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https://www.readbyqxmd.com/read/28719910/correlating-the-genetic-and-physical-map-of-barley-chromosome-3h-revealed-limitations-of-the-fish-based-mapping-of-nearby-single-copy-probes-caused-by-the-dynamic-structure-of-metaphase-chromosomes
#1
Fernanda O Bustamante, Lala Aliyeva-Schnorr, Jörg Fuchs, Sebastian Beier, Andreas Houben
Genetic maps are based on the recombination frequency of molecular markers which often show different positions in comparison to the corresponding physical maps. To decipher the position and order of DNA sequences genetically mapped to terminal and interstitial regions of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization (FISH) on mitotic metaphase chromosomes was performed with 16 genomic single-copy probes derived from fingerprinted BAC contigs. Long genetic distances at subterminal regions translated into short physical distances, confirming that recombination events occur more often at distal regions of chromosome 3H...
July 19, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28719907/tumor-heterogeneity-in-lymphomas-a-different-breed
#2
Christian M Schürch, Birgit Federmann, Leticia Quintanilla-Martinez, Falko Fend
The facts that cancer represents tissues consisting of heterogeneous neoplastic, as well as reactive, cell populations and that cancers of the same histotype may show profound differences in clinical behavior have long been recognized. With the advent of new technologies and the demands of precision medicine, the investigation of tumor heterogeneity has gained much interest. An understanding of intertumoral heterogeneity in patients with the same disease entity is necessary to optimally guide personalized treatment...
July 19, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28719906/a-common-ancestral-asn242ser-mutation-in-tmem67-identified-in-multiple-iranian-families-with-joubert-syndrome
#3
MohammadReza Dehghani, Majid Mojarad, Ehsan Ghayoor Karimiani, Mohammad Yahya Vahidi Mehrjardi, Afsaneh Sahebalzamani, Farah Ashrafzadeh, Mehran Beiraghi Toosi, Atiyeh Eslahi, Najmeh Ahangari, Seyed Mojtaba Yassini, Afsaneh Hassanbeigi, Azam Rasti, Seyed Mehdi Kalantar, Reza Maroofian
BACKGROUND: Joubert syndrome (JS) is a clinically and genetically heterogeneous group of rare neurodevelopmental disorder characterised by peculiar midbrain-hindbrain malformation, known as the "molar tooth" sign. JS can manifest a broad range of signs and symptoms. The most common features of JS are hypotonia, ataxia, developmental delay/intellectual disability, abnormal eye movements, and neonatal breathing abnormalities. To date, 29 genes have been shown to cause JS. METHODS: We employed whole-genome single nucleotide polymorphism genotyping in a group of Iranian families with JS and Sanger sequencing of a known mutation associated with JS located in a single homozygous regions shared by affected members of the families...
July 19, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28719877/functional-genomic-assessment-of-2-2-bis-bromomethyl-1-3-propanediol-induced-cytotoxicity-in-a-single-gene-knockout-library-of-e-%C3%A2-coli
#4
Miao Guan, Xiaowei Zhang
Functional gene fingerprinting of chemicals could be used to understand the direct gene-chemical interaction in the process of toxification from a genome-wide scale. 2, 2-bis (bromomethyl)-1, 3-propanediol (BMP) is a brominated flame retardant with widespread production but with very limited toxicological data. Here the cytotoxicity of BMP was assessed by Escherichia coli (E. coli) functional genome-wide knockout mutants screening and the underlying molecular mechanism was investigated. The median inhibition concentration (IC50) of BMP was 1...
July 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#5
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28719828/functional-analysis-of-pcsk2-coding-variants-a-founder-effect-in-the-old-order-amish-population
#6
Alexandra Winters, Bruno Ramos-Molina, Timothy S Jarvela, Laura Yerges-Armstrong, Toni I Pollin, Iris Lindberg
AIMS: In humans, noncoding variants of PCSK2, the gene encoding prohormone convertase 2 (PC2), have been previously associated with risk for and age of onset of type 2 diabetes (T2D). The aims of this study were to identify coding variants in PCSK2; to determine their possible association with glucose handling; and to determine functional outcomes for coding variants in biochemical studies. METHODS: Exome-wide genotyping was performed on 1725 Old Order Amish (OOA) subjects...
July 3, 2017: Diabetes Research and Clinical Practice
https://www.readbyqxmd.com/read/28719732/genome-wide-association-meta-analysis-reveals-novel-juvenile-idiopathic-arthritis-susceptibility-loci
#7
Laura A McIntosh, Miranda C Marion, Marc Sudman, Mary E Comeau, Mara L Becker, John F Bohnsack, Tasha E Fingerlin, Thomas A Griffin, J Peter Haas, Daniel J Lovell, Lisa A Maier, Peter A Nigrovic, Sampath Prahalad, Marilynn Punaro, Carlos D Rosé, Carol A Wallace, Carol A Wise, Halima Moncrieffe, Timothy D Howard, Carl D Langefeld, Susan D Thompson
OBJECTIVE: Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. This study focuses on identifying new associations among oligoarticular and polyarticular rheumatoid factor negative (RF(-) ) JIA, which are clinically similar and the most prevalent JIA disease subtypes. METHODS: Three cohorts totaling 2,751 oligoarticular and polyarticular RF(-) JIA cases were genotyped on the Affymetrix Genome-Wide SNP Array 6...
July 18, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28719649/differential-expression-of-small-rna-pathway-genes-associated-with-the-biomphalaria-glabrata-schistosoma-mansoni-interaction
#8
Fábio Ribeiro Queiroz, Luciana Maria Silva, Wander de Jesus Jeremias, Élio Hideo Babá, Roberta Lima Caldeira, Paulo Marcos Zech Coelho, Matheus de Souza Gomes
The World Health Organization (WHO) estimates that approximately 240 million people in 78 countries require treatment for schistosomiasis, an endemic disease caused by trematodes of the genus Schistosoma. In Brazil, Schistosoma mansoni is the only species representative of the genus whose passage through an invertebrate host, snails of the genus Biomphalaria, is obligatory before infecting a mammalian host, including humans. The availability of the genome and transcriptome of B. glabrata makes studying the regulation of gene expression, particularly the regulation of miRNA and piRNA processing pathway genes, possible...
2017: PloS One
https://www.readbyqxmd.com/read/28719641/inversion-of-the-imprinting-control-region-of-the-peg3-domain
#9
Joomyeong Kim, Hongzhi He, Hana Kim
The imprinting of the mouse Peg3 domain is controlled through a 4-kb genomic region encompassing the bidirectional promoter and 1st exons of Peg3 and Usp29. In the current study, this ICR was inverted to test its orientation dependency for the transcriptional and imprinting control of the Peg3 domain. The inversion resulted in the exchange of promoters and 1st exons between Peg3 and Usp29. Paternal transmission of this inversion caused 10-fold down-regulation of Peg3 and 2-fold up-regulation of Usp29 in neonatal heads, consistent with its original promoter strength in each direction...
2017: PloS One
https://www.readbyqxmd.com/read/28719630/oligo-and-dsdna-mediated-genome-editing-using-a-teta-dual-selection-system-in-escherichia-coli
#10
Young Shin Ryu, Sathesh-Prabu Chandran, Kyungchul Kim, Sung Kuk Lee
The ability to precisely and seamlessly modify a target genome is needed for metabolic engineering and synthetic biology techniques aimed at creating potent biosystems. Herein, we report on a promising method in Escherichia coli that relies on the insertion of an optimized tetA dual selection cassette followed by replacement of the same cassette with short, single-stranded DNA (oligos) or long, double-stranded DNA and the isolation of recombinant strains by negative selection using NiCl2. This method could be rapidly and successfully used for genome engineering, including deletions, insertions, replacements, and point mutations, without inactivation of the methyl-directed mismatch repair (MMR) system and plasmid cloning...
2017: PloS One
https://www.readbyqxmd.com/read/28719624/sequence-specific-dna-binding-by-myc-max-to-low-affinity-non-e-box-motifs
#11
Michael Allevato, Eugene Bolotin, Mark Grossman, Daniel Mane-Padros, Frances M Sladek, Ernest Martinez
The MYC oncoprotein regulates transcription of a large fraction of the genome as an obligatory heterodimer with the transcription factor MAX. The MYC:MAX heterodimer and MAX:MAX homodimer (hereafter MYC/MAX) bind Enhancer box (E-box) DNA elements (CANNTG) and have the greatest affinity for the canonical MYC E-box (CME) CACGTG. However, MYC:MAX also recognizes E-box variants and was reported to bind DNA in a "non-specific" fashion in vitro and in vivo. Here, in order to identify potential additional non-canonical binding sites for MYC/MAX, we employed high throughput in vitro protein-binding microarrays, along with electrophoretic mobility-shift assays and bioinformatic analyses of MYC-bound genomic loci in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/28719611/rna-sequencing-to-determine-the-contribution-of-kinase-receptor-transactivation-to-g-protein-coupled-receptor-signalling-in-vascular-smooth-muscle-cells
#12
Danielle Kamato, Venkata Vijayanand Bhaskarala, Nitin Mantri, Tae Gyu Oh, Dora Ling, Reearna Janke, Wenhua Zheng, Peter J Little, Narin Osman
G protein coupled receptor (GPCR) signalling covers three major mechanisms. GPCR agonist engagement allows for the G proteins to bind to the receptor leading to a classical downstream signalling cascade. The second mechanism is via the utilization of the β-arrestin signalling molecule and thirdly via transactivation dependent signalling. GPCRs can transactivate protein tyrosine kinase receptors (PTKR) to activate respective downstream signalling intermediates. In the past decade GPCR transactivation dependent signalling was expanded to show transactivation of serine/threonine kinase receptors (S/TKR)...
2017: PloS One
https://www.readbyqxmd.com/read/28719597/pharmacogenomics-study-of-thiazide-diuretics-and-qt-interval-in-multi-ethnic-populations-the-cohorts-for-heart-and-aging-research-in-genomic-epidemiology
#13
A A Seyerle, C M Sitlani, R Noordam, S M Gogarten, J Li, X Li, D S Evans, F Sun, M A Laaksonen, A Isaacs, K Kristiansson, H M Highland, J D Stewart, T B Harris, S Trompet, J C Bis, G M Peloso, J A Brody, L Broer, E L Busch, Q Duan, A M Stilp, C J O'Donnell, P W Macfarlane, J S Floyd, J A Kors, H J Lin, R Li-Gao, T Sofer, R Méndez-Giráldez, S R Cummings, S R Heckbert, A Hofman, I Ford, Y Li, L J Launer, K Porthan, C Newton-Cheh, M D Napier, K F Kerr, A P Reiner, K M Rice, J Roach, B M Buckley, E Z Soliman, R de Mutsert, N Sotoodehnia, A G Uitterlinden, K E North, C R Lee, V Gudnason, T Stürmer, F R Rosendaal, K D Taylor, K L Wiggins, J G Wilson, Y-DI Chen, R C Kaplan, K Wilhelmsen, L A Cupples, V Salomaa, C van Duijn, J W Jukema, Y Liu, D O Mook-Kanamori, L A Lange, R S Vasan, A V Smith, B H Stricker, C C Laurie, J I Rotter, E A Whitsel, B M Psaty, C L Avery
Thiazide diuretics, commonly used antihypertensives, may cause QT interval (QT) prolongation, a risk factor for highly fatal and difficult to predict ventricular arrhythmias. We examined whether common single-nucleotide polymorphisms (SNPs) modified the association between thiazide use and QT or its component parts (QRS interval, JT interval) by performing ancestry-specific, trans-ethnic and cross-phenotype genome-wide analyses of European (66%), African American (15%) and Hispanic (19%) populations (N=78 199), leveraging longitudinal data, incorporating corrected standard errors to account for underestimation of interaction estimate variances and evaluating evidence for pathway enrichment...
July 18, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28719574/ancient-european-dog-genomes-reveal-continuity-since-the-early-neolithic
#14
Laura R Botigué, Shiya Song, Amelie Scheu, Shyamalika Gopalan, Amanda L Pendleton, Matthew Oetjens, Angela M Taravella, Timo Seregély, Andrea Zeeb-Lanz, Rose-Marie Arbogast, Dean Bobo, Kevin Daly, Martina Unterländer, Joachim Burger, Jeffrey M Kidd, Krishna R Veeramah
Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. Here we sequence the genomes of an Early and End Neolithic dog from Germany, including a sample associated with an early European farming community. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. We find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication...
July 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28719321/association-of-interferon-%C3%AE-receptor-1-gene-polymorphism-with-nontuberculous-mycobacterial-lung-infection-among-iranian-patients-with-pulmonary-disease
#15
Poopak Farnia, Jalaledin Ghanavi, Shima Saif, Parissa Farnia, Ali Akbar Velayati
Nontuberculous mycobacteria (NTM) cause significant pulmonary infections in humans. Researchers have reported an association between interferon-gamma receptor-1 (IFN-γR1 or IFNGR1) deficiency and susceptibility to NTM, but the relevance of polymorphism within these genes is not yet clear. In this study, a single nucleotide polymorphism (SNP), T to C, at position-56 in NTM patients with pulmonary disease was investigated. Molecular identification of Mycobacterium isolates was performed with hsp65 genes using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP)...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719296/analysis-of-dengue-serotype-4-in-sri-lanka-during-the-2012-2013-dengue-epidemic
#16
Anna Uehara, Hasitha Aravinda Tissera, Champica K Bodinayake, Ananda Amarasinghe, Ajith Nagahawatte, L Gayani Tillekeratne, Jie Cui, Megan E Reller, Paba Palihawadana, Sunethra Gunasena, Aruna Dharshan Desilva, Annelies Wilder-Smith, Duane J Gubler, Christopher W Woods, October M Sessions
The four serotypes of dengue virus (DENV-1, -2, -3, and -4) have had a rapidly expanding geographic range and are now endemic in over 100 tropical and subtropical countries. Sri Lanka has experienced periodic dengue outbreaks since the 1960s, but since 1989 epidemics have become progressively larger and associated with more severe disease. The dominant virus in the 2012 epidemic was DENV-1, but DENV-4 infections were also commonly observed. DENV-4 transmission was first documented in Sri Lanka when it was isolated from a traveler in 1978, but has been comparatively uncommon since dengue surveillance began in the early 1980s...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719265/differences-in-inflammation-patterns-induced-by-african-and-asian-burkholderia-pseudomallei-isolates-in-mice
#17
Tassili A F Weehuizen, Emma Birnie, Bart Ferwerda, Joris J T H Roelofs, Alex F de Vos, Martin P Grobusch, W Joost Wiersinga
AbstractBurkholderia pseudomallei is the causative agent of melioidosis, an emerging tropical disease of high mortality. Sub-Saharan Africa represents potential melioidosis "hotspots"; however, to date, only a few cases have been reported. Here in, we compared the inflammatory patterns induced by a B. pseudomallei strain recently isolated from a fatal Gabonese case with the Thai reference strain B. pseudomallei-1026b and Burkholderia thailandensis-E264. Ex vivo, no differences were observed in terms of cellular responsiveness between strains...
June 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719243/genotyping-by-sequencing-based-genetic-analysis-of-african-rice-cultivars-and-association-mapping-of-blast-resistance-genes-against-magnaporthe-oryzae-populations-in-africa
#18
Emmanuel M Mgonja, Chan Ho Park, Houxiang Kang, Elias G Balimponya, Stephen Opiyo, Maria Bellizzi, Samuel K Mutiga, Felix Rotich, Veena Devi Ganeshan, Robert Mabagala, Clay Sneller, Jim Correll, Bo Zhou, Nicholas J Talbot, Thomas K Mitchell, Guo-Liang Wang
Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs)...
July 18, 2017: Phytopathology
https://www.readbyqxmd.com/read/28719180/heterologous-expression-purification-and-functional-analysis-of-plasmodium-falciparum-phosphatidylinositol-3-kinase
#19
Matthew Hassett, Anna Sternberg, Bryce Riegel, Craig J Thomas, Paul David Roepe
The Plasmodium falciparum malarial parasite genome appears to encode one and only one phosphatidylinositol 3'-kinase (PI3K) and sequence analysis suggests that the enzyme is a "class III" or "Vps34" type PI3K. The PfVps34 has generated excitement as a possible druggable target and potentially a key target of artemisinin-based antimalarials. In this study, we optimize the PfVps34 gene for heterologous expression in yeast, purify the protein to homogeneity, use a recently validated quantitative assay for phosphatidylinositol 3'-phosphate (PI3P) production from phosphatidylinositol (PI) (Hassett et al...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28719057/the-full-length-sequence-of-hla-b-59-01-01-01-confirmed-by-cloning-and-sequencing
#20
Z Li, H-Y Zou, D Zhou
The full-length sequence of HLA- B*59:01:01:01. The HLA genes are understood to be the most polymorphic in the human genome. According to the IPD-IMGT/HLA Database (release 3.27.0 2017-01), a total of 4,647 HLA-B alleles have been identified to date (1). However, members of the B*59 gene family are scarce and have only 10 alleles.
July 18, 2017: HLA
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