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Intermediate phenotypes

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https://www.readbyqxmd.com/read/28107053/diversity-and-coevolutionary-dynamics-in-high-dimensional-phenotype-spaces
#1
Michael Doebeli, Iaroslav Ispolatov
We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28105747/virulence-and-genotypes-of-white-spot-syndrome-virus-infecting-pacific-white-shrimp-litopenaeus-vannamei-in-north-western-mexico
#2
J Ramos-Paredes, J M Grijalva-Chon, J C Ibarra-Gámez
White spot syndrome virus (WSSV) has caused substantial global economic impact on aquaculture, and it has been determined that strains can vary in virulence. In this study, the effect of viral load was evaluated by infecting Litopenaeus vannamei with 10-fold serial dilution of tissue infected with strain WSSV Mx-H, and the virulence of four WSSV strains from north-western Mexico was assessed along with their variable number of tandem repeat (VNTR) genotypes in ORF75, ORF94 and ORF125. The LD50 of the Mx-H strain was a dilution dose of 10(-7...
January 20, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28105679/robust-immunoglobulin-class-switch-recombination-and-end-joining-in-parp9-deficient-mice
#3
Isabelle Robert, Léa Gaudot, Jose Yelamos, Aurélia Noll, Heng-Kuan Wong, Françoise Dantzer, Valérie Schreiber, Bernardo Reina-San-Martin
To mount highly specific and adapted immune responses, B lymphocytes assemble and diversify their antibody repertoire through mechanisms involving the formation of programmed DNA damage. Immunoglobulin class switch recombination (CSR) is triggered by DNA lesions induced by activation-induced cytidine deaminase, which are processed to double-stranded DNA break (DSB) intermediates. These DSBs activate the cellular DNA damage response and enroll numerous DNA repair factors, involving Poly(ADP-ribose) polymerases Parp1, Parp2 and Parp3 to promote appropriate DNA repair and efficient long-range recombination...
January 20, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28104410/the-drd2-rs1076560-polymorphism-and-schizophrenia-related-intermediate-phenotypes-a-systematic-review-and-meta-analysis
#4
REVIEW
Jurjen J Luykx, Juliette L Broersen, Max de Leeuw
Intermediate phenotypes may contribute to elucidate the genetic determinants of schizophrenia. A regulatory dopamine 2-receptor gene (DRD2) polymorphism (rs1076560; G > T) has been identified as a genetic risk factor for schizophrenia. Studies report conflicting results on its involvement in schizophrenia intermediate phenotypes and no systematic review on this topic has been published. Therefore, we aimed to assess whether this polymorphism is implicated in schizophrenia intermediate phenotypes by performing a systematic review and meta-analysis...
January 16, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28101535/the-case-for-adopting-the-species-complex-nomenclature-for-the-etiologic-agents-of-cryptococcosis
#5
Kyung J Kwon-Chung, John E Bennett, Brian L Wickes, Wieland Meyer, Christina A Cuomo, Kurt R Wollenburg, Tihana A Bicanic, Elizabeth Castañeda, Yun C Chang, Jianghan Chen, Massimo Cogliati, Françoise Dromer, David Ellis, Scott G Filler, Matthew C Fisher, Thomas S Harrison, Steven M Holland, Shigeru Kohno, James W Kronstad, Marcia Lazera, Stuart M Levitz, Michail S Lionakis, Robin C May, Popchai Ngamskulrongroj, Peter G Pappas, John R Perfect, Volker Rickerts, Tania C Sorrell, Thomas J Walsh, Peter R Williamson, Jianping Xu, Adrian M Zelazny, Arturo Casadevall
Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species...
January 2017: MSphere
https://www.readbyqxmd.com/read/28097061/contrasting-molecular-and-morphological-evidence-for-the-identification-of-an-anomalous-buteo-a-cautionary-tale-for-hybrid-diagnosis
#6
William S Clark, Spencer C Galen, Joshua M Hull, Megan A Mayo, Christopher C Witt
An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus;). It is now a specimen in the Museum of Wildlife and Fisheries Biology (WFB 4816) at the University of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus) and Red-shouldered Hawk (ssp elegans), leading us to hypothesize that the bird was a hybrid...
2017: PeerJ
https://www.readbyqxmd.com/read/28096473/vimentin-intermediate-filaments-control-actin-stress-fiber-assembly-through-gef-h1-and-rhoa
#7
Yaming Jiu, Johan Peränen, Niccole Schaible, Fang Cheng, John E Eriksson, Ramaswamy Krishnan, Pekka Lappalainen
The actin and intermediate filament cytoskeleltons contribute to numerous cellular processes, including morphogenesis, cytokinesis, and migration. These two cytoskeletal systems associate with each other, but the underlying mechanisms are incompletely understood. Here,we show that inactivation of vimentin leads to increased actin stress fiber assembly and contractility, and consequent elevation of myosin light chain phosphorylation and stabilization of tropomyosin-4.2. The vimentin knockout phenotypes can be rescued by re-expression of wild-type vimentin, but not by the non-filamentous 'unit length form' vimentin, demonstrating that intact vimentin intermediate filaments are required to facilitate the effects on the actin cytoskeleton...
January 17, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28096346/conserved-gtpase-lepa-elongation-factor-4-functions-in-biogenesis-of-the-30s-subunit-of-the-70s-ribosome
#8
Michelle R Gibbs, Kyung-Mee Moon, Menglin Chen, Rohan Balakrishnan, Leonard J Foster, Kurt Fredrick
The physiological role of LepA, a paralog of EF-G found in all bacteria, has been a mystery for decades. Here, we show that LepA functions in ribosome biogenesis. In cells lacking LepA, immature 30S particles accumulate. Four proteins are specifically underrepresented in these particles-S3, S10, S14, and S21-all of which bind late in the assembly process and contribute to the folding of the 3' domain of 16S rRNA. Processing of 16S rRNA is also delayed in the mutant strain, as indicated by increased levels of precursor 17S rRNA in assembly intermediates...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094999/specificity-of-executive-functioning-and-processing-speed-problems-in-common-psychopathology
#9
Joel T Nigg, Jennifer M Jester, Gillian M Stavro, Ka I Ip, Leon I Puttler, Robert A Zucker
OBJECTIVE: Interest continues in neuropsychological measures as cross-disorder intermediate phenotypes in understanding psychopathology. A central question concerns their specificity versus generalizability to particular forms of psychopathology, particularly for executive functioning (EF) and response speed. Three conceptual models examining these relationships were tested to clarify this picture at different levels in the diagnostic hierarchy. METHOD: Participants (total n = 641, age 18-60) yielded complete structured diagnostic interviews and a neuropsychological test battery comprising measures of executive function, processing speed, and IQ...
January 16, 2017: Neuropsychology
https://www.readbyqxmd.com/read/28094815/drd2-co-expression-network-and-a-related-polygenic-index-predict-imaging-behavioral-and-clinical-phenotypes-linked-to-schizophrenia
#10
G Pergola, P Di Carlo, E D'Ambrosio, B Gelao, L Fazio, M Papalino, A Monda, G Scozia, B Pietrangelo, M Attrotto, J A Apud, Q Chen, V S Mattay, A Rampino, G Caforio, D R Weinberger, G Blasi, A Bertolino
Genetic risk for schizophrenia (SCZ) is determined by many genetic loci whose compound biological effects are difficult to determine. We hypothesized that co-expression pathways of SCZ risk genes are associated with system-level brain function and clinical phenotypes of SCZ. We examined genetic variants related to the dopamine D2 receptor gene DRD2 co-expression pathway and associated them with working memory (WM) behavior, the related brain activity and treatment response. Using two independent post-mortem prefrontal messenger RNA (mRNA) data sets (total N=249), we identified a DRD2 co-expression pathway enriched for SCZ risk genes...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28092050/microwestern-arrays-for-systems-level-analysis-of-sh2-domain-containing-proteins
#11
Mark F Ciaccio, Richard B Jones
The Microwestern Array (MWA) method combines the scalability and miniaturization afforded by the Reverse Phase Lysate Array (RPLA) approach with the electrophoretic separation characteristic of the Western blot. This technology emulates the creation of an array of small Western blots on a single sheet of nitrocellulose allowing for the sensitive and quantitative measurement of hundreds of proteins from hundreds of cell lysates with minimal cost and maximal accuracy, precision, and reproducibility. The MWA is a versatile technology that can be easily configured for purposes such as antibody screening, cell signaling network inference, protein modification/phenotype regression analysis, and genomic/proteomic relationships...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28089668/ebio-does-not-induce-cardiomyogenesis-in-human-pluripotent-stem-cells-but-modulates-cardiac-subtype-enrichment-by-lineage-selective-survival
#12
Monica Jara-Avaca, Henning Kempf, Michael Rückert, Diana Robles-Diaz, Annika Franke, Jeanne de la Roche, Martin Fischer, Daniela Malan, Philipp Sasse, Wladimir Solodenko, Gerald Dräger, Andreas Kirschning, Ulrich Martin, Robert Zweigerdt
Subtype-specific human cardiomyocytes (CMs) are valuable for basic and applied research. Induction of cardiomyogenesis and enrichment of nodal-like CMs was described for mouse pluripotent stem cells (mPSCs) in response to 1-ethyl-2-benzimidazolinone (EBIO), a chemical modulator of small-/intermediate-conductance Ca(2+)-activated potassium channels (SKs 1-4). Investigating EBIO in human pluripotent stem cells (PSCs), we have applied three independent differentiation protocols of low to high cardiomyogenic efficiency...
January 4, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28089652/hippocampal-prefrontal-connectivity-as-a-translational-phenotype-for-schizophrenia
#13
REVIEW
Florian Bähner, Andreas Meyer-Lindenberg
Finding novel biological targets in psychiatry has been difficult, partly because current diagnostic categories are not defined by pathophysiology and difficult to model in animals. The study of species-conserved systems-level mechanisms implicated in psychiatric disease could be a promising strategy to address some of these difficulties. Altered hippocampal-prefrontal (HC-PFC) connectivity during working memory (WM) processing is a candidate for such a translational phenotype as it has been repeatedly associated with impaired cognition in schizophrenia patients and animal models for psychiatric risk factors...
January 12, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28088513/an-immunogram-for-the-cancer-immunity-cycle-towards-personalized-immunotherapy-of-lung-cancer
#14
Takahiro Karasaki, Kazuhiro Nagayama, Hideki Kuwano, Jun-Ichi Nitadori, Masaaki Sato, Masaki Anraku, Akihiro Hosoi, Hirokazu Matsushita, Yasuyuki Morishita, Kosuke Kashiwabara, Masaki Takazawa, Osamu Ohara, Kazuhiro Kakimi, Jun Nakajima
INTRODUCTION: The interaction of immune cells and cancer cells shapes the immunosuppressive tumor microenvironment. For successful cancer immunotherapy, comprehensive knowledge of anti-tumor immunity as a dynamic spacio-temporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle using next-generation sequencing. METHODS: Whole-exome sequencing and RNA-Seq was performed in 20 non-small cell lung cancer patients (12 adenocarcinoma, 7 squamous cell carcinoma, and 1 large cell neuroendocrine carcinoma)...
January 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28088345/phenotypic-characterization-of-perivascular-myoid-cell-neoplasms-using-myosin-1b-a-newly-identified-human-pericyte-marker
#15
Shiori Meguro, Taisuke Akamatsu, Sayomi Matsushima, Isao Kosugi, Hideya Kawasaki, Yosifumi Arai, Satoshi Baba, Takashi Tsuchida, Youji Shido, Takafumi Suda, Toshihide Iwashita
Our aim was to identify pericyte-specific markers for the analysis of formalin-fixed paraffin-embedded (FFPE) human tissue samples, and to characterize perivascular myoid cell neoplasms phenotypically. Previously identified pericyte markers failed to distinguish pericytes from other cellular types, such as vascular smooth muscle cells (vSMCs) and fibroblasts, in immunohistochemical (IHC) analysis. However, we compared gene expression profiles between pericytes, vSMCs, and fibroblasts, and performed human skin vasculature IHC analysis, which led to the identification of myosin 1B (MYO1B) as a novel pericyte marker...
January 11, 2017: Human Pathology
https://www.readbyqxmd.com/read/28088216/immunohistochemical-features-of-giant-cell-ependymoma-of-the-filum-terminale-with-unusual-clinical-and-radiological-presentation
#16
Fernando Candanedo-Gonzalez, Cindy Sharon Ortiz-Arce, Samuel Rosales-Perez, Ana Lilia Remirez-Castellanos, Candelaria Cordova-Uscanga, Armando Gamboa-Dominguez
BACKGROUND: Giant cell ependymoma of the filum terminale is a rare variant, generally manifested as a well-circunscribed intradural mass with an indolent biological behavior. CASE PRESENTATION: We describe the case of a 48-year-old Mexican female who non-relevant past medical history, that developed a GCE of the filum terminale. Magnetic resonance imaging and computed tomography revealed the presence of an intra-axial tumor extending from L3 to L5 with extra-medullary invasion...
January 14, 2017: Diagnostic Pathology
https://www.readbyqxmd.com/read/28088192/nucleotide-diversity-inflation-as-a-genome-wide-response-to-experimental-lifespan-extension-in-drosophila-melanogaster
#17
Pawel Michalak, Lin Kang, Pernille M Sarup, Mads F Schou, Volker Loeschcke
BACKGROUND: Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations. RESULTS: While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087677/incorporating-persistent-pain-in-phenotypic-frailty-measurement-and-prediction-of-adverse-health-outcomes
#18
Matthew C Lohman, Karen L Whiteman, Rebecca L Greenberg, Martha L Bruce
BACKGROUND: Frailty, a syndrome of physiological deficits, is prevalent among older adults and predicts elevated risk of adverse health outcomes. Although persistent pain predicts similar risk, it is seldom considered in frailty measurement. This article evaluated the construct and predictive validity of including persistent pain in phenotypic frailty measurement. METHODS: Frailty and persistent pain were operationalized using data from the Health and Retirement Study (2006-2012 waves)...
February 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28087438/dopa-responsive-dystonia-in-chinese-patients-including-a-novel-heterozygous-mutation-in-the-gch1-gene-with-an-intermediate-phenotype-and-one-case-of-prenatal-diagnosis
#19
Wen Zhang, Zhizi Zhou, Xiuzhen Li, Yonglan Huang, Taolin Li, Yunting Lin, Yongxian Shao, Hao Hu, Hongsheng Liu, Li Liu
Dopa-responsive dystonia (DRD) is a rare inherited disorder characterized by childhood-onset dystonia with diurnal fluctuation and dramatic response to levodopa. DRD is caused by the mutations in the genes encoding the enzymes involved in the dopamine and tetrahydrobiopterin (BH4) biosynthesis, including the GTP cyclohydrolase 1 (GCH1) gene and the tyrosine hydroxylase (TH) gene. In order to improve the diagnosis and expand the knowledge of the disease, we collected and analyzed relevant data of clinical diagnosis and molecular mutational analysis in five Chinese patients with DRD...
January 10, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28087064/effect-of-cyp2d6-polymorphisms-on-the-pharmacokinetics-of-propafenone-and-its-two-main-metabolites
#20
Mohammad-Reza Rouini, Minoo Afshar
AIM OF THE STUDY: Propafenone (PPF) is an antiarrhythmic drug, metabolized mainly by CYP2D6 to 5-hydroxypropafenone (5OH-PPF) and by CYP3A4 to norpropafenone (NOR-PPF). CYP2D6 shows a high degree of genetic polymorphism which is associated with diminished antiarrhythmic efficacy or cardiac seizures/cardiotoxicity. This study aimed to investigate the effect of the CYP2D6 polymorphism on the pharmacokinetics of PPF and its two main metabolites. The usefulness of PPF/5OH-PPF ratio for CYP2D6 phenotyping in healthy adults was also evaluated...
December 19, 2016: Thérapie
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