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  • 1
    In: Bioinformatics, 2014, Vol. 30(23), pp.3421-3423
    Description: Summary: RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. To draw biological conclusions based on RNA-Seq data, several steps, some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes and RNA immunoprecipitated with proteins, not only from bacteria but also from eukaryotes and archaea. Availability and implementation: READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849). Contact: cynthia.sharma@uni-wuerzburg.de and konrad.foerstner@uni-wuerzburg.de
    Keywords: Bacteria ; Computation ; Source Code ; Ribonucleic Acids ; Biological ; Licenses ; Tools ; Line Interfaces ; Life and Medical Sciences (Ci);
    ISSN: 1367-4803
    E-ISSN: 1460-2059
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  • 2
    In: The American Journal of Clinical Nutrition, 2018, Vol. 107(3), pp.484-494
    Description: Scientific progress depends on the quality and credibility of research methods. As discourse on rigor, transparency, and reproducibility joins the cacophony of nutrition information and misinformation in mass media, buttressing the real and perceived reliability of nutrition science is more important than ever. This broad topic was the focus of a 2016 plenary session, “Scientific Rigor and Competing Interests in the Nutrition Research Landscape.” This article summarizes and expands on this session in an effort to increase understanding and dialogue with regard to factors that limit the real and perceived reliability of nutrition science and steps that can be taken to mitigate those factors. The end goal is to both earn and merit greater trust in nutrition science by both the scientific community and the general public. The authors offer suggestions in each of the domains of education and training, communications, research conduct, and procedures and policies to help achieve this goal. The authors emphasize the need for adequate funding to support these efforts toward greater rigor and transparency, which will be resource demanding and may require either increased research funding or the recognition that a greater proportion of research funding may need to be allocated to these tasks.
    Keywords: Research Methods ; Scientific Rigor ; Nutrition ; Conflict Of Interests ; Transparency, Trust
    ISSN: 0002-9165
    E-ISSN: 1938-3207
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  • 3
    In: Environmental Entomology, 2019, Vol. 48(1), pp.12-21
    Description: To date, regulatory pesticide risk assessments have relied on the honey bee ( Apis mellifera L.) (Hymenoptera: Apidae) as a surrogate test species for estimating the risk of pesticide exposure to all bee species. However, honey bees and non- Apis bees may differ in their susceptibility and exposure to pesticides. In 2017, a workshop (‘Pesticide Exposure Assessment Paradigm for Non- Apis Bees’) was held to assess if honey bee risk assessment frameworks are reflective of non- Apis bee pesticide exposure. In this article, we summarize the workshop discussions on bumble bees ( Bombus spp.). We review the life history and foraging behavior of bumble bees and honey bees and discuss how these traits may influence routes and levels of exposure for both taxa. Overall, the major pesticide exposure routes for bumble bees and honey bees are similar; however, bumble bees face additional exposure routes (direct exposure of foraging queens and exposure of larvae and adults to soil residues). Furthermore, bumble bees may receive comparatively higher pesticide doses via contact or oral exposure. We conclude that honey bee pesticide risk assessments may not always be protective of bumble bees, especially queens, in terms of exposure. Data needed to reliably quantify pesticide exposure for bumble bees (e.g., food consumption rates, soil residue levels) are lacking. Addressing these knowledge gaps will be crucial before bumble bee exposure can be incorporated into the pesticide risk assessment process. Because bumble bees exhibit appreciable interspecific variation in colony and behavioral characteristics, data relevant to pesticide exposure should be generated for multiple species.
    Keywords: Bumble Bee ; Honey Bee ; Pesticide Exposure ; Risk Assessment
    ISSN: 0046-225X
    E-ISSN: 1938-2936
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  • 4
    In: Human Molecular Genetics, 2002, Vol.11(18), pp.2175-2187
    Description: Friedreich ataxia is commonly caused by large expansions of a GAA triplet-repeat (GAA-TR) sequence in the first intron of the FRDA gene. We used small-pool PCR to analyze somatic variability among 7190 individual FRDA molecules from peripheral blood DNA of subjects carrying 12 different expanded alleles, ranging in size from 241 to 1105 triplets. Expanded alleles showed a length-dependent increase in somatic variability, with mutation loads ranging from 47 to 78. We noted a strong contraction bias among long alleles (500 triplets), which showed a 4-fold higher frequency of large contractions versus expansions. Some contractions were very large; of all somatic mutations scored, 5 involved contractions of 50 of the original allele length, and 0.29 involved complete reversion to the normalpremutation length (60 triplets). These observations contrast sharply with the strong expansion bias seen in expanded CTG triplet repeats in myotonic dystrophy. No somatic variability was detected in 6000 individual FRDA molecules analyzed from 15 normal alleles (825 triplets). A premutation allele with 44 uninterrupted GAA repeats was found to be unstable, ranging in size from 6 to 113 triplets, thus establishing the threshold for somatic instability between 26 and 44 GAA triplets. Analysis of an additional 7850 FRDA molecules from serially passaged lymphoblastoid cell lines carrying nine expanded alleles (132933 triplets) showed very low mutation loads, ranging from 0 to 6.2. Our data indicate that expanded GAA-TR alleles in Friedreich ataxia are highly mutable and have a natural tendency to contract in vivo , and that these properties depend on multiple factors, including DNA sequence, triplet-repeat length and unknown cell-type-specific factors.
    Keywords: Medicine ; Biology;
    ISSN: 0964-6906
    E-ISSN: 14602083
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