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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/28931206/metabolic-engineering-a-yeast-to-produce-astaxanthin
#2
Yu-Ju Lin, Jui-Jen Chang, Hao-Yeh Lin, Caroline Thia, Yi-Ying Kao, Chieh-Chen Huang, Wen-Hsiung Li
In this study, an astaxanthin-biosynthesis Kluyveromyces marxianus strain Sm23 was first constructed, which could produce 31µg/g DCW astaxanthin. Then, repeated genome integration of the key astaxanthin biosynthesis genes Hpchyb and bkt was done to increase gene copy number and astaxanthin yield. Four improved strains were obtained and the yield of astaxanthin and the total yield of carotenoids in a strain increased with the copy numbers of Hpchyb and bkt. To improve the yield further, the gene Hpchyb from Haematococcus pluvialis was modified by site-directed mutagenesis to increase the enzyme efficiency or/and to prevent the heterologous protein degradation by ubiquitination...
July 23, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28931159/isolation-and-molecular-characterization-of-the-transformer-gene-from-bactrocera-cucurbitae-diptera-tephritidae
#3
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/28931158/new-mitogenomes-of-two-chinese-stag-beetles-coleoptera-lucanidae-and-their-implications-for-systematics
#4
Zi-Qi Lin, Fan Song, Teng Li, Yuan-Yuan Wu, Xia Wan
Although conspicuous and well-studied, stag beetles have been slow to join the genomic era. In this study, mitochondrial genomes of two stag beetles, Sinodendron yunnanense and Prosopocoilus confucius, are sequenced for the first time. Both of their genomes consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. The mitogenome of S. yunnanense was 16,921 bp in length, and P. confucius was 16,951 bp. The location of the gene trnL(UUR), between the A + T-rich and control region in S...
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
#5
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/28931092/the-genome-wide-associated-candidate-gene-znf804a-and-psychosis-proneness-evidence-of-sex-modulated-association
#6
Marta de Castro-Catala, Aurea Mora-Solano, Thomas R Kwapil, Paula Cristóbal-Narváez, Tamara Sheinbaum, Anna Racioppi, Neus Barrantes-Vidal, Araceli Rosa
BACKGROUND: The Zinc finger protein 804A (ZNF804A) is a promising candidate gene for schizophrenia and the broader psychosis phenotype that emerged from genome-wide association studies. It is related to neurodevelopment and associated to severe symptoms of schizophrenia and alterations in brain structure, as well as positive schizotypal personality traits in non-clinical samples. Moreover, a female-specific association has been observed between ZNF804A and schizophrenia. AIM: The present study examined the association of two ZNF804A polymorphisms (rs1344706 and rs7597593) with the positive dimension of schizotypy and psychotic-like experiences in a sample of 808 non-clinical subjects...
2017: PloS One
https://www.readbyqxmd.com/read/28931069/methylation-associated-transcriptional-repression-of-elovl5-in-novel-colorectal-cancer-cell-lines
#7
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/28931059/whole-genome-sequencing-of-mutants-with-increased-resistance-against-the-two-peptide-bacteriocin-plantaricin-jk-reveals-a-putative-receptor-and-potential-docking-site
#8
Bie Ekblad, Jon Nissen-Meyer, Tom Kristensen
By whole-genome sequencing of resistant mutants, a putative receptor for plantaricin JK, a two-peptide bacteriocin produced by some Lactobacillus plantarum strains, was identified in Lactobacillus plantarum NCFB 965 and Weissella viridescens NCFB 1655. The receptors of the two species had 66% identical amino acid sequences and belong to the amino acid-polyamine-organocation (APC) transporter protein family. The resistant mutants contained point mutations in the protein-encoding gene resulting in either premature stop codons, leading to truncated versions of the protein, or single amino acid substitutions...
2017: PloS One
https://www.readbyqxmd.com/read/28931058/molecular-characterization-of-neisseria-meningitidis-isolates-recovered-from-11-19-year-old-meningococcal-carriers-in-salvador-brazil
#9
Ana Rafaela Silva Simões Moura, Cécilia Batmalle Kretz, Italo Eustáquio Ferreira, Amélia Maria Pithon Borges Nunes, José Cássio de Moraes, Mitermayer Galvão Reis, Alan John Alexander McBride, Xin Wang, Leila Carvalho Campos
Characterization of meningococci isolated from the pharynx is essential towards understanding the dynamics of meningococcal carriage and disease. Meningococcal isolates, collected from adolescents resident in Salvador, Brazil during 2014, were characterized by multilocus sequence typing, genotyping or whole-genome sequencing. Most were nongroupable (61.0%), followed by genogroups B (11.9%) and Y (8.5%). We identified 34 different sequence types (STs), eight were new STs, distributed among 14 clonal complexes (cc), cc1136 represented 20...
2017: PloS One
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#10
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
#11
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/28931044/the-performance-of-a-new-local-false-discovery-rate-method-on-tests-of-association-between-coronary-artery-disease-cad-and-genome-wide-genetic-variants
#12
Shuyan Mei, Ali Karimnezhad, Marie Forest, David R Bickel, Celia M T Greenwood
The maximum entropy (ME) method is a recently-developed approach for estimating local false discovery rates (LFDR) that incorporates external information allowing assignment of a subset of tests to a category with a different prior probability of following the null hypothesis. Using this ME method, we have reanalyzed the findings from a recent large genome-wide association study of coronary artery disease (CAD), incorporating biologic annotations. Our revised LFDR estimates show many large reductions in LFDR, particularly among the genetic variants belonging to annotation categories that were known to be of particular interest for CAD...
2017: PloS One
https://www.readbyqxmd.com/read/28931025/the-clinical-and-microbiological-characteristics-of-enteric-fever-in-cambodia-2008-2015
#13
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/28931021/zoonotic-infection-of-brazilian-primate-workers-with-new-world-simian-foamy-virus
#14
Cláudia P Muniz, Liliane T F Cavalcante, Hongwei Jia, HaoQiang Zheng, Shaohua Tang, Anderson M Augusto, Alcides Pissinatti, Luiz P Fedullo, André F Santos, Marcelo A Soares, William M Switzer
Simian foamy viruses (SFVs) are retroviruses present in nearly all nonhuman primates (NHPs), including Old World primates (OWP) and New World primates (NWP). While all confirmed human infections with SFV are from zoonotic transmissions originating from OWP, little is known about the zoonotic transmission potential of NWP SFV. We conducted a longitudinal, prospective study of 56 workers occupationally exposed to NWP in Brazil. Plasma from these workers was tested using Western blot (WB) assays containing NWP SFV antigens...
2017: PloS One
https://www.readbyqxmd.com/read/28931002/enhanced-proofreading-governs-crispr-cas9-targeting-accuracy
#15
Janice S Chen, Yavuz S Dagdas, Benjamin P Kleinstiver, Moira M Welch, Alexander A Sousa, Lucas B Harrington, Samuel H Sternberg, J Keith Joung, Ahmet Yildiz, Jennifer A Doudna
The RNA-guided CRISPR-Cas9 nuclease from Streptococcus pyogenes (SpCas9) has been widely repurposed for genome editing(1-4). High-fidelity (SpCas9-HF1) and enhanced specificity (eSpCas9(1.1)) variants exhibit substantially reduced off-target cleavage in human cells, but the mechanism of target discrimination and the potential to further improve fidelity are unknown(5-9). Using single-molecule Förster resonance energy transfer (smFRET) experiments, we show that both SpCas9-HF1 and eSpCas9(1.1) are trapped in an inactive state(10) when bound to mismatched targets...
September 20, 2017: Nature
https://www.readbyqxmd.com/read/28930995/stereotactic-atlas-guided-laser-capture-microdissection-of-brain-regions-affected-by-traumatic-injury
#16
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/28930984/high-fat-diet-feeding-and-high-throughput-triacylglyceride-assay-in-drosophila-melanogaster
#17
Soda Balla Diop, Ryan T Birse, Rolf Bodmer
Heart disease is the number one cause of human death worldwide. Numerous studies have shown strong connections between obesity and cardiac malfunction in humans, but more tools and research efforts are needed to better elucidate the mechanisms involved. For over a century, the genetically highly tractable model of Drosophila has been instrumental in the discovery of key genes and molecular pathways that proved to be highly conserved across species. Many biological processes and disease mechanisms are functionally conserved in the fly, such as development (e...
September 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930971/determination-of-the-optimal-chromosomal-location-s-for-a-dna-element-in-escherichia-coli-using-a-novel-transposon-mediated-approach
#18
Jakob Frimodt-Møller, Godefroid Charbon, Karen A Krogfelt, Anders Løbner-Olesen
The optimal chromosomal position(s) of a given DNA element was/were determined by transposon-mediated random insertion followed by fitness selection. In bacteria, the impact of the genetic context on the function of a genetic element can be difficult to assess. Several mechanisms, including topological effects, transcriptional interference from neighboring genes, and/or replication-associated gene dosage, may affect the function of a given genetic element. Here, we describe a method that permits the random integration of a DNA element into the chromosome of Escherichia coli and select the most favorable locations using a simple growth competition experiment...
September 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930911/an-enrichment-strategy-yields-seven-novel-single-nucleotide-polymorphisms-associated-with-mortality-and-altered-th17-responses-following-blunt-trauma
#19
Lukas Schimunek, Rami A Namas, Jinling Yin, Dongmei Liu, Derek Barclay, Fayten El-Dehaibi, Andrew Abboud, Haley Lindberg, Ruben Zamora, R Billiar Timothy, Yoram Vodovotz
Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397...
September 19, 2017: Shock
https://www.readbyqxmd.com/read/28930865/presence-of-human-herpesvirus-6b-in-the-pancreas-of-subjects-with-and-without-type-1-diabetes
#20
Maja Ericsson, Oskar Skog
OBJECTIVES: The aims of this study were to investigate the presence of human herpesvirus 6 (HHV6) A and B in human pancreata and to search for signs of active infection in this organ of subjects with and without type 1 diabetes (T1D). METHODS: Pancreata from brain-dead organ donors with and without T1D were examined for the presence of HHV6 genomic sequences by polymerase chain reaction (PCR), transcripts by reverse transcriptase-PCR, and protein by immunohistochemistry...
September 19, 2017: Pancreas
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