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Sample records for genetically similar laboratory

  1. Authentication scheme for routine verification of genetically similar laboratory colonies: a trial with Anopheles gambiae

    Directory of Open Access Journals (Sweden)

    Sutcliffe Alice C

    2009-10-01

    Full Text Available Abstract Background When rearing morphologically indistinguishable laboratory strains concurrently, the threat of unintentional genetic contamination is constant. Avoidance of accidental mixing of strains is difficult due to the use of common equipment, technician error, or the possibility of self relocation by adult mosquitoes ("free fliers". In many cases, laboratory strains are difficult to distinguish because of morphological and genetic similarity, especially when laboratory colonies are isolates of certain traits from the same parental strain, such as eye color mutants, individuals with certain chromosomal arrangements or high levels of insecticide resistance. Thus, proving genetic integrity could seem incredibly time-consuming or impossible. On the other hand, lacking proof of genetically isolated laboratory strains could question the validity of research results. Results We present a method for establishing authentication matrices to routinely distinguish and confirm that laboratory strains have not become physically or genetically mixed through contamination events in the laboratory. We show a specific example with application to Anopheles gambiae sensu stricto strains at the Malaria Research and Reference Reagent Resource Center. This authentication matrix is essentially a series of tests yielding a strain-specific combination of results. Conclusion These matrix-based methodologies are useful for several mosquito and insect populations but must be specifically tailored and altered for each laboratory based on the potential contaminants available at any given time. The desired resulting authentication plan would utilize the least amount of routine effort possible while ensuring the integrity of the strains.

  2. Structural similarity of genetically interacting proteins

    Directory of Open Access Journals (Sweden)

    Nussinov Ruth

    2008-07-01

    Full Text Available Abstract Background The study of gene mutants and their interactions is fundamental to understanding gene function and backup mechanisms within the cell. The recent availability of large scale genetic interaction networks in yeast and worm allows the investigation of the biological mechanisms underlying these interactions at a global scale. To date, less than 2% of the known genetic interactions in yeast or worm can be accounted for by sequence similarity. Results Here, we perform a genome-scale structural comparison among protein pairs in the two species. We show that significant fractions of genetic interactions involve structurally similar proteins, spanning 7–10% and 14% of all known interactions in yeast and worm, respectively. We identify several structural features that are predictive of genetic interactions and show their superiority over sequence-based features. Conclusion Structural similarity is an important property that can explain and predict genetic interactions. According to the available data, the most abundant mechanism for genetic interactions among structurally similar proteins is a common interacting partner shared by two genetically interacting proteins.

  3. Similarity Arguments in the Genetic Modification Debate

    DEFF Research Database (Denmark)

    Christiansen, Andreas

    2017-01-01

    In the ethical debate on genetic modification (GM), it is common to encounter the claim that some anti-GM argument would also apply an established, ethically accepted technology, and that the anti-GM argument is therefore unsuccessful. The paper discusses whether this argumentative strategy...... transferability of reasons from one case to another; and (iii) it runs the risk of equivocations, especially in cases where the anti-genetic-modification argument relies on gradable features. The paper then shows how these issues play out in three specific Similarity Arguments that can be found in the literature....... Finally, the paper discusses what conclusions we can draw from the fact that genetic modification and established technologies are similar for the ethical status of genetic modification....

  4. Defining the role of laboratory genetic counselor.

    Science.gov (United States)

    Christian, Susan; Lilley, Margaret; Hume, Stacey; Scott, Patrick; Somerville, Martin

    2012-08-01

    An increasing number of genetic counselors are moving into non-clinical roles, where their primary duties do not involve direct patient contact. According to the National Society of Genetic Counselors Professional Status Survey in 2010, 23% of counselors working in non-clinical roles identified laboratory or genetic testing as their primary area of work. Using a survey, we identified 43 genetic counselors who work predominately in laboratory settings. The two primary tasks performed by participants, include acting as a customer liaison (95%) and calling out test results (88%). Nineteen participants (44.2%) also reported spending a considerable amount of time signing reports. The most prevalent areas of job satisfaction were support from laboratory directors (76.8%), autonomy (76.7%), interactions with clinicians (69.7%) and interaction with other genetics counselors (67.5%). This is the first study specifically looking at the roles of laboratory genetic counselors, which is an expanding area of genetic counseling.

  5. Mate choice and friendship in twins: evidence for genetic similarity.

    Science.gov (United States)

    Rushton, J Philippe; Bons, Trudy Ann

    2005-07-01

    This study examined the genetic and environmental contribution to people's preference for spouses and friends to be similar to themselves. In their responses to 130 personality, attitude, and demographic questions, 174 pairs of monozygotic (MZ) twins resembled each other (r= .53) more than did 148 pairs of dizygotic (DZ) twins (r= .32), 322 pairs of spouses (r= .32), and 563 pairs of best friends (r= .20). It was not previously recognized that spouses and friends are as similar as DZ twins. MZ twins also chose spouses and best friends more similar to their co-twins' friends and spouses than did DZ twins (mean rs = .22 vs. .14). The twins' preference for spouses and friends similar to themselves was about 34% due to the twins' genes, 12% due to the twins' common environment, and 54% due to the twins' unique (nonshared) environment. Similarity to partners was more pronounced on the more heritable items than the less heritable items. It is concluded that people are genetically inclined to choose as social partners those who resemble themselves at a genetic level.

  6. Perceived and actual similarities in biological and adoptive families: does perceived similarity bias genetic inferences?

    Science.gov (United States)

    Scarr, S; Scarf, E; Weinberg, R A

    1980-09-01

    Critics of the adoption method to estimate the relative effects of genetic and environmental differences on behavioral development claim that important biases are created by the knowledge of biological relatedness or adoptive status. Since the 1950s, agency policy has led to nearly all adopted children knowing that they are adopted. To test the hypothesis that knowledge of biological or adoptive status influences actual similarity, we correlated absolute differences in objective test scores with ratings of similarity by adolescents and their parents in adoptive and biological families. Although biological family members see themselves as more similar than adoptive family members, there are also important generational and gender differences in perceived similarity that cut across family type. There is moderate agreement among family members on the degree of perceived similarity, but there is no correlation between perceived and actual similarity in intelligence or temperament. However, family members are more accurate about shared social attitudes. Knowledge of adoptive or biological relatedness is related to the degree of perceived similarity, but perceptions of similarity are not related to objective similarities and thus do not constitute a bias in comparisons of measured differences in intelligence or temperament in adoptive and biological families.

  7. Skills training in laboratory and clerkship: connections, similarities, and differences

    Directory of Open Access Journals (Sweden)

    Berit Eika, MD, PhD

    2003-03-01

    Full Text Available Context: During the third semester of a 6 year long curriculum medical students train clinical skills in the skills laboratory (2 hours per week for 9 weeks as well as in an early, 8 week clinical clerkship at county hospitals. Objectives: to study students’ expectations and attitudes towards skills training in the skills laboratory and clerkship. Subjects: 126 medical students in their 3rd semester. Methods: During the fall of 2001 three consecutive, constructed questionnaires were distributed prior to laboratory training, following laboratory training but prior to clerkships, and following clerkships respectively. Results: Almost all (98% respondents found that training in skills laboratory improved the outcome of the early clerkship and 70% believed in transferability of skills from the laboratory setting to clerkship. Still, a majority (93% of students thought that the clerkship provided students with a better opportunity to learn clinical skills when compared to the skills laboratory. Skills training in laboratory as well as in clerkship motivated students for becoming doctors. Teachers in both settings were perceived as being committed to their teaching jobs, to demonstrate skills prior to practice, and to give students feed back with a small but significant more positive rating of the laboratory. Of the 22 skills that students had trained in the laboratory, a majority of students tried out skills associated with physical examination in the clerkship, whereas only a minority of students tried out more intimate skills. Female medical students tried significantly fewer skills during their clerkship compared to male students. Conclusions: Students believe that skills laboratory training prepare them for their subsequent early clerkship but favour the clerkship over the laboratory

  8. Learning, memory and exploratory similarities in genetically identical cloned dogs.

    Science.gov (United States)

    Shin, Chi Won; Kim, Geon A; Park, Won Jun; Park, Kwan Yong; Jeon, Jeong Min; Oh, Hyun Ju; Kim, Min Jung; Lee, Byeong Chun

    2016-12-30

    Somatic cell nuclear transfer allows generation of genetically identical animals using donor cells derived from animals with particular traits. To date, few studies have investigated whether or not these cloned dogs will show identical behavior patterns. To address this question, learning, memory and exploratory patterns were examined using six cloned dogs with identical nuclear genomes. The variance of total incorrect choice number in the Y-maze test among cloned dogs was significantly lower than that of the control dogs. There was also a significant decrease in variance in the level of exploratory activity in the open fields test compared to age-matched control dogs. These results indicate that cloned dogs show similar cognitive and exploratory patterns, suggesting that these behavioral phenotypes are related to the genotypes of the individuals.

  9. Laboratory Course on "Streptomyces" Genetics and Secondary Metabolism

    Science.gov (United States)

    Siitonen, Vilja; Räty, Kaj; Metsä-Ketelä, Mikko

    2016-01-01

    The "'Streptomyces' genetics and secondary metabolism" laboratory course gives an introduction to the versatile soil dwelling Gram-positive bacteria "Streptomyces" and their secondary metabolism. The course combines genetic modification of "Streptomyces"; growing of the strain and protoplast preparation, plasmid…

  10. Similarity

    Science.gov (United States)

    Apostol, Tom M. (Editor)

    1990-01-01

    In this 'Project Mathematics! series, sponsored by the California Institute for Technology (CalTech), the mathematical concept of similarity is presented. he history of and real life applications are discussed using actual film footage and computer animation. Terms used and various concepts of size, shape, ratio, area, and volume are demonstrated. The similarity of polygons, solids, congruent triangles, internal ratios, perimeters, and line segments using the previous mentioned concepts are shown.

  11. Learning, memory and exploratory similarities in genetically identical cloned dogs

    OpenAIRE

    Shin, Chi Won; Kim, Geon A; Park, Won Jun; Park, Kwan Yong; Jeon, Jeong Min; Oh, Hyun Ju; Kim, Min Jung; Lee, Byeong Chun

    2016-01-01

    Somatic cell nuclear transfer allows generation of genetically identical animals using donor cells derived from animals with particular traits. To date, few studies have investigated whether or not these cloned dogs will show identical behavior patterns. To address this question, learning, memory and exploratory patterns were examined using six cloned dogs with identical nuclear genomes. The variance of total incorrect choice number in the Y-maze test among cloned dogs was significantly lower...

  12. Escape from the laboratory: new horizons for plant genetics.

    Science.gov (United States)

    Rossetto, Maurizio; Henry, Robert J

    2014-09-01

    Next generation sequencing (NGS) is changing the way biologists work, as large amounts of genetic data can be easily outsourced commercially. Consequently, crucial research efforts in plant genetics can now be found outside the traditional laboratory setting, allowing for novel and more challenging scientific questions to be answered by virtual collaborative networks. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. The utilization of counseling skills by the laboratory genetic counselor.

    Science.gov (United States)

    Goodenberger, McKinsey L; Thomas, Brittany C; Wain, Karen E

    2015-02-01

    The number of available genetic testing options and the nuances associated with these options continue to expand. In addition, the scope of genetic testing has broadened to areas and specialties beyond Medical Genetics. In response to these changes, diagnostic laboratories have employed genetic counselors to help navigate the increasing complexity of genetic testing, given their expertise and training in human genetics. However a largely unrecognized aspect of this role involves the use of counseling skills. Counseling skills are used by laboratory genetic counselors in a variety of situations to convey information and facilitate understanding among clinicians and medical staff. This helps to reduce test ordering errors, promote optimal test utilization, and ensure best patient care practices. The specific counseling skills used by laboratory counselors will be explored using three fictional case vignettes, followed by a discussion of the applicability of these skills in other contexts. Exploration of the unique ways in which laboratory genetic counselors apply their counseling skills can be useful for professional development and instructive for graduate training programs.

  14. European registration process for Clinical Laboratory Geneticists in genetic healthcare

    OpenAIRE

    Liehr, Thomas; Carreira, Isabel M.; Aktas, Dilek; Bakker, Egbert; Rodr?guez de Alba, Marta; Coviello, Domenico A; Florentin, Lina; Scheffer, Hans; Rincic, Martina

    2017-01-01

    Tremendous progress in genetics and genomics led to a wide range of healthcare providers, genetic tests, and more patients who can benefit from these developments. To guarantee and improve the quality of genetic testing, a unified European-based registration for individuals qualified in biomedicine was realized. Therefore a Europe-wide recognition of the profession ?European registered Clinical Laboratory Geneticist (ErCLG)' based on a syllabus of core competences was established which allows...

  15. Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird

    Science.gov (United States)

    Mulard, Hervé; Danchin, E.; Talbot, S.L.; Ramey, A.M.; Hatch, Shyla A.; White, J.F.; Helfenstein, F.; Wagner, R.H.

    2009-01-01

    Background. Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results. Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i) genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii) offspring heterozygosity was positively correlated with growth rate and survival. Conclusion. These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure. ?? 2009 Mulard et al; licensee BioMed Central Ltd.

  16. Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird

    Directory of Open Access Journals (Sweden)

    Ramey Andrew M

    2009-06-01

    Full Text Available Abstract Background Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii offspring heterozygosity was positively correlated with growth rate and survival. Conclusion These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure.

  17. Genetic Algorithm-Based Relevance Feedback for Image Retrieval Using Local Similarity Patterns.

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    Stejic, Zoran; Takama, Yasufumi; Hirota, Kaoru

    2003-01-01

    Proposes local similarity pattern (LSP) as a new method for computing digital image similarity. Topics include optimizing similarity computation based on genetic algorithm; relevance feedback; and an evaluation of LSP on five databases that showed an increase in retrieval precision over other methods for computing image similarity. (Author/LRW)

  18. Further Defining the Role of the Laboratory Genetic Counselor.

    Science.gov (United States)

    Waltman, Lindsey; Runke, Cassandra; Balcom, Jessica; Riley, Jacquelyn D; Lilley, Margaret; Christian, Susan; Zetzsche, Lindsay; Goodenberger, McKinsey L

    2016-08-01

    Laboratory genetic counseling is becoming increasingly common as a result of increased laboratory services and genetic testing menus, as well as growing job responsibilities. Christian et al. (2012) provided the first quantitative data regarding the roles of the laboratory-based genetic counselor (LBGC) finding that two of the most prevalent roles are as customer liaisons and communicators of test results. The goal of the present study was to further delineate the role of the LBGC by addressing specific tasks that LBGCs are involved with on a day-to-day basis. A survey was designed to expand upon themes identified in the Christian et al. (2012) study by querying specific tasks performed in several categories of potential LBGC job duties. An invitation for LBGCs to participate was distributed via email to the membership of the National Society of Genetic Counselors (NSGC) and the Canadian Association of Genetic Counsellors (CAGC). We identified 121 genetic counselors who primarily work in the laboratory setting or whose job role includes a laboratory component. Almost all respondents performed customer liaison/case coordination (95 %), and interpretation and result reporting (88 %). The most frequently performed tasks within these categories involved addressing questions from clients, making phone calls with genetic testing results, obtaining clinical or family history information for results interpretation, and composing case-specific interpretations for unique results and/or obtaining literature references to support interpretations. The study results also point to trends of expanding roles in sales and marketing, variant interpretation and management responsibilities. Results of this study may be useful to further define the full scope of practice of LBGCs, aid in the development of new LBGC positions and expand current positions to include roles related to test development, research, and student supervision. It may also aid in curriculum updates for training

  19. European registration process for Clinical Laboratory Geneticists in genetic healthcare.

    Science.gov (United States)

    Liehr, Thomas; Carreira, Isabel M; Aktas, Dilek; Bakker, Egbert; Rodríguez de Alba, Marta; Coviello, Domenico A; Florentin, Lina; Scheffer, Hans; Rincic, Martina

    2017-05-01

    Tremendous progress in genetics and genomics led to a wide range of healthcare providers, genetic tests, and more patients who can benefit from these developments. To guarantee and improve the quality of genetic testing, a unified European-based registration for individuals qualified in biomedicine was realized. Therefore a Europe-wide recognition of the profession 'European registered Clinical Laboratory Geneticist (ErCLG)' based on a syllabus of core competences was established which allows for harmonization in professional education. The 'European Board of Medical Genetics division - Clinical Laboratory Geneticist' provides now since 3 years the possibility to register as an ErCLG. Applicants may be from all European countries and since this year also from outside of Europe. Five subtitles reflect the exact specialty of each ErCLG, who can reregister every 5 years. A previously not possible statistics based on ~300 individuals from 19 countries as holders of an ErCLG title provides interesting insights into the professionals working in human genetics. It could be substantiated that there are around twice as many females than males and that a PhD title was achieved by 80% of registered ErCLGs. Also most ErCLGs are still trained as generalists (66%), followed by such ErCLGs with focus on molecular genetics (23%); the remaining are concentrated either on clinical (6%), tumor (4%) or biochemical genetics (1%). In conclusion, besides MDs and genetic counselors/nurses an EU-wide recognition system for Clinical Laboratory Geneticist has been established, which strengthens the status of specialists working in human genetic diagnostics in Europe and worldwide.

  20. Genetics and molecular biology in laboratory medicine, 1963-2013.

    Science.gov (United States)

    Whitfield, John B

    2013-01-01

    The past 50 years have seen many changes in laboratory medicine, either as causes or consequences of increases in productivity and expansion of the range of information which can be provided. The drivers and facilitators of change in relation to clinical applications of molecular biology included the need for diagnostic tools for genetic diseases and technical advances such as PCR and sequencing. However, molecular biology techniques have proved to have far wider applications, from detection of infectious agents to molecular characterization of tumors. Journals such as Clinical Chemistry and Laboratory Medicine play an important role in communication of these advances to the laboratory medicine community and in publishing evaluations of their practical value.

  1. Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

    Science.gov (United States)

    Johnson, Ronald; Kennon, Tillman

    2009-01-01

    Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

  2. Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

    Science.gov (United States)

    Johnson, Ronald; Kennon, Tillman

    2009-01-01

    Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

  3. Living in a Genetic World: How Learning About Interethnic Genetic Similarities and Differences Affects Peace and Conflict.

    Science.gov (United States)

    Kimel, Sasha Y; Huesmann, Rowell; Kunst, Jonas R; Halperin, Eran

    2016-05-01

    Information about the degree of one's genetic overlap with ethnic outgroups has been emphasized in genocides, is frequently learned about through media reporting, and is increasingly being accessed via personal genetic testing services. However, the consequence of learning about whether your own ethnic group is either genetically related to or genetically distinct from a disliked ethnic group remains unknown. Across four experiments, using diverse samples, measures and contexts, we demonstrate that altering perceptions of genetic overlap between groups in conflict--in this case Arabs and Jews--impacts factors that are directly related to interethnic hostility (e.g., aggressive behaviors, support of conflict-related policies). Our findings indicate that learning about the genetic difference between oneself and an ethnic outgroup may contribute to the promotion of violence, whereas learning about the similarities may be a vital step toward fostering peace in some contexts. Possible interventions and implications are discussed. © 2016 by the Society for Personality and Social Psychology, Inc.

  4. The importance and value of EQA for diagnostic genetic laboratories.

    Science.gov (United States)

    Hastings, Ros J; Howell, Rod T

    2010-03-01

    Quality control in a laboratory setting requires the establishment of effective training, standard operating procedures, internal quality control, validation of tests and external quality assessment (EQA). A structured quality management system subject to regular internal and external audits will minimise the error rate. EQA, therefore, gives assurance, both to patients and referring clinicians, that the diagnostic laboratory is competent to produce results that are reliable and accurate. EQA is educational and aims to improve and validate the overall quality of genetic service to the user. Regular EQA assessment compares laboratory performance against set standards and also allows comparison between laboratories. Sometimes EQA can also help to define good standards (best practice), although this does depend on the type of EQA test. EQA interprets best practice standards (=quality) into a numerical score (=quantity). While international bodies or professional organisations set these standards, EQA is able to assess whether these standards are met, with any omissions resulting in a reduction in the total score. Although EQA has an educational role rather than a punitive role, critical errors affecting clinical management will result in a laboratory receiving a poor performance categorisation. Accurate analysis and interpretation are essential quality parameters that require extensive knowledge of the aetiology of genetic abnormalities/disease and risk factors. Training of staff in interpretation of the results together with a comprehensive means of reporting normal and abnormal genetic results underpins the diagnostic service to the patient. Poor-performing laboratories are, therefore, encouraged to review their internal processes. EQA schemes that have been established for many years have seen improvements in the analytical and reporting content over time, thereby improving the quality of diagnostic service available to patients.

  5. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences.

    Science.gov (United States)

    Othman, Razib M; Deris, Safaai; Illias, Rosli M

    2008-02-01

    A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search space of the Gene Ontology graph. The genetic similarity algorithm is implemented in the Gene Ontology browser named basic UTMGO to overcome the weaknesses of the existing Gene Ontology browsers which use a conventional approach based on keyword matching. To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO. The objective of developing the extended UTMGO is to provide a simple and practical tool that is capable of producing better results and requires a reasonable amount of running time with low computing cost specifically for offline usage. The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools.

  6. The genetic basis of laboratory adaptation in Caulobacter crescentus.

    Science.gov (United States)

    Marks, Melissa E; Castro-Rojas, Cyd Marie; Teiling, Clotilde; Du, Lei; Kapatral, Vinayak; Walunas, Theresa L; Crosson, Sean

    2010-07-01

    The dimorphic bacterium Caulobacter crescentus has evolved marked phenotypic changes during its 50-year history of culture in the laboratory environment, providing an excellent system for the study of natural selection and phenotypic microevolution in prokaryotes. Combining whole-genome sequencing with classical molecular genetic tools, we have comprehensively mapped a set of polymorphisms underlying multiple derived phenotypes, several of which arose independently in separate strain lineages. The genetic basis of phenotypic differences in growth rate, mucoidy, adhesion, sedimentation, phage susceptibility, and stationary-phase survival between C. crescentus strain CB15 and its derivative NA1000 is determined by coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. This study evidences multiple genetic mechanisms of bacterial evolution as driven by selection for growth and survival in a new selective environment and identifies a common polymorphic locus, zwf, between lab-adapted C. crescentus and clinical isolates of Pseudomonas aeruginosa that have adapted to a human host during chronic infection.

  7. Genetic Analyses in Health Laboratories: Current Status and Expectations

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    Finotti, Alessia; Breveglieri, Giulia; Borgatti, Monica; Gambari, Roberto

    Genetic analyses performed in health laboratories involve adult patients, newborns, embryos/fetuses, pre-implanted pre-embryos, pre-fertilized oocytes and should meet the major medical needs of hospitals and pharmaceutical companies. Recent data support the concept that, in addition to diagnosis and prognosis, genetic analyses might lead to development of personalized therapy. Novel frontiers in genetic testing involve the development of single cell analyses and non-invasive assays, including those able to predict outcome of cancer pathologies by looking at circulating tumor cells, DNA, mRNA and microRNAs. In this respect, PCR-free diagnostics appears to be one of the most interesting and appealing approaches.

  8. Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes.

    Science.gov (United States)

    Melamed, Rachel D; Emmett, Kevin J; Madubata, Chioma; Rzhetsky, Andrey; Rabadan, Raul

    2015-04-30

    Despite large-scale cancer genomics studies, key somatic mutations driving cancer, and their functional roles, remain elusive. Here, we propose that analysis of comorbidities of Mendelian diseases with cancers provides a novel, systematic way to discover new cancer genes. If germline genetic variation in Mendelian loci predisposes bearers to common cancers, the same loci may harbour cancer-associated somatic variation. Compilations of clinical records spanning over 100 million patients provide an unprecedented opportunity to assess clinical associations between Mendelian diseases and cancers. We systematically compare these comorbidities against recurrent somatic mutations from more than 5,000 patients across many cancers. Using multiple measures of genetic similarity, we show that a Mendelian disease and comorbid cancer indeed have genetic alterations of significant functional similarity. This result provides a basis to identify candidate drivers in cancers including melanoma and glioblastoma. Some Mendelian diseases demonstrate 'pan-cancer' comorbidity and shared genetics across cancers.

  9. Genetic similarity of island populations of tent caterpillars during successive outbreaks.

    Directory of Open Access Journals (Sweden)

    Michelle T Franklin

    Full Text Available Cyclic or fluctuating populations experience regular periods of low population density. Genetic bottlenecks during these periods could give rise to temporal or spatial genetic differentiation of populations. High levels of movement among increasing populations, however, could ameliorate any differences and could also synchronize the dynamics of geographically separated populations. We use microsatellite markers to investigate the genetic differentiation of four island and one mainland population of western tent caterpillars, Malacosoma californicum pluviale, in two periods of peak or pre-peak density separated by 8 years. Populations showed high levels of genetic variation and little genetic differentiation either temporally between peaks or spatially among sites. Mitochondrial haplotypes were also shared between one island population and one mainland population in the two years studied. An isolation-by-distance analysis showed the FST values of the two geographically closest populations to have the highest level of differentiation in both years. We conclude that high levels of dispersal among populations maintain both synchrony of population dynamics and override potential genetic differentiation that might occur during population troughs. As far we are aware, this is the first time that genetic similarity between temporally separated population outbreaks in insects has been investigated. A review of genetic data for both vertebrate and invertebrate species of cyclic animals shows that a lack of spatial genetic differentiation is typical, and may result from high levels of dispersal associated with fluctuating dynamics.

  10. Genetic similarity of island populations of tent caterpillars during successive outbreaks.

    Science.gov (United States)

    Franklin, Michelle T; Myers, Judith H; Cory, Jenny S

    2014-01-01

    Cyclic or fluctuating populations experience regular periods of low population density. Genetic bottlenecks during these periods could give rise to temporal or spatial genetic differentiation of populations. High levels of movement among increasing populations, however, could ameliorate any differences and could also synchronize the dynamics of geographically separated populations. We use microsatellite markers to investigate the genetic differentiation of four island and one mainland population of western tent caterpillars, Malacosoma californicum pluviale, in two periods of peak or pre-peak density separated by 8 years. Populations showed high levels of genetic variation and little genetic differentiation either temporally between peaks or spatially among sites. Mitochondrial haplotypes were also shared between one island population and one mainland population in the two years studied. An isolation-by-distance analysis showed the FST values of the two geographically closest populations to have the highest level of differentiation in both years. We conclude that high levels of dispersal among populations maintain both synchrony of population dynamics and override potential genetic differentiation that might occur during population troughs. As far we are aware, this is the first time that genetic similarity between temporally separated population outbreaks in insects has been investigated. A review of genetic data for both vertebrate and invertebrate species of cyclic animals shows that a lack of spatial genetic differentiation is typical, and may result from high levels of dispersal associated with fluctuating dynamics.

  11. On similarity of wind-waves spectral shapes in laboratory and in ocean

    Science.gov (United States)

    Shemer, Lev; Zavadsky, Andrey; Liberzon, Dan

    2012-11-01

    Wind-wave field evolving in a compact laboratory facility that consists of a wind tunnel capable of generating wind speed that may exceed 15 m/s atop of a 5 m long wave tank is studied. Surface elevation measurements were carried out at numerous positions along the test section and at different mean wind flow rates. For each experimental condition, the accumulated records were long enough to contain at least O(104) dominant waves; the wave power spectra computed from the recorded time series cover up to 5 decades. Similarity of the spectral shapes in the vicinity of the peak frequency fp obtained at various fetches and wind conditions was observed. This similarity manifests itself when normalized frequency deviation from the peak value is introduced. Detailed comparison is carried out of spectra obtained in the present measurements at all fetches and wind conditions, to the similarly normalized JONSWAP spectrum that represents field experiments. When estimating spectral tail behavior, care was taken to consider frequencies exceeding about 3.5fp to alleviate the effect of bound waves. The spectral tails dependence on frequency follows the power law f-n; the values of nbeing in the range 3 < n < 4 , depending on wave age. It thus can be concluded that the spectra of wind-waves in a small facility exhibit significant similarities to those obtained in field studies at much larger scales, as well as to theoretical estimates.

  12. Laboratory course on Streptomyces genetics and secondary metabolism.

    Science.gov (United States)

    Siitonen, Vilja; Räty, Kaj; Metsä-Ketelä, Mikko

    2016-09-10

    The "Streptomyces genetics and secondary metabolism" laboratory course gives an introduction to the versatile soil dwelling Gram-positive bacteria Streptomyces and their secondary metabolism. The course combines genetic modification of Streptomyces; growing of the strain and protoplast preparation, plasmid isolation by alkaline lysis and phenol precipitation, digestions, and ligations prior to protoplast transformation, as well as investigating the secondary metabolites produced by the strains. Thus, the course is a combination of microbiology, molecular biology, and chemistry. After the course the students should understand the relationship between genes, proteins, and the produced metabolites. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):492-499, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  13. The Genetic Counselor's Role in Managing Ethical Dilemmas Arising in the Laboratory Setting.

    Science.gov (United States)

    Balcom, Jessica R; Kotzer, Katrina E; Waltman, Lindsey A; Kemppainen, Jennifer L; Thomas, Brittany C

    2016-10-01

    Ethical dilemmas are encountered commonly in the setting of the clinical genetic testing laboratory due to the complexity of genetic testing and the number of relevant stakeholders involved in the genetic testing process. Based on their clinical training and role within the laboratory, genetic counselors are uniquely equipped to identify and facilitate management of ethical dilemmas. This paper reviews the historical context of ethical theory and its application to the field of genetic counseling. Theoretical and applied ethics are explored in the context of dilemmas arising in the laboratory setting, with a focus on the role of the laboratory genetic counselor in managing ethical dilemmas. Two illustrative case examples are provided.

  14. Looking back and moving forward: an historical perspective from laboratory genetic counselors.

    Science.gov (United States)

    Zetzsche, Lindsay H; Kotzer, Katrina E; Wain, Karen E

    2014-06-01

    Despite a consistent increase in genetic counselors who report working in laboratory positions, there is a relative dearth of literature on laboratory genetic counseling. Semi-structured interviews were completed with nine laboratory genetic counselors to document how positions were created and have changed with time. Interview transcriptions were analyzed for emerging themes. Several common themes were identified, including that early positions were often part-time, laboratory-initiated and had a lack of job definition. Laboratory genetic counselors commented on their evolving roles and responsibilities, with their positions becoming more technical and specialized over time and many taking on managerial and supervisory roles. All genetic counselors surveyed reported using core genetic counseling skills in their positions. The expansion of diagnostic testing and quickly evolving technology were common themes in regards to the future of laboratory genetic counselors, and participants commented on laboratory genetic counselors having expanding roles with data management, result interpretation and reporting, and guidance of other healthcare providers. Other comments included the impact of competition among laboratories and how training programs can better prepare genetic counseling students for a career in the laboratory setting. This study describes the emergence, and subsequent evolution, of laboratory genetic counseling positions as a significant subspecialty of genetic counseling.

  15. Lignocellulolytic mutants of Pleurotus ostreatus induced by gamma-ray radiation and their genetic similarities

    Science.gov (United States)

    Lee, Y.-K.; Chang, H.-H.; Kim, J.-S.; Kim, J. K.; Lee, K.-S.

    2000-02-01

    To induce the lignocellulolytic mutants of Pleurotus ostreatus, the mycelia were irradiated by gamma-ray radiation to doses of 1-2 kGy. Five strains were isolated by the criteria of clamp connection, fruiting body formation, growth rate and activities of extracellular enzymes. All isolated strains were able to form the fruiting bodies and grew similarly to the control. The extracellular enzymes activities in liquid media of isolated strains were up to 10 times higher than the control. Genetic similarities of the isolated strains ranged from 64.4% to 93.3% of the control. From these results, it seems that the genetic diversity of P. ostreatus could be changed and useful strains be induced by gamma-ray radiation to recycle or reuse biowastes.

  16. Lignocellulolytic mutants of Pleurotus ostreatus induced by gamma-ray radiation and their genetic similarities

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y-K. E-mail: yklee@nanum.kaeri.re.kr; Chang, H-H.; Kim, J-S.; Kim, J.K.; Lee, K-S

    2000-02-01

    To induce the lignocellulolytic mutants of Pleurotus ostreatus, the mycelia were irradiated by gamma-ray radiation to doses of 1-2 kGy. Five strains were isolated by the criteria of clamp connection, fruiting body formation, growth rate and activities of extracellular enzymes. All isolated strains were able to form the fruiting bodies and grew similarly to the control. The extracellular enzymes activities in liquid media of isolated strains were up to 10 times higher than the control. Genetic similarities of the isolated strains ranged from 64.4% to 93.3% of the control. From these results, it seems that the genetic diversity of P. ostreatus could be changed and useful strains be induced by gamma-ray radiation to recycle or reuse biowastes. (author)

  17. Dispersal similarly shapes both population genetics and community patterns in the marine realm

    KAUST Repository

    Chust, Guillem

    2016-06-27

    Dispersal plays a key role to connect populations and, if limited, is one of the main processes to maintain and generate regional biodiversity. According to neutral theories of molecular evolution and biodiversity, dispersal limitation of propagules and population stochasticity are integral to shaping both genetic and community structure. We conducted a parallel analysis of biological connectivity at genetic and community levels in marine groups with different dispersal traits. We compiled large data sets of population genetic structure (98 benthic macroinvertebrate and 35 planktonic species) and biogeographic data (2193 benthic macroinvertebrate and 734 planktonic species). We estimated dispersal distances from population genetic data (i.e., FST vs. geographic distance) and from β-diversity at the community level. Dispersal distances ranked the biological groups in the same order at both genetic and community levels, as predicted by organism dispersal ability and seascape connectivity: macrozoobenthic species without dispersing larvae, followed by macrozoobenthic species with dispersing larvae and plankton (phyto- and zooplankton). This ranking order is associated with constraints to the movement of macrozoobenthos within the seabed compared with the pelagic habitat. We showed that dispersal limitation similarly determines the connectivity degree of communities and populations, supporting the predictions of neutral theories in marine biodiversity patterns.

  18. Similarity in recombination rate estimates highly correlates with genetic differentiation in humans.

    Directory of Open Access Journals (Sweden)

    Hafid Laayouni

    Full Text Available Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans.

  19. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    Rafael Gustavo Ferreira Morales

    2011-12-01

    Full Text Available Most strawberry (Fragaria × ananassa Duchesne cultivars used in Brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. To start a breeding program is necessary the genetic characterization of the germplasm available. Molecular markers are important tools that can be used for this purpose. The objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using RAPD and ISSR molecular markers and to indicate the possible promising crosses. The DNA of the eleven strawberry cultivars was extracted and amplified by PCR with RAPD and ISSR primers. The DNA fragments were separated in agarose gel for the RAPD markers and in polyacrylamide gel for the ISSR markers. The genetic similarity matrix was estimated by the Jaccard coefficient. Based on this matrix, the cultivars were grouped using the UPGMA method. The dendogram generated by the RAPD markers distributed the cultivars in three groups while the ISSR markers generated two groups. There was no direct relationship between the marker groups when the two types of markers were compared. The grouping proposed by the ISSR markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the RAPD markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. The most promising crosses, based on the genetic divergence estimated from the RAPD and ISSR molecular data were between the Tudla and Ventana and the Oso Grande and Ventana cultivars, respectively.

  20. Genetic Similarities between Compulsive Overeating and Addiction Phenotypes: A Case for "Food Addiction"?

    Science.gov (United States)

    Carlier, Nina; Marshe, Victoria S; Cmorejova, Jana; Davis, Caroline; Müller, Daniel J

    2015-12-01

    There exists a continuous spectrum of overeating, where at the extremes there are casual overindulgences and at the other a 'pathological' drive to consume palatable foods. It has been proposed that pathological eating behaviors may be the result of addictive appetitive behavior and loss of ability to regulate the consumption of highly processed foods containing refined carbohydrates, fats, salt, and caffeine. In this review, we highlight the genetic similarities underlying substance addiction phenotypes and overeating compulsions seen in individuals with binge eating disorder. We relate these similarities to findings from neuroimaging studies on reward processing and clinical diagnostic criteria based on addiction phenotypes. The abundance of similarities between compulsive overeating and substance addictions puts forth a case for a 'food addiction' phenotype as a valid, diagnosable disorder.

  1. Evidence for multiple genetic forms with similar eyeless phenotypes in the blind cavefish, Astyanax mexicanus.

    Science.gov (United States)

    Dowling, Thomas E; Martasian, David P; Jeffery, William R

    2002-04-01

    A diverse group of animals has adapted to caves and lost their eyes and pigmentation, but little is known about how these animals and their striking phenotypes have evolved. The teleost Astyanax mexicanus consists of an eyed epigean form (surface fish) and at least 29 different populations of eyeless hypogean forms (cavefish). Current alternative hypotheses suggest that adaptation to cave environments may have occurred either once or multiple times during the evolutionary history of this species. If the latter is true, the unique phenotypes of different cave-dwelling populations may result from convergence of form, and different genetic changes and developmental processes may have similar morphological consequences. Here we report an analysis of variation in the mitochondrial NADH dehydrogenase 2 (ND2) gene among different surface fish and cavefish populations. The results identify a minimum of two genetically distinctive cavefish lineages with similar eyeless phenotypes. The distinction between these divergent forms is supported by differences in the number of rib-bearing thoracic vertebrae in their axial skeletons. The geographic distribution of ND2 haplotypes is consistent with roles for multiple founder events and introgressive hybridization in the evolution of cave-related phenotypes. The existence of multiple genetic lineages makes A. mexicanus an excellent model to study convergence and the genes and developmental pathways involved in the evolution of the eye and pigment degeneration.

  2. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

    Science.gov (United States)

    Hoehndorf, Robert; Schofield, Paul N.; Gkoutos, Georgios V.

    2015-06-01

    Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

  3. Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

    KAUST Repository

    Hoehndorf, Robert

    2015-06-08

    Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

  4. Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4.

    Science.gov (United States)

    Dyson, Zoe A; Tucci, Joseph; Seviour, Robert J; Petrovski, Steve

    2015-10-01

    Three Tsukamurella phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these Siphoviridae viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described Gordonia phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of Siphoviridae phages. All three phages appeared highly virulent on strains of Tsukamurella inchonensis and Tsukamurella paurometabola. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast.

    Directory of Open Access Journals (Sweden)

    Ben Lehner

    Full Text Available Gene inactivation often has little or no apparent consequence for the phenotype of an organism. This property-enetic (or mutational robustness-is pervasive, and has important implications for disease and evolution, but is not well understood. Dating back to at least Waddington, it has been suggested that mutational robustness may be related to the requirement to withstand environmental or stochastic perturbations. Here I show that global quantitative data from yeast are largely consistent with this idea. Considering the effects of mutations in all nonessential genes shows that genes that confer robustness to environmental or stochastic change also buffer the effects of genetic change, and with similar efficacy. This means that selection during evolution for environmental or stochastic robustness (also referred to as canalization may frequently have the side effect of increasing genetic robustness. A dynamic environment may therefore promote the evolution of phenotypic complexity. It also means that "hub" genes in genetic interaction (synthetic lethal networks are generally genes that confer environmental resilience and phenotypic stability.

  6. Phylogeny and prediction of genetic similarity of Cronobacter and related taxa by multilocus sequence analysis (MLSA).

    Science.gov (United States)

    Kuhnert, Peter; Korczak, Bozena M; Stephan, Roger; Joosten, Han; Iversen, Carol

    2009-12-31

    Multilocus sequence analysis (MLSA) based on recN, rpoA and thdF genes was done on more than 30 species of the family Enterobacteriaceae with a focus on Cronobacter and the related genus Enterobacter. The sequences provide valuable data for phylogenetic, taxonomic and diagnostic purposes. Phylogenetic analysis showed that the genus Cronobacter forms a homogenous cluster related to recently described species of Enterobacter, but distant to other species of this genus. Combining sequence information on all three genes is highly representative for the species' %GC-content used as taxonomic marker. Sequence similarity of the three genes and even of recN alone can be used to extrapolate genetic similarities between species of Enterobacteriaceae. Finally, the rpoA gene sequence, which is the easiest one to determine, provides a powerful diagnostic tool to identify and differentiate species of this family. The comparative analysis gives important insights into the phylogeny and genetic relatedness of the family Enterobacteriaceae and will serve as a basis for further studies and clarifications on the taxonomy of this large and heterogeneous family.

  7. Genetically modified laboratory mice with sebaceous glands abnormalities.

    Science.gov (United States)

    Ehrmann, Carmen; Schneider, Marlon R

    2016-12-01

    Sebaceous glands (SG) are exocrine glands that release their product by holocrine secretion, meaning that the whole cell becomes a secretion following disruption of the membrane. SG may be found in association with a hair follicle, forming the pilosebaceous unit, or as modified SG at different body sites such as the eyelids (Meibomian glands) or the preputial glands. Depending on their location, SG fulfill a number of functions, including protection of the skin and fur, thermoregulation, formation of the tear lipid film, and pheromone-based communication. Accordingly, SG abnormalities are associated with several diseases such as acne, cicatricial alopecia, and dry eye disease. An increasing number of genetically modified laboratory mouse lines develop SG abnormalities, and their study may provide important clues regarding the molecular pathways regulating SG development, physiology, and pathology. Here, we summarize in tabulated form the available mouse lines with SG abnormalities and, focusing on selected examples, discuss the insights they provide into SG biology and pathology. We hope this survey will become a helpful information source for researchers with a primary interest in SG but also as for researchers from unrelated fields that are unexpectedly confronted with a SG phenotype in newly generated mouse lines.

  8. Studying human disease genes in Caenorhabditis elegans: a molecular genetics laboratory project.

    Science.gov (United States)

    Cox-Paulson, Elisabeth A; Grana, Theresa M; Harris, Michelle A; Batzli, Janet M

    2012-01-01

    Scientists routinely integrate information from various channels to explore topics under study. We designed a 4-wk undergraduate laboratory module that used a multifaceted approach to study a question in molecular genetics. Specifically, students investigated whether Caenorhabditis elegans can be a useful model system for studying genes associated with human disease. In a large-enrollment, sophomore-level laboratory course, groups of three to four students were assigned a gene associated with either breast cancer (brc-1), Wilson disease (cua-1), ovarian dysgenesis (fshr-1), or colon cancer (mlh-1). Students compared observable phenotypes of wild-type C. elegans and C. elegans with a homozygous deletion in the assigned gene. They confirmed the genetic deletion with nested polymerase chain reaction and performed a bioinformatics analysis to predict how the deletion would affect the encoded mRNA and protein. Students also performed RNA interference (RNAi) against their assigned gene and evaluated whether RNAi caused a phenotype similar to that of the genetic deletion. As a capstone activity, students prepared scientific posters in which they presented their data, evaluated whether C. elegans was a useful model system for studying their assigned genes, and proposed future directions. Assessment showed gains in understanding genotype versus phenotype, RNAi, common bioinformatics tools, and the utility of model organisms.

  9. Genetic Similarity Assessment among Selected Naked Oat Cultivars and Breeding Lines Using ISSR Markers

    Directory of Open Access Journals (Sweden)

    Edyta PACZOS-GRZEDA

    2014-06-01

    Full Text Available Naked oat refers to a variety of Avena sativa with lemma and palea separating from the grains. Its spikelets are multiflorous and morphologically different from the husked oat. Problems with preharvest sprouting, threshability, rancidity, a wide range of kernel sizes, as well as its relatively low tolerance to limited soil water content, are its main drawbacks. Nevertheless it could be an alternative to a conventional oat. Unfortunately, its genetic variation is still poorly recognized.  In the given study a set of 26 naked oat cultivars and lines were analyzed with 25 inter-simple sequence repeats (ISSR primers that amplified as many as 429 DNA fragments among which 204 were polymorphic. The average number of markers amplified per primer pair and polymorphism information content (PIC value equaled to eight and 0.23, respectively. Forty four unique PCR products were identified for different genotypes. While Unweighted Pair-Group Method with Arithmetic Mean failed to distinguish the materials into main clusters it demonstrated that cultivars ‘Akt’, ‘Polar’, ‘Cacko’, ‘Siwek’, ‘Nagus’ and most of the DC lines were within a single group. Moreover, the cultivars that were closely related based on their breeding pedigree (related to ‘Akt’ were close to each other. Principal Coordinate Analysis explained 54.1% of variance and was in good agreement with the UPGMA. ISSR markers could be used for the evaluation of genetic similarity of cultivars and lines as well as the differentiation of individual genotypes. This study demonstrated that the available A. sativa naked type genetic pool is relatively wide and have the potential for further breeding progress.

  10. European registration process for Clinical Laboratory Geneticists in genetic healthcare

    NARCIS (Netherlands)

    Liehr, T.; Carreira, I.M.; Aktas, D.; Bakker, E. de; Rodriguez de Alba, M.; Coviello, D.A.; Florentin, L.; Scheffer, H.; Rincic, M.

    2017-01-01

    Tremendous progress in genetics and genomics led to a wide range of healthcare providers, genetic tests, and more patients who can benefit from these developments. To guarantee and improve the quality of genetic testing, a unified European-based registration for individuals qualified in biomedicine

  11. Feral Pigeons (Columba livia) Prefer Genetically Similar Mates despite Inbreeding Depression.

    Science.gov (United States)

    Jacob, Gwenaël; Prévot, Anne-Caroline; Baudry, Emmanuelle

    2016-01-01

    Avoidance of mating between related individuals is usually considered adaptive because it decreases the probability of inbreeding depression in offspring. However, mating between related partners can be adaptive if outbreeding depression is stronger than inbreeding depression or if females gain inclusive fitness benefits by mating with close kin. In the present study, we used microsatellite data to infer the parentage of juveniles born in a French colony of feral pigeons, which allowed us to deduce parent pairs. Despite detectable inbreeding depression, we found that pairwise relatedness between mates was significantly higher than between nonmates, with a mean coefficient of relatedness between mates of 0.065, approximately half the theoretical value for first cousins. This higher relatedness between mates cannot be explained by spatial genetic structure in this colonial bird; it therefore probably results from an active choice. As inbreeding but not outbreeding depression is observed in the study population, this finding accords with the idea that mating with genetically similar mates can confer a benefit in terms of inclusive fitness. Our results and published evidence suggest that preference for related individuals as mates might be relatively frequent in birds.

  12. Genetic similarity between cysticerci of Taenia solium isolated from human brain and from pigs.

    Science.gov (United States)

    Hinojosa-Juarez, Araceli Consuelo; Sandoval-Balanzario, Miguel; McManus, Donald Peter; Monroy-Ostria, Amalia

    2008-09-01

    Mitochondrial (mt) cox1 and ribosomal ITS1 DNA sequences from Taenia solium cysticercus isolates from pigs and cysticerci (racemose and cellulose types) from patients with neurocysticercosis were amplified by the polymerase chain reaction (PCR). The amplicons were sequenced in order to determine the genetic relationship between these types of cysticerci. Phylogenetic trees were constructed and evolutionary distances were calculated. ITS1 and mt cox1 cysticerci sequence data were compared with previously published Taenia spp. sequences. The variation in the ITS1 and cox1 sequences of samples collected from Mexico was minimal, regardless of geographical origin, size or colour of cysticerci from either pigs or human brain. These results suggest that the racemose and cellulose types represent genetically identical metacestodes of T. solium. Alignment of the mt cox1 sequences of the Mexican samples with sequences of other Taenia taxa showed that most were very similar to T. solium from Mexico and T. solium from Colombia; one T. solium Mexican isolate and Taenia hydatigena were placed in the same group close to Taenia crassiceps. The ITS1 sequences for the Mexican T. solium samples indicated the majority were in the same group as the Latin American T. solium. Two Mexican T. solium samples and T. solium from Philippines were placed together in a different group.

  13. Sir Francis Galton, epigenetic rules, genetic similarity theory, and human life-history analysis.

    Science.gov (United States)

    Rushton, J P

    1990-03-01

    In this article, an evolutionary perspective is applied to individual differences. Among the issues discussed are (a) the seminal contributions of Francis Galton and the subsequent ideological reaction, (b) the distal proximal continuum for understanding levels of explanation in social behavior, (c) consistent patterns of group differences in behavior (age, sex, social class,and race), (d) the heritability of personality and the role epigenetic rules play in guiding development in one direction over alternatives, (e) the genetic similarity theory perspective on friendship and mate choice, and (f) the view that personality is part of an r-K reproductive strategy involving a compensatory exchange between the production of gametes and parental care. It is suggested in conclusion that personality traits be considered aspects of a coordinated life cycle deeply embedded m evolutionary history.

  14. Improved Student Linkage of Mendelian and Molecular Genetic Concepts through a Yeast-Based Laboratory Module

    Science.gov (United States)

    Wolyniak, Michael J.

    2013-01-01

    A study of modern genetics requires students to successfully unite the principles of Mendelian genetics with the functions of DNA. Traditional means of teaching genetics are often successful in teaching Mendelian and molecular ideas but not in allowing students to see how the two subjects relate. The laboratory module presented here attempts to…

  15. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes

    DEFF Research Database (Denmark)

    Jahn, Leonie Johanna; Munck, Christian; Ellabaan, Mostafa M Hashim

    2017-01-01

    Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution....... However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes...... compare the geno- and phenotypes of Escherichia coli after evolution to Amikacin, Piperacillin, and Tetracycline under four different selection regimes. Interestingly, key mutations that confer antibiotic resistance as well as phenotypic changes like collateral sensitivity and cross-resistance emerge...

  16. Laboratory and histological similarities between Wilson's disease and rats with copper toxicity.

    Directory of Open Access Journals (Sweden)

    Narasaki,Mikio

    1980-04-01

    Full Text Available Rats were injected intraperitoneally with copper-lactate daily for over 160 days (total dose of 30 mg copper in each animal. At 120 to 160 days of copper administration, animals developed symptoms similar to those of Wilson's disease, i.e., kidney functional disturbances, proteinuria, aminoaciduria, decreased blood ceruloplasmin oxidase activity and increased urinary copper excretion. Cirrhosis was found in some animals. Tubular necrosis of the kidneys, liver fibrosis and tigrolysis of thalamic nerve cells were also found. Copper depositions were observed in liver parenchymal cells, renal tubular epithels, thalamus glia cells and on the Descemet's membrane of the cornea. The similarities between induced copper- intoxication in rats and Wilson's disease are discussed.

  17. Estimate Landslide Volume with Genetic Algorithms and Image Similarity Method from Single Satellite Image

    Science.gov (United States)

    Yu, Ting-To

    2013-04-01

    It is important to acquire the volume of landslide in short period of time. For hazard mitigation and also emergency response purpose, the traditional method takes much longer time than expected. Due to the weather limit, traffic accessibility and many regulations of law, it take months to handle these process before the actual carry out of filed work. Remote sensing imagery can get the data as long as the visibility allowed, which happened only few day after the event. While traditional photometry requires a stereo pairs images to produce the post event DEM for calculating the change of volume. Usually have to wait weeks or even months for gathering such data, LiDAR or ground GPS measurement might take even longer period of time with much higher cost. In this study we use one post event satellite image and pre-event DTM to compare the similarity between these by alter the DTM with genetic algorithms. The outcome of smartest guess from GAs shall remove or add exact values of height at each location, which been converted into shadow relief viewgraph to compare with satellite image. Once the similarity threshold been make then the guessing work stop. It takes only few hours to finish the entire task, the computed accuracy is around 70% by comparing to the high resolution LiDAR survey at a landslide, southern Taiwan. With extra GCPs, the estimate accuracy can improve to 85% and also within few hours after the receiving of satellite image. Data of this demonstration case is a 5 m DTM at 2005, 2M resolution FormoSat optical image at 2009 and 5M LiDAR at 2010. The GAs and image similarity code is developed on Matlab at windows PC.

  18. Genetic differentiation of Puccinia triticina populations in the Middle East and genetic similarity with populations in Central Asia.

    Science.gov (United States)

    Kolmer, J A; Ordoñez, M E; Manisterski, J; Anikster, Y

    2011-07-01

    Leaf rust of wheat, caused by Puccinia triticina, is a common and widespread disease in the Middle East. The objective of this study was to determine whether genetically differentiated groups of P. triticina are present in the Middle East region and to compare the population from the Middle East with the previously characterized population from Central Asia to determine whether genetically similar groups of isolates are found in the two regions. In total, 118 isolates of P. triticina collected from common wheat and durum wheat in Egypt, Israel, Turkey, Ethiopia, and Kenya were tested for virulence on 20 lines of wheat with single genes for leaf rust resistance and for molecular genotypes with 23 simple-sequence repeat (SSR) markers. After removal of isolates with identical virulence and SSR genotype in each country, 103 isolates were retained for further analysis. Clustering of SSR genotypes based on two-dimensional principal coordinates and virulence to wheat differential lines grouped the isolates into four Middle East (ME) groups. The two largest ME groups had virulence phenotypes typical of isolates collected from common wheat and two smaller ME groups had virulence typical of isolates collected from durum wheat. All pairs of ME groups were significantly differentiated for SSR genotype based on R(ST) and F(ST) statistics, and for virulence phenotype based on Φ(PT). All ME groups had observed values of heterozygosity greater than expected and significant fixation indices that indicated the clonal reproduction of urediniospores in the overall population. Linkage disequilibria for SSR genotypes was high across the entire population. The overall values of R(ST) and F(ST) were lower when isolates were grouped by country of origin that indicated the likely migration of isolates within the region. Although the two ME groups with virulence typical of isolates from common wheat were not differentiated for SSR genotype from groups of isolates from Central Asia based on

  19. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity.

    Science.gov (United States)

    Yang, Melinda A; Malaspinas, Anna-Sapfo; Durand, Eric Y; Slatkin, Montgomery

    2012-10-01

    Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site frequency spectrum [dcfs]), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans.

  20. SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil.

    Science.gov (United States)

    Lopes, Joao S; Marques, Isabel; Soares, Patricia; Nebenzahl-Guimaraes, Hanna; Costa, Joao; Miranda, Anabela; Duarte, Raquel; Alves, Adriana; Macedo, Rita; Duarte, Tonya A; Barbosa, Theolis; Oliveira, Martha; Nery, Joilda S; Boechat, Neio; Pereira, Susan M; Barreto, Mauricio L; Pereira-Leal, Jose; Gomes, Maria Gabriela Miranda; Penha-Goncalves, Carlos

    2013-08-01

    Human tuberculosis is an infectious disease caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Although spoligotyping and MIRU-VNTR are standard methodologies in MTBC genetic epidemiology, recent studies suggest that Single Nucleotide Polymorphisms (SNP) are advantageous in phylogenetics and strain group/lineages identification. In this work we use a set of 79 SNPs to characterize 1987 MTBC isolates from Portugal and 141 from Northeast Brazil. All Brazilian samples were further characterized using spolygotyping. Phylogenetic analysis against a reference set revealed that about 95% of the isolates in both populations are singly attributed to bacterial lineage 4. Within this lineage, the most frequent strain groups in both Portugal and Brazil are LAM, followed by Haarlem and X. Contrary to these groups, strain group T showed a very different prevalence between Portugal (10%) and Brazil (1.5%). Spoligotype identification shows about 10% of mis-matches compared to the use of SNPs and a little more than 1% of strains unidentifiability. The mis-matches are observed in the most represented groups of our sample set (i.e., LAM and Haarlem) in almost the same proportion. Besides being more accurate in identifying strain groups/lineages, SNP-typing can also provide phylogenetic relationships between strain groups/lineages and, thus, indicate cases showing phylogenetic incongruence. Overall, the use of SNP-typing revealed striking similarities between MTBC populations from Portugal and Brazil.

  1. Isolation of the rickettsial agent genetically similar to Candidatus Rickettsia kotlanii, from Haemaphysalis megaspinosa in Japan.

    Science.gov (United States)

    Andoh, Masako; Ogasawara, Yumiko; Sakata, Akiko; Ito, Takuya; Fujita, Hiromi; Kawabata, Hiroki; Ando, Shuji

    2014-09-01

    Two rickettsial isolates, HM-1 and HM-2, were isolated from Haemaphysalis megaspinosa collected in Japan in 2006 and 2011, respectively. The isolates were analyzed by DNA sequences of the outer membrane protein A gene, the outer membrane protein B gene, the citrate synthase gene, the genus Rickettsia-specific outer membrane protein 17-kDa gene, the 16S ribosome RNA gene, and the PS120 protein gene ("geneD"). HM-1 was identified as Rickettsia tamurae. HM-2 matched most closely with 'Candidatus Rickettsia kotlanii' DNA, which has only been reported from H. concinna in Hungary. This is the first report of isolation in Japan of the agent genetically similar to 'Candidatus R. kotlanii,' which belongs phylogenetically to the spotted fever group Rickettsia. Our study shows the possibility that 'Candidatus R. kotlanii' can be carried by at least two tick species. Furthermore, because the Rickettsia sp. has been found two distant countries, Hungary and Japan, it has potential for wider distribution.

  2. Basic principles and laboratory analysis of genetic variation.

    Science.gov (United States)

    Gonzalez-Bosquet, Jesus; Chanock, Stephen J

    2011-01-01

    With the draft of the human genome and advances in technology, the approach toward mapping complex diseases and traits has changed. Human genetics has evolved into the study of the genome as a complex structure harbouring clues for multifaceted disease risk with the majority still unknown. The discovery of new candidate regions by genome-wide association studies (GWAS) has changed strategies for the study of genetic predisposition. More genome-wide, "agnostic" approaches, with increasing numbers of participants from high-quality epidemiological studies are for the first time replicating results in different settings. However, new-found regions (which become the new candidate "genes") require extensive follow-up and investigation of their functional significance. Understanding the true effect of genetic variability on the risk of complex diseases is paramount. The importance of designing high-quality studies to assess environmental contributions, as well as the interactions between genes and exposures, cannot be stressed enough. This chapter will address the basic issues of genetic variation, including population genetics, as well as analytical platforms and tools needed to investigate the contribution of genetics to human diseases and traits.

  3. Genetic influence on blood pressure measured in the office, under laboratory stress and during real life

    National Research Council Canada - National Science Library

    Wang, Xiaoling; Ding, Xiuhua; Su, Shaoyong; Harshfield, Gregory; Treiber, Frank; Snieder, Harold

    To determine to what extent the genetic influences on blood pressure (BP) measured in the office, under psychologically stressful conditions in the laboratory and during real life are different from each other...

  4. The influence of space in genetic-environmental relationships when environmental heterogeneity and seed dispersal occur at similar scale.

    Science.gov (United States)

    Volis, S; Anikster, Y; Olsvig-Whittaker, L; Mendlinger, S

    2004-02-01

    We tested the importance of microenvironmental topographic parameters as predictors of emmer wheat genetic variation using three classes of single-locus (or at most several-loci) genetic markers (allozymes, glutenins, and qualitative traits) and two classes of markers of polygenic inheritance (phenological and morphological traits). Canonical correspondence analysis (CCA) and redundancy analysis (RDA) detected a significant effect of spatially structured environmental variation on genetic differences between plants for allozymes, glutenins, and quantitative morphological and phenological traits. However, after removing a spatial component of variation in partial CCA and partial RDA, the relationship of the remaining environmental variation with these genetic markers could be explained by chance alone, allowing us to rule out microniche topographic specialization in emmer wheat. Topographic autocorrelation exhibited a certain degree of similarity with genetic marker autocorrelation, indicating similar scales of environmental heterogeneity and seed flow. The detected population genetic structure agrees with one expected under isolation by distance as a result of limited gene flow. A negative relationship of genetic similarity with the logarithm of distance between plants was detected for both molecular markers and quantitative traits, which differed in the strength but not the pattern of association.

  5. [Teaching design and practice of human blood type traits in genetics comprehensive laboratory course].

    Science.gov (United States)

    Zhao, Jian; Hu, Dongmei; Yu, Dade; Dong, Mingliang; Li, Yun; Fan, Yingming; Wang, Yanwei; Zhang, Jinfeng

    2016-05-01

    Comprehensive laboratory courses, which enable students to aptly apply theoretic knowledge and master experiment skills, play an important role in the present educational reform of laboratory courses. We utilized human ABO blood type as the experimental subject, and designed the experiment--"Molecular Genotyping of Human ABO Blood Type and Analysis of Population Genetic Equilibrium". In the experiment, DNA in mucosal cells is extracted from students' saliva, and each student's genotype is identified using a series of molecular genetics technologies, including PCR amplification of target fragments, enzymatic digestion, and electrophoretic separation. Then, taking the whole class as an analogous Mendel population, a survey of genotype frequency of ABO blood type is conducted, followed with analyses of various population genetic parameters using Popgene. Through the open laboratory course, students can not only master molecular genetic experimental skills, but also improve their understanding of theoretic knowledge through independent design and optimization of molecular techniques. After five years of research and practice, a stable experimental system of molecular genetics has been established to identify six genotypes of ABO blood types, namely I(A)I(A), I(A)i, I(B)I(B), I(B)i, I(A)I(B) and ii. Laboratory courses of molecular and population genetics have been integrated by calculating the frequencies of the six genotypes and three multiple alleles and testing population genetic equilibrium. The goal of the open laboratory course with independent design and implementation by the students has been achieved. This laboratory course has proved effective and received good reviews from the students. It could be applied as a genetics laboratory course for the biology majors directly, and its ideas and methods could be promoted and applied to other biological laboratory courses.

  6. Genetically similar VHSV isolates are differentially virulent in olive flounder Paralichthys olivaceus.

    Science.gov (United States)

    Cho, Mi Young; Lee, Unn Hwa; Moon, Chang Hoon; Bang, Jong Deuk; Jee, Bo Young; Cha, Seung Ju; Kim, Jin Woo; Park, Myoung Ae; Do, Jeong Wan; Park, Jeong Woo

    2012-11-08

    Two viral hemorrhagic septicemia virus (VHSV) isolates, VHSV-KR-CJA and VHSV-KR-YGH, were isolated from viral hemorrhagic septicemia disease outbreaks in flounder farms in South Korea. The VHSV-KR-CJA isolate was isolated from a flounder farm with high mortality (80%), while the VHSV-KR-YGH isolate was isolated from a flounder farm with low mortality (15%), suggesting that these isolates differ in virulence. The virulence of these isolates was evaluated in juvenile flounder via intraperitoneal injection. Consistent with their virulence in the field, mortality data revealed that the VHSV-KR-CJA isolate was highly pathogenic (cumulative mortality of 80%), while the VHSV-KR-YGH isolate was less pathogenic in flounder (cumulative mortality of 20%). To characterize the genotypes of these viruses, the full open reading frames (ORFs) encoding nucleoprotein N, phosphoprotein P, matrix protein M, glycoprotein G, nonstructural viral protein NV, and polymerase L of these viruses were sequenced and analyzed. Sequence analysis revealed that both isolates are genetically very similar (identical amino acid sequences for P, M, NV, and L and >99.7 and 99.8% amino acid sequence identity for N and G, respectively). Phylogenetic analysis indicated that both of these viruses belong to the Genotype IVa group, suggesting that they originated from a common ancestral virus. The low pathogenicity VHSV strain may potentially evolve to become a more pathogenic strain through only a few nucleotide substitutions. Further functional analyses of mutations in VHSV genes are necessary to identify factors that determine VHSV pathogenicity in flounder.

  7. The U.S. Forest Service National Seed Laboratory and Fraxinus ex situ genetic conservation

    Science.gov (United States)

    Robert P. Karrfalt

    2010-01-01

    The U.S. Forest Service's National Seed Laboratory (NSL) has as part of its mission the conservation of genetic resources for the Forest Service and Forest Service cooperators through long-term seed storage. The Forest Service recognizes ash as one of four priority species for genetic conservation. The NSL is in charge of the Forest Service ash preservation plan...

  8. SSR ANALYSIS IN THE STUDY OF GENETIC DIVERSITY AND SIMILARITY OF BARLEY CULTIVARS

    Directory of Open Access Journals (Sweden)

    O. R. Lakhneko

    2016-06-01

    Full Text Available The aim of research was to develop an evaluation system of the genetic polymorphism for barley cultivars of Ukrainian and foreign origin based on the analysis of simple sequence repeats and valuable agricultural trait loci as well as to compose the molecular genetic passports for those cultivars. PCRs with the following separation of amplification products by agarose and polyacrylamide electrophoresis were performed to find out genetic polymorphism. Unweighted Pair Group Method with Arithmetic Mean was used for phylogenetic relationship detection. The dandrogram of phylogenetic relationships of 55 barley cultivars was constructed and molecular genetic passports were developed. Molecular genetic passports can be involved in verification for the compliance with standards cultivars, stability and seed purity.

  9. Genetically modified organisms in food and feed : annual report 2012 of the Dutch National Reference Laboratory

    NARCIS (Netherlands)

    Scholtens-Toma, I.M.J.; Molenaar, B.; Zaaijer, S.; Prins, T.W.; Kok, E.J.

    2013-01-01

    This is the annual report of the Dutch Reference Laboratory (NRL) for Genetically Modified Food and Feed (RIKILT Wageningen UR). The report gives an overview of the NRL activities carried out in 2012. In 2012 the two Dutch Official Laboratories participated in several proficiency tests with good res

  10. Genetically modified organisms in food and feed : annual report 2010 of the Dutch National Reference Laboratory

    NARCIS (Netherlands)

    Scholtens-Toma, I.M.J.; Molenaar, B.; Zaaijer, S.; Voorhuijzen, M.M.; Prins, T.W.; Kok, E.J.

    2011-01-01

    This is the annual report of the Dutch National Reference Laboratory (NRL) for Genetically Modified Food and Feed (RIKILT - Institue of Food Safety). The report gives an overview of the NRL activities carried out in 2010. In 2010 RIKILT participated in one ring trial for inter laboratory validation

  11. Genetically modified organisms in food and feed : annual report of the Dutch National Reference Laboratory

    NARCIS (Netherlands)

    Scholtens-Toma, I.M.J.; Molenaar, B.; Zaaijer, S.; Voorhuijzen, M.M.; Prins, T.W.; Kok, E.J.

    2012-01-01

    This is the annual report of the Dutch National Reference Laboratory (NRL) for Genetically Modified Food and Feed (RIKILT - Institute of Food Safety). The report gives an overview of the NRL activities carried out in 2011. In 2011 both RIKILT and the Routine Field Laboratory of the Netherlands Food

  12. One group of genetically similar Listeria monocytogenes strains frequently dominates and persists in several fish slaughter- and smokehouses

    DEFF Research Database (Denmark)

    Wulff, Gitte; Gram, Lone; Ahrens, Peter;

    2006-01-01

    Contamination of foods with the human pathogen Listeria monocytogenes may occur during processing, and the purpose of this study was to determine whether genetically similar strains colonize different processing plants or whether specific persistent strains are unique to each processing plant. We...... smokehouses and two slaughterhouses and was predominant in three of these plants. A subset of 35 strains was also analyzed by amplified fragment length polymorphism typing, which confirmed the genetic similarity of the groups. Moreover, strains of the dominant RAPD type were indistinguishable from strains...... related may be especially adapted to colonizing the processing equipment or especially resistant to cleaning and disinfection....

  13. Two Genetically Similar H9N2 Influenza A Viruses Show Different Pathogenicity in Mice

    Directory of Open Access Journals (Sweden)

    Qingtao Liu

    2016-11-01

    Full Text Available H9N2 Avian influenza virus has repeatedly infected humans and other mammals, which highlights the need to determine the pathogenicity and the corresponding mechanism of this virus for mammals. In this study, we found two H9N2 viruses with similar genetic background but with different pathogenicity in mice. The A/duck/Nanjing/06/2003 (NJ06 virus was highly pathogenic for mice, with a 50% mouse lethal dose of 102.83 50% egg infectious dose, whereas the A/duck/Nanjing/01/1999 (NJ01 virus was low pathogenic for mice, with a 50% mouse lethal dose of >106.81 50% egg infectious dose. Further studies showed that the NJ06 virus grew faster and reached significantly higher titers than NJ01 in vivo and in vitro. Moreover, the NJ06 virus induced more severe lung lesions, and higher levels of inflammatory cellular infiltration and cytokine response in lungs than NJ01 did. However, only twelve different amino acid residues (HA-K157E, NA-A9T, NA-R435K, PB2-T149P, PB2-K627E, PB1-R187K, PA-L548M, PA-M550L, NP-G127E, NP-P277H, NP-D340N, NS1-D171N were found between the two viruses, and all these residues except for NA-R435K were located in the known functional regions involved in interaction of viral proteins or between the virus and host factors. Summary, our results suggest that multiple amino acid differences may be responsible for the higher pathogenicity of the NJ06 virus for mice, resulting in lethal infection, enhanced viral replication, severe lung lesions, and excessive inflammatory cellular infiltration and cytokine response in lungs. These observations will be helpful for better understanding the pathogenic potential and the corresponding molecular basis of H9N2 viruses that might pose threats to human health in the future.

  14. Genetic, Clinical, and Laboratory Markers for DOCK8 Immunodeficiency Syndrome

    Directory of Open Access Journals (Sweden)

    Jeremiah C. Davis

    2010-01-01

    Full Text Available DOCK8 immunodeficiency syndrome (DIDS is a combined immunodeficiency characterized by recurrent viral infections, severe atopy, and early onset malignancy. Genetic studies revealed large, unique deletions in patients from different families and ethnic backgrounds. Clinical markers of DIDS include atopic dermatitis, allergies, cutaneous viral infections, recurrent respiratory tract infections, and malignancy. Immune assessments showed T cell lymphopenia, hyper-IgE, hypo-IgM, and eosinophilia. The impaired lymphocyte functions in DIDS patients appear central for disease pathogenesis.

  15. Laboratory Mass Production and Genetics of ’Anopheles Freeborni’

    Science.gov (United States)

    1990-07-19

    used for electrophoretic analysis. Buffer Buffer Adjusted Chemical Ingredients System Type pH per Liter H20 Ayala-c Gel 7.0 1.09 g Trizma Base 0.63 g...Base 66.00 g Citric Acid 5.5 Gel 5.50 2.60 g Trizma Base 1.80 g Citric Acid Electrode 5.20 20.25 g Trizma Base 14.64 g Citric Acid * The ca--hodc buffer ...and Joslyn (1979). Gels were prepared- as 12.5% solutions (w/v) of hydrolysed starch (Connaught Laboratories, Ontario, Canada) in an appropriate buffer

  16. Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains.

    Science.gov (United States)

    Lee, Kang-Hoon; Lim, Debora; Chiu, Sophia; Greenhalgh, David; Cho, Kiho

    2016-04-01

    Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.

  17. Patterns of cuticular hydrocarbon variation and genetic similarity between natural populations of Amblyomma cajennense (Acari: Ixodidae).

    Science.gov (United States)

    Estrada-Peña, A; Guglielmone, A A; Mangold, A J; Castellá, J

    1993-10-01

    Gas chromatography has been used to analyze the variation in cuticular hydrocarbon patterns between several populations of Amblyomma cajennense. 88 compounds were detected and these could be divided into 17 groups of hydrocarbons. Heterozygosis in the populations ranges from 0% to 25.84%. Isomers for pentacosane, heptacosane and nonatriacontane are the most variable, with 13, 10 and 11 variants, respectively. Nei's genetic identity and genetic distance show that populations may be considered as regional variants of only one species: the results do not indicate the presence of sibling species. However, a relatively high genetic distance has been observed between several Cuban and continental populations, suggesting a long reproductive isolation. Gas chromatography of cuticular hydrocarbons is a good alternative to isozyme analysis for population studies, when collecting conditions do not allow the use of live ticks and only alcohol-preserved collections are available. The high number of compounds available for genetic studies will provide excellent markers for evaluating the extent of gene flow and migration of tick species.

  18. Genetic and epigenetic similarities and differences between childhood and adult AML

    DEFF Research Database (Denmark)

    Juhl-Christensen, Caroline; Ommen, Hans Beier; Aggerholm, Anni

    2012-01-01

    The biology of acute myeloid leukemia (AML) is complex and includes both genetic and epigenetic aberrations. We addressed the combined consequences of promoter hypermethylation of p15, CDH1, ER, MDR1, and RARB2 and mutation of NPM1, CEBPA, FLT3, and WT1 in a Danish cohort of 70 pediatric and 383...

  19. Culturally relevant inquiry-based laboratory module implementations in upper-division genetics and cell biology teaching laboratories.

    Science.gov (United States)

    Siritunga, Dimuth; Montero-Rojas, María; Carrero, Katherine; Toro, Gladys; Vélez, Ana; Carrero-Martínez, Franklin A

    2011-01-01

    Today, more minority students are entering undergraduate programs than ever before, but they earn only 6% of all science or engineering PhDs awarded in the United States. Many studies suggest that hands-on research activities enhance students' interest in pursuing a research career. In this paper, we present a model for the implementation of laboratory research in the undergraduate teaching laboratory using a culturally relevant approach to engage students. Laboratory modules were implemented in upper-division genetics and cell biology courses using cassava as the central theme. Students were asked to bring cassava samples from their respective towns, which allowed them to compare their field-collected samples against known lineages from agricultural stations at the end of the implementation. Assessment of content and learning perceptions revealed that our novel approach allowed students to learn while engaged in characterizing Puerto Rican cassava. In two semesters, based on the percentage of students who answered correctly in the premodule assessment for content knowledge, there was an overall improvement of 66% and 55% at the end in the genetics course and 24% and 15% in the cell biology course. Our proposed pedagogical model enhances students' professional competitiveness by providing students with valuable research skills as they work on a problem to which they can relate.

  20. Genetic similarity among Agistemus pallinii Matioli et al (Acari: Stigmaeidae) found in citrus orchards in Vicosa, Minas Gerais state, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Matioli, Andre L. [Instituto Biologico, Campinas, SP (Brazil). Lab. de Entomologia Economica], e-mail: almatioli@biologico.sp.gov.br; Pallini, Angelo [Universidade Federal de Vicosa (UFV), MG (Brazil). Dept. de Biologia Animal], e-mail: pallini@ufv.br; Tavares, Mara G. [Universidade Federal de Vicosa (UFV), MG (Brazil). Dept. de Biologia Geral], e-mail: mtavares@ufv.br

    2009-03-15

    Stigmaeidae are very important predators of mite and insect pests on several crops in Brazil. It is considered the second most important family of predatory mites in citrus orchards in Brazil. However, their identification, especially that of the members of the genus Agistemus, is rather difficult based only on morphology. Hence, this study describes the use of random amplified polymorphic DNA (RAPD-PCR) markers to determine the genetic similarity of an Agistemus pallinii Matioli et al population found in 2004 in a citrus orchard in Vicosa, Minas Gerais State, Brazil, preying on Panonychus citri (McGregor). Amplifications were performed with 12 random primers (OPAA8, OPAA19, OPAB1, OPAB5, OPAB18, OPAC9, OPAC17, OPAC19, OPAD10, OPAE9, OPAE12 and OPAE17), which generated 119 bands, with 53.8% polymorphism. The coefficients of genetic similarity among the individuals ranged from 0.68 to 0.99, indicating a high genetic similarity among them. The 3D projection analysis clustered the majority of individuals confirming their high similarity. Though individuals of A. pallinii are minute ({+-} 360 {mu}m long), the PCR-RAPD technique can still be used for their identification, complementing morphological analyses or for comparison of populations collected in different geographic regions. This is the fi rst molecular study carried out with stigmaeid mites. (author)

  1. Genetic architecture of skewed X inactivation in the laboratory mouse.

    Directory of Open Access Journals (Sweden)

    John D Calaway

    Full Text Available X chromosome inactivation (XCI is the mammalian mechanism of dosage compensation that balances X-linked gene expression between the sexes. Early during female development, each cell of the embryo proper independently inactivates one of its two parental X-chromosomes. In mice, the choice of which X chromosome is inactivated is affected by the genotype of a cis-acting locus, the X-chromosome controlling element (Xce. Xce has been localized to a 1.9 Mb interval within the X-inactivation center (Xic, yet its molecular identity and mechanism of action remain unknown. We combined genotype and sequence data for mouse stocks with detailed phenotyping of ten inbred strains and with the development of a statistical model that incorporates phenotyping data from multiple sources to disentangle sources of XCI phenotypic variance in natural female populations on X inactivation. We have reduced the Xce candidate 10-fold to a 176 kb region located approximately 500 kb proximal to Xist. We propose that structural variation in this interval explains the presence of multiple functional Xce alleles in the genus Mus. We have identified a new allele, Xce(e present in Mus musculus and a possible sixth functional allele in Mus spicilegus. We have also confirmed a parent-of-origin effect on X inactivation choice and provide evidence that maternal inheritance magnifies the skewing associated with strong Xce alleles. Based on the phylogenetic analysis of 155 laboratory strains and wild mice we conclude that Xce(a is either a derived allele that arose concurrently with the domestication of fancy mice but prior the derivation of most classical inbred strains or a rare allele in the wild. Furthermore, we have found that despite the presence of multiple haplotypes in the wild Mus musculus domesticus has only one functional Xce allele, Xce(b. Lastly, we conclude that each mouse taxa examined has a different functional Xce allele.

  2. Similar genetic switch systems might integrate the floral inductive pathways in dicots and monocots

    DEFF Research Database (Denmark)

    Andersen, C.H.; Jensen, C.S.; Petersen, K.

    2004-01-01

    A recent paper by Million Tadege et A shows that a SOC1-like gene from rice, OsSOC1, can complement the Arabidopsis soc1 mutant, and that ectopic expression of the Arabidopsis floral repressor FLC in rice delays flowering and up-regulation of OsSOC1 These findings, together with the identificatio...... of the wheat vernalization VRN1 locus as an AP1 homologue, suggest that related genetic switch systems control floral transition in dicots and monocots but that they are based on different MADS-box transcription factors....

  3. Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

    Directory of Open Access Journals (Sweden)

    R. E. Schwartz

    2010-02-01

    Full Text Available Submicron particles collected at Whistler, British Columbia, at 1020 masl during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR and X-ray fluorescence (XRF techniques for organic functional groups (OFG and elemental composition. Organic mass (OM ranged from less than 0.5 to 3.1μg m−3, with a project mean and standard deviation of 1.3±1.0 μg m−3 and 0.21±0.16 μg m−3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and <1% of the average organic aerosol composition, respectively. Measurements of volatile organic compounds (VOC, including isoprene and monoterpenes from biogenic VOC (BVOC emissions and their oxidation products (methyl-vinylketone/methacrolein, MVK/MACR, were made using co-located proton transfer reaction mass spectrometry (PTR-MS. We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 2% organic hydroxyl, 16% ketone, and 6% amine groups was similar to that of secondary organic aerosol (SOA reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional group composition and

  4. Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

    Directory of Open Access Journals (Sweden)

    R. E. Schwartz

    2010-06-01

    Full Text Available Submicron particles collected at Whistler, British Columbia, at 1020 m a.s.l. during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR and X-ray fluorescence (XRF techniques for organic functional groups (OFG and elemental composition. Organic mass (OM concentrations ranged from less than 0.5 to 3.1 μg m−3, with a project mean and standard deviation of 1.3±1.0 μg m−3 and 0.21±0.16 μg m−3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and <1% of the average organic aerosol composition, respectively. Measurements of volatile organic compounds (VOC, including isoprene and monoterpenes from biogenic VOC (BVOC emissions and their oxidation products (methyl-vinylketone / methacrolein, MVK/MACR, were made using co-located proton transfer reaction mass spectrometry (PTR-MS. We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 21% organic hydroxyl, 16% ketone, and 6% amine groups was similar to that of secondary organic aerosol (SOA reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional

  5. Genetic Similarity between Cotton Leafroll Dwarf Virus and Chickpea Stunt Disease Associated Virus in India

    Directory of Open Access Journals (Sweden)

    Arup Kumar Mukherjee

    2016-12-01

    Full Text Available The cotton leafroll dwarf virus (CLRDV is one of the most devastating pathogens of cotton. This malady, known as cotton blue disease, is widespread in South America where it causes huge crop losses. Recently the disease has been reported from India. We noticed occurrence of cotton blue disease and chickpea stunt disease in adjoining cotton and chickpea fields and got interested in knowing if these two viral diseases have some association. By genetic studies, we have shown here that CLRDV is very close to chickpea stunt disease associated virus (CpSDaV. We were successful in transmitting the CLRDV from cotton to chickpea. Our studies indicate that CpSDaV and CLRDV in India are possibly two different strains of the same virus. These findings would be helpful in managing these serious diseases by altering the cropping patterns.

  6. Genetic Dissection of Acute Anterior Uveitis Reveals Similarities and Differences in Associations observed with Ankylosing Spondylitis

    Science.gov (United States)

    Robinson, Philip C.; Claushuis, Theodora A.M.; Cortes, Adrian; Martin, Tammy M.; Evans, David M.; Leo, Paul; Mukhopadhyay, Pamela; Bradbury, Linda A.; Cremin, Katie; Harris, Jessica; Maksymowych, Walter P.; Inman, Robert D.; Rahman, Proton; Haroon, Nigil; Gensler, Lianne; Powell, Joseph E.; van der Horst-Bruinsma, Irene E.; Hewitt, Alex W.; Craig, Jamie E.; Lim, Lyndell L.; Wakefield, Denis; McCluskey, Peter; Voigt, Valentina; Fleming, Peter; Degli-Esposti, Mariapia; Pointon, Jennifer J.; Weisman, Michael H.; Wordsworth, B. Paul; Reveille, John D.; Rosenbaum, James T.; Brown, Matthew A.

    2015-01-01

    Objective To use high density genotyping to investigate the genetic associations of acute anterior uveitis (AAU) in patients both with and without ankylosing spondylitis (AS). Method We genotyped 1,711 patients with AAU (either primary or with AAU and AS), 2,339 AS patients without AAU, and 10,000 controls on the Illumina Immunochip Infinium microarray. We also used data on AS patients from previous genomewide association studies to investigate the AS risk locus ANTXR2 for its putative effect in AAU. ANTXR2 expression in mouse eyes was investigated by RT-PCR. Results Comparing all AAU cases with HC, strong association was seen over HLA-B corresponding to the HLA-B27 tag SNP rs116488202. Three non-MHC loci IL23R, the intergenic region 2p15 and ERAP1 were associated at genome-wide significance (P < 5×10−8). Five loci harboring the immune-related genes IL10-IL19, IL18R1-IL1R1, IL6R, the chromosome 1q32 locus harboring KIF21B, as well as the eye related gene EYS, were also associated at a suggestive level of significance (P < 5×10−6). A number of previously confirmed AS associations demonstrated significant differences in effect size between AS patients with AAU and AS patients without AAU. ANTXR2 expression was found to vary across eye compartments. Conclusion These findings, with both novel AAU specific associations, and associations shared with AS demonstrate overlapping but also distinct genetic susceptibility loci for AAU and AS. The associations in IL10 and IL18R1 are shared with inflammatory bowel disease, suggesting common etiologic pathways. PMID:25200001

  7. Genetic regulation of bone metabolism in the chicken: similarities and differences to Mammalian systems.

    Directory of Open Access Journals (Sweden)

    Martin Johnsson

    2015-05-01

    Full Text Available Birds have a unique bone physiology, due to the demands placed on them through egg production. In particular their medullary bone serves as a source of calcium for eggshell production during lay and undergoes continuous and rapid remodelling. We take advantage of the fact that bone traits have diverged massively during chicken domestication to map the genetic basis of bone metabolism in the chicken. We performed a quantitative trait locus (QTL and expression QTL (eQTL mapping study in an advanced intercross based on Red Junglefowl (the wild progenitor of the modern domestic chicken and White Leghorn chickens. We measured femoral bone traits in 456 chickens by peripheral computerised tomography and femoral gene expression in a subset of 125 females from the cross with microarrays. This resulted in 25 loci for female bone traits, 26 loci for male bone traits and 6318 local eQTL loci. We then overlapped bone and gene expression loci, before checking for an association between gene expression and trait values to identify candidate quantitative trait genes for bone traits. A handful of our candidates have been previously associated with bone traits in mice, but our results also implicate unexpected and largely unknown genes in bone metabolism. In summary, by utilising the unique bone metabolism of an avian species, we have identified a number of candidate genes affecting bone allocation and metabolism. These findings can have ramifications not only for the understanding of bone metabolism genetics in general, but could also be used as a potential model for osteoporosis as well as revealing new aspects of vertebrate bone regulation or features that distinguish avian and mammalian bone.

  8. Witnessing Evolution First Hand: A K-12 Laboratory Exercise in Genetics & Evolution Using "Drosophila"

    Science.gov (United States)

    Heil, Caiti S. S.; Manzano-Winkler, Brenda; Hunter, Mika J.; Noor, Juliet K. F.; Noor, Mohamed A. F.

    2013-01-01

    We present a laboratory exercise that leverages student interest in genetics to observe and understand evolution by natural selection. Students begin with white-eyed fruit fly populations, to which they introduce a single advantageous variant (one male with red eyes). The superior health and vision associated with having the red-eye-color allele…

  9. Studying Human Disease Genes in "Caenorhabditis Elegans": A Molecular Genetics Laboratory Project

    Science.gov (United States)

    Cox-Paulson, Elisabeth A.; Grana, Theresa M.; Harris, Michelle A.; Batzli, Janet M.

    2012-01-01

    Scientists routinely integrate information from various channels to explore topics under study. We designed a 4-wk undergraduate laboratory module that used a multifaceted approach to study a question in molecular genetics. Specifically, students investigated whether "Caenorhabditis elegans" can be a useful model system for studying genes…

  10. Blue Genes: An Integrative Laboratory to Differentiate Genetic Transformation from Gene Mutation for Underclassmen

    Science.gov (United States)

    Militello, Kevin T.; Chang, Ming-Mei; Simon, Robert D.; Lazatin, Justine C.

    2016-01-01

    The ability of students to understand the relationship between genotype and phenotype, and the mechanisms by which genotypes and phenotypes can change is essential for students studying genetics. To this end, we have developed a four-week laboratory called Blue Genes, which is designed to help novice students discriminate between two mechanisms by…

  11. Studying Human Disease Genes in "Caenorhabditis Elegans": A Molecular Genetics Laboratory Project

    Science.gov (United States)

    Cox-Paulson, Elisabeth A.; Grana, Theresa M.; Harris, Michelle A.; Batzli, Janet M.

    2012-01-01

    Scientists routinely integrate information from various channels to explore topics under study. We designed a 4-wk undergraduate laboratory module that used a multifaceted approach to study a question in molecular genetics. Specifically, students investigated whether "Caenorhabditis elegans" can be a useful model system for studying genes…

  12. Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases

    Science.gov (United States)

    Greene, Daniel; Richardson, Sylvia; Turro, Ernest

    2016-01-01

    Rare genetic disorders, which can now be studied systematically with affordable genome sequencing, are often caused by high-penetrance rare variants. Such disorders are often heterogeneous and characterized by abnormalities spanning multiple organ systems ascertained with variable clinical precision. Existing methods for identifying genes with variants responsible for rare diseases summarize phenotypes with unstructured binary or quantitative variables. The Human Phenotype Ontology (HPO) allows composite phenotypes to be represented systematically but association methods accounting for the ontological relationship between HPO terms do not exist. We present a Bayesian method to model the association between an HPO-coded patient phenotype and genotype. Our method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease. We thus formalize a clinical approach to phenotyping that is lacking in standard regression techniques for rare disease research. We demonstrate the power of our method by uncovering a number of true associations in a large collection of genome-sequenced and HPO-coded cases with rare diseases. PMID:26924528

  13. Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases.

    Science.gov (United States)

    Greene, Daniel; Richardson, Sylvia; Turro, Ernest

    2016-03-01

    Rare genetic disorders, which can now be studied systematically with affordable genome sequencing, are often caused by high-penetrance rare variants. Such disorders are often heterogeneous and characterized by abnormalities spanning multiple organ systems ascertained with variable clinical precision. Existing methods for identifying genes with variants responsible for rare diseases summarize phenotypes with unstructured binary or quantitative variables. The Human Phenotype Ontology (HPO) allows composite phenotypes to be represented systematically but association methods accounting for the ontological relationship between HPO terms do not exist. We present a Bayesian method to model the association between an HPO-coded patient phenotype and genotype. Our method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease. We thus formalize a clinical approach to phenotyping that is lacking in standard regression techniques for rare disease research. We demonstrate the power of our method by uncovering a number of true associations in a large collection of genome-sequenced and HPO-coded cases with rare diseases.

  14. Repeated Rule Acquisition using Rule Ontology from Similar Web Sites Based on Genetic Algorithm

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    Shanmugapriya. D

    2014-01-01

    Full Text Available The Semantic Web, which is the key component of Web 2.0 and Web 3.0, is an evolving development of the World Wide Web in which the semantics of information and services on the Web are being defined. Knowledge is an essential part of most Semantic Web applications and ontology, which is a formal explicit description of concepts or classes in a domain of discussion, is the most important part of the knowledge. As a model for knowledge description and formalization, ontology’s are widely used to represent user profiles in personalized web information gathering. The ontology can decrease the amount of information and reduce the work of utilizing the information in rule acquisition, because it is generalized and specifically rearranged for rule acquisition. Moreover, the ontology can be accumulated and reused throughout repeated rule acquisition. The main contribution of existing work is that the complete and detailed rule composition process with examples and its evaluation. The enhancement work is, with the existing system concept we combining the concept of selecting exact parts that contain rules from Web pages to increase the accuracy in their result. In this proposed work we are combining the screen method from WebPages with use of genetic Techniques to extract the rule optimally.

  15. Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK.

    Science.gov (United States)

    Martin, Kate; Baddal, Buket; Mustafa, Nazim; Perry, Claire; Underwood, Anthony; Constantidou, Chrystala; Loman, Nick; Kenna, Dervla T; Turton, Jane F

    2013-07-01

    Variable number tandem repeat (VNTR) analysis at nine loci of isolates of Pseudomonas aeruginosa submitted to the national reference laboratory from UK hospitals, from over 2000 patients, between June 2010 and June 2012 revealed four widely found types that collectively were received from approximately a fifth of patients, including from those with cystic fibrosis. These types were also prevalent among related submissions from the clinical environment and were received from up to 54 (out of 143) hospitals. Multi-locus sequence typing and blaOXA-50-like sequencing confirmed the clonal relationship within each cluster, and representatives from multiple centres clustered within about 70 % by pulsed-field gel electrophoresis. Illumina sequencing of 12 isolates of cluster A of VNTR profile 8, 3, 4, 5, 2, 3, 5, 2, x (where the repeat number at the last, most discriminatory locus is variable) revealed a large number of variably present targets in the accessory genome and seven of these were sought by PCR among a larger set of isolates. Representatives from patients within a single centre mostly had distinct accessory gene profiles, suggesting that these patients acquired the strain independently, while those with clear epidemiological links shared the same profile. Profiles also varied between representatives from different centres. Epidemiological investigations of widely found types such as these require the use of finer-typing methods, which increasingly will be informed by next generation sequencing.

  16. Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex.

    Science.gov (United States)

    Ferris, Kathleen G; Rushton, Tullia; Greenlee, Anna B; Toll, Katherine; Blackman, Benjamin K; Willis, John H

    2015-08-01

    The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. Genetic Biomarker Prevalence Is Similar in Fecal Immunochemical Test Positive and Negative Colorectal Cancer Tissue.

    Science.gov (United States)

    Levin, Theodore R; Corley, Douglas A; Jensen, Christopher D; Marks, Amy R; Zhao, Wei K; Zebrowski, Alexis M; Quinn, Virginia P; Browne, Lawrence W; Taylor, William R; Ahlquist, David A; Lidgard, Graham P; Berger, Barry M

    2017-03-01

    Fecal immunochemical test (FIT) screening detects most asymptomatic colorectal cancers. Combining FIT screening with stool-based genetic biomarkers increases sensitivity for cancer, but whether DNA biomarkers (biomarkers) differ for cancers detected versus missed by FIT screening has not been evaluated in a community-based population. To evaluate tissue biomarkers among Kaiser Permanente Northern California patients diagnosed with colorectal cancer within 2 years after FIT screening. FIT-negative and FIT-positive colorectal cancer patients 50-77 years of age were matched on age, sex, and cancer stage. Adequate DNA was isolated from paraffin-embedded specimens in 210 FIT-negative and 211 FIT-positive patients. Quantitative allele-specific real-time target and signal amplification assays were performed for 7 K-ras mutations and 10 aberrantly methylated DNA biomarkers (NDRG4, BMP3, SFMBT2_895, SFMBT2_896, SFMBT2_897, CHST2_7890, PDGFD, VAV3, DTX1, CHST2_7889). One or more biomarkers were found in 414 of 421 CRCs (98.3%). Biomarker expression was not associated with FIT status, with the exception of higher SFMBT2_897 expression in FIT-negative (194 of 210; 92.4%) than in FIT-positive cancers (180 of 211; 85.3%; p = 0.02). There were no consistent differences in biomarker expression by FIT status within age, sex, stage, and cancer location subgroups. The biomarkers of a currently in-use multi-target stool DNA test (K-ras, NDRG4, and BMP3) and eight newly characterized methylated biomarkers were commonly expressed in tumor tissue specimens, independent of FIT result. Additional study using stool-based testing with these new biomarkers will allow assessment of sensitivity, specificity, and clinical utility.

  18. Gene Flow Results in High Genetic Similarity Between Sibiraea (Rosaceae species in the Qinghai-Tibetan Plateau

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    Peng-Cheng Fu

    2016-10-01

    Full Text Available Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of S. laevigata and S. angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45% rather than between species (4.39%. We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of these 2 species resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures between the species occurred.

  19. Genetically similar isolates of Klebsiella pneumoniae serotype K1 causing liver abscesses in three continents.

    Science.gov (United States)

    Turton, Jane F; Englender, Hilary; Gabriel, Samantha N; Turton, Sarah E; Kaufmann, Mary E; Pitt, Tyrone L

    2007-05-01

    The magA gene was sought in hypermucoviscous isolates of Klebsiella spp., the Klebsiella K serotype reference strains and in isolates of the K1 serotype of Klebsiella pneumoniae from the UK, Hong Kong, Israel, Taiwan and Australia. Only K1 isolates were PCR positive for magA; this gene was found in all such isolates tested. Hypermucoviscosity was not confined to magA positive isolates, nor was it found in all magA positive isolates. Comparison of XbaI PFGE profiles revealed that most (19/23) of the magA positive isolates clustered within 72 % similarity, with a further subcluster of isolates, from three different continents, clustering within >80 %. All of the 16 isolates tested within the main cluster had the same sequence type (ST 23) by multilocus sequence typing, with the exception of one isolate, which had a single nucleotide difference at one of the seven loci. This study indicates that a genotype strongly associated with highly invasive disease in Taiwan, where large numbers of cases have been reported, is geographically very widespread.

  20. Dynamics of genetic variability in Anastrepha fraterculus (Diptera: Tephritidae) during adaptation to laboratory rearing conditions.

    Science.gov (United States)

    Parreño, María A; Scannapieco, Alejandra C; Remis, María I; Juri, Marianela; Vera, María T; Segura, Diego F; Cladera, Jorge L; Lanzavecchia, Silvia B

    2014-01-01

    Anastrepha fraterculus is one of the most important fruit fly plagues in the American continent and only chemical control is applied in the field to diminish its population densities. A better understanding of the genetic variability during the introduction and adaptation of wild A. fraterculus populations to laboratory conditions is required for the development of stable and vigorous experimental colonies and mass-reared strains in support of successful Sterile Insect Technique (SIT) efforts. The present study aims to analyze the dynamics of changes in genetic variability during the first six generations under artificial rearing conditions in two populations: a) a wild population recently introduced to laboratory culture, named TW and, b) a long-established control line, named CL. Results showed a declining tendency of genetic variability in TW. In CL, the relatively high values of genetic variability appear to be maintained across generations and could denote an intrinsic capacity to avoid the loss of genetic diversity in time. The impact of evolutionary forces on this species during the adaptation process as well as the best approach to choose strategies to introduce experimental and mass-reared A. fraterculus strains for SIT programs are discussed.

  1. Zebrafish development and genetics: introducing undergraduates to developmental biology and genetics in a large introductory laboratory class.

    Science.gov (United States)

    D'Costa, Allison; Shepherd, Iain T

    2009-06-01

    We have taken advantage of the strengths of the zebrafish model system to introduce developmental biology and genetics to undergraduates in their second semester of the Introductory Biology course at Emory. We designed a 6-week laboratory module based on research being undertaken by faculty in the department, and incorporated experiments that used current research methods including bioinformatics. Students undertook a range of experiments including direct observation of live wild-type zebrafish at different stages of embryogenesis, whole-mount in situ hybridization of mutant and wild-type embryos, vital dye staining of mutant and wild-type embryos, and pharmacological treatments to perturb normal development. These laboratories engaged the students by providing a hands-on, research-centered experience, while also enhancing their written (worksheets and laboratory reports) and oral (group presentation) communication skills. We describe the proceedings of each lab and the logistics of preparing and running these labs for 400-500 students (120 students taking lab each day), and provide a preliminary assessment of the success of the laboratories data based on student evaluations.

  2. Evolutionary genetics of metamorphic failure using wild-caught vs. laboratory axolotls (Ambystoma mexicanum).

    Science.gov (United States)

    Voss, S R; Shaffer, H B

    2000-09-01

    In many organisms metamorphosis allows for an ecologically important habitat-shift from water to land. However, in some salamanders an adaptive life cycle mode has evolved that is characterized by metamorphic failure (paedomorphosis); these species remain in the aquatic habitat throughout the life cycle. Perhaps the most famous example of metamorphic failure is the Mexican axolotl (Ambystoma mexicanum), which has become a focal species for developmental biology since it was introduced into laboratory culture in the 1800s. Our previous genetic linkage mapping analysis, using an interspecific crossing design, demonstrated that a major gene effect underlies the expression of metamorphic failure in laboratory stocks of the Mexican axolotl. Here, we repeated this experiment using A. mexicanum that were sampled directly from their natural habitat at Lake Xochimilco, Mexico. We found no significant association between the major gene and metamorphic failure when wild-caught axolotls were used in the experimental design, although there is evidence of a smaller genetic effect. Thus, there appears to be genetic variation among Mexican axolotls (and possibly A. tigrinum tigrinum) at loci that contribute to metamorphic failure. This result suggests a role for more than one mutation and possibly artificial selection in the evolution of the major gene effect in the laboratory Mexican axolotl.

  3. Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method.

    Science.gov (United States)

    Vidal, A B; Colles, F M; Rodgers, J D; McCarthy, N D; Davies, R H; Maiden, M C J; Clifton-Hadley, F A

    2016-04-01

    The genetic diversity of Campylobacter jejuni and Campylobacter coliisolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645C. jejuniand 106C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuniisolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. ForC. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms forC. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% forC. coli). These results show the complexity of the population structure of Campylobacterin broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical.

  4. Newcastle Disease Viruses Causing Recent Outbreaks Worldwide Show Unexpectedly High Genetic Similarity to Historical Virulent Isolates from the 1940s.

    Science.gov (United States)

    Dimitrov, Kiril M; Lee, Dong-Hun; Williams-Coplin, Dawn; Olivier, Timothy L; Miller, Patti J; Afonso, Claudio L

    2016-05-01

    Virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), a devastating disease of poultry and wild birds. Phylogenetic analyses clearly distinguish historical isolates (obtained prior to 1960) from currently circulating viruses of class II genotypes V, VI, VII, and XII through XVIII. Here, partial and complete genomic sequences of recent virulent isolates of genotypes II and IX from China, Egypt, and India were found to be nearly identical to those of historical viruses isolated in the 1940s. Phylogenetic analysis, nucleotide distances, and rates of change demonstrate that these recent isolates have not evolved significantly from the most closely related ancestors from the 1940s. The low rates of change for these virulent viruses (7.05 × 10(-5) and 2.05 × 10(-5) per year, respectively) and the minimal genetic distances existing between these and historical viruses (0.3 to 1.2%) of the same genotypes indicate an unnatural origin. As with any other RNA virus, Newcastle disease virus is expected to evolve naturally; thus, these findings suggest that some recent field isolates should be excluded from evolutionary studies. Furthermore, phylogenetic analyses show that these recent virulent isolates are more closely related to virulent strains isolated during the 1940s, which have been and continue to be used in laboratory and experimental challenge studies. Since the preservation of viable viruses in the environment for over 6 decades is highly unlikely, it is possible that the source of some of the recent virulent viruses isolated from poultry and wild birds might be laboratory viruses. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  5. HLA similarities indicate shared genetic risk in 21-hydroxylase autoantibody positive South African and United States Addison's disease.

    Science.gov (United States)

    Ross, I L; Babu, S; Armstrong, T; Zhang, L; Schatz, D; Pugliese, A; Eisenbarth, G; Baker Ii, P

    2014-10-01

    Genetic similarities between patients from the United States and South African (SA) Addison's Disease (AD) strengthen evidence for genetic association. SA-AD (n = 73), SA healthy controls (N = 78), and US-AD patients (N = 83) were genotyped for DQA1, DQB1, DRB1, and HLA-B alleles. Serum was tested for the quantity of 21OH-AA and IFNα-AA at the Barbara Davis Center. Although not as profound as in US-AD, in SA-AD 21OH-AA + subjects the predominantly associated risk haplotypes were DRB1*0301-DQB1*0201 (DR3), DRB1*04xx-DQB1*0302 (DR4), and the combined DR3/4 genotype. DQB1*0302 associated DRB1*04xx haplotypes conferred higher risk than those DRB1*04xx haplotypes associated with other DQB1 alleles. We found negative association in 21OH-AA + SA-AD for DQA1*0201-DQB1*0202 and DQA1*0101-DQB1*0501 vs SA controls, and positive association for DQA1*0401-DQB1*0402 vs US-AD. Apart from the class II DR3 haplotype, HLA-B8 did not have an independent effect; however together DR3 and HLA-B8 conferred the highest risk vs 21OH-AA negative SA-AD and SA-controls. HLA-B7 (often with DR4) conferred novel risk in 21OH-AA + SA-AD vs controls. This study represents the first comparison between South African and United States AD populations utilizing genotyping and serology performed at the same center. SA-AD and US-AD 21OH-AA + patients share common HLA risk haplotypes including DR4 (with HLA-B7) and DR3 (with HLA-B8), strengthening previously described HLA associations and implicating similar genetic etiology. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Genetic variation of male reproductive success in a laboratory population of Anopheles gambiae

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    Voordouw Maarten J

    2007-07-01

    Full Text Available Abstract Background For Anopheline mosquitoes, the vectors of human malaria, genetic variation in male reproductive success can have important consequences for any control strategy based on the release of transgenic or sterile males. Methods A quantitative genetics approach was used to test whether there was a genetic component to variation in male reproductive success in a laboratory population of Anopheles gambiae. Swarms of full sibling brothers were mated with a fixed number of females and their reproductive success was measured as (1 proportion of ovipositing females, (2 proportion of ovipositing females that produced larvae, (3 proportion of females that produced larvae, (4 number of eggs laid per female, (5 number of larvae per ovipositing female and (6 number of larvae per female. Results The proportion of ovipositing females (trait 1 and the proportion of ovipositing females that produced larvae (trait 2 differed among full sib families, suggesting a genetic basis of mating success. In contrast, the other measures of male reproductive success showed little variation due to the full sib families, as their variation are probably mostly due to differences among females. While age at emergence and wing length of the males were also heritable, they were not associated with reproductive success. Larger females produced more eggs, but males did not prefer such partners. Conclusion The first study to quantify genetic variation for male reproductive success in A. gambiae found that while the initial stages of male reproduction (i.e. the proportion of ovipositing females and the proportion of ovipositing females that produced larvae had a genetic basis, the overall reproductive success (i.e. the mean number of larvae per female did not.

  7. Origins of albino and hooded rats: implications from molecular genetic analysis across modern laboratory rat strains.

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    Takashi Kuramoto

    Full Text Available Albino and hooded (or piebald rats are one of the most frequently used laboratory animals for the past 150 years. Despite this fact, the origin of the albino mutation as well as the genetic basis of the hooded phenotype remained unclear. Recently, the albino mutation has been identified as the Arg299His missense mutation in the Tyrosinase gene and the hooded (H locus has been mapped to the ∼460-kb region in which only the Kit gene exists. Here, we surveyed 172 laboratory rat strains for the albino mutation and the hooded (h mutation that we identified by positional cloning approach to investigate possible genetic roots and relationships of albino and hooded rats. All of 117 existing laboratory albino rats shared the same albino missense mutation, indicating they had only one single ancestor. Genetic fine mapping followed by de novo sequencing of BAC inserts covering the H locus revealed that an endogenous retrovirus (ERV element was inserted into the first intron of the Kit gene where the hooded allele maps. A solitary long terminal repeat (LTR was found at the same position to the ERV insertion in another allele of the H locus, which causes the so called Irish (h(i phenotype. The ERV and the solitary LTR insertions were completely associated with the hooded and Irish coat patterns, respectively, across all colored rat strains examined. Interestingly, all 117 albino rat strains shared the ERV insertion without any exception, which strongly suggests that the albino mutation had originally occurred in hooded rats.

  8. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

    DEFF Research Database (Denmark)

    Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O.

    2017-01-01

    Adaptive laboratory evolution (ALE) experiments are often designed to maintain a static culturing environment to minimize confounding variables that could influence the adaptive process, but dynamic nutrient conditions occur frequently in natural and bioprocessing settings. To study the nature...... of carbon substrate fitness tradeoffs, we evolved batch cultures of Escherichia coli via serial propagation into tubes alternating between glucose and either xylose, glycerol, or acetate. Genome sequencing of evolved cultures revealed several genetic changes preferentially selected for under dynamic...... to the observed distinct adaptive strategies. This study gives insight into the population dynamics of adaptation in an alternating environment and into the underlying metabolic and genetic mechanisms. Furthermore, ALE-generated optimized strains have phenotypes with potential industrial bioprocessing...

  9. MATLAB code to estimate landslide volume from single remote sensed image using genetic algorithm and imagery similarity measurement

    Science.gov (United States)

    Wang, Ting-Shiuan; Yu, Teng-To; Lee, Shing-Tsz; Peng, Wen-Fei; Lin, Wei-Ling; Li, Pei-Ling

    2014-09-01

    Information regarding the scale of a hazard is crucial for the evaluation of its associated impact. Quantitative analysis of landslide volume immediately following the event can offer better understanding and control of contributory factors and their relative importance. Such information cannot be gathered for each landslide event, owing to limitations in obtaining useable raw data and the necessary procedures of each applied technology. Empirical rules are often used to predict volume change, but the resulting accuracy is very low. Traditional methods use photogrammetry or light detection and ranging (LiDAR) to produce a post-event digital terrain model (DTM). These methods are both costly and time-intensive. This study presents a technique to estimate terrain change volumes quickly and easily, not only reducing waiting time but also offering results with less than 25% error. A genetic algorithm (GA) programmed MATLAB is used to intelligently predict the elevation change for each pixel of an image. This deviation from the pre-event DTM becomes a candidate for the post-event DTM. Thus, each changed DTM is converted into a shadow relief image and compared with a single post-event remotely sensed image for similarity ranking. The candidates ranked in the top two thirds are retained as parent chromosomes to produce offspring in the next generation according to the rules of GAs. When the highest similarity index reaches 0.75, the DTM corresponding to that hillshade image is taken as the calculated post-event DTM. As an example, a pit with known volume is removed from a flat, inclined plane to demonstrate the theoretical capability of the code. The method is able to rapidly estimate the volume of terrain change within an error of 25%, without the delays involved in obtaining stereo image pairs, or the need for ground control points (GCPs) or professional photogrammetry software.

  10. Mechanical design, analysis, and laboratory testing of a dental implant with axial flexibility similar to natural tooth with periodontal ligament.

    Science.gov (United States)

    Pektaş, Ömer; Tönük, Ergin

    2014-11-01

    At the interface between the jawbone and the roots of natural teeth, a thin, elastic, shock-absorbing tissue, called the periodontal ligament, forms a cushion which provides certain flexibility under mechanical loading. The dental restorations supported by implants, however, involve comparatively rigid connections to the jawbone. This causes overloading of the implant while bearing functional loading together with neighboring natural teeth, which leads to high stresses within the implant system and in the jawbone. A dental implant, with resilient components in the upper structure (abutment) in order to mimic the mechanical behavior of the periodontal ligament in the axial direction, was designed, analyzed in silico, and produced for mechanical testing. The aims of the design were avoiding high levels of stress, loosening of the abutment connection screw, and soft tissue irritations. The finite element analysis of the designed implant revealed that the elastic abutment yielded a similar axial mobility with the natural tooth while keeping stress in the implant at safe levels. The in vitro mechanical testing of the prototype resulted in similar axial mobility predicted by the analysis and as that of a typical natural tooth. The abutment screw did not loosen under repeated loading and there was no static or fatigue failure.

  11. The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics

    Energy Technology Data Exchange (ETDEWEB)

    Chesler, Elissa J [ORNL; Branstetter, Lisa R [ORNL; Churchill, Gary A [Jackson Laboratory, The, Bar Harbor, ME; Culiat, Cymbeline T [ORNL; Galloway, Leslie D [ORNL; Jackson, Barbara L [ORNL; Johnson, Dabney K [ORNL; Miller, Darla R [ORNL; Philip, Vivek M [ORNL; Threadgill, David [University of North Carolina, Chapel Hill; Voy, Brynn H [ORNL; Williams, Robert [University of Tennessee Health Science Center, Memphis; Manly, Kenneth [University of Tennessee Health Science Center, Memphis

    2008-01-01

    Complex traits and disease co-morbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of the resources needed to investigate biomolecular networks and ultimately systems level phenotypes, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include high levels of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independent recombination events. Implementation of the Collaborative Cross has been in progress at the Oak Ridge National Laboratory (ORNL) since May 2005. This is achieved through a software assisted breeding program with fully traceable lineages, performed in a uniform environment. Currently, there are 650 lines in production with almost 200 lines over seven generations of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analysis of recombination history, allele loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.

  12. Interferon response following infection with genetically similar isolates of viral haemorrhagic septicaemia virus (VHSV) exhibiting contrasting virulence in rainbow trout.

    Science.gov (United States)

    Campbell, S; McBeath, A; Secombes, C; Snow, M; Collet, B

    2011-01-01

    Isolates of viral haemorrhagic septicaemia virus (VHSV) were identified which are genetically similar yet, based on their isolation history were considered likely to differ in virulence in juvenile rainbow trout. An experimental infection study was performed in order to verify this hypothesis and provide an experimental infectivity model with which to investigate the basis for susceptibility of rainbow trout to this commercially important virus. Significant differences in mortality were obtained following both intraperitoneal (IP) injection and immersion challenges with an early marine (DK-M.Rhabdo) and early rainbow trout VHSV isolate (DK-F1) respectively. Expression of Type I IFN, Mx1 (an IFN-inducible protein), and viral genes (encoding nucleo-, phospho-, matrix, glyco- and non-viron proteins) was studied in sequential tissue samples using real-time quantitative PCR (QPCR). Resulting data revealed a significant increase in IFN and Mx1 expression detected in fish challenged by IP injection with both isolates. Expression levels of these genes were directly related to the degree of viral replication as measured by the expression of VHSV RNAs. In immersion-challenged fish a significant increase in Mx1 was observed only when using the virulent isolate DK-F1; however no elevated host response was detectable in fish challenged with the marine isolate DK-M.Rhabdo. Quintessentially the inability to detect any virus in trout challenged with the marine isolate via immersion suggests the virus was incapable of establishing infection. The mechanisms for this appear to be more related to initial cellular entry and replication rather than due to the overcoming of initial infection via an elevated host innate immune response.

  13. The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes

    NARCIS (Netherlands)

    Vijver, D.A. van de; Wensing, A.M.J.; Angarano, G.; Asjo, B.; Balotta, C.; Camacho, R.; Chaix, M.; Costagliola, D.; De Luca, A.; Derdelinckx, I.; Grossman, Z.; Hamouda, O.; Hatzakis, A.; Hemmer, R.; Hoepelman, A.I.M.; Horban, A.; Korn, K.; Kücherer, C.; Leitner, T.; Loveday, C.; MacRae, E.; Maljkovic, I.; Mendoza, C. de; Meyer, L.; Nielsen, C.; Op de Coul, E.L.M.; Omaasen, V.; Paraskevis, D.; Perrin, L.; Puchhammer-Stöckl, E.; Salminen, M.; Schmit, J.; Scheider, F.; Schuurman, R.; Soriano, V.; Stanczak, G.; Stanojevic, M.; Vandamme, A.; Laethem, K. van; Violin, M.; Wilde, K.; Yerly, S.; Zazzi, M.; Boucher, C.A.B.

    2006-01-01

    The genetic barrier, defined as the number of mutations required to overcome drug-selective pressure, is an important factor for the development of HIV drug resistance. Because of high variability between subtypes, particular HIV-1 subtypes could have different genetic barriers for drug resistance s

  14. Use of latent class models to accommodate inter-laboratory variation in assessing genetic polymorphisms associated with disease risk

    Directory of Open Access Journals (Sweden)

    Walter Stephen D

    2008-08-01

    Full Text Available Abstract Background Researchers wanting to study the association of genetic factors with disease may encounter variability in the laboratory methods used to establish genotypes or other traits. Such variability leads to uncertainty in determining the strength of a genotype as a risk factor. This problem is illustrated using data from a case-control study of cervical cancer in which some subjects were independently assessed by different laboratories for the presence of a genetic polymorphism. Inter-laboratory agreement was only moderate, which led to a very wide range of empirical odds ratios (ORs with the disease, depending on how disagreements were treated. This paper illustrates the use of latent class models (LCMs and to estimate OR while taking laboratory accuracy into account. Possible LCMs are characterised in terms of the number of laboratory measurements available, and if their error rates are assumed to be differential or non-differential by disease status and/or laboratory. Results The LCM results give maximum likelihood estimates of laboratory accuracy rates and the OR of the genetic variable and disease, and avoid the ambiguities of the empirical results. Having allowed for possible measurement error in the expure, the LCM estimates of exposure – disease associations are typically stronger than their empirical equivalents. Also the LCM estimates exploit all the available data, and hence have relatively low standard errors. Conclusion Our approach provides a way to evaluate the association of a polymorphism with disease, while taking laboratory measurement error into account. Ambiguities in the empirical data arising from disagreements between laboratories are avoided, and the estimated polymorphism-disease association is typically enhanced.

  15. A model of genetic guidance for hemoglobinopathy patients and laboratory diagnosis of family members as educational and preventive measures

    Directory of Open Access Journals (Sweden)

    Tatiana Dela-Sávia Ferreira

    2012-01-01

    Full Text Available BACKGROUND: The high frequency of hemoglobinopathies in Brazil constitutes a public health problem and thus educational and preventive measures are necessary to reduce the incidence. Genetic guidance, a modality of genetic counseling, and family screening are measures that can assist in reproductive decisions and mitigate clinical, psychological and social problems of families with these disorders. OBJETIVE: The objective of the current study was to evaluate the effectiveness of educational and preventive measures for hemoglobinopathies using genetic guidance and laboratory screening of families. METHODS: The diagnoses of patients with hemoglobinopathies were confirmed and then the level of knowledge about their disease was evaluated and genetic guidance was provided. Three months later, the level of assimilated information of these patients was evaluated. In addition, laboratory diagnosis of family members was carried out. RESULTS: Diagnosis of sickle cell anemia was confirmed for most patients. Moreover, the majority of the patients who had a low level of knowledge before genetic guidance (68.8% demonstrated a higher level of assimilated information after the process (81.8%. Almost 70% of the family members had hemoglobin changes and some had hemoglobinopathies (2.6%. They were duly informed about the results of the examinations, which made it possible to investigate further. CONCLUSION: Genetic guidance and family screening were effective preventive and educational measures that improved the quality of life of patients, preventing complications and sequels and allowed the referral of those who may transmit altered genes for clinical diagnosis and to genetic counseling services.

  16. Self-similarity of skeletal structures in laboratory high current electric discharges (plasmas and fractal dust deposits), severe weather phenomena and space

    Science.gov (United States)

    Kukushkin, A. B.; Rantsev-Kartinov, V. A.

    2003-10-01

    The phenomenon of skeletal structures (tubules, cartwheels, and their simple combinations) formerly found in laboratory plasmas, is extended to atmospheric and cosmic phenomena (Phys. Lett. A 306, 175, Dec. 2002). The long-lived filaments in plasmas have been suggested (1998) to possess a skeleton self-assembled during electric breakdown from wildly produced nanodust. The proof-of-concept studies revealed the skeletal structures in (1) plasmas in tokamaks, Z-pinches, plasma focus (in the range 0.01-10 cm), including the electric breakdown stage of discharge, (2) dust deposits in tokamak (10 nm - 10 microns), (3) hailstones (1-10 cm), tornado (10 m -1 km), (4) a wide class of objects in space (10^11-10^23 cm). The similarity of, and the trend toward self-similarity in, skeletal structures suggest all them to possess a fractal condensed matter of particular topology of the fractal. Here we discuss probable role of skeletal structures in the fast nonlocal transport of energy in strongly localized severe weather phenomena (tornado) and laboratory plasmas.

  17. Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

    Science.gov (United States)

    Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

    2005-01-01

    A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

  18. Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

    Science.gov (United States)

    Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

    2005-01-01

    A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

  19. DNA fingerprinting and anastomosis grouping reveal similar genetic diversity in Rhizoctonia species infecting turfgrasses in the transition zone of USA

    Science.gov (United States)

    Rhizoctonia blight (sensu lato) is a common and serious disease of many turfgrass species. The most widespread causal agent, R. solani, consists of several genetically different subpopulations. Though hyphal anastomosis reactions have been used to group Rhizoctonia species, they are time consuming a...

  20. Genetic similarities among four species of the Plectranthus (L’Hér. genus - DOI: 10.4025/actascibiolsci.v32i1.880 Genetic similarity among four species of Plectranthus genus - DOI: 10.4025/actascibiolsci.v32i1.880

    Directory of Open Access Journals (Sweden)

    Eugenia Jacira Bolacel Braga

    2009-12-01

    Full Text Available The Plectranthus genus comprises several species generally referred to as boldo, which are highly used in popular medicine due to their anti-dyspeptic, analgesic and digestion-stimulating properties. The amount of natural active principles can vary greatly in the related genotypes, which may lead to the inappropriate use of these plants. This work aimed to analyze the interspecific diversity among four species of the Plectranthus genus (P. grandis, P. barbatus, P. neochilus and P. amboinicus and the intraspecific diversity of P. barbatus collected from different places in southern Brazil, by means of the RAPD technique. A higher genetic similarity was observed between the P. neochilus and P. amboinicus species (80%, followed by P. grandis and P. barbatus (77%. P. barbatus genotypes from Passo Fundo and Porto Alegre showed a genetic similarity which was close to 100%, while the genetic similarity for P. barbatus genotypes from other locations was higher than 96%. Although a low variability among genotypes of this species was found in this study, RAPD markers allowed a clear differentiation among the analyzed genotypes, showing a 53% mean genetic similarity, with a high correlation value (r = 0.99, which proves a high agreement between the genetic similarity and clustering data.Medicinal plants are widely used by the population, therefore they are important sources of natural chemical products. Plectranthus includes species related as “boldo” that have anti-dyspeptics, analgesic and stimulants of digestion properties. Related species or genotypes can differ widely in the amount of natural active principles, in such case the lack of genetic fitness can lead to the use of not appropriate plants to the population health. Molecular techniques can be used for DNA-fingerprinting of plants providing its correct identification. This work aimed at verifying the genetic diversity among four species of Plectranthus genus (P. grandis, P. barbatus, P

  1. Plant Resistance to Virus Diseases through Genetic Engineering: Can a Similar Approach Control Plant-parasitic Nematodes?

    OpenAIRE

    Reimann-Philipp, Ulrich; Beachy, Roger N.

    1993-01-01

    Genetically engineered resistance against plant virus diseases has been achieved by transforming plants with gene constructs that encode viral sequences. Several successful field trials of virus-resistant transgenic plants have been carried out. Specific features of virus infection make it possible to interfere with different steps of the infection and disease cycle by accumulating products of chimeric genes introduced into transgenic plants. In this paper we describe the most common methods ...

  2. Similar patterns of mitochondrial vulnerability and rescue induced by genetic modification of alpha-synuclein, parkin, and DJ-1 in Caenorhabditis elegans.

    Science.gov (United States)

    Ved, Rina; Saha, Shamol; Westlund, Beth; Perier, Celine; Burnam, Lucinda; Sluder, Anne; Hoener, Marius; Rodrigues, Cecilia M P; Alfonso, Aixa; Steer, Clifford; Liu, Leo; Przedborski, Serge; Wolozin, Benjamin

    2005-12-30

    How genetic and environmental factors interact in Parkinson disease is poorly understood. We have now compared the patterns of vulnerability and rescue of Caenorhabditis elegans with genetic modifications of three different genetic factors implicated in Parkinson disease (PD). We observed that expressing alpha-synuclein, deleting parkin (K08E3.7), or knocking down DJ-1 (B0432.2) or parkin produces similar patterns of pharmacological vulnerability and rescue. C. elegans lines with these genetic changes were more vulnerable than nontransgenic nematodes to mitochondrial complex I inhibitors, including rotenone, fenperoximate, pyridaben, or stigmatellin. In contrast, the genetic manipulations did not increase sensitivity to paraquat, sodium azide, divalent metal ions (Fe(II) or Cu(II)), or etoposide compared with the nontransgenic nematodes. Each of the PD-related lines was also partially rescued by the antioxidant probucol, the mitochondrial complex II activator, D-beta-hydroxybutyrate, or the anti-apoptotic bile acid tauroursodeoxycholic acid. Complete protection in all lines was achieved by combining d-beta-hydroxybutyrate with tauroursodeoxycholic acid but not with probucol. These results show that diverse PD-related genetic modifications disrupt the mitochondrial function in C. elegans, and they raise the possibility that mitochondrial disruption is a pathway shared in common by many types of familial PD.

  3. Genetic similarity of polyploids - A new version of the computer program POPDIST (ver. 1.2.0) considers intraspecific genetic differentiation

    DEFF Research Database (Denmark)

    Tomiuk, Jürgen; Guldbrandtsen, Bernt; Loeschcke, Volker

    2009-01-01

    For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically eithe...

  4. Genetic effects of acute spermatogonial x-irradiation of the laboratory rat

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, J.R.; Chapman, A.B.

    1977-02-01

    The genetic effects of one generation of spermatogonial x-irradiation in rats, by a single dose of 600 r in one experiment and by a fractionated dose of 450 r in another, were measured in three generations of their descendants. Estimates of dominant lethal mutation rates, (2 to 3) x 10/sup -4//gamete/r, from litter size differences between irradiated and nonirradiated stock were consistent with previous estimates from rats and mice. Similar consistency was found for estimates of sex-linked recessive mutation rates, (1 to 2) x 10/sup -4/ chromosome/r, from male proportions within strains; however, when measured in crossbreds the proportion of males was higher in the irradiated than in the nonirradiated lines. This inconsistency in results is in keeping with the contradictory results reported for recessive sex-linked lethal mutation rates in mice. The effects used to estimate recessive lethal mutation rates which were unusually high, (2 to 14) x 10/sup -4//gamete/r, were not significant. Other factors that could have contributed to the observed effects are postulated.

  5. Comparison of saline tolerance among genetically similar species of Fusarium and Meloidogyne recovered from marine and terrestrial habitats

    Science.gov (United States)

    Elmer, W. H.; LaMondia, J. A.

    2014-08-01

    Successful plant pathogens co-evolve and adapt to the environmental constraints placed on host plants. We compared the salt tolerance of two salt marsh pathogens, Fusarium palustre and Meloidogyne spartinae, to genetically related terrestrial species, F. sporotrichioides and Meloidogyne hapla, to assess whether the salt marsh species had acquired selective traits for persisting in saline environments or if salt tolerance was comparable among Fusarium and Meloidogyne species. Comparisons of both species were made in vitro in vessels containing increasing concentration of NaCl. We observed that F. palustre was more tolerant to NaCl than F. sporotrichioides. The radial expansion of F. palustre on NaCl-amended agar plates was unaffected by increasing concentrations up to 0.3 M. F. sporotrichioides showed large reductions in growth at the same concentrations. Survival of M. hapla was greatest at 0 M, and reduced by half in a 0.3 M solution for 4 days. No juveniles survived exposure to 0.3 M NaCl for 12 days. M. spartinae survived at all NaCl concentrations tested, including 1.0 M for at least 12 days. These findings are consistent with the hypothesis that marine organisms in the upper tidal zone must osmoregulate to withstand a wide range of salinity and provide evidence that these pathogens evolved in saline conditions and are not recent introductions from terrestrial niches.

  6. [Plant genetic engineering in Monsanto company: from the first laboratory experiments to worldwide practical use].

    Science.gov (United States)

    Konov, A L; Velchev, M; Parcel, D

    2005-01-01

    The history of modern biotechnology of agricultural plants is briefly considered in the article. Methods of genetic transformation and regeneration of transgenic plants as well as the mechanisms of resistance of genetically modified plants to herbicides and pests are discussed. By the example of genetically modified varieties and hybrids there are shown the ways of solving the problem of weeds and pests. The questions of biosafety legislation in different countries are considered.

  7. Genetic modifiers of sickle cell anemia in the BABY HUG cohort: influence on laboratory and clinical phenotypes.

    Science.gov (United States)

    Sheehan, Vivien A; Luo, Zhaoyu; Flanagan, Jonathan M; Howard, Thad A; Thompson, Bruce W; Wang, Winfred C; Kutlar, Abdullah; Ware, Russell E

    2013-07-01

    The recently completed BABY HUG trial investigated the safety and efficacy of hydroxyurea in infants with sickle cell anemia (SCA). To investigate the effects of known genetic modifiers, genomic DNA on 190 randomized subjects were analyzed for alpha thalassemia, beta-globin haplotype, polymorphisms affecting endogenous fetal hemoglobin (HbF) levels (XmnI, BCL11A, and HBS1L-MYB), UGT1A1 promoter polymorphisms, and the common G6PD A(-) mutation. At study entry, infants with alpha thalassemia trait had significantly lower mean corpuscular volume, total bilirubin, and absolute reticulocyte count. Beta-globin haplotypes associated with milder disease had significantly higher hemoglobin and %HbF. BCL11A and XmnI polymorphisms had significant effects on baseline HbF, while UGT1A1 promoter polymorphisms significantly influenced baseline serum bilirubin. At study exit, subjects randomized to placebo still exhibited laboratory effects of alpha thalassemia and other modifiers, while those assigned hydroxyurea had treatment effects that exceeded most genetic influences. The pain phenotype was influenced by HbF modifiers in both treatment groups. These data document that genetic polymorphisms do modify laboratory and clinical phenotypes even in very young patients with SCA. The hydroxyurea effects are more potent, however, indicating that treatment criteria should not be limited to certain genetic subsets, and supporting the use of hydroxyurea for all young patients with SCA.

  8. The common ecotoxicology laboratory strain of Hyalella azteca is genetically distinct from most wild strains sampled in eastern North America.

    Science.gov (United States)

    Major, Kaley; Soucek, David J; Giordano, Rosanna; Wetzel, Mark J; Soto-Adames, Felipe

    2013-11-01

    The amphipod Hyalella azteca is commonly used as a model for determining safe concentrations of contaminants in freshwaters. The authors sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene for representatives of 38 populations of this species complex from US and Canadian toxicology research laboratories and eastern North American field sites to determine their genetic relationships. With 1 exception, all US and Canadian laboratory cultures sampled were identified as conspecific. In 22 wild populations spanning 5 US states and 1 Canadian province, the commonly occurring laboratory species was found only in northern Florida, USA. Therefore, the diversity of the H. azteca species complex detected in the wild is not accurately represented in North American laboratories, questioning the reliability of H. azteca cultures currently in use to accurately predict the responses of wild populations in ecotoxicological assays. The authors also examined the utility of different COI nucleotide fragments presently in use to determine phylogenetic relationships in this group and concluded that saturation in DNA sequences leads to inconsistent relationships between clades. Amino acid sequences for COI were not saturated and may allow a more accurate phylogeny estimate. Hyalella azteca is crucial for developing water-quality regulations; therefore, laboratories should know and standardize the strain(s) they use to confidently compare toxicity tests across laboratories and determine whether they are an appropriate surrogate for their regions.

  9. Similar genetic basis of resistance to Bt toxin Cry1Ac in Boll-selected and diet-selected strains of pink bollworm.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Fabrick

    Full Text Available Genetically engineered cotton and corn plants producing insecticidal Bacillus thuringiensis (Bt toxins kill some key insect pests. Yet, evolution of resistance by pests threatens long-term insect control by these transgenic Bt crops. We compared the genetic basis of resistance to Bt toxin Cry1Ac in two independently derived, laboratory-selected strains of a major cotton pest, the pink bollworm (Pectinophora gossypiella [Saunders]. The Arizona pooled resistant strain (AZP-R was started with pink bollworm from 10 field populations and selected with Cry1Ac in diet. The Bt4R resistant strain was started with a long-term susceptible laboratory strain and selected first with Bt cotton bolls and later with Cry1Ac in diet. Previous work showed that AZP-R had three recessive mutations (r1, r2, and r3 in the pink bollworm cadherin gene (PgCad1 linked with resistance to Cry1Ac and Bt cotton producing Cry1Ac. Here we report that inheritance of resistance to a diagnostic concentration of Cry1Ac was recessive in Bt4R. In interstrain complementation tests for allelism, F(1 progeny from crosses between AZP-R and Bt4R were resistant to Cry1Ac, indicating a shared resistance locus in the two strains. Molecular analysis of the Bt4R cadherin gene identified a novel 15-bp deletion (r4 predicted to cause the loss of five amino acids upstream of the Cry1Ac-binding region of the cadherin protein. Four recessive mutations in PgCad1 are now implicated in resistance in five different strains, showing that mutations in cadherin are the primary mechanism of resistance to Cry1Ac in laboratory-selected strains of pink bollworm from Arizona.

  10. Similar genetic basis of resistance to Bt toxin Cry1Ac in Boll-selected and diet-selected strains of pink bollworm.

    Science.gov (United States)

    Fabrick, Jeffrey A; Tabashnik, Bruce E

    2012-01-01

    Genetically engineered cotton and corn plants producing insecticidal Bacillus thuringiensis (Bt) toxins kill some key insect pests. Yet, evolution of resistance by pests threatens long-term insect control by these transgenic Bt crops. We compared the genetic basis of resistance to Bt toxin Cry1Ac in two independently derived, laboratory-selected strains of a major cotton pest, the pink bollworm (Pectinophora gossypiella [Saunders]). The Arizona pooled resistant strain (AZP-R) was started with pink bollworm from 10 field populations and selected with Cry1Ac in diet. The Bt4R resistant strain was started with a long-term susceptible laboratory strain and selected first with Bt cotton bolls and later with Cry1Ac in diet. Previous work showed that AZP-R had three recessive mutations (r1, r2, and r3) in the pink bollworm cadherin gene (PgCad1) linked with resistance to Cry1Ac and Bt cotton producing Cry1Ac. Here we report that inheritance of resistance to a diagnostic concentration of Cry1Ac was recessive in Bt4R. In interstrain complementation tests for allelism, F(1) progeny from crosses between AZP-R and Bt4R were resistant to Cry1Ac, indicating a shared resistance locus in the two strains. Molecular analysis of the Bt4R cadherin gene identified a novel 15-bp deletion (r4) predicted to cause the loss of five amino acids upstream of the Cry1Ac-binding region of the cadherin protein. Four recessive mutations in PgCad1 are now implicated in resistance in five different strains, showing that mutations in cadherin are the primary mechanism of resistance to Cry1Ac in laboratory-selected strains of pink bollworm from Arizona.

  11. Genetic similarity between Taenia solium cysticerci collected from the two distant endemic areas in North and North East India.

    Science.gov (United States)

    Sharma, Monika; Devi, Kangjam Rekha; Sehgal, Rakesh; Narain, Kanwar; Mahanta, Jagadish; Malla, Nancy

    2014-01-01

    Taenia solium taeniasis/cysticercosis is a major public health problem in developing countries. This study reports genotypic analysis of T. solium cysticerci collected from two different endemic areas of North (Chandigarh) and North East India (Dibrugarh) by the sequencing of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The variation in cox1 sequences of samples collected from these two different geographical regions located at a distance of 2585 km was minimal. Alignment of the nucleotide sequences with different species of Taenia showed the similarity with Asian genotype of T. solium. Among 50 isolates, 6 variant nucleotide positions (0.37% of total length) were detected. These results suggest that population in these geographical areas are homogenous.

  12. High similarity of Trypanosoma cruzi kDNA genetic profiles detected by LSSP-PCR within family groups in an endemic area of Chagas disease in Brazil

    Directory of Open Access Journals (Sweden)

    Sandra Maria Alkmim-Oliveira

    2014-10-01

    Full Text Available Introduction Determining the genetic similarities among Trypanosoma cruzi populations isolated from different hosts and vectors is very important to clarify the epidemiology of Chagas disease. Methods An epidemiological study was conducted in a Brazilian endemic area for Chagas disease, including 76 chronic chagasic individuals (96.1% with an indeterminate form; 46.1% with positive hemoculture. Results T. cruzi I (TcI was isolated from one child and TcII was found in the remaining (97.1% subjects. Low-stringency single-specific-primer-polymerase chain reaction (LSSP-PCR showed high heterogeneity among TcII populations (46% of shared bands; however, high similarities (80-100% among pairs of mothers/children, siblings, or cousins were detected. Conclusions LSSP-PCR showed potential for identifying similar parasite populations among individuals with close kinship in epidemiological studies of Chagas disease.

  13. Genetically similar strains of Escherichia coli O157:H7 isolated from sheep, cattle and human patients

    Directory of Open Access Journals (Sweden)

    Söderlund Robert

    2012-10-01

    Full Text Available Abstract Background Comparatively little is known about the prevalence or the molecular characteristics of the zoonotic pathogen E. coli O157:H7 in the sheep reservoir. To investigate this and determine the host specificity of subclones of the bacterium, we have conducted a slaughterhouse prevalence study in sheep and compared the collected isolates to O157:H7 previously isolated from cattle and human patients. Results Verotoxin-producing O157:H7 was found in 11/597 (1.8% of samples from sheep in Swedish slaughterhouses, 9/492 faecal (1.8% and 2/105 ear samples (1.9%. All positive sheep were eaeA, hlyA, cdtV-B, vtx1, and partial sequencing of vtx2. The observed profiles were similar to those of cattle strains investigated previously. Conclusions The same pathogenic subtypes of VTEC O157:H7, including the highly virulent clade 8, appear to be present in both sheep and cattle in Sweden, suggesting strains can circulate freely between ruminant reservoirs.

  14. Isolation and Genetic Analysis of an Environmental Bacteriophage: A 10-Session Laboratory Series in Molecular Virology

    Science.gov (United States)

    Williamson, Ryan P.; Barker, Brent T.; Drammeh, Hamidou; Scott, Jefferson; Lin, Joseph

    2014-01-01

    Bacterial viruses, otherwise known as bacteriophage (or phage), are some of the most abundant viruses found in the environment. They can be easily isolated from water or soil and are ideal for use in laboratory classrooms due to their ease of culture and inherent safety. Here, we describe a series of 10 laboratory exercises where students collect,…

  15. Isolation and Genetic Analysis of an Environmental Bacteriophage: A 10-Session Laboratory Series in Molecular Virology

    Science.gov (United States)

    Williamson, Ryan P.; Barker, Brent T.; Drammeh, Hamidou; Scott, Jefferson; Lin, Joseph

    2014-01-01

    Bacterial viruses, otherwise known as bacteriophage (or phage), are some of the most abundant viruses found in the environment. They can be easily isolated from water or soil and are ideal for use in laboratory classrooms due to their ease of culture and inherent safety. Here, we describe a series of 10 laboratory exercises where students collect,…

  16. IMPROVED GENETIC ALGORITHM BASED ON INDIVIDUAL SIMILARITY EVALUATION STRATEGY%基于个体相似性评价策略的改进遗传算法

    Institute of Scientific and Technical Information of China (English)

    汤可宗; 张彤; 罗立民

    2016-01-01

    Genetic algorithm is a method of searching the optimal solution by simulating natural evolutionary process.But it always requires longer computation time for the best solution in solving process.This paper presents an improved genetic algorithm,it is based on individual similarity evaluation strategy.In it a new rotation crossover operator is incorporated.The fitness value of each individual is assigned according to its similarity and reliability with its parents.The real fitness of individual is only evaluated when the reliability value is below a threshold.Experimental results show that the fitness values of individual derived from similarity evaluation strategy are close to the actual ones,and the number of evaluations required for seeking the optimal solution by the improved genetic algorithm is significantly less than that of traditional genetic algorithm.Additionally,the data on test criterion show that the performance of the proposed algorithm and the optimal solution derived from it are relatively better than the traditional genetic algorithm as well.%遗传算法是一种通过模拟自然进化过程搜索最优解的方法。但这种算法在求解最优解过程中总是以计算时间为代价来换得最优解的产生。对此,提出一种基于个体相似`性评价策略的改进遗传算法,融入了一种新的旋转交叉算子,每个子个体根据其与父个体的相似度和可信度来确定个体的适应度值,仅当可信度值低于某个阈值时,个体才做真实的适应度计算。实验结果显示,相似性评价策略计算得到的个体适应度值接近真实的适应度值,并且改进的算法求得最优解需要的评价次数明显要少于传统遗传算法,而在测试准测上的数据表明:提出的改进遗传算法相对于传统遗传算法,性能较好且求得的最优解也较为理想。

  17. Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes.

    Directory of Open Access Journals (Sweden)

    Marc Ciosi

    2014-02-01

    Full Text Available BACKGROUND: The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. METHODOLOGY/PRINCIPAL FINDINGS: We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC. There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. CONCLUSIONS/SIGNIFICANCE: All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.

  18. Evaluation of distal symmetric polyneuropathy: the role of laboratory and genetic testing (an evidence-based review).

    Science.gov (United States)

    England, J D; Gronseth, G S; Franklin, G; Carter, G T; Kinsella, L J; Cohen, J A; Asbury, A K; Szigeti, K; Lupski, J R; Latov, N; Lewis, R A; Low, P A; Fisher, M A; Herrmann, D; Howard, J F; Lauria, G; Miller, R G; Polydefkis, M; Sumner, A J

    2009-01-01

    Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP. A literature review using MEDLINE, EMBASE, Science Citation Index, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based on the level of evidence. (1) Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B(12) with metabolites (methylmalonic acid with or without homocysteine), and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). (2) Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities, which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).

  19. Genetic similarity between coriander genotypes using ISSR markers Similaridade genética entre genótipos de coentro por marcadores ISSR

    Directory of Open Access Journals (Sweden)

    Roberto de A Melo

    2011-12-01

    Full Text Available With the development of new cultivars, a precise genetic characterization is essential for improvement programs or for cultivar registration and protection. Molecular markers have been complementing the traditional morphological and agronomic characterization techniques because they are virtually unlimited, cover the whole genome and are not environmentally influenced. Genetic characterization constitutes the basis for studies involving estimates of genetic similarity. Therefore, the objective of the present study was to evaluate the genetic similarity between ten coriander genotypes (nine cultivars and one line using ISSR markers. The cultivars used were: Americano, Asteca, Palmeira, Português, Santo, Supéria, Tabocas, Tapacurá, Verdão and the experimental line HTV-9299. The genetic similarity between the cultivars was estimated using 227 banded regions of ISSR molecular markers. The UBC 897 oligonucleotide generated the highest number of fragments (16, resulting in a higher polymorphism. The results indicate that the twenty-nine oligonucleotides chosen were satisfactory for detecting polymorphism. Based on the grouping analysis determined from the similarity data, there were two groups and two sub-groups. The calculated similarity for the genotypes varied from 52 to 75%. The lowest similarity was observed between Português and Verdão, at 52%. The highest similarity was found between Português and Palmeira, at 75%. The ISSR is efficient for identifying DNA polymorphism in coriander.Com o surgimento de novas cultivares, uma caracterização genética precisa é essencial, visando à utilização em programas de melhoramento ou para fins de registros e ou proteção de cultivares. Marcadores moleculares vêm complementando a caracterização morfológica e agronômica tradicional, uma vez que são virtualmente ilimitados, cobrem todo o genoma e não são influenciados pelo ambiente. A caracterização genética constitui a base para

  20. LabSystem Gen, a tool for structuring and analyzing genetic data in histocompatibility laboratories.

    Science.gov (United States)

    Sousa, Luiz Cláudio Demes da Mata; dos Santos Neto, Pedro de Alcântara; de Souza, Fernando da Fonseca; do Monte, Semiramis Jamil Hadad

    2012-04-01

    Analysis of HLA data involves queries on web portals, whose search parameters are data stored in laboratories' databases. In order to automate these queries, one approach is to structure laboratory data into a database and to develop bioinformatic tools to perform the data mapping. In this context, we developed the LabSystem Gen tool that allows users to create a Laboratory Information System, without programming. Additionally we implemented a framework that provides bioinformatic tools, transparent access to public HLA (human leukocyte antigen) information resources. We demonstrated the LabSystemGen system by implementing BMDdb, which is a LIMS that manages data of recipients and donors of organ transplant.

  1. Recommendations for the design of laboratory studies on non-target arthropods for risk assessment of genetically engineered plants.

    Science.gov (United States)

    Romeis, Jörg; Hellmich, Richard L; Candolfi, Marco P; Carstens, Keri; De Schrijver, Adinda; Gatehouse, Angharad M R; Herman, Rod A; Huesing, Joseph E; McLean, Morven A; Raybould, Alan; Shelton, Anthony M; Waggoner, Annabel

    2011-02-01

    This paper provides recommendations on experimental design for early-tier laboratory studies used in risk assessments to evaluate potential adverse impacts of arthropod-resistant genetically engineered (GE) plants on non-target arthropods (NTAs). While we rely heavily on the currently used proteins from Bacillus thuringiensis (Bt) in this discussion, the concepts apply to other arthropod-active proteins. A risk may exist if the newly acquired trait of the GE plant has adverse effects on NTAs when they are exposed to the arthropod-active protein. Typically, the risk assessment follows a tiered approach that starts with laboratory studies under worst-case exposure conditions; such studies have a high ability to detect adverse effects on non-target species. Clear guidance on how such data are produced in laboratory studies assists the product developers and risk assessors. The studies should be reproducible and test clearly defined risk hypotheses. These properties contribute to the robustness of, and confidence in, environmental risk assessments for GE plants. Data from NTA studies, collected during the analysis phase of an environmental risk assessment, are critical to the outcome of the assessment and ultimately the decision taken by regulatory authorities on the release of a GE plant. Confidence in the results of early-tier laboratory studies is a precondition for the acceptance of data across regulatory jurisdictions and should encourage agencies to share useful information and thus avoid redundant testing.

  2. Similaridade genética entre acessos de Bidens pilosa resistentes aos herbicidas inibidores da ALS Genetic similarity among Bidens pilosa accesses resistant to ALS-inhibiting herbicides

    Directory of Open Access Journals (Sweden)

    R.A. Vidal

    2005-09-01

    Full Text Available Herbicidas inibidores da enzima acetolactato sintase (ALS têm sido amplamente utilizados no controle da planta daninha picão-preto (Bidens pilosa. A pressão de seleção causada pelo uso intensivo desses herbicidas tem selecionado biótipos de picão-preto resistentes. O objetivo deste trabalho foi avaliar o grau de similaridade genética entre acessos de picão-preto resistentes aos herbicidas inibidores da ALS, bem como a relação entre coeficiente de similaridade genética e distância geográfica desses acessos. Para isso, sementes de dois grupos de acessos de picão-preto, originárias de uma propriedade em Pato Branco, Paraná, resistentes aos herbicidas inibidores da ALS foram colhidas, e plântulas foram cultivadas em casa de vegetação na Universidade Federal do Rio Grande do Sul (UFRGS, Porto Alegre-RS, em outubro de 2004. Por meio do marcador molecular RAPD (polimorfismo de DNA amplificado ao acaso foi possível avaliar a similaridade genética entre os acessos de picão-preto. Na análise conjunta dos acessos, dos 20 primers utilizados, 17 apresentaram-se polimórficos, amplificando um total de 94 bandas. Houve baixa similaridade genética (38% entre acessos de picão-preto resistentes aos herbicidas inibidores da ALS originários de uma mesma propriedade. Não foi observada relação entre distância genética e distância geográfica entre os acessos avaliados.Acetolactate synthase (ALS-inhibiting herbicides have been widely used to control the weed hairy beggarticks (Bidens pilosa. The selection pressure caused by intensive herbicide use has selected hairy beggarticks resistant biotypes. The objectives of this work were to evaluate the degree of genetic similarity among hairy beggarticks accesses (Bidens pilosa resistant to ALS-inhibiting herbicides, and to evaluate the relation between genetic similarity and geographic distance. Seeds of two groups of hairy beggarticks accesses resistant to ALS-inhibitors were sampled from a

  3. New Genetics

    Science.gov (United States)

    ... Home > Science Education > The New Genetics The New Genetics Living Laboratories Classroom Poster Order a Free Copy ... Piece to a Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is ...

  4. Quantitative genetics of functional characters in Drosophila melanogaster populations subjected to laboratory selection

    Indian Academy of Sciences (India)

    Henrique Teotónio; Margarida Matos; Michael R. Rose

    2004-12-01

    What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantitative-genetic basis of divergence was characterized for outbred Drosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line-cross analysis using first-generation and second-generation hybrids from reciprocal crosses was conducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to starvation stress. The other type of cross was between the same set of ancestral-representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating single-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differentiation to adaptation.

  5. D-VASim: An Interactive Virtual Laboratory Environment for the Simulation and Analysis of Genetic Circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2016-01-01

    the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools...

  6. Analysis of a p53 Mutation Associated with Cancer Susceptibility for Biochemistry and Genetic Laboratory Courses

    Science.gov (United States)

    Soto-Cruz, Isabel; Legorreta-Herrera, Martha

    2009-01-01

    We have devised and implemented a module for an upper division undergraduate laboratory based on the amplification and analysis of a p53 polymorphism associated with cancer susceptibility. First, students collected a drop of peripheral blood cells using a sterile sting and then used FTA cards to extract the genomic DNA. The p53 region is then PCR…

  7. Analysis of a p53 Mutation Associated with Cancer Susceptibility for Biochemistry and Genetic Laboratory Courses

    Science.gov (United States)

    Soto-Cruz, Isabel; Legorreta-Herrera, Martha

    2009-01-01

    We have devised and implemented a module for an upper division undergraduate laboratory based on the amplification and analysis of a p53 polymorphism associated with cancer susceptibility. First, students collected a drop of peripheral blood cells using a sterile sting and then used FTA cards to extract the genomic DNA. The p53 region is then PCR…

  8. DNA-based genetic markers for Rapid Cycling Brassica rapa (Fast Plants type designed for the teaching laboratory.

    Directory of Open Access Journals (Sweden)

    Eryn E. Slankster

    2012-06-01

    Full Text Available We have developed DNA-based genetic markers for rapid-cycling Brassica rapa (RCBr, also known as Fast Plants. Although markers for Brassica rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP based markers and 14 variable number tandem repeat (VNTR-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a nongenic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

  9. Do Laboratory Results Concerning High-Viscosity Glass-Ionomers versus Amalgam for Tooth Restorations Indicate Similar Effect Direction and Magnitude than that of Controlled Clinical Trials? - A Meta-Epidemiological Study.

    Directory of Open Access Journals (Sweden)

    Steffen Mickenautsch

    Full Text Available A large percentage of evidence concerning dental interventions is based on laboratory research. The apparent wealth of laboratory evidence is sometimes used as basis for clinical inference and recommendations for daily dental practice. In this study two null-hypotheses are tested: whether trial results from laboratory and controlled clinical trials concerning the comparison of high-viscosity glass-ionomer cements (HVGIC to amalgam for restorations placed in permanent posterior teeth have: (i similar effect direction and (ii similar effect magnitude.7 electronic databases were searched, as well as reference lists. Odds ratios (OR and Standardised Mean Differences (SMD with 95% Confidence intervals were computed for extracted dichotomous and continuous data, respectively. Pooled effect estimates for laboratory and clinical data were computed to test for effect direction. Odds ratios were converted into SMDs. SMDs from laboratory and clinical data were statistically compared to test for differences in effect magnitude. The analysed results were further investigated within the context of potential influencing or confounding factors using a Directed acyclic graph.Of the accepted eight laboratory and nine clinical trials, 13 and 21 datasets could be extracted, respectively. The pooled results of the laboratory datasets were highly statistically significant in favor of amalgam. No statistically significant differences, between HVGICs and amalgam, were identified for clinical data. For effect magnitude, statistically significant differences between clinical and laboratory trial results were found. Both null-hypotheses were rejected.Laboratory results concerning high-viscosity glass-ionomers versus amalgam for tooth restorations do not indicate similar effect direction and magnitude than that of controlled clinical trials.

  10. The more the better - polyandry and genetic similarity are positively linked to reproductive success in a natural population of terrestrial salamanders (Salamandra salamandra).

    Science.gov (United States)

    Caspers, Barbara A; Krause, E Tobias; Hendrix, Ralf; Kopp, Michael; Rupp, Oliver; Rosentreter, Katrin; Steinfartz, Sebastian

    2014-01-01

    Although classically thought to be rare, female polyandry is widespread and may entail significant fitness benefits. If females store sperm over extended periods of time, the consequences of polyandry will depend on the pattern of sperm storage, and some of the potential benefits of polyandry can only be realized if sperm from different males is mixed. Our study aimed to determine patterns and consequences of polyandry in an amphibian species, the fire salamander, under fully natural conditions. Fire salamanders are ideal study objects, because mating, fertilization and larval deposition are temporally decoupled, females store sperm for several months, and larvae are deposited in the order of fertilization. Based on 18 microsatellite loci, we conducted paternity analysis of 24 female-offspring arrays with, in total, over 600 larvae fertilized under complete natural conditions. More than one-third of females were polyandrous and up to four males were found as sires. Our data clearly show that sperm from multiple males is mixed in the female's spermatheca. Nevertheless, paternity is biased, and the most successful male sires on average 70% of the larvae, suggesting a 'topping off' mechanism with first-male precedence. Female reproductive success increased with the number of sires, most probably because multiple mating ensured high fertilization success. In contrast, offspring number was unaffected by female condition and genetic characteristics, but surprisingly, it increased with the degree of genetic relatedness between females and their sires. Sires of polyandrous females tended to be genetically similar to each other, indicating a role for active female choice. © 2013 John Wiley & Sons Ltd.

  11. The Laboratory of the Dramaturge and Studies on Theatrical Genetics: experiments

    Directory of Open Access Journals (Sweden)

    Maria de Lourdes Rabetti

    2011-11-01

    Full Text Available This study is situated in the field of Theatrical Genetics and deals with the presence of the dramaturge in action. It assesses the relevance and uniqueness of the process of textual migration toward the theatrical scene caused by the combined exercises of translation and dramaturgy developed between the years 1985 and 1991 by Companhia de Encenação Teatral from the city of Rio de Janeiro. It updates and comments on accumulated experiences in the creation of a number of spectacles as a result of a long and continuous creative process. Theoretically, therefore, this text aims to understand Theatrical Genetics through the eyes of the dramaturge, the theatre historian.

  12. [Improvement of laboratory diagnostics of cholera due to genetically altered (hybrid) variants of cholera Vibrio biovar El Tor].

    Science.gov (United States)

    Savel'eva, I V; Khatsukov, K X; Savel'eva, E I; Moskvitina, S I; Kovalev, D A; Savel'ev, V N; Kulichenko, A N; Antonenko, A D; Babenyshev, B V

    2015-01-01

    Improvement of laboratory diagnostics of cholera taking into the account appearance of hybrid variants of cholera vibrio El Tor biovar in the 1990s. Phenotypic and molecular-genetic properties of typical toxigenic (151 strains) and hybrid (102 strains) variants of El Tor biovar cholera vibrios, isolated in the Caucuses in 1970-1990 and 1993-1998, respectively, were studied. Toxigenicity gene DNA fragments, inherent to El Tor biovars or classic, were detected by using a reagent kit "Genes of Vibrio cholerae variant ctxB-rstR-rstC, REF" developed by us. Reagent kit "Genes of V. cholerae variant ctxB-rstR-rstC, REF" is proposed to be used for laboratory diagnostics of cholera during study of material from humans or environmental objects and for identification of V. cholerae 01 on genome level in PCR-analysis as a necessary addition to the classic scheme of bacteriological analysis. Laboratory diagnostics of cholera due to genetically altered (hybrid) variants of cholera vibrio El Tor biovar is based on a complex study of material from humans and environmental objects by routine bacteriologic and PCR-analysis methods with the aim of detection of gene DNA fragments in the studied material, that determine biovar (classic or El Tor), identification of V. cholerae O1 strains with differentiation of El Tor vibrios into typical and altered, as well as determination of enterotoxin, produced by the specific cholera vibrio strain (by the presence ctxB(El) or ctxB(Cl) gene DNA fragment, coding biosynthesis of CT-2 or CT-1, respectively).

  13. Mutation-based learning to improve student autonomy and scientific inquiry skills in a large genetics laboratory course.

    Science.gov (United States)

    Wu, Jinlu

    2013-01-01

    Laboratory education can play a vital role in developing a learner's autonomy and scientific inquiry skills. In an innovative, mutation-based learning (MBL) approach, students were instructed to redesign a teacher-designed standard experimental protocol by a "mutation" method in a molecular genetics laboratory course. Students could choose to delete, add, reverse, or replace certain steps of the standard protocol to explore questions of interest to them in a given experimental scenario. They wrote experimental proposals to address their rationales and hypotheses for the "mutations"; conducted experiments in parallel, according to both standard and mutated protocols; and then compared and analyzed results to write individual lab reports. Various autonomy-supportive measures were provided in the entire experimental process. Analyses of student work and feedback suggest that students using the MBL approach 1) spend more time discussing experiments, 2) use more scientific inquiry skills, and 3) find the increased autonomy afforded by MBL more enjoyable than do students following regimented instructions in a conventional "cookbook"-style laboratory. Furthermore, the MBL approach does not incur an obvious increase in labor and financial costs, which makes it feasible for easy adaptation and implementation in a large class.

  14. Revised sections F7.5 (quantitative amino acid analysis) and F7.6 (qualitative amino acid analysis): American College of Medical Genetics Standards and Guidelines for Clinical Genetics Laboratories, 2003.

    Science.gov (United States)

    Grier, Robert E; Gahl, William A; Cowan, Tina; Bernardini, Isa; McDowell, Geraldine A; Rinaldo, Piero

    2004-01-01

    Determination of plasma amino acid levels has become a key piece of information in the diagnosis and clinical management of a group of metabolic genetic disorders. Appropriate laboratory methodologies have been published for amino acid analysis, yet there is a need for direction for the laboratory in performing this testing. The following guidelines were generated by a working group of the American College of Medical Genetics Laboratory Quality Assurance Committee. Based upon a body of knowledge and professional experience, these guidelines and standards are to be the benchmark for performance of amino acid analysis for clinical interpretation.

  15. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  16. Diversidade e similaridade genéticas em clones de pimenta-do-reino Genetic diversity and similarity in clones of black pepper

    Directory of Open Access Journals (Sweden)

    José M.D. Gaia

    2005-06-01

    Full Text Available Setenta e oito clones de pimenta-do-reino (Piper nigrum L. foram analisados por meio de eletroforese de isozimas para os sistemas ACP, GOT, SKDH, ACO, G6PDH, PGI, 6PGDH e FUM, para avaliar a diversidade por meio da porcentagem de locos polimórficos, número médio de alelos por locos e heterozigosidade média. A similaridade genética foi obtida por meio do coeficiente de semelhança simples e foi resumida num fenograma de média de grupo. Foram detectados 14 locos e 35 alelos. Os locos que apresentaram maior diversidade foram: G6pdh-1, Acp-1 e Skdh-1. A porcentagem de locos polimórficos variou de 3,57% a 64,29%; o número médio de alelos variou de 0,04 a 1,64; e a heterozigosidade média variou de 0,036 a 0,321. Os baixos valores observados no intervalo de variação da heterozigosidade média são consistentes com a estreita base genética dos genótipos e a amplitude deste intervalo pode estar relacionada com o grau de hibridação (artificial ou natural de cada clone. A similaridade genética variou de 65% a 100%, sendo que 70 clones estiveram contidos na faixa de 85% e 100%, o que ratifica o estreitamento da base genética da espécie e conseqüente homogeneidade dos genomas cultivados.Seventy eight black pepper clones (Piper nigrum L. were analyzed by means of isozyme electrophoresis for the systems ACP, GOT, SKDH, ACO, G6PDH, PGI, 6PGDH and FUM, in order to evaluate the diversity through the percentage of polymorphic loci, mean number of alleles per locus and mean heterozigosity. Genetic similarity was calculated by simple matching coefficient and summarized in the group average phenogram. Fourteen loci and 35 alleles were detected. The loci that presented larger diversity were G6pdh-1, Acp-1 and Skdh-1. The percentage of polymorphic loci ranged from 3.57% to 64.29%; the mean number of alleles ranged from 0.04 to 1.64 and; the mean heterozigosity varied from 0.036 to 0.321. The lower values observed in the interval of variation of the

  17. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution.

    Science.gov (United States)

    Zhang, Liqin; Yang, Zunyi; Le Trinh, Thu; Teng, I-Ting; Wang, Sai; Bradley, Kevin M; Hoshika, Shuichi; Wu, Qunfeng; Cansiz, Sena; Rowold, Diane J; McLendon, Christopher; Kim, Myong-Sang; Wu, Yuan; Cui, Cheng; Liu, Yuan; Hou, Weijia; Stewart, Kimberly; Wan, Shuo; Liu, Chen; Benner, Steven A; Tan, Weihong

    2016-09-26

    Laboratory in vitro evolution (LIVE) might deliver DNA aptamers that bind proteins expressed on the surface of cells. In this work, we used cell engineering to place glypican 3 (GPC3), a possible marker for liver cancer theranostics, on the surface of a liver cell line. Libraries were then built from a six-letter genetic alphabet containing the standard nucleobases and two added nucleobases (2-amino-8H-imidazo[1,2-a][1,3,5]triazin-4-one and 6-amino-5-nitropyridin-2-one), Watson-Crick complements from an artificially expanded genetic information system (AEGIS). With counterselection against non-engineered cells, eight AEGIS-containing aptamers were recovered. Five bound selectively to GPC3-overexpressing cells. This selection-counterselection scheme had acceptable statistics, notwithstanding the possibility that cells engineered to overexpress GPC3 might also express different off-target proteins. This is the first example of such a combination. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Genetic parameters for lactation traits of milking ewes: protein content and composition, fat, somatic cells and individual laboratory cheese yield

    Directory of Open Access Journals (Sweden)

    De la Fuente Luis

    2002-09-01

    Full Text Available Abstract The effects of some environmental variation factors and the genetic parameters for total milk traits (fat content, protein content, casein content, serum protein content, lactation mean of individual laboratory cheese yield (LILCY, lactation mean of somatic cell count (LSCC, and milk yield were estimated from the records of 1 111 Churra ewes. Genetic parameters were estimated by multivariate REML. Heritability for fat content was low (0.10 as is usually found in the Churra breed. Heritabilities for protein content, casein content, serum protein content, LILCY, milk yield and somatic cell count were 0.31, 0.30, 0.22, 0.09, 0.26 and 0.11, respectively. The highest heritability estimates were for protein and casein contents. Casein content is not advisable as an alternative to protein content as a selection criterion for cheese yield improvement; it does not have any compelling advantages and its measurement is costly. Our results for LSCC indicated that efforts should focus on improving the level of management rather than selecting for somatic cells, in the actual conditions of the Churra breed.

  19. Genetic antimicrobial susceptibility testing in Gram-negative sepsis - impact on time to results in a routine laboratory.

    Science.gov (United States)

    Kommedal, Øyvind; Aasen, Johanne Lind; Lindemann, Paul Christoffer

    2016-07-01

    Diagnostic testing of positive blood cultures is among the most critical tasks performed by clinical microbiology laboratories, and the total analysis time from sampling to results should be kept as short as possible. By providing identification of pelleted bacteria directly from positive blood-cultures, MALDI-TOF MS opens for relatively low-complex species-adjusted genetic susceptibility testing from the same bacterial pellet. In our lab routine, we prospectively evaluated a rapid in-house real-time PCR targeting the most common aminoglycoside and cephalosporin resistance genes in Escherichia coli and Klebsiella pneumoniae and measured time to preliminary susceptibility reporting for 138 samples. The results were compared to direct phenotypic susceptibility testing with interpretation after 6 h and overnight incubation respectively. Results from the genetic susceptibility testing were available for 69.5% (96/138) of the positive blood cultures within 24 h after sample collection. No phenotypic susceptibility results were available at this time. Compared to overnight direct susceptibility testing, the average time from sample collection to preliminary susceptibility reporting was reduced with 43%, from 45 h and 5 min to 25 h and 44 min, providing an earlier adjustment of antimicrobial therapy for 12 patients. Minor logistic adjustments have the potential to save yet another 4 h.

  20. Genetic variations of live attenuated plague vaccine strains (Yersinia pestis EV76 lineage) during laboratory passages in different countries.

    Science.gov (United States)

    Cui, Yujun; Yang, Xianwei; Xiao, Xiao; Anisimov, Andrey P; Li, Dongfang; Yan, Yanfeng; Zhou, Dongsheng; Rajerison, Minoarisoa; Carniel, Elisabeth; Achtman, Mark; Yang, Ruifu; Song, Yajun

    2014-08-01

    Plague, one of the most devastating infectious diseases in human history, is caused by the bacterial species Yersinia pestis. A live attenuated Y. pestis strain (EV76) has been widely used as a plague vaccine in various countries around the world. Here we compared the whole genome sequence of an EV76 strain used in China (EV76-CN) with the genomes of Y. pestis wild isolates to identify genetic variations specific to the EV76 lineage. We identified 6 SNPs and 6 Indels (insertions and deletions) differentiating EV76-CN from its counterparts. Then, we screened these polymorphic sites in 28 other strains of EV76 lineage that were stored in different countries. Based on the profiles of SNPs and Indels, we reconstructed the parsimonious dissemination history of EV76 lineage. This analysis revealed that there have been at least three independent imports of EV76 strains into China. Additionally, we observed that the pyrE gene is a mutation hotspot in EV76 lineages. The fine comparison results based on whole genome sequence in this study provide better understanding of the effects of laboratory passages on the accumulation of genetic polymorphisms in plague vaccine strains. These variations identified here will also be helpful in discriminating different EV76 derivatives. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Development and inter-laboratory assessment of droplet digital PCR assays for multiplex quantification of 15 genetically modified soybean lines.

    Science.gov (United States)

    Košir, Alexandra Bogožalec; Spilsberg, Bjørn; Holst-Jensen, Arne; Žel, Jana; Dobnik, David

    2017-08-17

    Quantification of genetically modified organisms (GMOs) in food and feed products is often required for their labelling or for tolerance thresholds. Standard-curve-based simplex quantitative polymerase chain reaction (qPCR) is the prevailing technology, which is often combined with screening analysis. With the rapidly growing number of GMOs on the world market, qPCR analysis becomes laborious and expensive. Innovative cost-effective approaches are therefore urgently needed. Here, we report the development and inter-laboratory assessment of multiplex assays to quantify GMO soybean using droplet digital PCR (ddPCR). The assays were developed to facilitate testing of foods and feed for compliance with current GMO regulations in the European Union (EU). Within the EU, the threshold for labelling is 0.9% for authorised GMOs per ingredient. Furthermore, the EU has set a technical zero tolerance limit of 0.1% for certain unauthorised GMOs. The novel multiplex ddPCR assays developed target 11 GMO soybean lines that are currently authorised, and four that are tolerated, pending authorisation in the EU. Potential significant improvements in cost efficiency are demonstrated. Performance was assessed for the critical parameters, including limits of detection and quantification, and trueness, repeatability, and robustness. Inter-laboratory performance was also determined on a number of proficiency programme and real-life samples.

  2. Similaridade genética entre clones de seringueira (Hevea brasiliensis, por meio de marcadores RAPD Genetic similarity among rubber tree (Hevea brasiliensis clones using RAPD markers

    Directory of Open Access Journals (Sweden)

    Karine Cristina Bicalho

    2008-10-01

    Full Text Available A seringueira [Hevea brasiliensis (Willd. ex. Adr. de Juss Muell.-Arg.] é uma espécie nativa da região amazônica e compreende a maior fonte produtora de borracha natural do mundo. Na busca de condições mais favoráveis ao cultivo, além da busca pela auto-suficiência na produção de borracha natural, o cultivo da seringueira migrou para outras regiões do país. Objetivou-se, com o presente trabalho, estimar a similaridade genética de genótipos de seringueira, provenientes de regiões distintas do país, Lavras-MG (UFLA e Campinas-SP (IAC, por meio de marcadores moleculares RAPD. A análise foi efetuada em 41 indivíduos, representados por 17 genótipos diferentes, com base em 19 primers, que geraram 121 fragmentos polimórficos. Os dados foram analisados utilizando o software NTSYS-pc - 2.1, por meio do coeficiente de Dice e pelo método das médias (UPGMA. A similaridade genética entre o material analisado variou de 0,56 a 1,00. Na análise do dendrograma, foram observados 18 grupos. Os clones (RRIM600, GT1, PB235, PL PIM e FX2261, utilizados em diferentes repetições, foram idênticos, quando comparados entre si, entretanto o mesmo não foi observado para os clones identificados como RRIM 701. Os resultados obtidos sugerem que o material avaliado na UFLA é o mesmo implantado no IAC, exceto o RRIM 701, mostrando uma ampla variabilidade genética, disponível para estudos e propagação da cultura.The rubber tree [Hevea brasiliensis (Willd. ex. Adr. de Juss Muell.-Arg.] is a native species from Amazon region, and represents the biggest source of natural rubber in the world.. However, the rubber tree culture has had an expansion to other brazilian regions, in search of more favorable conditions for its cultivation and self-sufficiency in natural rubber. The aim of this work was to estimate genetic similarity among rubber tree clones, from different Brazilian regions, Lavras (UFLA and Campinas (IAC, by using RAPD molecular markers

  3. Using a Molecular-Genetic Approach to Investigate Bacterial Physiology in a Continuous, Research-Based, Semester-Long Laboratory for Undergraduates †

    OpenAIRE

    Jeremiah Foster Ault; Betsey Marie Renfro; Andrea Kirsten White

    2011-01-01

    Designing investigative laboratory exercises that encourage critical thinking, problem solving, and independent thought for upper-division biology courses is a difficult but worthwhile task. In an effort to do so, we developed a semester-long, continuous, research-based investigative laboratory that integrates numerous genetic and molecular biology methods into the investigation of a bacterial physiological process. In this lab, students use random Tn5 transposon mutagenesis to create prodigi...

  4. The Effect of Ivermectin in Seven Strains of Aedes aegypti (Diptera: Culicidae) Including a Genetically Diverse Laboratory Strain and Three Permethrin Resistant Strains

    OpenAIRE

    Deus, K. M.; Saavedra-rodriguez, K.; Butters, M. P.; Black, W C; Foy, B.D.

    2012-01-01

    Seven different strains of Aedes aegypti (L.), including a genetically diverse laboratory strain, three laboratory-selected permethrin-resistant strains, a standard reference strain, and two recently colonized strains were fed on human blood containing various concentrations of ivermectin. Ivermectin reduced adult survival, fecundity, and hatch rate of eggs laid by ivermectin-treated adults in all seven strains. The LC50 of ivermectin for adults and the concentration that prevented 50% of egg...

  5. Web Similarity

    NARCIS (Netherlands)

    Cohen, A.R.; Vitányi, P.M.B.

    2015-01-01

    Normalized web distance (NWD) is a similarity or normalized semantic distance based on the World Wide Web or any other large electronic database, for instance Wikipedia, and a search engine that returns reliable aggregate page counts. For sets of search terms the NWD gives a similarity on a scale fr

  6. Similar Frequencies of Pseudomonas aeruginosa Isolates Producing KPC and VIM Carbapenemases in Diverse Genetic Clones at Tertiary-Care Hospitals in Medellín, Colombia

    Science.gov (United States)

    Vanegas, Johanna M.; Cienfuegos, Astrid V.; Ocampo, Ana M.; López, Lucelly; del Corral, Helena; Roncancio, Gustavo; Sierra, Patricia; Echeverri-Toro, Lina; Ospina, Sigifredo; Maldonado, Natalia; Robledo, Carlos; Restrepo, Andrea

    2014-01-01

    Carbapenem-resistant Pseudomonas aeruginosa has become a serious health threat worldwide due to the limited options available for its treatment. Understanding its epidemiology contributes to the control of antibiotic resistance. The aim of this study was to describe the clinical and molecular characteristics of infections caused by carbapenem-resistant P. aeruginosa isolates in five tertiary-care hospitals in Medellín, Colombia. A cross-sectional study was conducted in five tertiary-care hospitals from June 2012 to March 2014. All hospitalized patients infected by carbapenem-resistant P. aeruginosa were included. Clinical information was obtained from medical records. Molecular analyses included PCR for detection of blaVIM, blaIMP, blaNDM, blaOXA-48, and blaKPC genes plus pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for molecular typing. A total of 235 patients were enrolled: 91.1% of them were adults (n = 214), 88.1% (n = 207) had prior antibiotic use, and 14.9% (n = 35) had urinary tract infections. The blaVIM-2 and blaKPC-2 genes were detected in 13.6% (n = 32) and 11.5% (n = 27), respectively, of all isolates. Two isolates harbored both genes simultaneously. For KPC-producing isolates, PFGE revealed closely related strains within each hospital, and sequence types (STs) ST362 and ST235 and two new STs were found by MLST. With PFGE, VIM-producing isolates appeared highly diverse, and MLST revealed ST111 in four hospitals and five new STs. These results show that KPC-producing P. aeruginosa is currently disseminating rapidly and occurring at a frequency similar to that of VIM-producing P. aeruginosa isolates (approximately 1:1 ratio) in Medellín, Colombia. Diverse genetic backgrounds among resistant strains suggest an excessive antibiotic pressure resulting in the selection of resistant strains. PMID:25210071

  7. Genetic and environmental factors associated with laboratory rearing affect survival and assortative mating but not overall mating success in Anopheles gambiae sensu stricto.

    Science.gov (United States)

    Paton, Doug; Touré, Mahamoudou; Sacko, Adama; Coulibaly, Mamadou B; Traoré, Sékou F; Tripet, Frédéric

    2013-01-01

    Anopheles gambiae sensu stricto, the main vector of malaria in Africa, is characterized by its vast geographical range and complex population structure. Assortative mating amongst the reproductively isolated cryptic forms that co-occur in many areas poses unique challenges for programs aiming to decrease malaria incidence via the release of sterile or genetically-modified mosquitoes. Importantly, whether laboratory-rearing affects the ability of An. gambiae individuals of a given cryptic taxa to successfully mate with individuals of their own form in field conditions is still unknown and yet crucial for mosquito-releases. Here, the independent effects of genetic and environmental factors associated with laboratory rearing on male and female survival, mating success and assortative mating were evaluated in the Mopti form of An. gambiae over 2010 and 2011. In semi-field enclosures experiments and despite strong variation between years, the overall survival and mating success of male and female progeny from a laboratory strain was not found to be significantly lower than those of the progeny of field females from the same population. Adult progeny from field-caught females reared at the larval stage in the laboratory and from laboratory females reared outdoors exhibited a significant decrease in survival but not in mating success. Importantly, laboratory individuals reared as larvae indoors were unable to mate assortatively as adults, whilst field progeny reared either outdoors or in the laboratory, as well as laboratory progeny reared outdoors all mated significantly assortatively. These results highlight the importance of genetic and environment interactions for the development of An. gambiae's full mating behavioral repertoire and the challenges this creates for mosquito rearing and release-based control strategies.

  8. Lessons from the use of genetically modified Drosophila melanogaster in ecological studies: Hsf mutant lines show highly trait-specific performance in field and laboratory thermal assays

    DEFF Research Database (Denmark)

    Sørensen, Jesper Givskov; Loeschcke, Volker; Kristensen, Torsten Nygård

    2009-01-01

    1.  Laboratory studies on genetically modified strains may reveal important information on mechanisms involved in coping with thermal stress. However, to address the evolutionary significance of specific genes or physiological mechanisms, ecologically relevant field tests should also be performed....... 2.  We have tested the importance of inducible heat shock proteins (Hsps) under different thermal conditions using two heat shock factor (Hsf) mutant lines (either able (Hsf+) or unable (Hsf0) to mount a heat stress response) and an outbred laboratory adapted wild-type line of Drosophila...... that the ecological relevance of specific molecular mechanisms should be tested under a range of conditions both in the laboratory and in the field. Genetically modified lines cannot be assumed to represent the performance of natural populations, especially for field and/or ecologically relevant studies.6...

  9. Survival and catabolic activity of natural and genetically engineered bacteria in a laboratory-scale activated-sludge unit

    Energy Technology Data Exchange (ETDEWEB)

    McClure, N.C.; Fry, J.C.; Weightman, A.J. (Univ. of Wales College of Cardiff (Wales))

    1991-02-01

    The survival of selected naturally occurring and genetically engineered bacteria in a fully functional laboratory-scale activated-sludge unit (ASU) was investigated. The effect of the presence of 3-chlorobenzoate (3CB) on the survival of Pseudomonas putida UWC1, with or without a chimeric plasmid, pD10, which encodes 3CB catabolism, was determined. P. putida UWC1(pD10) did not enhance 3CB breakdown in the ASU, even following inoculation at a high concentration (3 x 10(8) CFU/ml). The emergence of a natural, 3CB-degrading population appeared to have a detrimental effect on the survival of strain UWC1 in the ASU. The fate of two 3CB-utilizing bacteria, derived from activated-sludge microflora, was studied in experiments in which these strains were inoculated into the ASU. Both strains, AS2, an unmanipulated natural isolate which flocculated readily in liquid media, and P. putida ASR2.8, a transconjugant containing the recombinant plasmid pD10, survived for long periods in the ASU and enhanced 3CB breakdown at 15 degrees C. The results reported in this paper illustrate the importance of choosing strains which are well adapted to environmental conditions if the use of microbial inoculants for the breakdown of target pollutants is to be successful.

  10. Assignment tests for variety identification compared to genetic similarity-based methods using experimental datasets from different marker systems in sugar beet

    NARCIS (Netherlands)

    Riek, de J.; Everaert, I.; Esselink, D.; Calsyn, E.; Smulders, M.J.M.; Vosman, B.

    2007-01-01

    High genetic variation within sugar beet (Beta vulgaris L.) varieties hampers reliable classification procedures independent of the type of marker technique applied. Datasets on amplified fragment length polymorphisms, sequence tagged microsatellite sites, and cleaved amplified polymorphic sites mar

  11. Similarity Scaling

    Science.gov (United States)

    Schnack, Dalton D.

    In Lecture 10, we introduced a non-dimensional parameter called the Lundquist number, denoted by S. This is just one of many non-dimensional parameters that can appear in the formulations of both hydrodynamics and MHD. These generally express the ratio of the time scale associated with some dissipative process to the time scale associated with either wave propagation or transport by flow. These are important because they define regions in parameter space that separate flows with different physical characteristics. All flows that have the same non-dimensional parameters behave in the same way. This property is called similarity scaling.

  12. Using a Molecular-Genetic Approach to Investigate Bacterial Physiology in a Continuous, Research-Based, Semester-Long Laboratory for Undergraduates

    Directory of Open Access Journals (Sweden)

    Jeremiah Foster Ault

    2011-09-01

    Full Text Available Designing investigative laboratory exercises that encourage critical thinking, problem solving, and independent thought for upper-division biology courses is a difficult but worthwhile task. In an effort to do so, we developed a semester-long, continuous, research-based investigative laboratory that integrates numerous genetic and molecular biology methods into the investigation of a bacterial physiological process. In this lab, students use random Tn5 transposon mutagenesis to create prodigiosin pigment mutants in the bacterium, Serratia marcescens. This is followed by phenotypic characterization, cloning, and sequencing the Tn insertion site to identify genes involved in pigment biosynthesis. During this lab, students gain ample experience performing basic lab techniques while learning about — and applying — methods for elucidating gene function. The approach to the laboratory and the outcomes are intimately integrated into the teaching of many fundamental physiological processes underlying prodigiosin production in bacteria. The result is a cohesive course that integrates the theory and application of molecular genetic techniques with the study of bacterial physiology. Assessments of student learning objectives demonstrated that students greatly improved their understanding of both physiological processes and the genetic techniques used to investigate them. In addition, students felt that this semester-long exercise provided the necessary laboratory experience they needed and desired in preparation for careers in molecular biology, microbiology, and biochemistry.

  13. Using a molecular-genetic approach to investigate bacterial physiology in a continuous, research-based, semester-long laboratory for undergraduates.

    Science.gov (United States)

    Ault, Jeremiah Foster; Renfro, Betsey Marie; White, Andrea Kirsten

    2011-01-01

    Designing investigative laboratory exercises that encourage critical thinking, problem solving, and independent thought for upper-division biology courses is a difficult but worthwhile task. In an effort to do so, we developed a semester-long, continuous, research-based investigative laboratory that integrates numerous genetic and molecular biology methods into the investigation of a bacterial physiological process. In this lab, students use random Tn5 transposon mutagenesis to create prodigiosin pigment mutants in the bacterium, Serratia marcescens. This is followed by phenotypic characterization, cloning, and sequencing the Tn insertion site to identify genes involved in pigment biosynthesis. During this lab, students gain ample experience performing basic lab techniques while learning about - and applying - methods for elucidating gene function. The approach to the laboratory and the outcomes are intimately integrated into the teaching of many fundamental physiological processes underlying prodigiosin production in bacteria. The result is a cohesive course that integrates the theory and application of molecular genetic techniques with the study of bacterial physiology. Assessments of student learning objectives demonstrated that students greatly improved their understanding of both physiological processes and the genetic techniques used to investigate them. In addition, students felt that this semester-long exercise provided the necessary laboratory experience they needed and desired in preparation for careers in molecular biology, microbiology, and biochemistry.

  14. Diagnostic algorithms in Charcot-Marie-Tooth neuropathies: experiences from a German genetic laboratory on the basis of 1206 index patients.

    Science.gov (United States)

    Rudnik-Schöneborn, S; Tölle, D; Senderek, J; Eggermann, K; Elbracht, M; Kornak, U; von der Hagen, M; Kirschner, J; Leube, B; Müller-Felber, W; Schara, U; von Au, K; Wieczorek, D; Bußmann, C; Zerres, K

    2016-01-01

    We present clinical features and genetic results of 1206 index patients and 124 affected relatives who were referred for genetic testing of Charcot-Marie-Tooth (CMT) neuropathy at the laboratory in Aachen between 2001 and 2012. Genetic detection rates were 56% in demyelinating CMT (71% of autosomal dominant (AD) CMT1/CMTX), and 17% in axonal CMT (24% of AD CMT2/CMTX). Three genetic defects (PMP22 duplication/deletion, GJB1/Cx32 or MPZ/P0 mutation) were responsible for 89.3% of demyelinating CMT index patients in whom a genetic diagnosis was achieved, and the diagnostic yield of the three main genetic defects in axonal CMT (GJB1/Cx32, MFN2, MPZ/P0 mutations) was 84.2%. De novo mutations were detected in 1.3% of PMP22 duplication, 25% of MPZ/P0, and none in GJB1/Cx32. Motor nerve conduction velocity was uniformly 40 m/s in MFN2, and more variable in GJB1/Cx32, MPZ/P0 mutations. Patients with CMT2A showed a broad clinical severity regardless of the type or position of the MFN2 mutation. Out of 75 patients, 8 patients (11%) with PMP22 deletions were categorized as CMT1 or CMT2. Diagnostic algorithms are still useful for cost-efficient mutation detection and for the interpretation of large-scale genetic data made available by next generation sequencing strategies.

  15. Relevance of JAK2V617F positivity to hematological diseases - survey of samples from a clinical genetics laboratory

    Directory of Open Access Journals (Sweden)

    Ho Wanting T

    2011-01-01

    Full Text Available Abstract Background JAK2V617F is found in the majority of patients with Ph- myeloproliferative neoplasms (MPNs and has become a valuable marker for diagnosis of MPNs. However, it has also been found in many other hematological diseases, and some studies even detected the presence of JAK2V617F in normal blood samples. This casts doubt on the primary role of JAK2V617F in the pathogenesis of MPNs and its diagnostic value. Methods In the present study, we analyzed JAK2V617F positivity with 232 normal blood samples and 2663 patient blood, bone marrow, and amniotic fluid specimens obtained from a clinical genetics laboratory by using a simple DNA extraction method and a sensitive nested allele-specific PCR strategy. Results We found JAK2V617F present in the majority (78% of MPN patients and in a small fraction (1.8-8.7% of patients with other specific hematological diseases but not at all in normal healthy donors or patients with non-hematological diseases. We also revealed associations of JAK2V617F with novel as well as known chromosomal abnormalities. Conclusions Our study suggests that JAK2V617F positivity is associated with specific hematological malignancies and is an excellent diagnostic marker for MPNs. The data also indicate that the nested allele-specific PCR method provides clinically relevant information and should be conducted for all cases suspected of having MPNs as well as for other related diseases.

  16. On the Revision of Introductory Genetics Laboratory Experiments%遗传学实验教材存在的问题及改革实践

    Institute of Scientific and Technical Information of China (English)

    杨大祥

    2012-01-01

    A laboratory guide is essential for effective classroom training. In this paper, the author self-reviewed the compilation and revision of Introductory Genetics Laboratory Experiments, a laboratory guide intended mainly for college students in China. The author suggested that a laboratory guide should be not only a guide to provide step-by-step protocols, but also a guide for laboratory investigation. Based on this viewpoint, the basic scientific research skills training, such as how to keep a laboratory note, how to write laboratory report, etc, which are usually neglected by the instructors, were incorporated into the basic genetic techniques training in the textbook. Besides, this textbook provides the learners with copious background knowledge to help students master techniques accurately and inspire their interests for further reading or thinking. In order to make the textbook more suitable for the beginner, both the review from peer reviewers and the meaningful and timely feedback from the students in the compiler's class over these years were taken into consideration.%基于目前遗传学实验教材一般存在背景知识介绍过于简单且陈旧、操作指导介绍过于笼统等不足,杨大祥在《遗传学实验》编写和修订时作了一些创新:注重实验背景知识、研究思路的介绍及实验结果的解释;注重学生科研基本功的训练;通过课后练习引申实验内容,让学生关注相关技术在实践中的应用等等,以此激发学生探索、发现的兴趣。

  17. ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics.

    Science.gov (United States)

    Monaghan, Kristin G; Lyon, Elaine; Spector, Elaine B

    2013-07-01

    Molecular genetic testing of the FMR1 gene is commonly performed in clinical laboratories. Mutations in the FMR1 gene are associated with fragile X syndrome, fragile X tremor ataxia syndrome, and premature ovarian insufficiency. This document provides updated information regarding FMR1 gene mutations, including prevalence, genotype-phenotype correlation, and mutation nomenclature. Methodological considerations are provided for Southern blot analysis and polymerase chain reaction amplification of the FMR1 gene, including triplet repeat-primed and methylation-specific polymerase chain reaction. In addition to report elements, examples of laboratory reports for various genotypes are also included.

  18. An approach for modeling cross-immunity of two strains, with application to variants of Bartonella in terms of genetic similarity.

    Science.gov (United States)

    Ahn, Kwang Woo; Kosoy, Michael; Chan, Kung-Sik

    2014-06-01

    We developed a two-strain susceptible-infected-recovered (SIR) model that provides a framework for inferring the cross-immunity between two strains of a bacterial species in the host population with discretely sampled co-infection time-series data. Moreover, the model accounts for seasonality in host reproduction. We illustrate an approach using a dataset describing co-infections by several strains of bacteria circulating within a population of cotton rats (Sigmodon hispidus). Bartonella strains were clustered into three genetically close groups, between which the divergence is correspondent to the accepted level of separate bacterial species. The proposed approach revealed no cross-immunity between genetic clusters while limited cross-immunity might exist between subgroups within the clusters. Copyright © 2014. Published by Elsevier B.V.

  19. Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

    Science.gov (United States)

    Vargas-Sanchez, Gie-Bele; Romero-Valdovinos, Mirza; Ramirez-Guerrero, Celedonio; Vargas-Hernandez, Ines; Ramirez-Miranda, Maria Elena; Martinez-Ocaña, Joel; Valadez, Alicia; Ximenez, Cecilia; Lopez-Escamilla, Eduardo; Hernandez-Campos, Maria Elena; Villalobos, Guiehdani; Martinez-Hernandez, Fernando; Maravilla, Pablo

    2015-01-01

    Blastocystis spp is a common intestinal parasite of humans and animals that has been associated to the etiology of irritable bowel syndrome (IBS); however, some studies have not found this association. Furthermore, many biological features of Blastocystis are little known. The objective of present study was to assess the generation times of Blastocystis cultures, from IBS patients and from asymptomatic carriers. A total of 100 isolates were obtained from 50 IBS patients and from 50 asymptomatic carriers. Up to 50 mg of feces from each participant were cultured in Barret's and in Pavlova's media during 48 h. Initial and final parasitological load were measured by microscopy and by quantitative PCR. Amplicons were purified, sequenced and submitted to GenBank; sequences were analysed for genetic diversity and a Bayesian inference allowed identifying genetic subtypes (ST). Generation times for Blastocystis isolates in both media, based on microscopic measures and molecular assays, were calculated. The clinical symptoms of IBS patients and distribution of Blastocystis ST 1, 2 and 3 in both groups was comparable to previous reports. Interestingly, the group of cases showed scarce mean nucleotide diversity (π) as compared to the control group (0.011±0.016 and 0.118±0.177, respectively), whilst high gene flow and small genetic differentiation indexes between different ST were found. Besides, Tajima's D test showed negative values for ST1-ST3. No statistical differences regarding parasitological load between cases and controls in both media, as searched by microscopy and by qPCR, were detected except that parasites grew faster in Barret's than in Pavlova's medium. Interestingly, slow growth of isolates recovered from cases in comparison to those of controls was observed (pBlastocystis might be easily affected by intestinal environmental changes due to IBS probably because virulent strains with slow growth may be selected, reducing their genetic variability.

  20. Blastocystis Isolates from Patients with Irritable Bowel Syndrome and from Asymptomatic Carriers Exhibit Similar Parasitological Loads, but Significantly Different Generation Times and Genetic Variability across Multiple Subtypes.

    Directory of Open Access Journals (Sweden)

    Gie-Bele Vargas-Sanchez

    Full Text Available Blastocystis spp is a common intestinal parasite of humans and animals that has been associated to the etiology of irritable bowel syndrome (IBS; however, some studies have not found this association. Furthermore, many biological features of Blastocystis are little known. The objective of present study was to assess the generation times of Blastocystis cultures, from IBS patients and from asymptomatic carriers. A total of 100 isolates were obtained from 50 IBS patients and from 50 asymptomatic carriers. Up to 50 mg of feces from each participant were cultured in Barret's and in Pavlova's media during 48 h. Initial and final parasitological load were measured by microscopy and by quantitative PCR. Amplicons were purified, sequenced and submitted to GenBank; sequences were analysed for genetic diversity and a Bayesian inference allowed identifying genetic subtypes (ST. Generation times for Blastocystis isolates in both media, based on microscopic measures and molecular assays, were calculated. The clinical symptoms of IBS patients and distribution of Blastocystis ST 1, 2 and 3 in both groups was comparable to previous reports. Interestingly, the group of cases showed scarce mean nucleotide diversity (π as compared to the control group (0.011±0.016 and 0.118±0.177, respectively, whilst high gene flow and small genetic differentiation indexes between different ST were found. Besides, Tajima's D test showed negative values for ST1-ST3. No statistical differences regarding parasitological load between cases and controls in both media, as searched by microscopy and by qPCR, were detected except that parasites grew faster in Barret's than in Pavlova's medium. Interestingly, slow growth of isolates recovered from cases in comparison to those of controls was observed (p<0.05. We propose that generation times of Blastocystis might be easily affected by intestinal environmental changes due to IBS probably because virulent strains with slow growth may be

  1. Increased prevalence of human cutaneous leishmaniasis in Israel and the Palestinian Authority caused by the recent emergence of a population of genetically similar strains of Leishmania tropica.

    Science.gov (United States)

    Azmi, Kifaya; Krayter, Lena; Nasereddin, Abedelmajeed; Ereqat, Suheir; Schnur, Lionel F; Al-Jawabreh, Amer; Abdeen, Ziad; Schönian, Gabriele

    2016-08-04

    Twelve unlinked microsatellite markers were used to determine the microsatellite profiles of 50 newly and 46 previously typed strains of L. tropica from various Israeli and Palestinian foci. Their microsatellite profiles were compared to those of 99 previously typed strains of L. tropica from 15 countries. Israeli and Palestinian strains of L. tropica fell into three different groups, one of which contained 75 of the 96 Israeli and Palestinian strains. This population separated from all the others at the first hierarchical level by Bayesian statistics and formed a distinct monophyletic group on applying genetic distance and allele frequency analyses. The second cluster contained ten Israeli strains from a specific focus north of the Sea of Galilee, which were previously shown to differ from all other strains of L. tropica in their serological, biochemical and molecular biological parameters. This cluster was closely related to clusters comprising strains of L. tropica from Africa. Four Israeli and five Palestinian strains fell into different genetic entities mostly related to strains from Asian foci of CL. Importation during numerous migrations of humans and, perhaps, infected reservoir animals in the past and, now, through modern travel is the most likely explanation for the existence of so many locally encountered genetic variants of L. tropica in the Israeli-Palestinian region. Geographical and ecological variation may play a role in expanding the genetic heterogeneity once given importations had become established in different foci. Currently, one population is expanding in the area comprising almost all of the Palestinian and Israeli strains of L. tropica isolated since 1996 and investigated in this study, which differ clearly from all other strains of whatsoever origin. This population seems to result from the re-emergence of a previously existing genotype owing to environmental changes and human activities.

  2. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  3. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history

    Science.gov (United States)

    Cobble, Kacy R.; Califf, Katy J.; Stone, Nathan E.; Shuey, Megan M.; Birdsell, Dawn; Colman, Rebecca E.; Schupp, James M.; Aziz, Maliha; Van Andel, Roger; Rocke, Tonie E.; Wagner, David M.; Busch, Joseph D.

    2016-01-01

    Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague-related die-offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two otherDRB1 alleles appear to be trans-species polymorphisms shared with the black-tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced theDRB1 locus because its level of differentiation was not different from that of microsatellites in anFST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.

  4. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties.

    Science.gov (United States)

    Rusanov, K; Kovacheva, N; Vosman, B; Zhang, L; Rajapakse, S; Atanassov, A; Atanassov, I

    2005-08-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed.

  5. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history.

    Science.gov (United States)

    Cobble, Kacy R; Califf, Katy J; Stone, Nathan E; Shuey, Megan M; Birdsell, Dawn N; Colman, Rebecca E; Schupp, James M; Aziz, Maliha; Van Andel, Roger; Rocke, Tonie E; Wagner, David M; Busch, Joseph D

    2016-04-01

    Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague-related die-offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67-0.87) in all colonies. Two other DRB1 alleles appear to be trans-species polymorphisms shared with the black-tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (F ST = 0.033) than at microsatellite markers (F ST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an F ST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.

  6. Human immunodeficiency virus type 1 gp120 envelope characteristics associated with disease progression differ in family members infected with genetically similar viruses.

    Science.gov (United States)

    Baan, Elly; van der Sluis, Renée M; Bakker, Margreet E; Bekker, Vincent; Pajkrt, Dasja; Jurriaans, Suzanne; Kuijpers, Taco W; Berkhout, Ben; Wolthers, Katja C; Paxton, William A; Pollakis, Georgios

    2013-01-01

    The human immunodeficiency virus type 1 (HIV-1) envelope protein provides the primary contact between the virus and host, and is the main target of the adaptive humoral immune response. The length of gp120 variable loops and the number of N-linked glycosylation events are key determinants for virus infectivity and immune escape, while the V3 loop overall positive charge is known to affect co-receptor tropism. We selected two families in which both parents and two children had been infected with HIV-1 for nearly 10 years, but who demonstrated variable parameters of disease progression. We analysed the gp120 envelope sequence and compared individuals that progressed to those that did not in order to decipher evolutionary alterations that are associated with disease progression when individuals are infected with genetically related virus strains. The analysis of the V3-positive charge demonstrated an association between higher V3-positive charges with disease progression. The ratio between the amino acid length and the number of potential N-linked glycosylation sites was also shown to be associated with disease progression with the healthier family members having a lower ratio. In conclusion in individuals initially infected with genetically linked virus strains the V3-positive charges and N-linked glycosylation are associated with HIV-1 disease progression and follow varied evolutionary paths for individuals with varied disease progression.

  7. Pathogenicity of Genetically Similar, H5N1 Highly Pathogenic Avian Influenza Virus Strains in Chicken and the Differences in Sensitivity among Different Chicken Breeds.

    Science.gov (United States)

    Matsuu, Aya; Kobayashi, Tomoko; Patchimasiri, Tuangthong; Shiina, Takashi; Suzuki, Shingo; Chaichoune, Kridsada; Ratanakorn, Parntep; Hiromoto, Yasuaki; Abe, Haruka; Parchariyanon, Sujira; Saito, Takehiko

    2016-01-01

    Differences in the pathogenicity of genetically closely related H5N1 highly pathogenic avian influenza viruses (HPAIVs) were evaluated in White Leghorn chickens. These viruses varied in the clinical symptoms they induced, including lethality, virus shedding, and replication in host tissues. A comparison of the host responses in the lung, brain, and spleen suggested that the differences in viral replication efficiency were related to the host cytokine response at the early phase of infection, especially variations in the proinflammatory cytokine IL-6. Based on these findings, we inoculated the virus that showed the mildest pathogenicity among the five tested, A/pigeon/Thailand/VSMU-7-NPT/2004, into four breeds of Thai indigenous chicken, Phadu-Hung-Dang (PHD), Chee, Dang, and Luang-Hung-Khao (LHK), to explore effects of genetic background on host response. Among these breeds, Chee, Dang, and LHK showed significantly longer survival times than White Leghorns. Virus shedding from dead Thai indigenous chickens was significantly lower than that from White Leghorns. Although polymorphisms were observed in the Mx and MHC class I genes, there was no significant association between the polymorphisms in these loci and resistance to HPAIV.

  8. Learning about Genetic Engineering in an Outreach Laboratory: Influence of Motivation and Gender on Students' Cognitive Achievement

    Science.gov (United States)

    Goldschmidt, Marlen; Bogner, Franz X.

    2016-01-01

    During the last 10 years, outreach science laboratories have become increasingly popular due to resource and time limitations in schools. Outreach laboratories offer hands-on projects in a situated and authentic learning setting, thereby promoting the development of students' scientific literacy. However, students' cognitive achievement within…

  9. Genetic Diversity of Brown Trout Populations Using Mitochondrial Markers In Relatively Similar Geographical and Ecological Conditions – a Carpathian Case Study

    Directory of Open Access Journals (Sweden)

    Popa Gina-Oana

    2013-12-01

    Full Text Available Analiza diversităţii genetice cu ajutorul markerilor mitocondriali, a unor populaţii de păstrav comun aflate în condiţii geografice şi ecologice relativ similare în Munţii Carpaţi.

  10. Accelerating discovery for complex neurological and behavioral disorders through systems genetics and integrative genomics in the laboratory mouse.

    Science.gov (United States)

    Bubier, Jason A; Chesler, Elissa J

    2012-04-01

    Recent advances in systems genetics and integrative functional genomics have greatly improved the study of complex neurological and behavioral traits. The methods developed for the integrated characterization of new, high-resolution mouse genetic reference populations and systems genetics enable behavioral geneticists an unprecedented opportunity to address questions of the molecular basis of neurological and psychiatric disorders and their comorbidities. Integrative genomics augment these strategies by enabling rapid informatics-assisted candidate gene prioritization, cross-species translation, and mechanistic comparison across related disorders from a wealth of existing data in mouse and other model organisms. Ultimately, through these complementary approaches, finding the mechanisms and sources of genetic variation underlying complex neurobehavioral disease related traits is becoming tractable. Furthermore, these methods enable categorization of neurobehavioral disorders through their underlying biological basis. Together, these model organism-based approaches can lead to a refinement of diagnostic categories and targeted treatment of neurological and psychiatric disease.

  11. Effect of genetic strain and gender on age-related changes in body composition of the laboratory rat.

    Data.gov (United States)

    U.S. Environmental Protection Agency — Body composition data for common laboratory strains of rat as a function of age. This dataset is associated with the following publication: Gordon , C., K. Jarema ,...

  12. Diagnosis of Wilson disease in young children: molecular genetic testing and a paradigm shift from the laboratory diagnosis.

    Science.gov (United States)

    Seo, Jeong Kee

    2012-12-01

    Wilson disease (WD) is an autosomal recessive disorder of copper metabolism that results in accumulation of copper primarily in the liver, brain and cornea. Mutations in the WD gene, ATP7B, cause failure of copper excretion from hepatocyte into bile and a defective synthesis of ceruloplasmin. More than 500 mutations are now recognized, scattered throughout the ATP7B gene. Since WD has protean clinical presentations, awareness of WD in clinical practice is important for the early diagnosis and prevention of accumulated copper toxicity. Molecular genetic testing is playing an increasingly important role in the diagnosis of WD in uncertain cases and family screening. Siblings should be screened for WD once an index case has been diagnosed. Discrimination of heterozygotes from asymptomatic patients is essential to avoid inappropriate lifelong therapy for heterozygotes. Genetic testing, either by haplotype analysis or by mutation analysis, is the only definite solution for differentiating heterozygote carriers from affected asymptomatic patients. Routine genetic testing, because of the multitude of documented mutations, has been thought to be impractical until recently. However, genetic testing is now being more actively applied to the diagnosis of WD, particularly in young children in whom conventional biochemical diagnosis has much limitation and only genetic testing is able to confirm WD. Because advancement of modern biochemical technology now allows more rapid, easier, and less expensive mutation detection, direct DNA sequencing could be actively considered as the primary mode of diagnostic investigation rather than a supplementary test to the conventional biochemical tests. This review will focus on the recent advancement of molecular genetics and genetic diagnosis of WD in very young children on the basis of research data of the Seoul National University Children's Hospital and recent literature.

  13. "Sickle cell anemia: tracking down a mutation": an interactive learning laboratory that communicates basic principles of genetics and cellular biology.

    Science.gov (United States)

    Jarrett, Kevin; Williams, Mary; Horn, Spencer; Radford, David; Wyss, J Michael

    2016-03-01

    "Sickle cell anemia: tracking down a mutation" is a full-day, inquiry-based, biology experience for high school students enrolled in genetics or advanced biology courses. In the experience, students use restriction endonuclease digestion, cellulose acetate gel electrophoresis, and microscopy to discover which of three putative patients have the sickle cell genotype/phenotype using DNA and blood samples from wild-type and transgenic mice that carry a sickle cell mutation. The inquiry-based, problem-solving approach facilitates the students' understanding of the basic concepts of genetics and cellular and molecular biology and provides experience with contemporary tools of biotechnology. It also leads to students' appreciation of the causes and consequences of this genetic disease, which is relatively common in individuals of African descent, and increases their understanding of the first principles of genetics. This protocol provides optimal learning when led by well-trained facilitators (including the classroom teacher) and carried out in small groups (6:1 student-to-teacher ratio). This high-quality experience can be offered to a large number of students at a relatively low cost, and it is especially effective in collaboration with a local science museum and/or university. Over the past 15 yr, >12,000 students have completed this inquiry-based learning experience and demonstrated a consistent, substantial increase in their understanding of the disease and genetics in general. Copyright © 2016 The American Physiological Society.

  14. Procedure for implementing the system of quality management in the testing laboratory of the Center for Genetic Engineering and Biotechnology in Sancti Spiritus.

    Directory of Open Access Journals (Sweden)

    Lídice Peraza Cruz

    2014-03-01

    Full Text Available Implementation of Quality Management System in testing laboratories offers the possibility of its accreditation and a frame for cooperation with other organizations, supporting information and experience exchange, as well as standards and procedures harmonization. To improve the performance of the Center for Genetic Engineering and Biotechnology of Sancti Spíritus testing laboratory, assuring technically valid data and results which promote technical competence and credibility of in vitro diagnostics and biological reagents products, a procedure was designed to implement a Quality Management System. This procedure applies Deming´s Quality Cycle and considers all relevant requirements in NC ISO/IEC 17025:2006 “General requirements for the competence of testing and calibration laboratories” and Regulation No. 20 2004 “Good Manufacturing Practices for in vitro Diagnostics” of Center for State Control of Drugs, Equipment and Medical Devices. We recommend an auto evaluation method, designed by authors, to verify quality management system accomplishment.

  15. "Sickle Cell Anemia: Tracking down a Mutation": An Interactive Learning Laboratory That Communicates Basic Principles of Genetics and Cellular Biology

    Science.gov (United States)

    Jarrett, Kevin; Williams, Mary; Horn, Spencer; Radford, David; Wyss, J. Michael

    2016-01-01

    "Sickle cell anemia: tracking down a mutation" is a full-day, inquiry-based, biology experience for high school students enrolled in genetics or advanced biology courses. In the experience, students use restriction endonuclease digestion, cellulose acetate gel electrophoresis, and microscopy to discover which of three putative patients…

  16. "Sickle Cell Anemia: Tracking down a Mutation": An Interactive Learning Laboratory That Communicates Basic Principles of Genetics and Cellular Biology

    Science.gov (United States)

    Jarrett, Kevin; Williams, Mary; Horn, Spencer; Radford, David; Wyss, J. Michael

    2016-01-01

    "Sickle cell anemia: tracking down a mutation" is a full-day, inquiry-based, biology experience for high school students enrolled in genetics or advanced biology courses. In the experience, students use restriction endonuclease digestion, cellulose acetate gel electrophoresis, and microscopy to discover which of three putative patients…

  17. A New Orbivirus Isolated from Mosquitoes in North-Western Australia Shows Antigenic and Genetic Similarity to Corriparta Virus but Does Not Replicate in Vertebrate Cells

    Directory of Open Access Journals (Sweden)

    Jessica J. Harrison

    2016-05-01

    Full Text Available The discovery and characterisation of new mosquito-borne viruses provides valuable information on the biodiversity of vector-borne viruses and important insights into their evolution. In this study, a broad-spectrum virus screening system, based on the detection of long double-stranded RNA in inoculated cell cultures, was used to investigate the presence of novel viruses in mosquito populations of northern Australia. We detected and isolated a new virus (tentatively named Parry’s Lagoon virus, PLV from Culex annulirostris, Culex pullus, Mansonia uniformis and Aedes normanensis mosquitoes that shares genomic sequence similarities to Corriparta virus (CORV, a member of the Orbivirus genus of the family Reoviridae. Despite moderate to high (72.2% to 92.2% amino acid identity across all proteins when compared to CORV, and demonstration of antigenic relatedness, PLV did not replicate in several vertebrate cell lines that were permissive to CORV. This striking phenotypic difference suggests that PLV has evolved to have a very restricted host range, indicative of a mosquito-only life cycle.

  18. Genetic Similarity and Population Structure in a Rice Drought Stress Adaptation Panel%一组水稻种质资源的遗传相似性及群体结构分析

    Institute of Scientific and Technical Information of China (English)

    肖宇龙; 雷建国; 余传元; Quirino D.Dela Cruz; Jonalyn M.Cstillo; Dindo A.Tabanao

    2012-01-01

    育种的成功基于试验材料中具有可利用的遗传变异,了解种质资源的群体机构及遗传变异范围是作物遗传改良的先决条件.本试验通过利用每3 Mb bin均匀分布于水稻染色体的156个SSR标记子,分析了一组(184个)用于干旱适应性研究的水稻种质资源的遗传相似性及群体结构.结果显示,水稻中确实存在着可供利用的遗传多样性,但也存在着普遍的遗传相似性,如国际水稻所的IR品种及菲律宾国家水稻所的PR及BP 水稻品种.通过利用Structure中的混合模型对该184个水稻品种在K=3和K=7时的分析表明,群体结构普遍存在于相同类型或亚种的水稻品种中,籼稻及粳稻品种具有相对明显的群体结构,同一亲本的衍生后代具有显著的遗传相似性和群体结构,不同的群体均存在一定程度的遗传混合.对该组干旱适应性水稻种质资源的遗传相似性及群体结构的研究为今后的抗旱性基因的联合作图,也为合理选择亲本进行水稻抗旱性改良提供了有价值的遗传信息.%The success of plant breeding is based on the availability of genetic variation. Understanding the population structure and range of diversity in available germplasm is fundamental for genetic improvement in all crop species. In this study, the authors analyzed the genetic diversity and the population structure of a drought stress adaptation panel (184 rice genotypes) through 156 SSR markers nearly evenly distributed across the rice genome at every 3 Mb bin. The results indicated that large range of genetic diversity existed among rice germplasms, while some accessions exhibited comparatively higher genetic similarity, such as IR designated varieties from IRRI and BP and PR designated varieties from PhilRice. The results of population structure of the 184 rice genotypes analyzed when K = 3 and K=7 through the mixed model of STRUCTURE indicated: population generally existed in the same type or rice

  19. Detection of an ABCA1 Variant Associated with Type 2 Diabetes Mellitus Susceptibility for Biochemistry and Genetic Laboratory Courses

    Science.gov (United States)

    Legorreta-Herrera, M.; Mosqueda-Romo, N. A.; Hernández-Clemente, F.; Soto-Cruz, I.

    2013-01-01

    We selected diabetes mellitus for this laboratory exercise to provide students with an explicit model for scientific research concerning the association between the R230C polymorphism and susceptibility to type 2 diabetes mellitus, which is highly prevalent in the Mexican population. We used a collaborative project-based learning to engage…

  20. Detection of an ABCA1 Variant Associated with Type 2 Diabetes Mellitus Susceptibility for Biochemistry and Genetic Laboratory Courses

    Science.gov (United States)

    Legorreta-Herrera, M.; Mosqueda-Romo, N. A.; Hernández-Clemente, F.; Soto-Cruz, I.

    2013-01-01

    We selected diabetes mellitus for this laboratory exercise to provide students with an explicit model for scientific research concerning the association between the R230C polymorphism and susceptibility to type 2 diabetes mellitus, which is highly prevalent in the Mexican population. We used a collaborative project-based learning to engage…

  1. American College of Medical Genetics and Genomics Standards and Guidelines for Clinical Genetics Laboratories, 2014 edition: technical standards and guidelines for Huntington disease.

    Science.gov (United States)

    Bean, Lora; Bayrak-Toydemir, Pinar

    2014-12-01

    Huntington disease is an autosomal-dominant neurodegenerative disease of mid-life onset caused by expansion of a polymorphic trinucleotide (CAG) repeat. Variable penetrance for alleles carrying 36-39 repeats has been noted, but the disease appears fully penetrant when the repeat numbers are >40. An abnormal CAG repeat may expand, contract, or be stably transmitted when passed from parent to child. Assays used to diagnose Huntington disease must be optimized to ensure the accurate and unambiguous quantitation of CAG repeat length. This document provides an overview of Huntington disease and methodological considerations for Huntington disease testing. Examples of laboratory reports are also included.

  2. Role of laboratory biomarkers in monitoring and prediction of the effectiveness of treatment of rheumatic diseases using genetically engineered drugs

    Directory of Open Access Journals (Sweden)

    Elena Nikolayevna Aleksandrova

    2014-01-01

    Full Text Available Significant progress in treating immunoinflammatory rheumatic diseases (RD is related to the design of a novel family of drugs, genetically engineered (GE drugs. Molecular and cellular biomarkers (antibodies, indicators of acute inflammation, cytokines, chemokines, growth factors, endothelial activation markers, immunoglobulins, cryoglobulins, T- and B-cell subpopulations, products of bone and cartilage metabolism, genetic and metabolic markers that allow one to conduct immunological monitoring and prediction of the effectiveness of RD therapy using tumor necrosis factor α inhibitors (infliximab, adalimumab, golimumab, etanercept, anti-B-cell drugs (rituximab, belimumab, interleukin-6 receptor antagonist (tocilizumab, and T-cell costimulation blocker (abatacept have been detected in blood, synovial fluid, urine, and bioptates of the affected tissues. In addition to the conventional uniplex immunodiagnostics techniques, multiplex analysis of marker, which is based on genetic, transcriptomic and proteomic technologies using DNA and protein microarrays, polymerase chain reaction, and flow cytometry, is becoming increasingly widespread. The search for and validation of immunological predictors of the effective response to GE drug therapy make it possible to optimize and reduce the cost of therapy using these drugs in future.

  3. Role of laboratory biomarkers in monitoring and prediction of the effectiveness of treatment of rheumatic diseases using genetically engineered drugs

    Directory of Open Access Journals (Sweden)

    Elena Nikolayevna Aleksandrova

    2014-03-01

    Full Text Available Significant progress in treating immunoinflammatory rheumatic diseases (RD is related to the design of a novel family of drugs, genetically engineered (GE drugs. Molecular and cellular biomarkers (antibodies, indicators of acute inflammation, cytokines, chemokines, growth factors, endothelial activation markers, immunoglobulins, cryoglobulins, T- and B-cell subpopulations, products of bone and cartilage metabolism, genetic and metabolic markers that allow one to conduct immunological monitoring and prediction of the effectiveness of RD therapy using tumor necrosis factor α inhibitors (infliximab, adalimumab, golimumab, etanercept, anti-B-cell drugs (rituximab, belimumab, interleukin-6 receptor antagonist (tocilizumab, and T-cell costimulation blocker (abatacept have been detected in blood, synovial fluid, urine, and bioptates of the affected tissues. In addition to the conventional uniplex immunodiagnostics techniques, multiplex analysis of marker, which is based on genetic, transcriptomic and proteomic technologies using DNA and protein microarrays, polymerase chain reaction, and flow cytometry, is becoming increasingly widespread. The search for and validation of immunological predictors of the effective response to GE drug therapy make it possible to optimize and reduce the cost of therapy using these drugs in future.

  4. 煤系古风化岩相似材料配比研究%LABORATORY STUDY ON PROPORTION OF SIMILAR MATERIAL FOR SIMULATING ANCIENT WEATHERED ROCK IN COAL STRATA

    Institute of Scientific and Technical Information of China (English)

    丁卿峰; 岳艳艳; 李文平; 白汉营

    2015-01-01

    为制备具有力学性质递变特征的相似材料试样,本文通过水泥石膏相似材料的配比试验,得到了两种骨料(标准砂和河沙)相似材料力学性质与配比间的关系。在拟合河沙相似材料的室内力学测试数据的基础上,得到了配比值关于抗压强度和弹性模量的确定公式。试验表明:用水量、成型压力和平均骨料粒径对相似材料的力学性质均有不同程度的影响,在制样过程中需要加以控制;低强度相似材料的抗拉强度不易控制,而单轴抗压强度和弹性模量对配比的变化有明显响应;河沙相似材料的力学性质与配比间呈明显的线性关系,而标准砂相似材料存在临界骨料含量和临界水泥含量表现出明显的非线性特征;在调整配比所能实现的抗压强度和弹性模量的变化范围内,相似材料能够较好地模拟单轴抗压强度大于3MPa 的风化岩。%This paper is to prepare the similar material specimens with gradual variation of mechanical properties. The proportion tests is used to achieve the relationship between mechanical properties and proportion of cement-gypsum similar materials with different aggregates.A defined formula of proportion based on compressive strength and elastic modulus is determined via fitting the laboratory mechanical testing data of river-sand material.The test result shows that:water dosage,forming pressure and average particle diameter have effect of different levels and should be controlled in specimen preparation process.The tensile strength of low-intensity similar material is uncontrollable while the compressive strength and the elastic modulus show an obvious response to the change of proportion.For river sand similar material,the mechanical properties and the proportion present a linear relationship.While the standard sand similar material presents a nonlinear relationship between the mechanical properties and the proportion due to

  5. Similaridade genética entre cultivares de cebola de diferentes tipos e origens, baseada em marcadores AFLP Genetic similarity among onion cultivars of different types and origins, based on AFLP markers

    Directory of Open Access Journals (Sweden)

    CAF Santos

    2011-03-01

    Full Text Available Foi estimada a similaridade genética entre cultivares de cebola de diferentes tipos e regiões geográficas, de forma a orientar programas de recursos genéticos e melhoramento da espécie no Nordeste brasileiro. Foram analisadas 41 cultivares, adotando-se para a visualização da similaridade genética o fenograma UPGMA gerado da matriz de distâncias genéticas estimadas pelo coeficiente de Jaccard e baseadas em 146 bandas polimórficas de Pst1 e Mse1 de AFLP. A correlação cofenética foi de 0,91, indicando boa confiabilidade da representação gráfica para a interpretação dos resultados. Foram observados dois grupos principais no fenograma, no ponto de corte de 0,55 de similaridade: 1 grupo formado por cultivares predominantemente brasileiras, com algumas inclusões de cultivares estrangeiras; e 2 grupo formado por três cultivares estrangeiras (Mercedes, Perfect e TEG 502 PRR. Rijnsburger Jumbo e IPA 8 apresentaram a maior similaridade (85%, enquanto Madrugada foi a mais divergente em relação às demais cultivares. As cultivares da série IPA se dividiram em subgrupos no grupo das cultivares brasileiras (IPA 8, IPA 10 e IPA 11; IPA 12, IPA 7, IPA 2 e IPA 6; IPA 3, IPA 4 e IPA 9, indicando haver variabilidade genética a ser explorada entre aquelas situadas em subgrupos distintos. Bola Precoce e BRS Cascata apresentaram a maior similaridade entre as cultivares de origem brasileira. Foi observada similaridade superior a 39%, refletindo a alta variabilidade genética da coleção de cebola estudada. A introdução de novos acessos deve considerar procedências outras que não norte americanas, para aumentar a variabilidade de germoplasma de cebola disponível no Nordeste do Brasil.The genetic similarity among onion cultivars of different origins was evaluated, in order to carry out genetic resources and breeding programs for this species on the Brazilian Northeast. Forty-one onion cultivars were analyzed for 146 polymorphic Pst1/Mse1

  6. Divergent evolution of molecular markers during laboratory adaptation in Drosophila subobscura.

    Science.gov (United States)

    Simões, Pedro; Pascual, Marta; Coelho, Maria Manuela; Matos, Margarida

    2010-10-01

    The impact of genetic drift in population divergence can be elucidated using replicated laboratory experiments. In the present study we used microsatellite loci to study the genetic variability and differentiation of laboratory populations of Drosophila subobscura derived from a common ancestral natural population after 49 generations in the laboratory. We found substantial genetic variability in all our populations. The high levels of genetic variability, similar across replicated populations, suggest that careful maintenance procedures can efficiently reduce the loss of genetic variability in captive populations undergoing adaptation, even without applying active management procedures with conservation purposes, in organisms that generate a high number of offspring such as Drosophila. Nevertheless, there was a significant genetic differentiation between replicated populations. This shows the importance of genetic drift, acting through changes in allele frequencies among populations, even when major changes in the degree of genetic diversity in each population are not involved.

  7. Genetic similarities among four species of the Plectranthus (L’Hér. genus = Similaridade genética de quatro espécies do gênero Plectranthus

    Directory of Open Access Journals (Sweden)

    Juliana de Magalhães Bandeira

    2010-01-01

    Full Text Available The Plectranthus genus comprises several species generally referred to as boldo, which are highly used in popular medicine due to their anti-dyspeptic, analgesic and digestion-stimulating properties. The amount of natural active principles can vary greatly in the related genotypes, which may lead to the inappropriate use of these plants. This work aimed to analyze the interspecific diversity among four species of the Plectranthus genus (P. grandis, P. barbatus, P. neochilus and P. amboinicus and the intraspecific diversity of P. barbatus collected from different places in southern Brazil, by means of the RAPD technique. A higher genetic similarity was observed between the P. neochilus and P. amboinicus species (80%, followed by P. grandis and P. barbatus (77%. P. barbatus genotypes from Passo Fundo and Porto Alegre showed a genetic similarity which was close to 100%, while the genetic similarity for P. barbatus genotypes from other locations was higher than 96%. Although a low variability among genotypes of this species was found in this study, RAPD markers allowed a clear differentiation among the analyzed genotypes, showing a 53% mean genetic similarity, with a high correlation value (r = 0.99, which proves a high agreement between the genetic similarity and clustering data.O gênero Plectranthus abrange plantas de diversas espécies, referidas como boldo, que são utilizadas na medicina popular pelas suas propriedades antidispépticas, analgésicas e estimulantes da digestão. Genótipos relacionados podem diferir amplamente na quantidade de princípios ativos naturais, resultando no uso de plantas não-apropriadas à saúde da população. O objetivo do presente estudo foi avaliar a diversidade genética interespecífica de quatro espécies do gênero Plectranthus (P. grandis, P. barbatus, P. neochilus e P. amboinicus e intraespecífica de P. barbatus, coletadas em diferentes localidades da região Sul do Brasil, por meio da técnica de RAPD

  8. Integrating clinical and laboratory data in genetic studies of complex phenotypes: a network-based data management system.

    Science.gov (United States)

    McMahon, F J; Thomas, C J; Koskela, R J; Breschel, T S; Hightower, T C; Rohrer, N; Savino, C; McInnis, M G; Simpson, S G; DePaulo, J R

    1998-05-01

    The identification of genes underlying a complex phenotype can be a massive undertaking, and may require a much larger sample size than thought previously. The integration of such large volumes of clinical and laboratory data has become a major challenge. In this paper we describe a network-based data management system designed to address this challenge. Our system offers several advantages. Since the system uses commercial software, it obviates the acquisition, installation, and debugging of privately-available software, and is fully compatible with Windows and other commercial software. The system uses relational database architecture, which offers exceptional flexibility, facilitates complex data queries, and expedites extensive data quality control. The system is particularly designed to integrate clinical and laboratory data efficiently, producing summary reports, pedigrees, and exported files containing both phenotype and genotype data in a virtually unlimited range of formats. We describe a comprehensive system that manages clinical, DNA, cell line, and genotype data, but since the system is modular, researchers can set up only those elements which they need immediately, expanding later as needed.

  9. Frequently Asked Questions about Genetic Testing

    Science.gov (United States)

    ... Care Specific Genetic Disorders Frequently Asked Questions About Genetic Testing What is genetic testing? What can I learn ... find more information about genetic testing? What is genetic testing? Genetic testing uses laboratory methods to look at ...

  10. IDENTIFYING GENETIC ASSOCIATIONS WITH VARIABILITY IN METABOLIC HEALTH AND BLOOD COUNT LABORATORY VALUES: DIVING INTO THE QUANTITATIVE TRAITS BY LEVERAGING LONGITUDINAL DATA FROM AN EHR.

    Science.gov (United States)

    Verma, Shefali S; Lucas, Anastasia M; Lavage, Daniel R; Leader, Joseph B; Metpally, Raghu; Krishnamurthy, Sarathbabu; Dewey, Frederick; Borecki, Ingrid; Lopez, Alexander; Overton, John; Penn, John; Reid, Jeffrey; Pendergrass, Sarah A; Breitwieser, Gerda; Ritchie, Marylyn D

    2016-01-01

    variance group and the low variance group for each lab variable. We found 717 PheWAS associations that replicated at a p-value less than 0.001. Next, we evaluated the results of this study by comparing the association results between the high and low variance groups. For example, we found 39 SNPs (in multiple genes) associated with ICD-9 250.01 (Type-I diabetes) in patients with high variance of plasma glucose levels, but not in patients with low variance in plasma glucose levels. Another example is the association of 4 SNPs in UMOD with chronic kidney disease in patients with high variance for aspartate aminotransferase (discovery p-value: 8.71×10-09 and replication p-value: 2.03×10-06). In general, we see a pattern of many more statistically significant associations from patients with high variance in the quantitative lab variables, in comparison with the low variance group across all of the 25 laboratory measurements. This study is one of the first of its kind to utilize quantitative trait variance from longitudinal laboratory data to find associations among genetic variants and clinical phenotypes obtained from an EHR, integrating laboratory values and diagnosis codes to understand the genetic complexities of common diseases.

  11. An RNA Phage Lab: MS2 in Walter Fiers' laboratory of molecular biology in Ghent, from genetic code to gene and genome, 1963-1976.

    Science.gov (United States)

    Pierrel, Jérôme

    2012-01-01

    The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück's phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers' laboratory at Ghent University (Belgium) and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his 'RNA phage lab' with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s.

  12. Paternity analysis based on NGM SElect system in the Medical and Forensic Genetics Laboratory, Department of Forensic Medicine, Medical University of Lodz

    Directory of Open Access Journals (Sweden)

    Beata Markiewicz-Knyziak

    2015-08-01

    Full Text Available The aim of the study was to evaluate the usefulness of the NGM SElect multiplex kit for paternity testing in the population of central Poland, and compare it with the IDENTIFILER system. The study material consisted of buccal swabs taken from individuals who reported to the Medical and Forensic Genetics Laboratory in Lodz. Samples from 450 trio cases of disputed paternity carried out in 2010–2014 were investigated. Genomic DNA was extracted from buccal swabs collected from 1,350 individuals using the Swab kit (A&A Biotechnology according to the manufacturer’s protocol. DNA amplification was performed using the AmpFℓSTR ® NGM Select TM PCR Amplification Kit (Life Technologies. PCR products were separated by capillary electrophoresis using HID 3500 Genetic Analyzer. In the analyzed cases with paternity confirmation in the NGM SElect system, the maximum value of PI was 3.9 × 10 12 , which corresponds to the probability of paternity W = 99.9999999999%. It was thus significantly higher than analogical parameters obtained in the IDENTIFILER system (PI = 6.0 × 10 10 , W = 99.99999999%. The NGM SElect kit was unable to resolve just one case out of 450, which represents only 0.2% of all analyzed disputed paternity cases. The study showed the SE33 (ACTBP2 locus to have the highest evidence value in paternity analysis out of all investigated autosomal STRs.

  13. Paternity analysis based on NGM SElect system in the Medical and Forensic Genetics Laboratory, Department of Forensic Medicine, Medical University of Lodz.

    Science.gov (United States)

    Markiewicz-Knyziak, B; Jędrzejczyk, M; Bąbol-Pokora, K; Wojtkiewicz, R; Jacewicz, R

    2015-01-01

    The aim of the study was to evaluate the usefulness of the NGM SElect multiplex kit for paternity testing in the population of central Poland, and compare it with the IDENTIFILER system. The study material consisted of buccal swabs taken from individuals who reported to the Medical and Forensic Genetics Laboratory in Lodz. Samples from 450 trio cases of disputed paternity carried out in 2010-2014 were investigated. Genomic DNA was extracted from buccal swabs collected from 1,350 individuals using the Swab kit (A and A Biotechnology) according to the manufacturer's protocol. DNA amplification was performed using the AmpFℓSTR® NGM SelectTM PCR Amplification Kit (Life Technologies). PCR products were separated by capillary electrophoresis using HID 3500 Genetic Analyzer. In the analyzed cases with paternity confirmation in the NGM SElect system, the maximum value of PI was 3.9 × 1012, which corresponds to the probability of paternity W = 99.9999999999%. It was thus significantly higher than analogical parameters obtained in the IDENTIFILER system (PI = 6.0 × 1010, W = 99.99999999%). The NGM SElect kit was unable to resolve just one case out of 450, which represents only 0.2% of all analyzed disputed paternity cases. The study showed the SE33 (ACTBP2) locus to have the highest evidence value in paternity analysis out of all investigated autosomal STRs.

  14. The effect of ivermectin in seven strains of Aedes aegypti (Diptera: Culicidae) including a genetically diverse laboratory strain and three permethrin resistant strains.

    Science.gov (United States)

    Deus, K M; Saavedra-Rodriguez, K; Butters, M P; Black, W C; Foy, B D

    2012-03-01

    Seven different strains of Aedes aegypti (L.), including a genetically diverse laboratory strain, three laboratory-selected permethrin-resistant strains, a standard reference strain, and two recently colonized strains were fed on human blood containing various concentrations of ivermectin. Ivermectin reduced adult survival, fecundity, and hatch rate of eggs laid by ivermectin-treated adults in all seven strains. The LC50 of ivermectin for adults and the concentration that prevented 50% of eggs from hatching was calculated for all strains. Considerable variation in adult survival after an ivermectin-bloodmeal occurred among strains, and all three permethrin-resistant strains were significantly less susceptible to ivermectin than the standard reference strain. The hatch rate after an ivermectin bloodmeal was less variable among strains, and only one of the permethrin-resistant strains differed significantly from the standard reference strain. Our studies suggest that ivermectin induces adult mortality and decreases the hatch rate of eggs through different mechanisms. A correlation analysis of log-transformed LC50 among strains suggests that permethrin and ivermectin cross-resistance may occur.

  15. Using student-generated UV-induced Escherichia coli mutants in a directed inquiry undergraduate genetics laboratory.

    Science.gov (United States)

    Healy, Frank G; Livingstone, Kevin D

    2010-09-01

    We report a thematic sequence of directed inquiry-based labs taking students from bacterial mutagenesis and phenotypic identification of their own self-created mutant, through identification of mutated genes by biochemical testing, to verification of mutant alleles by complementation, and finally to mutant allele characterization by DNA sequence analysis. The lab utilizes UV mutagenesis with wild-type Escherichia coli and a UV-sensitive isogenic derivative optimized for undergraduate use. The labs take advantage of the simplicity of E. coli in a realistic genetic investigation using safe UV irradiation methods for creation and characterization of novel mutants. Assessment data collected over three offerings of the course suggest that the labs, which combine original investigation in a scientifically realistic intellectual environment with learned techniques and concepts, were instrumental in improving students' learning in a number of areas. These include the development of critical thinking skills and understanding of concepts and methods. Student responses also suggest the labs were helpful in improving students' understanding of the scientific process as a rational series of experimental investigations and awareness of the interdisciplinary nature of scientific inquiry.

  16. The spectrum of FMF mutations and genotypes in the referrals to molecular genetic laboratory at Kirikkale University in Turkey.

    Science.gov (United States)

    Gunel-Ozcan, Aysen; Sayin, Derya Beyza; Misirlioğlu, Emine Dibek; Güliter, Sefa; Yakaryilmaz, Fahri; Ensari, Cuneyt

    2009-04-01

    Familial Mediterranean Fever (FMF) is an autosomal recessive genetic disorder characterised by recurrent and self-limited abdominal pain, synovitis and pleuritis. MEFV gene mutations are responsible from the disease and its protein product, pyrin or marenostrin, plays an essential role in the regulation of the inflammatory reactions. MEFV gene contains 10 exons and most of the mutations have been found on the last exon. Up to date, 152 mutations and polymorpisms have been reported inwhere V726A, M694V, M694I, M680I and E148Q are the most common mutations. In this study, MEFV allele frequencies of 136 individuals (60 from Pediatry, 76 from Internal Medicine) have been evaluated, and compared with each other. Asymptomatic individuals with FMF family history (4 from Pediatry, 6 from Internal Medicine) were excluded from the analysis. The prominent mutations indicated in the Pediatry group are V726A, M694V and M680I (G/C) and with the allele frequency of 0.06, 0.05 and 0.04 respectively while they were E148Q, M694V, M680I (G/C) in the Internal Medicine group with the allele frequency of 0.12, 0.08 and 0.04. The E148Q mutation is significantly overrepresented in the adult referrals (P = 0.02). Mutation on both alleles was observed in only 12% of cases. Overall mutation frequency was low, seen in 26.2% (66/252). However, when only diagnosed patients were analyzed it is 72.7% (16/22). It is also interesting that 63% of individuals are female that there may be sex influence on FMF phenotype.

  17. Genetic Diversity and Similarity of Global Faba Bean(Vcia faba L.)Germplasm Revealed by ISSR Markers%世界蚕豆种质资源遗传多样性和相似性的ISSR分析

    Institute of Scientific and Technical Information of China (English)

    王海飞; 关建平; 孙雪莲; 马钰; 宗绪晓

    2011-01-01

    [Objective] The purpose of this research is to analyze the genetic diversity of global faba bean germplasm, to explore their genetic similarity and population structure, and to provide essential information for germplasm evaluation and effective utilization of faba bean genetic resources. [Method] The genetic similarity of 383 faba bean accessions from 35 countries was analyzed by using ISSR marker. [Result] Eleven ISSR primers generated 229 unambiguous bands, of which 212 were polymorphic,and the rate of polymorphic bands was 0.93. Gene diversity index (H) and allelic richness (NA) of different geographic groups of germplasm ranged from 0.16 to 0.28 and from 104 to 193, respectively. Chinese spring-seeding area group showed the highest genetic diversity (H = 0.28, NA = 193), and America group showed the lowest (H = 0.16, NA = 104). The spring faba bean germplasm was clearly separated from winter faba bean germplasm of China in UPGMA clustering analysis based on ISSR molecular marker data. Germplasm from China is quite distinct to that from exotic accessions. The accessions from Europe had a closer genetic similarity with that from North Africa. While the germplasm resources from Asia, Europe and Africa are closely related to their geographical distribution. [Conclusion ] Accessions from spring-seeding area of China were most diverse. Germplasm from America showed lowest diversity. The results indicated that the genetic similarity and diversity of faba bean germplasm are closely associated with their growth habit, their geographical origin and ecological distribution.%[目的]分析国内外蚕豆种质资源的遗传多样性,探索其遗传相似性和遗传结构,为世界蚕豆资源的综合评价和优良种质资源的发掘利用提供依据.[方法]利用ISSR标记技术,对来自世界35个国家的383份蚕豆资源的遗传相似性进行分析.[结果]筛选出的11条ISSR引物共扩增出229条条带,其中多态性条带212条(占93%).不同地理

  18. Proceedings of the joint WHO/TDR, NIAD, IAEA and Frontis workshop on bridging laboratory and field research for genetic control of disease vectors, Nairobi, Kenya 14-16 July 2004

    NARCIS (Netherlands)

    Knols, B.G.J.; Bossin, H.

    2006-01-01

    Contemporary research on genetic control of disease-transmitting insects knows two kinds of scientists: those that work in the laboratory and those known as `field people¿. Over the last decade, both groups seem to have developed differing research priorities, address fundamentally different aspects

  19. Similaridade genética de acessos de mangueira de diferentes origens geográficas avaliadas por marcadores AFLP Genetic similarity of mango accessions of different geographic origins evaluated with AFLP markers

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2008-09-01

    accessions was extracted according to the CTAB protocol, the AFLP reactions were performed to EcoRI/MseI primers and the polymorphic bands analyzed to built a phenogram based on the Jaccard similarity coefficient. A hundred and fifty-seven and fifty-four polymorphic and monomorphic bands, respectively, were obtained from 13 AFLP primer combinations. The phenogram cophenetic value was estimated in 0.81. Five groups were observed: 1 Amrapali, Malika, Embrapa-CPAC hybrids and some American varieties forming a group, 2 other built, predominantly, by American varieties, with some inclusions of South African and Brazilian hybrids, 3 a large group composed by Brazilian accessions, with some inclusion of Australian, Indian and American accessions, 4 a group with some accessions of Espada, Rosa and others of different origins, and 5 a group formed by M. foetida and M. similis. Carabao and Manilla presented the largest similarity, 97%. The studied accessions presented similarity greater than 51%, suggesting a high genetic variability of the studied mango germplasm collection.

  20. Genetic diversity and genetic similarities between Iranian rose species

    NARCIS (Netherlands)

    Samiei, L.; Naderi, R.; Khalighi, A.; Shahnejat-Bushehri, A.A.; Mozaffarian, V.; Esselink, G.D.; Kazempour Osaloo, S.; Smulders, M.J.M.

    2010-01-01

    Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence

  1. Identification by 16S rDNA fragment amplification and determination of genetic diversity by random amplified polymorphic DNA analysis of Pasteurella pneumotropica isolated from laboratory rodents.

    Science.gov (United States)

    Kodjo, A; Villard, L; Veillet, F; Escande, F; Borges, E; Maurin, F; Bonnod, J; Richard, Y

    1999-02-01

    Pasteurella pneumotropica is an opportunistic bacterium frequently isolated from colonies of various laboratory rodents. Identification of this species, including its differentiation into two distinct biotypes (Jawetz and Heyl), is usually based on the use of conventional bacteriologic methods. In this study, a 16S rDNA fragment amplification procedure was developed for use as an alternative method for identification and differentiation of P. pneumotropica. Polymerase chain reaction (PCR) products were two distinctive fragments of 937 and 564 bp specific for biotypes Jawetz and Heyl, respectively. Specificity of PCR products could be achieved by EcoRI cleavage, leading to 596 plus 341-bp and 346 plus 218-bp fragments for each of the amplification products. Use of this procedure confirmed identification of 34 field isolates and allowed definitive identification of some strains that could not have been done by use of bacteriologic examinations. Field isolates subjected to random amplified polymorphic DNA (RAPD) analysis had high genetic diversity among biotype Jawetz strains in contrast to biotype Heyl strains. In conclusion, RAPD could represent an additional means for identification of ambiguous strains of biotype Heyl and a valuable epidemiologic tool for identification of biotype Jawetz strains of P. pneumotropica.

  2. Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system

    Directory of Open Access Journals (Sweden)

    Aguilar César

    2012-08-01

    Full Text Available Abstract Background Escherichia coli strains lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS, which is the major bacterial component involved in glucose transport and its phosphorylation, accumulate high amounts of phosphoenolpyruvate that can be diverted to the synthesis of commercially relevant products. However, these strains grow slowly in glucose as sole carbon source due to its inefficient transport and metabolism. Strain PB12, with 400% increased growth rate, was isolated after a 120 hours adaptive laboratory evolution process for the selection of faster growing derivatives in glucose. Analysis of the genetic changes that occurred in the PB12 strain that lacks PTS will allow a better understanding of the basis of its growth adaptation and, therefore, in the design of improved metabolic engineering strategies for enhancing carbon diversion into the aromatic pathways. Results Whole genome analyses using two different sequencing methodologies: the Roche NimbleGen Inc. comparative genome sequencing technique, and high throughput sequencing with Illumina Inc. GAIIx, allowed the identification of the genetic changes that occurred in the PB12 strain. Both methods detected 23 non-synonymous and 22 synonymous point mutations. Several non-synonymous mutations mapped in regulatory genes (arcB, barA, rpoD, rna and in other putative regulatory loci (yjjU, rssA and ypdA. In addition, a chromosomal deletion of 10,328 bp was detected that removed 12 genes, among them, the rppH, mutH and galR genes. Characterization of some of these mutated and deleted genes with their functions and possible functions, are presented. Conclusions The deletion of the contiguous rppH, mutH and galR genes that occurred simultaneously, is apparently the main reason for the faster growth of the evolved PB12 strain. In support of this interpretation is the fact that inactivation of the rppH gene in the parental PB11 strain substantially increased

  3. 牙鲆连续两代减数分裂雌核发育家系的遗传特征%Analysis of homozygosity and genetic similarity between two successive generations in a meiogynogenetic Japanese flounder family

    Institute of Scientific and Technical Information of China (English)

    王桂兴; 刘海金; 张晓彦; 刘永新; 王玉芬; 蒋丽

    2012-01-01

    The artificial induction of gynogenesis is a form of chromosome manipulation that has several applications, including the rapid establishment of inbred lines or strains. The technique offers a high degree of homozygosity, sex-control, and accelerated elimination of recessive deleterious genes from a cultured population. We produced two meiotic gynogenetic Japanese flounder (Paralichthys olivaceus) family lines: meio-Gl (the first generation) and meio-G2 (the second generation). We evaluated the efficacy of artificial meiotic gynogenesis for producing pure inbred lines by quantifying the homozygosity and genetic similarity of meio-Gl and meio-G2 using microsatellite markers The average homozygosity among 15 loci was 0.124 7 for meio-Gl and 0.221 5 for meio-G2, which was higher than that in the natural mating family (0.091 7). The average similarity indices among individuals within meio-Gl and meio-G2 were 0.891 7 and 0.923 8, which were higher than within the natural mating family (0.5603). The average similarity in meio-G2 was slightly higher than in meio-Gl. The observed heterozygosity in meio-Gl and meio-G2 was 1 at the Poli9-8tuf, Polil8tuf, Polil07tuf loci, all of which were located at some distance from the centromere (i.e., had high recombination frequencies). The loci {PoliHtuf, Poli24MHFS) closest to the centromere (i.e., with a low recombination frequency) were homozygous in meio-Gl and meio-G2. Our results suggest that artificially induced meiotic gynogenesis is an efficient method for inbreeding to purify the genome, increase genetic similarity, and fix maternal genetic traits in the Japanese flounder. The meiogynogenetic families cultured in our study may be used in further selective breeding research.%对牙鲆(Paralichthys olivaceus)减数分裂雌核发育二倍体(Meio-G1)再次诱导减数分裂雌核发育,获得连续两代雌核发育二倍体家系(Meio-G2),以Meio-G1亲本与1尾普通牙鲆雄鱼人工授精获得的

  4. Genetic Basis of Cry1F-Resistance in a Laboratory Selected Asian Corn Borer Strain and Its Cross-Resistance to Other Bacillus thuringiensis Toxins.

    Science.gov (United States)

    Wang, Yueqin; Wang, Yidong; Wang, Zhenying; Bravo, Alejandra; Soberón, Mario; He, Kanglai

    2016-01-01

    The Asian corn borer (ACB), Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae), is the most destructive insect pest of corn in China. Susceptibility to the Cry1F toxin derived from Bacillus thuringiensis has been demonstrated for ACB, suggesting the potential for Cry1F inclusion as part of an insect pest management program. Insects can develop resistance to Cry toxins, which threatens the development and use of Bt formulations and Bt crops in the field. To determine possible resistance mechanisms to Cry1F, a Cry1F-resistant colony of ACB (ACB-FR) that exhibited more than 1700-fold resistance was established through selection experiments after 49 generations of selection under laboratory conditions. The ACB-FR strain showed moderate cross-resistance to Cry1Ab and Cry1Ac of 22.8- and 26.9-fold, respectively, marginally cross-resistance to Cry1Ah (3.7-fold), and no cross-resistance to Cry1Ie (0.6-fold). The bioassay responses of progeny from reciprocal F1 crosses to different Cry1 toxin concentrations indicated that the resistance trait to Cry1Ab, Cry1Ac and Cry1F has autosomal inheritance with no maternal effect or sex linked. The effective dominance (h) of F1 offspring was calculated at different concentrations of Cry1F, showing that h decreased as concentration of Cry1F increased. Finally, the analysis of actual and expected mortality of the progeny from a backcross (F1 × resistant strain) indicated that the inheritance of the resistance to Cry1F in ACB-FR was due to more than one locus. The present study provides an understanding of the genetic basis of Cry1F resistance in ACB-FR and also shows that pyramiding Cry1F with Cry1Ah or Cry1Ie could be used as a strategy to delay the development of ACB resistance to Bt proteins.

  5. The non-structural (NS) gene segment of H9N2 influenza virus isolated from backyard poultry in Pakistan reveals strong genetic and functional similarities to the NS gene of highly pathogenic H5N1.

    Science.gov (United States)

    Munir, Muhammad; Zohari, Siamak; Iqbal, Munir; Abbas, Muhammad; Perez, Daniel Roberto; Berg, Mikael

    2013-10-01

    Apart from natural reassortment, co-circulation of different avian influenza virus strains in poultry populations can lead to generation of novel variants and reassortant viruses. In this report, we studied the genetics and functions of a reassorted non-structural gene (NS) of H9N2 influenza virus collected from back yard poultry (BYP) flock. Phylogenetic reconstruction based on hemagglutinin and neuraminidase genes indicates that an isolate from BYP belongs to H9N2. However, the NS gene-segment of this isolate cluster into genotype Z, clade 2.2 of the highly pathogenic H5N1. The NS gene plays essential roles in the host-adaptation, cell-tropism, and virulence of influenza viruses. However, such interpretations have not been investigated in naturally recombinant H9N2 viruses. Therefore, we compared the NS1 protein of H9N2 (H9N2/NS1) and highly pathogenic H5N1 (H5N1/NS1) in parallel for their abilities to regulate different signaling pathways, and investigated the molecular mechanisms of IFN-β production in human, avian, and mink lung cells. We found that H9N2/NS1 and H5N1/NS1 are comparably similar in inhibiting TNF-α induced nuclear factor κB and double stranded RNA induced activator protein 1 and interferon regulatory factor 3 transcription factors. Thus, the production of IFN-β was inhibited equally by both NS1s as demonstrated by IFN stimulatory response element and IFN-β promoter activation. Moreover, both NS1s predominantly localized in the nucleus when transfected to human A549 cells. This study therefore suggests the possible increased virulence of natural reassortant viruses for their efficient invasion of host immune responses, and proposes that these should not be overlooked for their epizootic and zoonotic potential.

  6. All about Genetics (For Parents)

    Science.gov (United States)

    ... or sequence) of these four bases determines each genetic code. The segments of DNA that contain the instructions ... laboratory dyes. continue Genetic Problems Errors in the genetic code or "gene recipe" can happen in a variety ...

  7. Bioassay Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Bioassay Laboratory is an accredited laboratory capable of conducting standardized and innovative environmental testing in the area of aquatic ecotoxicology. The...

  8. HYDROMECHANICS LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — Naval Academy Hydromechanics Laboratory The Naval Academy Hydromechanics Laboratory (NAHL) began operations in Rickover Hall in September 1976. The primary purpose...

  9. HYDROMECHANICS LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — Naval Academy Hydromechanics LaboratoryThe Naval Academy Hydromechanics Laboratory (NAHL) began operations in Rickover Hall in September 1976. The primary purpose of...

  10. Diagnostic laboratory testing for Charcot Marie Tooth disease (CMT): the spectrum of gene defects in Norwegian patients with CMT and its implications for future genetic test strategies

    National Research Council Canada - National Science Library

    Østern, Rune; Fagerheim, Toril; Hjellnes, Helene; Nygård, Bjørn; Mellgren, Svein I; Nilssen, Øivind

    2013-01-01

    Current genetic test algorithms for Charcot Marie Tooth (CMT) disease are based on family details and comprehensive clinical and neurophysiological data gathered under ideal conditions for clinical assessment...

  11. Genetic Basis of Cry1F-Resistance in a Laboratory Selected Asian Corn Borer Strain and Its Cross-Resistance to Other Bacillus thuringiensis Toxins

    Science.gov (United States)

    Wang, Yueqin; Wang, Yidong; Wang, Zhenying; Bravo, Alejandra; Soberón, Mario; He, Kanglai

    2016-01-01

    The Asian corn borer (ACB), Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae), is the most destructive insect pest of corn in China. Susceptibility to the Cry1F toxin derived from Bacillus thuringiensis has been demonstrated for ACB, suggesting the potential for Cry1F inclusion as part of an insect pest management program. Insects can develop resistance to Cry toxins, which threatens the development and use of Bt formulations and Bt crops in the field. To determine possible resistance mechanisms to Cry1F, a Cry1F-resistant colony of ACB (ACB-FR) that exhibited more than 1700-fold resistance was established through selection experiments after 49 generations of selection under laboratory conditions. The ACB-FR strain showed moderate cross-resistance to Cry1Ab and Cry1Ac of 22.8- and 26.9-fold, respectively, marginally cross-resistance to Cry1Ah (3.7-fold), and no cross-resistance to Cry1Ie (0.6-fold). The bioassay responses of progeny from reciprocal F1 crosses to different Cry1 toxin concentrations indicated that the resistance trait to Cry1Ab, Cry1Ac and Cry1F has autosomal inheritance with no maternal effect or sex linked. The effective dominance (h) of F1 offspring was calculated at different concentrations of Cry1F, showing that h decreased as concentration of Cry1F increased. Finally, the analysis of actual and expected mortality of the progeny from a backcross (F1 × resistant strain) indicated that the inheritance of the resistance to Cry1F in ACB-FR was due to more than one locus. The present study provides an understanding of the genetic basis of Cry1F resistance in ACB-FR and also shows that pyramiding Cry1F with Cry1Ah or Cry1Ie could be used as a strategy to delay the development of ACB resistance to Bt proteins. PMID:27518813

  12. 产地与种源对玛咖化学质量的影响%Contribution of environmental and genetic variation to chemical similarity of Maca (Lepidium meyenii Walp.)

    Institute of Scientific and Technical Information of China (English)

    周文彬; 成哲弘; 赵云鹏; 傅承新

    2016-01-01

    Summary Maca,Lepidiummeyenii Walp.(Brassicaceae),has been domesticated as a medicinal crop at high altitude of the Peruvian Andes for two millennia.Its cultivars or landraces with different chemical profiles were bred and introduced out of Peru to various countries for industrial cultivation as driven by the increasing demand. Maca,which was approved on the ChinaInventory of NewResource Food in 2011,was also massively cultivated in multiple regions in China.The applied Maca cultivars differed among the producers,which may result in significant inconsistency of Maca quality.Thus,it is increasingly urgent to assess the quality of Maca roots with different cultivars and cultivation localities. We simultaneously conducted both common garden and translocation experiments to address the contribution of both genetic and environmental variation to chemical similarity of Maca.Contents of mineral elements,amino acids,total alkaloid,and macamides were determined on five replicate samples of each Maca category using inductively coupled plasma mass spectrometer (ICP-MS), L8900 amino acid analyzer, UV-2700 spectrophotometer and ProStar 210 high performance liquid chromatograph.Both the chemical component contents and overall similarity coefficients were calculated and compared for the four parameters above using analysis of variance(ANOVA),principal component analysis (PCA),hierarchical clustering analysis (HCA) and cosine coefficient.Data analyses were conducted using SPSS version 22.0. The results showed that the same cultivar from the translocation experiment (H6 ,A6) demonstrated remarkably greater chemical dissimilarity than the four cultivars (H1 ,H2 ,H3 ,H6) from the common garden experiment.The former experimental pair significantly differed in 1 1 components,while the latter four cultivars differed in five components.Although different groups of components differed to different extents between either cultivars or localities,the contents of mineral elements were

  13. The current state of genetic counseling before and after amniocentesis for fetal karyotyping in Japan: a survey of obstetric hospital clients of a prenatal testing laboratory.

    Science.gov (United States)

    Nishiyama, Miyuki; Sawai, Hideaki; Kosugi, Shinji

    2013-12-01

    Pregnant women undergoing prenatal genetic testing should receive genetic counseling so they can make informed decisions. We examined the current state of providing genetic counseling in Japan to pregnant women before they elected amniocentesis for prenatal diagnosis of chromosome abnormalities and after test results were completed, and explored the opportunity for expanding access to certified genetic counselors (CGC) at clinical practices offering amniocentesis. An anonymous survey was mailed to the 298 hospitals that referred amniotic fluid specimens to LabCorp Japan in 2009. Most genetic counseling was provided by the obstetrician alone; 73.8 % (76/103) of pre-amniocentesis, 82.5 % (85/103) if normal results, and 49.4 % (44/89) if abnormal results. Respondents spent limited time in genetic counseling; 57.3 % spent amniocentesis, 88.3 % spent <10 min for normal results, and 54.0 % spent <20 min for abnormal results. While 45.8 % indicated that CGC do not have an essential role in clinical practice, responses that supported employment of CGC were more likely to come from hospitals that submitted more than ten specimens annually (p < 0.0001), university hospitals (p < 0.0001), and MD geneticists (p = 0.020). Currently, there is limited genetic counseling available in Japan. This indicates there are opportunities for the employment of CGC to improve the quality of genetic counseling.

  14. Consequences of Mycobacterium tuberculosis genetic diversity in the context of HIV co-infection for laboratory diagnosis of tuberculosis in Africa

    NARCIS (Netherlands)

    Ssengooba, W.

    2017-01-01

    Willy Ssengooba’s thesis evaluates the consequences of the genetic diversity of Mycobacterium tuberculosis, the causative agent of tuberculosis, for diagnosis of this disease tuberculosis in Africa, often in HIV co-infected patients. It addresses three main sub-themes around M. tuberculosis genetic

  15. Similarity transformations of MAPs

    Directory of Open Access Journals (Sweden)

    Andersen Allan T.

    1999-01-01

    Full Text Available We introduce the notion of similar Markovian Arrival Processes (MAPs and show that the event stationary point processes related to two similar MAPs are stochastically equivalent. This holds true for the time stationary point processes too. We show that several well known stochastical equivalences as e.g. that between the H 2 renewal process and the Interrupted Poisson Process (IPP can be expressed by the similarity transformations of MAPs. In the appendix the valid region of similarity transformations for two-state MAPs is characterized.

  16. Clustering by Pattern Similarity

    Institute of Scientific and Technical Information of China (English)

    Hai-xun Wang; Jian Pei

    2008-01-01

    The task of clustering is to identify classes of similar objects among a set of objects. The definition of similarity varies from one clustering model to another. However, in most of these models the concept of similarity is often based on such metrics as Manhattan distance, Euclidean distance or other Lp distances. In other words, similar objects must have close values in at least a set of dimensions. In this paper, we explore a more general type of similarity. Under the pCluster model we proposed, two objects are similar if they exhibit a coherent pattern on a subset of dimensions. The new similarity concept models a wide range of applications. For instance, in DNA microarray analysis, the expression levels of two genes may rise and fall synchronously in response to a set of environmental stimuli. Although the magnitude of their expression levels may not be close, the patterns they exhibit can be very much alike. Discovery of such clusters of genes is essential in revealing significant connections in gene regulatory networks. E-commerce applications, such as collaborative filtering, can also benefit from the new model, because it is able to capture not only the closeness of values of certain leading indicators but also the closeness of (purchasing, browsing, etc.) patterns exhibited by the customers. In addition to the novel similarity model, this paper also introduces an effective and efficient algorithm to detect such clusters, and we perform tests on several real and synthetic data sets to show its performance.

  17. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  18. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    In data science, there are important parameters that affect the accuracy of the algorithms used. Some of these parameters are: the type of data objects, the membership assignments, and distance or similarity functions. This paper discusses similarity functions as fundamental elements in membership...

  19. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    1998-01-01

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the formatio

  20. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    In data science, there are important parameters that affect the accuracy of the algorithms used. Some of these parameters are: the type of data objects, the membership assignments, and distance or similarity functions. This paper discusses similarity functions as fundamental elements in membership...... assignments. The paper introduces Weighted Feature Distance (WFD), and Prioritized Weighted Feature Distance (PWFD), two new distance functions that take into account the diversity in feature spaces. WFD functions perform better in supervised and unsupervised methods by comparing data objects on their feature...... spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets...

  1. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  2. Similar component analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hong; WANG Xin; LI Junwei; CAO Xianguang

    2006-01-01

    A new unsupervised feature extraction method called similar component analysis (SCA) is proposed in this paper. SCA method has a self-aggregation property that the data objects will move towards each other to form clusters through SCA theoretically,which can reveal the inherent pattern of similarity hidden in the dataset. The inputs of SCA are just the pairwise similarities of the dataset,which makes it easier for time series analysis due to the variable length of the time series. Our experimental results on many problems have verified the effectiveness of SCA on some engineering application.

  3. Gender similarities and differences.

    Science.gov (United States)

    Hyde, Janet Shibley

    2014-01-01

    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

  4. “Sickle cell anemia: tracking down a mutation”: an interactive learning laboratory that communicates basic principles of genetics and cellular biology

    Science.gov (United States)

    Jarrett, Kevin; Williams, Mary; Horn, Spencer; Radford, David

    2016-01-01

    “Sickle cell anemia: tracking down a mutation” is a full-day, inquiry-based, biology experience for high school students enrolled in genetics or advanced biology courses. In the experience, students use restriction endonuclease digestion, cellulose acetate gel electrophoresis, and microscopy to discover which of three putative patients have the sickle cell genotype/phenotype using DNA and blood samples from wild-type and transgenic mice that carry a sickle cell mutation. The inquiry-based, problem-solving approach facilitates the students' understanding of the basic concepts of genetics and cellular and molecular biology and provides experience with contemporary tools of biotechnology. It also leads to students' appreciation of the causes and consequences of this genetic disease, which is relatively common in individuals of African descent, and increases their understanding of the first principles of genetics. This protocol provides optimal learning when led by well-trained facilitators (including the classroom teacher) and carried out in small groups (6:1 student-to-teacher ratio). This high-quality experience can be offered to a large number of students at a relatively low cost, and it is especially effective in collaboration with a local science museum and/or university. Over the past 15 yr, >12,000 students have completed this inquiry-based learning experience and demonstrated a consistent, substantial increase in their understanding of the disease and genetics in general. PMID:26873898

  5. Colony fusion in Argentine ants is guided by worker and queen cuticular hydrocarbon profile similarity.

    Science.gov (United States)

    Vásquez, Gissella M; Schal, Coby; Silverman, Jules

    2009-08-01

    Introduced populations of the Argentine ant, Linepithema humile, have experienced moderate to severe losses of genetic diversity, which may have affected nestmate recognition to various degrees. We hypothesized that cuticular hydrocarbons (CHC) serve as nestmate recognition cues, and facilitate colony fusion of unrelated L. humile colonies that share similar CHC profiles. In this study, we paired six southeastern U.S. L. humile colonies in a 6-month laboratory fusion assay, and determined if worker and queen CHC profile similarity between colonies was associated with colony fusion and intercolony genetic similarity. We also compared worker and queen CHC profiles between fused colony pairs and unpaired controls to determine if worker and queen chemical profiles changed after fusion. We found that colony fusion correlated with the CHC similarity of workers and queens, with the frequency of fusion increasing with greater CHC profile similarity between colonies. Worker and queen CHC profile similarity between colonies also was associated with genetic similarity between colonies. Queen CHC profiles in fused colonies appeared to be a mix of the two colony phenotypes. In contrast, when only one of the paired colonies survived, the CHC profile of the surviving queens did not diverge from that of the colony of origin. Similarly, workers in non-fused colonies maintained their colony-specific CHC, whereas in fused colonies the worker CHC profiles were intermediate between those of the two colonies. These results suggest a role for CHC in regulating interactions among mutually aggressive L. humile colonies, and demonstrate that colony fusion correlates with both genetic and CHC similarities. Further, changes in worker and queen chemical profiles in fused colonies suggest that CHC plasticity may sustain the cohesion of unrelated L. humile colonies that had fused.

  6. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges.

    Science.gov (United States)

    Kanthaswamy, S

    2015-10-01

    This review highlights the importance of domestic animal genetic evidence sources, genetic testing, markers and analytical approaches as well as the challenges this field is facing in view of the de facto 'gold standard' human DNA identification. Because of the genetic similarity between humans and domestic animals, genetic analysis of domestic animal hair, saliva, urine, blood and other biological material has generated vital investigative leads that have been admitted into a variety of court proceedings, including criminal and civil litigation. Information on validated short tandem repeat, single nucleotide polymorphism and mitochondrial DNA markers and public access to genetic databases for forensic DNA analysis is becoming readily available. Although the fundamental aspects of animal forensic genetic testing may be reliable and acceptable, animal forensic testing still lacks the standardized testing protocols that human genetic profiling requires, probably because of the absence of monetary support from government agencies and the difficulty in promoting cooperation among competing laboratories. Moreover, there is a lack in consensus about how to best present the results and expert opinion to comply with court standards and bear judicial scrutiny. This has been the single most persistent challenge ever since the earliest use of domestic animal forensic genetic testing in a criminal case in the mid-1990s. Crime laboratory accreditation ensures that genetic test results have the courts' confidence. Because accreditation requires significant commitments of effort, time and resources, the vast majority of animal forensic genetic laboratories are not accredited nor are their analysts certified forensic examiners. The relevance of domestic animal forensic genetics in the criminal justice system is undeniable. However, further improvements are needed in a wide range of supporting resources, including standardized quality assurance and control protocols for sample

  7. Photometrics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose:The Photometrics Laboratory provides the capability to measure, analyze and characterize radiometric and photometric properties of light sources and filters,...

  8. Blackroom Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Enables evaluation and characterization of materials ranging from the ultraviolet to the longwave infrared (LWIR).DESCRIPTION: The Blackroom Laboratory is...

  9. Target Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — [Part of the ATLAS user facility.] The Physics Division operates a target development laboratory that produces targets and foils of various thickness and substrates,...

  10. Target Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — [Part of the ATLAS user facility.] The Physics Division operates a target development laboratory that produces targets and foils of various thickness and substrates,...

  11. Blackroom Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Enables evaluation and characterization of materials ranging from the ultraviolet to the longwave infrared (LWIR). DESCRIPTION: The Blackroom Laboratory is...

  12. Compression-based Similarity

    CERN Document Server

    Vitanyi, Paul M B

    2011-01-01

    First we consider pair-wise distances for literal objects consisting of finite binary files. These files are taken to contain all of their meaning, like genomes or books. The distances are based on compression of the objects concerned, normalized, and can be viewed as similarity distances. Second, we consider pair-wise distances between names of objects, like "red" or "christianity." In this case the distances are based on searches of the Internet. Such a search can be performed by any search engine that returns aggregate page counts. We can extract a code length from the numbers returned, use the same formula as before, and derive a similarity or relative semantics between names for objects. The theory is based on Kolmogorov complexity. We test both similarities extensively experimentally.

  13. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field......-shaped relation exists between expenditure strategy isomorphism and structure isomorphism in a longitudinal quantitative study of Danish municipalities....

  14. Segmentation Similarity and Agreement

    CERN Document Server

    Fournier, Chris

    2012-01-01

    We propose a new segmentation evaluation metric, called segmentation similarity (S), that quantifies the similarity between two segmentations as the proportion of boundaries that are not transformed when comparing them using edit distance, essentially using edit distance as a penalty function and scaling penalties by segmentation size. We propose several adapted inter-annotator agreement coefficients which use S that are suitable for segmentation. We show that S is configurable enough to suit a wide variety of segmentation evaluations, and is an improvement upon the state of the art. We also propose using inter-annotator agreement coefficients to evaluate automatic segmenters in terms of human performance.

  15. Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard

    DEFF Research Database (Denmark)

    Børsting, Claus; Rockenbauer, Eszter; Morling, Niels

    2009-01-01

    A multiplex assay with 49 autosomal single nucleotide polymorphisms (SNPs) developed for human identification was validated for forensic genetic casework and accredited according to the ISO 17025 standard. The multiplex assay was based on the SNPforID 52plex SNP assay [J.J. Sanchez, C. Phillips, C...

  16. Similaridade genética de populações naturais de pimenta-de-macaco por análise RAPD Genetic similarity of natural populations of pimenta-de-macaco (Piper aduncum L. obtained throug RAPD analysis

    Directory of Open Access Journals (Sweden)

    José Maria D. Gaia

    2004-12-01

    Full Text Available A espécie conhecida como pimenta-de-macaco (Piper aduncum L. possui grande potencial para exploração econômica em função da comprovada utilidade do seu óleo essencial na agricultura e saúde humana. O objetivo deste trabalho foi caracterizar a diversidade genética de populações naturais dessa planta. Um total de dezoito acessos da planta, provenientes de quatro procedências da Amazônia Brasileira, foi examinado por meio de locos de DNA, gerados por análise RAPD (polimorfismo de DNA amplificado ao acaso. O estudo evidenciou a existência de real diversidade entre as populações examinadas, sendo provável que dentro das localidades investigadas, os padrões da diversidade genética acompanhem os padrões de distribuição geográfica.The species known as pimenta-de-macaco (Piper aduncum L. has great economic explotation potential based on the proved usefulness of the essential oil in agriculture and human health. The genetic diversity of their natural populations was characterized. A total of eighteen accessions of the plant, obtained from four different origins in the Brazilian Amazon, was examined by means of DNA loci, generated by RAPD analysis. Real genetic diversity was observed between the analyzed populations and it appear that the patterns of the genetic diversity follow the patterns of the geographical distribution.

  17. Incremental Similarity and Turbulence

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole E.; Hedevang, Emil; Schmiegel, Jürgen

    This paper discusses the mathematical representation of an empirically observed phenomenon, referred to as Incremental Similarity. We discuss this feature from the viewpoint of stochastic processes and present a variety of non-trivial examples, including those that are of relevance for turbulence...

  18. Teaching design and practice of human blood type traits in genetics comprehensive laboratory course%人类血型性状综合遗传大实验的设计与教学实践

    Institute of Scientific and Technical Information of China (English)

    赵健; 胡冬梅; 于大德; 董明亮; 李云; 范英明; 王延伟; 张金凤

    2016-01-01

    综合大实验能够训练学生灵活应用理论知识并掌握实验技能,成为当前实验课教学改革的重要方式。本文以人类的 ABO 血型性状为实验对象,设计了―人类 ABO 血型分子基因分型与群体遗传平衡分析‖大实验。实验中提取同学唾液中黏膜细胞的 DNA,经过 PCR 扩增目的片段、酶切及电泳分离一系列分子遗传技术分析,鉴定出每位同学的基因型;然后以全班同学为一个类似孟德尔群体调查 ABO 血型的各种基因型频数,用Popgene 软件分析各种群体遗传参数。通过开放教学不仅让学生掌握了分子遗传实验技术和群体遗传分析技术及软件应用,还让学生自主设计方案优化分子技术环节,提高学生驾驭知识的能力。通过5年的教学探索与实践,建立了稳定的分子遗传实验体系,能够清楚地检测出 ABO 血型的6种基因型:IAIA、IAi、IBIB、IBi、IAIB、ii;综合了分子遗传与群体遗传的实验教学,统计全班同学6种基因型的频数,直接计算3个复等位基因的频率,进而应用软件分析群体遗传各种参数;实现了学生自主设计并完成实验的开放式实验教学;大实验教学获得了学生的好评,取得了很好的教学效果。该大实验可直接应用于生物类专业的遗传学实验教学,其中的教学理念和方法还可推广应用于其他生物学实验教学。%Comprehensive laboratory courses, which enable students to aptly apply theoretic knowledge and mas-ter experiment skills, play an important role in the present educational reform of laboratory courses. We utilized hu-man ABO blood type as the experimental subject, and designed the experiment——―Molecular Genotyping of Human ABO Blood Type and Analysis of Population Genetic Equilibrium‖. In the experiment, DNA in mucosal cells is ex-tracted from students’ saliva, and each student’s genotype is identified using a series

  19. Analyzsis of population genetic structure of laboratory orange tabby cat by microsatellite DNA markers%微卫星DNA标记技术对试验用虎皮猫群体遗传结构的分析

    Institute of Scientific and Technical Information of China (English)

    衣帅; 谢姗珊; 刘继峰; 杜小燕; 齐飞虎; 李益琛; 任文陟; 刘殿峰; 陈振文

    2013-01-01

    用筛选优化出的24个具有丰富多态性的微卫星位点对华北制药厂的34只虎皮猫基因组DNA进行PCR扩增,对扩增产物进行琼脂糖凝胶电泳和STR扫描,运用popgene3.2软件对试验用虎皮猫群体进行群体遗传结构分析.结果显示,虎皮猫群体平均观测等位基因数为4.083 3,平均有效等位基因数为2.632 3,平均有效杂合度为0.610 8,平均香隆指数为1.078 6.结果表明,微卫星DNA标记技术适于猫群体遗传结构分析;该试验用虎皮猫群体符合封闭群的遗传特性.%To evaluate the genetic structure of the laboratory orange tabby cat population. Twenty four refined polymorphic microsatellite loci were applied to amplify the genomic DNA from 34 orange tabby cats in Huabei Pharmaceutical factory by PCR. The PCR products were analyze by agarose gel electrophoresis,and short tandem repeat(STR) scanning. Software popgene 3. 2 was used to analyze the genetic structure. For the orange tabby cat population, the observed average number of alleles is 4. 083 3;the average effective number of alleles is 2. 632 3; the mean effective heterozygosity is 0. 610 8;the mean Shannon's information index is 1. 078 6. The microsatellite DNA markers are suitable for analyzing the genetic structure of cats and the laboratory orange tabby cat population has the characters of closed colony.

  20. More Similar Than Different

    DEFF Research Database (Denmark)

    Pedersen, Mogens Jin

    2015-01-01

    What role do employee features play into the success of different personnel management practices for serving high performance? Using data from a randomized survey experiment among 5,982 individuals of all ages, this article examines how gender conditions the compliance effects of different...... incentive treatments—each relating to the basic content of distinct types of personnel management practices. The findings show that males and females are more similar than different in terms of the incentive treatments’ effects: Significant average effects are found for three out of five incentive...

  1. Similar dissection of sets

    CERN Document Server

    Akiyama, Shigeki; Okazaki, Ryotaro; Steiner, Wolfgang; Thuswaldner, Jörg

    2010-01-01

    In 1994, Martin Gardner stated a set of questions concerning the dissection of a square or an equilateral triangle in three similar parts. Meanwhile, Gardner's questions have been generalized and some of them are already solved. In the present paper, we solve more of his questions and treat them in a much more general context. Let $D\\subset \\mathbb{R}^d$ be a given set and let $f_1,...,f_k$ be injective continuous mappings. Does there exist a set $X$ such that $D = X \\cup f_1(X) \\cup ... \\cup f_k(X)$ is satisfied with a non-overlapping union? We prove that such a set $X$ exists for certain choices of $D$ and $\\{f_1,...,f_k\\}$. The solutions $X$ often turn out to be attractors of iterated function systems with condensation in the sense of Barnsley. Coming back to Gardner's setting, we use our theory to prove that an equilateral triangle can be dissected in three similar copies whose areas have ratio $1:1:a$ for $a \\ge (3+\\sqrt{5})/2$.

  2. Laboratory Tests

    Science.gov (United States)

    ... evaluation of large parts of or the entire genetic code for an individual at relatively low cost. These ... of personalized medicine based on an individual’s unique genetic code, but when this will become reality at a ...

  3. Similarity transformed semiclassical dynamics

    Science.gov (United States)

    Van Voorhis, Troy; Heller, Eric J.

    2003-12-01

    In this article, we employ a recently discovered criterion for selecting important contributions to the semiclassical coherent state propagator [T. Van Voorhis and E. J. Heller, Phys. Rev. A 66, 050501 (2002)] to study the dynamics of many dimensional problems. We show that the dynamics are governed by a similarity transformed version of the standard classical Hamiltonian. In this light, our selection criterion amounts to using trajectories generated with the untransformed Hamiltonian as approximate initial conditions for the transformed boundary value problem. We apply the new selection scheme to some multidimensional Henon-Heiles problems and compare our results to those obtained with the more sophisticated Herman-Kluk approach. We find that the present technique gives near-quantitative agreement with the the standard results, but that the amount of computational effort is less than Herman-Kluk requires even when sophisticated integral smoothing techniques are employed in the latter.

  4. Determination of the genetic similarities of fingerprints from Escherichia coli O157:H7 isolated from different sources in the North West Province, South Africa using ISR, BOXAIR and REP-PCR analysis.

    Science.gov (United States)

    Ateba, Collins Njie; Mbewe, Moses

    2013-08-25

    The aim of this study was to determine the genetic relationships of Escherichia coli O157:H7 isolated from pigs, cattle, pork, beef, humans and water samples using REP, ISR and BOXAIR PCR analysis. A total of 94 isolates were subjected to the REP-PCR analysis while 95 were screened for ISR and BOXAIR PCR fingerprints. The band sizes for amplicons from the ISR-PCR analysis ranged from 0.173kb to 0.878kb. However, a large proportion of the isolates had four bands ranging from 0.447kb to 0.878kb. Cluster analysis of the BOXAIR PCR profiles based on banding patterns revealed seven main clusters. It was identified in the clusters III, IV and VII in the BOXAIR PCR that 17.9%, 16.8% and 18.9%, of E. coli O157:H7 isolates respectively were present from all the animal species, meat and water samples. REP-PCR analysis produced 9 different patterns with bands ranging from 0 to 12 per isolate. The band sizes ranged from 200bp to 8000bp. Nine major clusters (I-IX) were identified. From the three different species sampled cluster eight was the largest and a mixed cluster with 23.4% (22/94) of the E. coli O157:H7 isolates. These indicate that food products obtained from supermarkets in the study area are contaminated with E. coli O157:H7.

  5. Genetics Research Discovered in a Bestseller | Poster

    Science.gov (United States)

    By Nancy Parrish, Staff Writer One morning in early January, Amar Klar sat down at his computer and found an e-mail with a curious message from a colleague. While reading a bestselling novel, The Marriage Plot by Jeffrey Eugenides, his colleague, a professor at Princeton University, found a description of research on yeast genetics that was surprisingly similar to Klar’s early research. Even the laboratory in the novel was reminiscent of Cold Spring Harbor Laboratory, where Klar had conducted his research.

  6. Genetics Research Discovered in a Bestseller | Poster

    Science.gov (United States)

    By Nancy Parrish, Staff Writer One morning in early January, Amar Klar sat down at his computer and found an e-mail with a curious message from a colleague. While reading a bestselling novel, The Marriage Plot by Jeffrey Eugenides, his colleague, a professor at Princeton University, found a description of research on yeast genetics that was surprisingly similar to Klar’s early research. Even the laboratory in the novel was reminiscent of Cold Spring Harbor Laboratory, where Klar had conducted his research.

  7. Genetic similarity of Brazilian hull-less and malting barley varieties evaluated by RAPD markers Similaridade genética de variedades brasileiras de cevada nua e cevada cervejeira avaliada por marcadores RAPD

    Directory of Open Access Journals (Sweden)

    Mariela Aparecida Kroth

    2005-01-01

    Full Text Available Barley (Hordeum vulgare L. is widely used for brewing and animal feed. Recently, it has become desirable for human consumption due to its high nutritional significance, specially hull-less or naked barley. There are differences in nutritional and malting characteristics among barley varieties. RAPD procedure is able to separate barley varieties at various similarity levels. The aim of this work was the RAPD analysis of six Brazilian hull-less varieties and seven malting varieties. PCR reactions were performed with eleven random primers. A total of 34 RAPD fragments was obtained with five primers. A dendrogram was constructed based on the Jaccard similarity coefficient. Barley varieties displayed an average similarity coefficient of 0.53. Intravarietal monomorphic fragments allowed differentiation among varieties. The averages of intravarietal similarity coefficients ranged from 0.53 to 0.85. RAPD markers, detected in this work, were suitable for differentiation among Brazilian barley varieties.A cevada (Hordeum vulgare L. é amplamente empregada na produção de cerveja e na ração animal. Recentemente, este cereal tornou-se desejável na alimentação humana devido ao seu alto valor nutricional, principalmente da cevada nua ou sem casca. Existem diferenças nas características nutricionais e para malteação entre as diversas variedades de cevada. O procedimento RAPD é capaz de separar as variedades de cevada em vários níveis de similaridade. O objetivo desse trabalho foi analisar por RAPD seis variedades brasileiras de cevada nua e sete variedades de cevada cervejeira. Reações de PCR foram realizadas com onze iniciadores aleatórios. Um total de 34 fragmentos de amplificação foi obtido com cinco destes iniciadores. Baseado no coeficiente de similaridade de Jaccard, um dendrograma foi construído. As variedades de cevada apresentaram índice médio de similaridade de 0,53. Fragmentos monomórficos intravariedades permitiram a

  8. Computational Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains a number of commercial off-the-shelf and in-house software packages allowing for both statistical analysis as well as mathematical modeling...

  9. Analytical Laboratories

    Data.gov (United States)

    Federal Laboratory Consortium — NETL’s analytical laboratories in Pittsburgh, PA, and Albany, OR, give researchers access to the equipment they need to thoroughly study the properties of materials...

  10. Geomechanics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Geomechanics Laboratory allows its users to measure rock properties under a wide range of simulated service conditions up to very high pressures and complex load...

  11. Laboratory Tests

    Science.gov (United States)

    Laboratory tests check a sample of your blood, urine, or body tissues. A technician or your doctor ... compare your results to results from previous tests. Laboratory tests are often part of a routine checkup ...

  12. Genetic Factors in Systemic Lupus Erythematosus: Contribution to Disease Phenotype

    Science.gov (United States)

    Ceccarelli, Fulvia; Perricone, Carlo; Borgiani, Paola; Ciccacci, Cinzia; Rufini, Sara; Cipriano, Enrica; Alessandri, Cristiano; Spinelli, Francesca Romana; Sili Scavalli, Antonio; Novelli, Giuseppe; Valesini, Guido; Conti, Fabrizio

    2015-01-01

    Genetic factors exert an important role in determining Systemic Lupus Erythematosus (SLE) susceptibility, interplaying with environmental factors. Several genetic studies in various SLE populations have identified numerous susceptibility loci. From a clinical point of view, SLE is characterized by a great heterogeneity in terms of clinical and laboratory manifestations. As widely demonstrated, specific laboratory features are associated with clinical disease subset, with different severity degree. Similarly, in the last years, an association between specific phenotypes and genetic variants has been identified, allowing the possibility to elucidate different mechanisms and pathways accountable for disease manifestations. However, except for Lupus Nephritis (LN), no studies have been designed to identify the genetic variants associated with the development of different phenotypes. In this review, we will report data currently known about this specific association. PMID:26798662

  13. Genetic similarity between staphylococcus sp isolated from human and hospital settings, and susceptibility to different antimicrobials Similaridade genética entre estafilococos isolados de humanos e camas hospitalares e resistência à diferentes antimicrobianos

    Directory of Open Access Journals (Sweden)

    Telma Luciana Trovó Fabiano

    2008-12-01

    Full Text Available One hundred and forty-three samples from human hands and hospital beds were collected at a teaching hospital in the city of Ribeirão Preto/SP by swabs, and placed in BHI broth. Following a 24 h incubation period at 37ºC, they were seeded on Petri dishes containing Agar "Staphylococcus Medium 110". Colonies typical of the genus Staphylococcus were collected and stored at 4ºC until tested for catalase, mannitol, hemolysis, DNAse and coagulase. Strains were analyzed by RAPD-PCR to verify their similarity, and tested for sensitivity to ten different antibiotics. From the ninety-two isolated strains, 67 (72,8% were coagulase- negative and 25 (27,2% coagulase-positive. Similarity analysis showed a great heterogeneity among strains, but some presented 100% similarity. Resistance to oxacilin was encountered in 39 (42% of the strains. Two coagulase- negative strains were resistant to vancomycin, and eleven (12% were considered multiresistant. Measures such as hand disinfection of the staff and hospital beds and rationalization of antibiotic use could contribute to decrease pathogen transmission and selection pressure, diminishing the frequency and lethality of nosocomial infections.Foram coletadas 143 amostras de mãos de humanos e camas hospitalares, através de "swabs" no caldo BHI, em um hospital escola da cidade de Ribeirão Preto/SP. As amostras coletadas foram incubadas a 37ºC por 24 horas e após este período as culturas foram semeadas em placas de Petri contendo agar "Staphylococcus Médium 110". As colônias típicas do gênero Staphylococcus foram colhidas e estocados a 4ºC até o momento de elaboração das provas de catalase, manitol, hemólise, DNAse e coagulase. As cepas isoladas foram analisadas através da técnica de RAPD-PCR para verificar o grau de similaridade. A sensibilidade das cepas isoladas foi testada frente a 10 diferentes antibióticos. Das 92 cepas de Staphylococcus sp isoladas, 67 (72,8% foram identificados como

  14. Fast evolutionary genetic differentiation during experimental colonizations

    Indian Academy of Sciences (India)

    Josiane Santos; Marta Pascual; Pedro Simões; Inês Fragata; Michael R. Rose; Margarida Matos

    2013-08-01

    Founder effects during colonization of a novel environment are expected to change the genetic composition of populations, leading to differentiation between the colonizer population and its source population. Another expected outcome is differentiation among populations derived from repeated independent colonizations starting from the same source. We have previously detected significant founder effects affecting rate of laboratory adaptation among Drosophila subobscura laboratory populations derived from the wild. We also showed that during the first generations in the laboratory, considerable genetic differentiation occurs between foundations. The present study deepens that analysis, taking into account the natural sampling hierarchy of six foundations, derived from different locations, different years and from two samples in one of the years. We show that striking stochastic effects occur in the first two generations of laboratory culture, effects that produce immediate differentiation between foundations, independent of the source of origin and despite similarity among all founders. This divergence is probably due to powerful genetic sampling effects during the first few generations of culture in the novel laboratory environment, as a result of a significant drop in $N_{\\text{e}}$. Changes in demography as well as high variance in reproductive success in the novel environment may contribute to the low values of $N_{\\text{e}}$. This study shows that estimates of genetic differentiation between natural populations may be accurate when based on the initial samples collected in the wild, though considerable genetic differentiation may occur in the very first generations of evolution in a new, confined environment. Rapid and significant evolutionary changes can thus occur during the early generations of a founding event, both in the wild and under domestication, effects of interest for both scientific and conservation purposes.

  15. Estimativa da similaridade genética e identificação de cultivares do morangueiro por análise de RAPD Estimate of the genetic similarity and identification of strawberry cultivars by RAPD analysis

    Directory of Open Access Journals (Sweden)

    José Henrique Conti

    2002-06-01

    Full Text Available Caracteres moleculares do morango foram avaliados para conhecer cultivares que estão sendo introduzidas no Brasil. Utilizou-se o método do polimorfismo de DNA amplificado ao acaso (RAPD. Os caracteres moleculares com maior poder de discriminação foram os "marcadores" gerados pelos "primers" Operon B8, Operon B19 e Operon G5, que foram eficientes para discriminar as vinte e seis cultivares estudadas. Os dados foram interpretados com o auxílio de dendograma, mapa de bandas, quadro de identificação e chave dicotômica. Foi possível distinguir seis grupos de similaridade, dois deles com cultivares selecionadas no Brasil, sendo um com 'Campinas', 'Agf 80', 'Piedade', 'Jundiaí' e 'Monte Alegre' e o outro com 'Obaira' e 'Mantiqueira'; três grupos com cultivares introduzidas, sendo o primeiro com 'Lassen', 'Reiko', 'Chandler', 'Pajaro', 'Blackmore' e 'Seascape', o segundo com 'Fern' e 'Oso Grande' e o terceiro com 'Florida Belle' e 'Selva' O último grupo reuniu as cultivares 'Dover' e 'Dabreak' junto com 'Princesa Isabel'.Strawberry cultivars introduced in Brazil were identified through molecular study. The method of Random Amplified Polymorphic DNA (RAPD was used. Molecular characters with larger discrimination power were produced by the primers Operon B8, Operon B19 and Operon G5. These were efficient to discriminate the twenty six studied cultivars. Data were analised through dendogram, bandmap, picture and dicotomic key. Six similarity groups were distinguished: Two with cultivars selected in Brazil, one with 'Campinas', 'Agf 80', 'Piedade', 'Jundiaí' and 'Monte Alegre' and the other with 'Obaira' and 'Mantiqueira'; three with introduced cultivars the first of which 'Lassen', 'Reiko', 'Chandler', 'Pajaro', 'Blackmore' and 'Seascape', the second with 'Fern' and 'Oso Grande' and the third with 'Florida Belle' and 'Selva'. The last group united the cultivars 'Dover' and 'Dabreak' with 'Princesa Isabel'.

  16. Genetic analysis and cross-resistance spectrum of a laboratory-selected chlorfenapyr resistant strain of two-spotted spider mite (Acari: Tetranychidae).

    Science.gov (United States)

    Van Leeuwen, Thomas; Stillatus, Vincent; Tirry, Luc

    2004-01-01

    A laboratory susceptible strain of Tetranychus urticae was selected with chlorfenapyr resulting in a resistant strain. After 12 cycles of exposure, the resistance ratio (RR) calculated from the LC50s of susceptible and selected strain was 580. The resistant strain was screened with 16 currently used acaricides for cross-resistance. Cross-resistance was detected with amitraz (RR = 19.1), bifenthrin (RR = 1.3), bromopropylate (RR = 7.5), clofentezine (RR = 29.6) and dimethoate (RR = 17.6). No cross-resistance was detected with the new molecules acequinocyl, bifenazate and spirodiclofen. Mortality caused by chlorfenapyr in the F1 progeny from reciprocal crosses between both strains indicated that the mode of inheritance was incomplete recessive. Mortality in F2 progeny indicated that the resistance was under the control of more than one gene. Synergist experiments with S,S,S-tributylphosphorotrithioate (DEF), piperonylbutoxide (PBO) and diethylmaleate (DEM), which are inhibitors of esterases, monooxygenases and glutathion-S-transferases respectively, suggested a major role of esterases in the resistance to chlorfenapyr.

  17. Laboratory Building

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, Joshua M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-01

    This report is an analysis of the means of egress and life safety requirements for the laboratory building. The building is located at Sandia National Laboratories (SNL) in Albuquerque, NM. The report includes a prescriptive-based analysis as well as a performance-based analysis. Following the analysis are appendices which contain maps of the laboratory building used throughout the analysis. The top of all the maps is assumed to be north.

  18. Laboratory Building.

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, Joshua M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-01

    This report is an analysis of the means of egress and life safety requirements for the laboratory building. The building is located at Sandia National Laboratories (SNL) in Albuquerque, NM. The report includes a prescriptive-based analysis as well as a performance-based analysis. Following the analysis are appendices which contain maps of the laboratory building used throughout the analysis. The top of all the maps is assumed to be north.

  19. Visualization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Evaluates and improves the operational effectiveness of existing and emerging electronic warfare systems. By analyzing and visualizing simulation results...

  20. Dynamics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Dynamics Lab replicates vibration environments for every Navy platform. Testing performed includes: Flight Clearance, Component Improvement, Qualification, Life...

  1. Psychology Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This facility provides testing stations for computer-based assessment of cognitive and behavioral Warfighter performance. This 500 square foot configurable space can...

  2. Propulsion Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Propulsion Lab simulates field test conditions in a controlled environment, using standardized or customized test procedures. The Propulsion Lab's 11 cells can...

  3. Chemistry Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: To conduct fundamental studies of highway materials aimed at understanding both failure mechanisms and superior performance. New standard test methods are...

  4. Analytical Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Analytical Labspecializes in Oil and Hydraulic Fluid Analysis, Identification of Unknown Materials, Engineering Investigations, Qualification Testing (to support...

  5. Recovery geospatial objects using semantic similarity measures

    Directory of Open Access Journals (Sweden)

    Neili Machado-García

    2014-04-01

    Full Text Available In this paper we propose a methodology based on the semantic processing of geographic objects for the classification of soils according to the New Version of Genetic Classification of soils of Cuba. The method consists of five stages: conceptualization, synthesis, queries processing, retrieval and management. The result is a system of geospatial information management applying semantic similarity measure of Resnik. As a case study considering the region of San Jose de las Lajas located in the province of Mayabeque.

  6. Learning Laboratory.

    Science.gov (United States)

    Hay, Lyn; Callison, Daniel

    2000-01-01

    Considers the school library media center as an information learning laboratory. Topics include information literacy; Kuhlthau's Information Search Process model; inquiry theory and approach; discovery learning; process skills of laboratory science; the information scientist; attitudes of media specialists, teachers, and students; displays and Web…

  7. Estimating similarity of XML Schemas using path similarity measure

    Directory of Open Access Journals (Sweden)

    Veena Trivedi

    2012-07-01

    Full Text Available In this paper, an attempt has been made to develop an algorithm which estimates the similarity for XML Schemas using multiple similarity measures. For performing the task, the XML Schema element information has been represented in the form of string and four different similarity measure approaches have been employed. To further improve the similarity measure, an overall similarity measure has also been calculated. The approach used in this paper is a distinguished one, as it calculates the similarity between two XML schemas using four approaches and gives an integrated values for the similarity measure. Keywords-componen

  8. Laboratory Tests

    Science.gov (United States)

    ... specific genetic defects. This is particularly true of Severe Combined Immune Deficiency (SCID) where more than 12 different ... receptors. Looking to the Future Newborn screening for severe T-cell immunodeficiency is now recommended by the Secretary of the ...

  9. Genetics similarity among four breeds of goat in Saudi Arabia ...

    African Journals Online (AJOL)

    user

    2012-02-28

    Feb 28, 2012 ... environmental conditions and the different nutritional regimes under which .... statistical program analysis (Statistica® Version 5). RESULTS AND .... kids in Saudi Arabia at different ages and affecting factors. J. king. Saud Univ ...

  10. Semiconductor Electrical Measurements Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Semiconductor Electrical Measurements Laboratory is a research laboratory which complements the Optical Measurements Laboratory. The laboratory provides for Hall...

  11. Audio Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Provides an environment and facilities for auditory display research. A primary focus is the performance use of binaurally rendered 3D sound in conjunction...

  12. Elastomers Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Primary capabilities include: elastomer compounding in various sizes (micro, 3x5, 8x12, 8x15 rubber mills); elastomer curing and post curing (two 50-ton presses, one...

  13. A compendium of genetic variant data

    DEFF Research Database (Denmark)

    Cardoso, Joao; Schöning, Lars Yannik; Herrgard, Markus

    2014-01-01

    Laboratory strains are genetically unstable if exposed to selective pressure as encountered, for example, during molecular cloning, fermentation, or adaptive laboratory evolution experiments. This genetic variation is the consequence of an adaptation process of the microorganism to stress...... obtained from distinct experiments. This compendium of genetic variant is a critical step to develop approaches to automatically and systematically characterize mutated strains in the future....

  14. DNA Fingerprinting and RAPD for Genetic Monitoring of Laboratory Beagle%DNA指纹图及RAPD技术在比格犬群体遗传检测中的应用

    Institute of Scientific and Technical Information of China (English)

    战大伟; 陈振文; 李瑞生; 欧阳兆和

    2003-01-01

    With small somatotype, gentle temperament, balanced hematological and blood biochemical index, Beagle was ideal for laboratory use. Since 1980, beagle has been introducted into our country. They were successfully bred and multiplied in Guangdong , Shanghai and Beijing . But the control of heredity, balance of gene frequency, gene diversity and gene differentiation and protection of idioplasm has not been well studied. Falk & Holsinger( 1991 )point out: we can not protect what were unknowed. For operative preventing the inbreeding diminution , gene segregation and differentiation,the DFP and randomly amplified polymorphic (RAPD) technique were applied to assess the genetic variation and colony heredity structural analysis among the population of three internal beagle centers and Marshell beagle in America. The experimental exponent of the heredity analysis in different colony were from Guangdong, Shanghai, Beijing and Marshell (Amereca), and they were not relative. The experimental exponent of the different generation were from Beijing colony,and they were direct maternal side in different generation, but each individual were no relative in the same generation.

  15. Genetic Discrimination

    Science.gov (United States)

    ... in Genetics Archive Regulation of Genetic Tests Genetic Discrimination Overview Many Americans fear that participating in research ... I) and employment (Title II). Read more Genetic Discrimination and Other Laws Genetic Discrimination and Other Laws ...

  16. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformatio...

  17. Laboratory study of TLEs

    Science.gov (United States)

    Kochkin, P.; Van Deursen, A.; Ebert, U.

    2014-12-01

    Sprites are high-altitude kilometre-scale electrical discharges that happen above thundercloud. Pilot systems are pre-breakdown phenomena that usually attributed to stepped leader development. In Eindhoven University of Technology we investigate meter-scale laboratory discharges looking for similarities with natural lightning and its related phenomena. Negative lightning possesses step-like propagation behaviour which is associated with space leader formation in front of its main leader. Meter-scale laboratory sparks also develop via formation of a space stem that transforms into a pilot system and finally develops into a space leader in longer gaps. With ns-fast photography we investigated the pilot system formation and found striking similarities with high-altitude sprites. But sprites are different in size, environment and polarity. Laboratory pilot barely reaches 70 cm and develops in STP air, while high-altitude sprites reaches ionosphere stretching for dozens of kilometres. Also sprites are assumed to be of opposite to the pilot polarity. Besides that, the pilots are directly involved in x-ray generation in long laboratory sparks. The detailed pilot system development process will be shown, in particular focusing on similarities with natural sprites. Basic properties of the x-ray emission will be presented and discussed.

  18. Functional Similarity and Interpersonal Attraction.

    Science.gov (United States)

    Neimeyer, Greg J.; Neimeyer, Robert A.

    1981-01-01

    Students participated in dyadic disclosure exercises over a five-week period. Results indicated members of high functional similarity dyads evidenced greater attraction to one another than did members of low functional similarity dyads. "Friendship" pairs of male undergraduates displayed greater functional similarity than did…

  19. Functional Similarity and Interpersonal Attraction.

    Science.gov (United States)

    Neimeyer, Greg J.; Neimeyer, Robert A.

    1981-01-01

    Students participated in dyadic disclosure exercises over a five-week period. Results indicated members of high functional similarity dyads evidenced greater attraction to one another than did members of low functional similarity dyads. "Friendship" pairs of male undergraduates displayed greater functional similarity than did "nominal" pairs from…

  20. Feline genetics: clinical applications and genetic testing.

    Science.gov (United States)

    Lyons, Leslie A

    2010-11-01

    DNA testing for domestic cat diseases and appearance traits is a rapidly growing asset for veterinary medicine. Approximately 33 genes contain 50 mutations that cause feline health problems or alterations in the cat's appearance. A variety of commercial laboratories can now perform cat genetic diagnostics, allowing both the veterinary clinician and the private owner to obtain DNA test results. DNA is easily obtained from a cat via a buccal swab with a standard cotton bud or cytological brush, allowing DNA samples to be easily sent to any laboratory in the world. The DNA test results identify carriers of the traits, predict the incidence of traits from breeding programs, and influence medical prognoses and treatments. An overall goal of identifying these genetic mutations is the correction of the defect via gene therapies and designer drug therapies. Thus, genetic testing is an effective preventative medicine and a potential ultimate cure. However, genetic diagnostic tests may still be novel for many veterinary practitioners and their application in the clinical setting needs to have the same scrutiny as any other diagnostic procedure. This article will review the genetic tests for the domestic cat, potential sources of error for genetic testing, and the pros and cons of DNA results in veterinary medicine. Highlighted are genetic tests specific to the individual cat, which are a part of the cat's internal genome.

  1. LABORATORY FINDINGS IN PSORIATIC ARTHRITIS

    Directory of Open Access Journals (Sweden)

    S. Todesco

    2011-09-01

    Full Text Available Psoriatic arthritis (PsA has been classically defined as an inflammatory arthritis associated with psoriasis. However, in comparison with other relevant inflammatory arthropathies, in which a definite diagnosis is frequently possible only by means of laboratory investigations, in PsA true laboratory diagnostic markers are lacking. Some markers are utilised more to differentiate other diseases than to characterise PsA. For example in polyarticular PsA, which may be in some cases indistinguishable from RA, the rheumatoid factor (RF or the more specific and recently introduced antibodies to cyclic citrullinated peptides (anti-CCP, may be useful to better identify RA. However, RF was found in 5% to 13% of patients with PsA, and anti-CCP may be observed in almost similar percentage. The determination of ESR and/or CRP is frequently disappointing in PsA, since they are both elevated in only half of the patients with PsA. However, ESR and/or CRP are included in the most utilised response criteria for RA, such as ACR and DAS, and, in addition are also considered reliable in the assessment of PsA. Furthermore, elevated levels of ESR have been proposed as one of the best predictors of damage progression and, in addition, a low ESR seems protective, while an ESR >15 mm/h is one of the factors associated with an increased mortality in PsA. The synovial fluid (SF effusion is much higher in PsA, in comparison with other arthropathies. When available, SF analysis may offer additive information useful for the diagnosis, such as the increased number of leukocytes, which underlines the inflammatory nature of the effusion even in a patient with normal serum levels of acute phase response. We found that elevated IL-1 levels in SF of patients with early disease (<6 months, may be predictive of an evolution in polyarticular form at follow-up. This observation is in keeping with the crucial role that inflammatory cytokines play in PsA, probably related to a genetic

  2. Terrestrial plants require nutrients in similar proportions.

    Science.gov (United States)

    Knecht, Magnus F; Göransson, Anders

    2004-04-01

    Theoretical considerations based on nutrition experiments suggest that nutrient ratios of terrestrial plants are similar to the Redfield ratio found in marine phytoplankton. Laboratory experiments have shown that seedlings of many different plant species have similar nutrient concentration ratios when supplied with nutrients at free access. However, at free access, nutrients are likely to be taken up in amounts in excess of a plant's requirements for growth. In further experiments, therefore, the supply rate of each nutrient was reduced so that excessive uptake did not occur. Again, similar nutrient ratios were found among the plant species tested, although the ratios differed from those found in plants given free access to nutrients. Based on the law of the minimum, we suggest that optimum nutrient ratios be defined as the ratios found in plants when all nutrients are limiting growth simultaneously. The literature on nutrient concentrations was surveyed to investigate nutrient ratios in terrestrial ecosystems. Nutrients taken into consideration were nitrogen, phosphorus, potassium, calcium and magnesium. Based on the assumption that nitrogen is either the limiting nutrient or, when not limiting, is taken up only in small excess amounts, we calculated nutrient ratios from published data. The calculated ratios corresponded closely to the ratios determined in laboratory and field experiments.

  3. A COMPARISON OF SEMANTIC SIMILARITY MODELS IN EVALUATING CONCEPT SIMILARITY

    Directory of Open Access Journals (Sweden)

    Q. X. Xu

    2012-08-01

    Full Text Available The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  4. a Comparison of Semantic Similarity Models in Evaluating Concept Similarity

    Science.gov (United States)

    Xu, Q. X.; Shi, W. Z.

    2012-08-01

    The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  5. Learning Multi-modal Similarity

    CERN Document Server

    McFee, Brian

    2010-01-01

    In many applications involving multi-media data, the definition of similarity between items is integral to several key tasks, e.g., nearest-neighbor retrieval, classification, and recommendation. Data in such regimes typically exhibits multiple modalities, such as acoustic and visual content of video. Integrating such heterogeneous data to form a holistic similarity space is therefore a key challenge to be overcome in many real-world applications. We present a novel multiple kernel learning technique for integrating heterogeneous data into a single, unified similarity space. Our algorithm learns an optimal ensemble of kernel transfor- mations which conform to measurements of human perceptual similarity, as expressed by relative comparisons. To cope with the ubiquitous problems of subjectivity and inconsistency in multi- media similarity, we develop graph-based techniques to filter similarity measurements, resulting in a simplified and robust training procedure.

  6. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  7. Similarity Learning of Manifold Data.

    Science.gov (United States)

    Chen, Si-Bao; Ding, Chris H Q; Luo, Bin

    2015-09-01

    Without constructing adjacency graph for neighborhood, we propose a method to learn similarity among sample points of manifold in Laplacian embedding (LE) based on adding constraints of linear reconstruction and least absolute shrinkage and selection operator type minimization. Two algorithms and corresponding analyses are presented to learn similarity for mix-signed and nonnegative data respectively. The similarity learning method is further extended to kernel spaces. The experiments on both synthetic and real world benchmark data sets demonstrate that the proposed LE with new similarity has better visualization and achieves higher accuracy in classification.

  8. [Clinical laboratory in the 21st century].

    Science.gov (United States)

    Kawai, T

    1991-03-01

    Alvin Toffler has predicted that the "Third Wave" will be a society which be decentralized, diversified and customized, computer-dependent. Medical care and also clinical laboratory will be revolutionalized in a more or less similar direction to that predicted by him. Laboratory physicians and scientists should try to improve laboratory services, particularly establishment of adequate normal values, common expression of various laboratory results, introduction of medical decision making and recommended guideline for laboratory use in primary health care.

  9. Saxton Transportation Operations Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Saxton Transportation Operations Laboratory (Saxton Laboratory) is a state-of-the-art facility for conducting transportation operations research. The laboratory...

  10. Lunar laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Keaton, P.W.; Duke, M.B.

    1986-01-01

    An international research laboratory can be established on the Moon in the early years of the 21st Century. It can be built using the transportation system now envisioned by NASA, which includes a space station for Earth orbital logistics and orbital transfer vehicles for Earth-Moon transportation. A scientific laboratory on the Moon would permit extended surface and subsurface geological exploration; long-duration experiments defining the lunar environment and its modification by surface activity; new classes of observations in astronomy; space plasma and fundamental physics experiments; and lunar resource development. The discovery of a lunar source for propellants may reduce the cost of constructing large permanent facilities in space and enhance other space programs such as Mars exploration. 29 refs.

  11. Virtual Laboratories

    CERN Document Server

    Hut, P

    2006-01-01

    At the frontier of most areas in science, computer simulations play a central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and experimentation form three equally essential aspects, each with its own unique flavor and challenges. Yet, education in computational science is still lagging far behind, and the number of text books in this area is minuscule compared to the many text books on theoretical and experimental science. As a result, many researchers still carry out simulations in a haphazard way, without properly setting up the computational equivalent of a well equipped laboratory. The art of creating such a virtual laboratory, while providing proper extensibility and documentation, is still in its infancy. A new approach is described here, Open Knowledge, as an extension of the notion of Open Source software. Besides open source code, manuals, and primers, an open knowledge project provides simul...

  12. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

    A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

  13. Wavelet transform in similarity paradigm

    NARCIS (Netherlands)

    Z.R. Struzik; A.P.J.M. Siebes (Arno)

    1998-01-01

    textabstract[INS-R9802] Searching for similarity in time series finds still broader applications in data mining. However, due to the very broad spectrum of data involved, there is no possibility of defining one single notion of similarity suitable to serve all applications. We present a powerful

  14. Formal genetic maps

    African Journals Online (AJOL)

    Mohammad Saad Zaghloul Salem

    2014-12-24

    Dec 24, 2014 ... Abstract Formal genetic maps are databases, represented as text or graphic figures, that can be ..... cantly, to our current vague and scanty knowledge of many, ...... similar to reverse engineering techniques, might be worthy of.

  15. The genetics of deliria

    NARCIS (Netherlands)

    D. Adamis; B.C. van Munster; A.J.D. Macdonald

    2009-01-01

    Delirium not induced by alcohol or other psychoactive substance and alcohol withdrawal delirium (or delirium tremens) are both cerebral syndromes with similar presentations and are associated with various adverse outcomes. Recently, interest in identifying genetic predisposing factors that influence

  16. Similarity of samples and trimming

    CERN Document Server

    Álvarez-Esteban, Pedro C; Cuesta-Albertos, Juan A; Matrán, Carlos; 10.3150/11-BEJ351

    2012-01-01

    We say that two probabilities are similar at level $\\alpha$ if they are contaminated versions (up to an $\\alpha$ fraction) of the same common probability. We show how this model is related to minimal distances between sets of trimmed probabilities. Empirical versions turn out to present an overfitting effect in the sense that trimming beyond the similarity level results in trimmed samples that are closer than expected to each other. We show how this can be combined with a bootstrap approach to assess similarity from two data samples.

  17. Contextual Bandits with Similarity Information

    CERN Document Server

    Slivkins, Aleksandrs

    2009-01-01

    In a multi-armed bandit (MAB) problem, an online algorithm makes a sequence of choices. In each round it chooses from a time-invariant set of alternatives and receives the payoff associated with this alternative. While the case of small strategy sets is by now well-understood, a lot of recent work has focused on MAB problems with exponentially or infinitely large strategy sets, where one needs to assume extra structure in order to make the problem tractable. In particular, recent literature considered information on similarity between arms. We consider similarity information in the setting of "contextual bandits", a natural extension of the basic MAB problem where before each round an algorithm is given the "context" -- a hint about the payoffs in this round. Contextual bandits are directly motivated by placing advertisements on webpages, one of the crucial problems in sponsored search. A particularly simple way to represent similarity information in the contextual bandit setting is via a "similarity distance...

  18. Self-similar aftershock rates

    Science.gov (United States)

    Davidsen, Jörn; Baiesi, Marco

    2016-08-01

    In many important systems exhibiting crackling noise—an intermittent avalanchelike relaxation response with power-law and, thus, self-similar distributed event sizes—the "laws" for the rate of activity after large events are not consistent with the overall self-similar behavior expected on theoretical grounds. This is particularly true for the case of seismicity, and a satisfying solution to this paradox has remained outstanding. Here, we propose a generalized description of the aftershock rates which is both self-similar and consistent with all other known self-similar features. Comparing our theoretical predictions with high-resolution earthquake data from Southern California we find excellent agreement, providing particularly clear evidence for a unified description of aftershocks and foreshocks. This may offer an improved framework for time-dependent seismic hazard assessment and earthquake forecasting.

  19. Unmixing of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-01-01

    Full Text Available -bearing oxide/hydroxide/sulfate minerals in complex mixtures be obtained using hyperspectral data? Debba (CSIR) Unmixing of spectrally similar minerals MERAKA 2009 3 / 18 Method of spectral unmixing Old method: problem Linear Spectral Mixture Analysis (LSMA...

  20. Self-similar aftershock rates

    CERN Document Server

    Davidsen, Jörn

    2016-01-01

    In many important systems exhibiting crackling noise --- intermittent avalanche-like relaxation response with power-law and, thus, self-similar distributed event sizes --- the "laws" for the rate of activity after large events are not consistent with the overall self-similar behavior expected on theoretical grounds. This is in particular true for the case of seismicity and a satisfying solution to this paradox has remained outstanding. Here, we propose a generalized description of the aftershock rates which is both self-similar and consistent with all other known self-similar features. Comparing our theoretical predictions with high resolution earthquake data from Southern California we find excellent agreement, providing in particular clear evidence for a unified description of aftershocks and foreshocks. This may offer an improved way of time-dependent seismic hazard assessment and earthquake forecasting.

  1. Community Detection by Neighborhood Similarity

    Institute of Scientific and Technical Information of China (English)

    LIU Xu; XIE Zheng; YI Dong-Yun

    2012-01-01

    Detection of the community structure in a network is important for understanding the structure and dynamics of the network.By exploring the neighborhood of vertices,a local similarity metric is proposed,which can be quickly computed.The resulting similarity matrix retains the same support as the adjacency matrix.Based on local similarity,an agglomerative hierarchical clustering algorithm is proposed for community detection.The algorithm is implemented by an efficient max-heap data structure and runs in nearly linear time,thus is capable of dealing with large sparse networks with tens of thousands of nodes.Experiments on synthesized and real-world networks demonstrate that our method is efficient to detect community structures,and the proposed metric is the most suitable one among all the tested similarity indices.%Detection of the community structure in a network is important for understanding the structure and dynamics of the network. By exploring the neighborhood of vertices, a local similarity metric is proposed, which can be quickly computed. The resulting similarity matrix retains the same support as the adjacency matrix. Based on local similarity, an agglomerative hierarchical clustering algorithm is proposed for community detection. The algorithm is implemented by an efficient max-heap data structure and runs in nearly linear time, thus is capable of dealing with large sparse networks with tens of thousands of nodes. Experiments on synthesized and real-world networks demonstrate that our method is efficient to detect community structures, and the proposed metric is the most suitable one among all the tested similarity indices.

  2. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations...... a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single...

  3. Virtual Laboratories

    Science.gov (United States)

    Hut, P.

    At the frontier of most areas in science, computer simulations playa central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and experimentation form three equally essential aspects, each with its own unique flavor and challenges. Yet, education in computational science is still lagging far behind, and the number of text books in this area is minuscule compared to the many text books on theoretical and experimental science. As a result, many researchers still carry out simulations in a haphazard way, without properly setting up the computational equivalent of a well equipped laboratory. The art of creating such a virtual laboratory, while providing proper extensibility and documentation, is still in its infancy. A new approach is described here, Open Knowledge, as an extension of the notion of Open Source software. Besides open source code, manuals, and primers, an open knowledge project provides simulated dialogues between code developers, thus sharing not only the code, but also the motivations behind the code.

  4. Domain similarity based orthology detection.

    Science.gov (United States)

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  5. Similarity of atoms in molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cioslowski, J.; Nanayakkara, A. (Florida State Univ., Tallahassee, FL (United States))

    1993-12-01

    Similarity of atoms in molecules is quantitatively assessed with a measure that employs electron densities within respective atomic basins. This atomic similarity measure does not rely on arbitrary assumptions concerning basis functions or 'atomic orbitals', is relatively inexpensive to compute, and has straightforward interpretation. Inspection of similarities between pairs of carbon, hydrogen, and fluorine atoms in the CH[sub 4], CH[sub 3]F, CH[sub 2]F[sub 2], CHF[sub 3], CF[sub 4], C[sub 2]H[sub 2], C[sub 2]H[sub 4], and C[sub 2]H[sub 6] molecules, calculated at the MP2/6-311G[sup **] level of theory, reveals that the atomic similarity is greatly reduced by a change in the number or the character of ligands (i.e. the atoms with nuclei linked through bond paths to the nucleus of the atom in question). On the other hand, atoms with formally identical (i.e. having the same nuclei and numbers of ligands) ligands resemble each other to a large degree, with the similarity indices greater than 0.95 for hydrogens and 0.99 for non-hydrogens. 19 refs., 6 tabs.

  6. Quantifying Similarity in Seismic Polarizations

    Science.gov (United States)

    Eaton, D. W. S.; Jones, J. P.; Caffagni, E.

    2015-12-01

    Measuring similarity in seismic attributes can help identify tremor, low S/N signals, and converted or reflected phases, in addition to diagnosing site noise and sensor misalignment in arrays. Polarization analysis is a widely accepted method for studying the orientation and directional characteristics of seismic phases via. computed attributes, but similarity is ordinarily discussed using qualitative comparisons with reference values. Here we introduce a technique for quantitative polarization similarity that uses weighted histograms computed in short, overlapping time windows, drawing on methods adapted from the image processing and computer vision literature. Our method accounts for ambiguity in azimuth and incidence angle and variations in signal-to-noise (S/N) ratio. Using records of the Mw=8.3 Sea of Okhotsk earthquake from CNSN broadband sensors in British Columbia and Yukon Territory, Canada, and vertical borehole array data from a monitoring experiment at Hoadley gas field, central Alberta, Canada, we demonstrate that our method is robust to station spacing. Discrete wavelet analysis extends polarization similarity to the time-frequency domain in a straightforward way. Because histogram distance metrics are bounded by [0 1], clustering allows empirical time-frequency separation of seismic phase arrivals on single-station three-component records. Array processing for automatic seismic phase classification may be possible using subspace clustering of polarization similarity, but efficient algorithms are required to reduce the dimensionality.

  7. Gene functional similarity search tool (GFSST

    Directory of Open Access Journals (Sweden)

    Russo James J

    2006-03-01

    Full Text Available Abstract Background With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and their products have been discovered and their functions have begun to be understood. Increasing amounts of data about genes, gene products and their functions have been stored in databases. To facilitate selection of candidate genes for gene-disease research, genetic association studies, biomarker and drug target selection, and animal models of human diseases, it is essential to have search engines that can retrieve genes by their functions from proteome databases. In recent years, the development of Gene Ontology (GO has established structured, controlled vocabularies describing gene functions, which makes it possible to develop novel tools to search genes by functional similarity. Results By using a statistical model to measure the functional similarity of genes based on the Gene Ontology directed acyclic graph, we developed a novel Gene Functional Similarity Search Tool (GFSST to identify genes with related functions from annotated proteome databases. This search engine lets users design their search targets by gene functions. Conclusion An implementation of GFSST which works on the UniProt (Universal Protein Resource for the human and mouse proteomes is available at GFSST Web Server. GFSST provides functions not only for similar gene retrieval but also for gene search by one or more GO terms. This represents a powerful new approach for selecting similar genes and gene products from proteome databases according to their functions.

  8. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  9. Laboratory Activities

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Christopher F.; Serne, R. Jeffrey

    2008-01-17

    This chapter summarizes the laboratory activities performed by PNNL’s Vadose Zone Characterization Project in support of the Tank Farm Vadose Zone Program, led by CH2M HILL Hanford Group, Inc. The results of these studies are contained in numerous reports (Lindenmeier et al. 2002; Serne et al. 2002a, 2002b, 2002c, 2002d, 2002e; Lindenmeier et al. 2003; Serne et al. 2004a, 2004b; Brown et al. 2005, 2006a, 2007; Serne et al. 2007) and have generated much of the data reported in Chapter 22 (Geochemistry-Contaminant Movement), Appendix G (Geochemistry-Contaminant Movement), and Cantrell et al. (2007, SST WMA Geochemistry Data Package – in preparation). Sediment samples and characterization results from PNNL’s Vadose Zone Characterization Project are also shared with other science and technology (S&T) research projects, such as those summarized in Chapter 12 (Associated Science Activities).

  10. Genetic design of pigs as experimental models in the combat between chronic diseases and healthy aging

    DEFF Research Database (Denmark)

    Bolund, Lars

    2012-01-01

    pigs. We can also produce clones of pigs, some disease prone and some fluorescing, to perform experiments in regenerative medicine where the fate of healthy fluorescent cells can be followed in the, basically identical, disease prone animals. It is also our hope that our pig models can contribute...... with and without intervention. The genome of different pig breeds have been sequenced, revealing that the pig is genetically more similar to man than conventional laboratory animals - in agreement with the similarities in organ development, physiology and metabolism. Genetically designed minipigs (Göttingen...... and Yucatan) are obtained by genetic engineering of somatic cells and animal cloning by somatic cell nuclear transfer. Primary minipig fibroblasts are genetically modified in culture by transposon-based transgenesis and/or homologous recombination with AAV-transduced constructs. The designed pig cells...

  11. Distance learning for similarity estimation

    NARCIS (Netherlands)

    Yu, J.; Amores, J.; Sebe, N.; Radeva, P.; Tian, Q.

    2008-01-01

    In this paper, we present a general guideline to find a better distance measure for similarity estimation based on statistical analysis of distribution models and distance functions. A new set of distance measures are derived from the harmonic distance, the geometric distance, and their generalized

  12. Distance learning for similarity estimation.

    Science.gov (United States)

    Yu, Jie; Amores, Jaume; Sebe, Nicu; Radeva, Petia; Tian, Qi

    2008-03-01

    In this paper, we present a general guideline to find a better distance measure for similarity estimation based on statistical analysis of distribution models and distance functions. A new set of distance measures are derived from the harmonic distance, the geometric distance, and their generalized variants according to the Maximum Likelihood theory. These measures can provide a more accurate feature model than the classical Euclidean and Manhattan distances. We also find that the feature elements are often from heterogeneous sources that may have different influence on similarity estimation. Therefore, the assumption of single isotropic distribution model is often inappropriate. To alleviate this problem, we use a boosted distance measure framework that finds multiple distance measures which fit the distribution of selected feature elements best for accurate similarity estimation. The new distance measures for similarity estimation are tested on two applications: stereo matching and motion tracking in video sequences. The performance of boosted distance measure is further evaluated on several benchmark data sets from the UCI repository and two image retrieval applications. In all the experiments, robust results are obtained based on the proposed methods.

  13. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien

    2013-01-01

    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...

  14. Comparison of hydrological similarity measures

    Science.gov (United States)

    Rianna, Maura; Ridolfi, Elena; Manciola, Piergiorgio; Napolitano, Francesco; Russo, Fabio

    2016-04-01

    The use of a traditional at site approach for the statistical characterization and simulation of spatio-temporal precipitation fields has a major recognized drawback. Indeed, the weakness of the methodology is related to the estimation of rare events and it involves the uncertainty of the at-site sample statistical inference, because of the limited length of records. In order to overcome the lack of at-site observations, regional frequency approach uses the idea of substituting space for time to estimate design floods. The conventional regional frequency analysis estimates quantile values at a specific site from multi-site analysis. The main idea is that homogeneous sites, once pooled together, have similar probability distribution curves of extremes, except for a scaling factor. The method for pooling groups of sites can be based on geographical or climatological considerations. In this work the region of influence (ROI) pooling method is compared with an entropy-based one. The ROI is a flexible pooling group approach which defines for each site its own "region" formed by a unique set of similar stations. The similarity is found through the Euclidean distance metric in the attribute space. Here an alternative approach based on entropy is introduced to cluster homogeneous sites. The core idea is that homogeneous sites share a redundant (i.e. similar) amount of information. Homogeneous sites are pooled through a hierarchical selection based on the mutual information index (i.e. a measure of redundancy). The method is tested on precipitation data in Central Italy area.

  15. HOW DISSIMILARLY SIMILAR ARE BIOSIMILARS?

    Directory of Open Access Journals (Sweden)

    Ramshankar Vijayalakshmi

    2012-05-01

    Full Text Available Recently Biopharmaceuticals are the new chemotherapeutical agents that are called as “Biosimilars” or “follow on protein products” by the European Medicines Agency (EMA and the American regulatory agencies (Food and Drug Administration respectively. Biosimilars are extremely similar to the reference molecule but not identical, however close their similarities may be. A regulatory framework is therefore in place to assess the application for marketing authorisation of biosimilars. When a biosimilar is similar to the reference biopharmaceutical in terms of safety, quality, and efficacy, it can be registered. It is important to document data from clinical trials with a view of similar safety and efficacy. If the development time for a generic medicine is around 3 years, a biosimilar takes about 6-9 years. Generic medicines need to demonstrate bioequivalence only unlike biosimilars that need to conduct phase I and Phase III clinical trials. In this review, different biosimilars that are already being used successfully in the field on Oncology is discussed. Their similarity, differences and guidelines to be followed before a clinically informed decision to be taken, is discussed. More importantly the regulatory guidelines that are operational in India with a work flow of making a biosimilar with relevant dos and dont’s are discussed. For a large populous country like India, where with improved treatments in all sectors including oncology, our ageing population is increasing. For the health care of this sector, we need more newer, cheaper and effective biosimilars in the market. It becomes therefore important to understand the regulatory guidelines and steps to come up with more biosimilars for the existing population and also more information is mandatory for the practicing clinicians to translate these effectively into clinical practice.

  16. Pitfalls in genetic testing

    DEFF Research Database (Denmark)

    Djémié, Tania; Weckhuysen, Sarah; von Spiczak, Sarah

    2016-01-01

    BACKGROUND: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying...

  17. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  18. Genetic Mapping

    Science.gov (United States)

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers create ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human Genome ...

  19. High Resolution Laboratory Spectroscopy

    CERN Document Server

    Brünken, Sandra

    2016-01-01

    In this short review we will highlight some of the recent advancements in the field of high-resolution laboratory spectroscopy that meet the needs dictated by the advent of highly sensitive and broadband telescopes like ALMA and SOFIA. Among these is the development of broadband techniques for the study of complex organic molecules, like fast scanning conventional absorption spectroscopy based on multiplier chains, chirped pulse instrumentation, or the use of synchrotron facilities. Of similar importance is the extension of the accessible frequency range to THz frequencies, where many light hydrides have their ground state rotational transitions. Another key experimental challenge is the production of sufficiently high number densities of refractory and transient species in the laboratory, where discharges have proven to be efficient sources that can also be coupled to molecular jets. For ionic molecular species sensitive action spectroscopic schemes have recently been developed to overcome some of the limita...

  20. Genetic toxicology: web resources.

    Science.gov (United States)

    Young, Robert R

    2002-04-25

    Genetic toxicology is the scientific discipline dealing with the effects of chemical, physical and biological agents on the heredity of living organisms. The Internet offers a wide range of online digital resources for the field of Genetic Toxicology. The history of genetic toxicology and electronic data collections are reviewed. Web-based resources at US National Library of Medicine (NLM), including MEDLINE, PUBMED, Gateway, Entrez, and TOXNET, are discussed. Search strategies and Medical Subject Headings (MeSH) are reviewed in the context of genetic toxicology. The TOXNET group of databases are discussed with emphasis on those databases with genetic toxicology content including GENE-TOX, TOXLINE, Hazardous Substances Data Bank, Integrated Risk Information System, and Chemical Carcinogenesis Research Information System. Location of chemical information including chemical structure and linkage to health and regulatory information using CHEMIDPLUS at NLM and other databases is reviewed. Various government agencies have active genetic toxicology research programs or use genetic toxicology data to assist fulfilling the agency's mission. Online resources at the US Food and Drug Administration (FDA), the US Environmental Protection Agency (EPA), the National Institutes of Environmental Health Sciences, and the National Toxicology Program (NTP) are outlined. Much of the genetic toxicology for pharmaceuticals, industrial chemicals and pesticides that is performed in the world is regulatory-driven. Regulatory web resources are presented for the laws mandating testing, guidelines on study design, Good Laboratory Practice (GLP) regulations, and requirements for electronic data collection and reporting. The Internet provides a range of other supporting resources to the field of genetic toxicology. The web links for key professional societies and journals in genetic toxicology are listed. Distance education, educational media resources, and job placement services are also

  1. Distributed Energy Technology Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Distributed Energy Technologies Laboratory (DETL) is an extension of the power electronics testing capabilities of the Photovoltaic System Evaluation Laboratory...

  2. Bio Engineering Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry and biology laboratories The Bio Engineering Laboratory (BeL) is theonly full spectrum biotechnology capability within the Department...

  3. Advanced Chemistry Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry laboratory The Advanced Chemistry Laboratory (ACL) is a unique facility designed for working with the most super toxic compounds known...

  4. Bio Engineering Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry and biology laboratoriesThe Bio Engineering Laboratory (BeL) is theonly full spectrum biotechnology capability within the Department...

  5. FOOTWEAR PERFORMANCE LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory provides biomechanical and physical analyses for both military and commercial footwear. The laboratory contains equipment that is integral to the us...

  6. Physical Sciences Laboratory (PSL)

    Data.gov (United States)

    Federal Laboratory Consortium — PNNL's Physical Sciences Laboratory (PSL) houses 22 research laboratories for conducting a wide-range of research including catalyst formulation, chemical analysis,...

  7. Self-similarity Driven Demosaicking

    Directory of Open Access Journals (Sweden)

    Antoni Buades

    2011-06-01

    Full Text Available Digital cameras record only one color component per pixel, red, green or blue. Demosaicking is the process by which one can infer a whole color matrix from such a matrix of values, thus interpolating the two missing color values per pixel. In this article we propose a demosaicking method based on the property of non-local self-similarity of images.

  8. Sparse Similarity-Based Fisherfaces

    DEFF Research Database (Denmark)

    Fagertun, Jens; Gomez, David Delgado; Hansen, Mads Fogtmann;

    2011-01-01

    In this work, the effect of introducing Sparse Principal Component Analysis within the Similarity-based Fisherfaces algorithm is examined. The technique aims at mimicking the human ability to discriminate faces by projecting the faces in a highly discriminative and easy interpretative way. Pixel...... obtain the same recognition results as the technique in a dense version using only a fraction of the input data. Furthermore, the presented results suggest that using SPCA in the technique offers robustness to occlusions....

  9. Roget's Thesaurus and Semantic Similarity

    CERN Document Server

    Jarmasz, Mario

    2012-01-01

    We have implemented a system that measures semantic similarity using a computerized 1987 Roget's Thesaurus, and evaluated it by performing a few typical tests. We compare the results of these tests with those produced by WordNet-based similarity measures. One of the benchmarks is Miller and Charles' list of 30 noun pairs to which human judges had assigned similarity measures. We correlate these measures with those computed by several NLP systems. The 30 pairs can be traced back to Rubenstein and Goodenough's 65 pairs, which we have also studied. Our Roget's-based system gets correlations of .878 for the smaller and .818 for the larger list of noun pairs; this is quite close to the .885 that Resnik obtained when he employed humans to replicate the Miller and Charles experiment. We further evaluate our measure by using Roget's and WordNet to answer 80 TOEFL, 50 ESL and 300 Reader's Digest questions: the correct synonym must be selected amongst a group of four words. Our system gets 78.75%, 82.00% and 74.33% of ...

  10. Active browsing using similarity pyramids

    Science.gov (United States)

    Chen, Jau-Yuen; Bouman, Charles A.; Dalton, John C.

    1998-12-01

    In this paper, we describe a new approach to managing large image databases, which we call active browsing. Active browsing integrates relevance feedback into the browsing environment, so that users can modify the database's organization to suit the desired task. Our method is based on a similarity pyramid data structure, which hierarchically organizes the database, so that it can be efficiently browsed. At coarse levels, the similarity pyramid allows users to view the database as large clusters of similar images. Alternatively, users can 'zoom into' finer levels to view individual images. We discuss relevance feedback for the browsing process, and argue that it is fundamentally different from relevance feedback for more traditional search-by-query tasks. We propose two fundamental operations for active browsing: pruning and reorganization. Both of these operations depend on a user-defined relevance set, which represents the image or set of images desired by the user. We present statistical methods for accurately pruning the database, and we propose a new 'worm hole' distance metric for reorganizing the database, so that members of the relevance set are grouped together.

  11. Self-Similar Collisionless Shocks

    CERN Document Server

    Katz, B; Waxman, E; Katz, Boaz; Keshet, Uri; Waxman, Eli

    2006-01-01

    Observations of gamma-ray burst afterglows suggest that the correlation length of magnetic field fluctuations downstream of relativistic non-magnetized collisionless shocks grows with distance from the shock to scales much larger than the plasma skin depth. We argue that this indicates that the plasma properties are described by a self-similar solution, and derive constraints on the scaling properties of the solution. For example, we find that the scaling of the characteristic magnetic field amplitude with distance from the shock is B \\propto D^{s_B} with -1 \\propto x^{2s_B} (for x>>D). We show that the plasma may be approximated as a combination of two self-similar components: a kinetic component of energetic particles and an MHD-like component representing "thermal" particles. We argue that the latter may be considered as infinitely conducting, in which case s_B=0 and the scalings are completely determined (e.g. dn/dE \\propto E^{-2} and B \\propto D^0). Similar claims apply to non- relativistic shocks such a...

  12. Genetic Counseling

    Science.gov (United States)

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  13. Genetic mixture of multiple source populations accelerates invasive range expansion.

    Science.gov (United States)

    Wagner, Natalie K; Ochocki, Brad M; Crawford, Kerri M; Compagnoni, Aldo; Miller, Tom E X

    2017-01-01

    A wealth of population genetic studies have documented that many successful biological invasions stem from multiple introductions from genetically distinct source populations. Yet, mechanistic understanding of whether and how genetic mixture promotes invasiveness has lagged behind documentation that such mixture commonly occurs. We conducted a laboratory experiment to test the influence of genetic mixture on the velocity of invasive range expansion. The mechanistic basis for effects of genetic mixture could include evolutionary responses (mixed invasions may harbour greater genetic diversity and thus elevated evolutionary potential) and/or fitness advantages of between-population mating (heterosis). If driven by evolution, positive effects of source population mixture should increase through time, as selection sculpts genetic variation. If driven by heterosis, effects of mixture should peak following first reproductive contact and then dissipate. Using a laboratory model system (beetles spreading through artificial landscapes), we quantified the velocity of range expansion for invasions initiated with one, two, four or six genetic sources over six generations. Our experiment was designed to test predictions corresponding to the evolutionary and heterosis mechanisms, asking whether any effects of genetic mixture occurred in early or later generations of range expansion. We also quantified demography and dispersal for each experimental treatment, since any effects of mixture should be manifest in one or both of these traits. Over six generations, invasions with any amount of genetic mixture (two, four and six sources) spread farther than single-source invasions. Our data suggest that heterosis provided a 'catapult effect', leaving a lasting signature on range expansion even though the benefits of outcrossing were transient. Individual-level trait data indicated that genetic mixture had positive effects on local demography (reduced extinction risk and enhanced

  14. Laboratory Diagnostic Strategy for Thrombophilia

    Institute of Scientific and Technical Information of China (English)

    马西

    2010-01-01

    @@ Thrombophilia is described as a tendency to develop thrombosis as a consequence of predisposing factors that may be genetically determined, acquired, or both. The risk factors associated with venous thromboembolism are different from those associated with arterial thrombosis. Venous and arterial thromboses are also distinct clinical entities that differ in the microenvironment of clot formation and the structure of the clots formed. Therefore, the tests to be used in laboratory investigation of these two conditions are different.

  15. Assessing protein kinase target similarity

    DEFF Research Database (Denmark)

    Gani, Osman A; Thakkar, Balmukund; Narayanan, Dilip

    2015-01-01

    : focussed chemical libraries, drug repurposing, polypharmacological design, to name a few. Protein kinase target similarity is easily quantified by sequence, and its relevance to ligand design includes broad classification by key binding sites, evaluation of resistance mutations, and the use of surrogate......" of sequence and crystal structure information, with statistical methods able to identify key correlates to activity but also here, "the devil is in the details." Examples from specific repurposing and polypharmacology applications illustrate these points. This article is part of a Special Issue entitled...

  16. Theme: Laboratory Facilities Improvement.

    Science.gov (United States)

    Miller, Glen M.; And Others

    1993-01-01

    Includes "Laboratory Facilities Improvement" (Miller); "Remodeling Laboratories for Agriscience Instruction" (Newman, Johnson); "Planning for Change" (Mulcahy); "Laboratory Facilities Improvement for Technology Transfer" (Harper); "Facilities for Agriscience Instruction" (Agnew et al.); "Laboratory Facility Improvement" (Boren, Dwyer); and…

  17. Mechanisms for similarity based cooperation

    Science.gov (United States)

    Traulsen, A.

    2008-06-01

    Cooperation based on similarity has been discussed since Richard Dawkins introduced the term “green beard” effect. In these models, individuals cooperate based on an aribtrary signal (or tag) such as the famous green beard. Here, two different models for such tag based cooperation are analysed. As neutral drift is important in both models, a finite population framework is applied. The first model, which we term “cooperative tags” considers a situation in which groups of cooperators are formed by some joint signal. Defectors adopting the signal and exploiting the group can lead to a breakdown of cooperation. In this case, conditions are derived under which the average abundance of the more cooperative strategy exceeds 50%. The second model considers a situation in which individuals start defecting towards others that are not similar to them. This situation is termed “defective tags”. It is shown that in this case, individuals using tags to cooperate exclusively with their own kind dominate over unconditional cooperators.

  18. Interneurons targeting similar layers receive synaptic inputs with similar kinetics.

    Science.gov (United States)

    Cossart, Rosa; Petanjek, Zdravko; Dumitriu, Dani; Hirsch, June C; Ben-Ari, Yehezkel; Esclapez, Monique; Bernard, Christophe

    2006-01-01

    GABAergic interneurons play diverse and important roles in controlling neuronal network dynamics. They are characterized by an extreme heterogeneity morphologically, neurochemically, and physiologically, but a functionally relevant classification is still lacking. Present taxonomy is essentially based on their postsynaptic targets, but a physiological counterpart to this classification has not yet been determined. Using a quantitative analysis based on multidimensional clustering of morphological and physiological variables, we now demonstrate a strong correlation between the kinetics of glutamate and GABA miniature synaptic currents received by CA1 hippocampal interneurons and the laminar distribution of their axons: neurons that project to the same layer(s) receive synaptic inputs with similar kinetics distributions. In contrast, the kinetics distributions of GABAergic and glutamatergic synaptic events received by a given interneuron do not depend upon its somatic location or dendritic arborization. Although the mechanisms responsible for this unexpected observation are still unclear, our results suggest that interneurons may be programmed to receive synaptic currents with specific temporal dynamics depending on their targets and the local networks in which they operate.

  19. Genetic defects of iron transport.

    Science.gov (United States)

    Bannerman, R M

    1976-09-01

    Five genetic traits in man and laboratory animals have major effects on iron transport. The heterogeneous condition, hemochromatosis, in some families appears to segregate as a Mendelian trait, and is associated with defective control of intestinal iron absorption. In the very rare human autosomal recessive trait, atransferrinemia, there is an almost total lack of transferrin and gross maldistribution of iron through the body. In mice, sex-linked anemia (an X-linked recessive trait) causes iron deficiency through defective iron absorption, at the "exit" step; a similar defect probably exists in placental iron transfer. In microcytic anemia of mice, an autosomal recessive trait, iron absorption is also impaired because of a defect of iron entry into cells, which is probably generalized. Belgrade rat anemia, less understood at present, also may involve a major disorder of iron metabolism. Study of these mutations has provided new knowledge of iron metabolism and its genetic control Their phenotypic interaction with nutritional factors, especially the form and quantity of iron in the diet, may provide new insights for the study of nutrition.

  20. Semantically enabled image similarity search

    Science.gov (United States)

    Casterline, May V.; Emerick, Timothy; Sadeghi, Kolia; Gosse, C. A.; Bartlett, Brent; Casey, Jason

    2015-05-01

    Georeferenced data of various modalities are increasingly available for intelligence and commercial use, however effectively exploiting these sources demands a unified data space capable of capturing the unique contribution of each input. This work presents a suite of software tools for representing geospatial vector data and overhead imagery in a shared high-dimension vector or embedding" space that supports fused learning and similarity search across dissimilar modalities. While the approach is suitable for fusing arbitrary input types, including free text, the present work exploits the obvious but computationally difficult relationship between GIS and overhead imagery. GIS is comprised of temporally-smoothed but information-limited content of a GIS, while overhead imagery provides an information-rich but temporally-limited perspective. This processing framework includes some important extensions of concepts in literature but, more critically, presents a means to accomplish them as a unified framework at scale on commodity cloud architectures.

  1. SIMILARITIES AND DIFFERENCES BETWEEN COMPANIES

    Directory of Open Access Journals (Sweden)

    NAGY CRISTINA MIHAELA

    2015-05-01

    Full Text Available act: Similarities between the accounting of companies and territorial administrative units accounting are the following: organizing double entry accounting; accounting method both in terms of fundamental theoretical principles and specific practical tools. The differences between the accounting of companies and of territorial administrative units refer to: the accounting of territorial administrative units includes besides general accounting (financial also budgetary accounting, and the accounts system of the budgetary accounting is completely different from that of companies; financial statements of territorial administrative units to which leaders are not main authorizing officers are submitted to the hierarchically superior body (not at MPF; the accounts of territorial administrative units are opened at treasury and financial institutions, accounts at commercial banks being prohibited; equity accounts in territorial administrative units are structured into groups of funds; long term debts have a specific structure in territorial administrative units (internal local public debt and external local public debt.

  2. Performance Indexes: Similarities and Differences

    Directory of Open Access Journals (Sweden)

    André Machado Caldeira

    2013-06-01

    Full Text Available The investor of today is more rigorous on monitoring a financial assets portfolio. He no longer thinks only in terms of the expected return (one dimension, but in terms of risk-return (two dimensions. Thus new perception is more complex, since the risk measurement can vary according to anyone’s perception; some use the standard deviation for that, others disagree with this measure by proposing others. In addition to this difficulty, there is the problem of how to consider these two dimensions. The objective of this essay is to study the main performance indexes through an empirical study in order to verify the differences and similarities for some of the selected assets. One performance index proposed in Caldeira (2005 shall be included in this analysis.

  3. Features Based Text Similarity Detection

    CERN Document Server

    Kent, Chow Kok

    2010-01-01

    As the Internet help us cross cultural border by providing different information, plagiarism issue is bound to arise. As a result, plagiarism detection becomes more demanding in overcoming this issue. Different plagiarism detection tools have been developed based on various detection techniques. Nowadays, fingerprint matching technique plays an important role in those detection tools. However, in handling some large content articles, there are some weaknesses in fingerprint matching technique especially in space and time consumption issue. In this paper, we propose a new approach to detect plagiarism which integrates the use of fingerprint matching technique with four key features to assist in the detection process. These proposed features are capable to choose the main point or key sentence in the articles to be compared. Those selected sentence will be undergo the fingerprint matching process in order to detect the similarity between the sentences. Hence, time and space usage for the comparison process is r...

  4. Evaluating Gender Discrimination Claims: Is There a Gender Similarity Bias?

    Science.gov (United States)

    Elkins, Teri J.; Phillips, James S.; Konopaske, Robert; Townsend, Joellyn

    2001-01-01

    Investigated the possible existence of a gender similarity bias in evaluations of gender discrimination allegations, using a laboratory experiment in which the strength of evidence against a defendant company and the gender of the plaintiff were manipulated. Participants were ethnically diverse undergraduate students. Although female mock jurors…

  5. Laboratory Astrochemistry: Interstellar PAHs

    Science.gov (United States)

    Salama, Farid; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are now considered to be an important and ubiquitous component of the organic material in space. PAHs are found in a large variety of extraterrestrial materials such as interplanetary dust particles (IDPs) and meteoritic materials. PAHs are also good candidates to account for the infrared emission bands (UIRs) and the diffuse interstellar optical absorption bands (DIBs) detected in various regions of the interstellar medium. The recent observations made with the Infrared Space Observatory (ISO) have confirmed the ubiquitous nature of the UIR bands and their carriers. PAHs are thought to form through chemical reactions in the outflow from carbon-rich stars in a process similar to soot formation. Once injected in the interstellar medium, PAHs are further processed by the interstellar radiation field, interstellar shocks and energetic particles. A major, dedicated, laboratory effort has been undertaken to measure the physical and chemical characteristics of these complex molecules and their ions under experimental conditions that mimic the interstellar conditions. These measurements require collision-free conditions where the molecules and ions are cold and chemically isolated. The spectroscopy of PAHs under controlled conditions represents an essential diagnostic tool to study the evolution of extraterrestrial PAHs. The Astrochemistry Laboratory program will be discussed through its multiple aspects: (1) objectives, (2) approach and techniques adopted, (3) adaptability to the nature of the problem(s), and (4) results and implications for astronomy as well as for molecular spectroscopy. A review of the data generated through laboratory simulations of space environments and the role these data have played in our current understanding of the properties of interstellar PAHs will be presented. The discussion will also introduce the newest generation of laboratory experiments that are currently being developed in order to provide a

  6. Clinical characteristics and laboratory analyses of acute myeloid leukemia with t(16;21)(p11;q22)

    OpenAIRE

    Zhang, Zhifen; ZOU, JIANWEN; Li, Yuantang; Liu, Zhanfeng; Xu, Rui; TIAN, WENJUN; ZHAO, ZONGCHEN; Sun, Hui; Han, Jingying; Wang, Jia; Zhang, Bingchang; Ju, Ying

    2015-01-01

    The present study reviewed three patients with acute myeloid leukemia (AML) who had the specific genetic abnormality t(16;21)(p11;q22). To investigate the clinical and laboratory characteristics of AML with t(16;21)(p11;q22) translocation, the similarities and differences of clinical characteristics and laboratory examinations were compared, and a literature review was conducted. According to the French-American-British classification system, patient 1 was M4, patient 2 was M1 and patient 3 w...

  7. Genetics of Rapid and Extreme Size Evolution in Island Mice.

    Science.gov (United States)

    Gray, Melissa M; Parmenter, Michelle D; Hogan, Caley A; Ford, Irene; Cuthbert, Richard J; Ryan, Peter G; Broman, Karl W; Payseur, Bret A

    2015-09-01

    Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F(2) intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature. Copyright © 2015 by the Genetics Society of America.

  8. Pitfalls in genetic testing

    DEFF Research Database (Denmark)

    Djémié, Tania; Weckhuysen, Sarah; von Spiczak, Sarah;

    2016-01-01

    BACKGROUND: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying...... mutations. METHODS: We sent out a survey to 16 genetic centers performing SCN1A testing. RESULTS: We collected data on 28 mutations initially missed using Sanger sequencing. All patients were falsely reported as SCN1A mutation-negative, both due to technical limitations and human errors. CONCLUSION: We...

  9. Similarity analysis of the streamer zone of Blue Jets

    CERN Document Server

    Popov, N A; Milikh, G M

    2016-01-01

    Multiple observations of Blue Jets (BJ)) show that BJ emits a fan of streamers similar to a laboratory leader. Moreover,in the exponential atmosphere those long streamers grow preferentially upward, producing a narrow coneconfined by the aperture angle. It was also noticed that BJ are similar to the streamer zone of a leader (streamer corona) and the modeling studies based on the streamers fractal structure were conducted. Objective of this paper is to study the fractal dimension of the bunch of streamer channels emitted by BJ, at different altitude and under the varying reduced electric field. This similarity analysis has been done in three steps: First we described the dendritic structure of streamers in corona discharge applying the fractal theory. Then using this model and the data from existing laboratory experiments we obtained the fractal dimension of the branching streamer channels. Finally the model was validated by the observations of BJ available from the literature.

  10. Preimplantation genetic diagnosis: state of the art.

    Science.gov (United States)

    Basille, Claire; Frydman, René; El Aly, Abdelwahab; Hesters, Laetitia; Fanchin, Renato; Tachdjian, Gérard; Steffann, Julie; LeLorc'h, Marc; Achour-Frydman, Nelly

    2009-07-01

    Preimplantation genetic diagnosis (PGD) is used to analyze embryos genetically before their transfer into the uterus. It was developed first in England in 1990, as part of progress in reproductive medicine, genetic and molecular biology. PGD offers couples at risk the chance to have an unaffected child, without facing termination of pregnancy. Embryos are obtained by in vitro fertilization with intracytoplasmic sperm injection (ICSI), and are biopsied mostly on day 3; blastocyst biopsy is mentioned as a possible alternative. The genetic analysis is performed on one or two blastomeres, by fluorescent in situ hybridization (FISH) for cytogenetic diagnosis, or polymerase chain reaction (PCR) for molecular diagnosis. Genetic analysis of the first or second polar body can be used to study maternal genetic contribution. Only unaffected embryos are transferred into the uterus. To improve the accuracy of the diagnosis, new technologies are emerging, with comparative genomic hybridization (CGH) and microarrays. In Europe, depending on national regulations, PGD is either prohibited, or allowed, or practiced in the absence of recommendations. The indications are chromosomal abnormalities, X-linked diseases or single gene disorders. The number of disorders being tested increases. In Europe, data collection from the year 2004 reports that globally 69.6% of cycles lead to embryo transfer and implantation rate is 17%. European results from the year 2004 show a clinical pregnancy rate of 18% per oocyte retrieval and 25% per embryo transfer, leading to 528 babies born. The cohort studies concerning the paediatric follow-up of PGD babies show developmental outcomes similar to children conceived after IVF-ICSI. Recent advances include human leucocyte antigen (HLA) typing for PGD embryos, when an elder sibling is affected with a genetic disorder and needs stem cell transplantation. The HLA-matched offspring resulting can give cord blood at birth. Preimplantation genetic screening (PGS

  11. ENGL, the European Network of GMO Laboratories

    OpenAIRE

    KREYSA JOACHIM; Van den Eede, Guy; MAZZARA Marco

    2013-01-01

    When the current EU policy on Genetically Modified Organism (GMO) was designed, GMO-specific detection methods were not generally available. Under the leadership of the Joint Research Centre of the European Commission (JRC), a European Network of GMO Laboratories was formed, the ENGL. ENGL brings together the GMO control laboratories (including NRL) of the EU to establish standards, spread good practices, and discuss problems. Its standards are today used throughout the EU and beyond. ...

  12. Denver District Laboratory (DEN)

    Data.gov (United States)

    Federal Laboratory Consortium — Program CapabilitiesDEN-DO Laboratory is a multi-functional laboratory capable of analyzing most chemical analytes and pathogenic/non-pathogenic microorganisms found...

  13. NASA Space Radiation Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory is a NASA funded facility, delivering heavy ion beams to a target area where scientists...

  14. Lincoln Laboratory Grid

    Data.gov (United States)

    Federal Laboratory Consortium — The Lincoln Laboratory Grid (LLGrid) is an interactive, on-demand parallel computing system that uses a large computing cluster to enable Laboratory researchers to...

  15. Gun Dynamics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Gun Dynamics Laboratory is a research multi-task facility, which includes two firing bays, a high bay area and a second floor laboratory space. The high bay area...

  16. Advanced Chemistry Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry laboratoryThe Advanced Chemistry Laboratory (ACL) is a unique facility designed for working with the most super toxic compounds known...

  17. Genetic Disorders

    Science.gov (United States)

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  18. Systolic array IC for genetic computation

    Science.gov (United States)

    Anderson, D.

    1991-01-01

    Measuring similarities between large sequences of genetic information is a formidable task requiring enormous amounts of computer time. Geneticists claim that nearly two months of CRAY-2 time are required to run a single comparison of the known database against the new bases that will be found this year, and more than a CRAY-2 year for next year's genetic discoveries, and so on. The DNA IC, designed at HP-ICBD in cooperation with the California Institute of Technology and the Jet Propulsion Laboratory, is being implemented in order to move the task of genetic comparison onto workstations and personal computers, while vastly improving performance. The chip is a systolic (pumped) array comprised of 16 processors, control logic, and global RAM, totaling 400,000 FETS. At 12 MHz, each chip performs 2.7 billion 16 bit operations per second. Using 35 of these chips in series on one PC board (performing nearly 100 billion operations per second), a sequence of 560 bases can be compared against the eventual total genome of 3 billion bases, in minutes--on a personal computer. While the designed purpose of the DNA chip is for genetic research, other disciplines requiring similarity measurements between strings of 7 bit encoded data could make use of this chip as well. Cryptography and speech recognition are two examples. A mix of full custom design and standard cells, in CMOS34, were used to achieve these goals. Innovative test methods were developed to enhance controllability and observability in the array. This paper describes these techniques as well as the chip's functionality. This chip was designed in the 1989-90 timeframe.

  19. Laboratory-acquired brucellosis

    DEFF Research Database (Denmark)

    Fabiansen, C.; Knudsen, J.D.; Lebech, A.M.

    2008-01-01

    Brucellosis is a rare disease in Denmark. We describe one case of laboratory-acquired brucellosis from an index patient to a laboratory technician following exposure to an infected blood culture in a clinical microbiology laboratory Udgivelsesdato: 2008/6/9......Brucellosis is a rare disease in Denmark. We describe one case of laboratory-acquired brucellosis from an index patient to a laboratory technician following exposure to an infected blood culture in a clinical microbiology laboratory Udgivelsesdato: 2008/6/9...

  20. Exploring Genetic Drift and Natural Selection through a Simulation Activity.

    Science.gov (United States)

    Maret, Timothy J.; Rissing, Steven W.

    1998-01-01

    Reports on the development of a laboratory exercise that would allow students to explore the concept of genetic drift. Discusses the concept of genetic drift that is coincident with natural selection and that closely models the real world. (DDR)

  1. Genetic modification and genetic determinism.

    Science.gov (United States)

    Resnik, David B; Vorhaus, Daniel B

    2006-06-26

    In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  2. Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

    Science.gov (United States)

    Brandner, Diana L.

    2002-01-01

    Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

  3. Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

    Science.gov (United States)

    Brandner, Diana L.

    2002-01-01

    Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

  4. Tactical Systems Integration Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Tactical Systems Integration Laboratory is used to design and integrate computer hardware and software and related electronic subsystems for tactical vehicles....

  5. Combustion Research Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Combustion Research Laboratory facilitates the development of new combustion systems or improves the operation of existing systems to meet the Army's mission for...

  6. Semiconductor Laser Measurements Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Semiconductor Laser Measurements Laboratory is equipped to investigate and characterize the lasing properties of semiconductor diode lasers. Lasing features such...

  7. Research Combustion Laboratory (RCL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Research Combustion Laboratory (RCL) develops aerospace propulsion technology by performing tests on propulsion components and materials. Altitudes up to 137,000...

  8. Central Laboratories Services

    Data.gov (United States)

    Federal Laboratory Consortium — The TVA Central Laboratories Services is a comprehensive technical support center, offering you a complete range of scientific, engineering, and technical services....

  9. Rapid Prototyping Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The ARDEC Rapid Prototyping (RP) Laboratory was established in December 1992 to provide low cost RP capabilities to the ARDEC engineering community. The Stratasys,...

  10. Wind Structural Testing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This facility provides office space for industry researchers, experimental laboratories, computer facilities for analytical work, and space for assembling components...

  11. Vehicle Development Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Supports the development of prototype deployment platform vehicles for offboard countermeasure systems.DESCRIPTION: The Vehicle Development Laboratory is...

  12. Advanced Manufacturing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Manufacturing Laboratory at the University of Maryland provides the state of the art facilities for realizing next generation products and educating the...

  13. Intelligent Optics Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Intelligent Optics Laboratory supports sophisticated investigations on adaptive and nonlinear optics; advancedimaging and image processing; ground-to-ground and...

  14. Geospatial Services Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: To process, store, and disseminate geospatial data to the Department of Defense and other Federal agencies.DESCRIPTION: The Geospatial Services Laboratory...

  15. Wind Structural Testing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This facility provides office space for industry researchers, experimental laboratories, computer facilities for analytical work, and space for assembling components...

  16. Sandia National Laboratories

    Data.gov (United States)

    Federal Laboratory Consortium — For more than 60 years, Sandia has delivered essential science and technology to resolve the nation's most challenging security issues.Sandia National Laboratories...

  17. Fuels Processing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — NETL’s Fuels Processing Laboratory in Morgantown, WV, provides researchers with the equipment they need to thoroughly explore the catalytic issues associated with...

  18. Thermogravimetric Analysis Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — At NETL’s Thermogravimetric Analysis Laboratory in Morgantown, WV, researchers study how chemical looping combustion (CLC) can be applied to fossil energy systems....

  19. Acoustic Technology Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains an electro-magnetic worldwide data collection and field measurement capability in the area of acoustic technology. Outfitted by NASA Langley...

  20. Vehicle Development Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Supports the development of prototype deployment platform vehicles for offboard countermeasure systems. DESCRIPTION: The Vehicle Development Laboratory is...

  1. Laboratory of Chemical Physics

    Data.gov (United States)

    Federal Laboratory Consortium — Current research in the Laboratory of Chemical Physics is primarily concerned with experimental, theoretical, and computational problems in the structure, dynamics,...

  2. Space Weather Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Space Weather Computational Laboratory is a Unix and PC based modeling and simulation facility devoted to research analysis of naturally occurring electrically...

  3. ANALYTICAL MICROBIOLOGY LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains equipment that performs a broad array of microbiological analyses for pathogenic and spoilage microorganisms. It performs challenge studies...

  4. Engineered Natural Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — With its pressure vessels that simulate the pressures and temperatures found deep underground, NETL’s Engineered Natural Systems Laboratory in Pittsburgh, PA, gives...

  5. Coatings and Corrosion Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The mission of the Coatings and Corrosion Laboratory is to develop and analyze the effectiveness of innovative coatings test procedures while evaluating the...

  6. Environmental Microbiology Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Environmental Microbiology Laboratory, located in Bldg. 644 provides a dual-gas respirometer for measurement of oxygen consumption and carbon dioxide evolution...

  7. Research Combustion Laboratory (RCL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Research Combustion Laboratory (RCL) develops aerospace propulsion technology by performing tests on propulsion components and materials. Altitudes up to 137,000...

  8. Composites Characterization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The purpose of the Composites Characterization Laboratory is to investigate new and/or modified matrix materials and fibers for advanced composite applications both...

  9. Embedded Processor Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Embedded Processor Laboratory provides the means to design, develop, fabricate, and test embedded computers for missile guidance electronics systems in support...

  10. Photovoltaic Characterization Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — NIST's PV characterization laboratory is used to measure the electrical performance and opto-electronic properties of solar cells and modules. This facility consists...

  11. Wireless Emulation Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Wireless Emulation Laboratory (WEL) is a researchtest bed used to investigate fundamental issues in networkscience. It is a research infrastructure that emulates...

  12. Geospatial Services Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: To process, store, and disseminate geospatial data to the Department of Defense and other Federal agencies. DESCRIPTION: The Geospatial Services Laboratory...

  13. Neural Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — As part of the Electrical and Computer Engineering Department and The Institute for System Research, the Neural Systems Laboratory studies the functionality of the...

  14. Microgravity Emissions Laboratory (MEL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microgravity Emissions Laboratory (MEL) utilizes a low-frequency acceleration measurement system for the characterization of rigid body inertial forces generated...

  15. Optical Remote Sensing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Optical Remote Sensing Laboratory deploys rugged, cutting-edge electro-optical instrumentation for the collection of various event signatures, with expertise in...

  16. COGNITIVE PERFORMANCE LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory conducts basic and applied human research studies to characterize cognitive performance as influenced by militarily-relevant contextual and physical...

  17. Atmospheric Measurements Laboratory (AML)

    Data.gov (United States)

    Federal Laboratory Consortium — The Atmospheric Measurements Laboratory (AML) is one of the nation's leading research facilities for understanding aerosols, clouds, and their interactions. The AML...

  18. FOOD SAFETY TESTING LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory develops screening assays, tests and modifies biosensor equipment, and optimizes food safety testing protocols for the military and civilian sector...

  19. Virtual Training Devices Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Virtual Training Devices (VTD) Laboratory at the Life Cycle Software Engineering Center, Picatinny Arsenal, provides a software testing and support environment...

  20. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  1. Genetic principles.

    Science.gov (United States)

    Abuelo, D

    1987-01-01

    The author discusses the basic principles of genetics, including the classification of genetic disorders and a consideration of the rules and mechanisms of inheritance. The most common pitfalls in clinical genetic diagnosis are described, with emphasis on the problem of the negative or misleading family history.

  2. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  3. Molecular diversity of Clostridium botulinum and phenotypically similar strains.

    Science.gov (United States)

    Grenda, T; Kukier, E; Sieradzki, Z; Goldsztejn, M; Kwiatek, K

    2016-12-01

    This study was undertaken to examine phenotypic and genetic features of strains preliminary classified as Clostridium botulinum species. The phenotypic characteristics were assessed with different culture media and biochemical tests. The genetic characterization included detection of botulinum toxin genes by PCR and macrorestriction analysis with SmaI, XhoI and SacII by PFGE (Pulsed-field Gel Electrophoresis). Despite similar biochemical properties of all analysed strains, only 47% of them contained genes determining toxicity specific to C. botulinum species. The most valuable differentiation of C. botulinum and C. botulinum-like strains was obtained after SmaI digestion. The highest affinity was observed among C. botulinum type B profiles which was even up to 100%. It was found 100% of affinity between C. botulinum and C. botulinum-like strains, however, the similarity among C. botulinum and C. botulinum-like was generally lower than 80%.

  4. Diagnóstico laboratorial de hemoglobinas semelhantes à HbS Laboratorial diagnosis for hemoglobin like HbS

    Directory of Open Access Journals (Sweden)

    Paula Juliana Antoniazzo Zamaro

    2002-01-01

    Full Text Available A hemoglobina S (HbS está presente na população brasileira com prevalência variável, dependente dos grupos raciais formadores de cada região. A migração eletroforética em pH alcalino apresenta similaridade com outras hemoglobinas, e estudos complementares para sua correta caracterização são necessários. No presente estudo objetivamos traçar um fluxograma com as metodologias disponíveis para a caracterização da hemoglobina S e das hemoglobinas que apresentam migração semelhante em pH alcalino. No período de janeiro a junho de 2000, analisamos amostras de sangue com suspeita de hemoglobina S encaminhadas ao Laboratório de Hemoglobinas da Unesp. Caracterizamos diferentes mutantes e formas interativas com hemoglobina S, por procedimentos eletroforéticos, em variados pH, análises citológicas e testes bioquímicos específicos. Os procedimentos de análise aplicados resultaram em orientação fornecida aos laboratórios de rotina sobre como proceder no diagnóstico laboratorial destas alterações de hemoglobina. Desta forma contribuímos para um melhor conhecimento sobre a variabilidade genética das hemoglobinas em nossa população, auxiliando no acompanhamento clínico e no aconselhamento genético das hemoglobinopatias com fisiopatologia relacionada à alteração.The hemoglobin S is presented at Brazilian population with variable prevalence dependent of constitutive racial groups in each region. The electrophoretic migration on alkaline pH showed similarities with another hemoglobins. Complementary studies to the correct caracterization becomes necessary. At the present study we aimed make a fluxogram with the avaliable methodologies for the caracterization of hemoglobin S and hemoglobins that present similar migration on alkaline pH. During the period of January to June, 2000, we had analised blood samples with suspicious hemoglobin S sent to the Laboratory of Hemoglobins, Unesp. Were caracterized different mutants and

  5. Genetic modification and genetic determinism

    OpenAIRE

    Vorhaus Daniel B; Resnik David B

    2006-01-01

    Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound....

  6. Mating competitiveness of sterile genetic sexing strain males (GAMA) under laboratory and semi-field conditions: Steps towards the use of the Sterile Insect Technique to control the major malaria vector Anopheles arabiensis in South Africa.

    Science.gov (United States)

    Munhenga, Givemore; Brooke, Basil D; Gilles, Jeremie R L; Slabbert, Kobus; Kemp, Alan; Dandalo, Leonard C; Wood, Oliver R; Lobb, Leanne N; Govender, Danny; Renke, Marius; Koekemoer, Lizette L

    2016-03-02

    Anopheles arabiensis Patton is primarily responsible for malaria transmission in South Africa after successful suppression of other major vector species using indoor spraying of residual insecticides. Control of An. arabiensis using current insecticide based approaches is proving difficult owing to the development of insecticide resistance, and variable feeding and resting behaviours. The use of the sterile insect technique as an area-wide integrated pest management system to supplement the control of An. arabiensis was proposed for South Africa and is currently under investigation. The success of this technique is dependent on the ability of laboratory-reared sterile males to compete with wild males for mates. As part of the research and development of the SIT technique for use against An. arabiensis in South Africa, radio-sensitivity and mating competitiveness of a local An. arabiensis sexing strain were assessed. The optimal irradiation dose inducing male sterility without compromising mating vigour was tested using Cobalt 60 irradiation doses ranging from 70-100 Gy. Relative mating competitiveness of sterile laboratory-reared males (GAMA strain) compared to fertile wild-type males (AMAL strain) for virgin wild-type females (AMAL) was investigated under laboratory and semi-field conditions using large outdoor cages. Three different sterile male to fertile male to wild-type female ratios were evaluated [1:1:1, 5:1:1 and 10:1:1 (sterile males: fertile, wild-type males: fertile, wild-type females)]. Irradiation at the doses tested did not affect adult emergence but had a moderate effect on adult survivorship and mating vigour. A dose of 75 Gy was selected for the competitiveness assays. Mating competitiveness experiments showed that irradiated GAMA male mosquitoes are a third as competitive as their fertile AMAL counterparts under semi-field conditions. However, they were not as competitive under laboratory conditions. An inundative ratio of 10:1 induced the

  7. Textual and chemical information processing: different domains but similar algorithms

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2000-01-01

    Full Text Available This paper discusses the extent to which algorithms developed for the processing of textual databases are also applicable to the processing of chemical structure databases, and vice versa. Applications discussed include: an algorithm for distribution sorting that has been applied to the design of screening systems for rapid chemical substructure searching; the use of measures of inter-molecular structural similarity for the analysis of hypertext graphs; a genetic algorithm for calculating term weights for relevance feedback searching for determining whether a molecule is likely to exhibit biological activity; and the use of data fusion to combine the results of different chemical similarity searches.

  8. Population genetic structure and ecotoxicology.

    OpenAIRE

    Guttman, S I

    1994-01-01

    Electrophoretic analyses of population genetic structure, both in the laboratory and in the field, have documented significant shifts in allozyme genotype frequencies in a variety of aquatic taxa as a result of environmental impacts. Studies are documented which indicate that contaminants may select for individuals with tolerant allozyme genotypes, causing the potential loss of individuals with sensitive genotypes. This may diminish the genetic variability and fitness of affected populations ...

  9. Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models.

    Directory of Open Access Journals (Sweden)

    Sangwon Lee

    Full Text Available We are developing a laboratory-scale model to improve our understanding and capacity to assess the biological risks of genetically engineered bacteria and their genetic elements in the natural environment. Our hypothetical scenario concerns an industrial bioreactor failure resulting in the introduction of genetically engineered bacteria to a downstream municipal wastewater treatment plant (MWWTP. As the first step towards developing a model for this scenario, we sampled microbial communities from the aeration basin of a MWWTP at three seasonal time points. Having established a baseline for community composition, we investigated how the community changed when propagated in the laboratory, including cell culture media conditions that could provide selective pressure in future studies. Specifically, using PhyloChip 16S-rRNA-gene targeting microarrays, we compared the compositions of sampled communities to those of inocula propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources (glucose, chloroacetate, D-threonine or the ionic liquid 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl. Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in both aeration basin and laboratory-cultured communities. Laboratory-cultured communities were enriched in γ-Proteobacteria. Enterobacteriaceae, and Aeromonadaceae were enriched by glucose, Pseudomonadaceae by chloroacetate and D-threonine, and Burkholderiacea by high (50 mM concentrations of chloroacetate. Microbial communities cultured with chloroacetate and D-threonine were more similar to sampled field communities than those cultured with glucose or [C2mim]Cl. Although observed relative richness in operational taxonomic units (OTUs was lower for laboratory cultures than for field communities, both flask and reactor systems supported phylogenetically diverse communities. These results importantly provide a foundation for laboratory models of industrial

  10. Inequalities between similarities for numerical data

    NARCIS (Netherlands)

    Warrens, Matthijs J.

    2016-01-01

    Similarity measures are entities that can be used to quantify the similarity between two vectors with real numbers. We present inequalities between seven well known similarities. The inequalities are valid if the vectors contain non-negative real numbers.

  11. Laboratory Information Systems.

    Science.gov (United States)

    Henricks, Walter H

    2015-06-01

    Laboratory information systems (LISs) supply mission-critical capabilities for the vast array of information-processing needs of modern laboratories. LIS architectures include mainframe, client-server, and thin client configurations. The LIS database software manages a laboratory's data. LIS dictionaries are database tables that a laboratory uses to tailor an LIS to the unique needs of that laboratory. Anatomic pathology LIS (APLIS) functions play key roles throughout the pathology workflow, and laboratories rely on LIS management reports to monitor operations. This article describes the structure and functions of APLISs, with emphasis on their roles in laboratory operations and their relevance to pathologists.

  12. Energy Materials Research Laboratory (EMRL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Energy Materials Research Laboratory at the Savannah River National Laboratory (SRNL) creates a cross-disciplinary laboratory facility that lends itself to the...

  13. Genetic barcodes

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  14. Genetic Characterization of Bacillus anthracis 17 JB strain

    Directory of Open Access Journals (Sweden)

    Sakineh Seyed-Mohamadi

    2015-11-01

    Full Text Available Background and Objectives: Bacillus anthracis is one of the most homogenous bacteria ever described. Bacillus anthracis 17JB is a laboratory strain. It is broadly used as a challenge strain in guinea pigs for potency test of anthrax vaccine.Material and Methods: This work describes genetic characterization of B. anthracis 17 JB strain using the SNPs and MLVA genotyping.Results and Conclusion: In SNPs typing, the originally French 17JB strain represented the A. Br. 008/009 subgroup. In Levy's genotyping method, 843, 451 and 864 bp long fragments were identified at AA03, AJ03 and AA07 loci, respectively. In the vaccine manufacturer perspective these findings are much valuable on their own account, but similar research is required to extend molecular knowledge of B. anthracis epidemiology in Persia.Keywords: Bacillus anthracis 17JB, Genetic characterization, SNPs typing

  15. Mammalian developmental genetics in the twentieth century.

    Science.gov (United States)

    Artzt, Karen

    2012-12-01

    This Perspectives is a review of the breathtaking history of mammalian genetics in the past century and, in particular, of the ways in which genetic thinking has illuminated aspects of mouse development. To illustrate the power of that thinking, selected hypothesis-driven experiments and technical advances are discussed. Also included in this account are the beginnings of mouse genetics at the Bussey Institute, Columbia University, and The Jackson Laboratory and a retrospective discussion of one of the classic problems in developmental genetics, the T/t complex and its genetic enigmas.

  16. Genetic modification and genetic determinism

    Directory of Open Access Journals (Sweden)

    Vorhaus Daniel B

    2006-06-01

    Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  17. Genetics & sport: bioethical concerns.

    Science.gov (United States)

    Miah, Andy

    2012-12-01

    This paper provides an overview of the ethical issues pertaining to the use of genetic insights and techniques in sport. Initially, it considers a range of scientific findings that have stimulated debate about the ethical issues associated with genetics applied to sport. It also outlines some of the early policy responses to these discoveries from world leading sports organizations, along with knowledge about actual use of gene technologies in sport. Subsequently, it considers the challenges with distinguishing between therapeutic use and human enhancement within genetic science, which is a particularly important issue for the world of sport. Next, particular attention is given to the use of genetic information, which raises questions about the legitimacy and reliability of genetic tests, along with the potential public value of having DNA databanks to economize in health care. Finally, the ethics of gene transfer are considered, inviting questions into the values of sport and humanity. It argues that, while gene modification may seem conceptually similar to other forms of doping, the requirements upon athletes are such that new forms of enhancement become increasingly necessary to discover. Insofar as genetic science is able to create safer, more effective techniques of human modification, then it may be an appealing route through which to modify athletes to safeguard the future of elite sports as enterprises of human excellence.

  18. How to design a genetic mating scheme: a basic training package for Drosophila genetics.

    Science.gov (United States)

    Roote, John; Prokop, Andreas

    2013-02-01

    Drosophila melanogaster is a powerful model organism for biological research. The essential and common instrument of fly research is genetics, the art of applying Mendelian rules in the specific context of Drosophila with its unique classical genetic tools and the breadth of modern genetic tools and strategies brought in by molecular biology, transgenic technologies and the use of recombinases. Training newcomers to fly genetics is a complex and time-consuming task but too important to be left to chance. Surprisingly, suitable training resources for beginners currently are not available. Here we provide a training package for basic Drosophila genetics, designed to ensure that basic knowledge on all key areas is covered while reducing the time invested by trainers. First, a manual introduces to fly history, rationale for mating schemes, fly handling, Mendelian rules in fly, markers and balancers, mating scheme design, and transgenic technologies. Its self-study is followed by a practical training session on gender and marker selection, introducing real flies under the dissecting microscope. Next, through self-study of a PowerPoint presentation, trainees are guided step-by-step through a mating scheme. Finally, to consolidate knowledge, trainees are asked to design similar mating schemes reflecting routine tasks in a fly laboratory. This exercise requires individual feedback but also provides unique opportunities for trainers to spot weaknesses and strengths of each trainee and take remedial action. This training package is being successfully applied at the Manchester fly facility and may serve as a model for further training resources covering other aspects of fly research.

  19. Genetic Engineering

    Science.gov (United States)

    Phillips, John

    1973-01-01

    Presents a review of genetic engineering, in which the genotypes of plants and animals (including human genotypes) may be manipulated for the benefit of the human species. Discusses associated problems and solutions and provides an extensive bibliography of literature relating to genetic engineering. (JR)

  20. Genetic Counseling

    Science.gov (United States)

    ... for certain types of genetic conditions (such as Down syndrome) in the baby if mother-to-be is 35 years of age or more, or is concerned at any age about her chances of having a child with a genetic condition To learn about the ...

  1. Genetic variation in the zebrafish

    NARCIS (Netherlands)

    Guryev, V.; Koudijs, M.J.; Berezikov, E.; Johnson, S.L.; Plasterk, R.; van Eeden, F.; Cuppen, E.

    2006-01-01

    Although zebrafish was introduced as a laboratory model organism several decades ago and now serves as a primary model for developmental biology, there is only limited data on its genetic variation. An establishment of a dense polymorphism map becomes a requirement for effective linkage analysis and

  2. Manipulating Genetic Material in Bacteria

    Science.gov (United States)

    1998-01-01

    Lisa Crawford, a graduate research assistant from the University of Toledo, works with Laurel Karr of Marshall Space Flight Center (MSFC) in the molecular biology laboratory. They are donducting genetic manipulation of bacteria and yeast for the production of large amount of desired protein. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  3. Family Assessment and Genetic Counseling.

    Science.gov (United States)

    Carpenter, Pat; And Others

    Presented are two papers from a panel discussion on prenatal diagnosis and genetic counseling with families. D. Blackston (director of the Developmental Evaluation Clinic, Decatur, Georgia) points out that a concise family history, pregnancy and birth data, developmental history, careful physical examination, and appropriate laboratory studies are…

  4. Differences in ultrasonic vocalizations between wild and laboratory California mice (Peromyscus californicus.

    Directory of Open Access Journals (Sweden)

    Matina C Kalcounis-Rueppell

    Full Text Available BACKGROUND: Ultrasonic vocalizations (USVs emitted by muroid rodents, including laboratory mice and rats, are used as phenotypic markers in behavioral assays and biomedical research. Interpretation of these USVs depends on understanding the significance of USV production by rodents in the wild. However, there has never been a study of muroid rodent ultrasound function in the wild and comparisons of USVs produced by wild and laboratory rodents are lacking to date. Here, we report the first comparison of wild and captive rodent USVs recorded from the same species, Peromyscus californicus. METHODOLOGY AND PRINCIPAL FINDINGS: We used standard ultrasound recording techniques to measure USVs from California mice in the laboratory (Peromyscus Genetic Stock Center, SC, USA and the wild (Hastings Natural History Reserve, CA, USA. To determine which California mouse in the wild was vocalizing, we used a remote sensing method that used a 12-microphone acoustic localization array coupled with automated radio telemetry of all resident Peromyscus californicus in the area of the acoustic localization array. California mice in the laboratory and the wild produced the same types of USV motifs. However, wild California mice produced USVs that were 2-8 kHz higher in median frequency and significantly more variable in frequency than laboratory California mice. SIGNIFICANCE: The similarity in overall form of USVs from wild and laboratory California mice demonstrates that production of USVs by captive Peromyscus is not an artifact of captivity. Our study validates the widespread use of USVs in laboratory rodents as behavioral indicators but highlights that particular characteristics of laboratory USVs may not reflect natural conditions.

  5. Genetic Romanticism

    DEFF Research Database (Denmark)

    Tupasela, Aaro

    2016-01-01

    . This article compares and contrasts the work of two doctors in Finland, Elias Lönnrot and Reijo Norio, working over a century and a half apart, to examine the ways in which they have contributed to the formation of national identity and unity. The notion of genetic romanticism is introduced as a term...... to complement the notion of national romanticism that has been used to describe the ways in which nineteenth-century scholars sought to create and deploy common traditions for national-romantic purposes. Unlike national romanticism, however, strategies of genetic romanticism rely on the study of genetic...... inheritance as a way to unify populations within politically and geographically bounded areas. Thus, new genetics have contributed to the development of genetic romanticisms, whereby populations (human, plant, and animal) can be delineated and mobilized through scientific and medical practices to represent...

  6. Detroit District Laboratory (DET)

    Data.gov (United States)

    Federal Laboratory Consortium — Program Capabilities DET-DO Laboratory is equipped with the usual instrumentation necessary to perform a wide range of analyses of food, drugs and cosmetics. Program...

  7. Aquatic Research Laboratory (ARL)

    Data.gov (United States)

    Federal Laboratory Consortium — Columbia River and groundwater well water sources are delivered to the Aquatic Research Laboratory (ARL), where these resources are used to conduct research on fish...

  8. Product Evaluation Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory offers the services of highly trained and experienced specialists that have a full complement of measuring equipment. It is equipped with two optical...

  9. Protective Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory is a 40 by 28 by 9 foot facility that is equipped with tools for the development of various items of control technology related to the transmission...

  10. Laboratory Demographics Lookup Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — This website provides demographic information about laboratories, including CLIA number, facility name and address, where the laboratory testing is performed, the...

  11. Neutral Buoyancy Laboratory (NBL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Neutral Buoyancy Laboratory (NBL) is an astronaut training facility and neutral buoyancy pool operated by NASA and located at the Sonny Carter Training Facility,...

  12. Aircraft Fire Protection Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Navy Aircraft Protection Laboratory provides complete test support for all Navy air vehicle fire protection systems. The facility allows for the simulation of a...

  13. Geometric Design Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The mission of the Geometric Design Laboratory (GDL) is to support the Office of Safety Research and Development in research related to the geometric design...

  14. Laboratory of Biological Modeling

    Data.gov (United States)

    Federal Laboratory Consortium — The Laboratory of Biological Modeling is defined by both its methodologies and its areas of application. We use mathematical modeling in many forms and apply it to...

  15. Aircraft Fire Protection Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Navy Aircraft Protection Laboratory provides complete test support for all Navy air vehicle fire protection systems.The facility allows for the simulation of a...

  16. Radiochemical Processing Laboratory (RPL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Radiochemical Processing Laboratory (RPL)�is a scientific facility funded by DOE to create and implement innovative processes for environmental clean-up and...

  17. Mechanical Testing Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — NETL’s Mechanical Testing Laboratory in Albany, OR, helps researchers investigate materials that can withstand the heat and pressure commonly found in fossil energy...

  18. Laboratory of Biological Modeling

    Data.gov (United States)

    Federal Laboratory Consortium — The Laboratory of Biological Modeling is defined by both its methodologies and its areas of application. We use mathematical modeling in many forms and apply it to a...

  19. High Bay Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory is a specially constructed facility with elevated (37 feet) ceilings and an overhead catwalk, and which is dedicated to research efforts in reducing...

  20. FLEXIBLE FOOD PACKAGING LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains equipment to fabricate and test prototype packages of many types and sizes (e.g., bags, pouches, trays, cartons, etc.). This equipment can...

  1. Los Alamos National Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Lab has a proud history and heritage of almost 70 years of science and innovation. The people at the Laboratory work on advanced technologies to provide the best...

  2. Geological Services Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Researchers use computed tomography (CT) scanners at NETL’s Geological Services Laboratory in Morgantown, WV, to peer into geologic core samples to determine how...

  3. Clinical Laboratory Fee Schedule

    Data.gov (United States)

    U.S. Department of Health & Human Services — Outpatient clinical laboratory services are paid based on a fee schedule in accordance with Section 1833(h) of the Social Security Act. The clinical laboratory fee...

  4. Philadelphia District Laboratory (PHI)

    Data.gov (United States)

    Federal Laboratory Consortium — Program Capabilities PHI-DO Pharmaceutical Laboratory specializes in the analyses of all forms and types of drug products.Its work involves nearly all phases of drug...

  5. Energetics Laboratory Facilities

    Data.gov (United States)

    Federal Laboratory Consortium — These energetic materials laboratories are equipped with explosion proof hoods with blow out walls for added safety, that are certified for safe handling of primary...

  6. Human Factors Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The purpose of the Human Factors Laboratory is to further the understanding of highway user needs so that those needs can be incorporated in roadway design,...

  7. Space Systems Laboratory (SSL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Space Systems Laboratory (SSL) is part of the Aerospace Engineering Department and A. James Clark School of Engineering at the University of Maryland in College...

  8. Aquatic Research Laboratory (ARL)

    Data.gov (United States)

    Federal Laboratory Consortium — Columbia River and groundwater well water sources are delivered to the Aquatic Research Laboratory (ARL), where these resources are used to conduct research on fish...

  9. Philadelphia District Laboratory (PHI)

    Data.gov (United States)

    Federal Laboratory Consortium — Program CapabilitiesPHI-DO Pharmaceutical Laboratory specializes in the analyses of all forms and types of drug products.Its work involves nearly all phases of drug...

  10. Moriah Wind System Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — Purpose: The Moriah Wind System Laboratory provides in-service support for the more than 50 U.S. Navy, U.S. Coast Guard and Military Sealift Command ships on which...

  11. Detroit District Laboratory (DET)

    Data.gov (United States)

    Federal Laboratory Consortium — Program CapabilitiesDET-DO Laboratory is equipped with the usual instrumentation necessary to perform a wide range of analyses of food, drugs and cosmetics. Program...

  12. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    Directory of Open Access Journals (Sweden)

    Annalise B. Paaby

    2016-06-01

    Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

  13. Cryptic Genetic Variation in Evolutionary Developmental Genetics.

    Science.gov (United States)

    Paaby, Annalise B; Gibson, Greg

    2016-06-13

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes-processes that cannot be fully observed in continuously varying visible traits.

  14. Reconstructing propagation networks with temporal similarity metrics

    CERN Document Server

    Liao, Hao

    2014-01-01

    Node similarity is a significant property driving the growth of real networks. In this paper, based on the observed spreading results we apply the node similarity metrics to reconstruct propagation networks. We find that the reconstruction accuracy of the similarity metrics is strongly influenced by the infection rate of the spreading process. Moreover, there is a range of infection rate in which the reconstruction accuracy of some similarity metrics drops to nearly zero. In order to improve the similarity-based reconstruction method, we finally propose a temporal similarity metric to take into account the time information of the spreading. The reconstruction results are remarkably improved with the new method.

  15. Photobiology Research Laboratory (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-06-01

    This fact sheet provides information about Photobiology Research Laboratory capabilities and applications at NREL. The photobiology group's research is in four main areas: (1) Comprehensive studies of fuel-producing photosynthetic, fermentative, and chemolithotrophic model microorganisms; (2) Characterization and engineering of redox enzymes and proteins for fuel production; (3) Genetic and pathway engineering of model organisms to improve production of hydrogen and hydrocarbon fuels; and (4) Studies of nanosystems using biological and non-biological materials in hybrid generation. NREL's photobiology research capabilities include: (1) Controlled and automated photobioreactors and fermenters for growing microorganisms under a variety of environmental conditions; (2) High-and medium-throughput screening of H{sub 2}-producing organisms; (3) Homologous and heterologous expression, purification, and biochemical/biophysical characterization of redox enzymes and proteins; (4) Qualitative and quantitative analyses of gases, metabolites, carbohydrates, lipids, and proteins; (5) Genetic and pathway engineering and development of novel genetic toolboxes; and (6) Design and spectroscopic characterization of enzyme-based biofuel cells and energy conversion nanodevices.

  16. EPA Environmental Chemistry Laboratory

    Science.gov (United States)

    1993-01-01

    The Environmental Protection Agency's (EPA) Chemistry Laboratory (ECL) is a national program laboratory specializing in residue chemistry analysis under the jurisdiction of the EPA's Office of Pesticide Programs in Washington, D.C. At Stennis Space Center, the laboratory's work supports many federal anti-pollution laws. The laboratory analyzes environmental and human samples to determine the presence and amount of agricultural chemicals and related substances. Pictured, ECL chemists analyze environmental and human samples for the presence of pesticides and other pollutants.

  17. Genetic biomarkers in hypertrophic cardiomyopathy.

    Science.gov (United States)

    Coats, Caroline J; Elliott, Perry M

    2013-08-01

    Hypertrophic cardiomyopathy is a common inherited heart muscle disorder associated with sudden cardiac death, arrhythmias and heart failure. Genetic mutations can be identified in approximately 60% of patients; these are commonest in genes that encode proteins of the cardiac sarcomere. Similar to other Mendelian diseases these mutations are characterized by incomplete penetrance and variable clinical expression. Our knowledge of this genetic diversity is rapidly evolving as high-throughput DNA sequencing technology is now used to characterize an individual patient's disease. In addition, the genomic basis of several multisystem diseases associated with a hypertrophic cardiomyopathy phenotype has been elucidated. Genetic biomarkers can be helpful in making an accurate diagnosis and in identifying relatives at risk of developing the condition. In the clinical setting, genetic testing and genetic screening should be used pragmatically with appropriate counseling. Here we review the current role of genetic biomarkers in hypertrophic cardiomyopathy, highlight recent progress in the field and discuss future challenges.

  18. Genetic specificity of face recognition.

    Science.gov (United States)

    Shakeshaft, Nicholas G; Plomin, Robert

    2015-10-13

    Specific cognitive abilities in diverse domains are typically found to be highly heritable and substantially correlated with general cognitive ability (g), both phenotypically and genetically. Recent twin studies have found the ability to memorize and recognize faces to be an exception, being similarly heritable but phenotypically substantially uncorrelated both with g and with general object recognition. However, the genetic relationships between face recognition and other abilities (the extent to which they share a common genetic etiology) cannot be determined from phenotypic associations. In this, to our knowledge, first study of the genetic associations between face recognition and other domains, 2,000 18- and 19-year-old United Kingdom twins completed tests assessing their face recognition, object recognition, and general cognitive abilities. Results confirmed the substantial heritability of face recognition (61%), and multivariate genetic analyses found that most of this genetic influence is unique and not shared with other cognitive abilities.

  19. Genetic variation and population substructure in outbred CD-1 mice: implications for genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Kimberly A Aldinger

    Full Text Available Outbred laboratory mouse populations are widely used in biomedical research. Since little is known about the degree of genetic variation present in these populations, they are not widely used for genetic studies. Commercially available outbred CD-1 mice are drawn from an extremely large breeding population that has accumulated many recombination events, which is desirable for genome-wide association studies. We therefore examined the degree of genome-wide variation within CD-1 mice to investigate their suitability for genetic studies. The CD-1 mouse genome displays patterns of linkage disequilibrium and heterogeneity similar to wild-caught mice. Population substructure and phenotypic differences were observed among CD-1 mice obtained from different breeding facilities. Differences in genetic variation among CD-1 mice from distinct facilities were similar to genetic differences detected between closely related human populations, consistent with a founder effect. This first large-scale genetic analysis of the outbred CD-1 mouse strain provides important considerations for the design and analysis of genetic studies in CD-1 mice.

  20. Los Alamos National Laboratory.

    Science.gov (United States)

    Hammel, Edward F., Jr.

    1982-01-01

    Current and post World War II scientific research at the Los Alamos National Laboratory (New Mexico) is discussed. The operation of the laboratory, the Los Alamos consultant program, and continuation education, and continuing education activities at the laboratory are also discussed. (JN)

  1. Conditional Similarity Solutions of the Boussinesq Equation

    Institute of Scientific and Technical Information of China (English)

    TANG Xiao-Yan; LIN Ji; LOU Sen-Yue

    2001-01-01

    The direct method proposed by Clarkson and Kruskal is modified to obtain some conditional similarity solutions of a nonlinear physics model. Taking the (1+ 1 )-dimensional Boussinesq equation as a simple example, six types of conditional similarity reductions are obtained.

  2. Shape Similarity Measures of Linear Entities

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The essential of feature matching technology lies in how to measure the similarity of spatial entities.Among all the possible similarity measures,the shape similarity measure is one of the most important measures because it is easy to collect the necessary parameters and it is also well matched with the human intuition.In this paper a new shape similarity measure of linear entities based on the differences of direction change along each line is presented and its effectiveness is illustrated.

  3. Similarity spectra analysis of high-performance jet aircraft noise.

    Science.gov (United States)

    Neilsen, Tracianne B; Gee, Kent L; Wall, Alan T; James, Michael M

    2013-04-01

    Noise measured in the vicinity of an F-22A Raptor has been compared to similarity spectra found previously to represent mixing noise from large-scale and fine-scale turbulent structures in laboratory-scale jet plumes. Comparisons have been made for three engine conditions using ground-based sideline microphones, which covered a large angular aperture. Even though the nozzle geometry is complex and the jet is nonideally expanded, the similarity spectra do agree with large portions of the measured spectra. Toward the sideline, the fine-scale similarity spectrum is used, while the large-scale similarity spectrum provides a good fit to the area of maximum radiation. Combinations of the two similarity spectra are shown to match the data in between those regions. Surprisingly, a combination of the two is also shown to match the data at the farthest aft angle. However, at high frequencies the degree of congruity between the similarity and the measured spectra changes with engine condition and angle. At the higher engine conditions, there is a systematically shallower measured high-frequency slope, with the largest discrepancy occurring in the regions of maximum radiation.

  4. Exploration Laboratory Analysis FY13

    Science.gov (United States)

    Krihak, Michael; Perusek, Gail P.; Fung, Paul P.; Shaw, Tianna, L.

    2013-01-01

    The Exploration Laboratory Analysis (ELA) project supports the Exploration Medical Capability (ExMC) risk, which is stated as the Risk of Inability to Adequately Treat an Ill or Injured Crew Member, and ExMC Gap 4.05: Lack of minimally invasive in-flight laboratory capabilities with limited consumables required for diagnosing identified Exploration Medical Conditions. To mitigate this risk, the availability of inflight laboratory analysis instrumentation has been identified as an essential capability in future exploration missions. Mission architecture poses constraints on equipment and procedures that will be available to treat evidence-based medical conditions according to the Space Medicine Exploration Medical Conditions List (SMEMCL), and to perform human research studies on the International Space Station (ISS) that are supported by the Human Health and Countermeasures (HHC) element. Since there are significant similarities in the research and medical operational requirements, ELA hardware development has emerged as a joint effort between ExMC and HHC. In 2012, four significant accomplishments were achieved towards the development of exploration laboratory analysis for medical diagnostics. These achievements included (i) the development of high priority analytes for research and medical operations, (ii) the development of Level 1 functional requirements and concept of operations documentation, (iii) the selection and head-to-head competition of in-flight laboratory analysis instrumentation, and (iv) the phase one completion of the Small Business Innovation Research (SBIR) projects under the topic Smart Phone Driven Blood-Based Diagnostics. To utilize resources efficiently, the associated documentation and advanced technologies were integrated into a single ELA plan that encompasses ExMC and HHC development efforts. The requirements and high priority analytes was used in the selection of the four in-flight laboratory analysis performers. Based upon the

  5. Underground laboratory in China

    Science.gov (United States)

    Chen, Heshengc

    2012-09-01

    The underground laboratories and underground experiments of particle physics in China are reviewed. The Jinping underground laboratory in the Jinping mountain of Sichuan, China is the deepest underground laboratory with horizontal access in the world. The rock overburden in the laboratory is more than 2400 m. The measured cosmic-ray flux and radioactivities of the local rock samples are very low. The high-purity germanium experiments are taking data for the direct dark-matter search. The liquid-xenon experiment is under construction. The proposal of the China National Deep Underground Laboratory with large volume at Jinping for multiple discipline research is discussed.

  6. Genetic Transformation in Citrus

    Directory of Open Access Journals (Sweden)

    Dicle Donmez

    2013-01-01

    Full Text Available Citrus is one of the world’s important fruit crops. Recently, citrus molecular genetics and biotechnology work have been accelerated in the world. Genetic transformation, a biotechnological tool, allows the release of improved cultivars with desirable characteristics in a shorter period of time and therefore may be useful in citrus breeding programs. Citrus transformation has now been achieved in a number of laboratories by various methods. Agrobacterium tumefaciens is used mainly in citrus transformation studies. Particle bombardment, electroporation, A. rhizogenes, and a new method called RNA interference are used in citrus transformation studies in addition to A. tumefaciens. In this review, we illustrate how different gene transformation methods can be employed in different citrus species.

  7. Characterizing the Laboratory Market

    Energy Technology Data Exchange (ETDEWEB)

    Shehabi, Arman; Ganeshalingam, Mohan; DeMates, Lauren; Mathew, Paul; Sartor, Dale

    2017-04-11

    Laboratories are estimated to be 3-5 times more energy intensive than typical office buildings and offer significant opportunities for energy use reductions. Although energy intensity varies widely, laboratories are generally energy intensive due to ventilation requirements, the research instruments used, and other health and safety concerns. Because the requirements of laboratory facilities differ so dramatically from those of other buildings, a clear need exists for an initiative exclusively targeting these facilities. The building stock of laboratories in the United States span different economic sectors, include governmental and academic institution, and are often defined differently by different groups. Information on laboratory buildings is often limited to a small subsection of the total building stock making aggregate estimates of the total U.S. laboratories and their energy use challenging. Previous estimates of U.S. laboratory space vary widely owing to differences in how laboratories are defined and categorized. A 2006 report on fume hoods provided an estimate of 150,000 laboratories populating the U.S. based in part on interviews of industry experts, however, a 2009 analysis of the 2003 Commercial Buildings Energy Consumption Survey (CBECS) generated an estimate of only 9,000 laboratory buildings. This report draws on multiple data sources that have been evaluated to construct an understanding of U.S. laboratories across different sizes and markets segments. This 2016 analysis is an update to draft reports released in October and December 2016.

  8. Safe genetically engineered plants

    Science.gov (United States)

    Rosellini, D.; Veronesi, F.

    2007-10-01

    The application of genetic engineering to plants has provided genetically modified plants (GMPs, or transgenic plants) that are cultivated worldwide on increasing areas. The most widespread GMPs are herbicide-resistant soybean and canola and insect-resistant corn and cotton. New GMPs that produce vaccines, pharmaceutical or industrial proteins, and fortified food are approaching the market. The techniques employed to introduce foreign genes into plants allow a quite good degree of predictability of the results, and their genome is minimally modified. However, some aspects of GMPs have raised concern: (a) control of the insertion site of the introduced DNA sequences into the plant genome and of its mutagenic effect; (b) presence of selectable marker genes conferring resistance to an antibiotic or an herbicide, linked to the useful gene; (c) insertion of undesired bacterial plasmid sequences; and (d) gene flow from transgenic plants to non-transgenic crops or wild plants. In response to public concerns, genetic engineering techniques are continuously being improved. Techniques to direct foreign gene integration into chosen genomic sites, to avoid the use of selectable genes or to remove them from the cultivated plants, to reduce the transfer of undesired bacterial sequences, and make use of alternative, safer selectable genes, are all fields of active research. In our laboratory, some of these new techniques are applied to alfalfa, an important forage plant. These emerging methods for plant genetic engineering are briefly reviewed in this work.

  9. Personalized laboratory medicine

    DEFF Research Database (Denmark)

    Pazzagli, M.; Malentacchi, F.; Mancini, I.

    2015-01-01

    Developments in "omics" are creating a paradigm shift in Laboratory Medicine leading to Personalised Medicine. This allows the increasing in diagnostics and therapeutics focused on individuals rather than populations. In order to investigate whether Laboratory Medicine is able to implement new...... diagnostic tools and expertise and commands proper state-of-the-art knowledge about Personalized Medicine and Laboratory Medicine in Europe, the joint Working Group "Personalized Laboratory Medicine" of the EFLM and ESPT societies compiled and conducted the Questionnaire "Is Laboratory Medicine ready...... for the era of Personalized Medicine?". 48 laboratories from 18 European countries participated at this survey. The answers of the participating Laboratory Medicine professionals indicate that they are aware that Personalized Medicine can represent a new and promising health model. Whereas they are aware...

  10. Personalized laboratory medicine

    DEFF Research Database (Denmark)

    Pazzagli, M.; Malentacchi, F.; Mancini, I.

    2015-01-01

    Developments in "omics" are creating a paradigm shift in Laboratory Medicine leading to Personalised Medicine. This allows the increasing in diagnostics and therapeutics focused on individuals rather than populations. In order to investigate whether Laboratory Medicine is able to implement new...... diagnostic tools and expertise and commands proper state-of-the-art knowledge about Personalized Medicine and Laboratory Medicine in Europe, the joint Working Group "Personalized Laboratory Medicine" of the EFLM and ESPT societies compiled and conducted the Questionnaire "Is Laboratory Medicine ready...... for the era of Personalized Medicine?". 48 laboratories from 18 European countries participated at this survey. The answers of the participating Laboratory Medicine professionals indicate that they are aware that Personalized Medicine can represent a new and promising health model. Whereas they are aware...

  11. Genetic testing in cardiovascular diseases.

    Science.gov (United States)

    Arndt, Anne-Karin; MacRae, Calum A

    2014-05-01

    The review is designed to outline the major developments in genetic testing in the cardiovascular arena in the past year or so. This is an exciting time in genetic testing as whole exome and whole genome approaches finally reach the clinic. These new approaches offer insight into disease causation in families in which this might previously have been inaccessible, and also bring a wide range of interpretative challenges. Among the most significant recent findings has been the extent of physiologic rare coding variation in the human genome. New disease genes have been identified through whole exome studies in neonatal arrhythmia, congenital heart disease and coronary artery disease that were simply inaccessible with other techniques. This has not only shed light on the challenges of genetic testing at this scale, but has also sharply defined the limits of prior gene-panel focused testing. As novel therapies targeting specific genetic subsets of disease become available, genetic testing will become a part of routine clinical care. The pace of change in sequencing technologies has begun to transform clinical medicine, and cardiovascular disease is no exception. The complexity of such studies emphasizes the importance of real-time communication between the genetics laboratory and genetically informed clinicians. New efforts in data and knowledge management will be central to the continued advancement of genetic testing.

  12. Stability of similarity measurements for bipartite networks

    CERN Document Server

    Liu, Jian-Guo; Pan, Xue; Guo, Qiang; Zhou, Tao

    2015-01-01

    Similarity is a fundamental measure in network analyses and machine learning algorithms, with wide applications ranging from personalized recommendation to socio-economic dynamics. We argue that an effective similarity measurement should guarantee the stability even under some information loss. With six bipartite networks, we investigate the stabilities of fifteen similarity measurements by comparing the similarity matrixes of two data samples which are randomly divided from original data sets. Results show that, the fifteen measurements can be well classified into three clusters according to their stabilities, and measurements in the same cluster have similar mathematical definitions. In addition, we develop a top-$n$-stability method for personalized recommendation, and find that the unstable similarities would recommend false information to users, and the performance of recommendation would be largely improved by using stable similarity measurements. This work provides a novel dimension to analyze and eval...

  13. Similarity analysis of the streamer zone of Blue jets

    Science.gov (United States)

    Popov, N. A.; Shneider, M. N.; Milikh, G. M.

    2016-09-01

    Multiple observations of Blue Jets (BJ) and Gigantic Blue Jets (GBJ) show that BJ and GBJ emits a fan of streamers similar to a laboratory leader. Moreover, in the exponential atmosphere those long streamers grow preferentially upward, producing a narrow cone confined by the aperture angle. It was also noticed that BJ are similar to the streamer zone of a leader (streamer corona) and the modeling studies based on the streamers fractal structure were conducted. Objective of this paper is to study the fractal dimension of the bunch of streamer channels emitted by BJ and GBJ, at different altitude and under the varying electric field. This similarity analysis has been done in three steps: first we described the dendritic structure of streamers in corona discharge applying the fractal theory. Then using this model and the data from existing laboratory experiments we obtained the fractal dimension of the branching streamer channels. Finally the model was validated by the observations of BJ available from the literature.

  14. Genetic Breakthrough

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new calf breeding technique shows promise for treating malignant tumors Chinese scientists have successfully bred a genetically altered cow capable of producing cancer-curing proteins for human beings.

  15. Mitochondrial genetics

    OpenAIRE

    Chinnery, Patrick Francis; Hudson, Gavin

    2013-01-01

    Introduction In the last 10 years the field of mitochondrial genetics has widened, shifting the focus from rare sporadic, metabolic disease to the effects of mitochondrial DNA (mtDNA) variation in a growing spectrum of human disease. The aim of this review is to guide the reader through some key concepts regarding mitochondria before introducing both classic and emerging mitochondrial disorders. Sources of data In this article, a review of the current mitochondrial genetics literature was con...

  16. The art and design of genetic screens: mouse.

    Science.gov (United States)

    Kile, Benjamin T; Hilton, Douglas J

    2005-07-01

    Humans are mammals, not bacteria or plants, yeast or nematodes, insects or fish. Mice are also mammals, but unlike gorilla and goat, fox and ferret, giraffe and jackal, they are suited perfectly to the laboratory environment and genetic experimentation. In this review, we will summarize the tools, tricks and techniques for executing forward genetic screens in the mouse and argue that this approach is now accessible to most biologists, rather than being the sole domain of large national facilities and specialized genetics laboratories.

  17. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji

    2016-07-14

    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  18. Quality Assurance Program for Molecular Medicine Laboratories

    OpenAIRE

    Hajia, M; Safadel, N; Samiee, S Mirab; Dahim, P; Anjarani, S; N Nafisi; Sohrabi, A; M Rafiee; Sabzavi, F; B Entekhabi

    2013-01-01

    Background: Molecular diagnostic methods have played and continuing to have a critical role in clinical laboratories in recent years. Therefore, standardization is an evolutionary process that needs to be upgrade with increasing scientific knowledge, improvement of the instruments and techniques. The aim of this study was to design a quality assurance program in order to have similar conditions for all medical laboratories engaging with molecular tests. Methods: We had to design a plan for al...

  19. Using the Domestic Cat in the Teaching of Genetics.

    Science.gov (United States)

    Kinnear, Judith F.

    1986-01-01

    Focuses on genetic concepts that form key components of transmission genetics and illustrates how the domestic cat can be used in the teaching of these concepts. Offers examples of how laboratory experiences with the cat can enhance student learning of genetics. (ML)

  20. Genetic counseling of the cancer survivor

    Energy Technology Data Exchange (ETDEWEB)

    Mulvihill, J.J.; Byrne, J.

    1989-02-01

    Each year, tens of thousands of persons are diagnosed with cancer, are treated, and become survivors while still in their reproductive years. Their concerns about possible germ-cell damage as a result of life-saving radiation, chemotherapy, or both are plausible, based on evidence from animal models and from somatic cell mutations in human beings. A 40-year follow-up of survivors of the atomic bomb blasts in Japan showed no detectable genetic damage and suggested that the human gonad is more resistant to radiogenic mutation than the laboratory mouse. The pooled results of studying 12 series of offspring of cancer patients showed a 4% rate of major birth defects (similar to that of the general population) and an excess of fetal loss and low birth weight in offspring of women who received abdominal radiotherapy. According to preliminary evaluation of a new National Cancer Institute collaboration with five cancer registries, offspring of survivors of childhood cancers had no more birth defects than expected and, beyond an increase in probably familial cancers in children younger than 5, no overall increase in childhood cancer. Ideally, genetic and reproductive counseling should take place as soon as cancer is diagnosed (before therapy starts) and again when pregnancy is contemplated. 28 references.