in a Tunisian university hospital.

PubMed

Ktari, Sonia; Ksibi, Boutheina; Gharsallah, Houda; Mnif, Basma; Maalej, Sonda; Rhimi, Fouzia; Hammami, Adnene

2016-03-01

Enteritidis, Typhimurium and Livingstone are the main Salmonella enterica serovars recovered in Tunisia. Here, we aimed to assess the genetic diversity of fifty-seven Salmonella enterica strains from different sampling periods, origins and settings using pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and multi-locus variable-number tandem repeat analysis (MLVA). Salmonella Enteritidis, isolated from human and food sources from two regions in Sfax in 2007, were grouped into one cluster using PFGE. However, using MLVA these strains were divided into two clusters. Salmonella Typhimurium strains, recovered in 2012 and represent sporadic cases of human clinical isolates, were included in one PFGE cluster. Nevertheless, the MLVA technique, divided Salmonella Typhimurium isolates into six clusters with diversity index reaching (DI = 0.757). For Salmonella Livingstone which was responsible of two nosocomial outbreaks during 2000-2003, the PFGE and MLVA methods showed that these strains were genetically closely related. Salmonella Enteritidis and Salmonella Livingstone populations showed a single ST lineage ST11 and ST543 respectively. For Salmonella Typhimurium, two MLST sequence types ST19 and ST328 were defined. Salmonella Enteritidis and Salmonella Typhimurium strains were clearly differentiated by MLVA which was not the case using PFGE. © 2015 APMIS. Published by John Wiley & Sons Ltd.

Defining the electronic and geometric structure of one-electron oxidized copper-bis-phenoxide complexes.

PubMed

Storr, Tim; Verma, Pratik; Pratt, Russell C; Wasinger, Erik C; Shimazaki, Yuichi; Stack, T Daniel P

2008-11-19

The geometric and electronic structure of an oxidized Cu complex ([CuSal](+); Sal = N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-(1R,2R)-diamine) with a non-innocent salen ligand has been investigated both in the solid state and in solution. Integration of information from UV-vis-NIR spectroscopy, magnetic susceptibility, electrochemistry, resonance Raman spectroscopy, X-ray crystallography, X-ray absorption spectroscopy, and density functional theory calculations provides critical insights into the nature of the localization/delocalization of the oxidation locus. In contrast to the analogous Ni derivative [NiSal](+) (Storr, T.; et al. Angew. Chem., Int. Ed. 2007, 46, 5198), which exists solely in the Ni(II) ligand-radical form, the locus of oxidation is metal-based for [CuSal](+), affording exclusively a Cu(III) species in the solid state (4-300 K). Variable-temperature solution studies suggest that [CuSal](+) exists in a reversible spin-equilibrium between a ligand-radical species [Cu(II)Sal(*)](+) (S = 1) and the high-valent metal form [Cu(III)Sal](+) (S = 0), indicative of nearly isoenergetic species. It is surprising that a bis-imine-bis-phenolate ligation stabilizes the Cu(III) oxidation state, and even more surprising that in solution a spin equilibrium occurs without a change in coordination number. The oxidized tetrahydrosalen analogue [CuSal(red)](+) (Sal(red) = N,N'-bis(3,5-di- tert-butylhydroxybenzyl)-1,2-cyclohexane-(1R,2R)-diamine) exists as a temperature-invariant Cu(II)-ligand-radical complex in solution, demonstrating that ostensibly simple variations of the ligand structure affect the locus of oxidation in Cu-bis-phenoxide complexes.

Defining the Electronic and Geometric Structure of One-Electron Oxidized Copper–Bis-phenoxide Complexes

PubMed Central

Storr, Tim; Verma, Pratik; Pratt, Russell C.; Wasinger, Erik C.; Shimazaki, Yuichi; Stack, T. Daniel P.

2009-01-01

The geometric and electronic structure of an oxidized Cu complex ([CuSal]+; Sal = N, N′-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-(1R,2R)-diamine) with a non-innocent salen ligand has been investigated both in the solid state and in solution. Integration of information from UV–vis–NIR spectroscopy, magnetic susceptibility, electrochemistry, resonance Raman spectroscopy, X-ray crystallography, X-ray absorption spectroscopy, and density functional theory calculations provides critical insights into the nature of the localization/delocalization of the oxidation locus. In contrast to the analogous Ni derivative [NiSal]+ (Storr, T.; et al. Angew. Chem., Int. Ed. 2007, 46, 5198), which exists solely in the Ni(II) ligand-radical form, the locus of oxidation is metal-based for [CuSal]+, affording exclusively a Cu(III) species in the solid state (4–300 K). Variable-temperature solution studies suggest that [CuSal]+ exists in a reversible spin-equilibrium between a ligand-radical species [Cu(II)Sal•]+ (S = 1) and the high-valent metal form [Cu(III)Sal]+ (S = 0), indicative of nearly isoenergetic species. It is surprising that a bis-imine–bis-phenolate ligation stabilizes the Cu(III) oxidation state, and even more surprising that in solution a spin equilibrium occurs without a change in coordination number. The oxidized tetrahydrosalen analogue [CuSalred]+ (Salred = N, N′-bis(3,5-di-tert-butylhydroxybenzyl)-1,2-cyclohexane-(1R,2R)-diamine) exists as a temperature-invariant Cu(II)–ligand-radical complex in solution, demonstrating that ostensibly simple variations of the ligand structure affect the locus of oxidation in Cu–bis-phenoxide complexes. PMID:18939830

Trends and differences in tuberculosis incidences and clustering among natives in Denmark, Sweden and Finland: comparison of native incidences and molecular epidemiology among three low-incidence countries.

PubMed

Pedersen, M K; Lillebaek, T; Andersen, A B; Soini, H; Haanperä, M; Groenheit, R; Jonsson, J; Svensson, E

2018-07-01

To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control. TB incidence trends from 1990 through 2015 were compared among the countries. In addition, for the periods 2012-2013 and 2014-2015, genotyping data were compared. Genotyping was performed using the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) method in Denmark and Sweden. For Finland, spoligotyping in conjunction with the 15-locus MIRU-VNTR method was used for 2012-2013 and translated into the 24-locus MIRU-VNTR when feasible, and for 2014-2015 only MIRU-VNTR was used. Both incidence trends and molecular epidemiology were assessed for native cases. The average annual rate of change in TB incidence for native Danes was -2.4% vs. -6.1% and -6.9% for native Swedes and Finns respectively. In 2012-2013 Denmark had 52 native cases in the largest transmission chain vs. three cases in Sweden and ten in Finland, and during the same period the clustering rate for native Danes was 48.8% vs. 6.5% and 18.2% for native Swedes and Finns respectively. For 2014-2015, a similar pattern was seen. The decline of TB among natives in Denmark is slower than for Sweden and Finland, and it seems Denmark has more active transmission among natives. The focused assessment on basic native TB epidemiology reveals striking differences in TB transmission among otherwise similar low-TB-incidence countries. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Attitudes toward euthanasia and physician-assisted suicide: a study of the multivariate effects of healthcare training, patient characteristics, religion and locus of control.

PubMed

Hains, Carrie-Anne Marie; Hulbert-Williams, Nicholas J

2013-11-01

Public and healthcare professionals differ in their attitudes towards euthanasia and physician-assisted suicide (PAS), the legal status of which is currently in the spotlight in the UK. In addition to medical training and experience, religiosity, locus of control and patient characteristics (eg, patient age, pain levels, number of euthanasia requests) are known influencing factors. Previous research tends toward basic designs reporting on attitudes in the context of just one or two potentially influencing factors; we aimed to test the comparative importance of a larger range of variables in a sample of nursing trainees and non-nursing controls. One hundred and fifty-one undergraduate students (early-stage nursing training, late-stage nursing training and non-nursing controls) were approached on a UK university campus and asked to complete a self-report questionnaire. Participants were of mixed gender and were on average 25.5 years old. No significant differences in attitude were found between nursing and non-nursing students. There was a significant positive correlation between higher religiosity and positive attitude toward euthanasia (r=0.19, p<0.05) and a significant negative relationship between internal locus of control and positive attitude toward PAS (r=-0.263, p<0.01). Multivariate analyses revealed differing predictor models for attitudes towards euthanasia and PAS, and confirm the importance of individual differences in determining these attitudes. The unexpected direction of association between religiosity and attitudes may reflect a broader cultural shift in attitudes since earlier research in this area. Furthermore, these findings suggest it possible that experience, more than training itself, may be a bigger influence on attitudinal differences in healthcare professionals.

Pleiotropy in microdeletion syndromes: Neurologic and spermatogenic abnormalities in mice homozygous for the p{sup 6H} deletion are likely due to dysfunction of a single gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinchik, E.M.; Carpenter, D.A.; Handel, M.A.

1995-07-03

Variability and complexity of phenotypes observed in microdeletion syndromes can be due to deletion of a single gene whose product participates in several aspects of development or can be due to the deletion of a number of tightly linked genes, each adding its own effect to the syndrome. The p{sup 6H} deletion in mouse chromosome 7 presents a good model with which to address this question of multigene vs. single-gene pleiotropy. Mice homozygous for the p{sup 6H} deletion are diluted in pigmentation, are smaller than their littermates, and manifest a nervous jerky-gait phenotype. Male homozygotes are sterile and exhibit profoundmore » abnormalities in spermiogenesis. By using N-ethyl-N-nitrosourea (EtNU) mutagenesis and a breeding protocol designed to recover recessive mutations expressed hemizygously opposite a large p-locus deletion, we have generated three noncomplementing mutations that map to the p{sup 6H} deletion. Each of these EtNU-induced mutations has adverse effects on the size, nervous behavior, and progression of spermiogenesis that characterize p{sup 6H} deletion homozygotes. Because etNU is thought to induce primarily intragenic (point) mutations in mouse stem-cell spermatogonia, we propose that the trio of phenotypes (runtiness, nervous jerky gait, and male sterility) expressed in p{sup 6H} deletion homozygotes is the result of deletion of a single highly pleiotropic gene. We also predict that a homologous single locus, quite possibly tightly linked and distal to the D15S12 (P) locus in human chromosome 15q11-q13, may be associated with similar developmental abnormalities in humans. 29 refs., 3 figs., 1 tab.« less

Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

PubMed Central

Mujic, Alija Bajro; Kuo, Alan; Tritt, Andrew; Lipzen, Anna; Chen, Cindy; Johnson, Jenifer; Sharma, Aditi; Barry, Kerrie; Grigoriev, Igor V.; Spatafora, Joseph W.

2017-01-01

Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)—the first genomes available for Basidiomycota truffles—and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A-locus as well as pheromone receptor and pheromone precursor homologs at the mating type B-locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B-locus pheromone receptor and precursor genes than R. vesiculosus, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B-locus compared to a single copy in R. vesiculosus. Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B-locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B-locus region structure intermediate between bipolar and tetrapolar Boletales. PMID:28450370

Genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay

USGS Publications Warehouse

Duda, T. F.

1994-01-01

The genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay was described using starch gel electrophoresis at eight presumptive loci. Specimens were taken from five environmentally distinct sites located throughout the bay. The population maintains a high degree of genetic variation, with a mean heterozygosity of 0.295, a mean polymorphism of 0.75, and an average of 3.70 alleles per locus. The population is genetically homogeneous, as evidenced from genetic distance values and F-statistics. However, heterogeneity of populations was indicated from a contingency chi-square test. Significant deviations from Hardy-Weinberg equilibrium and heterozygote deficiencies were found at the Lap-1 locus for all populations and at the Lap-2 locus for a single population. High levels of variability could represent a universal characteristic of invading species, the levels of variability in the source population(s), and/or the dynamics of the introduction. Lack of differentiation between subpopulations may be due to the immaturity of the San Francisco Bay population, the “general purpose” phenotype genetic strategy of the species, high rates of gene flow in the population, and/or the selective neutrality of the loci investigated.

Variable Number of Tandem Repeats in Salmonella enterica subsp. enterica for Typing Purposes

PubMed Central

Ramisse, Vincent; Houssu, Perrine; Hernandez, Eric; Denoeud, France; Hilaire, Valérie; Lisanti, Olivier; Ramisse, Françoise; Cavallo, Jean-Didier; Vergnaud, Gilles

2004-01-01

The genomic sequences of Salmonella enterica subsp. enterica strains CT18, Ty2 (serovar Typhi), and LT2 (serovar Typhimurium) were analyzed for potential variable number tandem repeats (VNTRs). A multiple-locus VNTR analysis (MLVA) of 99 strains of S. enterica supsp. enterica based on 10 VNTRs distinguished 52 genotypes and placed them into four groups. All strains tested were independent human isolates from France and did not reflect isolates from outbreak episodes. Of these 10 VNTRs, 7 showed variability within serovar Typhi, whereas 1 showed variability within serovar Typhimurium. Four VNTRs showed high Nei's diversity indices (DIs) of 0.81 to 0.87 within serovar Typhi (n = 27). Additionally, three of these more variable VNTRs showed DIs of 0.18 to 0.58 within serovar Paratyphi A (n = 10). The VNTR polymorphic site within multidrug-resistant (MDR) serovar Typhimurium isolates (n = 39; resistance to ampicillin, chloramphenicol, spectinomycin, sulfonamides, and tetracycline) showed a DI of 0.81. Cluster analysis not only identified three genetically distinct groups consistent with the present serovar classification of salmonellae (serovars Typhi, Paratyphi A, and Typhimurium) but also discriminated 25 subtypes (93%) within serovar Typhi isolates. The analysis discriminated only eight subtypes within serovar Typhimurium isolates resistant to ampicillin, chloramphenicol, spectinomycin, sulfonamides, and tetracycline, possibly reflecting the emergence in the mid-1990s of the DT104 phage type, which often displays such an MDR spectrum. Coupled with the ongoing improvements in automated procedures offered by capillary electrophoresis, use of these markers is proposed in further investigations of the potential of MLVA in outbreaks of salmonellosis, especially outbreaks of typhoid fever. PMID:15583305

Professional Women: Job Role Stresses and Psychosocial Variables.

ERIC Educational Resources Information Center

Robinson, Sharon E.; Skarie, Elizabeth K.

1986-01-01

A study of 91 professional women revealed that internal locus of control was significantly related to three job role stresses (role ambiguity, nonparticipation in decision making, and role overload) and to fear of success. (Author/ABB)

The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.

PubMed

Nguyen, Hoang T; Merriman, Tony R; Black, Michael A

2014-01-01

Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN) at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralog ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust the results across multiple populations, in combination with a Bayesian normal mixture model to cluster segmentation scores into groups for individual CN counts. The performance of CNVrd2 was compared to that of two other read depth-based methods (CNVnator, cn.mops) at the CCL3L1 and DEFB103A loci. The highest concordance with the paralog ratio test method was observed for CNVrd2 (77.8/90.4% for CNVrd2, 36.7/4.8% for cn.mops and 7.2/1% for CNVnator at CCL3L1 and DEF103A). CNVrd2 is available as an R package as part of the Bioconductor project: http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html.

The WWW as a research medium: an illustrative survey on paranormal belief.

PubMed

Göritz, A S; Schumacher, J

2000-06-01

Data collected with a short World Wide Web (WWW) survey on paranormal belief, age, sex, locus of control, extraversion, emotional and physical well-being, and mood were compared with findings from recent literature while controlling for effects of self-selection. Each variable was measured with one item. The sample comprised 342 women, 648 men, and 8 participants of unknown sex, of whom 76.7% were self-selected and 23.3% did not select themselves. There was a weak but, given the large sample, significant effect of self-selection regarding paranormal belief (rpb 932 = .08) but no relationships for paranormal belief and the examined variables. In the entire sample, statistically significant correlations ranging from .13 to .07 between paranormal belief and female sex, scores on external locus of control, good mood, extraversion, and emotional well-being corresponded with previous offline results.

Self-Esteem, Locus of Control, and First-Time NCLEX-RN Passage of BSN Students at Historically Black Colleges and Universities.

PubMed

Chavis, Pamella Ivey

Relationships between self-esteem, locus of control (LOC), and first-time passage of National Council Licensure Examination for Registered Nurses (NCLEX-RN®) were examined at baccalaureate nursing programs at two historically black colleges and universities. Shortages continue to exceed demands for RNs prepared at the baccalaureate level. Inconsistent pass rates on the NCLEX-RN for graduates of historically black colleges and universities impede the supply of RNs. Surveys and archival data were used to examine characteristics of the sample and explore relationships among variables. All participants (N = 90) reported high self-esteem and internal LOC. Models suggested that all those with high self-esteem and internal LOC would pass the NCLEX-RN; only 85 percent passed the first time. Statistical analysis revealed a lack of statistical significance between self-esteem, LOC, and first-time passage. Variables not included in the study may have affected first-time passage.

Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants.

PubMed

Maloukh, Lina; Kumarappan, Alagappan; Jarrar, Mohammad; Salehi, Jawad; El-Wakil, Houssam; Rajya Lakshmi, T V

2017-06-01

DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.

Haldane, Waddington and recombinant inbred lines: extension of their work to any number of genes.

PubMed

Samal, Areejit; Martin, Olivier C

2017-11-01

In the early 1930s, J. B. S. Haldane and C. H. Waddington collaborated on the consequences of genetic linkage and inbreeding. One elegant mathematical genetics problem solved by them concerns recombinant inbred lines (RILs) produced via repeated self or brother-sister mating. In this classic contribution, Haldane and Waddington derived an analytical formula for the probabilities of 2-locus and 3-locus RIL genotypes. Specifically, the Haldane-Waddington formula gives the recombination rate R in such lines as a simple function of the per generation recombination rate r. Interestingly, for more than 80 years, an extension of this result to four or more loci remained elusive. In 2015, we generalized the Haldane-Waddington self-mating result to any number of loci. Our solution used self-consistent equations of the multi-locus probabilities 'for an infinite number of generations' and solved these by simple algebraic operations. In practice, our approach provides a quantum leap in the systems that can be handled: the cases of up to six loci can be solved by hand while a computer program implementing our mathematical formalism tackles up to 20 loci on standard desktop computers.

Familial migraine: Exclusion of the susceptibility gene from the reported locus of familial hemiplegic migraine on 19p

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hovatta, I.; Peltonen, L.; Kallela, M.

1994-10-01

Genetic isolates are highly useful in analyses of the molecular background of complex diseases since the enrichment of a limited number of predisposing genes can be predicted in representative families or in specific geographical regions. It has been suggested that the pathophysiology and etiology of familial hemiplegic migraine (FHM) and typical migraine with aura are most probably the same. Recent assignment of FHM locus to chromosome 19p in two French families makes it now possible to test this hypothesis. We report here linkage data on four families with multiple cases of migraine disorder originating from the genetically isolated population ofmore » Finland. We were interested to discover whether the migraine in these families would also show linkage to the markers on 19p. We could exclude a region of 50 cM, flanking the reported FHM locus, as a site of migraine locus in our four families. It seems evident that locus heterogeneity exists between different diagnostic classes of migraine spectrum of diseases and also between different ethnic groups. 10 refs., 2 figs., 1 tab.« less

Locus of control and academic efficacy in the thoughts of life and death of young Quebec university students.

PubMed

Labelle, Réal; Lachance, Lise

2003-01-01

This study evaluated the role of control and efficacy expectations in the thoughts of life and death of 50 male and 50 female university students and investigated sex differences in this regard. It followed a correlational design and employed measures of tridimensional locus of control, expectations of academic efficacy, thoughts of life and death. A comparison of means revealed that male students did not differ from their female counterparts on any of the variables under study. Stepwise regression coefficients indicated that the two cognitive factors accounted more for thoughts of death than for thoughts of life; expectations of academic efficacy were the single variable that most explained variance. Regression equations by sex showed that thoughts of life were associated with internality and expectations of academic efficacy in females, and that thoughts of death were associated with expectations of academic inefficacy in males. The university counseling personnel should be especially sensitive to youths presenting with expectations of externality and of academic inefficacy. The latter variable seems to be particularly important, regardless of sex.

Extension of the root-locus method to a certain class of fractional-order systems.

PubMed

Merrikh-Bayat, Farshad; Afshar, Mahdi; Karimi-Ghartemani, Masoud

2009-01-01

In this paper, the well-known root-locus method is developed for the special subset of linear time-invariant systems commonly known as fractional-order systems. Transfer functions of these systems are rational functions with polynomials of rational powers of the Laplace variable s. Such systems are defined on a Riemann surface because of their multi-valued nature. A set of rules for plotting the root loci on the first Riemann sheet is presented. The important features of the classical root-locus method such as asymptotes, roots condition on the real axis and breakaway points are extended to the fractional case. It is also shown that the proposed method can assess the closed-loop stability of fractional-order systems in the presence of a varying gain in the loop. Moreover, the effect of perturbation on the root loci is discussed. Three illustrative examples are presented to confirm the effectiveness of the proposed algorithm.

A structural equations model of stress, locus of control, social support, psychiatric symptoms, and propensity to leave a job.

PubMed

Afzalur Rahim, M; Psenicka, C

1996-02-01

The main effects of (a) job stress on psychiatric symptoms and propensity to leave a job and of (b) psychiatric symptoms on propensity to leave a job and the (c) moderating effects of locus of control and social support on the relationships of job stress to psychiatric symptoms and propensity to leave a job were examined. Data collected with questionnaires completed by 526 members of the Chamber of Commerce in a southern state were analyzed using LISREL 7 (Jöreskog & Sörbom, 1988). The results indicate that role overload and role insufficiency positively influenced psychiatric symptoms and that role insufficiency, role ambiguity, and role conflict positively influenced propensity to leave a job. Overall, the moderating effects of locus of control on the relationships of stress variables to psychiatric symptoms and propensity to leave a job were significant, but similar moderating effects for social support were not.

FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae).

PubMed

Aguilera, Patricia M; Debat, Humberto J; Scaldaferro, Marisel A; Martí, Dardo A; Grabiele, Mauro

2016-03-01

We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus.

New microsatellite loci isolated via next-generation sequencing for two endangered pronghorn from the Sonoran Desert

USGS Publications Warehouse

Munguia-Vega, Adrian; Klimova, Anastasia; Culver, Melanie

2013-01-01

We isolated 16 novel microsatellite loci in two subspecies of endangered desert pronghorns (Antilocapra americana sonoriensis and Antilocapra americana peninsularis) using a shotgun pyrosequencing approach. All and 87.5 % of the loci were polymorphic within each subspecies, respectively. The mean number of alleles per locus was 4.86 (range 2–8) and 2.5 alleles per locus (range 1–4 alleles), and observed heterozygosity ranged from 0.13 to 0.78 (mean 0.48) and 0.00 to 0.61 (mean 0.31), respectively. We did not find significant linkage disequilibrium among loci pairs and only one locus deviated significantly from Hardy–Weinberg equilibrium in peninsularis.

The Mycobacterium marinum mel2 locus displays similarity to bacterial bioluminescence systems and plays a role in defense against reactive oxygen and nitrogen species

PubMed Central

Subbian, Selvakumar; Mehta, Parmod K; Cirillo, Suat LG; Cirillo, Jeffrey D

2007-01-01

Background Mycobacteria have developed a number of pathways that provide partial protection against both reactive oxygen species (ROS) and reactive nitrogen species (RNS). We recently identified a locus in Mycobacterium marinum, mel2, that plays a role during infection of macrophages. The molecular mechanism of mel2 action is not well understood. Results To better understand the role of the M. marinum mel2 locus, we examined these genes for conserved motifs in silico. Striking similarities were observed between the mel2 locus and loci that encode bioluminescence in other bacterial species. Since bioluminescence systems can play a role in resistance to oxidative stress, we postulated that the mel2 locus might be important for mycobacterial resistance to ROS and RNS. We found that an M. marinum mutant in the first gene in this putative operon, melF, confers increased susceptibility to both ROS and RNS. This mutant is more susceptible to ROS and RNS together than either reactive species alone. Conclusion These observations support a role for the M. marinum mel2 locus in resistance to oxidative stress and provide additional evidence that bioluminescence systems may have evolved from oxidative defense mechanisms. PMID:17239244

Recombination Can Initiate and Terminate at a Large Number of Sites within the Rosy Locus of Drosophila Melanogaster

PubMed Central

Clark, S. H.; Hilliker, A. J.; Chovnick, A.

1988-01-01

This report presents the results of a recombination experiment designed to question the existence of special sites for the initiation or termination of a recombination heteroduplex within the region of the rosy locus. Intragenic recombination events were monitored between two physically separated rosy mutant alleles ry(301) and ry(2) utilizing DNA restriction site polymorphisms as genetic markers. Both ry(301) and ry(2) are known from previous studies to be associated with gene conversion frequencies an order of magnitude lower than single site mutations. The mutations are associated with large, well defined insertions located as internal sites within the locus in prior intragenic mapping studies. On the molecular map, they represent large insertions approximately 2.7 kb apart in the second and third exons, respectively, of the XDH coding region. The present study monitors intragenic recombination in a mutant heterozygous genotype in which DNA homology is disrupted by these large discontinuities, greater than the region of DNA homology and flanking both sides of the locus. If initiation/or termination requires separate sites at either end of the locus, then intragenic recombination within the rosy locus of the heterozygote should be eliminated. Contrary to expectation, significant recombination between these sites is seen. PMID:2834266

Genetic variability in Melipona scutellaris from Recôncavo, Bahia, Brazil.

PubMed

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.

Identification of the Rare, Four Repeat Allele of IL-4 Intron-3 VNTR Polymorphism in Indian Populations.

PubMed

Verma, Henu Kumar; Jha, Aditya Nath; Khodiar, Prafulla Kumar; Patra, Pradeep Kumar; Bhaskar, Lakkakula Venkata Kameswara Subrahmanya

2016-06-01

Cytokines are cell signaling molecules which upon release by cells facilitate the recruitment of immune-modulatory cells towards the sites of inflammation. Genetic variations in cytokine genes are shown to regulate their production and affect the risk of infectious as well as autoimmune diseases. Intron-3 of interleukin-4 gene (IL-4) harbors 70-bp variable number of tandem repeats (VNTR) that may alter the expression level of IL-4 gene. To determine the distribution of IL-4 70-bp VNTR polymorphism in seven genetically heterogeneous populations of Chhattisgarh, India and their comparison with the finding of other Indian and world populations. A total of 371 healthy unrelated individuals from 5 caste and 2 tribal populations were included in the present study. The IL-4 70-bp VNTR genotyping was carried out using PCR and electrophoresis. Overall, 3 alleles of IL-4 70-bp VNTR (a2, a3 and a4) were detected. The results demonstrated the variability of the IL-4 70-bp VNTR polymorphism in Chhattisgarh populations. Allele a3 was the most common allele at the 70-bp VNTR locus in all populations followed by a2 allele. This study reports the presence four repeat allele a4 at a low frequency in the majority of the Chhattisgarh populations studied. Further, the frequency of the minor allele (a2) in Chhattisgarh populations showed similarity with the frequencies of European populations but not with the East Asian populations where the a2 allele is a major allele. Our study provides a baseline for future research into the role of the IL-4 locus in diseases linked to inflammation in Indian populations.

Characterization of Genomic Island 3 and Genetic Variability of Chilean Field Strains of Brucella abortus▿

PubMed Central

Céspedes, Sandra; Salgado, Paulina; Valenzuela, Patricio; Vidal, Roberto; Oñate, Angel A.

2011-01-01

One of the capabilities developed by bacteria is the ability to gain large fragments of DNA from other bacteria or to lose portions of their own genomes. Among these exchangeable fragments are the genomic islands (GIs). Nine GIs have been identified in Brucella, and genomic island 3 (GI-3) is shared by two pathogenic species, B. melitensis and B. abortus. GI-3 encodes mostly unknown proteins. One of the aims of this study was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of B. abortus from Chile to determine whether these isolates are clonally related. Furthermore, we focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of B. abortus from Chile, showed that the strains were genetically homogeneous. To increase the power of genetic discrimination among these strains, we used multiple locus variable-number tandem-repeat (VNTR) analysis with 16 loci (MLVA-16). The results obtained by MLVA-16 showed that the strains of B. abortus were genetically heterogeneous and that most of them clustered according to their geographic origin. Of the genetic loci studied, panel 2B was the one describing the highest diversity in the analysis, as well as locus Bruce19 in panel 2A. In relation to the study of GI-3, our experimental analysis by TP-PCR identified and confirmed that GI-3 is present in all wild strains of B. abortus, demonstrating the high stability of gene cluster GI-3 in Chilean field strains. PMID:21543580

Dynamic of Mutational Events in Variable Number Tandem Repeats of Escherichia coli O157:H7

PubMed Central

Bustamante, A. V.; Sanso, A. M.; Segura, D. O.; Parma, A. E.; Lucchesi, P. M. A.

2013-01-01

VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenic E. coli O157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05 to 1.8 × 10−03 mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03 mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study. PMID:24093095

Impact of donor mismatches at individual HLA-A, -B, -C, -DR, and -DQ loci on the development of HLA-specific antibodies in patients listed for repeat renal transplantation.

PubMed

Kosmoliaptsis, Vasilios; Gjorgjimajkoska, Olivera; Sharples, Linda D; Chaudhry, Afzal N; Chatzizacharias, Nikolaos; Peacock, Sarah; Torpey, Nicholas; Bolton, Eleanor M; Taylor, Craig J; Bradley, J Andrew

2014-11-01

We have analyzed the relationship between donor mismatches at each HLA locus and development of HLA locus-specific antibodies in patients listed for repeat transplantation. HLA antibody screening was undertaken using single-antigen beads in 131 kidney transplant recipients returning to the transplant waiting list following first graft failure. The number of HLA mismatches and the calculated reaction frequency of antibody reactivity against 10,000 consecutive deceased organ donors were determined for each HLA locus. Two-thirds of patients awaiting repeat transplantation were sensitized (calculated reaction frequency over 15%) and half were highly sensitized (calculated reaction frequency of 85% and greater). Antibody levels peaked after re-listing for repeat transplantation, were independent of graft nephrectomy and were associated with length of time on the waiting list (odds ratio 8.4) and with maintenance on dual immunosuppression (odds ratio 0.2). Sensitization was independently associated with increasing number of donor HLA mismatches (odds ratio 1.4). All mismatched HLA loci contributed to the development of HLA locus-specific antibodies (HLA-A: odds ratio 3.2, HLA-B: odds ratio 3.4, HLA-C: odds ratio 2.5, HLA-DRB1: odds ratio 3.5, HLA-DRB3/4/5: odds ratio 3.9, and HLA-DQ: odds ratio 3.0 (all significant)). Thus, the risk of allosensitization following failure of a first renal transplant increases incrementally with the number of mismatches at all HLA loci assessed. Maintenance of re-listed patients on dual immunosuppression was associated with a reduced risk of sensitization.

Measurement of locus copy number by hybridisation with amplifiable probes

PubMed Central

Armour, John A. L.; Sismani, Carolina; Patsalis, Philippos C.; Cross, Gareth

2000-01-01

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicroscopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader–Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications. PMID:10606661

Measurement of locus copy number by hybridisation with amplifiable probes.

PubMed

Armour, J A; Sismani, C; Patsalis, P C; Cross, G

2000-01-15

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicro-scopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader-Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications.

Intergenic Variable-Number Tandem-Repeat Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes.

PubMed

Zhu, Luchang; Olsen, Randall J; Horstmann, Nicola; Shelburne, Samuel A; Fan, Jia; Hu, Ye; Musser, James M

2016-07-01

Variable-number tandem-repeat (VNTR) polymorphisms are ubiquitous in bacteria. However, only a small fraction of them has been functionally studied. Here, we report an intergenic VNTR polymorphism that confers an altered level of toxin production and increased virulence in Streptococcus pyogenes The nature of the polymorphism is a one-unit deletion in a three-tandem-repeat locus upstream of the rocA gene encoding a sensor kinase. S. pyogenes strains with this type of polymorphism cause human infection and produce significantly larger amounts of the secreted cytotoxins S. pyogenes NADase (SPN) and streptolysin O (SLO). Using isogenic mutant strains, we demonstrate that deleting one or more units of the tandem repeats abolished RocA production, reduced CovR phosphorylation, derepressed multiple CovR-regulated virulence factors (such as SPN and SLO), and increased virulence in a mouse model of necrotizing fasciitis. The phenotypic effect of the VNTR polymorphism was nearly the same as that of inactivating the rocA gene. In summary, we identified and characterized an intergenic VNTR polymorphism in S. pyogenes that affects toxin production and virulence. These new findings enhance understanding of rocA biology and the function of VNTR polymorphisms in S. pyogenes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

[Self-esteem, resilience, locus of control and suicide risk in nursing students].

PubMed

Montes-Hidalgo, Javier; Tomás-Sábado, Joaquín

2016-01-01

Assuming that suicide is the result of a series of factors acting cumulatively, the aim of this paper was to study the association of self-esteem, resilience and locus of control with the risk of suicidal behavior in a sample of nursing students. Observational, cross-sectional and correlational study with 186 nursing students who answered a questionnaire that contained, in addition to demographic data, the Spanish forms of Rosenberg self-esteem scale, the brief resilient coping scale, the Plutchik scale of suicide risk and the Rotter's internal-external locus of control scale. The scores of males and females are very similar on all scales except Locus of Control, where a significantly greater tendency of females attributed to external control. 6.4% of students have scores indicating suicide risk. Suicide risk scores correlated negatively and significantly with self-esteem and resilience and positively with locus of control. The multiple linear regression analysis identified self-esteem as the main variable related to suicide risk. The results suggest that students who have low self-esteem, have difficulty in adjusting to adverse situations and tend to the external attribution of the consequences of their actions may have an increased risk of suicidal behavior. Furthermore, the identification of self-esteem as the important factor involved in suicide risk can help in designing prevention programs. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

Dissemination of streptococcal pyrogenic exotoxin G (spegg) with an IS-like element in fish isolates of Streptococcus dysgalactiae.

PubMed

Abdelsalam, Mohamed; Chen, Shih-Chu; Yoshida, Terutoyo

2010-08-01

The Lancefield group C alpha-hemolytic Streptococcus dysgalactiae ssp. dysgalactiae (GCSD) causes systemic granulomatous inflammatory disease and high mortality rates in infected fish. Superantigen and streptolysin S genes are the most important virulence factors contributing to an invasive streptococcal infection. PCR amplification revealed that all strains isolated from moribund fish harbored the streptolysin S structural gene (sagA). GCSD fish isolates were PCR negative for emm, speA, speB, speC, speM, smeZ, and ssa. However, the size of the streptococcal pyrogenic exotoxin G (spegg) locus, a superantigen, in positive S. dysgalactiae fish and pig strains was variable. The ORF of the spegg locus of 26 GCSD fish strains and one GCSD pig strain was inserted with IS981SC. Interestingly, the ORF of the spegg locus of two fish strains of GCSD collected in Malaysia was inserted with an IS981SC-IS1161 hybrid IS element. The hybrid IS element was found in all of the GCSD fish isolates and one GCSD pig through PCR screening. Although no insertion sequence (IS) was detected in the spegg locus of S. dysgalactiae ssp. equisimilis (GCSE) strains, a five-nucleotide deletion mutation was detected in the ORF of the spegg locus of one GCSE strain at the supposed site of IS981SC insertion, resulting in a frameshift mutation.

Influence of health locus of control and fear of hypoglycaemia on glycaemic control and treatment satisfaction in people with Type 1 diabetes on insulin pump therapy.

PubMed

Indelicato, L; Mariano, V; Galasso, S; Boscari, F; Cipponeri, E; Negri, C; Frigo, A; Avogaro, A; Bonora, E; Trombetta, M; Bruttomesso, D

2017-05-01

To assess the influence of health locus of control and fear of hypoglycaemia on metabolic control and treatment satisfaction in people with Type 1 diabetes mellitus on continuous subcutaneous insulin infusion. People with Type 1 diabetes on continuous subcutaneous insulin infusion for at least 1 year, sub-classified as an 'acceptable glucose control' group [HbA 1c ≤ 58 mmol/mol (7.5%)] and a 'suboptimum glucose control' group [HbA 1c > 58 mmol/mol (7.5%)], were consecutively enrolled in a multicentre cross-sectional study. Questionnaires were administered to assess health locus of control [Multidimensional Health Locus of Control (MHLC) scale, with internal and external subscales], fear of hypoglycaemia [Hypoglycaemia Fear Survey II (HFS-II)] and treatment satisfaction [Diabetes Treatment Satisfaction Questionnaire (DTSQ)]. We enrolled 214 participants (mean ± sd age 43.4 ± 12.1 years). The suboptimum glucose control group (n = 127) had lower mean ± sd internal MHLC and DTSQ scores than the acceptable glucose control group (19.6 ± 5.2 vs 21.0 ± 5.0, P = 0.04 and 28.8 ± 4.8 vs 30.9 ± 4.5, P < 0.001). HFS-II scores did not differ between the two groups. Internal MHLC score was negatively associated with HbA 1c (r = -0.15, P < 0.05) and positively associated with the number of mild and severe hypoglycaemic episodes (r = 0.16, P < 0.05 and r = 0.18, P < 0.001, respectively) and with DTSQ score (r = 0.17, P < 0.05). HFS-II score was negatively associated with DTSQ score (r = -0.18, P < 0.05) and positively with number of severe hypoglycaemic episodes (r = 0.16, P < 0.5). In adults with Type 1 diabetes receiving continuous subcutaneous insulin infusion, high internal locus represents the most important locus of control pattern for achieving good metabolic control. © 2017 Diabetes UK.

Aluminum tolerance is associated with higher MATE1 gene copy-number in maize

USDA-ARS?s Scientific Manuscript database

Genome structure variation, including copy-number (CNV) and presence/absence variation (PAV), comprise a large extent of maize genetic diversity but their effect on phenotypes remains largely unexplored. Here we describe how copy-number variation in a major aluminum (Al) tolerance locus contributes ...

Relations Between Embedded Figures Test Performance and Dimensions of the I-E Scale

ERIC Educational Resources Information Center

Strahan, Robert; Huth, Helga

1975-01-01

Relations between an embedded figures measure of field independence and various dimensions of Rotter's Internal-External Locus of Control Scale were investigated. The general absence of significant correlations suggests that these variables are essentially unrelated. (Author)

Locus of decision making in multinational corporations and its relationship to subsidiary performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goehle, D.G.

1978-01-01

A conceptual model was developed which drew from the existing research in organization theory, comparative management, and international business which assisted in the delineation of the relevant variables and suggested the nature of their relationship to the locus of decision making. The conceptual model incorporated certain corporate and subsidiary factors considered an influence on the determination of the locus of decision making. Corporate factors included product line or industry, size and complexity of international operations, organization structure, availability of managerial talent, and corporate philosophy. Subsidiary characteristics included subsidiary age and size, availability of local managerial talent, geographic distance from headquartersmore » and other affiliated units, and subsidiary environmental characteristics. The locus of desicion making was measured by the level of participation the headquarters and subsidiary management had in decision making for twenty-nine decisions, representing six functional areas. Levels of participation for headquarters and subsidiary managers were measured for each decision based on responses to a five-point scale of decision process categories which indicated varying levels of headquarters and subsidiary participation. The sample included ten US multinational corporations representing five industries: pharmaceuticals, tire and rubber, automobiles, capital equipment, and food processing.« less

Coat color genetics of Peromyscus: IV. Variable white, a new dominant mutation in the deer mouse.

PubMed

Cowling, K; Robbins, R J; Haigh, G R; Teed, S K; Dawson, W D

1994-01-01

The variable white mutation arose spontaneously in 1983 within a laboratory stock of wild-type deer mice (Peromyscus maniculatus). The original mutant animal was born to a wild-type pair that had previously produced several entirely wild-type litters. Other variable white animals were bred from the initial individual. Variable white deer mice exhibit extensive areas of white on the head, sides, and tail. Usually a portion of pigmented pelage occurs dorsally and on the shoulders, but the extent of white varies from nearly all white to patches of white on the muzzle, tip of tail, and sides. The pattern is irregular, but not entirely asymmetrical. Eyes are pigmented, but histologically reveal a decrease in thickness and pigmentation of the choroid layer. Many variable white animals do not respond to auditory stimuli, an effect that is particularly evident in animals in which the head is entirely white. Ataxic behavior is also prevalent. Pigment distribution, together with auditory and retinal deficiencies, suggests a neural crest cell migration defect. Breeding data are consistent with an autosomal semidominant, lethal mode of inheritance. The trait differs from two somewhat similar variants in Peromyscus: from dominant spot (S) in extent and pattern of pigmentation and from whiteside (ws), an autosomal recessive trait, in the mode of inheritance and viability. Evidence for possible homology with the Va (varitint-waddler) locus in house mouse (Mus) is presented. The symbol Vw is tentatively assigned for the variable white locus in Peromyscus.

Restriction fragment length polymorphism among Israeli Holstein-Friesian dairy bulls.

PubMed

Beckmann, J S; Kashi, Y; Hallerman, E M; Nave, A; Soller, M

1986-01-01

Israeli Holstein-Friesian dairy bulls were screened for restriction fragment length polymorphisms by hybridizing cloned DNA probes for bovine growth hormone, for chymosin, and for rat muscle beta-actin to restriction endonuclease-digested DNA immobilized on nitrocellulose filters. The population proved to be polymorphic at the growth hormone locus, with evidence consistent with the phenotypes being inherited in allelic fashion. A low level of polymorphism was also observed at one of the beta-actin gene family loci. The chymosin locus was monomorphic with the restriction enzymes utilized. The results illustrate the power of restriction fragment length polymorphism methodology in visualizing genetic variability in dairy cattle populations.

Testing for time-based correlates of perceived gender discrimination.

PubMed

Blau, Gary; Tatum, Donna Surges; Ward-Cook, Kory; Dobria, Lidia; McCoy, Keith

2005-01-01

Using a sample of 201 medical technologists (MTs) over a five-year period, this study extends initial findings on perceived gender discrimination (PGD) by Blau and Tatum (2000) by applying organizational justice variables and internal-external locus of control as hypothesized correlates of PGD. Three types of organizational justice were measured: distributive, procedural, and interactional. General relationships found include locus of control being related to PGD such that internals perceived lower PGD. Also, distributive, procedural, and interactional justice were negatively related to PGD. However, increasing the time interval between these correlates weakened their relationships. The relationship of interactional justice to PGD remained the most "resistant" to attenuation over time.

Multiple-locus variable-number tandem repeat analysis potentially reveals the existence of two groups of Anaplasma phagocytophilum circulating in cattle in France with different wild reservoirs.

PubMed

Dugat, Thibaud; Zanella, Gina; Véran, Luc; Lesage, Céline; Girault, Guillaume; Durand, Benoît; Lagrée, Anne-Claire; Boulouis, Henri-Jean; Haddad, Nadia

2016-11-22

Anaplasma phagocytophilum is the causative agent of tick-borne fever, a disease with high economic impact for domestic ruminants in Europe. Epidemiological cycles of this species are complex, and involve different ecotypes circulating in various host species. To date, these epidemiological cycles are poorly understood, especially in Europe, as European reservoir hosts (i.e. vertebrate hosts enabling long-term maintenance of the bacterium in the ecosystem), of the bacterium have not yet been clearly identified. In this study, our objective was to explore the presence, the prevalence, and the genetic diversity of A. phagocytophilum in wild animals, in order to better understand their implications as reservoir hosts of this pathogen. The spleens of 101 wild animals were collected from central France and tested for the presence of A. phagocytophilum DNA by msp2 qPCR. Positive samples were then typed by multi-locus variable-number tandem repeat (VNTR) analysis (MLVA), and compared to 179 previously typed A. phagocytophilum samples. Anaplasma phagocytophilum DNA was detected in 82/101 (81.2%) animals including 48/49 red deer (98%), 20/21 roe deer (95.2%), 13/29 wild boars (44.8%), and 1/1 red fox. MLVA enabled the discrimination of two A. phagocytophilum groups: group A contained the majority of A. phagocytophilum from red deer and two thirds of those from cattle, while group B included a human strain and variants from diverse animal species, i.e. sheep, dogs, a horse, the majority of variants from roe deer, and the remaining variants from cattle and red deer. Our results suggest that red deer and roe deer are promising A. phagocytophilum reservoir host candidates. Moreover, we also showed that A. phagocytophilum potentially circulates in at least two epidemiological cycles in French cattle. The first cycle may involve red deer as reservoir hosts and cattle as accidental hosts for Group A strains, whereas the second cycle could involve roe deer as reservoir hosts and at least domestic ruminants, dogs, horses, and humans as accidental hosts for Group B strains.

A Symmetric Two-Locus Fertility Model

PubMed Central

Feldman, Marcus W.; Liberman, Uri

1985-01-01

A model in which selection is mediated by differential fertilities among the genotypes at two diallelic loci is proposed. Fertility depends only on the number of heterozygous loci participating in the mating. Classes analogous to symmetric equilibria in symmetric viability models are determined explicitly and shown to exhibit stability behavior very different from the viability results. Linkage equilibrium is shown to occur in a relatively asymmetric fashion and to overlap in stability with linkage disequilibrium. In many cases single-locus or two-locus polymorphism is shown to be stable simultaneously with chromosome fixation even under very tight linkage. It is suggested that historical effects may be of great significance in the evolution of systems in which fertility is the primary agent of natural selection. PMID:3967817

A mathematical model for evolution and SETI.

PubMed

Maccone, Claudio

2011-12-01

Darwinian evolution theory may be regarded as a part of SETI theory in that the factor f(l) in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor f(l) is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factors increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions (b-lognormals) constrained between the time axis and the exponential growth curve. Finally, since each b-lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

Modelling Evolution and SETI Mathematically

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2012-05-01

Darwinian evolution theory may be regarded as a part of SETI theory in that the factor fl in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor fl is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factor increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions constrained between the time axis and the exponential growth curve. Finally, since each lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

A Mathematical Model for Evolution and SETI

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2011-12-01

Darwinian evolution theory may be regarded as a part of SETI theory in that the factor fl in the Drake equation represents the fraction of planets suitable for life on which life actually arose. In this paper we firstly provide a statistical generalization of the Drake equation where the factor fl is shown to follow the lognormal probability distribution. This lognormal distribution is a consequence of the Central Limit Theorem (CLT) of Statistics, stating that the product of a number of independent random variables whose probability densities are unknown and independent of each other approached the lognormal distribution when the number of factors increased to infinity. In addition we show that the exponential growth of the number of species typical of Darwinian Evolution may be regarded as the geometric locus of the peaks of a one-parameter family of lognormal distributions (b-lognormals) constrained between the time axis and the exponential growth curve. Finally, since each b-lognormal distribution in the family may in turn be regarded as the product of a large number (actually "an infinity") of independent lognormal probability distributions, the mathematical way is paved to further cast Darwinian Evolution into a mathematical theory in agreement with both its typical exponential growth in the number of living species and the Statistical Drake Equation.

First Worldwide Proficiency Study on Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Complex Strains

PubMed Central

de Beer, Jessica L.; Kremer, Kristin; Ködmön, Csaba; Supply, Philip

2012-01-01

Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future. PMID:22170917

Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates.

PubMed

Noller, Anna C; McEllistrem, M Catherine; Pacheco, Antonio G F; Boxrud, David J; Harrison, Lee H

2003-12-01

Escherichia coli O157:H7 is a major cause of food-borne illness in the United States. Outbreak detection involves traditional epidemiological methods and routine molecular subtyping by pulsed-field gel electrophoresis (PFGE). PFGE is labor-intensive, and the results are difficult to analyze and not easily transferable between laboratories. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a fast, portable method that analyzes multiple VNTR loci, which are areas of the bacterial genome that evolve quickly. Eighty isolates, including 21 isolates from five epidemiologically well-characterized outbreaks from Pennsylvania and Minnesota, were analyzed by PFGE and MLVA. Strains in PFGE clusters were defined as strains that differed by less than or equal to one band by using XbaI and the confirmatory enzyme SpeI. MLVA was performed by comparing the number of tandem repeats at seven loci. From 6 to 30 alleles were found at the seven loci, resulting in 64 MLVA types among the 80 isolates. MLVA correctly identified the isolates from all five outbreaks if only a single-locus variant was allowed. MLVA differentiated strains with unique PFGE types. Additionally, MLVA discriminated strains within PFGE-defined clusters that were not known to be part of an outbreak. In addition to being a simple and validated method for E. coli O157:H7 outbreak detection, MLVA appears to have a sensitivity equal to that of PFGE and a specificity superior to that of PFGE.

Genome-wide association analysis identifies a meningioma risk locus at 11p15.5.

PubMed

Claus, Elizabeth B; Cornish, Alex J; Broderick, Peter; Schildkraut, Joellen M; Dobbins, Sara E; Holroyd, Amy; Calvocoressi, Lisa; Lu, Lingeng; Hansen, Helen M; Smirnov, Ivan; Walsh, Kyle M; Schramm, Johannes; Hoffmann, Per; Nöthen, Markus M; Jöckel, Karl-Heinz; Swerdlow, Anthony; Larsen, Signe Benzon; Johansen, Christoffer; Simon, Matthias; Bondy, Melissa; Wrensch, Margaret; Houlston, Richard; Wiemels, Joseph L

2018-05-12

Meningioma are adult brain tumors originating in the meningeal coverings of the brain and spinal cord, with significant heritable basis. Genome-wide association studies (GWAS) have previously identified only a single risk locus for meningioma, at 10p12.31. To identify a susceptibility locus for meningioma, we conducted a meta-analysis of two GWAS, imputed using a merged reference panel of 1,000 Genomes and UK10K data, with validation in two independent sample series totaling 2,138 cases and 12,081 controls. We identified a new susceptibility locus for meningioma at 11p15.5 (rs2686876, odds ratio = 1.44, P = 9.86 × 10-9). A number of genes localize to the region of linkage disequilibrium encompassing rs2686876, including RIC8A, which plays a central role in the development of neural crest-derived structures, such as the meninges. This finding advances our understanding of the genetic basis of meningioma development and provides additional support for a polygenic model of meningioma.

The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage

PubMed Central

Chaumeil, Julie; Micsinai, Mariann; Ntziachristos, Panagiotis; Roth, David B.; Aifantis, Iannis; Kluger, Yuval; Deriano, Ludovic; Skok, Jane A.

2013-01-01

Tight control of antigen-receptor gene rearrangement is required to preserve genome integrity and prevent the occurrence of leukemia and lymphoma. Nonetheless, mistakes can happen, leading to the generation of aberrant rearrangements, such as Tcra/d-Igh inter-locus translocations that are a hallmark of ATM deficiency. Current evidence indicates that these translocations arise from the persistence of unrepaired breaks converging at different stages of thymocyte differentiation. Here we show that a defect in feedback control of RAG2 activity gives rise to bi-locus breaks and damage on Tcra/d and Igh in the same T cell at the same developmental stage, which provides a direct mechanism for generating these inter-locus rearrangements. Both the RAG2 C-terminus and ATM prevent bi-locus RAG-mediated cleavage through modulation of 3D conformation (higher order loops) and nuclear organization of the two loci. This limits the number of potential substrates for translocation and provides an important mechanism for protecting genome stability. PMID:23900513

Personality traits associated with genetic counselor compassion fatigue: the roles of dispositional optimism and locus of control.

PubMed

Injeyan, Marie C; Shuman, Cheryl; Shugar, Andrea; Chitayat, David; Atenafu, Eshetu G; Kaiser, Amy

2011-10-01

Compassion fatigue (CMF) arises as a consequence of secondary exposure to distress and can be elevated in some health practitioners. Locus of control and dispositional optimism are aspects of personality known to influence coping style. To investigate whether these personality traits influence CMF risk, we surveyed 355 genetic counselors about their CMF, locus of control orientation, and degree of dispositional optimism. Approximately half of respondents reported they experience CMF; 26.6% had considered leaving their job due to CMF symptoms. Mixed-method analyses revealed that genetic counselors having an external locus of control and low optimism were at highest risk for CMF. Those at highest risk experienced moderate-to-high burnout, low-to-moderate compassion satisfaction, and tended to rely on religion/spirituality when coping with stress. CMF risk was not influenced by years in practice, number of genetic counselor colleagues in the workplace, or completion of graduate training in this area. Recommendations for practice and education are outlined.

Population genetics of apolipoprotein A-4, E, and H polymorphisms in Yanomami Indians of northwestern Brazil: associations with lipids, lipoproteins, and carbohydrate metabolism.

PubMed

Crews, D E; Kamboh, M I; Mancilha-Carvalho, J J; Kottke, B

1993-04-01

Using isoelectric focusing and immunoblotting techniques, we screened 96 serum samples from Yanomami Indians of northwestern Brazil to determine structural variation at three apolipoprotein loci: A4, E, and H. The APO-H locus, which is commonly polymorphic in white and black samples, was found to be monomorphic. At the APO-E locus only two alleles, APOE*3 and APOE*4, rather than the three-allele polymorphism commonly seen in Caucasians, was observed. At the APO-A4 locus no example of the APOA4*2 allele, found in Caucasians, was detected. However, the frequency of the less common APOA4*4 allele was above what has been observed in any other population. We investigated the impact of genetic variation at both polymorphic loci on quantitative differences in lipids, apolipoproteins, serum glucose, glycated hemoglobin, and uric acid. Contrary to the cholesterol-elevating effect of APOE*4 reported elsewhere, in both univariate analyses and after adjustments for age, sex, weight, and height, APOE*4 was associated with about a 4% lower mean serum cholesterol. Only after adjustment was this association statistically significant. The APOE*4 allele was significantly associated with unadjusted APO-A1 and APO-E levels but not with any other dependent variable; associations with adjusted APO-A1, APO-C2, and uric acid also approached standard levels of statistical significance (p < or = 0.05). In univariate analyses the APOA4*4 allele was significantly associated with APO-B, serum glucose, percent glycated hemoglobin, and uric acid, but no significant associations were observed after dependent variables were adjusted for age, sex, weight, and height. These results support the notion that apolipoprotein distributions and their associations with lipid and carbohydrate metabolism show ethnic variability.

Coping Styles Mediate the Relationship Between Self-esteem, Health Locus of Control, and Health-Promoting Behavior in Chinese Patients With Coronary Heart Disease.

PubMed

Zou, Huijing; Tian, Qian; Chen, Yuxia; Cheng, Cheng; Fan, Xiuzhen

Health-promoting behavior plays an important role in reducing the burden of coronary heart disease. Self-esteem and health locus of control may contribute to health-promoting behavior, and coping styles may mediate these associations. The aims of our study were to examine whether self-esteem and health locus of control are associated with health-promoting behavior and examine the possible mediating effect of coping styles in patients with coronary heart disease. Health-promoting behavior, self-esteem, health locus of control, and coping styles were assessed in 272 hospitalized patients (60 ± 12 years, 61% male) with coronary heart disease. Hierarchical regression analysis was conducted to analyze the relationships between health-promoting behavior and other variables. Mediation effect was examined according to the methods of Baron and Kenny. The mean score for health-promoting behavior was 2.57 ± 0.51; 38.2% of patients (n = 104) scored lower than 2.5. Self-esteem (β = .139, P < .05), confrontation coping style (β = .491, P < .001), disease duration (≥6 months, β = .147, P < .05), and monthly income (≥1000 RMB [approximately US$154], β = .111, P < .05) were positively associated with health-promoting behavior, accounting for 47.5% of its variance (F = 19.828). Confrontation partly mediated the association between self-esteem and health-promoting behavior and completely mediated the relationship between internal health locus of control and health-promoting behavior. Confrontation plays a mediating role in the association among self-esteem, internal health locus of control, and health-promoting behavior. Strategies should be undertaken to encourage the use of confrontation coping style, which will facilitate health-promoting behavior.

Genetic and environmental influences on the relationship between flow proneness, locus of control and behavioral inhibition.

PubMed

Mosing, Miriam A; Pedersen, Nancy L; Cesarini, David; Johannesson, Magnus; Magnusson, Patrik K E; Nakamura, Jeanne; Madison, Guy; Ullén, Fredrik

2012-01-01

Flow is a psychological state of high but subjectively effortless attention that typically occurs during active performance of challenging tasks and is accompanied by a sense of automaticity, high control, low self-awareness, and enjoyment. Flow proneness is associated with traits and behaviors related to low neuroticism such as emotional stability, conscientiousness, active coping, self-esteem and life satisfaction. Little is known about the genetic architecture of flow proneness, behavioral inhibition and locus of control--traits also associated with neuroticism--and their interrelation. Here, we hypothesized that individuals low in behavioral inhibition and with an internal locus of control would be more likely to experience flow and explored the genetic and environmental architecture of the relationship between the three variables. Behavioral inhibition and locus of control was measured in a large population sample of 3,375 full twin pairs and 4,527 single twins, about 26% of whom also scored the flow proneness questionnaire. Findings revealed significant but relatively low correlations between the three traits and moderate heritability estimates of .41, .45, and .30 for flow proneness, behavioral inhibition, and locus of control, respectively, with some indication of non-additive genetic influences. For behavioral inhibition we found significant sex differences in heritability, with females showing a higher estimate including significant non-additive genetic influences, while in males the entire heritability was due to additive genetic variance. We also found a mainly genetically mediated relationship between the three traits, suggesting that individuals who are genetically predisposed to experience flow, show less behavioral inhibition (less anxious) and feel that they are in control of their own destiny (internal locus of control). We discuss that some of the genes underlying this relationship may include those influencing the function of dopaminergic neural systems.

Relationships Between Health Behaviors, Self-Efficacy, and Health Locus of Control of Students at the Universities of the Third Age.

PubMed

Zielińska-Więczkowska, Halina

2016-02-16

BACKGROUND This study aimed to determine the relationship of health behaviors with the health locus of control and the sense of self-efficacy against the background of socio-economic factors and self-rated health among students of the Universities of the Third Age (U3As). MATERIAL AND METHODS The study included 320 U3A students, with mean age of 67.5 years. The following research tools were used: Health Behavior Inventory (HBI), Multidimensional Health Locus of Control Scale (MHLC), Generalized Self-Efficacy Scale (GSES), and an original survey of the author's own design. RESULTS Mean total HBI and GSES scores were 90.63 and 30.12, respectively. These results are satisfactory. A slight predominance of internal health locus of control was documented. A number of significant correlations were found between the HBI, GSES, and MHLC scores, except for the MHLC subscale expressing the influence of chance. Educational attainment was shown to have a significant impact on the scores for the positive attitude and proper dietary habits subscales of HBI, as well as on the GSES scores. Economic status of the participants influenced the levels of positive attitude, internal health locus of control, and self-efficacy. Furthermore, internal health locus of control was found to be modulated by subjective health of the respondents. The scores for external health locus of control and the influence of chance increased significantly with age. CONCLUSIONS The currently noticeable emphasis placed on lifelong education should serve as a good prognostic factor for health behaviors and personal health resources for years to come.

A single nucleotide polymorphism in the FADS1/FADS2 gene is associated with plasma lipid profiles in two genetically similar Asian ethnic groups with distinctive differences in lifestyle.

PubMed

Nakayama, Kazuhiro; Bayasgalan, Tumenbayer; Tazoe, Fumiko; Yanagisawa, Yoshiko; Gotoh, Takaya; Yamanaka, Kazuhiro; Ogawa, Ayumi; Munkhtulga, Lkhagvasuren; Chimedregze, Ulziiburen; Kagawa, Yasuo; Ishibashi, Shun; Iwamoto, Sadahiko

2010-06-01

Recent genome-wide association studies (GWASs) showed that single nucleotide polymorphisms (SNPs) in FADS1/FADS2 were associated with plasma lipid concentrations in populations with European ancestry. We investigated the associations between the SNPs in FADS1/FADS2 and plasma concentrations of triglycerides, high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) in two Asian groups, i.e., Japanese and Mongolians. The genotype of rs174547 (T/C), found to be associated with triglyceride and HDL-C concentrations in the GWAS, was determined in 21,004 Japanese and 1,203 Mongolian individuals. Genotype-phenotype association was assessed by using multiple linear regression models, assuming an additive model of inheritance. The copy number of the rs174547 C allele was significantly associated with increased triglyceride levels (P = 1.5 x 10(-6)) and decreased HDL-C levels (P = 0.03) in the Japanese population. On the other hand, in the Mongolian population, the rs174547 C allele copy number was strongly associated with decreased LDL-C levels (P = 2.6 x 10(-6)), but was not associated with triglyceride and HDL-C levels. The linkage disequilibrium pattern and haplotype structures of SNPs around the FADS1/FADS2 locus showed no marked dissimilarity between Japanese and Mongolian individuals. The present data indicate that the FADS1/FADS2 locus can be added to the growing list of loci involved in polygenic dyslipidemia in Asians. Furthermore, the variable effects of FADS1/FADS2 on plasma lipid profiles in Asians may result from differences in the dietary intake of polyunsaturated fatty acids, which serve as substrates for enzymes encoded by FADS1/FADS2.

A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.

PubMed

Clerc-Blain, Jessica L E; Starr, Julian R; Bull, Roger D; Saarela, Jeffery M

2010-01-01

Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies. © 2009 Blackwell Publishing Ltd.

Correspondence between EQ-5D health state classifications and EQ VAS scores.

PubMed

Whynes, David K

2008-11-07

The EQ-5D health-related quality of life instrument comprises a health state classification followed by a health evaluation using a visual analogue scale (VAS). The EQ-5D has been employed frequently in economic evaluations, yet the relationship between the two parts of the instrument remains ill-understood. In this paper, we examine the correspondence between VAS scores and health state classifications for a large sample, and identify variables which contribute to determining the VAS scores independently of the health states as classified. A UK trial of management of low-grade abnormalities detected on screening for cervical pre-cancer (TOMBOLA) provided EQ-5D data for over 3,000 women. Information on distress and multi-dimensional health locus of control had been collected using other instruments. A linear regression model was fitted, with VAS score as the dependent variable. Independent variables comprised EQ-5D health state classifications, distress, locus of control, and socio-demographic characteristics. Equivalent EQ-5D and distress data, collected at twelve months, were available for over 2,000 of the women, enabling us to predict changes in VAS score over time from changes in EQ-5D classification and distress. In addition to EQ-5D health state classification, VAS score was influenced by the subject's perceived locus of control, and by her age, educational attainment, ethnic origin and smoking behaviour. Although the EQ-5D classification includes a distress dimension, the independent measure of distress was an additional determinant of VAS score. Changes in VAS score over time were explained by changes in both EQ-5D severities and distress. Women allocated to the experimental management arm of the trial reported an increase in VAS score, independently of any changes in health state and distress. In this sample, EQ VAS scores were predictable from the EQ-5D health state classification, although there also existed other group variables which contributed systematically and independently towards determining such scores. These variables comprised psychological disposition, socio-demographic factors such as age and education, clinically-important distress, and the clinical intervention itself. ISRCTN34841617.

Association of CLEC16A with human common variable immunodeficiency disorder and role in murine B cells.

PubMed

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.

Differential sequence diversity at merozoite surface protein-1 locus of Plasmodium knowlesi from humans and macaques in Thailand.

PubMed

Putaporntip, Chaturong; Thongaree, Siriporn; Jongwutiwes, Somchai

2013-08-01

To determine the genetic diversity and potential transmission routes of Plasmodium knowlesi, we analyzed the complete nucleotide sequence of the gene encoding the merozoite surface protein-1 of this simian malaria (Pkmsp-1), an asexual blood-stage vaccine candidate, from naturally infected humans and macaques in Thailand. Analysis of Pkmsp-1 sequences from humans (n=12) and monkeys (n=12) reveals five conserved and four variable domains. Most nucleotide substitutions in conserved domains were dimorphic whereas three of four variable domains contained complex repeats with extensive sequence and size variation. Besides purifying selection in conserved domains, evidence of intragenic recombination scattering across Pkmsp-1 was detected. The number of haplotypes, haplotype diversity, nucleotide diversity and recombination sites of human-derived sequences exceeded that of monkey-derived sequences. Phylogenetic networks based on concatenated conserved sequences of Pkmsp-1 displayed a character pattern that could have arisen from sampling process or the presence of two independent routes of P. knowlesi transmission, i.e. from macaques to human and from human to humans in Thailand. Copyright © 2013 Elsevier B.V. All rights reserved.

E. coli O157 from sheep in northeast Scotland: prevalence, concentration shed, and molecular characterization by multilocus variable tandem repeat analysis.

PubMed

Solecki, Olivia; MacRae, Marion; Strachan, Norval; Lindstedt, Bjørn-Arne; Ogden, Iain

2009-09-01

We report the prevalence, concentrations, and strain diversity of Escherichia coli O157 shed by sheep fed on root crops during a winter period in northeast Scotland. E. coli O157 was isolated on 6 farms from 14 studied during January to March 2005. The individual sheep prevalence was 5.8% and concentration excreted was <10(2) colony-forming units/g for all but one fecal sample. Verocytotoxigenic E. coli O157, determined by polymerase chain reaction and verocell assay, was recovered from 27% of samples. Four farms had sheep shedding the same strain as determined by multiple-locus variable analysis and no within-farm diversity was observed. The low numbers shed and the high levels of atoxigenic strains indicate a lower risk to human health from these animals compared to many ruminants grazing pasture during summer months. These data will be valuable for quantitative risk assessments and provide preliminary information that feeding sheep on root crops may be a practical intervention to reduce E. coli O157 infection in animals and ultimately humans.

Perceptions of control in adults with epilepsy.

PubMed

Gehlert, S

1994-01-01

That psychosocial problems are extant in epilepsy is evidenced by a suicide rate among epileptic persons five times that of the general population and an unemployment rate estimated to be more than twice that of the population as a whole. External perceptions of control secondary to repeated episodes of seizure activity that generalize to the social sphere have been implicated as causes of these problems. The hypothesis that individuals who continue to have seizures become more and more external in perceptions of control was tested by a survey mailed to a sample of individuals with epilepsy in a metropolitan area of the Midwest. Dependent variables were, scores on instruments measuring locus of control and attributional style. The independent variable was a measure of seizure control based on present age, age at onset, and length of time since last seizure. Gender, socioeconomic status, and certain parenting characteristics were included as control variables, as they are also known to affect perceptions of control. Analysis by multiple regression techniques supported the study's hypothesis when perceptions of control was conceptualized as learned helplessness for bad, but not for good, events. The hypothesis was not confirmed when perceptions of control was conceptualized as either general or health locus of control.

Genetic variation in lipoprotein (a) levels in families enriched for coronary artery disease is determined almost entirely by the apolipoprotein (a) gene locus.

PubMed Central

DeMeester, C A; Bu, X; Gray, R J; Lusis, A J; Rotter, J I

1995-01-01

Lipoprotein (a) (Lp[a]) is a cholesterol-rich lipoprotein resembling LDL but also containing a large polypeptide designated apolipoprotein (a) (apo[a]). Its levels are highly variable among individuals and, in a number of studies, are strongly correlated with the risk of coronary artery disease (CAD). In an effort to determine which genes control Lp(a) levels, we have studied 25 multiplex families (comprising 298 members) enriched for CAD. The apo(a) gene was genotyped among the families, using a highly informative pulse-field gel electrophoresis procedure. In addition, polymorphisms of the gene for the other major protein of Lp(a), apolipoprotein B (apoB), were examined. Quantitative sib-pair linkage analysis indicates that apo(a) is the major gene controlling Lp(a) levels in this CAD population (P = .001; 99 sib pairs), whereas the apoB gene demonstrated no significant quantitative linkage effect. We estimate that the apo(a) locus accounts for < or = 98% of variance of Lp(a) serum levels. Approximately 43% of this variation is explained by size polymorphisms within the apo(a) gene. These results indicate that the apo(a) gene is the major determinant of Lp(a) serum levels not only in the general population but also in a high-risk CAD population. Images Figure 2 PMID:7825589

Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction.

PubMed

Zhao, Yao; Schreiner, Sarah M; Koo, Peter K; Colombi, Paolo; King, Megan C; Mochrie, Simon G J

2016-07-12

Many aspects of chromatin biology are influenced by the nuclear compartment in which a locus resides, from transcriptional regulation to DNA repair. Further, the dynamic and variable localization of a particular locus across cell populations and over time makes analysis of a large number of cells critical. As a consequence, robust and automatable methods to measure the position of individual loci within the nuclear volume in populations of cells are necessary to support quantitative analysis of nuclear position. Here, we describe a three-dimensional membrane reconstruction approach that uses fluorescently tagged nuclear envelope or endoplasmic reticulum membrane marker proteins to precisely map the nuclear volume. This approach is robust to a variety of nuclear shapes, providing greater biological accuracy than alternative methods that enforce nuclear circularity, while also describing nuclear position in all three dimensions. By combining this method with established approaches to reconstruct the position of diffraction-limited chromatin markers-in this case, lac Operator arrays bound by lacI-GFP-the distribution of loci positions within the nuclear volume with respect to the nuclear periphery can be quantitatively obtained. This stand-alone image analysis pipeline should be of broad practical utility for individuals interested in various aspects of chromatin biology, while also providing, to our knowledge, a new conceptual framework for investigators who study organelle shape. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Distribution of Bartonella henselae Variants in Patients, Reservoir Hosts and Vectors in Spain

PubMed Central

Gil, Horacio; Escudero, Raquel; Pons, Inmaculada; Rodríguez-Vargas, Manuela; García-Esteban, Coral; Rodríguez-Moreno, Isabel; García-Amil, Cristina; Lobo, Bruno; Valcárcel, Félix; Pérez, Azucena; Jiménez, Santos; Jado, Isabel; Juste, Ramón; Segura, Ferrán; Anda, Pedro

2013-01-01

We have studied the diversity of B. henselae circulating in patients, reservoir hosts and vectors in Spain. In total, we have fully characterized 53 clinical samples from 46 patients, as well as 78 B. henselae isolates obtained from 35 cats from La Rioja and Catalonia (northeastern Spain), four positive cat blood samples from which no isolates were obtained, and three positive fleas by Multiple Locus Sequence Typing and Multiple Locus Variable Number Tandem Repeats Analysis. This study represents the largest series of human cases characterized with these methods, with 10 different sequence types and 41 MLVA profiles. Two of the sequence types and 35 of the profiles were not described previously. Most of the B. henselae variants belonged to ST5. Also, we have identified a common profile (72) which is well distributed in Spain and was found to persist over time. Indeed, this profile seems to be the origin from which most of the variants identified in this study have been generated. In addition, ST5, ST6 and ST9 were found associated with felines, whereas ST1, ST5 and ST8 were the most frequent sequence types found infecting humans. Interestingly, some of the feline associated variants never found on patients were located in a separate clade, which could represent a group of strains less pathogenic for humans. PMID:23874563

Multiple locus VNTR analysis highlights that geographical clustering and distribution of Dichelobacter nodosus, the causal agent of footrot in sheep, correlates with inter-country movements☆

PubMed Central

Russell, Claire L.; Smith, Edward M.; Calvo-Bado, Leonides A.; Green, Laura E.; Wellington, Elizabeth M.H.; Medley, Graham F.; Moore, Lynda J.; Grogono-Thomas, Rosemary

2014-01-01

Dichelobacter nodosus is a Gram-negative, anaerobic bacterium and the causal agent of footrot in sheep. Multiple locus variable number tandem repeat (VNTR) analysis (MLVA) is a portable technique that involves the identification and enumeration of polymorphic tandem repeats across the genome. The aims of this study were to develop an MLVA scheme for D. nodosus suitable for use as a molecular typing tool, and to apply it to a global collection of isolates. Seventy-seven isolates selected from regions with a long history of footrot (GB, Australia) and regions where footrot has recently been reported (India, Scandinavia), were characterised. From an initial 61 potential VNTR regions, four loci were identified as usable and in combination had the attributes required of a typing method for use in bacterial epidemiology: high discriminatory power (D > 0.95), typeability and reproducibility. Results from the analysis indicate that D. nodosus appears to have evolved via recombinational exchanges and clonal diversification. This has resulted in some clonal complexes that contain isolates from multiple countries and continents; and others that contain isolates from a single geographic location (country or region). The distribution of alleles between countries matches historical accounts of sheep movements, suggesting that the MLVA technique is sufficiently specific and sensitive for an epidemiological investigation of the global distribution of D. nodosus. PMID:23748018

Machado Joseph disease maps to the same region of chromosome 14 as the spinocerebellar ataxia type 3 locus.

PubMed Central

Twist, E C; Casaubon, L K; Ruttledge, M H; Rao, V S; Macleod, P M; Radvany, J; Zhao, Z; Rosenberg, R N; Farrer, L A; Rouleau, G A

1995-01-01

Machado Joseph disease (MJD) is an autosomal dominantly inherited neuro-degenerative disorder primarily affecting the motor system. It can be divided into three phenotypes based on the variable combination of a range of clinical symptoms including pyramidal and extra-pyramidal features, cerebellar deficits, and distal muscle atrophy. MJD is thought to be caused by mutation of a single gene which has recently been mapped, using genetic linkage analysis, to a 29 cM region on chromosome 14q24.3-q32 in five Japanese families. A second disorder, spinocerebellar ataxia type 3 (SCA3), which has clinical symptoms similar to MJD, has also been linked to the same region of chromosome 14q in two French families. In order to narrow down the region of chromosome 14 which contains the MJD locus and to determine if this region overlaps with the predisposing locus for SCA3, we have performed genetic linkage analysis in seven MJD families, six of Portuguese/Azorean origin and one of Brazilian origin, using nine microsatellite markers mapped to 14q24.3-q32. Our results localise the MJD locus in these families to an 11 cM interval flanked by the markers D14S68 and AFM343vf1. In addition we show that this 11 cM interval maps within the 15 cM interval containing the SCA3 locus, suggesting that these diseases are allelic. PMID:7897622

Genomewide scan identifies susceptibility locus for dyslexia on Xq27 in an extended Dutch family.

PubMed

de Kovel, C G F; Hol, F A; Heister, J G A M; Willemen, J J H T; Sandkuijl, L A; Franke, B; Padberg, G W

2004-09-01

Dyslexia is a common disorder with a strong genetic component, but despite significant research effort, the aetiology is still largely unknown. To identify loci contributing to dyslexia risk. This was a genomewide linkage analysis in a single large family. Dutch families with at least two first degree relatives suffering from dyslexia participated in the study. Participants were recruited through an advertisement campaign in papers and magazines. The main outcome measure was linkage between genetic markers and dyslexia phenotype. Using parametric linkage analysis, we found strong evidence for a locus influencing dyslexia on Xq27.3 (multipoint lod = 3.68). Recombinations in two family members flanked an 8 cM region, comprising 11 currently confirmed genes. All four males carrying the risk haplotype had very low scores on the reading tests. The presentation in females was more variable, but 8/9 females carrying the risk haplotype were diagnosed dyslexic by our composite score, so we considered the putative risk allele to be dominant with reduced penetrance. Linkage was not found in an additional collection of affected sibling pairs. A locus influencing dyslexia risk is probably located between markers DXS1227 and DXS8091 on the X chromosome, closely situated to a locus indicated by a published genome scan of English sibling pairs. Although the locus may not be a common cause for dyslexia, the relatively small and gene poor region offers hope to identify the responsible gene.

Genomewide scan identifies susceptibility locus for dyslexia on Xq27 in an extended Dutch family

PubMed Central

de Kovel, C G F; Hol, F; Heister, J; Willemen, J; Sandkuijl, L; Franke, B; Padberg, G

2004-01-01

Context: Dyslexia is a common disorder with a strong genetic component, but despite significant research effort, the aetiology is still largely unknown. Objective: To identify loci contributing to dyslexia risk. Methods: This was a genomewide linkage analysis in a single large family. Dutch families with at least two first degree relatives suffering from dyslexia participated in the study. Participants were recruited through an advertisement campaign in papers and magazines. The main outcome measure was linkage between genetic markers and dyslexia phenotype. Results: Using parametric linkage analysis, we found strong evidence for a locus influencing dyslexia on Xq27.3 (multipoint lod = 3.68). Recombinations in two family members flanked an 8 cM region, comprising 11 currently confirmed genes. All four males carrying the risk haplotype had very low scores on the reading tests. The presentation in females was more variable, but 8/9 females carrying the risk haplotype were diagnosed dyslexic by our composite score, so we considered the putative risk allele to be dominant with reduced penetrance. Linkage was not found in an additional collection of affected sibling pairs. Conclusions: A locus influencing dyslexia risk is probably located between markers DXS1227 and DXS8091 on the X chromosome, closely situated to a locus indicated by a published genome scan of English sibling pairs. Although the locus may not be a common cause for dyslexia, the relatively small and gene poor region offers hope to identify the responsible gene. PMID:15342694

Metallo-β-lactamase-producing Pseudomonas aeruginosa in the Netherlands: the nationwide emergence of a single sequence type.

PubMed

Van der Bij, A K; Van der Zwan, D; Peirano, G; Severin, J A; Pitout, J D D; Van Westreenen, M; Goessens, W H F

2012-09-01

Recently, the first outbreak of clonally related VIM-2 metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa in a Dutch tertiary-care centre was described. Subsequently, a nationwide surveillance study was performed in 2010-2011, which identified the presence of VIM-2 MBL-producing P. aeruginosa in 11 different hospitals. Genotyping by multiple-locus variable-number tandem-repeat analysis (MLVA) showed that the majority of the 82 MBL-producing isolates found belonged to a single MLVA type (n = 70, 85%), identified as ST111 by multilocus sequence typing (MLST). As MBL-producing isolates cause serious infections that are difficult to treat, the presence of clonally related isolates in various hospitals throughout the Netherlands is of nationwide concern. © 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.

Isolation of microsatellite loci for Rhodiola alsia (Crassulaceae), an important ethno-medicinal herb endemic to the Qinghai-Tibetan plateau.

PubMed

Zhang, F Q; Lei, S Y; Gao, Q B; Khan, G; Xing, R; Yang, H L; Chen, S L

2015-05-18

Rhodiola alsia, which has been used widely in traditional Chinese medicine for a considerable time, grows on moist habitats at high altitude near the snow line. Microsatellite loci were developed for R. alsia to investigate its population genetics. In total, 17 polymorphic microsatellites were developed based on ESTs from the Illumina HiSeq(TM) 2000 platform. The microsatellite loci were checked for variability using 80 individuals of R. alsia sampled from four locations on the Qinghai-Tibet Plateau. The total number of alleles per locus ranged from 10 to 20, and the observed heterozygosity ranged from 0.000 to 1.000. The null allele frequency ranged from 0.000 to 0.324. These microsatellites are expected to be helpful in future studies of population genetics in R. alsia and related species.

An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome-wide association studies.

PubMed

Setsirichok, Damrongrit; Tienboon, Phuwadej; Jaroonruang, Nattapong; Kittichaijaroen, Somkit; Wongseree, Waranyu; Piroonratana, Theera; Usavanarong, Touchpong; Limwongse, Chanin; Aporntewan, Chatchawit; Phadoongsidhi, Marong; Chaiyaratana, Nachol

2013-01-01

This article presents the ability of an omnibus permutation test on ensembles of two-locus analyses (2LOmb) to detect pure epistasis in the presence of genetic heterogeneity. The performance of 2LOmb is evaluated in various simulation scenarios covering two independent causes of complex disease where each cause is governed by a purely epistatic interaction. Different scenarios are set up by varying the number of available single nucleotide polymorphisms (SNPs) in data, number of causative SNPs and ratio of case samples from two affected groups. The simulation results indicate that 2LOmb outperforms multifactor dimensionality reduction (MDR) and random forest (RF) techniques in terms of a low number of output SNPs and a high number of correctly-identified causative SNPs. Moreover, 2LOmb is capable of identifying the number of independent interactions in tractable computational time and can be used in genome-wide association studies. 2LOmb is subsequently applied to a type 1 diabetes mellitus (T1D) data set, which is collected from a UK population by the Wellcome Trust Case Control Consortium (WTCCC). After screening for SNPs that locate within or near genes and exhibit no marginal single-locus effects, the T1D data set is reduced to 95,991 SNPs from 12,146 genes. The 2LOmb search in the reduced T1D data set reveals that 12 SNPs, which can be divided into two independent sets, are associated with the disease. The first SNP set consists of three SNPs from MUC21 (mucin 21, cell surface associated), three SNPs from MUC22 (mucin 22), two SNPs from PSORS1C1 (psoriasis susceptibility 1 candidate 1) and one SNP from TCF19 (transcription factor 19). A four-locus interaction between these four genes is also detected. The second SNP set consists of three SNPs from ATAD1 (ATPase family, AAA domain containing 1). Overall, the findings indicate the detection of pure epistasis in the presence of genetic heterogeneity and provide an alternative explanation for the aetiology of T1D in the UK population.

Population-specific variation in haplotype composition and heterozygosity at the POLB locus.

PubMed

Yamtich, Jennifer; Speed, William C; Straka, Eva; Kidd, Judith R; Sweasy, Joann B; Kidd, Kenneth K

2009-05-01

DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

Examining maternal age, breastfeeding self-efficacy and health locus of control in psychological wellbeing of mothers.

PubMed

Lawal, Abiodun Musbau; Idemudia, Erhabor Sunday

2017-12-01

We investigated the direct and interaction influence of maternal age, breastfeeding self-efficacy (BSE), health locus of control (HLOC) on six dimensions of psychological wellbeing of breastfeeding mothers in Lagos, Nigeria. Data were collected from a convenience sample of 291 mothers attending health facilities in two suburb local government areas. The survey included socio-demographics (maternal age, marital status, ethnicity, education level and position of the baby currently breastfeeding), breastfeeding self-efficacy, health locus of control and psychological wellbeing scales. Independent variables were tested against sense of autonomy, positive relations with others, purpose in life, self-acceptance, environmental mastery and personal growth using factorial Multivariate Analysis of Variance. Results showed direct influence of BSE, HLOC and maternal age on various dimensions of psychological wellbeing. Interaction influences indicate BSE and HLOC on environmental mastery; BSE and maternal age on self-acceptance and HLOC and maternal age on sense of autonomy, positive relationship with others and self-acceptance respectively. In conclusion, maternal age, breastfeeding self-efficacy and health locus of control are vital for mothers to enjoy plenty dimensions of psychological wellbeing. Breastfeeding mothers need to be confident in their abilities to breastfeed and have control over their health-related behaviour in order to enjoy sufficient dimensions of psychological wellbeing.

Inheritance pattern of platelet membrane fluidity in Alzheimer disease.

PubMed Central

Chakravarti, A; Slaugenhaupt, S A; Zubenko, G S

1989-01-01

The fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene in labeled platelet membranes, an index of membrane fluidity, is a stable, familial trait that is associated with a clinically distinct subtype of Alzheimer disease. Complex segregation analysis of this continuous variable was performed on 95 members of 14 pedigrees identified through probands who had autopsy-confirmed or clinically diagnosed Alzheimer disease. The results suggest that platelet membrane fluidity is controlled by a single genetic locus, PMF, with two alleles that have additive effects. The PMF locus appears to explain approximately 80% of the total variation in platelet membrane fluidity within the families of patients with Alzheimer disease. PMID:2729275

Murine Lupus Susceptibility Locus Sle1a Requires the Expression of two Subloci to Induce Inflammatory T Cells

PubMed Central

Cuda, Carla M.; Zeumer, Leilani; Sobel, Eric S.; Croker, Byron P.; Morel, Laurence

2010-01-01

The NZM2410-derived Sle1a lupus susceptibility locus induces activated autoreactive CD4+ T cells and reduces the number and function of Foxp3+ regulatory T cells. In this study, we first showed that Sle1a contributes to autoimmunity by increasing anti-nuclear antibody production when expressed on either NZB or NZW heterozygous genomes, and by enhancing the chronic graft vs. host disease response indicating an expansion of the autoreactive B cell pool. Screening two non-overlapping recombinants, the Sle1a.1 and Sle1a.2 intervals that cover the entire Sle1a locus, revealed that both Sle1a.1 and Sle1a.2 were necessary for the full Sle1a phenotype. Sle1a.1, and to a lesser extent Sle1a.2, significantly affected CD4+ T cell activation as well as Treg differentiation and function. Sle1a.2 also increased the production of autoreactive B cells. Since the Sle1a.1 and Sle1a.2 intervals contain only one and 15 known genes, respectively, this study considerably reduces the number of candidate genes responsible for the production of autoreactive T cells. These results also demonstrate that the Sle1 locus is an excellent model for the genetic architecture of lupus, in which a major obligate phenotype results from the co-expression of multiple genetic variants with individual weak effects. PMID:20445563

Conserved Organisation of 45S rDNA Sites and rDNA Gene Copy Number among Major Clades of Early Land Plants

PubMed Central

Rosato, Marcela; Kovařík, Aleš; Garilleti, Ricardo; Rosselló, Josep A.

2016-01-01

Genes encoding ribosomal RNA (rDNA) are universal key constituents of eukaryotic genomes, and the nuclear genome harbours hundreds to several thousand copies of each species. Knowledge about the number of rDNA loci and gene copy number provides information for comparative studies of organismal and molecular evolution at various phylogenetic levels. With the exception of seed plants, the range of 45S rDNA locus (encoding 18S, 5.8S and 26S rRNA) and gene copy number variation within key evolutionary plant groups is largely unknown. This is especially true for the three earliest land plant lineages Marchantiophyta (liverworts), Bryophyta (mosses), and Anthocerotophyta (hornworts). In this work, we report the extent of rDNA variation in early land plants, assessing the number of 45S rDNA loci and gene copy number in 106 species and 25 species, respectively, of mosses, liverworts and hornworts. Unexpectedly, the results show a narrow range of ribosomal locus variation (one or two 45S rDNA loci) and gene copies not present in vascular plant lineages, where a wide spectrum is recorded. Mutation analysis of whole genomic reads showed higher (3-fold) intragenomic heterogeneity of Marchantia polymorpha (Marchantiophyta) rDNA compared to Physcomitrella patens (Bryophyta) and two angiosperms (Arabidopsis thaliana and Nicotiana tomentosifomis) suggesting the presence of rDNA pseudogenes in its genome. No association between phylogenetic position, taxonomic adscription and the number of rDNA loci and gene copy number was found. Our results suggest a likely evolutionary rDNA stasis during land colonisation and diversification across 480 myr of bryophyte evolution. We hypothesise that strong selection forces may be acting against ribosomal gene locus amplification. Despite showing a predominant haploid phase and infrequent meiosis, overall rDNA homogeneity is not severely compromised in bryophytes. PMID:27622766

The evolution of dominance in sporophytic self-incompatibility systems. II. Mate availability and recombination.

PubMed

Schoen, Daniel J; Busch, Jeremiah W

2009-08-01

Sporophytic self-incompatibility (SSI) is a self-pollen recognition system that enforces outcrossing in plants. Recognition in SSI systems is typically controlled by a complex locus (S-locus) with separate genes that determine pollen and stigma specificity. Experimental studies show that S-alleles can be dominant, recessive, or codominant, and that the dominance level of a given S-allele can depend upon whether pollen or stigma specificity is examined. Here and in the companion paper by Llaurens and colleagues, the evolution of dominance in single-locus SSI is explored using numerical models and simulation. Particular attention is directed at factors that can cause S-allele dominance to differ in pollen versus stigma. The effect of recombination between the S-locus and modifier locus is also examined. The models predict that limitation in the number of compatible mates is required for the evolution of S-allele dominance in the stigma but not in the pollen. Tight linkage between the S-locus and modifier promotes the evolution of S-allele dominance hierarchies. Model results are interpreted with respect to published information on the molecular basis of dominance in SSI systems, and reported S-allele dominance relationships in a variety of species. These studies show that dominant S-alleles are more common in the pollen than in the stigma, a pattern that when interpreted in light of model predictions, suggests that mate limitation may be relatively infrequent in natural populations with SSI.

A PQL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition.

PubMed

Bourgeois, Michael; Jacquin, Françoise; Cassecuelle, Florence; Savois, Vincent; Belghazi, Maya; Aubert, Grégoire; Quillien, Laurence; Huart, Myriam; Marget, Pascal; Burstin, Judith

2011-05-01

Legume seeds are a major source of dietary proteins for humans and animals. Deciphering the genetic control of their accumulation is thus of primary significance towards their improvement. At first, we analysed the genetic variability of the pea seed proteome of three genotypes over 3 years of cultivation. This revealed that seed protein composition variability was under predominant genetic control, with as much as 60% of the spots varying quantitatively among the three genotypes. Then, by combining proteomic and quantitative trait loci (QTL) mapping approaches, we uncovered the genetic architecture of seed proteome variability. Protein quantity loci (PQL) were searched for 525 spots detected on 2-D gels obtained for 157 recombinant inbred lines. Most protein quantity loci mapped in clusters, suggesting that the accumulation of the major storage protein families was under the control of a limited number of loci. While convicilin accumulation was mainly under the control of cis-regulatory regions, vicilins and legumins were controlled by both cis- and trans-regulatory regions. Some loci controlled both seed protein composition and protein content and a locus on LGIIa appears to be a major regulator of protein composition and of protein in vitro digestibility. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic Divergence and Chemotype Diversity in the Fusarium Head Blight Pathogen Fusarium poae.

PubMed

Vanheule, Adriaan; De Boevre, Marthe; Moretti, Antonio; Scauflaire, Jonathan; Munaut, Françoise; De Saeger, Sarah; Bekaert, Boris; Haesaert, Geert; Waalwijk, Cees; van der Lee, Theo; Audenaert, Kris

2017-08-23

Fusarium head blight is a disease caused by a complex of Fusarium species. F. poae is omnipresent throughout Europe in spite of its low virulence. In this study, we assessed a geographically diverse collection of F. poae isolates for its genetic diversity using AFLP (Amplified Fragment Length Polymorphism). Furthermore, studying the mating type locus and chromosomal insertions, we identified hallmarks of both sexual recombination and clonal spread of successful genotypes in the population. Despite the large genetic variation found, all F. poae isolates possess the nivalenol chemotype based on Tri7 sequence analysis. Nevertheless, Tri gene clusters showed two layers of genetic variability. Firstly, the Tri1 locus was highly variable with mostly synonymous mutations and mutations in introns pointing to a strong purifying selection pressure. Secondly, in a subset of isolates, the main trichothecene gene cluster was invaded by a transposable element between Tri5 and Tri6 . To investigate the impact of these variations on the phenotypic chemotype, mycotoxin production was assessed on artificial medium. Complex blends of type A and type B trichothecenes were produced but neither genetic variability in the Tri genes nor variability in the genome or geography accounted for the divergence in trichothecene production. In view of its complex chemotype, it will be of utmost interest to uncover the role of trichothecenes in virulence, spread and survival of F. poae .

HvFT1 polymorphism and effect—survey of barley germplasm and expression analysis

PubMed Central

Loscos, Jorge; Igartua, Ernesto; Contreras-Moreira, Bruno; Gracia, M. Pilar; Casas, Ana M.

2014-01-01

Flowering time in plants is a tightly regulated process. In barley (Hordeum vulgare L.), HvFT1, ortholog of FLOWERING LOCUS T, is the main integrator of the photoperiod and vernalization signals leading to the transition from vegetative to reproductive state of the plant. This gene presents sequence polymorphisms affecting flowering time in the first intron and in the promoter. Recently, copy number variation (CNV) has been described for this gene. An allele with more than one copy was linked to higher gene expression, earlier flowering, and an overriding effect of the vernalization mechanism. This study aims at (1) surveying the distribution of HvFT1 polymorphisms across barley germplasm and (2) assessing gene expression and phenotypic effects of HvFT1 alleles. We analyzed HvFT1 CNV in 109 winter, spring, and facultative barley lines. There was more than one copy of the gene (2–5) only in spring or facultative barleys without a functional vernalization VrnH2 allele. CNV was investigated in several regions inside and around HvFT1. Two models of the gene were found: one with the same number of promoters and transcribed regions, and another with one promoter and variable number of transcribed regions. This last model was found in Nordic barleys only. Analysis of HvFT1 expression showed that association between known polymorphisms at the HvFT1 locus and the expression of the gene was highly dependent on the genetic background. Under long day conditions the earliest flowering lines carried a sensitive PpdH1 allele. Among spring cultivars with different number of copies, no clear relation was found between CNV, gene expression and flowering time. This was confirmed in a set of doubled haploid lines of a population segregating for HvFT1 CNV. Earlier flowering in the presence of several copies of HvFT1 was only seen in cultivar Tammi, which carries one promoter, suggesting a relation of gene structure with its regulation. HvCEN also affected to a large extent flowering time. PMID:24936204

Relationships Between Health Behaviors, Self-Efficacy, and Health Locus of Control of Students at the Universities of the Third Age

PubMed Central

Zielińska-Więczkowska, Halina

2016-01-01

Background This study aimed to determine the relationship of health behaviors with the health locus of control and the sense of self-efficacy against the background of socio-economic factors and self-rated health among students of the Universities of the Third Age (U3As). Material/Methods The study included 320 U3A students, with mean age of 67.5 years. The following research tools were used: Health Behavior Inventory (HBI), Multidimensional Health Locus of Control Scale (MHLC), Generalized Self-Efficacy Scale (GSES), and an original survey of the author’s own design. Results Mean total HBI and GSES scores were 90.63 and 30.12, respectively. These results are satisfactory. A slight predominance of internal health locus of control was documented. A number of significant correlations were found between the HBI, GSES, and MHLC scores, except for the MHLC subscale expressing the influence of chance. Educational attainment was shown to have a significant impact on the scores for the positive attitude and proper dietary habits subscales of HBI, as well as on the GSES scores. Economic status of the participants influenced the levels of positive attitude, internal health locus of control, and self-efficacy. Furthermore, internal health locus of control was found to be modulated by subjective health of the respondents. The scores for external health locus of control and the influence of chance increased significantly with age. Conclusions The currently noticeable emphasis placed on lifelong education should serve as a good prognostic factor for health behaviors and personal health resources for years to come. PMID:26879981

Material Hardship and Internal Locus of Control Over the Prevention of Child Obesity in Low-Income Hispanic Pregnant Women.

PubMed

Gross, Rachel S; Mendelsohn, Alan L; Gross, Michelle B; Scheinmann, Roberta; Messito, Mary Jo

2016-07-01

To determine the relations between household material hardships and having a low internal locus of control over the prevention of child obesity in low-income Hispanic pregnant women. We performed a cross-sectional analysis of baseline data collected during a third trimester prenatal visit from women participating in the Starting Early Study, a randomized controlled trial to test the efficacy of a primary care-based family-centered early child obesity prevention intervention. Using multiple logistic regression analyses, we determined whether 4 domains of material hardship (food insecurity, difficulty paying bills, housing disrepair, neighborhood stress), considered individually and also cumulatively, were associated with having a low internal locus of control over the prevention of child obesity. The sample included 559 low-income Hispanic pregnant women, with 60% having experienced at least 1 hardship. Food insecurity was independently associated with a low internal locus of control over the prevention of child obesity (adjusted odds ratio, 2.38; 95% confidence interval, 1.50-3.77), controlling for other hardships and confounders. Experiencing a greater number of material hardships was associated in a dose-dependent relationship with an increased odds of having a low internal locus of control. Prenatal material hardships, in particular food insecurity, were associated with having a lower prenatal internal locus of control over the prevention of child obesity. Longitudinal follow-up of this cohort is needed to determine how relations between material hardships and having a low internal locus of control will ultimately affect infant feeding practices and child weight trajectories. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Salmonella Typhimurium DT193 and DT99 are present in great and blue tits in Flanders, Belgium

PubMed Central

Verbrugghe, E.; Dekeukeleire, D.; De Beelde, R.; Rouffaer, L. O.; Haesendonck, R.; Strubbe, D.; Mattheus, W.; Bertrand, S.; Pasmans, F.; Bonte, D.; Verheyen, K.; Lens, L.; Martel, A.

2017-01-01

Endemic infections with the common avian pathogen Salmonella enterica subspecies enterica serovar Typhimurium (Salmonella Typhimurium) may incur a significant cost on the host population. In this study, we determined the potential of endemic Salmonella infections to reduce the reproductive success of blue (Cyanistes caeruleus) and great (Parus major) tits by correlating eggshell infection with reproductive parameters. The fifth egg of each clutch was collected from nest boxes in 19 deciduous forest fragments. Out of the 101 sampled eggs, 7 Salmonella Typhimurium isolates were recovered. The low bacterial prevalence was reflected by a similarly low serological prevalence in the fledglings. In this study with a relatively small sample size, presence of Salmonella did not affect reproductive parameters (egg volume, clutch size, number of nestlings and number of fledglings), nor the health status of the fledglings. However, in order to clarify the impact on health and reproduction a larger number of samples have to be analyzed. Phage typing showed that the isolates belonged to the definitive phage types (DT) 193 and 99, and multi-locus variable number tandem repeat analysis (MLVA) demonstrated a high similarity among the tit isolates, but distinction to human isolates. These findings suggest the presence of passerine-adapted Salmonella strains in free-ranging tit populations with host pathogen co-existence. PMID:29112955

Race Differences and Type II Errors: A Comment on Borkowski and Krause.

ERIC Educational Resources Information Center

Jensen, Arthur R.

1985-01-01

Borkowski and Krause (1983) concluded that the locus of black-white intelligence differences lies in metaprocesses not elementary cognitive processes. However, some variables were difference scores with unacceptably low reliability. Magnitude comparisons of racial differences give a different picture of results; comparable differences in measures…

A Longitudinal Study of Adolescents' Future Orientation (Time Perspective).

ERIC Educational Resources Information Center

Trommsdorff, Gisela; And Others

1979-01-01

Vocational or college-bound students responded to four futures orientation variables (personality, physical well-being, family, and occupation) along several dimensions, including hopes and fears, locus of control, and optimism. The same students took the same survey two years later. Age, sex, and educational status differences were noted. (CP)

The Relationship between Birth Order and Academic Achievement.

ERIC Educational Resources Information Center

Cherry, Crystal M.

This paper reviews the literature on the relationship between birth order and several variables, especially academic achievement. One study found a relationship between leadership skills and birth order for males. Several studies found no relationship between birth order and academic achievement; grade point average; self-esteem; locus of control…

The Relationship of Intelligence, Self-Concept and Locus of Control to School Achievement for Aboriginal and Non-Aboriginal Children.

ERIC Educational Resources Information Center

Wright, Marilyn M.; Parker, J. L.

1978-01-01

To examine variables related to the school achievement of Aboriginal and non-Aboriginal students, 35 indigenous students and 58 non-Aboriginals in grade 8 completed a Coopersmith Self-Esteem Inventory and the Intellectual Responsibility Questionnaire. (Author/SBH)

Racial Prejudice, Interracial Contact, and Personality Variables.

ERIC Educational Resources Information Center

Moore, J. William; And Others

1984-01-01

This study examined the relationship of childrens' racial prejudice to child's race, interracial contact, grade, sex, intelligence, locus of control, anxiety, and self-concept. Five facets of racial prejudice were examined: a total index of racial prejudice, dating and marriage, school, social relationships, and racial interactions in restaurants.…

Efficacy of Incorporating Experiencing Exercises into a Smoking Cessation Curriculum.

ERIC Educational Resources Information Center

Watt, Celia A.; Manaster, Guy

2003-01-01

Examines the impact of experiential exercises, combined with a traditional smoking cessation intervention, on quit rates and social learning theory variables known to impact smoking cessation. Measures of self-efficacy and locus of control did not significantly differ between the experimental and control conditions. Quit rates did not differ…

The Effect of Logo on Attributions toward Success.

ERIC Educational Resources Information Center

Horner, Charlotte M.; Maddux, Cleborne D.

1985-01-01

A study was conducted to determine Logo's effect on problem solving, locus of control, math attitudes, and angle recognition in learning-disabled and nonlearning-disabled junior high school students. No significant differences were found on the variables under investigation, but more students reported internal attributions toward Logo than…

Examining Depressive Symptoms and Their Predictors in Malaysia: Stress, Locus of Control, and Occupation

PubMed Central

Yeoh, Si H.; Tam, Cai L.; Wong, Chee P.; Bonn, Gregory

2017-01-01

The 2015 National Health and Morbidity Survey estimated that over 29% of the adult population of Malaysia suffers from mental distress, a nearly 3-fold increase from the 10.7% estimated by the NHMS in 1996 pointing to the potential beginnings of a public health crisis. This study aimed to better understand this trend by assessing depressive symptoms and their correlates in a cross-section of Malaysians. Specifically, it assesses stress, perceived locus of control, and various socio-demographic variables as possible predictors of depressive symptoms in the Malaysian context. A total of 728 adults from three Malaysian states (Selangor, Penang, Terengganu) completed Beck’s depression inventory as well as several other measures: 10% of respondents reported experiencing severe levels of depressive symptoms, 11% reported moderate and 15% reported mild depressive symptoms indicating that Malaysians are experiencing high levels of emotional distress. When controlling for the influence of other variables, depressive symptoms were predictably related to higher levels of stress and lower levels of internal locus of control. Ethnic Chinese Malaysians, housewives and those engaged in professional-type occupations reported less depressive symptoms. Business owners reported more depressive symptoms. Further research should look more into Malaysians’ subjective experience of stress and depression as well as explore environmental factors that may be contributing to mental health issues. It is argued that future policies can be designed to better balance individual mental health needs with economic growth. PMID:28878710

Examining Depressive Symptoms and Their Predictors in Malaysia: Stress, Locus of Control, and Occupation.

PubMed

Yeoh, Si H; Tam, Cai L; Wong, Chee P; Bonn, Gregory

2017-01-01

The 2015 National Health and Morbidity Survey estimated that over 29% of the adult population of Malaysia suffers from mental distress, a nearly 3-fold increase from the 10.7% estimated by the NHMS in 1996 pointing to the potential beginnings of a public health crisis. This study aimed to better understand this trend by assessing depressive symptoms and their correlates in a cross-section of Malaysians. Specifically, it assesses stress, perceived locus of control, and various socio-demographic variables as possible predictors of depressive symptoms in the Malaysian context. A total of 728 adults from three Malaysian states (Selangor, Penang, Terengganu) completed Beck's depression inventory as well as several other measures: 10% of respondents reported experiencing severe levels of depressive symptoms, 11% reported moderate and 15% reported mild depressive symptoms indicating that Malaysians are experiencing high levels of emotional distress. When controlling for the influence of other variables, depressive symptoms were predictably related to higher levels of stress and lower levels of internal locus of control. Ethnic Chinese Malaysians, housewives and those engaged in professional-type occupations reported less depressive symptoms. Business owners reported more depressive symptoms. Further research should look more into Malaysians' subjective experience of stress and depression as well as explore environmental factors that may be contributing to mental health issues. It is argued that future policies can be designed to better balance individual mental health needs with economic growth.

12p13.33 microdeletion including ELKS/ERC1, a new locus associated with childhood apraxia of speech

PubMed Central

Thevenon, Julien; Callier, Patrick; Andrieux, Joris; Delobel, Bruno; David, Albert; Sukno, Sylvie; Minot, Delphine; Mosca Anne, Laure; Marle, Nathalie; Sanlaville, Damien; Bonnet, Marlène; Masurel-Paulet, Alice; Levy, Fabienne; Gaunt, Lorraine; Farrell, Sandra; Le Caignec, Cédric; Toutain, Annick; Carmignac, Virginie; Mugneret, Francine; Clayton-Smith, Jill; Thauvin-Robinet, Christel; Faivre, Laurence

2013-01-01

Speech sound disorders are heterogeneous conditions, and sporadic and familial cases have been described. However, monogenic inheritance explains only a small proportion of such disorders, in particular in cases with childhood apraxia of speech (CAS). Deletions of <5 Mb involving the 12p13.33 locus is one of the least commonly deleted subtelomeric regions. Only four patients have been reported with such a deletion diagnosed with fluorescence in situ hybridisation telomere analysis or array CGH. To further delineate this rare microdeletional syndrome, a French collaboration together with a search in the Decipher database allowed us to gather nine new patients with a 12p13.33 subtelomeric or interstitial rearrangement identified by array CGH. Speech delay was found in all patients, which could be defined as CAS when patients had been evaluated by a speech therapist (5/9 patients). Intellectual deficiency was found in 5/9 patients only, and often associated with psychiatric manifestations of various severity. Two such deletions were inherited from an apparently healthy parent, but reevaluation revealed abnormal speech production at least in childhood, suggesting variable expressivity. The ELKS/ERC1 gene, which encodes for a synaptic factor, is found in the smallest region of overlap. These results reinforce the hypothesis that deletions of the 12p13.33 locus may be responsible for variable phenotypes including CAS associated with neurobehavioural troubles and that the presence of CAS justifies a genetic work-up. PMID:22713806

Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA.

PubMed

Siarkou, Victoria I; Vorimore, Fabien; Vicari, Nadia; Magnino, Simone; Rodolakis, Annie; Pannekoek, Yvonne; Sachse, Konrad; Longbottom, David; Laroucau, Karine

2015-01-01

Chlamydia abortus, an obligate intracellular bacterium, is the most common infectious cause of abortion in small ruminants worldwide and has zoonotic potential. We applied multilocus sequence typing (MLST) together with multiple-locus variable-number tandem repeat analysis (MLVA) to genotype 94 ruminant C. abortus strains, field isolates and samples collected from 1950 to 2011 in diverse geographic locations, with the aim of delineating C. abortus lineages and clones. MLST revealed the previously identified sequence types (STs) ST19, ST25, ST29 and ST30, plus ST86, a recently-assigned type on the Chlamydiales MLST website and ST87, a novel type harbouring the hemN_21 allele, whereas MLVA recognized seven types (MT1 to MT7). Minimum-spanning-tree analysis suggested that all STs but one (ST30) belonged to a single clonal complex, possibly reflecting the short evolutionary timescale over which the predicted ancestor (ST19) has diversified into three single-locus variants (ST86, ST87 and ST29) and further, through ST86 diversification, into one double-locus variant (ST25). ST descendants have probably arisen through a point mutation evolution mode. Interestingly, MLVA showed that in the ST19 population there was a greater genetic diversity than in other STs, most of which exhibited the same MT over time and geographical distribution. However, the evolutionary pathways of C. abortus STs seem to be diverse across geographic distances with individual STs restricted to particular geographic locations. The ST30 singleton clone displaying geographic specificity and represented by the Greek strains LLG and POS was effectively distinguished from the clonal complex lineage, supporting the notion that possibly two separate host adaptations and hence independent bottlenecks of C. abortus have occurred through time. The combination of MLST and MLVA assays provides an additional level of C. abortus discrimination and may prove useful for the investigation and surveillance of emergent C. abortus clonal populations.

Associations of the interleukin-1 gene locus polymorphisms with risk to hip and knee osteoarthritis: gender and subpopulation differences.

PubMed

Kaarvatn, M H; Jotanovic, Z; Mihelic, R; Etokebe, G E; Mulac-Jericevic, B; Tijanic, T; Balen, S; Sestan, B; Dembic, Z

2013-02-01

Genetic predisposition to the complex hereditary disease like osteoarthritis (OA) of the large joints (hip and knee) includes the interleukin-1 gene (IL-1) cluster on chromosome 2. Using a case-control study with 500 OA patients (240 knee and 260 hip OA patients, all with joint replacement), we analysed frequencies of IL-1 gene cluster polymorphisms in Croatian Caucasian population. The control samples came from 531 healthy individuals including blood donors. We genotyped two single nucleotide polymorphisms in the IL-1 gene locus at IL-1A (-889, C>T, rs1800587) and IL-1B (+3594, C>T, rs1143634) and compared their frequencies between patients and controls. We predicted haplotypes by combining current data with our previous results on gene polymorphisms (IL-1B, rs16944 and the IL-1 receptor antagonist gene [IL-1RN] variable number tandem repeat [VNTR]) for the same population. Haplotype analyses revealed gender disparities and showed that women carriers of the 1-2-1-1 haplotype [IL-1A(rs1800587) - IL-1B(rs1143634) - IL-1B(rs16944) - IL-1RN(VNTR)] had sixfold lower risk to develop knee OA. However, carriers of the 1-1-1-2 haplotype of both sexes had over twofold higher predisposition to hip OA. Our results differ from some earlier studies in Caucasian subpopulations, which may be due to the fact that this is the first study to separate genders in assessing the IL-1-locus genetic risk of OA. The results suggest that inflammatory mediators like IL-1 might be implicated in the pathogenesis of primary OA in large joints and that as yet unidentified gender-specific factors exist in a Croatian Caucasian population. © 2012 The Authors. Scandinavian Journal of Immunology © 2012 Blackwell Publishing Ltd.

Resistance to temptation: the interaction of external and internal control on alcohol use during residential treatment for alcohol use disorder.

PubMed

Soravia, Leila M; Schläfli, Katrin; Stutz, Sonja; Rösner, Susanne; Moggi, Franz

2015-11-01

There is evidence that drinking during residential treatment is related to various factors, such as patients' general control beliefs and self-efficacy, as well as to external control of alcohol use by program's staff and situations where there is temptation to drink. As alcohol use during treatment has been shown to be associated with the resumption of alcohol use after discharge from residential treatment, we aimed to investigate how these variables are related to alcohol use during abstinence-oriented residential treatment programs for alcohol use disorders (AUD). In total, 509 patients who entered 1 of 2 residential abstinence-oriented treatment programs for AUD were included in the study. After detoxification, patients completed a standardized diagnostic procedure including interviews and questionnaires. Drinking was assessed by patients' self-report of at least 1 standard drink or by positive breathalyzer testing. The 2 residential programs were categorized as high or low control according to the average number of tests per patient. Regression analysis revealed a significant interaction effect between internal and external control suggesting that patients with high internal locus of control and high frequency of control by staff demonstrated the least alcohol use during treatment (16.7%) while patients with low internal locus of control in programs with low external control were more likely to use alcohol during treatment (45.9%). No effects were found for self-efficacy and temptation. As alcohol use during treatment is most likely associated with poor treatment outcomes, external control may improve treatment outcomes and particularly support patients with low internal locus of control, who show the highest risk for alcohol use during treatment. High external control may complement high internal control to improve alcohol use prevention while in treatment. Copyright © 2015 The Authors. Alcoholism: Clinical and Experimental Research published by Wiley Periodicals, Inc. on behalf of Research Society on Alcoholism.

Ratings of perceived exertion by women with internal or external locus of control.

PubMed

Hassmén, P; Koivula, N

1996-10-01

Ratings of perceived exertion are frequently used to estimate the strain and effort experienced subjectively by individuals during various forms of physical activity. A number of factors, both physiological and psychological in origin, have been suggested to work as modifiers of the exertion perceived by the individual. It has been reported in nonsport-related research that individuals with an internal locus of control seem to pay more attention to relevant information and use the available information more adequately than individuals with an external locus of control. The reputed inferior information-processing abilities of externals compared with internals could possibly also influence the ratings of perceived exertion, with externals being less accurate in their ratings. Whether locus of control might be such a factor was investigated. Fifty women worked on an ergometer cycle at four different work loads. The results showed statistically significant differences in subjective ratings of perceived exertion between externals and internals, especially at heavier work loads. Such differences might be because of unequal information-processing abilities, as the observed discrepancies occurred at higher work intensities, when more cues are available for processing.

Protein variants in Hiroshima and Nagasaki: tales of two cities.

PubMed Central

Neel, J V; Satoh, C; Smouse, P; Asakawa, J; Takahashi, N; Goriki, K; Fujita, M; Kageoka, T; Hazama, R

1988-01-01

The results of 1,465,423 allele product determinations based on blood samples from Hiroshima and Nagasaki, involving 30 different proteins representing 32 different gene products, are analyzed in a variety of ways, with the following conclusions: (1) Sibships and their parents are included in the sample. Our analysis reveals that statistical procedures designed to reduce the sample to equivalent independent genomes do not in population comparisons compensate for the familial cluster effect of rare variants. Accordingly, the data set was reduced to one representative of each sibship (937,427 allele products). (2) Both chi 2-type contrasts and a genetic distance measure (delta) reveal that rare variants (P less than .01) are collectively as effective as polymorphisms in establishing genetic differences between the two cities. (3) We suggest that rare variants that individually exhibit significant intercity differences are probably the legacy of tribal private polymorphisms that occurred during prehistoric times. (4) Despite the great differences in the known histories of the two cities, both the overall frequency of rare variants and the number of different rare variants are essentially identical in the two cities. (5) The well-known differences in locus variability are confirmed, now after adjustment for sample size differences for the various locus products; in this large series we failed to detect variants at only three of 29 loci for which sample size exceeded 23,000. (6) The number of alleles identified per locus correlates positively with subunit molecular weight. (7) Loci supporting genetic polymorphisms are characterized by more rare variants than are loci at which polymorphisms were not encountered. (8) Loci whose products do not appear to be essential for health support more variants than do loci the absence of whose product is detrimental to health. (9) There is a striking excess of rare variants over the expectation under the neutral mutation/drift/equilibrium theory. We suggest that this finding is primarily due to the relatively recent (in genetic time) agglomeration of previously separated tribal populations; efforts to test for agreement with the expectations of this theory by using data from modern cosmopolitan populations are exercises in futility. (10) All of these findings should characterize DNA variants in exons as more data become available, since the finding are the protein expression of such variants. PMID:3195587

Protein variants in Hiroshima and Nagasaki: tales of two cities.

PubMed

Neel, J V; Satoh, C; Smouse, P; Asakawa, J; Takahashi, N; Goriki, K; Fujita, M; Kageoka, T; Hazama, R

1988-12-01

The results of 1,465,423 allele product determinations based on blood samples from Hiroshima and Nagasaki, involving 30 different proteins representing 32 different gene products, are analyzed in a variety of ways, with the following conclusions: (1) Sibships and their parents are included in the sample. Our analysis reveals that statistical procedures designed to reduce the sample to equivalent independent genomes do not in population comparisons compensate for the familial cluster effect of rare variants. Accordingly, the data set was reduced to one representative of each sibship (937,427 allele products). (2) Both chi 2-type contrasts and a genetic distance measure (delta) reveal that rare variants (P less than .01) are collectively as effective as polymorphisms in establishing genetic differences between the two cities. (3) We suggest that rare variants that individually exhibit significant intercity differences are probably the legacy of tribal private polymorphisms that occurred during prehistoric times. (4) Despite the great differences in the known histories of the two cities, both the overall frequency of rare variants and the number of different rare variants are essentially identical in the two cities. (5) The well-known differences in locus variability are confirmed, now after adjustment for sample size differences for the various locus products; in this large series we failed to detect variants at only three of 29 loci for which sample size exceeded 23,000. (6) The number of alleles identified per locus correlates positively with subunit molecular weight. (7) Loci supporting genetic polymorphisms are characterized by more rare variants than are loci at which polymorphisms were not encountered. (8) Loci whose products do not appear to be essential for health support more variants than do loci the absence of whose product is detrimental to health. (9) There is a striking excess of rare variants over the expectation under the neutral mutation/drift/equilibrium theory. We suggest that this finding is primarily due to the relatively recent (in genetic time) agglomeration of previously separated tribal populations; efforts to test for agreement with the expectations of this theory by using data from modern cosmopolitan populations are exercises in futility. (10) All of these findings should characterize DNA variants in exons as more data become available, since the finding are the protein expression of such variants.

Characterization of a hypoxia-response element in the Epo locus of the pufferfish, Takifugu rubripes.

PubMed

Kulkarni, Rashmi P; Tohari, Sumanty; Ho, Adrian; Brenner, Sydney; Venkatesh, Byrappa

2010-06-01

Animals respond to hypoxia by increasing synthesis of the glycoprotein hormone erythropoietin (Epo) which in turn stimulates the production of red blood cells. The gene encoding Epo has been recently cloned in teleost fishes such as the pufferfish Takifugu rubripes (fugu) and zebrafish (Danio rerio). It has been shown that the transcription levels of Epo in teleost fishes increase in response to anemia or hypoxia in a manner similar to its human ortholog. However, the cis-regulatory element(s) mediating the hypoxia response of Epo gene in fishes has not been identified. In the present study, using the human hepatoma cell line (Hep3B), we have identified and characterized a hypoxia response element (HRE) in the fugu Epo locus. The sequence of the fugu HRE (ACGTGCTG) is identical to that of the HRE in the human EPO locus. However, unlike the HRE in the mammalian Epo locus, which is located in the 3' region of the gene, the fugu HRE is located in the 5' flanking region and on the opposite strand of DNA. This HRE is conserved in other teleosts such as Tetraodon and zebrafish in a similar location. A 365-bp fragment containing the fugu HRE was able to drive GFP expression in the liver of transgenic zebrafish. However, we could not ascertain if the expression of transgene is induced by hypoxia in vivo due to the low and variable levels of GFP expression in transgenic zebrafish. Our investigations also revealed that the Epo locus has experienced extensive rearrangements during vertebrate evolution. Copyright © 2010 Elsevier B.V. All rights reserved.

Clonal structure in Ichthyobacterium seriolicida, the causative agent of bacterial haemolytic jaundice in yellowtail, Seriola quinqueradiata, inferred from molecular epidemiological analysis.

PubMed

Matsuyama, T; Fukuda, Y; Sakai, T; Tanimoto, N; Nakanishi, M; Nakamura, Y; Takano, T; Nakayasu, C

2017-08-01

Bacterial haemolytic jaundice caused by Ichthyobacterium seriolicida has been responsible for mortality in farmed yellowtail, Seriola quinqueradiata, in western Japan since the 1980s. In this study, polymorphic analysis of I. seriolicida was performed using three molecular methods: amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Twenty-eight isolates were analysed using AFLP, while 31 isolates were examined by MLST and MLVA. No polymorphisms were identified by AFLP analysis using EcoRI and MseI, or by MLST of internal fragments of eight housekeeping genes. However, MLVA revealed variation in repeat numbers of three elements, allowing separation of the isolates into 16 sequence types. The unweighted pair group method using arithmetic averages cluster analysis of the MLVA data identified four major clusters, and all isolates belonged to clonal complexes. It is likely that I. seriolicida populations share a common ancestor, which may be a recently introduced strain. © 2016 John Wiley & Sons Ltd.

Prognostic relevance of the expressions of CAV1 and TES genes on 7q31 in melanoma.

PubMed

Vizkeleti, Laura; Ecsedi, Szilvia; Rakosy, Zsuzsa; Begany, Agnes; Emri, Gabriella; Toth, Reka; Orosz, Adrienn; Szollosi, Attila Gabor; Mehes, Gabor; Adany, Roza; Balazs, Margit

2012-01-01

The 7q31 locus contains several genes affected in cancer progression. Although evidences exist regarding its impact on tumorigenesis, the role of genetic alterations and the expressions of locus-related genes are still controversial. Our study aimed to define the 7q31 copy number alterations in primary melanomas, primary-metastatic tumor pairs and cell lines. Data were correlated with clinical-pathological parameters. Genetic data show that 7q31 copy number distribution was heterogeneous in both primary and metastatic tumors. Extra copies were highly accompanied by chromosome 7 polisomy, and significantly increased in primary lesions with poor prognosis. Additionally, we determined the mRNA and protein levels of the locus-related CAV1 and TES genes. TES mRNA level was associated with metastatic location. CAV1 mRNA and protein levels were significantly higher in thicker tumors, however, lack of protein was also observed in a subpopulation of thin lesions. Expressions of CAV1 and TES were not associated with 7q31 alterations. In conclusion, 7q31 amplification can predict unfavorable outcome. Alterations of TES mRNA level may predict the location of metastasis. CAV1 possibly affect the cancer cell invasion.

A bayesian analysis for identifying DNA copy number variations using a compound poisson process.

PubMed

Chen, Jie; Yiğiter, Ayten; Wang, Yu-Ping; Deng, Hong-Wen

2010-01-01

To study chromosomal aberrations that may lead to cancer formation or genetic diseases, the array-based Comparative Genomic Hybridization (aCGH) technique is often used for detecting DNA copy number variants (CNVs). Various methods have been developed for gaining CNVs information based on aCGH data. However, most of these methods make use of the log-intensity ratios in aCGH data without taking advantage of other information such as the DNA probe (e.g., biomarker) positions/distances contained in the data. Motivated by the specific features of aCGH data, we developed a novel method that takes into account the estimation of a change point or locus of the CNV in aCGH data with its associated biomarker position on the chromosome using a compound Poisson process. We used a Bayesian approach to derive the posterior probability for the estimation of the CNV locus. To detect loci of multiple CNVs in the data, a sliding window process combined with our derived Bayesian posterior probability was proposed. To evaluate the performance of the method in the estimation of the CNV locus, we first performed simulation studies. Finally, we applied our approach to real data from aCGH experiments, demonstrating its applicability.

Genetic variation affecting host-parasite interactions: major-effect quantitative trait loci affect the transmission of sigma virus in Drosophila melanogaster.

PubMed

Bangham, Jenny; Knott, Sara A; Kim, Kang-Wook; Young, Robert S; Jiggins, Francis M

2008-09-01

In natural populations, genetic variation affects resistance to disease. Whether that genetic variation comprises lots of small-effect polymorphisms or a small number of large-effect polymorphisms has implications for adaptation, selection and how genetic variation is maintained in populations. Furthermore, how much genetic variation there is, and the genes that underlie this variation, affects models of co-evolution between parasites and their hosts. We are studying the genetic variation that affects the resistance of Drosophila melanogaster to its natural pathogen--the vertically transmitted sigma virus. We have carried out three separate quantitative trait locus mapping analyses to map gene variants on the second chromosome that cause variation in the rate at which males transmit the infection to their offspring. All three crosses identified a locus in a similar chromosomal location that causes a large drop in the rate at which the virus is transmitted. We also found evidence for an additional smaller-effect quantitative trait locus elsewhere on the chromosome. Our data, together with previous experiments on the sigma virus and parasitoid wasps, indicate that the resistance of D. melanogaster to co-evolved pathogens is controlled by a limited number of major-effect polymorphisms.

Construction of the physical map of the gpa7 locus reveals that a large segment was deleted during rice domestication.

PubMed

Li, Xianran; Tian, Feng; Huang, Haiyan; Tan, Lubin; Zhu, Zuofeng; Hu, Songnian; Sun, Chuanqing

2008-06-01

To facilitate cloning gene(s) underlying gpa7, a deep-coverage BAC library was constructed for an isolate of common wild rice (Oryza rufipogon Griff.) collected from Dongxiang, Jiangxi Province, China (DXCWR). gpa7, a quantitative trait locus corresponding to grain number per panicle, is positioned in the short arm of chromosome 7. The BAC library containing 96,768 clones represents approximate 18 haploid genome equivalents. The contig spanning DXCWR gpa7 was constructed with a series of ordered markers. The putative physical map near the gpa7 locus of another accession of O. rufipogon (Accession: IRGC 105491) was also isolated in silico. Analysis of the physical maps of gpa7 indicated that a segment of about 150 kb was deleted during domestication of common wild rice.

Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode1[W][OPEN

PubMed Central

Cook, David E.; Bayless, Adam M.; Wang, Kai; Guo, Xiaoli; Song, Qijian; Jiang, Jiming; Bent, Andrew F.

2014-01-01

Copy number variation of kilobase-scale genomic DNA segments, beyond presence/absence polymorphisms, can be an important driver of adaptive traits. Resistance to Heterodera glycines (Rhg1) is a widely utilized quantitative trait locus that makes the strongest known contribution to resistance against soybean cyst nematode (SCN), Heterodera glycines, the most damaging pathogen of soybean (Glycine max). Rhg1 was recently discovered to be a complex locus at which resistance-conferring haplotypes carry up to 10 tandem repeat copies of a 31-kb DNA segment, and three disparate genes present on each repeat contribute to SCN resistance. Here, we use whole-genome sequencing, fiber-FISH (fluorescence in situ hybridization), and other methods to discover the genetic variation at Rhg1 across 41 diverse soybean accessions. Based on copy number variation, transcript abundance, nucleic acid polymorphisms, and differentially methylated DNA regions, we find that SCN resistance is associated with multicopy Rhg1 haplotypes that form two distinct groups. The tested high-copy-number Rhg1 accessions, including plant introduction (PI) 88788, contain a flexible number of copies (seven to 10) of the 31-kb Rhg1 repeat. The identified low-copy-number Rhg1 group, including PI 548402 (Peking) and PI 437654, contains three copies of the Rhg1 repeat and a newly identified allele of Glyma18g02590 (a predicted α-SNAP [α-soluble N-ethylmaleimide–sensitive factor attachment protein]). There is strong evidence for a shared origin of the two resistance-conferring multicopy Rhg1 groups and subsequent independent evolution. Differentially methylated DNA regions also were identified within Rhg1 that correlate with SCN resistance. These data provide insights into copy number variation of multigene segments, using as the example a disease resistance trait of high economic importance. PMID:24733883

Retroviral vectors encoding ADA regulatory locus control region provide enhanced T-cell-specific transgene expression.

PubMed

Trinh, Alice T; Ball, Bret G; Weber, Erin; Gallaher, Timothy K; Gluzman-Poltorak, Zoya; Anderson, French; Basile, Lena A

2009-12-30

Murine retroviral vectors have been used in several hundred gene therapy clinical trials, but have fallen out of favor for a number of reasons. One issue is that gene expression from viral or internal promoters is highly variable and essentially unregulated. Moreover, with retroviral vectors, gene expression is usually silenced over time. Mammalian genes, in contrast, are characterized by highly regulated, precise levels of expression in both a temporal and a cell-specific manner. To ascertain if recapitulation of endogenous adenosine deaminase (ADA) expression can be achieved in a vector construct we created a new series of Moloney murine leukemia virus (MuLV) based retroviral vector that carry human regulatory elements including combinations of the ADA promoter, the ADA locus control region (LCR), ADA introns and human polyadenylation sequences in a self-inactivating vector backbone. A MuLV-based retroviral vector with a self-inactivating (SIN) backbone, the phosphoglycerate kinase promoter (PGK) and the enhanced green fluorescent protein (eGFP), as a reporter gene, was generated. Subsequent vectors were constructed from this basic vector by deletion or addition of certain elements. The added elements that were assessed are the human ADA promoter, human ADA locus control region (LCR), introns 7, 8, and 11 from the human ADA gene, and human growth hormone polyadenylation signal. Retroviral vector particles were produced by transient three-plasmid transfection of 293T cells. Retroviral vectors encoding eGFP were titered by transducing 293A cells, and then the proportion of GFP-positive cells was determined using fluorescence-activated cell sorting (FACS). Non T-cell and T-cell lines were transduced at a multiplicity of infection (MOI) of 0.1 and the yield of eGFP transgene expression was evaluated by FACS analysis using mean fluorescent intensity (MFI) detection. Vectors that contained the ADA LCR were preferentially expressed in T-cell lines. Further improvements in T-cell specific gene expression were observed with the incorporation of additional cis-regulatory elements, such as a human polyadenylation signal and intron 7 from the human ADA gene. These studies suggest that the combination of an authentically regulated ADA gene in a murine retroviral vector, together with additional locus-specific regulatory refinements, will yield a vector with a safer profile and greater efficacy in terms of high-level, therapeutic, regulated gene expression for the treatment of ADA-deficient severe combined immunodeficiency.

The population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae): the number, frequency, and dominance interactions of S alleles across its British range.

PubMed

Brennan, Adrian C; Harris, Stephen A; Hiscock, Simon J

2006-02-01

Sporophytic self-incompatibility (SSI) was studied in 11 British Senecio squalidus populations to quantify mating system variation and determine how its recent colonization of the United Kingdom has influenced its mating behavior. S allele number, frequency, and dominance interactions in populations were assessed using full diallels of controlled pollinations. A mean of 5.1 S alleles per population was observed, and no population contained more than six S alleles. Numbers of S alleles within populations of S. squalidus declined with increasing distance from the center of its introduction (Oxford). Cross-classification of S alleles allowed an estimate of approximately seven and no more than 11 S alleles for the entire British S. squalidus population. The low number of S alleles observed in British S. squalidus compared to other SI species is consistent with the population bottleneck associated with S. squalidus' introduction to the Oxford Botanic Garden and subsequent colonization of Britain. Extensive S allele dominance interactions were observed to be a feature of the S. squalidus SSI system and may represent an adaptive response to improve limited mate availability imposed by the presence of so few S alleles. Multilocus allozyme genotypes were also identified for individuals in all populations and geographic patterns of S locus and allozyme loci variation investigated. Less interpopulation structure was observed for the S locus than for allozyme diversity--a finding indicative of the effects of negative frequency-dependent selection at the S locus maintaining equal S phenotypes within populations and enhancing effective migration between populations.

Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA).

PubMed

Bergonier, Dominique; Sobral, Daniel; Feßler, Andrea T; Jacquet, Eric; Gilbert, Florence B; Schwarz, Stefan; Treilles, Michaël; Bouloc, Philippe; Pourcel, Christine; Vergnaud, Gilles

2014-10-02

Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes.

Evaluating the Use of Multilocus Variable Number Tandem Repeat Analysis of Shiga Toxin-Producing Escherichia coli O157 as a Routine Public Health Tool in England

PubMed Central

Byrne, Lisa; Elson, Richard; Dallman, Timothy J.; Perry, Neil; Ashton, Philip; Wain, John; Adak, Goutam K.; Grant, Kathie A.; Jenkins, Claire

2014-01-01

Multilocus variable number tandem repeat analysis (MLVA) provides microbiological support for investigations of clusters of cases of infection with Shiga toxin-producing E. coli (STEC) O157. All confirmed STEC O157 isolated in England and submitted to the Gastrointestinal Bacteria Reference Unit (GBRU) during a six month period were typed using MLVA, with the aim of assessing the impact of this approach on epidemiological investigations. Of 539 cases investigated, 341 (76%) had unique (>2 single locus variants) MLVA profiles, 12% of profiles occurred more than once due to known household transmission and 12% of profiles occurred as part of 41 clusters, 21 of which were previously identified through routine public health investigation of cases. The remaining 20 clusters were not previously detected and STEC enhanced surveillance data for associated cases were retrospectively reviewed for epidemiological links including shared exposures, geography and/or time. Additional evidence of a link between cases was found in twelve clusters. Compared to phage typing, the number of sporadic cases was reduced from 69% to 41% and the diversity index for MLVA was 0.996 versus 0.782 for phage typing. Using MLVA generates more data on the spatial and temporal dispersion of cases, better defining the epidemiology of STEC infection than phage typing. The increased detection of clusters through MLVA typing highlights the challenges to health protection practices, providing a forerunner to the advent of whole genome sequencing as a diagnostic tool. PMID:24465775

Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England.

PubMed

Byrne, Lisa; Elson, Richard; Dallman, Timothy J; Perry, Neil; Ashton, Philip; Wain, John; Adak, Goutam K; Grant, Kathie A; Jenkins, Claire

2014-01-01

Multilocus variable number tandem repeat analysis (MLVA) provides microbiological support for investigations of clusters of cases of infection with Shiga toxin-producing E. coli (STEC) O157. All confirmed STEC O157 isolated in England and submitted to the Gastrointestinal Bacteria Reference Unit (GBRU) during a six month period were typed using MLVA, with the aim of assessing the impact of this approach on epidemiological investigations. Of 539 cases investigated, 341 (76%) had unique (>2 single locus variants) MLVA profiles, 12% of profiles occurred more than once due to known household transmission and 12% of profiles occurred as part of 41 clusters, 21 of which were previously identified through routine public health investigation of cases. The remaining 20 clusters were not previously detected and STEC enhanced surveillance data for associated cases were retrospectively reviewed for epidemiological links including shared exposures, geography and/or time. Additional evidence of a link between cases was found in twelve clusters. Compared to phage typing, the number of sporadic cases was reduced from 69% to 41% and the diversity index for MLVA was 0.996 versus 0.782 for phage typing. Using MLVA generates more data on the spatial and temporal dispersion of cases, better defining the epidemiology of STEC infection than phage typing. The increased detection of clusters through MLVA typing highlights the challenges to health protection practices, providing a forerunner to the advent of whole genome sequencing as a diagnostic tool.

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion.

PubMed

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-10-07

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model, F = 11.81, p < 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12-162.41; p < 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes.

Hookworm infection, anaemia and genetic variability of the New Zealand sea lion

PubMed Central

Acevedo-Whitehouse, Karina; Petetti, Laura; Duignan, Padraig; Castinel, Aurelie

2009-01-01

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model, F = 11.81, p < 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12–162.41; p < 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes. PMID:19605394

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

PubMed Central

Bader, Douglas E.

2012-01-01

Environmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park. Bacillus anthracis spores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. Confirmed B. anthracis isolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA). B. anthracis isolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing of Bacillus anthracis. PMID:22773624

Clinical and genetic diversity of SMN1-negative proximal spinal muscular atrophies

PubMed Central

Jordanova, Albena

2014-01-01

Hereditary spinal muscular atrophy is a motor neuron disorder characterized by muscle weakness and atrophy due to degeneration of the anterior horn cells of the spinal cord. Initially, the disease was considered purely as an autosomal recessive condition caused by loss-of-function SMN1 mutations on 5q13. Recent developments in next generation sequencing technologies, however, have unveiled a growing number of clinical conditions designated as non-5q forms of spinal muscular atrophy. At present, 16 different genes and one unresolved locus are associated with proximal non-5q forms, having high phenotypic variability and diverse inheritance patterns. This review provides an overview of the current knowledge regarding the phenotypes, causative genes, and disease mechanisms associated with proximal SMN1-negative spinal muscular atrophies. We describe the molecular and cellular functions enriched among causative genes, and discuss the challenges in the post-genomics era of spinal muscular atrophy research. PMID:24970098

Persistence of the same genetic type of Mycoplasma hyopneumoniae in a closed herd for at least two years.

PubMed

Rebaque, Florencia; Camacho, Pablo; Parada, Julián; Lucchesi, Paula; Ambrogi, Arnaldo; Tamiozzo, Pablo

2017-10-20

Two cross-sectional studies were carried out in 2013 and 2015 monitoring for Mycoplasma hyopneumoniae presence in a swine farm. In these studies, the genetic diversity of M. hyopneumoniae was assessed in clinical specimens using a Multiple Locus Variable-number tandem repeat Analysis (MLVA) targeting P97 R1, P146 R3 and H4 loci. The samples from August 2015 showed the MLVA profile prevalent in June 2013, therefore it can be concluded that a same genetic type of M. hyopneumoniae can persist for at least two years in a closed herd. In addition, the nested PCR reactions implemented in this study showed to be useful for MLVA typing in non-invasive clinical samples. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

[Paternity study in Chilean families using DNA fingerprints and erythrocyte blood markers].

PubMed

Aguirre, R; Blanco, R; Cifuentes, L; Chiffelle, I; Armanet, L; Vargas, J; Jara, L

1992-10-01

In the last decade, the electromorphic phenotype corresponding to extremely polymorphic zones of DNA, that include variable number of tandem repeat loci (VNTR) of oligonucleotide sequences, have been added to classical markers to elucidate the problems of parenthood identification and ascription in human beings. Using VNTR of several loci, a band profile practically unique for each individual is obtained (DNA-fingerprints). Since the pattern of VNTR electrophoretic bands is inherited from parents in a proportion of 50% from each one, this system is extremely useful for paternity ascription or exclusion. Nine nuclear families were studied, randomly selected from a group of 170 families that were analyzed using 5 erythrocyte genetic markers and with VNTRs detected using the multi locus probe (CAC)5, aiming to explore the concordance of both methods. Results were similar for both methods; however for VNTR, there is no information available on population frequency of polymorphisms.

Telomerase reverse transcriptase locus polymorphisms and cancer risk: a field synopsis and meta-analysis.

PubMed

Mocellin, Simone; Verdi, Daunia; Pooley, Karen A; Landi, Maria T; Egan, Kathleen M; Baird, Duncan M; Prescott, Jennifer; De Vivo, Immaculata; Nitti, Donato

2012-06-06

Several recent studies have provided evidence that polymorphisms in the telomerase reverse transcriptase (TERT) gene sequence are associated with cancer development, but a comprehensive synopsis is not available. We conducted a systematic review and meta-analysis of the available molecular epidemiology data regarding the association between TERT locus polymorphisms and predisposition to cancer. A systematic review of the English literature was conducted by searching PubMed, Embase, Cancerlit, Google Scholar, and ISI Web of Knowledge databases for studies on associations between TERT locus polymorphisms and cancer risk. Random-effects meta-analysis was performed to pool per-allele odds ratios for TERT locus polymorphisms and risk of cancer, and between-study heterogeneity and potential bias sources (eg, publication and chasing bias) were assessed. Because the TERT locus includes the cleft lip and palate transmembrane 1-like (CLPTM1L) gene, which is in linkage disequilibrium with TERT, CLPTM1L polymorphisms were also analyzed. Cumulative evidence for polymorphisms with statistically significant associations was graded as "strong," "moderate," and "weak" according to the Venice criteria. The joint population attributable risk was calculated for polymorphisms with strong evidence of association. Eighty-five studies enrolling 490 901 subjects and reporting on 494 allelic contrasts were retrieved. Data were available on 67 TERT locus polymorphisms and 24 tumor types, for a total of 221 unique combinations of polymorphisms and cancer types. Upon meta-analysis, a statistically significant association with the risk of any cancer type was found for 22 polymorphisms. Strong, moderate, and weak cumulative evidence for association with at least one tumor type was demonstrated for 11, 9, and 14 polymorphisms, respectively. For lung cancer, which was the most studied tumor type, the estimated joint population attributable risk for three polymorphisms (TERT rs2736100, intergenic rs4635969, and CLPTM1L rs402710) was 41%. Strong evidence for lack of association was identified for five polymorphisms in three tumor types. To our knowledge, this is the largest collection of data for associations between TERT locus polymorphisms and cancer risk. Our findings support the hypothesis that genetic variability in this genomic region can modulate cancer susceptibility in humans.

Deregulated HOX genes in ameloblastomas are located in physical contiguity to keratin genes.

PubMed

Schiavo, Giulia; D'Antò, Vincenzo; Cantile, Monica; Procino, Alfredo; Di Giovanni, Stefano; Valletta, Rossella; Terracciano, Luigi; Baumhoer, Daniel; Jundt, Gernot; Cillo, Clemente

2011-11-01

The expression of the HOX gene network in mid-stage human tooth development mostly concerns the epithelial tooth germ compartment and involves the C and D HOX loci. To further dissect the HOX gene implication with tooth epithelium differentiation we compared the expression of the whole HOX network in human ameloblastomas, as paradigm of epithelial odontogenic tumors, with tooth germs. We identified two ameloblastoma molecular types with respectively low and high number of active HOX C genes. The highly expressing HOX C gene ameloblastomas were characterized by a strong keratinized phenotype. Locus C HOX genes are located on chromosome 12q13-15 in physical contiguity with one of the two keratin gene clusters included in the human genome. The most posterior HOX C gene, HOX C13, is capable to interact with hair keratin genes located on the other keratin gene cluster in physical contiguity with the HOX B locus on chromosome 17q21-22. Inside the HOX C locus, a 2.2 kb ncRNA (HOTAIR) able to repress transcription, in cis, along the entire HOX C locus and, in trans, at the posterior region of the HOX D locus has recently been identified. Interestingly both loci are deregulated in ameloblastomas. Our finding support an important role of the HOX network in characterizing the epithelial tooth compartment. Furthermore, the physical contiguity between locus C HOX and keratin genes in normal tooth epithelium and their deregulation in the neoplastic counterparts suggest they may act on the same mechanism potentially involved with epithelial tumorigenesis. Copyright © 2011 Wiley Periodicals, Inc.

The pink-eyed dilution locus controls the biogenesis of melanosomes and levels of melanosomal proteins in the eye.

PubMed

Orlow, S J; Brilliant, M H

1999-02-01

The pink-eyed dilution (p) locus is known to control the quantity of melanin pigment made within melanocytes and retinal pigment epithelium (RPE) in the eye. We have examined the effects of several mutant allele combinations at the murine p locus on the number and morphology of melanosomes in choroidal melanocytes and RPE cells as well as on the levels of four proteins known to be present within melanosomes: tyrosinase, tyrosinase-related proteins 1 and 2 (TRP-1 and TRP-2) and lysosome-associated membrane protein-1 (LAMP-1). By electron microscopy, we observed a modest diminution in the size and number of choroidal melanosomes in pbs/pJ mice but a more dramatic decrease in the RPE in comparison with wild-type P/P mice. By contrast, a drastic reduction in melanosome size and number was present in the choroid and RPE of pun/pun and p6H/pcp mice, and in the RPE of p6H/pcp mice, melanosomes were essentially undetectable. In wild-type mice, levels of tyrosinase, TRP-1 and TRP-2 were high at birth and showed a second peak of expression at 10-14 days of age, declining to undetectable levels by 42 days. All three mutant allele combinations reduced the levels of these melanosomal proteins with the relative severity of effects being p6H/pcp>pun/pun>pbs/pJ. In the null p6H/pcp mice, levels of these proteins were extremely low at birth, no postnatal peak was observed, and levels declined to undetectable by 14 days. Levels of LAMP-1 in wild-type mice rose initially and then declined whereas in the mutant mice, levels decreased gradually from birth. Higher levels of LAMP-1 were observed in each of the mutants than in the wild-type mice at 21 days of age. Our results demonstrate that mutations at the p locus affect the size, number, shape and contents of melanosomes, implicating the p gene product in the normal biogenesis of this organelle. Copyright 1999 Academic Press.

Photoreceptor dysplasia (pd) in miniature schnauzer dogs: evaluation of candidate genes by molecular genetic analysis.

PubMed

Zhang, Q; Baldwin, V J; Acland, G M; Parshall, C J; Haskel, J; Aguirre, G D; Ray, K

1999-01-01

Photoreceptor dysplasia (pd) is one of a group of at least six distinct autosomal and one X-linked retinal disorders identified in dogs which are collectively known as progressive retinal atrophy (PRA). It is an early onset retinal disease identified in miniature schnauzer dogs, and pedigree analysis and breeding studies have established autosomal recessive inheritance of the disease. Using a gene-based approach, a number of retina-expressed genes, including some members of the phototransduction pathway, have been causally implicated in retinal diseases of humans and other animals. Here we examined seven such potential candidate genes (opsin, RDS/peripherin, ROM1, rod cGMP-gated cation channel alpha-subunit, and three subunits of transducin) for their causal association with the pd locus by testing segregation of intragenic markers with the disease locus, or, in the absence of informative polymorphisms, sequencing of the coding regions of the genes. Based on these results, we have conclusively excluded four photoreceptor-specific genes as candidates for pd by linkage analysis. For three other photoreceptor-specific genes, we did not find any mutation in the coding sequences of the genes and have excluded them provisionally. Formal exclusion would require investigation of the levels of expression of the candidate genes in pd-affected dogs relative to age-matched controls. At present we are building suitable informative pedigrees for the disease locus with a sufficient number of meiosis to be useful for genomewide screening. This should identify markers linked to the disease locus and eventually permit progress toward the identification of the photoreceptor dysplasia gene and the disease-causing mutation.

Crowding, visual awareness, and their respective neural loci

PubMed Central

Shin, Kilho; Chung, Susana T. L.; Tjan, Bosco S.

2017-01-01

In peripheral vision, object identification can be impeded when a target object is flanked by other objects. This phenomenon of crowding has been attributed to basic processes associated with image encoding by the visual system, but the neural origin of crowding is not known. Determining whether crowding depends on subjective awareness of the flankers can provide information on the neural origin of crowding. However, recent studies that manipulated flanker awareness have yielded conflicting results. In the current study, we suppressed flanker awareness with two methods: interocular suppression (IOS) and adaptation-induced blindness (AIB). We tested two different types of stimuli: gratings and letters. With IOS, we found that the magnitude of crowding increased as the number of physical flankers increased, even when the observers did not report seeing any of the flankers. In contrast, when flanker awareness was manipulated with AIB, the magnitude of crowding increased with the number of perceived flankers. Our results show that whether crowding is contingent on awareness of the flankers depends on the method used to suppress awareness. In addition, our results imply that the locus of crowding is upstream from the neural locus of IOS and close to or downstream from that of AIB. Neurophysiology and neuroimaging studies jointly implicate mid-to-high level visual processing stages for IOS, while direct evidence regarding the neural locus of AIB is limited. The most consistent interpretation of our empirical findings is to place the neural locus of crowding at an early cortical site, such as V1 or V2. PMID:28549353

Look Before You Leap: What Are the Obstacles to Risk Calculation in the Equestrian Sport of Eventing?

PubMed Central

O’Brien, Denzil

2016-01-01

Simple Summary This paper examines a number of methods for calculating injury risk for riders in the equestrian sport of eventing, and suggests that the primary locus of risk is the action of the horse jumping, and the jump itself. The paper argues that risk calculation should therefore focus first on this locus. Abstract All horse-riding is risky. In competitive horse sports, eventing is considered the riskiest, and is often characterised as very dangerous. But based on what data? There has been considerable research on the risks and unwanted outcomes of horse-riding in general, and on particular subsets of horse-riding such as eventing. However, there can be problems in accessing accurate, comprehensive and comparable data on such outcomes, and in using different calculation methods which cannot compare like with like. This paper critically examines a number of risk calculation methods used in estimating risk for riders in eventing, including one method which calculates risk based on hours spent in the activity and in one case concludes that eventing is more dangerous than motorcycle racing. This paper argues that the primary locus of risk for both riders and horses is the jump itself, and the action of the horse jumping. The paper proposes that risk calculation in eventing should therefore concentrate primarily on this locus, and suggests that eventing is unlikely to be more dangerous than motorcycle racing. The paper proposes avenues for further research to reduce the likelihood and consequences of rider and horse falls at jumps. PMID:26891334

A Novel Quantitative Trait Locus on Mouse Chromosome 18, “era1,” Modifies the Entrainment of Circadian Rhythms

PubMed Central

Wisor, Jonathan P.; Striz, Martin; DeVoss, Jason; Murphy, Greer M.; Edgar, Dale M.; O'Hara, Bruce F.

2007-01-01

Study Objectives: The mammalian circadian clock in the suprachiasmatic nuclei (SCN) of the hypothalamus conveys 24-h rhythmicity to sleep-wake cycles, locomotor activity, and other behavioral and physiological processes. The timing of rhythms relative to the light/dark (LD12:12) cycle is influenced in part by the endogenous circadian period and the time of day specific sensitivity of the clock to light. We now describe a novel circadian rhythm phenotype, and a locus influencing that phenotype, in a segregating population of mice. Methods: By crossbreeding 2 genetically distinct nocturnal strains of mice (Cast/Ei and C57BL/6J) and backcrossing the resulting progeny to Cast/Ei, we have produced a novel circadian phenotype, called early runner mice. Results: Early runner mice entrain to a light/dark cycle at an advanced phase, up to 9 hours before dark onset. This phenotype is not significantly correlated with circadian period in constant darkness and is not associated with disruption of molecular circadian rhythms in the SCN, as assessed by analysis of period gene expression. We have identified a genomic region that regulates this phenotype—a major quantitative trait locus on chromosome 18 (near D18Mit184) that we have named era1 for Early Runner Activity locus one. Phase delays caused by light exposure early in the subjective night were of smaller magnitude in backcross offspring that were homozygous Cast/Ei at D18Mit184 than in those that were heterozygous at this locus. Conclusion: Genetic variability in the circadian response to light may, in part, explain the variance in phase angle of entrainment in this segregating mouse population. Citation: Wisor JP; Striz M; DeVoss J; Murphy GM; Edgar DM; O'Hara BF. A novel quantitative trait locus on mouse chromosome 18, “era1,” modifies the entrainment of circadian rhythms. SLEEP 2007;30(10):1255-1263. PMID:17969459

The relation of locus-of-control orientation and task structure to problem-solving performance of sixth-grade student pairs

NASA Astrophysics Data System (ADS)

Main, June Dewey; Budd Rowe, Mary

This study investigated the relationship of locus-of-control orientations and task structure to the science problem-solving performance of 100 same-sex, sixth-grade student pairs. Pairs performed a four-variable problem-solving task, racing cylinders down a ramp in a series of trials to determine the 3 fastest of 18 different cylinders. The task was completed in one of two treatment conditions: the structured condition with moderate cuing and the unstructured condition with minimal cuing. Pairs completed an after-task assessment, predicting the results of proposed cylinder races, to measure the ability to understand and apply task concepts. Overall conclusions were: (1) There was no relationship between locus-of-control orientation and effectiveness of problem-solving strategy; (2) internality was significantly related to higher accuracy on task solutions and on after-task predictions; (3) there was no significant relationship between task structure and effectiveness of problem-solving strategy; (4) solutions to the task were more accurate in the unstructured task condition; (5) internality related to more accurate solutions in the unstructured task condition.

Ribosomal DNA, tri- and bi-partite pericentromeres in the permanent translocation heterozygote Rhoeo spathacea.

PubMed

Golczyk, Hieronim; Hasterok, Robert; Szklarczyk, Marek

2010-12-01

High- and low-stringency FISH and base-specific fluorescence were performed on the permanent translocation heterozygote Rhoeo spathacea (2n = 12). Our results indicate that 45S rDNA arrays, rDNA-related sequences and other GC-rich DNA fraction(s) are located within the pericentromeric regions of all twelve chromosomes, usually colocalizing with the chromomycin A(3)-positive bands. Homogenization of the pericentromeric regions appears to result from the concerted spread of GC-rich sequences, with differential amplification likely. We found new 5S rDNA patterns, which suggest a variability in the breakpoints and in the consequent chromosome reorganizations. It was found that the large 5S rDNA locus residing on each of the 8E and 9E arms consisted of two smaller loci. On each of the two chromosome arms 3b and 4b, in addition to the major subtelomeric 5S rDNA locus, a new minor locus was found interstitially about 40% along the arm length. The arrangement of cytotogenetic landmarks and chromosome arm measurements are discussed with regard to genome repatterning in Rhoeo.

FRAXE mutation analysis in three Spanish families

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carbonell, P.; Lopez, I.; Gabarron, J.

Very little is known about the phenotype of FRAXE-positive individuals and the relation between the genotype/phenotype and genotype/cytogenetic expression. We describe three families with normal and mildly affected individuals and a severely retarded male expressing fragility at the FRAXE locus or presenting different expansions at the CGG FRAXE triplet. In addition, we analyze the FRAXE mutation in sperm DNA from a retarded male carrier with a handicapped daughter expressing fragility at the FRAXE locus. Mental status in FRAXE individuals is highly variable and, although mild mental retardation is observed in most cases, several carrier males are apparently normal. It seemsmore » that methylation is not as strictly associated with size of CGG triplets in the FRAXE locus as in FRAXA, and it is possible that normal carrier individuals with fully methylated increments in lymphocytes have a certain proportion of unmethylated alleles in the critical (i.e., neural) tissues. FRAXE mutation is apparently similar to FRAXA in that males with somatic large methylated increments are carriers of small unmethylated ones in germinal cells. 12 refs., 2 figs., 1 tab.« less

A Pilot Comparison of Purging and Non-Purging Bulimics.

ERIC Educational Resources Information Center

Grace, Pamela S.; And Others

1985-01-01

Compared purging bulimics (N=26), non-purging bulimics (N=24), and controls with no apparent eating problems, on personality and demographic variables. Results linked bulimics with low self-esteem, high anxiety, external locus of control, and high incidence of maternal and family obesity. No significant differences were found between purgers and…

MHC ANTIGEN BINDING LOCUS DRB1 SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETERCLITUS POPULATIONS

EPA Science Inventory

The major histocompatibility system provides a unique complex of genetic loci in vertebrates to assess genetic diversity and to look for the effects of selection on the adaptive immune system. Studies using mammals and birds
have demonstrated relationships between MHC genotyp...

High-speed Internet Use and Academic Gratifications in the College Residence.

ERIC Educational Resources Information Center

Matthews, Denise; Schrum, Lynne

2003-01-01

A multimethod exploration of undergraduates' high-speed Internet use in residence halls took a uses-and-gratifications approach and revealed Internet use as integral to students' lives. Students' negative comments about Internet distractions from academic work led to identification of an individual difference variable, internal locus of control of…

Examining the Relevance of Emotional Intelligence within Educational Programs for the Gifted and Talented

ERIC Educational Resources Information Center

Bellamy, Al; Gore, David; Sturgis, Judy

2005-01-01

This study explored the relationships between emotional intelligence, locus of control, and self-efficacy among gifted and talented students participating in a two week long summer educational program. Results revealed statistically significant correlations between these variables. Gender was found to moderate the relationships. The study also…

Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number.

PubMed

Sukumaran, Sivakumar; Lopes, Marta; Dreisigacker, Susanne; Reynolds, Matthew

2018-04-01

GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa. The panel genotyped with the 90 K Illumina Infinitum SNP array resulted in 26,814 SNPs for genome-wide association study (GWAS). Statistical analysis of the multi-environmental data for GY, GN, and TGW observed repeatability estimates of 0.76, 0.62, and 0.95, respectively. GWAS on BLUPs of combined environment analysis identified 38 loci associated with the traits. Among them four loci-6A (85 cM), 5A (98 cM), 3B (99 cM), and 2B (96 cM)-were associated with multiple traits. The study identified two loci that showed positive association between GY and TGW, with allelic substitution effects of 4% (GY) and 1.7% (TGW) for 6A locus and 0.2% (GY) and 7.2% (TGW) for 2B locus. The locus in chromosome 6A (79-85 cM) harbored a gene TaGW2-6A. We also identified that a combination of markers associated with GY, TGW, and GN together explained higher variation for GY (32%), than the markers associated with GY alone (27%). The marker-trait associations from the present study can be used for marker-assisted selection (MAS) and to discover the underlying genes for these traits in spring wheat.

Effects of a didactic and guided-imagery intervention regarding horrendous death by nuclear war upon fear of death, health locus of control, and social responsibility in health education college students

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campanelli, L.C.

1987-01-01

This investigation studied the effects of a videotaped lecture explaining horrendous death theory, with a guided imagery component describing horrendous death of a beloved other, upon action toward anti-nuclearism and three individual difference variables. The primary purpose of this study was to determine the effects of a videotaped lecture on college students' fear of death, health locus of control, and social responsibility. A second purpose was to determine whether participants who viewed the videotape were likely to sign a petition against nuclear war, in support of the Physicians for Social Responsibility's position against nuclearism. One hundred fifty-two (152) college studentsmore » participated in this study; approximately 55% were female and 50% were seniors. No significant differences were found regarding individual difference variables, except concerning fear of death of self between death education and non-death education experimental groups. Although an interaction effect was found, the hypothesis that experimental groups would be more likely to sign the petition against nuclear was not confirmed.« less

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

PubMed Central

Plantegenet, Stephanie; Weber, Johann; Goldstein, Darlene R; Zeller, Georg; Nussbaumer, Cindy; Thomas, Jérôme; Weigel, Detlef; Harshman, Keith; Hardtke, Christian S

2009-01-01

In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5′ regulatory sequence variation in the corresponding genes is indeed increased. However, ∼42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL. PMID:19225455

Preferential Mating in Symmetric Multilocus Systems: Limits for Multiallelism and for Many Loci

PubMed Central

Raper, J.

1982-01-01

Models in which general forms of preferential mating have been superimposed on the framework of the symmetric heterozygosity selection regime have been examined previously with respect to the existence and local stability of a central polymorphic equilibrium. The results are now extended to produce the limiting form of the stability conditions in two cases: First, where the number of alleles per locus is assumed to be very large; second, where the number of loci affecting the character is very large. It is argued that some type of frequency dependence in the mating pattern must be included, and a particular case is examined in detail. It is shown that multiallelism is ambiguous in its effect on stability, while an increasing number of loci, at least under zero linkage, leads to a simple stability condition which is analogous to the one-locus heterosis principle. Assortative mating appears to be more likely to produce a stable central polymorphism under high levels of allelism than is sexual selection, but is relatively very much weaker than sexual or viability selection if the number of loci involved is large. PMID:17246061

X-linked dominant cone-rod degeneration: Linkage mapping of a new locus for retinitis pigmentosa (RP15) to Xp22.13-p22.11

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuire, R.E.; Sullivan, L.S.; Daiger, S.P.

1995-07-01

Retinitis pigmentosa is the name given to a heterogeneous group of hereditary retinal degenerations characterized by progressive visual field loss, pigmentary changes of the retina, abnormal electroretinograms, and, frequently, night blindness. In this study, we investigated a family with dominant cone-rod degeneration, a variant form of retinitis pigmentosa. We used microsatellite markers to test for linkage to the disease locus and exluded all mapped autosomal loci. However, a marker from the short arm of the X chromosome, DXS989, showed 0% recombination to the disease locus, with a maximum lod (log-odds) score of 3.3. On the basis of this marker, themore » odds favoring X-linked dominant versus autosomal dominant inheritance are > 10{sup 5}:1. Haplotype analysis using an additional nine microsatellite markers places the disease locus in the Xp22.13-p22.11 region and excludes other X-linked disease loci causing retinal degeneration. The clinical expression of the retinal degeneration is consistent with X-linked dominant inheritance with milder, variable effects of Lyonization affecting expression in females. On the basis of these data we propose that this family has a novel form of dominant, X-linked cone-rod degeneration with the gene symbol {open_quotes}RP15{close_quotes}. 17 refs., 2 figs., 4 tabs.« less

Health locus of control as manifested in individuals attending a state-run medical dispensary in northern India.

PubMed

Berg, Michael B; Anshika, Avi

2017-04-01

To investigate the health locus of control (HLOC) beliefs of patients and visitors at a free, state-run medical clinic in Faridabad, India, in order to establish a norm for this population and to explore potential associations between the different categories of causal health beliefs. Participants (110 men, 96 women) were interviewed in Hindi and asked a shortened version of the Multidimensional Health Locus of Control Scale assessing both internal HLOC and three aspects of external HLOC (chance, powerful others, and God). Additional variables of interest included a Traditional Values Scale, a measure of spirituality, an assessment of health status, and demographic information including gender, age, employment status, and religion. Participants rated the external-God factor as a stronger determinant of their health than the internal or other external HLOC factors. Internal HLOC was positively correlated with external HLOC in terms of chance and the role of powerful others and these associations were strongest for the most interdependent participants (i.e. women and the unemployed). For patients and visitors at the Faridabad clinic, religion played a significant role in their causal health beliefs. In addition, internal HLOC was positively associated with aspects of external locus of control, suggesting that causal health beliefs were viewed in a holistic, integrated fashion. Interventions based on these findings are suggested.

Surface Diversity in Mycoplasma agalactiae Is Driven by Site-Specific DNA Inversions within the vpma Multigene Locus

PubMed Central

Glew, Michelle D.; Marenda, Marc; Rosengarten, Renate; Citti, Christine

2002-01-01

The ruminant pathogen Mycoplasma agalactiae possesses a family of abundantly expressed variable surface lipoproteins called Vpmas. Phenotypic switches between Vpma members have previously been correlated with DNA rearrangements within a locus of vpma genes and are proposed to play an important role in disease pathogenesis. In this study, six vpma genes were characterized in the M. agalactiae type strain PG2. All vpma genes clustered within an 8-kb region and shared highly conserved 5′ untranslated regions, lipoprotein signal sequences, and short N-terminal sequences. Analyses of the vpma loci from consecutive clonal isolates showed that vpma DNA rearrangements were site specific and that cleavage and strand exchange occurred within a minimal region of 21 bp located within the 5′ untranslated region of all vpma genes. This process controlled expression of vpma genes by effectively linking the open reading frame (ORF) of a silent gene to a unique active promoter sequence within the locus. An ORF (xer1) immediately adjacent to one end of the vpma locus did not undergo rearrangement and had significant homology to a distinct subset of genes belonging to the λ integrase family of site-specific xer recombinases. It is proposed that xer1 codes for a site-specific recombinase that is not involved in chromosome dimer resolution but rather is responsible for the observed vpma-specific recombination in M. agalactiae. PMID:12374833

Designing an optimum pulsed magnetic field by a resistance/self-inductance/capacitance discharge system and alignment of carbon nanotubes embedded in polypyrrole matrix

NASA Astrophysics Data System (ADS)

Kazemikia, Kaveh; Bonabi, Fahimeh; Asadpoorchallo, Ali; Shokrzadeh, Majid

2015-02-01

In this work, an optimized pulsed magnetic field production apparatus is designed based on a RLC (Resistance/Self-inductance/Capacitance) discharge circuit. An algorithm for designing an optimum magnetic coil is presented. The coil is designed to work at room temperature. With a minor physical reinforcement, the magnetic flux density can be set up to 12 Tesla with 2 ms duration time. In our design process, the magnitude and the length of the magnetic pulse are the desired parameters. The magnetic field magnitude in the RLC circuit is maximized on the basis of the optimal design of the coil. The variables which are used in the optimization process are wire diameter and the number of coil layers. The coil design ensures the critically damped response of the RLC circuit. The electrical, mechanical, and thermal constraints are applied to the design process. A locus of probable magnetic flux density values versus wire diameter and coil layer is provided to locate the optimum coil parameters. Another locus of magnetic flux density values versus capacitance and initial voltage of the RLC circuit is extracted to locate the optimum circuit parameters. Finally, the application of high magnetic fields on carbon nanotube-PolyPyrrole (CNT-PPy) nano-composite is presented. Scanning probe microscopy technique is used to observe the orientation of CNTs after exposure to a magnetic field. The result shows alignment of CNTs in a 10.3 Tesla, 1.5 ms magnetic pulse.

Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast.

PubMed

Maio, Elisa; Begeman, Lineke; Bisselink, Yvette; van Tulden, Peter; Wiersma, Lidewij; Hiemstra, Sjoukje; Ruuls, Robin; Gröne, Andrea; Roest, Hendrik-Ido-Jan; Willemsen, Peter; van der Giessen, Joke

2014-09-17

The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265) Brucella positive tissue samples were Brucella positive by culture and these were all confirmed by real-time polymerase chain reaction (real-time PCR) based on the insertion element 711 (IS711). In addition, two more Brucella-positive tissue samples from two animals collected in 2011 were identified using real-time PCR resulting in an overall Brucella prevalence of 6.3% (7/112 animals). Brucella spp. were obtained from lungs (n=3), pulmonary lymph node (n=3) and lungworms (n=2). Multi Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) typing based on the MLVA-16 showed that the Brucella isolates were B. ceti. Additional in silico Multi Locus Sequence typing (MLST) after whole genome sequencing of the 6 Brucella isolates confirmed B. ceti ST 23. According to the Brucella 2010 MLVA database, the isolated Brucella strains encountered were of five genotypes, in two distinct subclusters divided in two different time periods of harbour porpoises collection. This study is the first population based analyses for Brucella spp. infections in cetaceans stranded along the Dutch coast. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Ancient Evolutionary Trade-Offs between Yeast Ploidy States

PubMed Central

Zörgö, Enikö; Chwialkowska, Karolina; Gjuvsland, Arne B.; Garré, Elena; Sunnerhagen, Per; Liti, Gianni; Blomberg, Anders; Omholt, Stig W.; Warringer, Jonas

2013-01-01

The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy–environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%–17% of ploidy–environment interactions. The mechanism of the cell size–based superior reproductive efficiency of haploids during Li+ exposure was traced to the Li+ exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li+ tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots. PMID:23555297

Molecular epidemiology of Bordetella pertussis in the Philippines in 2012-2014.

PubMed

Galit, Salvacion Rosario L; Otsuka, Nao; Furuse, Yuki; Almonia, Daryl Joy V; Sombrero, Lydia T; Capeding, Rosario Z; Lupisan, Socorro P; Saito, Mariko; Oshitani, Hitoshi; Hiramatsu, Yukihiro; Shibayama, Keigo; Kamachi, Kazunari

2015-06-01

The present study was designed to determine the genotypes of circulating Bordetella pertussis in the Philippines by direct molecular typing of clinical specimens. Nasopharyngeal swabs (NPSs) were collected from 50 children hospitalized with pertussis in three hospitals during 2012-2014. Multilocus variable-number tandem repeat analysis (MLVA) was performed on the DNA extracts from NPSs. B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter, ptxP, were also investigated by DNA sequence-based typing. Twenty-six DNA extracts yielded a complete MLVA profile, which were sorted into 10 MLVA types. MLVA type 34 (MT34), which is rare in Australia, Europe, Japan, and the USA, was the predominant strain (50%). Seven MTs (MT29, MT32, MT33, and MT283-286, total 42%) were single-locus variants of MT34, while two (MT141 and MT287, total 8%) were double-locus variants of MT34. All MTs had the combination of virulence-associated allelic genes, ptxP1-ptxA1-prn1-fim3A. The B. pertussis population in the Philippines comprises genetically related strains. These strains are markedly different from those found in patients from other countries where acellular pertussis vaccines are used. The differences in vaccine types between these other countries and the Philippines, where the whole-cell vaccine is still used, may select for distinct populations of B. pertussis. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Predominance of Central Asian and European families among Mycobacterium tuberculosis isolates in Kashmir Valley, India.

PubMed

Bashir, Gulnaz; Wani, Tehmeena; Sharma, Pragya; Katoch, V M; Lone, Rubina; Shah, Azra; Katoch, Kiran; Kakru, D K; Chauhan, Devendra Singh

2017-10-01

As there are no data available regarding the strains of Mycobacterium tuberculosis circulating in Kashmir Valley, India, the current study aimed at describing the genetic diversity of M. tuberculosis strains in this region, by spoligotyping and 12-locus-based MIRU-VNTR typing (Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat). Sputa from 207 smear positive cases with newly diagnosed pulmonary tuberculosis were subjected to culture for M. tuberculosis. Eighty-five isolates confirmed as M. tuberculosis were subjected to drug susceptibility testing and molecular typing by spoligotyping and MIRU-VNTRs. Drug susceptibility results of 72 isolates revealed 76.3% as fully sensitive while 5.5% as multidrug resistant (MDR). Spoligotyping of 85 isolates detected 42 spoligotypes with 50 isolates (58.8%) clustered into seven spoligotypes. SIT26/CAS1_Del was the major spoligotype (23, 27%) followed by SIT127/H4 (12, 14.1%); CAS lineage (37.6%) was predominant, followed by Haarlem (25.8%) and ill-defined T clade (23.5%). MIRU-VNTR analysis displayed 82 MIRU patterns from 85 strains, including 3 small clusters and 79 unique. MIRU 26 was found to be the most discriminatory locus. Kashmir Valley has CAS as the predominant lineage of M. tuberculosis similar to the rest of the Indian sub-continent, while it is peculiar in having Euro American lineages such as Haarlem and ill-defined T clade. Copyright © 2017 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.

IDLN-MSP: Idiolocal normalization of real-time methylation-specific PCR for genetic imbalanced DNA specimens.

PubMed

Santourlidis, Simeon; Ghanjati, Foued; Beermann, Agnes; Hermanns, Thomas; Poyet, Cédric

2016-02-01

Sensitive, accurate, and reliable measurements of tumor cell-specific DNA methylation changes are of fundamental importance in cancer diagnosis, prognosis, and monitoring. Real-time methylation-specific PCR (MSP) using intercalating dyes is an established method of choice for this purpose. Here we present a simple but crucial adaptation of this widely applied method that overcomes a major obstacle: genetic abnormalities in the DNA samples, such as aneuploidy or copy number variations, that could result in inaccurate results due to improper normalization if the copy numbers of the target and reference sequences are not the same. In our idiolocal normalization (IDLN) method, the locus for the normalizing, methylation-independent reference amplification is chosen close to the locus of the methylation-dependent target amplification. This ensures that the copy numbers of both the target and reference sequences will be identical in most cases if they are close enough to each other, resulting in accurate normalization and reliable comparative measurements of DNA methylation in clinical samples when using real-time MSP.

Selection of high heterozygosity popcorn varieties in Brazil based on SSR markers.

PubMed

Eloi, I B O; Mangolin, C A; Scapim, C A; Gonçalves, C S; Machado, M F P S

2012-07-19

We analyzed genetic structure and diversity among eight populations of popcorn, using SSR loci as genetic markers. Our objectives were to select SSR loci that could be used to estimate genetic diversity within popcorn populations, and to analyze the genetic structure of promising populations with high levels of heterozygosity that could be used in breeding programs. Fifty-seven alleles (3.7 alleles per locus) were detected; the highest effective number of alleles (4.21) and the highest gene diversity (0.763) were found for the Umc2226 locus. A very high level of population differentiation was found (F(ST) = 0.3664), with F(ST) for each locus ranging from 0.1029 (Umc1664) to 0.6010 (Umc2350). This analysis allowed us to identify SSR loci with high levels of heterozygosity and heterozygous varieties, which could be selected for production of inbred lines and for developing new cultivars.

Slow-fast stochastic diffusion dynamics and quasi-stationarity for diploid populations with varying size.

PubMed

Coron, Camille

2016-01-01

We are interested in the long-time behavior of a diploid population with sexual reproduction and randomly varying population size, characterized by its genotype composition at one bi-allelic locus. The population is modeled by a 3-dimensional birth-and-death process with competition, weak cooperation and Mendelian reproduction. This stochastic process is indexed by a scaling parameter K that goes to infinity, following a large population assumption. When the individual birth and natural death rates are of order K, the sequence of stochastic processes indexed by K converges toward a new slow-fast dynamics with variable population size. We indeed prove the convergence toward 0 of a fast variable giving the deviation of the population from quasi Hardy-Weinberg equilibrium, while the sequence of slow variables giving the respective numbers of occurrences of each allele converges toward a 2-dimensional diffusion process that reaches (0,0) almost surely in finite time. The population size and the proportion of a given allele converge toward a Wright-Fisher diffusion with stochastically varying population size and diploid selection. We insist on differences between haploid and diploid populations due to population size stochastic variability. Using a non trivial change of variables, we study the absorption of this diffusion and its long time behavior conditioned on non-extinction. In particular we prove that this diffusion starting from any non-trivial state and conditioned on not hitting (0,0) admits a unique quasi-stationary distribution. We give numerical approximations of this quasi-stationary behavior in three biologically relevant cases: neutrality, overdominance, and separate niches.

The SH2B1 obesity locus is associated with myocardial infarction in diabetic patients and with NO synthase activity in endothelial cells.

PubMed

Prudente, Sabrina; Morini, Eleonora; Larmon, Jay; Andreozzi, Francesco; Di Pietro, Natalia; Nigro, Angela; Gervino, Ernest V; Mannino, Gaia Chiara; Bacci, Simonetta; Hauser, Thomas H; Bellacchio, Emanuele; Formoso, Gloria; Pellegrini, Fabio; Proto, Vittoria; Menzaghi, Claudia; Frittitta, Lucia; Pandolfi, Assunta; Sesti, Giorgio; Doria, Alessandro; Trischitta, Vincenzo

2011-12-01

Obesity and cardiovascular disease recognize a common metabolic soil and may therefore share part of their genetic background. Genome-wide association studies have identified variability at the SH2B1 locus as a predictor of obesity. We investigated whether SNP rs4788102, which captures the entire SH2B1 variability, is associated with coronary artery disease (CAD) and/or myocardial infarction (MI) in patients with type 2 diabetes mellitus (T2DM). SNP rs4788102 was typed in 2015 White subjects with T2DM from three CAD case-control studies [n=740 from the Gargano Hearth Study (GHS, Italy); n=818 from the Joslin Hearth Study (JHS, Boston); n=457 from the University of Catanzaro (CZ, Italy)]. SNP rs4788102 (G/A) was not associated with CAD (overall allelic OR=1.06, 95% CI=0.93-1.21; p=0.37). On the contrary, it was associated with MI in GHS (1.42, 1.12-1.81; p=0.004) and in the three samples analyzed together (1.21, 1.04-1.41; p=0.016). Insulin stimulated nitric oxide synthase (NOS) activity in human vein endothelial cells from G/G (n=4, p=0.03) but not the G/A (n=5, p=0.83) genotype. Of the SNPs in perfect LD with rs4788102, one (rs7498665) affects amino acid polarity (Ala484Thr) and falls into a highly conserved protein segment of SH2B1 containing a class II SH3 domain binding site. Variability at the SH2B1 obesity locus is associated with MI in diabetic patients and with reduced insulin-stimulated NOS activity in human endothelial cells. Further studies are needed to replicate this association and dissect the biology underlying this finding. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

The effect of intimate exposure to alcohol abuse on the acquisition of knowledge about drinking.

PubMed

Rainer, J P

1994-01-01

This study explored how an alcohol education program might be structured to effectively educate college students about the consequences of alcohol use. The primary hypothesis tested stated that individuals would vary significantly in the amount of knowledge learned from a structured alcohol education workshop, based on the degree of familial or social exposure s/he has had to alcohol abuse. Social learning variables of locus of control, dogmatism, and expectancy for risk were tested for interaction with degree of exposure, to determine their influence on learning. A pretest-posttest control group was employed with a sample of 66 undergraduate college students. A four hour alcohol education program was administered to teach cognitive information and fact about alcohol, with a goal of facilitating responsible use/nonuse of alcohol. The Student Drinking Questionnaire measured acquisition of knowledge. The Adult Nowicki-Strickland Internal/External Scale measured locus of control, and Schultze's Short Dogmatism Scale measured dogmatism. The researcher developed an instrument for expectancy for risk. Multiple regression analyses yielded prediction equations for the variables under study. For the sample group, results demonstrated that a significant portion of the variance in the residualized posttest scores was accounted for by level of exposure and dogmatism. When the sample was blocked according to intimate or social exposure, dogmatism was the only construct entering the regression equation at a significant level for the intimate exposure group. None of the constructs were able to predict any of the residualized posttest scores for the social exposure group. It was concluded that: (1) Students in the sample learned differentially based on the degree of intimate exposure of alcohol; (2) Dogmatism is a moderating variable with acquisition of knowledge for those intimately exposed to alcohol abuse, but locus of control and expectancy for risk are not; and (3) Further research is needed to study the effects of differential learning goals set for different populations.

Molecular identification and typing of Burkholderia pseudomallei and Burkholderia mallei: when is enough enough?

PubMed

Antonov, Valery A; Tkachenko, Galina A; Altukhova, Viktoriya V; Savchenko, Sergey S; Zinchenko, Olga V; Viktorov, Dmitry V; Zamaraev, Valery S; Ilyukhin, Vladimir I; Alekseev, Vladimir V

2008-12-01

Burkholderia mallei and B. pseudomallei are highly pathogenic microorganisms for both humans and animals. Moreover, they are regarded as potential agents of bioterrorism. Thus, rapid and unequivocal detection and identification of these dangerous pathogens is critical. In the present study, we describe the use of an optimized protocol for the early diagnosis of experimental glanders and melioidosis and for the rapid differentiation and typing of Burkholderia strains. This experience with PCR-based identification methods indicates that single PCR targets (23S and 16S rRNA genes, 16S-23S intergenic region, fliC and type III secretion gene cluster) should be used with caution for identification of B. mallei and B. pseudomallei, and need to be used alongside molecular methods such as gene sequencing. Several molecular typing procedures have been used to identify genetically related B. pseudomallei and B. mallei isolates, including ribotyping, pulsed-field gel electrophoresis and multilocus sequence typing. However, these methods are time consuming and technically challenging for many laboratories. RAPD, variable amplicon typing scheme, Rep-PCR, BOX-PCR and multiple-locus variable-number tandem repeat analysis have been recommended by us for the rapid differentiation of B. mallei and B. pseudomallei strains.

[Multiple-locus variable number tandem repeat analysis of Bordetella pertussis strains collected in the Czech Republic in 1967-2015: spread of a variant adapted to the population with a high vaccination coverage].

PubMed

Lžičařová, D; Zavadilová, J; Musílek, M; Jandová, Z; Křížová, P; Fabiánová, K

To perform multiple-locus variable number tandem repeat analysis (MLVA) of B. pertussis strains from the collection of the National Reference Laboratory for Diphtheria and Pertussis (NRL/DIPE), National Institute of Public Health (NIPH), Prague. The study strains were isolated from clinical specimens collected mostly in the Czech Republic over a nearly 50-year period from 1967 to 2015 (June). The isolates from three periods characterized by different vaccination strategies and trends in pertussis are compared for genetic diversity and distribution of MLVA types (MT). Based on the results obtained, the suitability for use of MLVA in the analysis of epidemic outbreaks of B. pertussis in the Czech Republic is considered. DNA samples extracted from B. pertussis strains included in the present study were examined by MLVA using the standard protocol. Data were processed by means of the eBURST algorithm and the calculation of the Simpson diversity index (DI) was used for the statistical analysis. Data were analyzed as a whole and also separately for strains from the three periods: 1967-1980, 1990-2007, and 2008-2015 (June). Fourteen different MT were detected in the study strains, with three of them not being reported before. The most common MTs were MT27 and MT29. MT29 was predominant in 1967-1980 while MT27 was the most prevalent in 1990-2007 and 2008-2015 (June). The DI was the lowest (0.49) in 2008-2015 (June), and comparably higher DIs were calculated for the two previous periods (i.e. 0.667 for 1967-1980 and 0.654 for 1990-2007). MLVA revealed a decrease in genetic diversity and shifts in MT distribution of B. pertussis strains isolated from clinical specimens in the Czech Republic from 1967 to 2015 (June). These shifts in the Czech Republic can be characterized as a progressive increase in global MTs at the expense of the locally unique ones. The most common MT, similarly to other geographical areas with long-term high vaccination coverage, is MT27. The results of MLVA of 136 B. pertussis strains can provide a background for using this method in molecular epidemiological analysis of smaller groups of strains.

Locus of control and depression as a function of sex role orientation in two age groups of mental health nurses.

PubMed

Napholz, L

1991-01-01

The purpose of the study reported in this article was to examine the relationships between locus of control and level of depression in younger adult and midlife registered mental health nurses (MHNs) in relation to each other and as a function of sex role orientation. On the basis of C. G. Jung's (1954) theory of individuation, the following hypotheses were derived: (a) MHNs with an androgynous sex role orientation will have a higher internal locus of control than MHNs with a nonandrogynous sex role orientation; (b) MHNs with an androgynous sex role orientation will be less depressed than nonandrogynous sex role-oriented MHNs, and (c) midlife MHNs will be more androgynous in sex role orientation than younger MHNs. Thirty-six participants, all working female registered mental health nurses between the ages of 30 and 59, were placed in the midlife group (age 41-59) or the young adult group (age 31-40) on the basis of self-indicated age. Two groups of female MHNs (younger adult and midlife women) were compared with each other by means of the Personal Attributes Questionnaire (Spence, Helmreich, & Stapp, 1975), used to assess sex role orientation (androgynous or nonandrogynous: cross-typed, sex-typed, or undifferentiated); Rotter's (1966) Locus of Control Scale, used to assess internal or external (I-E) locus of control; and the Beck Depression Inventory (Beck, Ward, Mendelson, Mock, & Erbaugh, 1961), used to assess level of depression. In regards to all three hypotheses, no statistically significant associations were found among the study variables. The strengths and weakness of the present study were reviewed. The theoretical and practical implications of the results were discussed, and directions for future research were considered.

Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response

PubMed Central

Juneja, Punita; Ariani, Cristina V.; Ho, Yung Shwen; Akorli, Jewelna; Palmer, William J.; Pain, Arnab; Jiggins, Francis M.

2015-01-01

Many mosquito species are naturally polymorphic for their abilities to transmit parasites, a feature which is of great interest for controlling vector-borne disease. Aedes aegypti, the primary vector of dengue and yellow fever and a laboratory model for studying lymphatic filariasis, is genetically variable for its capacity to harbor the filarial nematode Brugia malayi. The genome of Ae. aegypti is large and repetitive, making genome resequencing difficult and expensive. We designed exome captures to target protein-coding regions of the genome, and used association mapping in a wild Kenyan population to identify a single, dominant, sex-linked locus underlying resistance. This falls in a region of the genome where a resistance locus was previously mapped in a line established in 1936, suggesting that this polymorphism has been maintained in the wild for the at least 80 years. We then crossed resistant and susceptible mosquitoes to place both alleles of the gene into a common genetic background, and used RNA-seq to measure the effect of this locus on gene expression. We found evidence for Toll, IMD, and JAK-STAT pathway activity in response to early stages of B. malayi infection when the parasites are beginning to die in the resistant genotype. We also found that resistant mosquitoes express anti-microbial peptides at the time of parasite-killing, and that this expression is suppressed in susceptible mosquitoes. Together, we have found that a single resistance locus leads to a higher immune response in resistant mosquitoes, and we identify genes in this region that may be responsible for this trait. PMID:25815506

Development and characterization of polymorphic microsatellite markers in Dysosma pleiantha (Berberidaceae).

PubMed

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.

Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands

PubMed Central

Kamst, Miranda; van Hunen, Rianne; de Zwaan, Carolina Catherina; Mulder, Arnout; Supply, Philip; Anthony, Richard; van der Hoek, Wim; van Soolingen, Dick

2017-01-01

ABSTRACT Since 2004, variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the period from 2004 to 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, with 186 (2.2%) of these exhibiting double alleles at one locus. Double alleles were most common in loci 4052 and 2163b. The variables significantly associated with double alleles were urban living (odds ratio [OR], 1.503; 95% confidence interval [CI], 1.084 to 2.084; P = 0.014) and pulmonary TB (OR, 1.703; 95% CI, 1.216 to 2.386; P = 0.002). Single-colony cultures of double-allele strains were produced and revealed single-allele profiles; a maximum of five single nucleotide polymorphisms (SNPs) was observed between the single- and double-allele isolates from the same patient when whole-genome sequencing (WGS) was applied. This indicates the presence of two bacterial populations with slightly different VNTR profiles in the parental population, related to genetic drift. This observation is confirmed by the fact that secondary cases from TB source cases with double-allele isolates sometimes display only one of the two alleles present in the source case. Double alleles occur at a frequency of 2.2% in VNTR patterns in The Netherlands. They are caused by biological variation rather than by technical aberrations and can be transmitted either as single- or double-allele variants. PMID:29142049

Dopamine Transporter Genetic Variants and Pesticides in Parkinson’s Disease

PubMed Central

Ritz, Beate R.; Manthripragada, Angelika D.; Costello, Sadie; Lincoln, Sarah J.; Farrer, Matthew J.; Cockburn, Myles; Bronstein, Jeff

2009-01-01

Background Research suggests that independent and joint effects of genetic variability in the dopamine transporter (DAT) locus and pesticides may influence Parkinson’s disease (PD) risk. Materials Methods: In 324 incident PD patients and 334 population controls from our rural California case–control study, we genotyped rs2652510, rs2550956 (for the DAT 5′ clades), and the 3′ variable number of tandem repeats (VNTR). Using geographic information system methods, we determined residential exposure to agricultural maneb and paraquat applications. We also collected occupational pesticide use data. Employing logistic regression, we calculated odds ratios (ORs) for clade diplotypes, VNTR genotype, and number of susceptibility (A clade and 9-repeat) alleles and assessed susceptibility allele–pesticide interactions. Results PD risk was increased separately in DAT A clade diplotype carriers [AA vs. BB: OR = 1.66; 95% confidence interval (CI), 1.08–2.57] and 3′ VNTR 9/9 carriers (9/9 vs. 10/10: OR = 1.8; 95% CI, 0.96–3.57), and our data suggest a gene dosing effect. Importantly, high exposure to paraquat and maneb in carriers of one susceptibility allele increased PD risk 3-fold (OR = 2.99; 95% CI, 0.88–10.2), and in carriers of two or more alleles more than 4-fold (OR = 4.53; 95% CI, 1.70–12.1). We obtained similar results for occupational pesticide measures. Discussion Using two independent pesticide measures, we a) replicated previously reported gene–environment interactions between DAT genetic variants and occupational pesticide exposure in men and b) overcame previous limitations of nonspecific pesticide measures and potential recall bias by employing state records and computer models to estimate residential pesticide exposure. Conclusion Our results suggest that DAT genetic variability and pesticide exposure interact to increase PD risk. PMID:19590691

Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F2 Population.

PubMed

Zhu, Dan; Zhou, Gang; Xu, Caiguo; Zhang, Qifa

2016-02-20

Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an "immortalized F2" population composed of 105 hybrids produced by intercrossing recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance (epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F1 hybrid. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Copy number aberrations landscape of a breast tumor, connection with the efficiency of neoadjuvant chemotherapy

NASA Astrophysics Data System (ADS)

Ibragimova, M. K.; Tsyganov, M. M.; Slonimskaya, E. M.; Litviakov, N. V.

2017-09-01

The research involved 80 patients diagnosed with breast cancer (BC). Each patient had their tumor biopsy material sampled before their treatment. We studied the tumor tissue using the CytoScan HD Array (Affymetrix, USA) microarray to evaluate the CNA landscape. We studied the frequency of segmental and numerical CNA occurrence, their association with the efficiency of neoadjuvant chemotherapy (NAC). We found that the biggest number of amplifications (with frequency over 60%) were found on in the following locuses; 1q32.1 1q32.3, 1q42.13, 1q42.2, 1q43. The biggest frequency of deletions (more than in 58% of the patients) was found in these locuses: 16q21, 16q23.2, 16q23.3, 17p12, 17p13.1. However, we found the locuses with full absence of segmental chromosome anomalies. We observed trisomy most frequently in the 7, 8, 12, and 17 chromosomes, and monosomy in the 3, 4, 9, 11, 18, and X-chromosomes. We demonstrated the connection between the high frequency of cytobands with CNA in the patients' tumors and the efficiency of NAC. We also identified the cytobands, whose CNA are linked to the response to NAC.

De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters.

PubMed

Chiara, Matteo; Horner, David S; Spada, Alberto

2013-01-01

De novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Indeed, closely related paralogous transcripts are often merged into single clusters by current approaches. Here, a novel heuristic method for locus-specific clustering is compared to that implemented in the de novo assembler Oases, using the same initial transcript collections, derived from Arabidopsis thaliana and the developmental model Streptocarpus rexii. We show that the proposed approach improves cluster specificity in the A. thaliana dataset for which the reference genome is available. Furthermore, for the S. rexii data our filtered transcript collection matches a larger number of distinct annotated loci in reference genomes than the Oases set, while containing a reduced overall number of loci. A detailed discussion of advantages and limitations of our approach in processing de novo transcriptome reconstructions is presented. The proposed method should be widely applicable to other organisms, irrespective of the transcript assembly method employed. The S. rexii transcriptome is available as a sophisticated and augmented publicly available online database.

[Modelling of selection acting upon the pleioptropic locus in an asynchronous population].

PubMed

Zhdanov, O L; Frisman, E Ia

2014-08-01

We created and examined a mathematical model describing the size and genetic composition dynamics in a population with two age classes, where the survival of both zygotes and adult individuals is determined by one pleioptropic locus. Even under present limitations, as the outside effects of a complex multigenic system are reduced to the case of single locus, our model demonstrates a wide range of different evolutionary scenarios for possible changes in the population dynamics. An increase in the reproductive potential and survival is accompanied by a transition from stable to oscillating population numbers. However, the evolutionary growth of these parameters may be nonmonotonic and may fluctuate significantly. In the case of antagonistic pleioptropy, an increase in one of these parameters usually leads to a predictable decrease in the other. This, in turn, may even stabilize the numbers and genetic compositions of the age groups. We demonstrated that selection acting on later stages of the life cycle is accompanied by destabilization of the Hardy-Weinberg equilibriums that link allele and genotype frequencies. We obtained a balance ratio, which allowed us to compare the combined fitness of the genotypes and to demonstrate that selection leads to the exclusion of the least adapted genotypes. Initial conditionsmay in some cases determine the genetic composition and pattern of population size dynamics.

Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.

PubMed

Tost, Jörg

2016-01-01

DNA methylation is the most studied epigenetic modification, and altered DNA methylation patterns have been identified in cancer and more recently also in many other complex diseases. Furthermore, DNA methylation is influenced by a variety of environmental factors, and the analysis of DNA methylation patterns might allow deciphering previous exposure. Although a large number of techniques to study DNA methylation either genome-wide or at specific loci have been devised, they all are based on a limited number of principles for differentiating the methylation state, viz., methylation-specific/methylation-dependent restriction enzymes, antibodies or methyl-binding proteins, chemical-based enrichment, or bisulfite conversion. Second-generation sequencing has largely replaced microarrays as readout platform and is also becoming more popular for locus-specific DNA methylation analysis. In this chapter, the currently used methods for both genome-wide and locus-specific analysis of 5-methylcytosine and as its oxidative derivatives, such as 5-hydroxymethylcytosine, are reviewed in detail, and the advantages and limitations of each approach are discussed. Furthermore, emerging technologies avoiding PCR amplification and allowing a direct readout of DNA methylation are summarized, together with novel applications, such as the detection of DNA methylation in single cells or in circulating cell-free DNA.

Impaired glucose homeostasis in transgenic mice expressing the human transient neonatal diabetes mellitus locus, TNDM

PubMed Central

Ma, Dan; Shield, Julian P.H.; Dean, Wendy; Leclerc, Isabelle; Knauf, Claude; Burcelin, Rémy; Rutter, Guy A.; Kelsey, Gavin

2004-01-01

Transient neonatal diabetes mellitus (TNDM) is a rare inherited diabetic syndrome apparent in the first weeks of life and again during early adulthood. The relative contributions of reduced islet β cell number and impaired β cell function to the observed hypoinsulinemia are unclear. The inheritance pattern of this imprinted disorder implicates overexpression of one or both genes within the TNDM locus: ZAC, which encodes a proapoptotic zinc finger protein, and HYMAI, which encodes an untranslated mRNA. To investigate the consequences for pancreatic function, we have developed a high-copy transgenic mouse line, TNDM29, carrying the human TNDM locus. TNDM29 neonates display hyperglycemia, and older adults, impaired glucose tolerance. Neonatal hyperglycemia occurs only on paternal transmission, analogous to paternal dependence of TNDM in humans. Embryonic pancreata of TNDM29 mice showed reductions in expression of endocrine differentiation factors and numbers of insulin-staining structures. By contrast, β cell mass was normal or elevated at all postnatal stages, whereas pancreatic insulin content in neonates and peak serum insulin levels after glucose infusion in adults were reduced. Expression of human ZAC and HYMAI in these transgenic mice thus recapitulates key features of TNDM and implicates impaired development of the endocrine pancreas and β cell function in disease pathogenesis. PMID:15286800

Beyond the Personal Learning Environment: Attachment and Control in the Classroom of the Future

ERIC Educational Resources Information Center

Johnson, Mark William; Sherlock, David

2014-01-01

The Personal Learning Environment (PLE) has been presented in a number of guises over a period of 10 years as an intervention which seeks the reorganisation of educational technology through shifting the "locus of control" of technology towards the learner. In the intervening period to the present, a number of initiatives have attempted…

QTL mapping of flowering time, fruit size and number in populations involving andromonoecious true lemon cucumber

USDA-ARS?s Scientific Manuscript database

Andromonoecious sex expression in cucumber is controlled by the m locus, which encodes the 1-aminocyclopropane-1 –carboxylic acid synthase (ACS) in the ethylene biosynthesis pathway. This gene seems to have pleotropic effects on fruit size and number, but the genetic basis is unknown. The True Lemon...

Isozyme variation and linkage in six conifer species

Treesearch

M. Thompson Conkle

1981-01-01

Isozymes of female gametophyte tissue were analyzed for allelic variation in knobcone, lodgepole, loblolly, Jeffrey, and sugar pines and in Douglas-fir. Linkage was studied in the five pines. The average number of alleles and average herozygosity per enzyme locus were estimated. Knobcone pine ranked lowest among the six species in number of alleles and average...

S locus-linked F-box genes expressed in anthers of Hordeum bulbosum.

PubMed

Kakeda, Katsuyuki

2009-09-01

Diploid Hordeum bulbosum (a wild relative of cultivated barley) exhibits a two-locus self-incompatibility (SI) system gametophytically controlled by the unlinked multiallelic loci S and Z. This unique SI system is observed in the grasses (Poaceae) including the tribe Triticeae. This paper describes the identification and characterization of two F-box genes cosegregating with the S locus in H. bulbosum, named Hordeum S locus-linked F-box 1 (HSLF1) and HSLF2, which were derived from an S (3) haplotype-specific clone (HAS175) obtained by previous AMF (AFLP-based mRNA fingerprinting) analysis. Sequence analysis showed that both genes encode similar F-box proteins with a C-terminal leucine-rich repeat (LRR) domain, which are distinct from S locus (or S haplotype-specific) F-box protein (SLF/SFB), a class of F-box proteins identified as the pollen S determinant in S-RNase-based gametophytic SI systems. A number of homologous F-box genes with an LRR domain were found in the rice genome, although the functions of the gene family are unknown. One allele of the HSLF1 gene (HSLF1-S (3)) was expressed specifically in mature anthers, whereas no expression was detected from the other two alleles examined. Although the degree of sequence polymorphism among the three HSLF1 alleles was low, a frameshift mutation was found in one of the unexpressed alleles. The HSLF2 gene showed a low level of expression with no tissue specificity as well as little sequence polymorphism among the three alleles. The multiplicity of S locus-linked F-box genes is discussed in comparison with those found in the S-RNase-based SI system.

Variants in SKP1, PROB1, and IL17B genes at keratoconus 5q31.1–q35.3 susceptibility locus identified by whole-exome sequencing

PubMed Central

Karolak, Justyna A; Gambin, Tomasz; Pitarque, Jose A; Molinari, Andrea; Jhangiani, Shalini; Stankiewicz, Pawel; Lupski, James R; Gajecka, Marzena

2017-01-01

Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in impairment of visual function. The extreme genetic heterogeneity makes it difficult to discover factors unambiguously influencing the KTCN phenotype. In this study, we used whole-exome sequencing (WES) and Sanger sequencing to reduce the number of candidate genes at the 5q31.1–q35.3 locus and to prioritize other potentially relevant variants in an Ecuadorian family with KTCN. We applied WES in two affected KTCN individuals from the Ecuadorian family that showed a suggestive linkage between the KTCN phenotype and the 5q31.1–q35.3 locus. Putative variants identified by WES were further evaluated in this family using Sanger sequencing. Exome capture discovered a total of 173 rare (minor allele frequency <0.001 in control population) nonsynonymous variants in both affected individuals. Among them, 16 SNVs were selected for further evaluation. Segregation analysis revealed that variants c.475T>G in SKP1, c.671G>A in PROB1, and c.527G>A in IL17B in the 5q31.1–q35.3 linkage region, and c.850G>A in HKDC1 in the 10q22 locus completely segregated with the phenotype in the studied KTCN family. We demonstrate that a combination of various techniques significantly narrowed the studied genomic region and reduced the list of the putative exonic variants. Moreover, since this locus overlapped two other chromosomal regions previously recognized in distinct KTCN studies, our findings suggest that this 5q31.1–q35.3 locus might be linked with KTCN. PMID:27703147

Genotype and cardiovascular phenotype correlations with TBX1 in 1,022 velo-cardio- facial/DiGeorge/22q11.2 deletion syndrome patients

PubMed Central

Guo, Tingwei; McGinn, Donna McDonald; Blonska, Anna; Shanske, Alan; Bassett, Anne; Chow, Eva; Bowser, Mark; Sheridan, Molly; Beemer, Frits; Devriendt, Koen; Swillen, Ann; Breckpot, Jeroen; Digilio, M. Cristina; Marino, Bruno; Dallapiccola, Bruno; Carpenter, Courtney; Zheng, Xin; Johnson, Jacob; Chung, Jonathan; Higgins, Anne Marie; Philip, Nicole; Simon, Tony J.; Coleman, Karlene; Heine-Suner, Damian; Rosell, Jordi; Kates, Wendy; Devoto, Marcella; Goldmuntz, Elizabeth; Zackai, Elaine; Wang, Tao; Shprintzen, Robert; Emanuel, Beverly; Morrow, Bernice

2011-01-01

Haploinsufficiency of TBX1, encoding a T-box transcription factor, is largely responsible for the physical malformations in velo-cardio-facial/DiGeorge/22q11.2 deletion syndrome (22q11DS) patients. Cardiovascular malformations in these patients are highly variable, raising the question as to whether DNA variations in the TBX1 locus on the remaining allele of 22q11.2, could be responsible. To test this, a large sample size is needed. The TBX1 gene was sequenced in 360 consecutive 22q11DS patients. Rare and common variations were identified. We did not detect enrichment in rare SNP number in those with or without a congenital heart defect. One exception was that there was increased number of very rare SNPs between those with normal heart anatomy compared to those with right-sided aortic arch or persistent truncus arteriosus, suggesting potentially protective roles in the SNPs for these phenotype enrichment groups. Nine common SNPs (MAF >0.05) were chosen and used to genotype the entire cohort of 1,022 22q11DS subjects. We did not find a correlation between common SNPs or haplotypes and cardiovascular phenotype. This work demonstrates that common DNA variations in TBX1 do not explain variable cardiovascular expression in 22q11DS patients, implicating existence of modifiers in other genes on 22q11.2 or elsewhere in the genome. PMID:21796729

Resistance to Phakopsora pachyrhizi in soybean PI 587905 maps to the Rpp1 locus and exhibits variable dominance associated with plant ontogeny

USDA-ARS?s Scientific Manuscript database

Soybean rust, caused by Phakopsora pachyrhizi Sydow, results in significant yield loss worldwide. Soybean accession PI 587905, previously identified as having resistance to P. pachyrhizi, was used to create two independent populations (F2 plants and F2-derived F3 lines) segregating for resistance. ...

Microevolution of the Direct Repeat Locus of Mycobacterium tuberculosis in a Strain Prevalent in San Francisco

PubMed Central

Aga, Roxanne S.; Fair, Elizabeth; Abernethy, Neil F.; DeRiemer, Kathryn; Paz, E. Antonio; Kawamura, L. Masae; Small, Peter M.; Kato-Maeda, Midori

2006-01-01

We describe a microevolutionary event of a prevalent strain of Mycobacterium tuberculosis that caused two outbreaks in San Francisco. During the second outbreak, a direct variable repeat was lost. We discuss the mechanisms of this change and the implications of analyzing multiple genetic loci in this context. PMID:16597893

Fine mapping of Ur-3, a historically important rust resistance locus in common bean

USDA-ARS?s Scientific Manuscript database

Resistance in common bean to the highly variable bean rust pathogen is conditioned by single and dominant genes. The Ur-3 gene confers resistance to 55 of 94 races of this pathogen maintained at Beltsville, MD, Ur-3 is also resistant to many races that overcome all other rust resistance genes in com...

Human-Computer Interaction: A Review of the Research on Its Affective and Social Aspects.

ERIC Educational Resources Information Center

Deaudelin, Colette; Dussault, Marc; Brodeur, Monique

2003-01-01

Discusses a review of 34 qualitative and non-qualitative studies related to affective and social aspects of student-computer interactions. Highlights include the nature of the human-computer interaction (HCI); the interface, comparing graphic and text types; and the relation between variables linked to HCI, mainly trust, locus of control,…

The Effects of an Environmental Studies Course on Selected Variables Related To Environmentally Responsible Behavior.

ERIC Educational Resources Information Center

Smith-Sebasto, N. J.

1995-01-01

Reports that students completing an environmental studies course displayed significant gains when compared with students not completing such a course. These gains were made in acquiring a more internally-oriented locus of control of reinforcement for environmentally responsible behavior, a higher perception of their knowledge of and skill in using…

APOA5 gene variation interacts with dietary fat intake to modulate obesity and circulating triglycerides in a Mediterranean population

USDA-ARS?s Scientific Manuscript database

APOA5 is one of the strongest regulators of plasma TG concentrations; nevertheless, its mechanisms of action are poorly characterized. Genetic variability at the APOA5 locus has also been associated with increased cardiovascular disease risk; however, this predisposition could be attenuated in the c...

The Role of Personality Factors in Predicting the Reported Physical Health Symptoms of Turkish College Students

ERIC Educational Resources Information Center

Ustundag-Budak, Meltem; Mocan-Aydin, Gul

2005-01-01

This study investigates the role of optimism, health control beliefs, perceived health competence, and medical help-seeking variables in predicting the frequency of reported physical symptoms. A total of 345 college students (207 male and 138 female) were presented with the Life Orientation Test, Multidimensional Health Locus of Control, Perceived…

Relations of Cognitive and Motivational Variables with Students' Human Circulatory System Achievement in Traditional and Learning Cycle Classrooms

ERIC Educational Resources Information Center

Sadi, Özlem; Çakiroglu, Jale

2014-01-01

This study is aimed at investigating the relationships among students' relevant prior knowledge, meaningful learning orientation, reasoning ability, self-efficacy, locus of control, attitudes toward biology and achievement with the human circulatory system (HCS) using the learning cycle (LC) and the traditional classroom setting. The study was…

Preconditions for Post-Employment Learning: Preliminary Results from Ongoing Research

ERIC Educational Resources Information Center

Salter, Linda

2011-01-01

This article describes the first phase of a two-phase, mixed-method study. The study, now in progress, explores how and to what extent willingness to engage in learning in mature adulthood is influenced by prior experiences and specific individual personality variables, such as perceived locus of control and degree of self-efficacy. Study…

Newly developed primers for complete YCF1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility

Treesearch

Matthew Parks; Aaron Liston; Rich Cronn

2011-01-01

Primers were designed to amplify the highly variable locus ycf1 from all 11 subsections of Pinus to facilitate plastome assemblies based on short sequence reads as well as future phylogenetic and population genetic analyses. Primer design was based on alignment of 33 Pinus and four Pinaceae plastomes with...

Gender, College Major Selections, Classifications within Majors, and Its Relationship with Locus of Control: An Empirical Evidence for Counseling Educators

ERIC Educational Resources Information Center

Jemi-Alade, Tunji

2008-01-01

To help counselors develop strategies to enhance students' social, personal, and psychological well-being, this research provides an understanding of how students perceive their environment. Specifically examining graduate and undergraduate students, the researcher was concerned with ascertaining the effect of the college-major variable (Business…

Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation

PubMed Central

Heilbronner, Simon; Brozyna, Jeremy R.; Heinrichs, David E.; Skaar, Eric P.; Peschel, Andreas; Foster, Timothy J.

2016-01-01

Staphylococcus lugdunensis is a coagulase negative bacterial pathogen that is particularly associated with severe cases of infectious endocarditis. Unique amongst the coagulase-negative staphylococci, S. lugdunensis harbors an iron regulated surface determinant locus (isd). This locus facilitates the acquisition of heme as a source of nutrient iron during infection and allows iron limitation caused by “nutritional immunity” to be overcome. The isd locus is duplicated in S. lugdunensis HKU09-01 and we show here that the duplication is intrinsically unstable and undergoes accordion-like amplification and segregation leading to extensive isd copy number variation. Amplification of the locus increased the level of expression of Isd proteins and improved binding of hemoglobin to the cell surface of S. lugdunensis. Furthermore, Isd overexpression provided an advantage when strains were competing for a limited amount of hemoglobin as the sole source of iron. Gene duplications and amplifications (GDA) are events of fundamental importance for bacterial evolution and are frequently associated with antibiotic resistance in many species. As such, GDAs are regarded as evolutionary adaptions to novel selective pressures in hostile environments pointing towards a special importance of isd for S. lugdunensis. For the first time we show an example of a GDA that involves a virulence factor of a Gram-positive pathogen and link the GDA directly to a competitive advantage when the bacteria were struggling with selective pressures mimicking “nutritional immunity”. PMID:27575058

Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation.

PubMed

Heilbronner, Simon; Monk, Ian R; Brozyna, Jeremy R; Heinrichs, David E; Skaar, Eric P; Peschel, Andreas; Foster, Timothy J

2016-08-01

Staphylococcus lugdunensis is a coagulase negative bacterial pathogen that is particularly associated with severe cases of infectious endocarditis. Unique amongst the coagulase-negative staphylococci, S. lugdunensis harbors an iron regulated surface determinant locus (isd). This locus facilitates the acquisition of heme as a source of nutrient iron during infection and allows iron limitation caused by "nutritional immunity" to be overcome. The isd locus is duplicated in S. lugdunensis HKU09-01 and we show here that the duplication is intrinsically unstable and undergoes accordion-like amplification and segregation leading to extensive isd copy number variation. Amplification of the locus increased the level of expression of Isd proteins and improved binding of hemoglobin to the cell surface of S. lugdunensis. Furthermore, Isd overexpression provided an advantage when strains were competing for a limited amount of hemoglobin as the sole source of iron. Gene duplications and amplifications (GDA) are events of fundamental importance for bacterial evolution and are frequently associated with antibiotic resistance in many species. As such, GDAs are regarded as evolutionary adaptions to novel selective pressures in hostile environments pointing towards a special importance of isd for S. lugdunensis. For the first time we show an example of a GDA that involves a virulence factor of a Gram-positive pathogen and link the GDA directly to a competitive advantage when the bacteria were struggling with selective pressures mimicking "nutritional immunity".

Multivariate Analysis of the Visual Information Processing of Numbers

ERIC Educational Resources Information Center

Levine, David M.

1977-01-01

Nonmetric multidimensional scaling and hierarchical clustering procedures are applied to a confusion matrix of numerals. Two dimensions were interpreted: straight versus curved, and locus of curvature. Four major clusters of numerals were developed. (Author/JKS)

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

PubMed

De Bellis, Fabien; Malapa, Roger; Kagy, Valérie; Lebegin, Stéphane; Billot, Claire; Labouisse, Jean-Pierre

2016-08-01

Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19. The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management.

Genotyping of Mycobacterium leprae strains from a region of high endemic leprosy prevalence in India.

PubMed

Lavania, Mallika; Jadhav, Rupendra; Turankar, Ravindra P; Singh, Itu; Nigam, Astha; Sengupta, U

2015-12-01

Leprosy is still a major health problem in India which has the highest number of cases. Multiple locus variable number of tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) have been proposed as tools of strain typing for tracking the transmission of leprosy. However, empirical data for a defined population from scale and duration were lacking for studying the transmission chain of leprosy. Seventy slit skin scrapings were collected from Purulia (West Bengal), Miraj (Maharashtra), Shahdara (Delhi), and Naini (UP) hospitals of The Leprosy Mission (TLM). SNP subtyping and MLVA on 10 VNTR loci were applied for the strain typing of Mycobacterium leprae. Along with the strain typing conventional epidemiological investigation was also performed to trace the transmission chain. In addition, phylogenetic analysis was done on variable number of tandem repeat (VNTR) data sets using sequence type analysis and recombinational tests (START) software. START software performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. Diversity was observed in the cross-sectional survey of isolates obtained from 70 patients. Similarity in fingerprinting profiles observed in specimens of cases from the same family or neighborhood locations indicated a possible common source of infection. The data suggest that these VNTRs including subtyping of SNPs can be used to study the sources and transmission chain in leprosy, which could be very important in monitoring of the disease dynamics in high endemic foci. The present study strongly indicates that multi-case families might constitute epidemic foci and the main source of M. leprae in villages, causing the predominant strain or cluster infection leading to the spread of leprosy in the community. Copyright © 2015 Elsevier B.V. All rights reserved.

Analysis of Salmonella enterica Serovar Typhimurium Variable-Number Tandem-Repeat Data for Public Health Investigation Based on Measured Mutation Rates and Whole-Genome Sequence Comparisons

PubMed Central

Dimovski, Karolina; Cao, Hanwei; Wijburg, Odilia L. C.; Strugnell, Richard A.; Mantena, Radha K.; Whipp, Margaret; Hogg, Geoff

2014-01-01

Variable-number tandem repeats (VNTRs) mutate rapidly and can be useful markers for genotyping. While multilocus VNTR analysis (MLVA) is increasingly used in the detection and investigation of food-borne outbreaks caused by Salmonella enterica serovar Typhimurium (S. Typhimurium) and other bacterial pathogens, MLVA data analysis usually relies on simple clustering approaches that may lead to incorrect interpretations. Here, we estimated the rates of copy number change at each of the five loci commonly used for S. Typhimurium MLVA, during in vitro and in vivo passage. We found that loci STTR5, STTR6, and STTR10 changed during passage but STTR3 and STTR9 did not. Relative rates of change were consistent across in vitro and in vivo growth and could be accurately estimated from diversity measures of natural variation observed during large outbreaks. Using a set of 203 isolates from a series of linked outbreaks and whole-genome sequencing of 12 representative isolates, we assessed the accuracy and utility of several alternative methods for analyzing and interpreting S. Typhimurium MLVA data. We show that eBURST analysis was accurate and informative. For construction of MLVA-based trees, a novel distance metric, based on the geometric model of VNTR evolution coupled with locus-specific weights, performed better than the commonly used simple or categorical distance metrics. The data suggest that, for the purpose of identifying potential transmission clusters for further investigation, isolates whose profiles differ at one of the rapidly changing STTR5, STTR6, and STTR10 loci should be collapsed into the same cluster. PMID:24957617

A recall-by-genotype study of CHRNA5-A3-B4 genotype, cotinine and smoking topography: study protocol.

PubMed

Ware, Jennifer J; Timpson, Nic; Davey Smith, George; Munafò, Marcus R

2014-01-22

Genome-wide association studies have revealed an association between several loci in the nicotinic acetylcholine receptor gene cluster CHRNA5-A3-B4 and daily cigarette consumption. Recent studies have sought to refine this phenotype, and have shown that a locus within this cluster, marked primarily by rs1051730 and rs16969968, is also associated with levels of cotinine, the primary metabolite of nicotine. This association remains after adjustment for self-reported smoking, which suggests that even amongst people who smoke the same number of cigarettes there is still genetically-influenced variation in nicotine consumption. This is likely to be due to differences in smoking topography, that is, how a cigarette is smoked (e.g., volume of smoke inhaled per puff, number of puffs taken per cigarette). The aim of this study is to determine potential mediation of the relationship between the rs1051730 locus and cotinine levels by smoking topography. Adopting a recall-by-genotype design, we will recruit 200 adults from the Avon Longitudinal Study of Parents and Children on the basis of minor or major homozygote status at rs1051730 (100 in each genotype group). All participants will be current, daily smokers. Our primary study outcome measures will be measures of smoking topography: total volume of smoke (ml) inhaled per cigarette, total volume of smoke (ml) inhaled over of the course of one day, and salivary cotinine level (ng/ml). This study will extend our understanding of the biological basis of inter-individual variability in heaviness of smoking, and therefore in exposure to smoking-related toxins. The novel recall-by-genotype approach we will use is efficient, maximising statistical power, and enables the collection of extremely precise phenotypic data that are impractical to collect in a larger sample. The methods described within this protocol also hold the potential for wider application in the field of molecular genetics.

Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates.

PubMed

Liu, Fei; Hu, Yongfei; Wang, Qi; Li, Hong Min; Gao, George F; Liu, Cui Hua; Zhu, Baoli

2014-06-13

Due to excessive antibiotic use, drug-resistant Mycobacterium tuberculosis has become a serious public health threat and a major obstacle to disease control in many countries. To better understand the evolution of drug-resistant M. tuberculosis strains, we performed whole genome sequencing for 7 M. tuberculosis clinical isolates with different antibiotic resistance profiles and conducted comparative genomic analysis of gene variations among them. We observed that all 7 M. tuberculosis clinical isolates with different levels of drug resistance harbored similar numbers of SNPs, ranging from 1409-1464. The numbers of insertion/deletions (Indels) identified in the 7 isolates were also similar, ranging from 56 to 101. A total of 39 types of mutations were identified in drug resistance-associated loci, including 14 previously reported ones and 25 newly identified ones. Sixteen of the identified large Indels spanned PE-PPE-PGRS genes, which represents a major source of antigenic variability. Aside from SNPs and Indels, a CRISPR locus with varied spacers was observed in all 7 clinical isolates, suggesting that they might play an important role in plasticity of the M. tuberculosis genome. The nucleotide diversity (Л value) and selection intensity (dN/dS value) of the whole genome sequences of the 7 isolates were similar. The dN/dS values were less than 1 for all 7 isolates (range from 0.608885 to 0.637365), supporting the notion that M. tuberculosis genomes undergo purifying selection. The Л values and dN/dS values were comparable between drug-susceptible and drug-resistant strains. In this study, we show that clinical M. tuberculosis isolates exhibit distinct variations in terms of the distribution of SNP, Indels, CRISPR-cas locus, as well as the nucleotide diversity and selection intensity, but there are no generalizable differences between drug-susceptible and drug-resistant isolates on the genomic scale. Our study provides evidence strengthening the notion that the evolution of drug resistance among clinical M. tuberculosis isolates is clearly a complex and diversified process.

Evidence for a major retinitis pigmentosa locus on 19q13.4 (RP11), and association with a unique bimodal expressivity phenotype

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Maghtheh, M.; Vithana, E.; Tarttelin, E.

Retinitis pigmentosa (RP) is the name given to a heterogeneous group of retinal degenerations mapping to at least 16 loci. The autosomal dominant form (adRP), accounting for {approximately}25% of cases, can be caused by mutations in two genes, rhodopsin and peripherin/RDS, and by at least six other loci identified by linkage analysis. The RP11 locus for adRP has previously been mapped to chromosome 19q13.4 in a large English family. This linkage has been independently confirmed in a Japanese family, and we now report three additional unrelated linked U.K. families, suggesting that this is a major locus for RP. Linkage analysismore » in the U.K. families refines the RP11 interval to 5 cM between markers D19S180 and AFMc001yb1. All linked families exhibit incomplete penetrance; some obligate gene carriers remain asymptomatic throughout their lives, whereas symptomatic individuals experience night blindness and visual field loss in their teens and are generally registered as blind by their 30s. This {open_quotes}bimodal expressivity{close_quotes} contrasts with the variable-expressivity RP mapping to chromosome 7p (RP9) in another family, which has implications for diagnosis and counseling of RP11 families. These results may also imply that a proportion of sporadic RP, previously assumed to be recessive, might result from mutations at this locus. 27 refs., 3 figs., 1 tab.« less

Telomerase Reverse Transcriptase Locus Polymorphisms and Cancer Risk: A Field Synopsis and Meta-Analysis

PubMed Central

Verdi, Daunia; Pooley, Karen A.; Landi, Maria T.; Egan, Kathleen M.; Baird, Duncan M.; Prescott, Jennifer; De Vivo, Immaculata; Nitti, Donato

2012-01-01

Background Several recent studies have provided evidence that polymorphisms in the telomerase reverse transcriptase (TERT) gene sequence are associated with cancer development, but a comprehensive synopsis is not available. We conducted a systematic review and meta-analysis of the available molecular epidemiology data regarding the association between TERT locus polymorphisms and predisposition to cancer. Methods A systematic review of the English literature was conducted by searching PubMed, Embase, Cancerlit, Google Scholar, and ISI Web of Knowledge databases for studies on associations between TERT locus polymorphisms and cancer risk. Random-effects meta-analysis was performed to pool per-allele odds ratios for TERT locus polymorphisms and risk of cancer, and between-study heterogeneity and potential bias sources (eg, publication and chasing bias) were assessed. Because the TERT locus includes the cleft lip and palate transmembrane 1-like (CLPTM1L) gene, which is in linkage disequilibrium with TERT, CLPTM1L polymorphisms were also analyzed. Cumulative evidence for polymorphisms with statistically significant associations was graded as “strong,” “moderate,” and “weak” according to the Venice criteria. The joint population attributable risk was calculated for polymorphisms with strong evidence of association. Results Eighty-five studies enrolling 490 901 subjects and reporting on 494 allelic contrasts were retrieved. Data were available on 67 TERT locus polymorphisms and 24 tumor types, for a total of 221 unique combinations of polymorphisms and cancer types. Upon meta-analysis, a statistically significant association with the risk of any cancer type was found for 22 polymorphisms. Strong, moderate, and weak cumulative evidence for association with at least one tumor type was demonstrated for 11, 9, and 14 polymorphisms, respectively. For lung cancer, which was the most studied tumor type, the estimated joint population attributable risk for three polymorphisms (TERT rs2736100, intergenic rs4635969, and CLPTM1L rs402710) was 41%. Strong evidence for lack of association was identified for five polymorphisms in three tumor types. Conclusions To our knowledge, this is the largest collection of data for associations between TERT locus polymorphisms and cancer risk. Our findings support the hypothesis that genetic variability in this genomic region can modulate cancer susceptibility in humans. PMID:22523397

The SH2B1 obesity locus and abnormal glucose homeostasis: lack of evidence for association from a meta-analysis in individuals of European ancestry.

PubMed

Prudente, S; Copetti, M; Morini, E; Mendonca, C; Andreozzi, F; Chandalia, M; Baratta, R; Pellegrini, F; Mercuri, L; Bailetti, D; Abate, N; Frittitta, L; Sesti, G; Florez, J C; Doria, A; Trischitta, V

2013-11-01

The development of type 2 diabetes (T2D) is influenced both by environmental and by genetic determinants. Obesity is an important risk factor for T2D, mostly mediated by obesity-related insulin resistance. Obesity and insulin resistance are also modulated by the genetic milieu; thus, genes affecting risk of obesity and insulin resistance might also modulate risk of T2D. Recently, 32 loci have been associated with body mass index (BMI) by genome-wide studies, including one locus on chromosome 16p11 containing the SH2B1 gene. Animal studies have suggested that SH2B1 is a physiological enhancer of the insulin receptor and humans with rare deletions or mutations at SH2B1 are obese with a disproportionately high insulin resistance. Thus, the role of SH2B1 in both obesity and insulin resistance makes it a strong candidate for T2D. However, published data on the role of SH2B1 variability on the risk for T2D are conflicting, ranging from no effect at all to a robust association. The SH2B1 tag SNP rs4788102 (SNP, single nucleotide polymorphism) was genotyped in 6978 individuals from six studies for abnormal glucose homeostasis (AGH), including impaired fasting glucose, impaired glucose tolerance or T2D, from the GENetics of Type 2 Diabetes in Italy and the United States (GENIUS T2D) consortium. Data from these studies were then meta-analyzed, in a Bayesian fashion, with those from DIAGRAM+ (n = 47,117) and four other published studies (n = 39,448). Variability at the SH2B1 obesity locus was not associated with AGH either in the GENIUS consortium (overall odds ratio (OR) = 0.96; 0.89-1.04) or in the meta-analysis (OR = 1.01; 0.98-1.05). Our data exclude a role for the SH2B1 obesity locus in the modulation of AGH. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina).

PubMed

Dentinger, Bryn T M; Didukh, Maryna Y; Moncalvo, Jean-Marc

2011-01-01

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (~450 bp) representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (~1500 bp) at variable locations were detected in ~5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (~30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.

Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

PubMed Central

Dentinger, Bryn T. M.; Didukh, Maryna Y.; Moncalvo, Jean-Marc

2011-01-01

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (∼450 bp) representing ∼100 morphospecies from ∼650 collections of Agaricomycotina using several sets of new primers. Large introns (∼1500 bp) at variable locations were detected in ∼5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (∼30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms. PMID:21966418

Dominant root locus in state estimator design for material flow processes: A case study of hot strip rolling.

PubMed

Fišer, Jaromír; Zítek, Pavel; Skopec, Pavel; Knobloch, Jan; Vyhlídal, Tomáš

2017-05-01

The purpose of the paper is to achieve a constrained estimation of process state variables using the anisochronic state observer tuned by the dominant root locus technique. The anisochronic state observer is based on the state-space time delay model of the process. Moreover the process model is identified not only as delayed but also as non-linear. This model is developed to describe a material flow process. The root locus technique combined with the magnitude optimum method is utilized to investigate the estimation process. Resulting dominant roots location serves as a measure of estimation process performance. The higher the dominant (natural) frequency in the leftmost position of the complex plane the more enhanced performance with good robustness is achieved. Also the model based observer control methodology for material flow processes is provided by means of the separation principle. For demonstration purposes, the computer-based anisochronic state observer is applied to the strip temperatures estimation in the hot strip finishing mill composed of seven stands. This application was the original motivation to the presented research. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Application of mixsep software package: Performance verification of male-mixed DNA analysis

PubMed Central

HU, NA; CONG, BIN; GAO, TAO; CHEN, YU; SHEN, JUNYI; LI, SHUJIN; MA, CHUNLING

2015-01-01

An experimental model of male-mixed DNA (n=297) was constructed according to the mixed DNA construction principle. This comprised the use of the Applied Biosystems (ABI) 7500 quantitative polymerase chain reaction system, with scientific validation of mixture proportion (Mx; root-mean-square error ≤0.02). Statistical analysis was performed on locus separation accuracy using mixsep, a DNA mixture separation R-package, and the analytical performance of mixsep was assessed by examining the data distribution pattern of different mixed gradients, short tandem repeat (STR) loci and mixed DNA types. The results showed that locus separation accuracy had a negative linear correlation with the mixed gradient (R2=−0.7121). With increasing mixed gradient imbalance, locus separation accuracy first increased and then decreased, with the highest value detected at a gradient of 1:3 (≥90%). The mixed gradient, which is the theoretical Mx, was one of the primary factors that influenced the success of mixed DNA analysis. Among the 16 STR loci detected by Identifiler®, the separation accuracy was relatively high (>88%) for loci D5S818, D8S1179 and FGA, whereas the median separation accuracy value was lowest for the D7S820 locus. STR loci with relatively large numbers of allelic drop-out (ADO; >15) were all located in the yellow and red channels, including loci D18S51, D19S433, FGA, TPOX and vWA. These five loci featured low allele peak heights, which was consistent with the low sensitivity of the ABI 3130xl Genetic Analyzer to yellow and red fluorescence. The locus separation accuracy of the mixsep package was substantially different with and without the inclusion of ADO loci; inclusion of ADO significantly reduced the analytical performance of the mixsep package, which was consistent with the lack of an ADO functional module in this software. The present study demonstrated that the mixsep software had a number of advantages and was recommended for analysis of mixed DNA. This software was easy to operate and produced understandable results with a degree of controllability. PMID:25936428

A Copy Number Variant at the KITLG Locus Likely Confers Risk for Canine Squamous Cell Carcinoma of the Digit

PubMed Central

Karyadi, Danielle M.; Karlins, Eric; Decker, Brennan; vonHoldt, Bridgett M.; Carpintero-Ramirez, Gretchen; Parker, Heidi G.; Wayne, Robert K.; Ostrander, Elaine A.

2013-01-01

The domestic dog is a robust model for studying the genetics of complex disease susceptibility. The strategies used to develop and propagate modern breeds have resulted in an elevated risk for specific diseases in particular breeds. One example is that of Standard Poodles (STPOs), who have increased risk for squamous cell carcinoma of the digit (SCCD), a locally aggressive cancer that causes lytic bone lesions, sometimes with multiple toe recurrence. However, only STPOs of dark coat color are at high risk; light colored STPOs are almost entirely unaffected, suggesting that interactions between multiple pathways are necessary for oncogenesis. We performed a genome-wide association study (GWAS) on STPOs, comparing 31 SCCD cases to 34 unrelated black STPO controls. The peak SNP on canine chromosome 15 was statistically significant at the genome-wide level (Praw = 1.60×10−7; Pgenome = 0.0066). Additional mapping resolved the region to the KIT Ligand (KITLG) locus. Comparison of STPO cases to other at-risk breeds narrowed the locus to a 144.9-Kb region. Haplotype mapping among 84 STPO cases identified a minimal region of 28.3 Kb. A copy number variant (CNV) containing predicted enhancer elements was found to be strongly associated with SCCD in STPOs (P = 1.72×10−8). Light colored STPOs carry the CNV risk alleles at the same frequency as black STPOs, but are not susceptible to SCCD. A GWAS comparing 24 black and 24 light colored STPOs highlighted only the MC1R locus as significantly different between the two datasets, suggesting that a compensatory mutation within the MC1R locus likely protects light colored STPOs from disease. Our findings highlight a role for KITLG in SCCD susceptibility, as well as demonstrate that interactions between the KITLG and MC1R loci are potentially required for SCCD oncogenesis. These findings highlight how studies of breed-limited diseases are useful for disentangling multigene disorders. PMID:23555311

Ectopic Expression of O Antigen in Bordetella pertussis by a Novel Genomic Integration System

PubMed Central

Shinzawa, Naoaki; Nishikawa, Sayaka; Suzuki, Koichiro; Fukui-Miyazaki, Aya

2018-01-01

ABSTRACT We describe a novel genome integration system that enables the introduction of DNA fragments as large as 50 kbp into the chromosomes of recipient bacteria. This system, named BPI, comprises a bacterial artificial chromosome vector and phage-derived gene integration machinery. We introduced the wbm locus of Bordetella bronchiseptica, which is required for O antigen biosynthesis, into the chromosome of B. pertussis, which intrinsically lacks O antigen, using the BPI system. After the introduction of the wbm locus, B. pertussis presented an additional substance in the lipooligosaccharide fraction that was specifically recognized by the anti-B. bronchiseptica antibody but not the anti-B. pertussis antibody, indicating that B. pertussis expressed O antigen corresponding to that of B. bronchiseptica. O antigen-expressing B. pertussis was less sensitive to the bactericidal effects of serum and polymyxin B than the isogenic parental strain. In addition, an in vivo competitive infection assay showed that O antigen-expressing B. pertussis dominantly colonized the mouse respiratory tract over the parental strain. These results indicate that the BPI system provides a means to alter the phenotypes of bacteria by introducing large exogenous DNA fragments. IMPORTANCE Some bacterial phenotypes emerge through the cooperative functions of a number of genes residing within a large genetic locus. To transfer the phenotype of one bacterium to another, a means to introduce the large genetic locus into the recipient bacterium is needed. Therefore, we developed a novel system by combining the advantages of a bacterial artificial chromosome vector and phage-derived gene integration machinery. In this study, we succeeded for the first time in introducing a gene locus involved in O antigen biosynthesis of Bordetella bronchiseptica into the chromosome of B. pertussis, which intrinsically lacks O antigen, and using this system we analyzed phenotypic alterations in the resultant mutant strain of B. pertussis. The present results demonstrate that this system successfully accomplished the above-described purpose. We consider this system to be applicable to a number of bacteria other than Bordetella. PMID:29404410

Ectopic Expression of O Antigen in Bordetella pertussis by a Novel Genomic Integration System.

PubMed

Ishigaki, Keisuke; Shinzawa, Naoaki; Nishikawa, Sayaka; Suzuki, Koichiro; Fukui-Miyazaki, Aya; Horiguchi, Yasuhiko

2018-01-01

We describe a novel genome integration system that enables the introduction of DNA fragments as large as 50 kbp into the chromosomes of recipient bacteria. This system, named BPI, comprises a bacterial artificial chromosome vector and phage-derived gene integration machinery. We introduced the wbm locus of Bordetella bronchiseptica , which is required for O antigen biosynthesis, into the chromosome of B. pertussis , which intrinsically lacks O antigen, using the BPI system. After the introduction of the wbm locus, B. pertussis presented an additional substance in the lipooligosaccharide fraction that was specifically recognized by the anti- B. bronchiseptica antibody but not the anti- B. pertussis antibody, indicating that B. pertussis expressed O antigen corresponding to that of B. bronchiseptica . O antigen-expressing B. pertussis was less sensitive to the bactericidal effects of serum and polymyxin B than the isogenic parental strain. In addition, an in vivo competitive infection assay showed that O antigen-expressing B. pertussis dominantly colonized the mouse respiratory tract over the parental strain. These results indicate that the BPI system provides a means to alter the phenotypes of bacteria by introducing large exogenous DNA fragments. IMPORTANCE Some bacterial phenotypes emerge through the cooperative functions of a number of genes residing within a large genetic locus. To transfer the phenotype of one bacterium to another, a means to introduce the large genetic locus into the recipient bacterium is needed. Therefore, we developed a novel system by combining the advantages of a bacterial artificial chromosome vector and phage-derived gene integration machinery. In this study, we succeeded for the first time in introducing a gene locus involved in O antigen biosynthesis of Bordetella bronchiseptica into the chromosome of B. pertussis , which intrinsically lacks O antigen, and using this system we analyzed phenotypic alterations in the resultant mutant strain of B. pertussis . The present results demonstrate that this system successfully accomplished the above-described purpose. We consider this system to be applicable to a number of bacteria other than Bordetella .

A Specific Construction of a Conic from an Ellipse

ERIC Educational Resources Information Center

Lee, J. Todd

2004-01-01

The interesting construction of a conic from an ellipse given by Manuel Santos-Trigo is evaluated. The validity of the conclusion that the locus is a conic section, the nature of which is determined in a simple way by the location of the variable point R relative to its center point O and the major vertices of the ellipse are proved.

If You Had My Brain, Where Would I Be? Children's Understanding of the Brain and Identity.

ERIC Educational Resources Information Center

Johnson, Carl Nils

1990-01-01

Reveals that during the elementary school years, children acquire a firm understanding of the brain as the primary locus of psychological attributes and identity. The early school years, when children are five to seven years old, appear to be a transitional phase, when performance is variable and subject to task conditions. (RH)

Course Selection Theory and College Transition Seminars: An Adaptation of College Choice Models to Explain First-Year Students' Course Enrollment Behavior

ERIC Educational Resources Information Center

Graff, Curt Gerard

2011-01-01

This dissertation examines the course-enrollment behavior of first-year students at a public Midwestern university. Using the student choice construct, modern college choice theory, and the constructs of habitus, human capital, financial capital, social capital, cultural capital, along with background variables such as gender and locus of control,…

Williams-Beuren syndrome: phenotypic variability and deletions of chromosomes 7, 11, and 22 in a series of 52 patients.

PubMed Central

Joyce, C A; Zorich, B; Pike, S J; Barber, J C; Dennis, N R

1996-01-01

Fluorescence in situ hybridisation (FISH) and conventional chromosome analysis were performed on a series of 52 patients with classical Williams-Beuren syndrome (WBS), suspected WBS, or supravalvular aortic stenosis (SVAS). In the classical WBS group, 22/23 (96%) had a submicroscopic deletion of the elastin locus on chromosome 7, but the remaining patient had a unique interstitial deletion of chromosome 11 (del(11)(q13.5q14.2)). In the suspected WBS group 2/22 (9%) patients had elastin deletions but a third patient had a complex karyotype including a ring chromosome 22 with a deletion of the long arm (r(22)(p11-->q13)). In the SVAS group, 1/7 (14%) had an elastin gene deletion, despite having normal development and minimal signs of WBS. Overall, some patients with submicroscopic elastin deletions have fewer features of Williams-Beuren syndrome than those with other cytogenetic abnormalities. These results, therefore, emphasise the importance of a combined conventional and molecular cytogenetic approach to diagnosis and suggest that the degree to which submicroscopic deletions of chromosome 7 extend beyond the elastin locus may explain some of the phenotypic variability found in Williams-Beuren syndrome. Images PMID:9004128

Perception of economic crisis among Spanish nursing students: Its relation to burnout and engagement.

PubMed

Manzano-García, Guadalupe; Montañés, Pilar; Megías, Jesús L

2017-05-01

The high levels of indebtedness and deficit of Spain's autonomous communities as a consequence of the national and European economic crisis have caused radical changes in the Spanish National Health Service. At the present time, the economic crisis is seriously affecting nurses in several European countries, and especially in Spain. The aim of this study was to analyse whether nursing students' perceptions of economic crisis influence their levels of burnout and engagement in relation to their studies. We have also tried to clarify the relationship of sociodemographic variables (age and gender) and personal control factors (self-efficacy, locus of control and success) with these factors. This was a transversal study based on descriptive and inferential statistical analysis. Analysis of the quantitative data was performed using Statistical Package for Social Sciences, IBM 19.0 (SPSS, 2010). 166 nursing students participated in the study, comprising 142 women and 24 men studying in Schools of Nursing in the North of Spain. They completed various questionnaires to gather information on sociodemographic variables and measure burnout, engagement, locus of control, expectations of success and perceptions of threat due to the economic crisis. Higher perception of economic crisis by the students is related to higher scores for burnout and lower scores for engagement. The scores for burnout were also positively predicted by external locus of control and negatively predicted by perception of self-efficacy. The age of participants is related to lower levels of burnout and higher levels of engagement. Finally, expectation of success also positively predicted the level of engagement. The results demonstrate the importance of the perceptions of the economic crisis on the development of burnout and engagement among nursing students. Copyright © 2017 Elsevier Ltd. All rights reserved.

Number of discernible colors for color-deficient observers estimated from the MacAdam limits.

PubMed

Perales, Esther; Martínez-Verdú, Francisco Miguel; Linhares, João Manuel Maciel; Nascimento, Sérgio Miguel Cardoso

2010-10-01

We estimated the number of colors perceived by color normal and color-deficient observers when looking at the theoretic limits of object-color stimuli. These limits, the optimal color stimuli, were computed for a color normal observer and CIE standard illuminant D65, and the resultant colors were expressed in the CIELAB and DIN99d color spaces. The corresponding color volumes for abnormal color vision were computed using models simulating for normal trichromatic observers the appearance for dichromats and anomalous trichomats. The number of colors perceived in each case was then computed from the color volumes enclosed by the optimal colors also known as MacAdam limits. It was estimated that dichromats perceive less than 1% of the colors perceived by normal trichromats and that anomalous trichromats perceive 50%-60% for anomalies in the medium-wavelength-sensitive and 60%-70% for anomalies in the long-wavelength-sensitive cones. Complementary estimates obtained similarly for the spectral locus of monochromatic stimuli suggest less impairment for color-deficient observers, a fact that is explained by the two-dimensional nature of the locus.

Retroviral vectors encoding ADA regulatory locus control region provide enhanced T-cell-specific transgene expression

PubMed Central

2009-01-01

Background Murine retroviral vectors have been used in several hundred gene therapy clinical trials, but have fallen out of favor for a number of reasons. One issue is that gene expression from viral or internal promoters is highly variable and essentially unregulated. Moreover, with retroviral vectors, gene expression is usually silenced over time. Mammalian genes, in contrast, are characterized by highly regulated, precise levels of expression in both a temporal and a cell-specific manner. To ascertain if recapitulation of endogenous adenosine deaminase (ADA) expression can be achieved in a vector construct we created a new series of Moloney murine leukemia virus (MuLV) based retroviral vector that carry human regulatory elements including combinations of the ADA promoter, the ADA locus control region (LCR), ADA introns and human polyadenylation sequences in a self-inactivating vector backbone. Methods A MuLV-based retroviral vector with a self-inactivating (SIN) backbone, the phosphoglycerate kinase promoter (PGK) and the enhanced green fluorescent protein (eGFP), as a reporter gene, was generated. Subsequent vectors were constructed from this basic vector by deletion or addition of certain elements. The added elements that were assessed are the human ADA promoter, human ADA locus control region (LCR), introns 7, 8, and 11 from the human ADA gene, and human growth hormone polyadenylation signal. Retroviral vector particles were produced by transient three-plasmid transfection of 293T cells. Retroviral vectors encoding eGFP were titered by transducing 293A cells, and then the proportion of GFP-positive cells was determined using fluorescence-activated cell sorting (FACS). Non T-cell and T-cell lines were transduced at a multiplicity of infection (MOI) of 0.1 and the yield of eGFP transgene expression was evaluated by FACS analysis using mean fluorescent intensity (MFI) detection. Results Vectors that contained the ADA LCR were preferentially expressed in T-cell lines. Further improvements in T-cell specific gene expression were observed with the incorporation of additional cis-regulatory elements, such as a human polyadenylation signal and intron 7 from the human ADA gene. Conclusion These studies suggest that the combination of an authentically regulated ADA gene in a murine retroviral vector, together with additional locus-specific regulatory refinements, will yield a vector with a safer profile and greater efficacy in terms of high-level, therapeutic, regulated gene expression for the treatment of ADA-deficient severe combined immunodeficiency. PMID:20042112

Rex and a Suppressor of Rex Are Repeated Neomorphic Loci in the Drosophila Melanogaster Ribosomal DNA

PubMed Central

Rasooly, R. S.; Robbins, L. G.

1991-01-01

The Rex locus of Drosophila melanogaster induces a high frequency of mitotic exchange between two separated ribosomal DNA arrays on a single chromosome. The exchanges take place in the progeny of Rex mothers and occur very early, before the third mitotic division. A number of common laboratory stocks have also been found to carry dominant suppressors of Rex (Su(Rex)). Rex was mapped to the X centric heterochromatin, proximal to su(f), by genetic and molecular analysis of two spontaneous recombinants. Using deficiencies and duplications of the heterochromatin, both Rex and one Su(Rex) were shown to behave as neomorphs. Rex-induced exchange in a target chromosome bearing both Rex and Su(Rex) was then used to map these functions to the bb locus itself. Molecular analysis of the recombinants, using length variants of the ribosomal DNA intergenic spacer as genetic markers, mapped Su(Rex) and Rex within the bb locus and demonstrated that both are repeated elements. PMID:1936953

Perceived health promotion practice by older women: use of herbal products.

PubMed

Yoon, Saunjoo Lee; Horne, Claydell H

2004-07-01

Women age 65 and older appear to use herbal products as well as multiple prescribed and non-prescribed drugs as part of their health-promoting practice. The purpose of this study was to identify changes in herbal-product use in a sample of older women during an 18-month period and to explore differences in locus of control and perceived health competence between herbal-product users and non-users. A longitudinal and descriptive study design was used. Instruments used to guide the two sets of structured interviews included the Multidimensional Health Locus of Control (MHLC), the Perceived Health Competence Scale (PHCS), and a questionnaire about herbal-product use. The prevalence of herbal-product usage and the number of products used remained consistent between the initial and follow-up interviews, with 43% of the participants using an average of 2.6 herbal products. Neither MHLC nor PHCS scores differed between herbal-product users and non-users. Mean scores of women in the study indicated higher internal than external locus of control.

Genomic analysis reveals extensive gene duplication within the bovine TRB locus

PubMed Central

Connelley, Timothy; Aerts, Jan; Law, Andy; Morrison, W Ivan

2009-01-01

Background Diverse TR and IG repertoires are generated by V(D)J somatic recombination. Genomic studies have been pivotal in cataloguing the V, D, J and C genes present in the various TR/IG loci and describing how duplication events have expanded the number of these genes. Such studies have also provided insights into the evolution of these loci and the complex mechanisms that regulate TR/IG expression. In this study we analyze the sequence of the third bovine genome assembly to characterize the germline repertoire of bovine TRB genes and compare the organization, evolution and regulatory structure of the bovine TRB locus with that of humans and mice. Results The TRB locus in the third bovine genome assembly is distributed over 5 scaffolds, extending to ~730 Kb. The available sequence contains 134 TRBV genes, assigned to 24 subgroups, and 3 clusters of DJC genes, each comprising a single TRBD gene, 5–7 TRBJ genes and a single TRBC gene. Seventy-nine of the TRBV genes are predicted to be functional. Comparison with the human and murine TRB loci shows that the gene order, as well as the sequences of non-coding elements that regulate TRB expression, are highly conserved in the bovine. Dot-plot analyses demonstrate that expansion of the genomic TRBV repertoire has occurred via a complex and extensive series of duplications, predominantly involving DNA blocks containing multiple genes. These duplication events have resulted in massive expansion of several TRBV subgroups, most notably TRBV6, 9 and 21 which contain 40, 35 and 16 members respectively. Similarly, duplication has lead to the generation of a third DJC cluster. Analyses of cDNA data confirms the diversity of the TRBV genes and, in addition, identifies a substantial number of TRBV genes, predominantly from the larger subgroups, which are still absent from the genome assembly. The observed gene duplication within the bovine TRB locus has created a repertoire of phylogenetically diverse functional TRBV genes, which is substantially larger than that described for humans and mice. Conclusion The analyses completed in this study reveal that, although the gene content and organization of the bovine TRB locus are broadly similar to that of humans and mice, multiple duplication events have led to a marked expansion in the number of TRB genes. Similar expansions in other ruminant TR loci suggest strong evolutionary pressures in this lineage have selected for the development of enlarged sets of TR genes that can contribute to diverse TR repertoires. PMID:19393068

Tracking and responding to an outbreak of tuberculosis using MIRU-VNTR genotyping and whole genome sequencing as epidemiological tools.

PubMed

Black, Anne T; Hamblion, Esther L; Buttivant, Helen; Anderson, Sarah R; Stone, Madeline; Casali, Nicola; Drobniewski, Francis; Nwoguh, Francisca; Marshall, Ben G; Booth, Linda

2017-07-05

We describe an outbreak that contributed to a near doubling of the incidence of tuberculosis in Southampton, UK. We examine the importance of 24 locus mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) genotyping in its identification and management and the role of whole genome sequencing (WGS) in tracing the spread of the strain. Outbreak cases were defined as those diagnosed between January and December 2011 with indistinguishable 24 locus-MIRU-VNTR genotypes or, cases linked epidemiologically. A cluster questionnaire was administered by TB nurses to identify contacts and social settings. Overall, 25 patients fulfilled the case definition. No cases with this MIRU-VNTR genotype had been detected in the UK previously. Connections were found between all cases through household contacts or social venues including a football club, Internet cafe and barber's shop. Public health actions included extended contact tracing, venue screening and TB awareness-raising. The outbreak resulted in a high rate of transmission and high incidence of clinical disease among contacts. This outbreak illustrates the value of combining active case-finding with prospective MIRU-VNTR genotyping to identify settings to undertake public health action. In addition WGS revealed that the VNTR-defined cluster was a single outbreak and that active TB transmission not reactivation was responsible for this outbreak in non-UK born individuals. © The Author 2017. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Development and evaluation of a multi-locus sequence typing scheme for Mycoplasma synoviae.

PubMed

Dijkman, R; Feberwee, A; Landman, W J M

2016-08-01

Reproducible molecular Mycoplasma synoviae typing techniques with sufficient discriminatory power may help to expand knowledge on its epidemiology and contribute to the improvement of control and eradication programmes of this mycoplasma species. The present study describes the development and validation of a novel multi-locus sequence typing (MLST) scheme for M. synoviae. Thirteen M. synoviae isolates originating from different poultry categories, farms and lesions, were subjected to whole genome sequencing. Their sequences were compared to that of M. synoviae reference strain MS53. A high number of single nucleotide polymorphisms (SNPs) indicating considerable genetic diversity were identified. SNPs were present in over 40 putative target genes for MLST of which five target genes were selected (nanA, uvrA, lepA, ruvB and ugpA) for the MLST scheme. This scheme was evaluated analysing 209 M. synoviae samples from different countries, categories of poultry, farms and lesions. Eleven clonal clusters and 76 different sequence types (STs) were obtained. Clustering occurred following geographical origin, supporting the hypothesis of regional population evolution. M. synoviae samples obtained from epidemiologically linked outbreaks often harboured the same ST. In contrast, multiple M. synoviae lineages were found in samples originating from swollen joints or oviducts from hens that produce eggs with eggshell apex abnormalities indicating that further research is needed to identify the genetic factors of M. synoviae that may explain its variations in tissue tropism and disease inducing potential. Furthermore, MLST proved to have a higher discriminatory power compared to variable lipoprotein and haemagglutinin A typing, which generated 50 different genotypes on the same database.

Somatic cell mutations at the glycophorin A locus in erythrocytes of atomic bomb survivors: Implications for radiation carcinogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyoizumi, Seishi; Akiyama, Mitoshi; Tanabe, Kazumi

To clarify the relationship between somatic cell mutations and radiation exposure, the frequency of hemizygous mutant erythrocytes at the glycophorin A (GPA) locus was measured by flow cytometry for 1,226 heterozygous atomic bomb (A-bomb) survivors in HIroshima and Nagasaki. For statistical analysis, both GPA mutant frequency and radiation dose were log-transformed to normalize skewed distributions of these variables. The GPA mutant frequency increased slightly but significantly with age at testing and with the number of cigarettes smoked. Also, mutant frequency was significantly higher in males than in females even with adjustment for smoking and was higher to Hiroshima than inmore » Nagasaki. These characteristics of background GPA mutant frequency are qualitatively similar to those of background solid cancer incidence or mortality obtained from previous epidemiological studies of survivors. An analysis of the mutant frequency dose response using a descriptive model showed that the doubling dose is about 1.20 Sv [95% confidence interval (CI): 0.95-1.56], whereas the minimum dose for detecting a significant increase in mutant frequency is about 0.24 Sv (95% CI: 0.041-0.51). No significant effects of sex, city or age at the time of exposure on the dose response were detected. Interestingly, the doubling dose of the GPA mutant frequency was similar to that of solid cancer incidence in A-bomb survivors. This observation is in line with the hypothesis that radiation-induced somatic cell mutations are the major cause of excess cancer risk after radiation. 49 refs., 6 figs., 2 tabs.« less

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.

PubMed

Viñuelas, José; Kaneko, Gaël; Coulon, Antoine; Vallin, Elodie; Morin, Valérie; Mejia-Pous, Camila; Kupiec, Jean-Jacques; Beslon, Guillaume; Gandrillon, Olivier

2013-02-25

A number of studies have established that stochasticity in gene expression may play an important role in many biological phenomena. This therefore calls for further investigations to identify the molecular mechanisms at stake, in order to understand and manipulate cell-to-cell variability. In this work, we explored the role played by chromatin dynamics in the regulation of stochastic gene expression in higher eukaryotic cells. For this purpose, we generated isogenic chicken-cell populations expressing a fluorescent reporter integrated in one copy per clone. Although the clones differed only in the genetic locus at which the reporter was inserted, they showed markedly different fluorescence distributions, revealing different levels of stochastic gene expression. Use of chromatin-modifying agents showed that direct manipulation of chromatin dynamics had a marked effect on the extent of stochastic gene expression. To better understand the molecular mechanism involved in these phenomena, we fitted these data to a two-state model describing the opening/closing process of the chromatin. We found that the differences between clones seemed to be due mainly to the duration of the closed state, and that the agents we used mainly seem to act on the opening probability. In this study, we report biological experiments combined with computational modeling, highlighting the importance of chromatin dynamics in stochastic gene expression. This work sheds a new light on the mechanisms of gene expression in higher eukaryotic cells, and argues in favor of relatively slow dynamics with long (hours to days) periods of quiet state.

Deciphering amphibian diversity through DNA barcoding: chances and challenges.

PubMed

Vences, Miguel; Thomas, Meike; Bonett, Ronald M; Vieites, David R

2005-10-29

Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I (cox1) sequences in this taxon. High intraspecific cox1 divergences of 7-14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1.

Methylation of avpr1a in the cortex of wild prairie voles: effects of CpG position and polymorphism

PubMed Central

Maguire, S. M.; Phelps, S. M.

2017-01-01

DNA methylation can cause stable changes in neuronal gene expression, but we know little about its role in individual differences in the wild. In this study, we focus on the vasopressin 1a receptor (avpr1a), a gene extensively implicated in vertebrate social behaviour, and explore natural variation in DNA methylation, genetic polymorphism and neuronal gene expression among 30 wild prairie voles (Microtus ochrogaster). Examination of CpG density across 8 kb of the locus revealed two distinct CpG islands overlapping promoter and first exon, characterized by few CpG polymorphisms. We used a targeted bisulfite sequencing approach to measure DNA methylation across approximately 3 kb of avpr1a in the retrosplenial cortex, a brain region implicated in male space use and sexual fidelity. We find dramatic variation in methylation across the avrp1a locus, with pronounced diversity near the exon–intron boundary and in a genetically variable putative enhancer within the intron. Among our wild voles, differences in cortical avpr1a expression correlate with DNA methylation in this putative enhancer, but not with the methylation status of the promoter. We also find an unusually high number of polymorphic CpG sites (polyCpGs) in this focal enhancer. One polyCpG within this enhancer (polyCpG 2170) may drive variation in expression either by disrupting transcription factor binding motifs or by changing local DNA methylation and chromatin silencing. Our results contradict some assumptions made within behavioural epigenetics, but are remarkably concordant with genome-wide studies of gene regulation. PMID:28280564

Motivating contributions to online forums: can locus of control moderate the effects of interface cues?

PubMed

Kim, Hyang-Sook; Sundar, S Shyam

2016-01-01

In an effort to encourage users to participate rather than lurk, online health forums provide authority badges (e.g., guru) to frequent contributors and popularity indicators (e.g., number of views) to their postings. Studies have shown the latter to be more effective, implying that bulletin-board users are motivated by external validation of their contributions. However, no consideration has yet been given to individual differences in the influence of such popularity indicators. Personality psychology suggests that individuals with external, rather than internal, locus of control are more likely to be other-directed and therefore more likely to be motivated by interface cues showing the bandwagon effect of their online posts. We investigate this hypothesis by analyzing data from a 2 (high vs. low authority cue) × 2 (strong vs. weak bandwagon cue) experiment with an online health community. Results show that strong bandwagon cues promote sense of community among users with internal, rather than external, locus of control. When bandwagon cues are weak, bestowal of high authority serves to heighten their sense of agency. Contrary to prediction, weak bandwagon cues appear to promote sense of community and sense of agency among those with external locus of control. Theoretical and practical implications are discussed.

A local duplication of the Melanocortin receptor 1 locus in Astyanax

PubMed Central

Gross, Joshua B.; Weagley, James; Stahl, Bethany A.; Ma, Li; Espinasa, Luis; McGaugh, Suzanne E.

2017-01-01

In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ~820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ~89% sequence similarity, and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus, and if this novel copy number variant may have adaptive significance for the Astyanax lineage. PMID:28738163

Hierarchical Naive Bayes for genetic association studies.

PubMed

Malovini, Alberto; Barbarini, Nicola; Bellazzi, Riccardo; de Michelis, Francesca

2012-01-01

Genome Wide Association Studies represent powerful approaches that aim at disentangling the genetic and molecular mechanisms underlying complex traits. The usual "one-SNP-at-the-time" testing strategy cannot capture the multi-factorial nature of this kind of disorders. We propose a Hierarchical Naïve Bayes classification model for taking into account associations in SNPs data characterized by Linkage Disequilibrium. Validation shows that our model reaches classification performances superior to those obtained by the standard Naïve Bayes classifier for simulated and real datasets. In the Hierarchical Naïve Bayes implemented, the SNPs mapping to the same region of Linkage Disequilibrium are considered as "details" or "replicates" of the locus, each contributing to the overall effect of the region on the phenotype. A latent variable for each block, which models the "population" of correlated SNPs, can be then used to summarize the available information. The classification is thus performed relying on the latent variables conditional probability distributions and on the SNPs data available. The developed methodology has been tested on simulated datasets, each composed by 300 cases, 300 controls and a variable number of SNPs. Our approach has been also applied to two real datasets on the genetic bases of Type 1 Diabetes and Type 2 Diabetes generated by the Wellcome Trust Case Control Consortium. The approach proposed in this paper, called Hierarchical Naïve Bayes, allows dealing with classification of examples for which genetic information of structurally correlated SNPs are available. It improves the Naïve Bayes performances by properly handling the within-loci variability.

Can an Internal Locus of Control and Social Support Reduce Work-Related Levels of Stress and Strain?: A Comparative Study Between Spanish Owners and Managers.

PubMed

Ariza-Montes, Antonio; Leal-Rodríguez, Antonio L; Rodríguez-Félix, Lucía; Albort-Morant, Gema

2017-09-01

The aim of this article is to assess the role played by both individual and contextual factors in reducing the manager's levels of stress and strain within the workplace setting. This article also highlights the manager's locus of control (LOC) as an internal factor and emphasizes the social support variable as a contextual factor. We use a sample of 332 respondents belonging to Spanish manufacturing and services firms and a structural equation modeling technique (partial least squares path modeling). The results reveal that there are significant differences between managers and owners about stress-strain relationship. The study provides support for the literature on stress management, which emphasizes the importance of a LOC and social support in influencing stress and strain between managers and owners.

The normal huntington disease (HD) allele, or a closely linked gene, influences age at onset of HD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farrer, L.A.; Cupples, L.A.; Conneally, P.M.

1993-07-01

The authors evaluated the hypothesis that Huntington disease (HD) is influenced by the normal HD allele by comparing transmission patterns of genetically linked markers at the D4S10 locus in the normal parent against age at onset in the affected offspring. Analysis of information from 21 sibships in 14 kindreds showed a significant tendency for sibs who have similar onset ages to share the same D4S10 allele from the normal parent. Affected sibs who inherited different D4S10 alleles from the normal parent tended to have more variable ages at onset. These findings suggest that the expression of HD is modulated bymore » the normal HD allele or by a closely linked locus. 38 refs., 2 figs., 1 tab.« less

Identification of Stmm3 locus Conferring Resistance to Late-stage Chemically Induced Skin Papillomas on Mouse Chromosome 4 by Congenic Mappingand Allele-specific Alteration Analysis

PubMed Central

Saito, Megumi; Okumura, Kazuhiro; Miura, Ikuo; Wakana, Shigeharu; Kominami, Ryo; Wakabayashi, Yuichi

2014-01-01

Genome-wide association studies have revealed that many low-penetrance cancer susceptibility loci are located throughout the genome; however, a very limited number of genes have been identified so far. Using a forward genetics approach to map such loci in a mouse skin cancer model, we previously identified strong genetic loci conferring resistance to chemically induced skin papillomas on chromosome 4 and 7 with a large number of [(FVB/N × MSM/Ms) F1 × FVB/N] backcross mice. In this report, we describe a combination of congenic mapping and allele-specific alteration analysis of the loci on chromosome 4. We used linkage analysis and a congenic mouse strain, FVB.MSM-Stmm3 to refine the location of Stmm3 (Skin tumor modifier of MSM 3) locus within a physical interval of about 34 Mb on distal chromosome 4. In addition, we used patterns of allele-specific imbalances in tumors from N2 and N10 congenic mice to narrow down further the region of Stmm3 locus to a physical distance of about 25 Mb. Furthermore, immunohistochemical analysis showed papillomas from congenic mice had less proliferative activity. These results suggest that Stmm3 responsible genes may have an influence on papilloma formation in the two-stage skin carcinogenesis by regulating papilloma growth rather than development. PMID:25077764

Analysis of Cooperative Education as a Work/Education Joint Venture.

ERIC Educational Resources Information Center

Wilson, James W.

1984-01-01

Examines why joint ventures are formed and discusses a number of factors related to the success of such interaction. Focus is on four factors: goal compatibility, boundary-spanning structures and processes, locus of need satisfaction, and organizational incentives. (CT)

Characteristics of polymorphism at a VNTR locus 3[prime] to the apolipoprotein B gene in five human populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deka, R.; DeCroo, S.; Ferrell, R.E.

1992-12-01

The authors have analyzed the allele frequency distribution at the hypervariable locus 3[prime] to the apolipoprotein B gene (ApoB 3[prime] VNTR) in five well-defined human populations (Kacharis of northeast India, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, and a relatively homogeneous Caucasian population of northern German extraction) by using the PCR technique. A total of 12 segregating alleles were detected in the pooled sample of 319 individuals. A fairly consistent bimodal pattern of allele frequency distribution, apparent in most of these geographically and genetically diverse populations, suggests that the ApoB 3[prime] VNTRmore » polymorphism predates the geographic dispersal of ancestral human populations. In spite of the observed high degree of polymorphism at this locus (expected heterozygosity levels 55%-78%), the genotype distributions in all populations (irrespective of their tribal or cosmopolitan nature) conform to their respective Hardy-Weinberg predictions. Furthermore, analysis of the congruence between expected heterozygosity and the observed number of alleles reveals that, in general, the allele frequency distributions at this locus are in agreement with the predictions of the classical mutation-drift models. The data also show that alleles that are shared by all populations have the highest average frequency within populations. These findings demonstrate the potential utility of highly informative hypervariable loci such as the ApoB 3[prime] VNTR locus in population genetic research, as well as in forensic medicine and determination of biological relatedness of individuals. 38 refs., 2 figs., 3 tabs.« less

Composition, variation, expression and evolution of low-molecular-weight glutenin subunit genes in Triticum urartu.

PubMed

Luo, Guangbin; Zhang, Xiaofei; Zhang, Yanlin; Yang, Wenlong; Li, Yiwen; Sun, Jiazhu; Zhan, Kehui; Zhang, Aimin; Liu, Dongcheng

2015-02-28

Wheat (AABBDD, 2n = 6x = 42) is a major dietary component for many populations across the world. Bread-making quality of wheat is mainly determined by glutenin subunits, but it remains challenging to elucidate the composition and variation of low-molecular-weight glutenin subunits (LMW-GS) genes, the major components for glutenin subunits in hexaploid wheat. This problem, however, can be greatly simplified by characterizing the LMW-GS genes in Triticum urartu, the A-genome donor of hexaploid wheat. In the present study, we exploited the high-throughput molecular marker system, gene cloning, proteomic methods and molecular evolutionary genetic analysis to reveal the composition, variation, expression and evolution of LMW-GS genes in a T. urartu population from the Fertile Crescent region. Eight LMW-GS genes, including four m-type, one s-type and three i-type, were characterized in the T. urartu population. Six or seven genes, the highest number at the Glu-A3 locus, were detected in each accession. Three i-type genes, each containing more than six allelic variants, were tightly linked because of their co-segregation in every accession. Only 2-3 allelic variants were detected for each m- and s-type gene. The m-type gene, TuA3-385, for which homologs were previously characterized only at Glu-D3 locus in common wheat and Aegilops tauschii, was detected at Glu-A3 locus in T. urartu. TuA3-460 was the first s-type gene identified at Glu-A3 locus. Proteomic analysis showed 1-4 genes, mainly i-type, expressed in individual accessions. About 62% accessions had three active i-type genes, rather than one or two in common wheat. Southeastern Turkey might be the center of origin and diversity for T. urartu due to its abundance of LMW-GS genes/genotypes. Phylogenetic reconstruction demonstrated that the characterized T. urartu might be the direct donor of the Glu-A3 locus in common wheat varieties. Compared with the Glu-A3 locus in common wheat, a large number of highly diverse LMW-GS genes and active genes were characterized in T. urartu, demonstrating that this progenitor might provide valuable genetic resources for LMW-GS genes to improve the quality of common wheat. The phylogenetic analysis provided molecular evidence and confirmed that T. urartu was the A-genome donor of hexaploid wheat.

Low α-defensin gene copy number increases the risk for IgA nephropathy and renal dysfunction.

PubMed

Ai, Zhen; Li, Ming; Liu, Wenting; Foo, Jia-Nee; Mansouri, Omniah; Yin, Peiran; Zhou, Qian; Tang, Xueqing; Dong, Xiuqing; Feng, Shaozhen; Xu, Ricong; Zhong, Zhong; Chen, Jian; Wan, Jianxin; Lou, Tanqi; Yu, Jianwen; Zhou, Qin; Fan, Jinjin; Mao, Haiping; Gale, Daniel; Barratt, Jonathan; Armour, John A L; Liu, Jianjun; Yu, Xueqing

2016-06-29

Although a major source of genetic variation, copy number variations (CNVs) and their involvement in disease development have not been well studied. Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. We performed association analysis of the DEFA1A3 CNV locus in two independent IgAN cohorts of southern Chinese Han (total of 1189 cases and 1187 controls). We discovered three independent copy number associations within the locus: DEFA1A3 [P = 3.99 × 10(-9); odds ratio (OR), 0.88], DEFA3 (P = 6.55 × 10(-5); OR, 0.82), and a noncoding deletion variant (211bp) (P = 3.50 × 10(-16); OR, 0.75) (OR per copy, fixed-effects meta-analysis). While showing strong association with an increased risk for IgAN (P = 9.56 × 10(-20)), low total copy numbers of the three variants also showed significant association with renal dysfunction in patients with IgAN (P = 0.03; hazards ratio, 3.69; after controlling for the effects of known prognostic factors) and also with increased serum IgA1 (P = 0.02) and galactose-deficient IgA1 (P = 0.03). For replication, we confirmed the associations of DEFA1A3 (P = 4.42 × 10(-4); OR, 0.82) and DEFA3 copy numbers (P = 4.30 × 10(-3); OR, 0.74) with IgAN in a Caucasian cohort (531 cases and 198 controls) and found the 211bp variant to be much rarer in Caucasians. We also observed an association of the 211bp copy number with membranous nephropathy (P = 1.11 × 10(-7); OR, 0.74; in 493 Chinese cases and 500 matched controls), but not with diabetic kidney disease (in 806 Chinese cases and 786 matched controls). By explaining 4.96% of disease risk and influencing renal dysfunction in patients with IgAN, the DEFA1A3 CNV locus may be a potential therapeutic target for developing treatments for this disease. Copyright © 2016, American Association for the Advancement of Science.

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

PubMed Central

Rigal, Mélanie; Becker, Claude; Pélissier, Thierry; Pogorelcnik, Romain; Devos, Jane; Ikeda, Yoko; Weigel, Detlef; Mathieu, Olivier

2016-01-01

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation. PMID:27001853

Molecular typing of monophasic Salmonella 4,[5]:i:- strains isolated in Belgium (2008-2011).

PubMed

Boland, Cécile; Bertrand, Sophie; Mattheus, Wesley; Dierick, Katelijne; Wattiau, Pierre

2014-01-31

To assess the distribution of Salmonella 4,[5]:i:- subtypes in the Belgian food chain and compare it to the subtypes associated with human infections, a molecular assessment was initiated. Two hundred fifty-three Salmonella isolates serotyped as 4,[5]:i:- during the period 2008-2011 in Belgium and originating from animal productions, food or human clinical samples were analysed by a specific duplex PCR. One hundred ninety-four isolates (76.7%) fit the profile of a S. Typhimurium monophasic variant as defined by the European Food Safety Authority. The other isolates possessed but did not express the phase II flagellin gene (23.3%). Multiple Locus Variable Number of Tandem Repeats Analysis (MLVA) revealed many but closely related profiles in the fljB-negative S. Typhimurium monophasic variant isolates. Some MLVA types were associated with both human and animal isolates but no unique source of human contamination could be demonstrated. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular characterization of Mycobacterium tuberculosis isolates from elephants of Nepal.

PubMed

Paudel, Sarad; Mikota, Susan K; Nakajima, Chie; Gairhe, Kamal P; Maharjan, Bhagwan; Thapa, Jeewan; Poudel, Ajay; Shimozuru, Michito; Suzuki, Yasuhiko; Tsubota, Toshio

2014-05-01

Mycobacterium tuberculosis was cultured from the lung tissues of 3 captive elephants in Nepal that died with extensive lung lesions. Spoligotyping, TbD1 detection and multi-locus variable number of tandem repeat analysis (MLVA) results suggested 3 isolates belonged to a specific lineage of Indo-Oceanic clade, EAI5 SIT 138. One of the elephant isolates had a new synonymous single nucleotide polymorphism (SNP) T231C in the gyrA sequence, and the same SNP was also found in human isolates in Nepal. MLVA results and transfer history of the elephants suggested that 2 of them might be infected with M. tuberculosis from the same source. These findings indicated the source of M. tuberculosis infection of those elephants were local residents, presumably their handlers. Further investigation including detailed genotyping of elephant and human isolates is needed to clarify the infection route and eventually prevent the transmission of tuberculosis to susceptible hosts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular typing of isolates obtained from aborted foetuses in Brucella-free Holstein dairy cattle herd after immunisation with Brucella abortus RB51 vaccine in Egypt.

PubMed

Wareth, Gamal; Melzer, Falk; Böttcher, Denny; El-Diasty, Mohamed; El-Beskawy, Mohamed; Rasheed, Nesma; Schmoock, Gernot; Roesler, Uwe; Sprague, Lisa D; Neubauer, Heinrich

2016-12-01

Bovine brucellosis is endemic in Egypt in spite of application of surveillance and control measures. An increase of abortions was reported in a Holstein dairy cattle herd with 600 animals in Damietta governorate in Egypt after immunisation with Brucella (B.) abortus RB51 vaccine. Twenty one (10.6%) of 197 vaccinated cows aborted after 3 months. All aborted cows had been tested seronegative for brucellosis in the past 3 years. B. abortus was isolated from four foetuses. Conventional biochemical and bacteriological identification and polymerase chain reaction (PCR) confirmed two B. abortus biovar (bv.) 1 smooth and two B. abortus rough strains. None of the B. abortus isolates were identified as RB51. Genotyping analysis by multiple locus of variable number tandem repeats analysis based on 16 markers (MLVA-16) revealed two different profiles with low genetic diversity. B. abortus bv1 was introduced in the herd and caused abortions. Copyright © 2016 Elsevier B.V. All rights reserved.

Tuberculosis Caused by Mycobacterium africanum, United States, 2004-2013.

PubMed

Sharma, Aditya; Bloss, Emily; Heilig, Charles M; Click, Eleanor S

2016-03-01

Mycobacterium africanum is endemic to West Africa and causes tuberculosis (TB). We reviewed reported cases of TB in the United States during 2004-2013 that had lineage assigned by genotype (spoligotype and mycobacterial interspersed repetitive unit variable number tandem repeats). M. africanum caused 315 (0.4%) of 73,290 TB cases with lineage assigned by genotype. TB caused by M. africanum was associated more with persons from West Africa (adjusted odds ratio [aOR] 253.8, 95% CI 59.9-1,076.1) and US-born black persons (aOR 5.7, 95% CI 1.2-25.9) than with US-born white persons. TB caused by M. africanum did not show differences in clinical characteristics when compared with TB caused by M. tuberculosis. Clustered cases defined as >2 cases in a county with identical 24-locus mycobacterial interspersed repetitive unit genotypes, were less likely for M. africanum (aOR 0.1, 95% CI 0.1-0.4), which suggests that M. africanum is not commonly transmitted in the United States.

Quantitative studies on the mating system of jute (Corchorus olitorius L.).

PubMed

Basak, S L; Gupta, S

1972-01-01

More than 100,000 individuals of C. olitorius were scored for selfing versus outcrossing in various populations, at several locations, over a number of years and seasons. Different marker loci, such as A (d) /a (0), Sh/sh, Cr/cr and Pl/pl, were used to determine the male gametes which had effected fertilization. The results showed that the frequency of outcrossing was extremely variable among loci, crosses and samples within a single locus. The outcrossing parameter, α, was found to differ with years, locations and seasons within years. It was also found that outcrossing, in general, was nonrandom. Nonrandomness was also independent of flowering dates. The amount of outcrossing was directly associated with the frequency of F 2 plants flowering at different dates. A recalculated outcrossing parameter from different authors' reported data, representing different years and locations, has been found to be nonrandom. It was observed that the propensity to outcross was not a simple function of changing gene frequency but was associated with the genotype of individual selected.

Genotypes of pathogenic Leptospira spp isolated from rodents in Argentina

PubMed Central

Loffler, Sylvia Grune; Pavan, Maria Elisa; Vanasco, Bibiana; Samartino, Luis; Suarez, Olga; Auteri, Carmelo; Romero, Graciela; Brihuega, Bibiana

2014-01-01

Leptospirosis is the most widespread zoonosis in the world and significant efforts have been made to determine and classify pathogenic Leptospira strains. This zoonosis is maintained in nature through chronic renal infections of carrier animals, with rodents and other small mammals serving as the most important reservoirs. Additionally, domestic animals, such as livestock and dogs, are significant sources of human infection. In this study, a multiple-locus variable-number tandem repeat analysis (MLVA) was applied to genotype 22 pathogenic Leptospira strains isolated from urban and periurban rodent populations from different regions of Argentina. Three MLVA profiles were identified in strains belonging to the species Leptospira interrogans (serovars Icterohaemorrhagiae and Canicola); one profile was observed in serovar Icterohaemorrhagiae and two MLVA profiles were observed in isolates of serovars Canicola and Portlandvere. All strains belonging to Leptospira borgpetersenii serovar Castellonis exhibited the same MLVA profile. Four different genotypes were isolated from urban populations of rodents, including both mice and rats and two different genotypes were isolated from periurban populations. PMID:24676656