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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/28931159/isolation-and-molecular-characterization-of-the-transformer-gene-from-bactrocera-cucurbitae-diptera-tephritidae
#2
Ya Luo, Santao Zhao, Jiahui Li, Peizheng Li, Rihui Yan
transformer (tra) is a switch gene of sex determination in many insects, particularly in Dipterans. However, the sex determination pathway in Bactrocera cucurbitae (Coquillett), a very destructive pest on earth, remains largely uncharacterized. In this study, we have isolated and characterized one female-specific and two male-specific transcripts of the tra gene (Bcutra) of B. cucurbitae. The genomic structure of Bcutra has been determined and the presence of multiple conserved Transformer (TRA)/TRA-2 binding sites in Bcutra has been found...
January 1, 2017: Journal of Insect Science
https://www.readbyqxmd.com/read/28931093/synthesis-of-udp-apiose-in-bacteria-the-marine-phototroph-geminicoccus-roseus-and-the-plant-pathogen-xanthomonas-pisi
#3
James Amor Smith, Maor Bar-Peled
The branched-chain sugar apiose was widely assumed to be synthesized only by plant species. In plants, apiose-containing polysaccharides are found in vascularized plant cell walls as the pectic polymers rhamnogalacturonan II and apiogalacturonan. Apiosylated secondary metabolites are also common in many plant species including ancestral avascular bryophytes and green algae. Apiosyl-residues have not been documented in bacteria. In a screen for new bacterial glycan structures, we detected small amounts of apiose in methanolic extracts of the aerobic phototroph Geminicoccus roseus and the pathogenic soil-dwelling bacteria Xanthomonas pisi...
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/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#5
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28931056/heterogeneity-in-the-expression-and-subcellular-localization-of-polyol-monosaccharide-transporter-genes-in-lotus-japonicus
#6
Lu Tian, Leru Liu, Yehu Yin, Mingchao Huang, Yanbo Chen, Xinlan Xu, Pingzhi Wu, Meiru Li, Guojiang Wu, Huawu Jiang, Yaping Chen
Polyols can serve as a means for the translocation of carbon skeletons and energy between source and sink organs as well as being osmoprotective solutes and antioxidants which may be involved in the resistance of some plants to biotic and abiotic stresses. Polyol/Monosaccharide transporter (PLT) proteins previously identified in plants are involved in the loading of polyols into the phloem and are reported to be located in the plasma membrane. The functions of PLT proteins in leguminous plants are not yet clear...
2017: PloS One
https://www.readbyqxmd.com/read/28931025/the-clinical-and-microbiological-characteristics-of-enteric-fever-in-cambodia-2008-2015
#7
Laura M F Kuijpers, Thong Phe, Chhun H Veng, Kruy Lim, Sovann Ieng, Chun Kham, Nizar Fawal, Laetitia Fabre, Simon Le Hello, Erika Vlieghe, François-Xavier Weill, Jan Jacobs, Willy E Peetermans
BACKGROUND: Enteric fever remains a major public health problem in low resource settings and antibiotic resistance is increasing. In Asia, an increasing proportion of infections is caused by Salmonella enterica serovar Paratyphi A, which for a long time was assumed to cause a milder clinical syndrome compared to Salmonella enterica serovar Typhi. METHODOLOGY: A retrospective chart review study was conducted of 254 unique cases of blood culture confirmed enteric fever who presented at a referral adult hospital in Phnom Penh, Cambodia between 2008 and 2015...
September 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28930995/stereotactic-atlas-guided-laser-capture-microdissection-of-brain-regions-affected-by-traumatic-injury
#8
Harris A Weisz, Deborah R Boone, Stacy L Sell, Helen L Hellmich
The ability to isolate specific brain regions of interest can be impeded in tissue disassociation techniques that do not preserve their spatial distribution. Such techniques also potentially skew gene expression analysis because the process itself can alter expression patterns in individual cells. Here we describe a laser capture microdissection (LCM) method to selectively collect specific brain regions affected by traumatic brain injury (TBI) by using a modified Nissl (cresyl violet) staining protocol and the guidance of a rat brain atlas...
September 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930567/molecular-mechanisms-of-chlamydia-trachomatis-resistance-to-antimicrobial-drugs
#9
Tomislav Mestrovic, Suncanica Ljubin-Sternak
Chlamydia trachomatis (C. trachomatis) is a leading cause of bacterial sexually transmitted infections in developed and undeveloped countries, and therefore a global public health issue. In an era of increasing bacterial resistance to antibiotics, resistance has been an exceedingly rare phenomenon in C. trachomatis; however, clinical treatment failures attributed to multidrug-resistant C. trachomatis strains have been described on several occasions. Cell culture systems using McCoy cells and subsequent immunofluorescent staining are still the most common methodology used for antimicrobial susceptibility testing, but the presence of resistance markers should be appraised by further genetic analysis...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930563/mass-spectrometry-based-proteomic-analysis-of-the-dna-damage-response
#10
Matthew P Stokes, Yiying Zhu, Charles L Farnsworth
In response to DNA damage, cells have evolved mechanisms to halt cell cycle progression, activate repair, or initiate apoptosis. These DNA damage response (DDR) pathways are critical for cellular survival in response to genomic insult, and play important roles in growth, development, and disease. Historically, mediators of DNA damage response signaling have been studied one or a few proteins at a time. Advances in mass spectrometry instrumentation and enrichment methods now allow for more global analysis of the DDR in cells and tissues...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930152/proteomic-analysis-of-the-chlorophyta-dunaliella-new-strain-al-1-revealed-global-changes-of-metabolism-during-high-carotenoid-production
#11
Faten Ben Amor, Fatma Elleuch, Hajer Ben Hlima, Matthieu Garnier, Bruno Saint-Jean, Mohamed Barkallah, Chantal Pichon, Slim Abdelkafi, Imen Fendri
The green microalgae Dunaliella genus is known for the production of high added value molecules. In this study, strain AL-1 was isolated from the Sebkha of Sidi El Hani (Sousse, Tunisia). This isolate was identified both morphologically and genetically via 18S rRNA gene sequence as a member of the genus Dunaliella. Strain AL-1 was found to be closely related to Dunaliella salina, Dunaliella quartolecta and Dunaliella polymorpha with more than 97% similarity. Response surface methodology was used to maximize carotenoid production by strain AL-1 by optimizing its growth conditions...
September 20, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28930031/spread-of-chikungunya-virus-east-central-south-african-genotype-in-northeast-brazil
#12
Antonio Charlys da Costa, Julien Thézé, Shirley Cavalcante Vasconcelos Komninakis, Rodrigo Lopes Sanz-Duro, Marta Rejane Lemos Felinto, Lúcia Cristina Corrêa Moura, Ivoneide Moreira de Oliveira Barroso, Lucineide Eliziario Correia Santos, Mardjane Alves de Lemos Nunes, Adriana Avila Moura, José Lourenço, Xutao Deng, Eric L Delwart, Maria Raquel Dos Anjos Silva Guimarães, Oliver G Pybus, Ester C Sabino, Nuno R Faria
We investigated an outbreak of exanthematous illness in Maceió by using molecular surveillance; 76% of samples tested positive for chikungunya virus. Genetic analysis of 23 newly generated genomes identified the East/Central/South African genotype, suggesting that this lineage has persisted since mid-2014 in Brazil and may spread in the Americas and beyond.
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28930029/berlin-squirrelpox-virus-a-new-poxvirus-in-red-squirrels-berlin-germany
#13
Gudrun Wibbelt, Simon H Tausch, Piotr W Dabrowski, Olivia Kershaw, Andreas Nitsche, Livia Schrick
Near Berlin, Germany, several juvenile red squirrels (Sciurus vulgaris) were found with moist, crusty skin lesions. Histology, electron microscopy, and cell culture isolation revealed an orthopoxvirus-like infection. Subsequent PCR and genome analysis identified a new poxvirus (Berlin squirrelpox virus) that could not be assigned to any known poxvirus genera.
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28930002/investigation-of-outbreaks-of-salmonella-enterica-serovar-typhimurium-and-its-monophasic-variants-using-whole-genome-sequencing-denmark
#14
Pernille Gymoese, Gitte Sørensen, Eva Litrup, John Elmerdal Olsen, Eva Møller Nielsen, Mia Torpdahl
Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases...
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28929973/vermont-a-multi-perspective-visual-interactive-platform-for-mutational-analysis
#15
Alexandre V Fassio, Pedro M Martins, Samuel da S Guimarães, Sócrates S A Junior, Vagner S Ribeiro, Raquel C de Melo-Minardi, Sabrina de A Silveira
BACKGROUND: A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease association and effects on protein structure and function. Therefore, reliable computational approaches are needed to support the understanding of mutations and their impacts. Here, we present VERMONT 2.0, a visual interactive platform that combines sequence and structural parameters with interactive visualizations to make the impact of protein point mutations more understandable...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929505/high-level-glyoxalase-1-glo1-expression-is-linked-to-poor-prognosis-in-prostate-cancer
#16
Christoph Burdelski, Rami Shihada, Andrea Hinsch, Alexander Angerer, Cosima Göbel, Emily Friedrich, Claudia Hube-Magg, Susanne Burdak-Rothkamm, Martina Kluth, Ronald Simon, Christina Möller-Koop, Guido Sauter, Franzika Büscheck, Corinna Wittmer, Till S Clauditz, Till Krech, Maria C Tsourlakis, Sarah Minner, Markus Graefen, Thorsten Schlomm, Waldemar Wilczak, Frank Jacobsen
BACKGROUND: Glyoxalase 1 (GLO1) is an enzyme involved in removal of toxic byproducts accumulating during glycolysis from the cell. GLO1 is up regulated in many cancer types but its role in prostate cancer is largely unknown. METHODS: Here, we employed GLO1 immunohistochemistry on a tissue microarray including 11 152 tumors and an attached clinical and molecular database. RESULTS: Normal prostate epithelium was negative for GLO1, whereas 2059 (27...
September 19, 2017: Prostate
https://www.readbyqxmd.com/read/28929377/opposing-roles-of-the-aldo-keto-reductases-akr1b1-and-akr1b10-in-colorectal-cancer
#17
Betul Taskoparan, Esin Gulce Seza, Secil Demirkol, Sinem Tuncer, Milan Stefek, Ali Osmay Gure, Sreeparna Banerjee
PURPOSE: Aldo-keto reductases (including AKR1B1 and AKR1B10) constitute a family of oxidoreductases that have been implicated in the pathophysiology of diabetes and cancer, including colorectal cancer (CRC). Available data indicate that, despite their similarities in structure and enzymatic functions, their roles in CRC may be divergent. Here, we aimed to determine the expression and functional implications of AKR1B1 and AKR1B10 in CRC. METHODS: AKR1B1 and AKR1B10 gene expression levels were analyzed using publicly available microarray data and ex vivo CRC-derived cDNA samples...
September 19, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28929317/risk-alleles-for-iga-nephropathy-associated-snps-conferred-completely-opposite-effects-to-idiopathic-membranous-nephropathy-in-chinese-han
#18
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/28929285/genomic-disorders-in-psychiatry-what-does-the-clinician-need-to-know
#19
REVIEW
Chelsea Lowther, Gregory Costain, Danielle A Baribeau, Anne S Bassett
PURPOSE OF REVIEW: The purpose of this review is to summarize the role of genomic disorders in various psychiatric conditions and to highlight important recent advances in the field that are of potential clinical relevance. RECENT FINDINGS: Genomic disorders are caused by large rare recurrent deletions and duplications at certain chromosomal "hotspots" (e.g., 22q11.2, 16p11.2, 15q11-q13, 1q21.1, 15q13.3) across the genome. Most overlap multiple genes, affect development, and are associated with variable cognitive and other neuropsychiatric expression...
September 20, 2017: Current Psychiatry Reports
https://www.readbyqxmd.com/read/28929273/complete-genome-sequence-of-a-novel-lytic-bacteriophage-isolated-from-ralstonia-solanacearum
#20
Jingfang Su, Hongwei Sun, Junjie Liu, Zhaokui Guo, Guoquan Fan, Gang Gu, Guanghua Wang
A lytic podophage RSPI1 was isolated from tobacco field soil collected in Fujian Province, South China using host bacterium Ralstonia solanacearum Tb15-14. Whole genome sequencing of this phage was performed using the high-throughput Ion Torrent PGM Sequencer. The complete genome of RSPI1 was 43,211 bp in length with a mean DNA G + C content of 61.5%. A total of 48 open reading frames were identified with lengths ranging from 132 bp to 5,061 bp, of which, 11, 12 and 25 were identified as functional, structural and unknown genes, respectively...
September 19, 2017: Archives of Virology
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