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https://www.readbyqxmd.com/read/28636232/a-genetic-stochastic-process-model-for-genome-wide-joint-analysis-of-biomarker-dynamics-and-disease-susceptibility-with-longitudinal-data
#1
Liang He, Ilya Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin, Alexander M Kulminski
Unraveling the underlying biological mechanisms or pathways behind the effects of genetic variations on complex diseases remains one of the major challenges in the post-GWAS (where GWAS is genome-wide association study) era. To further explore the relationship between genetic variations, biomarkers, and diseases for elucidating underlying pathological mechanism, a huge effort has been placed on examining pleiotropic and gene-environmental interaction effects. We propose a novel genetic stochastic process model (GSPM) that can be applied to GWAS and jointly investigate the genetic effects on longitudinally measured biomarkers and risks of diseases...
June 21, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28636169/a-novel-double-nucleotide-variant-in-the-ferritin-l-iron-responsive-element-in-a-finnish-patient-with-hereditary-hyperferritinaemia-cataract-syndrome
#2
Roosa-Maria Mattila, Annele Sainio, Marketta Järveläinen, Juha Pursiheimo, Hannu Järveläinen
PURPOSE: To present a novel Finnish double nucleotide variant in the iron-responsive element (IRE) of the ferritin L-chain gene (FTL) leading to hyperferritinaemia-cataract syndrome (HHCS). METHODS: Genomic DNA extracted from peripheral blood leucocytes and synthetized with three different primers flanking the IRE in the FTL 5'-untranslated region of the FTL was used in polymerase chain reaction (PCR). Thereafter, Sanger sequencing was performed on the 487-bp and 602-bp PCR amplification products with specific primers to reveal FTL IRE mutations...
June 21, 2017: Acta Ophthalmologica
https://www.readbyqxmd.com/read/28636095/suppression-or-knockout-of-saf-sam-overcomes-the-sa-mediated-hybrid-male-sterility-in-rice
#3
Yongyao Xie, Baixiao Niu, Yunming Long, Gousi Li, Jintao Tang, Yaling Zhang, Ding Ren, Yao-Guang Liu, Letian Chen
Hybrids between the indica and japonica subspecies of rice (Oryza sativa) are usually sterile, which hinders utilization of heterosis in the inter-subspecific hybrid breeding. The complex locus Sa comprises two adjacently located genes, SaF and SaM, which interact to cause abortion of pollen grains carrying the japonica allele in japonica-indica hybrids. Here we showed that silencing of SaF or SaM by RNA interference restored male fertility in indica-japonica hybrids with heterozygous Sa. We further used CRISPR/Cas9-based genome editing to knockout the SaF and SaM alleles respectively of an indica rice line to create hybrid-compatible lines...
June 21, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28636075/molecular-cloning-mrna-expression-and-biological-activity-of-the-pheromone-biosynthesis-activating-neuropeptide-pban-from-the-european-corn-borer-ostrinia-nubilalis
#4
J Fodor, G Köblös, Á Kákai, Z Kárpáti, B P Molnár, T Dankó, G Bozsik, C Bognár, G Szőcs, A Fónagy
Pheromone biosynthesis activating neuropeptide (PBAN) is a member of the pyrokinin (FXPRLamide) insect neuropeptides. Here, we report the cloning of the gene Ostnu-PBAN from the E and Z pheromone strains of the European corn borer (ECB), Ostrinia nubilalis (Lepidoptera: Crambidae), a major pest of maize. The Ostnu-PBAN genomic sequence is > 5 kb in length and consists of six exons. The deduced amino acid sequence revealed a 200-residue precursor protein including a signal peptide, a 24-amino acid (aa) diapause hormone, a 37-aa PBAN and three other FXPRLamide neuropeptides...
June 21, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28635675/co-infection-with-marek-s-disease-virus-and-reticuloendotheliosis-virus-increases-illness-severity-and-reduces-marek-s-disease-vaccine-efficacy
#5
Guo-Rong Sun, Yan-Ping Zhang, Lin-Yi Zhou, Hong-Chao Lv, Feng Zhang, Kai Li, Yu-Long Gao, Xiao-Le Qi, Hong-Yu Cui, Yong-Qiang Wang, Li Gao, Qing Pan, Xiao-Mei Wang, Chang-Jun Liu
Marek's disease virus (MDV) and reticuloendotheliosis virus (REV) cause Marek's disease (MD) and reticuloendotheliosis (RE), respectively. Co-infection with MDV and REV is common in chickens, causing serious losses to the poultry industry. However, experimental studies of such co-infection are lacking. In this study, Chinese field strains of MDV (ZW/15) and REV (JLR1501) were used as challenge viruses to evaluate the pathogenicity of co-infection and the influence of MD vaccination in chickens. Compared to the MDV-challenged group, the mortality and tumor rates increased significantly by 20...
June 21, 2017: Viruses
https://www.readbyqxmd.com/read/28635674/exploring-wound-healing-genomic-machinery-with-a-network-based-approach
#6
Francesca Vitali, Simone Marini, Martina Balli, Hanne Grosemans, Maurilio Sampaolesi, Yves A Lussier, Maria Gabriella Cusella De Angelis, Riccardo Bellazzi
The molecular mechanisms underlying tissue regeneration and wound healing are still poorly understood despite their importance. In this paper we develop a bioinformatics approach, combining biology and network theory to drive experiments for better understanding the genetic underpinnings of wound healing mechanisms and for selecting potential drug targets. We start by selecting literature-relevant genes in murine wound healing, and inferring from them a Protein-Protein Interaction (PPI) network. Then, we analyze the network to rank wound healing-related genes according to their topological properties...
June 21, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28635668/the-role-of-cccdna-in-hbv-maintenance
#7
REVIEW
Lena Allweiss, Maura Dandri
Chronic hepatitis B virus (HBV) infection continues to be a major health burden worldwide; it can cause various degrees of liver damage and is strongly associated with the development of liver cirrhosis and hepatocellular carcinoma. The molecular mechanisms determining HBV persistence are not fully understood, but these appear to be multifactorial and the unique replication strategy employed by HBV enables its maintenance in infected hepatocytes. Both the stability of the HBV genome, which forms a stable minichromosome, the covalently closed circular DNA (cccDNA) in the hepatocyte nucleus, and the inability of the immune system to resolve chronic HBV infection are believed to be key mechanisms of HBV chronicity...
June 21, 2017: Viruses
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#8
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635635/identifying-bird-remains-using-ancient-dna-barcoding
#9
Love Dalén, Vendela K Lagerholm, Johan A A Nylander, Nick Barton, Zbigniew M Bochenski, Teresa Tomek, David Rudling, Per G P Ericson, Martin Irestedt, John R Stewart
Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635630/development-of-a-high-density-snp-based-linkage-map-and-detection-of-qtl-for-%C3%AE-glucans-protein-content-grain-yield-per-spike-and-heading-time-in-durum-wheat
#10
Ilaria Marcotuli, Agata Gadaleta, Giacomo Mangini, Antonio Massimo Signorile, Silvana Addolorata Zacheo, Antonio Blanco, Rosanna Simeone, Pasqualina Colasuonno
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#11
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635598/sickle-cell-disease-tipping-the-balance-of-genomic-research-to-catalyse-discoveries-in-africa
#12
Julie Makani, Solomon F Ofori-Acquah, Furahini Tluway, Nicola Mulder, Ambroise Wonkam
No abstract text is available yet for this article.
June 17, 2017: Lancet
https://www.readbyqxmd.com/read/28635594/translation-repression-via-modulation-of-the-cytoplasmic-poly-a-binding-protein-in-the-inflammatory-response
#13
Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu
Gene expression is precisely regulated during the inflammatory response to control infection and limit the detrimental effects of inflammation. Here, we profiled global mRNA translation dynamics in the mouse primary macrophage-mediated inflammatory response and identified hundreds of differentially translated mRNAs. These mRNAs' 3'UTRs have enriched binding motifs for several RNA-binding proteins, which implies extensive translational regulatory networks. We characterized one such protein, Zfp36, as a translation repressor...
June 21, 2017: ELife
https://www.readbyqxmd.com/read/28635590/imbalance-between-innate-antiviral-and-pro-inflammatory-immune-responses-may-contribute-to-different-outcomes-involving-low-and-highly-pathogenic-avian-influenza-h5n3-infections-in-chickens
#14
John Pasick, Sandra Diederich, Yohannes Berhane, Carissa Embury-Hyatt, Wanhong Xu
In order to gain further insight into the early virus-host interactions associated with highly pathogenic avian influenza virus infections in chickens, genome-wide expression profiling of chicken lung and brain was carried out at 24 and 72 h post-inoculation (h p.i.). For this purpose two recombinant H5N3 viruses were utilized, each possessing a polybasic HA0 cleavage site but differing in pathogenicity. The original rH5N3 P0 virus, which has a low-pathogenic phenotype, was passaged six times through chickens to give rise to the derivative rH5N3 P6 virus, which is highly pathogenic (Diederich S, Berhane Y, Embury-Hyatt C, Hisanaga T, Handel K et al...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28635588/genome-sequence-variation-in-the-constricta-strain-dramatically-alters-the-protein-interaction-and-localization-map-of-potato-yellow-dwarf-virus
#15
Chanyong Jang, Renyuan Wang, Joseph Wells, Fabian Leon, Mark Farman, John Hammond, Michael M Goodin
The genome sequence of the constricta strain of Potato yellow dwarf virus (CYDV) was determined to be 12 792 nt long and organized into seven ORFs with the gene order 3'-N-X-P-Y-M-G-L-5', which encodes the nucleocapsid, phospho, movement, matrix, glyco, and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. Cloned ORFs for each gene, except L, were used to construct a protein interaction and localization map (PILM) for this virus, which shares greater than 80 % amino acid similarity in all ORFs except X and P with the sanguinolenta strain of this species (SYDV)...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28635587/ictv-virus-taxonomy-profile-ophioviridae
#16
María Laura García, Elena Dal Bó, John V da Graça, Selma Gago-Zachert, John Hammond, Pedro Moreno, Tomohide Natsuaki, Vicente Pallás, Jose A Navarro, Carina A Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis E Tzanetakis, Anna María Vaira, Martin Verbeek, Ictv Report Consortium
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots...
June 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28635542/gene-expression-study-of-mitochondrial-complex-i-in-schizophrenia-and-paranoid-personality-disorder
#17
Arvin Haghighatfard, Sarah Andalib, Mozhdeh Amini Faskhodi, Soha Sadeghi, Amir Hossein Ghaderi, Shadi Moradkhani, Jalal Rostampour, Zeinab Tabrizi, Ali Mahmoodi, Talie Karimi, Zakieh Ghadimi
OBJECTIVES: The aetiology and molecular mechanisms of schizophrenia (SCZ) and paranoid personality disorder (PPD) are not yet clarified. The present study aimed to assess the role of mitochondrial complex I and cell bioenergetic pathways in the aetiology and characteristics of SCZ and PPD. METHODS: mRNA levels of all genomic and mitochondrial genes which encode mitochondrial complex I subunits (44 genes) were assessed in blood in 634 SCZ, 340 PPD patients and 528 non-psychiatric subjects using quantitative real-time PCR, and associated comprehensive psychiatric, neurological and biochemical assessments...
February 20, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28635424/genome-wide-linkage-and-haplotype-sharing-analysis-implicates-the-mcdr3-locus-as-a-candidate-region-for-a-developmental-macular-disorder-in-association-with-digit-abnormalities
#18
Valentina Cipriani, Ambreen Kalhoro, Gavin Arno, Raquel S Silva, Nikolas Pontikos, Virginie Puech, Michelle E McClements, David M Hunt, Veronica van Heyningen, Michel Michaelides, Andrew R Webster, Anthony T Moore, Bernard Puech
BACKGROUND: Developmental macular disorders are a heterogeneous group of rare retinal conditions that can cause significant visual impairment from childhood. Among these disorders, autosomal dominant North Carolina macular dystrophy (NCMD) has been mapped to 6q16 (MCDR1) with recent support for a non-coding disease mechanism of PRDM13. A second locus on 5p15-5p13 (MCDR3) has been implicated in a similar phenotype, but the disease-causing mechanism still remains unknown. METHODS: Two families affected by a dominant developmental macular disorder that closely resembles NCMD in association with digit abnormalities were included in the study...
March 2, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28635365/nucleosomal-organization-and-dna-base-composition-patterns
#19
Alicia García, Sara González, Francisco Antequera
Nucleosomes are the basic units of chromatin. They compact the genome inside the nucleus and regulate the access of proteins to DNA. In the yeast genome, most nucleosomes occupy well-defined positions, which are maintained under many different physiological situations and genetic backgrounds. Although several short sequence elements have been described that favour or reduce the affinity between histones and DNA, the extent to which the DNA sequence affects nucleosome positioning in the genomic context remains unclear...
June 21, 2017: Nucleus
https://www.readbyqxmd.com/read/28635326/encapsulins-molecular-biology-of-the-shell
#20
Robert J Nichols, Caleb Cassidy-Amstutz, Thawatchai Chaijarasphong, David F Savage
Compartmentalization is both a fundamental principle of cellular organization and an emerging theme in prokaryotic biology. Work in the past few decades has shown that protein-based organelles called microcompartments enhance the function of encapsulated cargo proteins. More recently, the repertoire of known prokaryotic organelles has expanded beyond microcompartments to include a new class of smaller proteinaceous compartments, termed nanocompartments (also known as encapsulins). Nanocompartments are icosahedral capsids that are smaller and less complex than microcompartments...
June 21, 2017: Critical Reviews in Biochemistry and Molecular Biology
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