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https://www.readbyqxmd.com/read/29777949/evaluation-of-skin-or-sweat-characteristic-mrnas-for-inferring-the-human-origin-of-touched-contact-traces
#1
Tomoko Akutsu, Ken Watanabe, Ayari Takamura, Koichi Sakurada
The source of small amounts of touch DNA, which is transferred from the skin to an object when it is handled or touched, could be an issue in the forensic analysis of criminal cases. Here, we performed an extended evaluation of skin- or sweat-characteristic mRNAs to investigate their usability to infer whether an object has been handled or touched by someone. First, we compared the expression levels of candidate genes between skin swabs and other body fluids by quantitative RT-PCR analysis. Among the analyzed genes, corneodesmosin (CDSN), late cornified envelope 1C (LCE1C), filaggrin (FLG), desmocollin 1, and dermcidin were selected for further analysis on the basis of their specificities and sensitivities...
May 14, 2018: Legal Medicine
https://www.readbyqxmd.com/read/29777820/accuracy-and-precision-of-quantitative-dce-mri-parameters-how-should-one-estimate-contrast-concentration
#2
Nicole Wake, Hersh Chandarana, Henry Rusinek, Koji Fujimoto, Linda Moy, Daniel K Sodickson, Sungheon Gene Kim
INTRODUCTION: Pharmacokinetic parameters derived from dynamic contrast-enhanced MRI (DCE-MRI) data are sensitive to acquisition and post-processing techniques, which makes it difficult to compare results obtained using different methods. In particular, one of the most important factors affecting estimation of model parameters is how to convert MRI signal intensities to contrast agent concentration. The purpose of our study was to quantitatively compare a linear signal-to-concentration conversion (LC) as an approximation and a non-linear conversion (NLC) based on the MRI signal equation, in terms of the accuracy and precision of the pharmacokinetic parameters in T1 -weighted DCE-MRI...
May 16, 2018: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/29777594/il-3-producing-basophils-are-required-to-exacerbate-airway-hyper-responsiveness-in-a-murine-inflammatory-model
#3
Rachel Rignault-Bricard, François Machavoine, Salah Mecheri, Olivier Hermine, Elke Schneider, Michel Dy, Maria Leite-de-Moraes
BACKGROUND: Basophils are commonly associated with allergic responses because of their ability to produce large amounts of pro-Th2 cytokines and histamine. However, the mechanisms through which bone marrow-resident basophils (BMRB) become fully competent cytokine and histamine producers in response to IgE crosslinking are poorly understood. Here, we sought to determine the role of IL-3 in promoting pro-Th2 basophils. METHODS: BMRB and basophils exposed to IL-3 in vitro and in vivo were evaluated for their production of Th2 cytokines and histamine in response to FcεRI crosslinking on both protein and gene expression levels...
May 19, 2018: Allergy
https://www.readbyqxmd.com/read/29777226/genetic-contribution-to-waist-to-hip-ratio-in-mexican-children-and-adolescents-based-on-12-loci-validated-in-european-adults
#4
Michelle Turcotte, Arkan Abadi, Jesus Peralta-Romero, Fernando Suarez, Hudson Reddon, Jaime Gomez-Zamudio, Ana I Burguete-Garcia, Miguel Cruz, David Meyre
BACKGROUND/OBJECTIVES: The prevalence of abdominal obesity in Mexican children has risen dramatically in the past decade. Genome-wide association studies (GWAS) for waist-to-hip ratio (WHR) performed predominantly in European descent adult  populations have identified multiple single-nucleotide polymorphisms (SNPs) with larger effects in women. The contribution of these SNPs to WHR in non-European children is unknown. SUBJECTS/METHODS: Mexican children and adolescents (N = 1421, 5-17 years) were recruited in Mexico City...
March 13, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29776125/post-transcriptional-bursting-in-genes-regulated-by-small-rna-molecules
#5
Guillermo Rodrigo
Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775756/pkm2-a-potential-target-for-regulating-cancer
#6
REVIEW
Yu-Huan Li, Xiao-Feng Li, Jia-Tao Liu, Hua Wang, Lu-Lu Fan, Jun Li, Guo-Ping Sun
Aberrated glucose metabolism is a key future of cancer cells. Unlike normal cells, tumor cells favor glycolysis even in the presence of sufficient oxygen. Pyruvate kinase (PK), a key glucose metabolic enzyme, converts phosphoenolpyruvate (PEP) to pyruvate by transferring the high-energy phosphate group to adenosine diphosphate (ADP) to produce adenosine triphosphate (ATP). Pyruvate kinase M2 (PKM2), one of the four isozyme of PK, which universally expressed in rapidly proliferating cells such as embryonic cells and cancer cells...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775685/phenotypic-and-genetic-resistance-traits-in-pseudomonas-aeruginosa-strains-infecting-cystic-fibrosis-patients-a-french-cohort-study
#7
Nathalie Courtois, Yvan Caspar, Max Maurin
Pseudomonas aeruginosa is responsible for chronic respiratory tract colonisation and acute exacerbations in cystic fibrosis (CF) patients. This Gram-negative bacterium often develops multidrug resistance, which represents a therapeutic challenge. Our objective was to characterize the phenotypic and genetic β-lactam resistance traits of P. aeruginosa strains isolated from CF patients followed at Grenoble Alpes university hospital. The susceptibility to β-lactam compounds of 123 P. aeruginosa strains collected from the lower respiratory tract of 45 CF patients, between 2010 and 2014, was evaluated...
May 15, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#8
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29773850/comparative-genomic-analysis-of-acinetobacter-spp-plasmids-originating-from-clinical-settings-and-environmental-habitats
#9
Ileana P Salto, Gonzalo Torres Tejerizo, Daniel Wibberg, Alfred Pühler, Andreas Schlüter, Mariano Pistorio
Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773668/plants-send-small-rnas-in-extracellular-vesicles-to-fungal-pathogen-to-silence-virulence-genes
#10
Qiang Cai, Lulu Qiao, Ming Wang, Baoye He, Feng-Mao Lin, Jared Palmquist, Hsien-Da Huang, Hailing Jin
Some pathogens and pests deliver small RNAs (sRNAs) into host cells to suppress host immunity. Conversely, hosts also transfer sRNAs into pathogens and pests to inhibit their virulence. Although sRNA trafficking has been observed in a wide variety of interactions, how sRNAs are transferred, especially from hosts to pathogens/pests, is still unknown. Here we show that host Arabidopsis cells secrete exosome-like extracellular vesicles to deliver sRNAs into fungal pathogen Botrytis cinerea These sRNA-containing vesicles accumulate at the infection sites and are taken up by the fungal cells...
May 17, 2018: Science
https://www.readbyqxmd.com/read/29773659/modeling-leaderless-transcription-and-atypical-genes-results-in-more-accurate-gene-prediction-in-prokaryotes
#11
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang, Mark Borodovsky
In a conventional view of the prokaryotic genome organization, promoters precede operons and RBS sites with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS 2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of pre-computed "heuristic" models designed to identify harder-to-detect genes (likely horizontally transferred)...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29772393/unexpected-mechanisms-of-resistance-in-dutch-pseudomonas-aeruginosa-isolates-collected-during-fourteen-years-of-surveillance
#12
P D Croughs, C H W Klaassen, J van Rosmalen, D M Maghdid, S A Boers, J P Hays, W H F Goessens
Pseudomonas aeruginosa is one of the most important causes of infection in the intensive care unit. It is intrinsically resistant to many antibiotics and easily acquires additional resistance genes via horizontal gene transfer of mobile genetic elements. In the present study, 1,528 P. aeruginosa isolates, obtained from a Dutch national surveillance program between the years 1998 and 2011, were analyzed for the presence of Extended Spectrum β-Lactamase (ESBL) genes blaCTX-M , blaSHV , blaTEM , blaBEL , blaPER , blaVEB , blaOXA-10 and metallo-β-Lactamase (MBL) genes blaIMP , blaVIM and blaNDM ...
May 14, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#13
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29771284/non-cell-autonomous-otx2-homeoprotein-regulates-visual-cortex-plasticity-through-gadd45b-g
#14
Jessica Apulei, Namsuk Kim, Damien Testa, Jérôme Ribot, David Morizet, Clémence Bernard, Laurent Jourdren, Corinne Blugeon, Ariel A Di Nardo, Alain Prochiantz
The non-cell autonomous transfer of OTX2 homeoprotein transcription factor into juvenile mouse cerebral cortex regulates parvalbumin interneuron maturation and critical period timing. By analyzing gene expression in primary visual cortex of wild-type and Otx2+/GFP mice at plastic and nonplastic ages, we identified several putative genes implicated in Otx2-dependent visual cortex plasticity for ocular dominance. Cortical OTX2 infusion in juvenile mice induced Gadd45b/g expression through direct regulation of transcription...
May 16, 2018: Cerebral Cortex
https://www.readbyqxmd.com/read/29770865/the-agrobacterium-phenotypic-plasticity-plast-genes
#15
Léon Otten
The transfer of T-DNA sequences from Agrobacterium to plant cells is a well-understood process of natural genetic engineering. The expression of T-DNA genes in plants leads to tumors, hairy roots, or transgenic plants. The transformed cells multiply and synthesize small molecules, called opines, used by Agrobacteria for their growth. Several T-DNA genes stimulate or influence plant growth. Among these, iaaH and iaaM encode proteins involved in auxin synthesis, whereas ipt encodes a protein involved in cytokinin synthesis...
May 17, 2018: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/29770657/-cloning-expression-and-immunity-analysis-of-transketolase-of-echinococcus-granulosus
#16
Cao De-Ping, Zhang Yao-Gang, Li Chao-Qun, Liu Jia, Jiang Bo-Fan
OBJECTIVE: To obtain the prokaryotic expression of transketolase genes and analyze its value as a diagnostic antigen for echinococcosis. METHODS: TK gene was amplified by PCR and cloned into prokaryotic vector pMD19-EgTK, and then subcloned into the expression vector pET-28a. The target gene TK prokaryotic expression plasmid pET-28a was constructed and transferred into BL21. The purified protein was identified by SDS-PAGE and Western blotting. The blood samples of patients with cystic echinococcosis (CE group), alveolar echinococcosis (AE group) and healthy people (healthy group) were collected and detected by ELISA with the recombinant EgTK protein as a diagnostic antigen...
April 20, 2018: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
https://www.readbyqxmd.com/read/29770326/characterization-and-comparative-analysis-of-the-complete-chloroplast-genome-of-the-critically-endangered-species-streptocarpus-teitensis-gesneriaceae
#17
Cornelius M Kyalo, Andrew W Gichira, Zhi-Zhong Li, Josphat K Saina, Itambo Malombe, Guang-Wan Hu, Qing-Feng Wang
Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29769695/genomic-and-functional-characterisation-of-incx3-plasmids-encoding-bla-shv-12-in-escherichia-coli-from-human-and-animal-origin
#18
Apostolos Liakopoulos, Jeanet van der Goot, Alex Bossers, Jonathan Betts, Michael S M Brouwer, Arie Kant, Hilde Smith, Daniela Ceccarelli, Dik Mevius
The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12 -encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769396/bulk-electroporation-mediated-gene-transfer-into-xenopus-tadpole-brain
#19
Cristina Sáenz de Miera, Ethan Parr, Robert J Denver
In vivo gene transfer is a powerful tool for investigating protein function and gene regulation in living organisms. Delivery of plasmid DNA to the brain of Xenopus tadpoles by bulk electroporation-mediated (EM) gene transfer can be used to study the effects of ectopic gene expression on development, physiology, and behavior. It can also be used to mark cells for lineage tracing, investigate the in vivo function of gene regulatory elements when linked to a reporter gene, and introduce mutations into the genome of transfected cells, among other applications...
May 16, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29769342/cotesia-congregata-bracovirus-circles-encoding-ptp-and-ankyrin-genes-integrate-into-the-dna-of-parasitized-manduca-sexta-hemocytes
#20
Germain Chevignon, Georges Periquet, Gabor Gyapay, Nathalie Vega-Czarny, Karine Musset, Jean-Michel Drezen, Elisabeth Huguet
Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as template for the production of double stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production hence impeding viral replication in caterpillar hosts during parasitism. Here we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta , by the wasp Cotesia congregata Sequences sharing similarities with Host integration Motifs (HIM) involved in integration into DNA of Microplitis demolitor bracovirus (MdBV) circles, could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption...
May 16, 2018: Journal of Virology
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