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https://www.readbyqxmd.com/read/29474985/optimal-reference-gene-selection-for-expression-studies-in-human-reticulocytes
#1
Anu Aggarwal, Manu Jamwal, Ganesh Kumar V, Prashant Sharma, Man Updesh Singh Sachdeva, Deepak Bansal, Pankaj Malhotra, Reena Das
Reference genes are indispensable for normalizing mRNA levels across samples in real-time quantitative PCR. Their expression levels vary under different experimental conditions and due to several inherent characteristics. Appropriate reference gene selection is thus critical for gene-expression studies. This study aimed at selecting optimal reference genes for gene-expression analysis of reticulocytes and validating them in hereditary spherocytosis (HS) and β-thalassemia intermedia (βTI) patients. Seven reference genes (PGK1, MPP1, HPRT1, ACTB, GAPDH, RN18S1, and SDHA) were selected from published literature...
February 20, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29474581/thermopriming-triggers-splicing-memory-in-arabidopsis
#2
Yu Ling, Natalia Serrano, Ge Gao, Mohamed Atia, Morad Mokhtar, Yong H Woo, Jeremie Bazin, Alaguraj Veluchamy, Moussa Benhamed, Martin Crespi, Christoph Gehring, A S N Reddy, Magdy M Mahfouz
Abiotic and biotic stresses limit crop productivity. Exposure to a non-lethal stress, referred to as priming, can allow plants to survive subsequent and otherwise lethal conditions; the priming effect persists even after a prolonged stress-free period. However, the molecular mechanisms underlying priming are not fully understood. Here, we investigated the molecular basis of heat shock memory and the role of priming in Arabidopsisthaliana. Comprehensive analysis of transcriptome-wide changes in gene expression and alternative splicing in primed and non-primed plants revealed that alternative splicing functions as a novel component of heat shock memory...
February 21, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29473327/epidemiological-investigation-of-pseudorabies-in-shandong-province-from-2013-to-2016
#3
J Gu, D Hu, T Peng, Y Wang, Z Ma, Z Liu, F Meng, Y Shang, S Liu, Y Xiao
In late 2011, a variant pseudorabies virus (vPRV) emerged in Bartha-K61-vaccinated pig herds, resulting in high morbidity and mortality of piglets in China. Since 2013, the autopsy lesions, histological examinations, virus isolation, phylogenetic analysis and selection pressure analysis of the gE gene of vPRV were recorded for 395 clinical cases, and 5,033 pig serum samples were detected by PRV gE-coated enzyme-linked immunosorbent assay. The major clinical symptoms were abortion in pregnant sows, fatal neurological signs in piglets and respiratory disease in growing pigs...
February 22, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29473046/duplications-at-19q13-33-in-patients-with-neurodevelopmental-disorders
#4
Eduardo Pérez-Palma, Elmo Saarentaus, Marie Ravoet, Giancarlo V De Ferrari, Peter Nürnberg, Bertrand Isidor, Bernd A Neubauer, Dennis Lal
Objective: After the recent publication of the first patients with disease-associated missense variants in the GRIN2D gene, we evaluate the effect of copy number variants (CNVs) overlapping this gene toward the presentation of neurodevelopmental disorders (NDDs). Methods: We explored ClinVar (number of CNVs = 50,794) and DECIPHER (number of CNVs = 28,085) clinical databases of genomic variations for patients with copy number changes overlapping the GRIN2D gene at the 19q13...
February 2018: Neurology. Genetics
https://www.readbyqxmd.com/read/29472760/genetic-diversity-and-functional-analysis-of-sigma-factors-in-enterobacter-cloacae-complex-resourced-from-various-niche
#5
Farah Nazir, Muhammad Ibrahim, Ghunva Zaman, Annam Hussain, Asma Muhammad Yar, Zhu Bo
Sigma factors are bacterial transcription factors that bind the core RNA polymerase and direct transcription initiation at a specific promoter site. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions and selectively increase the transcription of those genes. Here, we attempt to identify sigma factors in 5 genomes belonging to the Enterobacter cloacae complex (Ecc), a group of gram-negative bacteria that are important nosocomial pathogens. This process includes the identification of orthologous sequences, conserved motifs, domains, families, phylogenetic profiles, and protein-protein associations of these components...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29472617/whole-genome-diversity-of-inherited-chromosomally-integrated-hhv-6-derived-from-healthy-individuals-of-diverse-geographic-origin
#6
Marco Telford, Arcadi Navarro, Gabriel Santpere
Human herpesviruses 6-A and -B (HHV-6A, HHV-6B) are ubiquitous in human populations worldwide. These viruses have been associated with several diseases such as multiple sclerosis, Hodgkin's lymphoma or encephalitis. Despite of the need to understand the genetic diversity and geographic stratification of these viruses, the availability of complete viral sequences from different populations is still limited. Here, we present nine new inherited chromosomally integrated HHV-6 sequences from diverse geographical origin which were generated through target DNA enrichment on lymphoblastoid cell lines derived from healthy individuals...
February 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29471822/direct-whole-genome-sequencing-of-plasmodium-falciparum-specimens-from-dried-erythrocyte-spots
#7
Sidsel Nag, Poul-Erik Kofoed, Johan Ursing, Camilla Koldbæk Lemvigh, Rosa Lundbye Allesøe, Amabelia Rodrigues, Christina Aaby Svendsen, Jacob Dyring Jensen, Michael Alifrangis, Ole Lund, Frank M Aarestrup
BACKGROUND: Plasmodium falciparum malaria remains a major health burden and genomic research represents one of the necessary approaches for continued progress towards malaria control and elimination. Sample acquisition for this purpose is troublesome, with the majority of malaria-infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain...
February 23, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29471274/accession-specific-life-strategies-affect-responses-in-leaves-of-arabidopsis-thaliana-plants-exposed-to-excess-cu-and-cd
#8
Rafaela Amaral Dos Reis, Els Keunen, Miguel Pedro Mourato, Luísa Louro Martins, Jaco Vangronsveld, Ann Cuypers
The natural accession Columbia (Col-0) is considered as the reference genome of the model plant Arabidopsis thaliana. Nonetheless, Col-0 plants are more sensitive to excess copper (Cu) and cadmium (Cd) than other widely used accessions such as Wassilewskija (Ws) plants. In the current study, this accession-specific metal sensitivity is further explored by comparing the responses in leaves of Col-0 and Ws plants exposed to excess Cu and Cd. Our results suggest that different life strategies favored by both accessions under physiological conditions affect their response to metal exposure...
February 6, 2018: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29470392/gja4-connexin-37-mutations-correlate-with-secondary-lymphedema-following-surgery-in-breast-cancer-patients
#9
Mahrooyeh Hadizadeh, Seiied Mojtaba Mohaddes Ardebili, Mansoor Salehi, Chris Young, Fariborz Mokarian, James McClellan, Qin Xu, Mohammad Kazemi, Elham Moazam, Behzad Mahaki, Maziar Ashrafian Bonab
Lymphedema is a condition resulting from mutations in various genes essential for lymphatic development and function, which leads to obstruction of the lymphatic system. Secondary lymphedema is a progressive and incurable condition, most often manifesting after surgery for breast cancer. Although its causation appears complex, various lines of evidence indicate that genetic predisposition may play a role. Previous studies show that mutations in connexin 47 are associated with secondary lymphedema. We have tested the hypothesis that connexin 37 gene mutations in humans are associated with secondary lymphedema following breast cancer surgery...
February 22, 2018: Biomedicines
https://www.readbyqxmd.com/read/29469357/-correlation-between-hla-db1-genes-and-susceptibility-to-echinococcosis-in-tibetan-population-in-tibetan-plateau
#10
Gao Shu-Feng, Han Xiu-Min, Zhang Xue-Fei, Wang Yong-Shun, Wang Wei, Guo Ya-Min, Li Yong-Shou
OBJECTIVE: To determine the susceptibility genes and resistance genes in HLA-DRB1 alleles in Tibetan patients with cystic and alveolar hydatid diseases, so as to provide the references for the research of the genetic characteristics and infection mechanism of Tibetan hydatid diseases. METHODS: The case control method was applied. The Tibetan patients with cystic and alveolar hydatid diseases (63 and 73 cases respectively) in Yushu and Guoluo Tibetan Autonomous Prefecture, and unrelated healthy people (60 cases) in this area were selected as the study subjects...
October 23, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
https://www.readbyqxmd.com/read/29469323/-molecular-epidemiology-of-cryptosporidium-infection-in-infants-with-diarrhea-in-wuhan-city
#11
Liu Xiao-Jie, Mao Tie-Bo, Wu Peng, Zhou Rui
OBJECTIVE: To understand the prevalence of Cryptosporidium infection in diarrhea infants under 2 years old in Wuhan City, so as to provide the epidemiological evidence for the prevention and treatment of cryptosporidiosis. METHODS: The fecal samples from infants under 2 years old with diarrhea were collected in Hubei General Hospital and Central South Hospital in Wuhan City, Hubei Province from August 2014 to July 2015. The fecal samples were stored in 2.5% potassium dichromate at 4 ℃ after filtered...
March 14, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
https://www.readbyqxmd.com/read/29468853/the-effect-of-hydroxyapatite-nanoparticles-on-adipogenic-differentiation-of-human-mesenchymal-stem-cells
#12
Xing Yang, Yuanyuan Li, Qianli Huang, Xujie Liu, Ranran Zhang, Qingling Feng
Due to its excellent biocompatibility, nanosized hydroxyapatite (nHA) has drawn much attention for various applications in biomedical fields. There are growing concerns about its biosecurity, however, little is known about its effects on adipogenesis. In the present study, nHA with three different sizes were synthesized and the in vitro effects of nHA on cell proliferation and adipogenic differentiation of human mesenchymal stem cells (hMSCs) were investigated. The results clearly show that nHA does not affect the cell viability, the lipids droplets formation, triglyceride (TG) synthesis and the expression of adipogenic marker genes/proteins of hMSCs at the concentrations lower than 50 μg/ml...
February 22, 2018: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/29468460/two-dominant-loci-determine-resistance-to-phomopsis-cane-lesions-in-f-1-families-of-hybrid-grapevines
#13
Paola Barba, Jacquelyn Lillis, R Stephen Luce, Renaud Travadon, Michael Osier, Kendra Baumgartner, Wayne F Wilcox, Bruce I Reisch, Lance Cadle-Davidson
Rapid characterization of novel NB-LRR-associated resistance to Phomopsis cane spot on grapevine using high-throughput sampling and low-coverage sequencing for genotyping, locus mapping and transcriptome analysis provides insights into genetic resistance to a hemibiotrophic fungus. Phomopsis cane and leaf spot, caused by the hemibiotrophic fungus Diaporthe ampelina (syn = Phomopsis viticola), reduces the productivity in grapevines. Host resistance was studied on three F1 families derived from crosses involving resistant genotypes 'Horizon', Illinois 547-1, Vitis cinerea B9 and V...
February 21, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29467750/the-peroxygenase-activity-of-the-aspergillus-flavus-caleosin-afpxg-modulates-the-biosynthesis-of-aflatoxins-and-their-trafficking-and-extracellular-secretion-via-lipid-droplets
#14
Abdulsamie Hanano, Mari Alkara, Ibrahem Almousally, Mouhnad Shaban, Farzana Rahman, Mehedi Hassan, Denis J Murphy
Aflatoxins (AF) are highly detrimental to human and animal health. We recently demonstrated that the Aspergillus flavus caleosin, AfPXG, had peroxygenase activity and mediated fungal development and AF accumulation. We now report the characterization of an AfPXG -deficient line using reference strain NRRL3357. The resulting fungal phenotype included a severe decrease in mycelium growth, failure to sporulate, and reduced AF production. Increasing cellular oxidative status by administration of hydrogen peroxide and cumene hydroperoxide did not restore the AfPXG -deficient phenotype, which suggests that AfPXG -deficiency is not directly related to oxidative stress...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29465750/identification-of-pyrg-used-as-an-endogenous-reference-gene-in-qualitative-and-real-time-quantitative-pcr-detection-of-pleurotus-ostreatus
#15
Shi Zheng, Luying Shan, Yongliang Zhuang, Ying Shang
As a well-known edible fungus rich in nutrients, Pleurotus ostreatus has been used as an alternative to expensive wild edible fungi. Specifically, the fact that using P. ostreatus instead of other expensive wild edible fungi has damaged the rights and interests of consumers. Among the existing methods for detection of food adulteration, the amplification of endogenous reference gene is the most accurate method. However, an ideal endogenous reference gene for P. ostreatus has yet to be developed. In this study, a DNA extraction method for P...
February 21, 2018: Journal of Food Science
https://www.readbyqxmd.com/read/29463845/identification-of-stable-reference-genes-for-quantitative-pcr-in-koalas
#16
N Sarker, J Fabijan, R D Emes, F Hemmatzadeh, J Meers, J Moreton, H Owen, J M Seddon, G Simmons, N Speight, D Trott, L Woolford, R E Tarlinton
To better understand host and immune response to diseases, gene expression studies require identification of reference genes with stable expression for accurate normalisation. This study describes the identification and testing of reference genes with stable expression profiles in koala lymph node tissues across two genetically distinct koala populations. From the 25 most stable genes identified in transcriptome analysis, 11 genes were selected for verification using reverse transcription quantitative PCR, in addition to the commonly used ACTB and GAPDH genes...
February 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29463659/a-near-complete-haplotype-phased-genome-of-the-dikaryotic-wheat-stripe-rust-fungus-puccinia-striiformis-f-sp-tritici-reveals-high-interhaplotype-diversity
#17
Benjamin Schwessinger, Jana Sperschneider, William S Cuddy, Diana P Garnica, Marisa E Miller, Jennifer M Taylor, Peter N Dodds, Melania Figueroa, Robert F Park, John P Rathjen
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29463655/-de-novo-assembly-and-phasing-of-dikaryotic-genomes-from-two-isolates-of-puccinia-coronata-f-sp-avenae-the-causal-agent-of-oat-crown-rust
#18
Marisa E Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M Palmer, Diana Garnica, Narayana Upadhyaya, John Rathjen, Jennifer M Taylor, Robert F Park, Peter N Dodds, Cory D Hirsch, Shahryar F Kianian, Melania Figueroa
Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae , is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29463577/evaluation-of-the-quality-of-rna-extracted-from-archival-ffpe-glioblastoma-and-epilepsy-surgical-samples-for-gene-expression-assays
#19
Harry R Haynes, Clare L Killick-Cole, Kelly M Hares, Juliana Redondo, Kevin C Kemp, Karwan A Moutasim, Claire Faulkner, Alastair Wilkins, Kathreena M Kurian
AIMS: Histopathological tissue samples are being increasingly used as sources of nucleic acids in molecular pathology translational research. This study investigated the suitability of glioblastoma and control central nervous system (CNS) formalin-fixed paraffin embedded (FFPE) tissue-derived RNA for gene expression analyses. METHODS: Total RNA was extracted from control (temporal lobe resection tissue) and glioblastoma FFPE tissue samples. RNA purity (260/280 ratios) was determined and RNA integrity number (RIN) analysis was performed...
February 20, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29463413/a-genomic-approach-to-identify-and-monitor-a-novel-pyrethroid-resistance-mutation-in-the-redlegged-earth-mite-halotydeus-destructor
#20
Owain R Edwards, Thomas K Walsh, Suzanne Metcalfe, Wee Tek Tay, Ary A Hoffmann, Peter Mangano, Alan Lord, Svetlana Micic, Paul A Umina
Resistance mechanisms are typically uncovered by identifying sequence variation in known candidate genes, however this strategy can be problematic for species with no reference data in known relatives. Here we take a genomic approach to identify resistance to pyrethroids in the redlegged earth mite, Halotydeus destructor, a member of the Penthalidae family of mites that are virtually uncharacterized genetically. Based on shallow genome sequencing followed by a genome assembly, we first identified contigs of the H...
January 2018: Pesticide Biochemistry and Physiology
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