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Nature Genetics

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https://www.readbyqxmd.com/read/27933683/genetics-and-the-conservation-of-natural-populations-allozymes-to-genomes
#1
Fred W Allendorf
I consider how the study of genetic variation has influenced efforts to conserve natural populations over the last 50 years. Studies with allozymes in the 1970s provided the first estimates of the amount of genetic variation within and between natural populations at multiple loci. These early studies played an important role in developing plans to conserve species. The description of genetic variation in mitochondrial DNA in the early 1980s laid the foundation for the field of phylogeography, which provided a deeper look in time of the relationships and connectivity among populations...
December 9, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27933533/systems-genetics-as-a-tool-to-identify-master-genetic-regulators-in-complex-disease
#2
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, Enrico Petretto
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933520/mouse-genome-informatics-mgi-resources-for-mining-mouse-genetic-genomic-and-biological-data-in-support-of-primary-and-translational-research
#3
Janan T Eppig, Cynthia L Smith, Judith A Blake, Martin Ringwald, James A Kadin, Joel E Richardson, Carol J Bult
The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933342/prediction-of-nk-cell-licensing-level-in-selection-of-hematopoietic-stem-cell-donor-initial-results
#4
Marta Rogatko-Koroś, Renata Mika-Witkowska, Katarzyna Bogunia-Kubik, Barbara Wysoczańska, Emilia Jaskuła, Katarzyna Kościńska, Klaudia Nestorowicz, Joanna Dziopa, Urszula Szlendak, Sławomir Gwozdowicz, Elżbieta Graczyk-Pol, Andrzej Lange, Jacek Nowak
Natural killer (NK) cell licensing status depends on clonal expression of inhibitory killer cell immunoglobulin-like receptors (iKIR) and short term HLA environment. Licensed NK cells are more efficient in tumor killing than unlicensed NK cells. Cognate KIR-HLA pairs in hematopoietic stem cell transplant (HSCT) donor and recipient are decisive for the possible change in the NK cell licensing status after HSCT. We assessed clinical outcomes in 297 patients with lymphoproliferative or myeloproliferative malignancies, or myelodysplastic syndrome in a model with upward licensing, downward resetting, and unchanged licensing genetics status after T cell replate HSCT from unrelated donors...
December 8, 2016: Archivum Immunologiae et Therapiae Experimentalis
https://www.readbyqxmd.com/read/27933279/is-there-a-role-for-genetic-information-in-risk-assessment-and-decision-making-in-prostate-cancer
#5
Mohamadreza Nowroozi, Mohsen Ayati, Erfan Amini, Reza Mahdian, Behzad Yousefi, Amir Arbab, Mansour Jamali Zawarei, Hasan Niroomand, Hamidreza Ghorbani, Alireza Ghadian
OBJECTIVES: Prostate cancer is a neoplasm with a variable natural history and clinical behavior. There is much debate on the use of inherited genetic information in clinical application including risk assessment and treatment decisions. This study was performed to evaluate the relationship between clinical parameters of prostate cancer (PSA, Gleason score, and metastasis) and expression of NKX3.1, AMACR, TMPRSS2-ERG, ERG, and SPINK1 genes. METHODS: Newly diagnosed cases of prostate cancer were selected for this study...
November 2016: Nephro-urology Monthly
https://www.readbyqxmd.com/read/27933102/a-polysaccharide-utilization-locus-from-flavobacterium-johnsoniae-enables-conversion-of-recalcitrant-chitin
#6
Johan Larsbrink, Yongtao Zhu, Sampada S Kharade, Kurt J Kwiatkowski, Vincent G H Eijsink, Nicole M Koropatkin, Mark J McBride, Phillip B Pope
BACKGROUND: Chitin is the second most abundant polysaccharide on earth and as such a great target for bioconversion applications. The phylum Bacteroidetes is one of nature's most ubiquitous bacterial lineages and is essential in the global carbon cycle with many members being highly efficient degraders of complex carbohydrates. However, despite their specialist reputation in carbohydrate conversion, mechanisms for degrading recalcitrant crystalline polysaccharides such as chitin and cellulose are hitherto unknown...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27933061/ncr1-expression-identifies-canine-natural-killer-cell-subsets-with-phenotypic-similarity-to-human-natural-killer-cells
#7
Jennifer A Foltz, Srinivas S Somanchi, Yanwen Yang, Arianexys Aquino-Lopez, Erin E Bishop, Dean A Lee
Canines spontaneously develop many cancers similar to humans - including osteosarcoma, leukemia, and lymphoma - offering the opportunity to study immune therapies in a genetically heterogeneous and immunocompetent environment. However, a lack of antibodies recognizing canine NK cell markers has resulted in suboptimal characterization and unknown purity of NK cell products, hindering the development of canine models of NK cell adoptive immunotherapy. To this end, we generated a novel antibody to canine NCR1 (NKp46), the putative species-wide marker of NK cells, enabling purification of NK cells for further characterization...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27932930/testing-the-global-malaise-trap-program-how-well-does-the-current-barcode-reference-library-identify-flying-insects-in-germany
#8
Matthias F Geiger, Jerome Moriniere, Axel Hausmann, Gerhard Haszprunar, Wolfgang Wägele, Paul D N Hebert, Björn Rulik
BACKGROUND: Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27932927/the-avian-collection-of-the-zoological-museum-of-the-university-of-athens-zmua
#9
Gabriella Papastefanou, Anastasios Legakis, Igor Shogolev
BACKGROUND: The Zoological Museum of the University of Athens (ZMUA) was established in 1858. It is the oldest natural history museum of Greece. The museum began its operation with the acquisition of a core collection and has been expanding ever since. One of the most substantial parts of the museum's collection consists of the avian exhibits, originating from around the world. NEW INFORMATION: Today, the avian collection consists of 2,948 specimens, preserved mostly through taxidermy, along with a significant number of eggs...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27932576/mammalian-synthetic-biology-for-studying-the-cell
#10
REVIEW
Melina Mathur, Joy S Xiang, Christina D Smolke
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes...
December 8, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27932545/population-genomics-of-daphnia-pulex
#11
Michael Lynch, Ryan Gutenkunst, Matthew Ackerman, Ken Spitze, Zhiqiang Ye, Takahiro Maruki, Zhiyuan Jia
Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short (< 100 bp) distances in D. melanogaster and at long distances in D...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932544/improving-the-identification-of-phenotypic-abnormalities-and-sexual-dimorphism-in-mice-when-studying-rare-event-categorical-characteristics
#12
Natasha A Karp, Ruth Heller, Shay Yaacoby, Jacqueline K White, Yoav Benjamini
Biological research frequently involves the study of phenotyping data. Many of these studies focus on rare event categorical data, and in functional genomics typically study the presence or absence of an abnormal phenotype. With the growing interest in the role of sex, there is a need to assess the phenotype for sexual dimorphism. The identification of abnormal phenotypes for downstream research is challenged by the small sample size, the rare event nature, and the multiple testing problem, as many variables are monitored simultaneously...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932479/progress-in-understanding-the-genetics-of-calcium-containing-nephrolithiasis
#13
John A Sayer
Renal stone disease is a frequent condition, causing a huge burden on health care systems globally. Calcium-based calculi account for around 75% of renal stone disease and the incidence of these calculi is increasing, suggesting environmental and dietary factors are acting upon a preexisting genetic background. The familial nature and significant heritability of stone disease is known, and recent genetic studies have successfully identified genes that may be involved in renal stone formation. The detection of monogenic causes of renal stone disease has been made more feasible by the use of high-throughput sequencing technologies and has also facilitated the discovery of novel monogenic causes of stone disease...
December 8, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27931534/advances-in-clinical-immunology-in-2015
#14
REVIEW
Javier Chinen, Luigi D Notarangelo, William T Shearer
Advances in clinical immunology in the past year included the report of practice parameters for the diagnosis and management of primary immunodeficiencies to guide the clinician in the approach to these relatively uncommon disorders. We have learned of new gene defects causing immunodeficiency and of new phenotypes expanding the spectrum of conditions caused by genetic mutations such as a specific regulator of telomere elongation (RTEL1) mutation causing isolated natural killer cell deficiency and mutations in ras-associated RAB (RAB27) resulting in immunodeficiency without albinism...
December 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27931250/tracing-the-origin-of-disseminated-tumor-cells-in-breast-cancer-using-single-cell-sequencing
#15
Jonas Demeulemeester, Parveen Kumar, Elen K Møller, Silje Nord, David C Wedge, April Peterson, Randi R Mathiesen, Renathe Fjelldal, Masoud Zamani Esteki, Koen Theunis, Elia Fernandez Gallardo, A Jason Grundstad, Elin Borgen, Lars O Baumbusch, Anne-Lise Børresen-Dale, Kevin P White, Vessela N Kristensen, Peter Van Loo, Thierry Voet, Bjørn Naume
BACKGROUND: Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer. RESULTS: We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients...
December 9, 2016: Genome Biology
https://www.readbyqxmd.com/read/27931223/pattern-and-prognostic-value-of-cardiac-involvement-in-patients-with-late-onset-pompe-disease-a-comprehensive-cardiovascular-magnetic-resonance-approach
#16
Matthias Boentert, Anca Florian, Bianca Dräger, Peter Young, Ali Yilmaz
BACKGROUND: Pompe disease is an autosomal recessive disorder caused by deficiency of the lysosomal α-1,4-glucosidase leading to accumulation of glycogen in target tissues with progressive organ failure. While the early infantile-onset form is characterized by early severe hypertrophic cardiomyopathy with cardiac and respiratory failure, clinically relevant cardiomyopathy seems to be uncommon in patients with late-onset Pompe disease, and the prevalence and nature of myocardial abnormalities are still to be clarified...
December 7, 2016: Journal of Cardiovascular Magnetic Resonance
https://www.readbyqxmd.com/read/27931140/phylogeography-of-the-endangered-orchid-dendrobium-moniliforme-in-east-asia-inferred-from-chloroplast-dna-sequences
#17
Meirong Ye, Wei Liu, Qingyun Xue, Beiwei Hou, Jing Luo, Xiaoyu Ding
The aim of the current study was to elucidate the phylogeographic history of Dendrobium moniliforme, an endangered orchid species, based on two chloroplast DNA (cpDNA) markers (trnC-petN and trnE-trnT). One hundred and thirty-five samples were collected from 18 natural populations of D. moniliforme covering the entire range of the Sino-Japanese Floristic Region (SJFR) of East Asia. A total of 35 distinct cpDNA haplotypes were identified in these populations, of which 23 haplotypes were each present in only one sample and thus restricted to a single population...
December 8, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/27930701/natural-and-undetermined-sudden-death-value-of-post-mortem-genetic-investigation
#18
Olallo Sanchez, Oscar Campuzano, Anna Fernández-Falgueras, Georgia Sarquella-Brugada, Sergi Cesar, Irene Mademont, Jesus Mates, Alexandra Pérez-Serra, Monica Coll, Ferran Pico, Anna Iglesias, Coloma Tirón, Catarina Allegue, Esther Carro, María Ángeles Gallego, Carles Ferrer-Costa, Anna Hospital, Narcís Bardalet, Juan Carlos Borondo, Albert Vingut, Elena Arbelo, Josep Brugada, Josep Castellà, Jordi Medallo, Ramon Brugada
BACKGROUND: Sudden unexplained death may be the first manifestation of an unknown inherited cardiac disease. Current genetic technologies may enable the unraveling of an etiology and the identification of relatives at risk. The aim of our study was to define the etiology of natural deaths, younger than 50 years of age, and to investigate whether genetic defects associated with cardiac diseases could provide a potential etiology for the unexplained cases. METHODS AND FINDINGS: Our cohort included a total of 789 consecutive cases (77...
2016: PloS One
https://www.readbyqxmd.com/read/27930550/role-of-immune-cells-in-pancreatic-cancer-from-bench-to-clinical-application-an-updated-review
#19
Jae Hyuck Chang, Yongjian Jiang, Venu G Pillarisetty
BACKGROUND: Pancreatic cancer (PC) remains difficult to treat, despite the recent advances in various anticancer therapies. Immuno-inflammatory response is considered to be a major risk factor for the development of PC in addition to a combination of genetic background and environmental factors. Although patients with PC exhibit evidence of systemic immune dysfunction, the PC microenvironment is replete with immune cells. METHODS: We searched PubMed for all relevant English language articles published up to March 2016...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27930436/self-peeling-epiretinal-membrane
#20
Cem Ozgonul, Cagri G Besirli
PURPOSE: To present a self-peeling epiretinal membrane (ERM) in a patient with spontaneously improved retinal capillary hemangioma in the left eye. METHODS: We demonstrate the improvement of an untreated retinal capillary hemangioma and resolution of ERM with fundus photography, fluorescein angiography, and spectral domain optical coherence tomography. Genetic testing excluded von Hippel-Lindau disease in this patient. RESULTS: Evaluation of a patient with rheumatoid arthritis revealed retinal capillary hemangioma with retinal exudates at the temporal peripheral fundus and an ERM in the left eye...
December 7, 2016: Retinal Cases & Brief Reports
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