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Genomics

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https://www.readbyqxmd.com/read/28088090/degradation-in-forensic-trace-dna-samples-explored-by-massively-parallel-sequencing
#1
Eirik Nataas Hanssen, Robert Lyle, Thore Egeland, Peter Gill
Routine forensic analysis using STRs will fail if the DNA is too degraded. The DNA degradation process in biological stain material is not well understood. In this study we sequenced old semen and blood stains by massively parallel sequencing. The sequence data coverage was used to measure degradation across the genome. The results supported the contention that degradation is uniform across the genome, showing no evidence of regions with increased or decreased resistance towards degradation. Thus the lack of genetic regions robust to degradation removes the possibility of using such regions to further optimize analysis performance for degraded DNA...
January 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28088031/the-timing-of-zygotic-genome-activation
#2
REVIEW
Máté Pálfy, Shai R Joseph, Nadine L Vastenhouw
After fertilization, the embryonic genome is inactive until transcription is initiated during the maternal-to-zygotic transition. How the onset of transcription is regulated in a precisely timed manner, however, is a long standing question in biology. Several mechanisms have been shown to contribute to the temporal regulation of genome activation but none of them can fully explain the general absence of transcription as well the gene specific onset that follows. Here we review the work that has been done toward elucidating the mechanisms underlying the temporal regulation of transcription in embryos...
January 11, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28088028/role-of-small-rnas-in-epigenetic-reprogramming-during-plant-sexual-reproduction
#3
REVIEW
German Martinez, Claudia Köhler
Sexual reproduction, the formation of a new individual from specialized reproductive cells after fertilization, involves the precise orchestration of different developmental and genomic processes. These processes are to a large extent governed by small RNAs (sRNAs) that either belong to the class of micro RNAs (miRNAs) or small-interfering RNAs (siRNAs). The latter are derived from transposable elements (TEs) and involved in genome defense and transgenerational inheritance of heterochromatin identity, ensuring genome stability...
January 11, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28088010/challenges-and-opportunities-for-improving-food-quality-and-nutrition-through-plant-biotechnology
#4
REVIEW
David Francis, John J Finer, Erich Grotewold
Plant biotechnology has been around since the advent of humankind, resulting in tremendous improvements in plant cultivation through crop domestication, breeding and selection. The emergence of transgenic approaches involving the introduction of defined DNA sequences into plants by humans has rapidly changed the surface of our planet by further expanding the gene pool used by plant breeders for plant improvement. Transgenic approaches in food plants have raised concerns on the merits, social implications, ecological risks and true benefits of plant biotechnology...
January 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28087944/laboratory-diagnosis-and-susceptibility-testing-for-mycobacterium-tuberculosis
#5
Gary W Procop
The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of Mycobacterium tuberculosis. Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087943/rna-interference-in-fungi-retention-and-loss
#6
Francisco E Nicolás, Victoriano Garre
RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in Neurospora crassa, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087931/evolution-of-cell-autonomous-effector-mechanisms-in-macrophages-versus-non-immune-cells
#7
Ryan G Gaudet, Clinton J Bradfield, John D MacMicking
Specialized adaptations for killing microbes are synonymous with phagocytic cells including macrophages, monocytes, inflammatory neutrophils, and eosinophils. Recent genome sequencing of extant species, however, reveals that analogous antimicrobial machineries exist in certain non-immune cells and also within species that ostensibly lack a well-defined immune system. Here we probe the evolutionary record for clues about the ancient and diverse phylogenetic origins of macrophage killing mechanisms and how some of their properties are shared with cells outside the traditional bounds of immunity in higher vertebrates such as mammals...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087927/genome-wide-approaches-to-defining-macrophage-identity-and-function
#8
Gregory J Fonseca, Jason S Seidman, Christopher K Glass
Macrophages play essential roles in the response to injury and infection and contribute to the development and/or homeostasis of the various tissues they reside in. Conversely, macrophages also influence the pathogenesis of metabolic, neurodegenerative, and neoplastic diseases. Mechanisms that contribute to the phenotypic diversity of macrophages in health and disease remain poorly understood. Here we review the recent application of genome-wide approaches to characterize the transcriptomes and epigenetic landscapes of tissue-resident macrophages...
October 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087895/crohn-disease-risk-prediction-best-practices-and-pitfalls-with-exome-data
#9
Manuel Giollo, David T Jones, Marco Carraro, Emanuela Leonardi, Carlo Ferrari, Silvio C E Tosatto
The Critical Assessment of Genome Interpretation (CAGI) experiment is the first attempt to evaluate the state-of-the-art in genetic data interpretation. Among the proposed challenges, Crohn disease (CD) risk prediction has become the most classic problem spanning three editions. The scientific question is very hard: can anybody assess the risk to develop CD given the exome data alone? This is one of the ultimate goals of genetic analysis, which motivated most CAGI participants to look for powerful new methods...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#10
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087820/emerging-functional-roles-of-nuclear-receptors-in-breast-cancer
#11
Tram B Doan, Justine Graham, Christine Clarke
Nuclear receptors (NRs) have been targets of intensive drug development for decades due to their roles as key regulators of multiple developmental, physiological and disease processes. In breast cancer, expression of the estrogen and progesterone receptor remains clinically important in predicting prognosis and determining therapeutic strategies. More recently, there is growing evidence supporting the involvement of multiple nuclear receptors other than the estrogen and progesterone receptors, in the regulation of various processes important to the initiation and progression of breast cancer...
January 13, 2017: Journal of Molecular Endocrinology
https://www.readbyqxmd.com/read/28087781/deleterious-variants-in-asian-rice-and-the-potential-cost-of-domestication
#12
Qingpo Liu, Yongfeng Zhou, Peter L Morrell, Brandon S Gaut
Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a 'cost of domestication'. Here we investigated the numbers and frequencies of deleterious variants in Asian rice (O. sativa), focusing on two varieties (japonica and indica) and their wild relative (O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087780/oncogenes-without-a-neighboring-tumor-suppressor-gene-are-more-prone-to-amplification
#13
William K K Wu, Xiangchun Li, Xiansong Wang, Rudin Z W Dai, Alfred S L Cheng, Maggie H T Wang, Thomas Kwong, Tai C Chow, Jun Yu, Matthew T V Chan, Sunny H Wong
Focal copy number gains or losses are important genomic hallmarks of cancer. The genomic distribution of oncogenes and tumor-suppressor genes (TSG) in relation to focal copy number aberrations is unclear. Our analysis revealed that the mean distance of TSGs from oncogenes was significantly shorter than that of non-cancer genes, suggesting that oncogenes and TSGs tend to be in close physical proximity in the human genome. Such relationship was conserved in mouse and drosophila. Pan-cancer analysis using data from The Cancer Genome Atlas indicated that oncogenes without a nearby TSG are more prone to amplification...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087779/genomics-of-parallel-experimental-evolution-in-drosophila
#14
J L Graves, K L Hertweck, M A Phillips, M V Han, L G Cabral, T T Barter, L F Greer, M K Burke, L D Mueller, M R Rose
What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly forty-year laboratory radiation featuring three selection regimes, each shared by ten populations for up to 837 generations, with moderately large effective population sizes. Each of three sets of ten populations that shared a selection regime consist of five populations that have long been maintained under that selection regime, paired with five populations that had only recently been subjected to that selection regime...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087778/no-evidence-for-phylostratigraphic-bias-impacting-inferences-on-patterns-of-gene-emergence-and-evolution
#15
Tomislav Domazet-Lošo, Anne-Ruxandra Carvunis, M Mar Albà, Martin Sebastijan Šestak, Robert Bakarić, Rafik Neme, Diethard Tautz
Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087777/genome-sequencing-reveals-the-origin-of-the-allotetraploid-arabidopsis-suecica
#16
Polina Yu Novikova, Takashi Tsuchimatsu, Samson Simon, Viktoria Nizhynska, Viktor Voronin, Robin Burns, Olga M Fedorenko, Svante Holm, Torbjörn Säll, Elisa Prat, William Marande, Vincent Castric, Magnus Nordborg
Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual - a bona fide speciation event. The extent to which this happens is not known...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087776/seed-plant-specific-gene-lineages-involved-in-carpel-development
#17
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot Arabidopsis thaliana To unravel the evolution of the carpel GRN and to discriminate between "early" and "late" steps in carpel evolution we calculated thorough phylogeny reconstructions based on sequenced genomes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087772/possible-roles-of-new-mutations-shared-by-asian-and-american-zika-viruses
#18
Shozo Yokoyama, William T Starmer
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 x 10(-3)/nucleotide site/year and subsequently increased significantly in most of its descendants...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087771/genome-wide-convergence-during-evolution-of-mangroves-from-woody-plants
#19
Shaohua Xu, Ziwen He, Zixiao Guo, Zhang Zhang, Gerald J Wyckoff, Anthony Greenberg, Chung-I Wu, Suhua Shi
When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia and other stressors in the new habitat might have affected both genomic features and protein structures...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087770/article-discoveries
#20
Anke Konrad, Owen Thompson, Robert H Waterston, Donald G Moerman, Peter D Keightley, Ulfar Bergthorsson, Vaishali Katju
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10 and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection...
January 12, 2017: Molecular Biology and Evolution
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