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https://www.readbyqxmd.com/read/28527390/on-filter-direct-amplification-of-legionella-pneumophila-for-rapid-assessment-of-its-abundance-and-viability
#1
Farag A Samhan, Tiffany M Stedtfeld, Hassan Waseem, Maggie R Williams, Robert D Stedtfeld, Syed A Hashsham
Guidelines and regulations to control Legionella pneumophila in cooling water systems of large buildings are evolving due to the increasing number of outbreaks. Rapid, on-site, simple, and sensitive quantification methods that are also able to assess viability may be extremely useful in monitoring and control. Culture-based methods for measuring L. pneumophila may take 4-10 days and qPCR-based methods are also slow, requiring at least a day from sample to result, albeit mainly due to the need for sample transport to a centralized laboratory...
May 13, 2017: Water Research
https://www.readbyqxmd.com/read/28526432/quantitative-susceptibility-mapping-using-principles-of-echo-shifting-with-a-train-of-observations-sequence-on-1-5t-mri
#2
Hirohito Kan, Nobuyuki Arai, Harumasa Kasai, Hiroshi Kunitomo, Yasujiro Hirose, Yuta Shibamoto
PURPOSE: To evaluate the accuracy of susceptibility estimated from the principles of echo shifting with a train of observations (PRESTO) sequence using a 1.5T MRI system, we conducted experiments on the human brain using the PRESTO sequence and compared our results with the susceptibility obtained from spoiled gradient-recalled echo (GRE) sequence with flow compensation using quantitative susceptibility mapping (QSM) reconstruction. MATERIALS AND METHODS: Experiments on the human brain were conducted on 12 healthy volunteers (27±4years) using PRESTO and spoiled GRE sequences on a 1...
May 16, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#3
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28526036/molecular-characterization-of-dirofilaria-spp-circulating-in-portugal
#4
Cátia Ferreira, Ana Afonso, Manuela Calado, Isabel Maurício, Ana Margarida Alho, José Meireles, Luís Madeira de Carvalho, Silvana Belo
BACKGROUND: Dirofilariosis is a potentially zoonotic parasitic disease, mainly transmitted by mosquito vectors in many parts of the world. Data concerning the canine Dirofilaria species currently circulating in Portugal is scarce. Thereby, a large-scale study was conducted to determine the Dirofilaria spp. present in Portugal, based on a molecular approach, and also to optimize a reliable and highly sensitive species-specific polymerase chain reaction (PCR) assay that could be used for the simultaneous detection and differentiation of Dirofilaria immitis, Dirofilaria repens, and other concurrent filarial species in animal reservoirs...
May 19, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28525966/gene-expression-of-vibrio-parahaemolyticus-growing-in-laboratory-isolation-conditions-compared-to-those-common-in-its-natural-ocean-environment
#5
Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor, Romilio T Espejo
BACKGROUND: Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525954/construction-of-various-%C3%AE-34-5-deleted-fluorescent-expressing-oncolytic-herpes-simplex-type-1-ohsv-for-generation-and-isolation-of-hsv-based-vectors
#6
REVIEW
Shahriyar Abdoli, Farzin Roohvand, Ladan Teimoori-Toolabi, Mohammad Ali Shokrgozar, Mina Bahrololoumi, Kayhan Azadmanesh
Background: Oncolytic herpes simplex virus (oHSV)-based vectors lacking γ34.5 gene, are considered as ideal templates to construct efficient vectors for (targeted) cancer gene therapy. Herein, we reported the construction of three single/dually-flourescence labeled and γ34.5-deleted, recombinant HSV-1 vectors for rapid generation and easy selection/isolation of different HSV-Based vectors. Methods: Generation of recombinant viruses was performed with conventional homologous recombination methods using green fluorescent protein (GFP) and BleCherry harboring shuttle vectors...
July 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28525772/implementation-of-glycanbuilder-to-draw-a-wide-variety-of-ambiguous-glycans
#7
Shinichiro Tsuchiya, Nobuyuki P Aoki, Daisuke Shinmachi, Masaaki Matsubara, Issaku Yamada, Kiyoko F Aoki-Kinoshita, Hisashi Narimatsu
GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) was proposed during the early stages of the GlyTouCan project. GlyTouCan uses WURCS as its base representation for glycans because existing formats were insufficient in their flexibility to represent any and all glycans universally. Therefore, in order to obtain WURCS strings for existing or new glycan structures, conversion tools or glycan structure editors that can export WURCS became necessary...
April 19, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28525653/predicted-philogeny-secondary-conformational-structure-and-epitope-antigenicity-of-immunological-sequences-in-poultry
#8
L J Lara, A P Peconick, É J Fassani, A M P Júnior, P R B Chalfun, D L Raymundo, T A Barçante, J M de P Barçante
Poultry production is faced with different types of stresses that are responsible for issues of animal welfare as well as for economic losses. Moreover, the immunity decreases when animals are stressed. In silico analyses are important in reducing the cost and in increasing the accuracy of scientific results. A bioinformatics tool was used to perform ontology studies on 15 different immunological sequences of poultry. The mRNA structures and sequences with maximum antigenic residues were also predicted. No homology was found between the sequences of poultry and mammals...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28524363/donor-transmitted-mutation-of-the-abcb11-gene-and-ensuing-intra-hepatic-cholestasis-of-pregnancy-in-a-liver-transplant-recipient
#9
Tiong Yeng Lim, Iona Coltart, Pierre Foskett, Richard Thompson, Sandra Strautnieks, Leonie Penna, Catherine Williamson, Rosa Miquel, Michael A Heneghan
In liver transplant (LT) recipients, the cause of graft dysfunction in pregnancy is often difficult to ascertain. Moreover, a liver biopsy in late pregnancy is often avoided as a consequence of patient and physician factors. Management of graft dysfunction can be difficult in this setting. We report a 30-year-old female LT recipient who developed acutely deranged liver biochemistry during the third trimester of her first pregnancy. At 29 weeks gestation, her liver function test (LFT) became abnormal; AST peaked at 978 IU/L (normal range 10-50), GGT 25 IU/L (normal range 1-55), bilirubin 1...
May 19, 2017: Liver Transplantation
https://www.readbyqxmd.com/read/28524227/computational-approaches-for-interpreting-scrna-seq-data
#10
REVIEW
R Rostom, V Svensson, S A Teichmann, G Kar
The recent developments in high throughput single-cell RNA sequencing technology (scRNA-seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data analysis, building on high-dimensional data mining techniques. Here, we consider biological questions for which scRNA-seq data is used, both at a cell and gene level, and describe tools available for these types of analyses. This is an exciting and rapidly evolving field, where clustering, pseudotime inference, branching inference and gene-level analyses are particularly informative areas of computational analysis...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28523555/alzheimer-s-disease-and-ncrnas
#11
Rotem Maoz, Benjamin P Garfinkel, Hermona Soreq
Alzheimer's disease is a devastating neurodegenerative disorder affecting a significant portion of the world's rapidly growing aging population. In spite of its prevalence, the etiology of the disease is still poorly understood, and effective therapy is all but unavailable. Over the past decade, noncoding RNA, including microRNA (miRNA), has emerged as a major class of regulatory molecules involved in virtually all physiological and disease states. The specificity provided by miRNA sequence complementarity, together with the ability of these molecules to regulate complex networks of genes, has made them exciting novel targets for therapeutic agents...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523344/role-of-g3bp1-in-glucocorticoid-receptor-mediated-microrna-15b-and-microrna-23a-biogenesis-in-endothelial-cells
#12
Hoi-Hin Kwok, Po-Ying Poon, Kylie Hin-Man Mak, Lin-Yao Zhang, Pei Liu, Huoming Zhang, Nai-Ki Mak, Patrick Ying-Kit Yue, Ricky Ngok-Shun Wong
MicroRNAs (miRNAs) are a family of non-coding RNAs that play crucial roles in regulating various normal cellular responses. Recent studies revealed that the canonical miRNA biogenesis pathway is subject to sophisticated regulation. Hormonal control of miRNA biogenesis by androgen and estrogen has been demonstrated, but the direct effects of the glucocorticoid receptor (GR) on miRNA biogenesis are unknown. This study revealed the role of GR in miRNA maturation. We showed that two GR agonists, dexamethasone and ginsenoside-Rg1 rapidly suppressed the expression of mature miR-15b, miR-23a, and miR-214 in human endothelial cells...
May 18, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28523290/complex-modular-architecture-around-a-simple-toolkit-of-wing-pattern-genes
#13
Steven M Van Belleghem, Pasi Rastas, Alexie Papanicolaou, Simon H Martin, Carlos F Arias, Megan A Supple, Joseph J Hanly, James Mallet, James J Lewis, Heather M Hines, Mayte Ruiz, Camilo Salazar, Mauricio Linares, Gilson R P Moreira, Chris D Jiggins, Brian A Counterman, W Owen McMillan, Riccardo Papa
Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern...
2017: Nat Ecol Evol
https://www.readbyqxmd.com/read/28523090/penetrating-craniomaxillofacial-injury-caused-by-a-pneumatic-nail-gun
#14
Kevin Jae Choi, Marisa Ann Ryan, Tracy Cheng, David Powers
Craniomaxillofacial injuries can be complex, requiring a multidisciplinary approach. The primary survey is always the first step in trauma management prior to proceeding with further evaluation and treatment. A 26-year-old man presented with a penetrating nail gun injury through the oral and nasal cavities. He did not present in extremis but required elective endotracheal intubation for intraoperative assessment and treatment. Airway management was enhanced by the use of lingual nerve and inferior alveolar nerve blocks via the Vazirani-Akinosi technique to maintain spontaneous respiration while the tongue was distracted from the palate...
June 2017: Craniomaxillofacial Trauma & Reconstruction
https://www.readbyqxmd.com/read/28522818/efficient-modification-of-%C3%AE-dna-substrates-for-single-molecule-studies
#15
Yoori Kim, Armando de la Torre, Andrew A Leal, Ilya J Finkelstein
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522803/precise-genome-wide-base-editing-by-the-crispr-nickase-system-in-yeast
#16
Atsushi Satomura, Ryosuke Nishioka, Hitoshi Mori, Kosuke Sato, Kouichi Kuroda, Mitsuyoshi Ueda
The CRISPR/Cas9 system has been applied to efficient genome editing in many eukaryotic cells. However, the bases that can be edited by this system have been limited to those within the protospacer adjacent motif (PAM) and guide RNA-targeting sequences. In this study, we developed a genome-wide base editing technology, "CRISPR Nickase system" that utilizes a single Cas9 nickase. This system was free from the limitation of editable bases that was observed in the CRISPR/Cas9 system, and was able to precisely edit bases up to 53 bp from the nicking site...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522775/purpura-fulminans-mimicking-toxic-epidermal-necrolysis-additional-value-of-16s-rrna-sequencing-and-skin-biopsy
#17
K H W Dautzenberg, F N Polderman, R J van Suylen, M A M Moviat
Both purpura fulminans and toxic epidermal necrolysis (TEN) are rare and life-threatening disorders with a high mortality. We present a case of suspected rapidly progressive, severe pneumococcal sepsis-induced purpura fulminans complicated by multiple organ failure, severe epidermolysis and cutaneous necrosis. We show the diagnostic challenge to differentiate between purpura fulminans and TEN, as the extensive epidermolysis in purpura fulminans may mimic TEN and we highlight the additional value of repeated skin biopsies and 16S rRNA gene sequencing...
May 2017: Netherlands Journal of Medicine
https://www.readbyqxmd.com/read/28522638/a-self-consistent-structural-perturbation-approach-for-determining-the-magnitude-and-extent-of-allosteric-coupling-in-proteins
#18
Nandakumar Rajasekaran, Athi N Naganathan
Elucidating the extent of energetic coupling between residues in single-domain proteins, a fundamental determinant of allostery, information transfer and folding cooperativity, has remained a grand challenge. While several sequence- and structure-based approaches have been proposed, a self-consistent description that is simultaneously compatible with unfolding thermodynamics is lacking. We had recently developed a simple structural perturbation protocol that captures the changes in thermodynamic stabilities induced by point mutations within the protein interior...
May 18, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#19
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28522372/effective-antimicrobial-activity-of-a-peptide-mutant-cbf-14-2-against-penicillin-resistant-bacteria-based-on-its-unnatural-amino-acids
#20
Wei Kang, Hanhan Liu, Lingman Ma, Mengxiao Wang, Shanshan Wei, Pengbo Sun, Meiling Jiang, Min Guo, Changlin Zhou, Jie Dou
Broad spectrum activities, a unique mode of actions and rare resistant variants make antimicrobial peptide (AMP) a potential alternative to antibiotics. However, AMPs still have limitations in clinical development due to their physiological stability, toxicity and manufacturing costs. Cbf-14, derived from cathelicidin-BF has been proven to be effective against drug-resistant bacteria. Herein, a series of Cbf-14 mutants were designed to overcome these limitations. Design strategies included substitutions of lysine (Lys) or leucine (Leu) with similar residues such as ornithine (Orn) and norleucine (Ile), which are unnatural amino acids, to generate AMPs with enhanced therapeutic potential...
May 15, 2017: European Journal of Pharmaceutical Sciences
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