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https://www.readbyqxmd.com/read/28821942/rapid-detection-of-serratia-fonticola-by-taqman-quantitative-real-time-pcr-using-primers-targeting-the-gyrb-gene
#1
Jing Hua Ruan, Wu Jun Wang, Ti Yin Zhang, Quan Yang Bai, Teng Zheng, Zhi Deng Zhang, Li Yun Wu, Yi Fan Huang, Dao Jin Yu
A gyrB gene is present in the majority of bacterial species, and encodes the ATPase domain of DNA gyraseB-subunit protein, which is essential for transcription and replication of bacteria. The gyrB gene exhibits higher nucleotide sequence variability than the 16S rDNA gene and thus could be more reliable in differentiating Serratia fonticola. A species-specific primer pair and probe were designed for quantitative real-time PCR detection of S. fonticola using gyrB as the target gene. Nine members of the Serratia family (representing nine Serratia species) were chosen to verify the specificity of the primers...
August 18, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28821935/age-related-t2-relaxation-times-at-3-tesla-as-a-biomarker-of-infratentorial-brain-maturation
#2
Eva Bültmann, Loukia M Spineli, Friederike Göhner, Hans Hartmann, Heinrich Lanfermann
PURPOSE: The purpose of this study was to examine age-related, infratentorial changes in T2 relaxation times during infancy and childhood using routine MRI data at 3 Tesla. METHODS: One hundred patients (0-199 months) without signal abnormalities on conventional MRI were retrospectively selected from our pool of pediatric MRI examinations. T2 maps based on our routinely acquired triple-echo turbo spin-echo (TSE) sequence were created. Based on their clinical symptoms, the children were divided into 43 controls and 57 diseased children with different clinical diseases...
August 18, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28821546/a-supervised-statistical-learning-approach-for-accurate-legionella-pneumophila-source-attribution-during-outbreaks
#3
Andrew H Buultjens, Kyra Y L Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Gonçalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#4
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820399/repetitive-muscle-compression-reduces-vascular-mechano-sensitivity-and-the-hyperemic-response-to-muscle-contraction
#5
A Messere, M Turturici, G Millo, S Roatta
Animal studies have shown that the rapid hyperemic response to external muscle compression undergoes inactivation upon repetitive stimulation, but this phenomenon has never been observed in humans. The aim of the present study was to determine whether 1) the vascular mechano-sensitivity underlying muscle compression-induced hyperemia is inactivated in an inter-stimulus interval (ISI)-dependent fashion upon repetitive stimulation, as suggested by animal studies, and 2) whether such inactivation also attenuates contraction-induced hyperemia...
June 2017: Journal of Physiology and Pharmacology: An Official Journal of the Polish Physiological Society
https://www.readbyqxmd.com/read/28820087/reinstating-mycobacterium-massiliense-and-mycobacterium-bolletii-as-species-of-the-mycobacterium-abscessus-complex
#6
Toidi Adekambi, Mohamed Sassi, Jakko van Ingen, Michel Drancourt
TheMycobacterium abscessus complex is a group of rapidly growing, multiresistant mycobacteria previously divided into three species. Proposal for the union of Mycobacterium bolletii and Mycobacterium massiliense into one subspecies, so-called M. abscessus subsp. massiliense, created much confusion about the routine identification and reporting of M. abscessus clinical isolates for clinicians. Results derived from multigene sequencing unambiguously supported the reinstatement of M. massiliense and M. bolletii as species, culminating in the presence of erm(41)-encoded macrolide resistance in M...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28819973/mobile-platform-for-multiplexed-detection-and-differentiation-of-disease-specific-nucleic-acid-sequences-using-microfluidic-loop-mediated-isothermal-amplification-and-smartphone-detection
#7
Weili Chen, Hojeong Yu, Fu Sun, Akid Ornob, Ryan Brisbin, Anurup Ganguli, Vinay Kumar Vemuri, Piotr Strzebonski, Guangzhe Cui, Karen J Allen, Smit A Desai, Weiran Lin, David M Nash, David Hirschberg, Ian Brooks, Rashid Bashir, Brian T Cunningham
New tools are needed to enable rapid detection, identification, and reporting of infectious viral and microbial pathogens in a wide variety of point-of-care applications that impact human and animal health. We report the design, construction, and characterization of a platform for multiplexed analysis of disease-specific DNA sequences that utilizes a smartphone camera as the sensor in conjunction with a handheld "cradle" that interfaces the phone with a silicon-based microfluidic chip embedded within a credit card-sized cartridge...
August 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28819248/a-portable-microfluidic-platform-for-rapid-molecular-diagnostic-testing-of-patients-with-myeloproliferative-neoplasms
#8
Hua Wang, Xinju Zhang, Xiao Xu, Qunfeng Zhang, Hengliang Wang, Dong Li, Zhihua Kang, Zhiyuan Wu, Yigui Tang, Zhenhua An, Ming Guan
The ability to simultaneously detect JAK2 V617F and MPL W515K/L mutations would substantially improve the early diagnosis of myeloproliferative neoplasms (MPNs) and decrease the risk of arterial thrombosis. The goal of this study is to achieve a point of care testing platform for simultaneous analysis of major genetic alterations in MPN. Here, we report a microfluidic platform including a glass capillary containing polypropylene matrix that extracts genomic DNA from a drop of whole blood, a microchip for simultaneous multi-gene mutation screening, and a handheld battery-powered heating device...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819006/increased-tissue-oxygenation-explains-the-attenuation-of-hyperaemia-upon-repetitive-pneumatic-compression-of-the-lower-leg
#9
Alessandro Messere, Gianluca Ceravolo, Walter Franco, Daniela Maffiodo, Carlo Ferraresi, Silvestro Roatta
Aim The rapid hyperaemia evoked by muscle compression is short-lived and was recently shown to undergo a rapid decrease even in spite of continuing mechanical stimulation. The present study aims at investigating the mechanisms underlying this attenuation which include local metabolic mechanisms, desensitization of mechano-sensitive pathways, and reduced efficacy of the muscle pump. Methods In 10 healthy subjects short sequences of mechanical compressions (n=3-6; 150 mmHg) of the lower leg were delivered at different inter-stimulus intervals (ranging from 20 to 160 s) through a customized pneumatic device...
August 17, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28818953/new-horizons-for-precision-medicine-in-biliary-tract-cancers
#10
REVIEW
Juan W Valle, Angela Lamarca, Lipika Goyal, Jorge Barriuso, Andrew X Zhu
Biliary tract cancers (BTC), including cholangiocarcinoma and gallbladder cancer, are poor-prognosis and low-incidence cancers, although the incidence of intrahepatic cholangiocarcinoma is rising. A minority of patients present with resectable disease but relapse rates are high; benefit from adjuvant capecitabine chemotherapy has been demonstrated. Cisplatin/gemcitabine combination chemotherapy has emerged as the reference first-line treatment regimen; there is no standard second-line therapy. Selected patients may be suitable for liver-directed therapy (e...
August 17, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28818905/complete-genome-sequence-of-mycobacterium-stephanolepidis
#11
Hanako Fukano, Mitsunori Yoshida, Yukie Katayama, Tsutomu Omatsu, Tetsuya Mizutani, Osamu Kurata, Shinpei Wada, Yoshihiko Hoshino
Mycobacterium stephanolepidis is a rapid-growing nonpigmented species isolated from marine teleost fish (Stephanolepis cirrhifer) and is closely related to Mycobacterium chelonae Here, we report the complete sequence of its genome, comprising a 4.9-Mb chromosome. The sequence represents essential data for future phylogenetic and comparative genome studies of this fish pathogen.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818886/draft-genome-sequences-of-two-pseudomonas-aeruginosa-bloodstream-infection-isolates-associated-with-rapid-patient-death
#12
K L McCarthy, A V Jennison, A M Wailan, D L Paterson
The morbidity and mortality associated with Pseudomonas aeruginosa bloodstream infections are significant. New strategies are required to treat such infections. We report here the draft genome sequences of two antibiotic-sensitive P. aeruginosa bloodstream infection isolates that were associated with rapid death in nonneutropenic patients.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818691/multi-center-evaluation-of-the-cobas-%C3%A2-liat-%C3%A2-influenza-a-b-rsv-assay-for-rapid-point-of-care-diagnosis
#13
Jane Gibson, Elissa M Schechter-Perkins, Patricia Mitchell, Sharon Mace, Yu Tian, Kemi Williams, Robert Luo, Belinda Yen-Lieberman
Point of Care Testing (POCT) provides the capability for rapid laboratory test results in patient care environments where a traditional clinical laboratory is not available. POCTs have shorter turn-around times (TATs), they may be performed by non-laboratory personnel, and the need for transport time is eliminated. The Food and Drug Administration (FDA) recently granted Clinical Laboratory Improvements Amendment (CLIA) waiver status to the cobas(®) Influenza A/B & RSV assay, a rapid, accurate point-of-care test for Influenza and respiratory syncytial virus (RSV) performed on the Liat(®) System...
August 8, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#14
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) greater than approximately 50bp. Since these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required resulting in increased labor, costs, and turnaround times...
August 14, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28818557/dna-aptamer-identification-and-characterization-for-e-coli-o157-detection-using-cell-based-selex-method
#15
Masoum Amraee, Mana Oloomi, Afsaneh Yavari, Saeid Bouzari
Escherichia coli (E. coli) O157:H7 is a foodborne pathogen that causes symptoms in humans. Its rapid identification should be considered to avoid toxic effects of the pathogen. In this study, systematic evolution of ligands by exponential enrichment using whole cells (Cell-SELEX) method was used for recognizing E. coli strain, O157 by single-stranded DNA library of aptamer. Nine rounds of cell-selex procedure were applied using O157, as a whole-cell target, with O42, K12, Top10, DH5α E. coli cells, Shigella flexneri and Salmonella typhi as counterparts...
August 14, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28817704/analysis-of-multidrug-resistant-group-b-streptococci-with-reduced-penicillin-susceptibility-forming-small-less-hemolytic-colonies
#16
Hirotsugu Banno, Kouji Kimura, Yosuke Tanaka, Tsuyoshi Sekizuka, Makoto Kuroda, Wanchun Jin, Jun-Ichi Wachino, Keiko Yamada, Keigo Shibayama, Yoshichika Arakawa
Group B streptococci (GBS; Streptococcus agalactiae) are the leading cause of neonatal invasive diseases and are also important pathogens for elderly adults. Until now, nearly all GBS with reduced penicillin susceptibility (PRGBS) have shown β-hemolytic activity and grow on sheep blood agar. However, we have previously reported three PRGBS clinical isolates harboring a CylK deletion that form small less hemolytic colonies. In this study, we examined the causes of small, less hemolytic colony formation in these clinical isolates...
2017: PloS One
https://www.readbyqxmd.com/read/28817385/novel-molecular-defects-associated-with-very-early-onset-inflammatory-bowel
#17
Sara Ciullini Mannurita, Eleonora Gambineri
PURPOSE OF REVIEW: Immune dysregulation disorders present with common clinical features of multiorgan autoimmunity. Gastrointestinal involvement is the hallmark of an impaired immune homeostasis. This review will give an overview on the novel phenotypes, highlighting the major points that will help to enable early diagnosis and treatment. RECENT FINDINGS: The rapid progress on DNA sequencing technologies have led to the identification of monogenic defects that adversely impact the control of immune homeostasis...
August 16, 2017: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28815912/assembly-and-rna-free-annotation-of-highly-heterozygous-genomes-the-case-of-the-thick-billed-murre-uria-lomvia
#18
Anna Tigano, Timothy B Sackton, Vicki L Friesen
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats, and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird...
August 16, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28815890/a-semi-synthetic-glycoconjugate-vaccine-candidate-for-carbapenem-resistant-klebsiella-pneumoniae
#19
Peter H Seeberger, Claney L Pereira, Naeem Khan, Guozhi Xiao, Elizabeth Diago-Navarro, Katrin Reppe, Bastian Opitz, Bettina C Fries, Martin Witzenrath
Hospital acquired infections are an increasingly serious health concern. Infections caused by carpabenem-resistant Klebsiella pneumoniae (CR-Kp) are especially problematic, with a 50% average survival rate. CR-Kp are isolated from patients with ever greater frequency: 7% within the EU but 62% in Greece. At a time when antibiotics are becoming less effective, no vaccines to protect from this severe bacterial infection exist. Here, we describe the convergent [3+3] synthesis of the hexasaccharide repeating unit from its capsular polysaccharide and related sequences...
August 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#20
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
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