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https://www.readbyqxmd.com/read/28931241/association-of-a-novel-mutation-in-the-plasmodium-falciparum-chloroquine-resistance-transporter-with-decreased-piperaquine-sensitivity
#1
Sonia Agrawal, Kara A Moser, Lindsay Morton, Michael P Cummings, Ankita Parihar, Ankit Dwivedi, Amol C Shetty, Elliott F Drabek, Christopher G Jacob, Philipp P Henrich, Christian M Parobek, Krisada Jongsakul, Rekol Huy, Michele D Spring, Charlotte A Lanteri, Suwanna Chaorattanakawee, Chanthap Lon, Mark M Fukuda, David L Saunders, David A Fidock, Jessica T Lin, Jonathan J Juliano, Christopher V Plowe, Joana C Silva, Shannon Takala-Harrison
Background: Amplified copy number in the plasmepsin II/III genes within Plasmodium falciparum has been associated with decreased sensitivity to piperaquine. To examine this association and test whether additional loci might also contribute, we performed a genome-wide association study of ex vivo P. falciparum susceptibility to piperaquine. Methods: Plasmodium falciparum DNA from 183 samples collected primarily from Cambodia was genotyped at 33716 genome-wide single nucleotide polymorphisms (SNPs)...
August 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28931078/microgeographic-population-structuring-of-aedes-aegypti-diptera-culicidae
#2
André Barretto Bruno Wilke, Ramon Wilk-da-Silva, Mauro Toledo Marrelli
Aedes aegypti is one of the species most favored by changes in the environment caused by urbanization. Its abundance increases rapidly in the face of such changes, increasing the risk of disease transmission. Previous studies have shown that mosquito species that have adapted to anthropogenic environmental changes benefit from urbanization and undergo population expansion. In light of this, we used microsatellite markers to explore how urbanization processes may be modulating Ae. aegypti populations collected from three areas with different levels of urbanization in the city of São Paulo, Brazil...
2017: PloS One
https://www.readbyqxmd.com/read/28931071/the-origin-of-multiple-clones-in-the-parthenogenetic-lizard-species-darevskia-rostombekowi
#3
Alexey P Ryskov, Fedor A Osipov, Andrey V Omelchenko, Seraphima K Semyenova, Anastasiya E Girnyk, Vitaly I Korchagin, Andrey A Vergun, Robert W Murphy
The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species...
2017: PloS One
https://www.readbyqxmd.com/read/28931069/methylation-associated-transcriptional-repression-of-elovl5-in-novel-colorectal-cancer-cell-lines
#4
Arnoud Boot, Jan Oosting, Jaap D H van Eendenburg, Peter J K Kuppen, Hans Morreau, Tom van Wezel
Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines...
2017: PloS One
https://www.readbyqxmd.com/read/28930861/targeted-gene-panel-sequencing-for-early-onset-inflammatory-bowel-disease-and-chronic-diarrhea
#5
Britt-Sabina Petersen, Dietrich August, Renate Abt, Moudjahed Alddafari, Lida Atarod, Safa Baris, Hemant Bhavsar, Florian Brinkert, Mary Buchta, Alla Bulashevska, Ronnie Chee, Ana I Cordeiro, Naghi Dara, Gregor Dückers, Aisha Elmarsafy, Natalie Frede, Nermeen Galal, Patrick Gerner, Erik-Oliver Glocker, Sigune Goldacker, Jutta Hammermann, Peter Hasselblatt, Zuzana Havlicekova, Katrin Hübscher, Milos Jesenak, Neslihan E Karaca, Elif Karakoc-Aydiner, Mahboubeh M Kharaghani, Sara S Kilic, Ayca Kiykim, Christoph Klein, Christian Klemann, Robin Kobbe, Daniel Kotlarz, Martin W Laass, T Ronan Leahy, Mehrnaz Mesdaghi, Sally Mitton, João F Neves, Birol Öztürk, Luis F Pereira, Jan Rohr, Jessica L R Restrepo, Gunda Ruzaike, Nadia Saleh, Suranjith Seneviratne, Ebru Senol, Carsten Speckmann, Daniel Tegtmeyer, Paul Thankam, Jutte van der Werff Ten Bosch, Horst von Bernuth, Sebastian Zeissig, Yvonne Zeissig, Andre Franke, Bodo Grimbacher
BACKGROUND: In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients...
September 19, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28930579/using-comparative-genomics-to-decode-the-genetics-of-acaricide-resistance
#6
Janice P Van Zee, Catherine A Hill
The availability of genome assemblies and other genomic resources is facilitating investigations of complex genetic traits for several species of ticks. Understanding the genetics of acaricide resistance is a priority for tick and tick-borne disease control. The synaptic enzyme acetylcholinesterase (ACE) is recognized as the target of organophosphates (OPs) and carbamates, and mutations in ACE have been tied to resistance. Multiple studies support three ACE (ace) loci in R. microplus but the molecular basis of OP-resistance in this tick remains elusive...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929968/c-state-an-interactive-web-app-for-simultaneous-multi-gene-visualization-and-comparative-epigenetic-pattern-search
#7
Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K Mishra
BACKGROUND: Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. RESULTS: We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929370/a-termite-symbiotic-mushroom-maximizing-sexual-activity-at-growing-tips-of-vegetative-hyphae
#8
Huei-Mei Hsieh, Mei-Chu Chung, Pao-Yang Chen, Fei-Man Hsu, Wen-Wei Liao, Ai-Ning Sung, Chun-Ru Lin, Chung-Ju Rachel Wang, Yu-Hsin Kao, Mei-Jane Fang, Chi-Yung Lai, Chieh-Chen Huang, Jyh-Ching Chou, Wen-Neng Chou, Bill Chia-Han Chang, Yu-Ming Ju
BACKGROUND: Termitomyces mushrooms are mutualistically associated with fungus-growing termites, which are widely considered to cultivate a monogenotypic Termitomyces symbiont within a colony. Termitomyces cultures isolated directly from termite colonies are heterokaryotic, likely through mating between compatible homokaryons. RESULTS: After pairing homokaryons carrying different haplotypes at marker gene loci MIP and RCB from a Termitomyces fruiting body associated with Odontotermes formosanus, we observed nuclear fusion and division, which greatly resembled meiosis, during each hyphal cell division and conidial formation in the resulting heterokaryons...
September 19, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28929317/risk-alleles-for-iga-nephropathy-associated-snps-conferred-completely-opposite-effects-to-idiopathic-membranous-nephropathy-in-chinese-han
#9
Xiaosong Qin, Chen Wang, Guanting Lu, Mengle Peng, Guixue Cheng, Hongquan Zhu, Yun Cao, Jianhua Liu, Yuzhong Li, Hong Cai, Funing Yang, Yanhong Liu, Xiaoyu Chen, Liubing Li, Nan Wan, Xiaoting Wen, Shijun Li, Ruili Nie, Dongchun Qin, Yongzhe Li, Yong Liu
The coexistence of immunoglobulin A nephropathy (IgAN) and idiopathic membranous nephropathy (IMN) in a few cases suggested that there could be existed a similar mechanism in pathogenesis of these two types of primary glomerulonephritis. In order to verify this hypothesis, a total of 23 reported IgAN-associated SNPs were genotyped in a cohort of 485 IMN patients and 569 healthy controls with Chinese Han origin. After Cochran-Armitage test for trend analysis, seven IgAN-associated SNPs located in the major histocompatibility complex (MHC) region were found to be significantly associated with the susceptibility of IMN, with rs9275596 as the top one (p = 1...
September 19, 2017: Immunologic Research
https://www.readbyqxmd.com/read/28929106/common-expression-quantitative-trait-loci-shared-by-histone-genes
#10
Hanseol Kim, Yujin Suh, Chaeyoung Lee
A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28929021/allele-specific-expression-and-methylation-in-the-bumblebee-bombus-terrestris
#11
Zoë Lonsdale, Kate Lee, Maria Kiriakidu, Harindra Amarasinghe, Despina Nathanael, Catherine J O'Connor, Eamonn B Mallon
The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee...
2017: PeerJ
https://www.readbyqxmd.com/read/28929008/early-branching-euteleost-relationships-areas-of-congruence-between-concatenation-and-coalescent-model-inferences
#12
Matthew A Campbell, Michael E Alfaro, Max Belasco, J Andrés López
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements...
2017: PeerJ
https://www.readbyqxmd.com/read/28928752/climate-clever-clovers-new-paradigm-to-reduce-the-environmental-footprint-of-ruminants-by-breeding-low-methanogenic-forages-utilizing-haplotype-variation
#13
Parwinder Kaur, Rudi Appels, Philipp E Bayer, Gabriel Keeble-Gagnere, Jiankang Wang, Hideki Hirakawa, Kenta Shirasawa, Philip Vercoe, Katia Stefanova, Zoey Durmic, Phillip Nichols, Clinton Revell, Sachiko N Isobe, David Edwards, William Erskine
Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H(2) = 0.4) and allelic variation in a region of Chr 8 accounted for 7...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928442/genome-wide-association-and-hla-region-fine-mapping-studies-identify-susceptibility-loci-for-multiple-common-infections
#14
Chao Tian, Bethann S Hromatka, Amy K Kiefer, Nicholas Eriksson, Suzanne M Noble, Joyce Y Tung, David A Hinds
Infectious diseases have a profound impact on our health and many studies suggest that host genetics play a major role in the pathogenesis of most of them. We perform 23 genome-wide association studies for common infections and infection-associated procedures, including chickenpox, shingles, cold sores, mononucleosis, mumps, hepatitis B, plantar warts, positive tuberculosis test results, strep throat, scarlet fever, pneumonia, bacterial meningitis, yeast infections, urinary tract infections, tonsillectomy, childhood ear infections, myringotomy, measles, hepatitis A, rheumatic fever, common colds, rubella and chronic sinus infection, in over 200,000 individuals of European ancestry...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928368/detection-of-clinically-relevant-copy-number-alterations-in-oral-cancer-progression-using-multiplexed-droplet-digital-pcr
#15
Curtis B Hughesman, X J David Lu, Kelly Y P Liu, Yuqi Zhu, Rebecca M Towle, Charles Haynes, Catherine F Poh
Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928236/histone-deacetylase-inhibition-ameliorates-hypertension-and-hyperglycemia-in-a-model-of-cushing-s-syndrome
#16
Hae-Ahm Lee, Seol-Hee Kang, Mina Kim, Eunjo Lee, Hyun-Min Cho, Eun-Kyung Moon, Inkyeom Kim
Cushing's syndrome (CS) caused by hypercortisolism is occasionally accompanied by metabolic disorders such as hypertension, diabetes mellitus (DM), dyslipidemia and central obesity. Thus, morbidity and mortality, observed in cardiovascular disease, are elevated in patients with CS. We hypothesized that HDAC inhibition (HDACi) decreased transcriptional activity of glucocorticoid receptor (GR), which ameliorates hypertension and hyperglycemia in patients with CS. To establish an animal model of hypercortisolism, Sprague-Dawley rats were infused with adrenocorticotropic hormone (ACTH, 40 ng/day) or dexamethasone (Dex, 10 μg/day) via osmotic minipumps for 4 weeks...
September 19, 2017: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#17
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28928151/comparative-analysis-reveals-genomic-features-of-stress-induced-transcriptional-readthrough
#18
Anna Vilborg, Niv Sabath, Yuval Wiesel, Jenny Nathans, Flonia Levy-Adam, Therese A Yario, Joan A Steitz, Reut Shalgi
Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28928088/20-s-ginsenoside-rh2-suppresses-proliferation-and-migration-of-hepatocellular-carcinoma-cells-by-targeting-ezh2-to-regulate-cdkn2a-2b-gene-cluster-transcription
#19
Qi Li, Bai Li, Chengya Dong, Yajie Wang, Qi Li
20(S)-Ginsenoside Rh2 (20(S)-GRh2) exerts important pharmacological effects with regard to the control of human hepatocellular carcinoma (HCC). EZH2 is a potent histone methyltransferase of H3K27me(3), which has been determined as an oncogene in many malignancies. The CDKN2A-2B gene cluster encodes three important tumor suppressors, P14, P15 and P16. In this study, the anticancer effect and molecular mechanism of 20(S)-GRh2 on HCC was investigated. Treatment of HCC cells with 20(S)-GRh2 inhibited cell proliferation, migration and induced cell cycle arrest at the G0/G1 phase, and inhibited tumor growth in vivo...
September 16, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28927971/the-interaction-of-polymorphisms-in-extracellular-matrix-genes-and-underlying-mirna-motifs-that-modulate-susceptibility-to-anterior-cruciate-ligament-rupture
#20
Kyle Willard, Sasha Mannion, Colleen J Saunders, Malcolm Collins, Alison V September
OBJECTIVES: Variants within genes that encode proteins regulating fibrillogenesis such as BGN (rs1126499 C>T, rs1042103 C>T), COL5A1 (rs12722 C>T) and DCN (rs516115 C>T) have been associated with susceptibility to anterior cruciate ligament (ACL) ruptures. A miRNA mediated transcript instability was proposed for the COL5A1 association. The study aims were: (i) to investigate the association of inferred allele combinations across the COL5A1 3'-UTR, BGN and DCN genes with susceptibility to ACL rupture; and (ii) to use an in silico approach to identify miRNA binding sites common to these risk associated allele combinations...
September 1, 2017: Journal of Science and Medicine in Sport
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