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https://www.readbyqxmd.com/read/29778045/massively-parallel-sequencing-of-124-snps-included-in-the-precision-id-identity-panel-in-three-east-asian-minority-ethnicities
#1
Jing Liu, Zheng Wang, Guanglin He, Xueying Zhao, Mengge Wang, Tao Luo, Chengtao Li, Yiping Hou
Massively parallel sequencing (MPS) technologies can sequence many targeted regions of multiple samples simultaneously and are gaining great interest in the forensic community. The Precision ID Identity Panel contains 90 autosomal SNPs and 34 upper Y-Clade SNPs, which was designed with small amplicons and optimized for forensic degraded or challenging samples. Here, 184 unrelated individuals from three East Asian minority ethnicities (Tibetan, Uygur and Hui) were analyzed using the Precision ID Identity Panel and the Ion PGM System...
May 15, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29778030/retrospective-genotype-phenotype-analysis-in-a-305-patient-cohort-referred-for-testing-of-a-targeted-epilepsy-panel
#2
Andrew N Hesse, Jennifer Bevilacqua, Kritika Shankar, Honey V Reddi
PURPOSE: Epilepsy is a diverse neurological condition with extreme genetic and phenotypic heterogeneity. The introduction of next-generation sequencing into the clinical laboratory has made it possible to investigate hundreds of associated genes simultaneously for a patient, even in the absence of a clearly defined syndrome. This has resulted in the detection of rare and novel mutations at a rate well beyond our ability to characterize their effects. This retrospective study reviews genotype data in the context of available phenotypic information on 305 patients spanning the epileptic spectrum to identify established and novel patterns of correlation...
May 16, 2018: Epilepsy Research
https://www.readbyqxmd.com/read/29777876/poly-adenine-mediated-fluorescent-spherical-nucleic-acid-probes-for-live-cell-imaging-of-endogenous-tumor-related-mrna
#3
Dan Zhu, Dongxia Zhao, Jiaxuan Huang, Yu Zhu, Jie Chao, Shao Su, Jiang Li, Lihua Wang, Jiye Shi, Xiaolei Zuo, Lixing Weng, Qian Li, Lianhui Wang
Identification of tumor-related mRNA in living cells hold great promise for early cancer diagnosis and pathological research. Herein, we present poly-adenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) probes for intracellular mRNA detection with regulable sensitivities by programmably adjusting the loading density of DNA on gold nano-interface. Gold nanoparticles (AuNPs) functionalized with polyA-tailed recognition sequences were hybridized to fluorescent "reporter" strands to fabricate fluorescence-quenched FSNA probes...
May 16, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/29777734/gga-mir-454-suppresses-infectious-bursal-disease-virus-ibdv-replication-via-directly-targeting-ibdv-genomic-segment-b-and-cellular-suppressors-of-cytokine-signaling-6-socs6
#4
Mengjiao Fu, Bin Wang, Xiang Chen, Zhiyuan He, Yongqiang Wang, Xiaoqi Li, Hong Cao, Shijun J Zheng
MicroRNAs (miRNAs), as post-transcriptional regulators, play important roles in the process of viral infection through inhibiting virus replication or modulating host immune response. However, the role of miRNAs in host response against infectious bursal disease virus (IBDV) infection is still unclear. In this study, we found that gga-miR-454 of the host was decreased in response to IBDV infection and that transfection of DF-1 cells with miR-454 inhibited IBDV replication via directly targeting the specific sequence of IBDV genomic segment B, while blockage of endogenous miR-454 by inhibitors enhanced virus replication...
May 16, 2018: Virus Research
https://www.readbyqxmd.com/read/29777630/microrna-493-is-a-prognostic-factor-in-triple-negative-breast-cancer
#5
Ling Yao, Yirong Liu, Zhigang Cao, Junjing Li, Yanni Huang, Xin Hu, Zhiming Shao
Breast cancer is one of the most common malignant diseases in women, in which triple-negative breast cancer (TNBC) exhibits higher aggressiveness and recurrence rates, while there are no effective targets or tailored treatments for patients with this subtype. Thus, finding effective prognostic markers for TNBC might help clinicians in their ability to care for their patients. We used tissue microarrays (TMAs) to detect miR-493 expression in breast cancer samples. A miRCURY LNATM detection probe specific for miR-493 was used in in situ hybridization assays...
May 19, 2018: Cancer Science
https://www.readbyqxmd.com/read/29777484/identification-of-differentially-expressed-micrornas-in-sahiwal-bos-indicus-breed-of-cattle-during-thermal-stress
#6
Gyanendra Singh Sengar, Rajib Deb, Umesh Singh, Vivek Junghare, Saugata Hazra, T V Raja, Rani Alex, Ashish Kumar, R R Alyethodi, Rajiv Kant, Subhash Jakshara, C G Joshi
microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in post transcriptional gene regulation that influence various fundamental cellular processes, including the cellular responses during environmental stresses. However, perusal of literatures revealed few reports on the differential expression of miRNA during thermal stress in Indian native (Bos indicus) cattle breeds. The present investigation aimed to identify differentially expressed miRNAs during thermal stress in Sahiwal (Bos indicus) dairy cattle breed of India, adapted with tropical climate over a long period of time...
May 18, 2018: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/29777440/mir-27a-b-regulates-liver-regeneration-by-posttranscriptional-modification-of-tmub1
#7
Xiang Lan, Guangyao Li, Hongming Liu, Hangwei Fu, Ping Chen, Menggang Liu
BACKGROUND: Transmembrane and ubiquitin-like domain-containing 1 protein (Tmub1) negatively regulates liver regeneration. However, whether this regulation involves posttranscriptional modification of Tmub1 expression is unknown. AIM: The aim of the study was to investigate whether microRNA (miR)-27a/b regulates posttranscriptional modification of Tmub1 and cell proliferation during liver regeneration. METHODS: Tmub1 mRNA 3'-untranslated region (UTR) sequences were analyzed using online software...
May 17, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29777113/synaptic-mechanisms-of-interference-in-working-memory
#8
Zachary P Kilpatrick
Information from preceding trials of cognitive tasks can bias performance in the current trial, a phenomenon referred to as interference. Subjects performing visual working memory tasks exhibit interference in their responses: the recalled target location is biased in the direction of the target presented on the previous trial. We present modeling work that develops a probabilistic inference model of this history-dependent bias, and links our probabilistic model to computations of a recurrent network wherein short-term facilitation accounts for the observed bias...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#9
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776928/enrichment-of-clinically-relevant-organisms-in-spontaneous-preterm-delivered-placenta-and-reagent-contamination-across-all-clinical-groups-in-a-large-uk-pregnancy-cohort
#10
Lydia J Leon, Ronan Doyle, Ernest Diez-Benavente, Taane G Clark, Nigel Klein, Philip Stanier, Gudrun E Moore
In this study differences in the placental microbiota of term and preterm deliveries from a large UK pregnancy cohort were studied using 16S targeted amplicon sequencing. The impact of contamination from DNA extraction, PCR reagents, as well as those from delivery itself were also examined. A total of 400 placental samples from 256 singleton pregnancies were analysed and differences investigated between spontaneous preterm, non-spontaneous preterm, and term delivered placenta. DNA from recently delivered placenta was extracted, and screening for bacterial DNA was carried out using targeted sequencing of the 16S rRNA gene on the Illumina MiSeq platform...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29776924/tools-for-rapid-genetic-engineering-of-vibrio-fischeri
#11
Karen L Visick, Kelsey M Hodge-Hanson, Alice H Tischler, Allison K Bennett, Vincent Mastrodomenico
Vibrio fischeri is used as a model for number of processes, including symbiosis, quorum sensing, bioluminescence, and biofilm formation. Many of these studies depend on generating deletion mutants and complementing them. Engineering such strains, however, is a time-consuming, multi-step process that relies on cloning and subcloning. Here, we describe a set of tools that can be used to rapidly engineer deletions and insertions in the V. fischeri chromosome without cloning. We developed a uniform approach for generating deletions using PCR SOEing (Splicing by Overlap Extension) with antibiotic cassettes flanked by standardized linker sequences...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29776391/the-clinical-implications-of-g1-g6-transcriptomic-signature-and-5-gene-score-in-korean-patients-with-hepatocellular-carcinoma
#12
Sung-Min Ahn, Farhan Haq, Inkeun Park, Jean-Charles Nault, Jessica Zucman-Rossi, Eunsil Yu
BACKGROUND: Efforts have been made to classify Hepatocellular Carcinoma (HCC) at surgically curable stages because molecular classification, which is prognostically informative, can accurately identify patients in need of additional early therapeutic interventions. Recently, HCC classification based French studies on the expression of 16 genes and 5 genes were proposed. In 16-gene classification, transcriptomic signatures (G1-G6) were used to classify HCC patients into clinical, genomic and pathway-specific subgroups...
May 18, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29776375/range-wide-genetic-analysis-of-dermacentor-variabilis-and-its-francisella-like-endosymbionts-demonstrates-phylogeographic-concordance-between-both-taxa
#13
Emily L Kaufman, Nathan E Stone, Glen A Scoles, Crystal M Hepp, Joseph D Busch, David M Wagner
BACKGROUND: The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete. METHODS: We carried out a phylogenetic analysis of D. variabilis using samples collected from 26 USA states and five Canadian provinces. Tick samples (n = 1053 in total) originated from two main sources: existing archives (2000-2011), and new collections made from 2012 to 2013...
May 18, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29776373/metabolic-therapy-with-peg-arginase-induces-a-sustained-complete-remission-in-immunotherapy-resistant-melanoma
#14
Carmela De Santo, Paul Cheng, Andrew Beggs, Sharon Egan, Alberto Bessudo, Francis Mussai
BACKGROUND: Metastatic melanoma is an aggressive skin cancer with a poor prognosis. Current treatment strategies for high-stage melanoma are based around the use of immunotherapy with immune checkpoint inhibitors such as anti-PDL1 or anti-CTLA4 antibodies to stimulate anti-cancer T cell responses, yet a number of patients will relapse and die of disease. Here, we report the first sustained complete remission in a patient with metastatic melanoma who failed two immunotherapy strategies, by targeting tumour arginine metabolism...
May 18, 2018: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/29776341/different-adaptive-strategies-in-e-coli-populations-evolving-under-macronutrient-limitation-and-metal-ion-limitation
#15
Omar M Warsi, Dan I Andersson, Daniel E Dykhuizen
BACKGROUND: Adaptive responses to nutrient limitation involve mutations that increase the efficiency of usage or uptake of the limiting nutrient. However, starvation of different nutrients has contrasting effects on physiology, resulting in different evolutionary responses. Most studies performed to understand these evolutionary responses have focused only on macronutrient limitation. Hence our understanding of adaptation under limitation of other forms of nutrients is limited. In this study, we compared the evolutionary response in populations evolving under growth-limiting conditions for a macronutrient and a major cation...
May 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29776336/phylogenomic-analysis-of-apoidea-sheds-new-light-on-the-sister-group-of-bees
#16
Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, Michael Ohl
BACKGROUND: Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families...
May 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29775961/antioxidant-response-elements-discovery-classes-regulation-and-potential-applications
#17
REVIEW
Azhwar Raghunath, Kiruthika Sundarraj, Raju Nagarajan, Frank Arfuso, Jinsong Bian, Alan P Kumar, Gautam Sethi, Ekambaram Perumal
Exposure to antioxidants and xenobiotics triggers the expression of a myriad of genes encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer protection against oxidative stress. This articulated universal mechanism is regulated through the cis-acting elements in an array of Nrf2 target genes called antioxidant response elements (AREs), which play a critical role in redox homeostasis. Though the Keap1/Nrf2/ARE system involves many players, AREs hold the key in transcriptional regulation of cytoprotective genes...
May 7, 2018: Redox Biology
https://www.readbyqxmd.com/read/29775857/enzyme-free-homogeneous-electrochemical-biosensor-for-dna-assay-using-toehold-triggered-strand-displacement-reaction-coupled-with-host-guest-recognition-of-fe-3-o-4-sio-2-%C3%AE-cd-nanocomposites
#18
Jingjing Jiang, Xinyi Lin, Dong Ding, Guowang Diao
Taking advantages of the toehold-triggered strand displacement reaction (TSDR) and host-guest interaction of β-cyclodextrin (β-CD), a facile enzyme-free and homogeneous electrochemical sensing strategy was designed for the sensitive assay of target DNA using Fe3 O4 @SiO2 @β-CD nanocomposites and ferrocene-labeled hairpin DNA (H-1) as the capture and electrochemical probes, respectively. Upon addition of target molecule, the initiated TSDR process induced the conformational change of H-1, and subsequently stimulated the dynamic assembly of assist probes (A-1 and A-2) to generate H-1:A-1:A-2 duplex along with the release of target sequence...
April 17, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29775838/deconstructing-skill-learning-and-its-physiological-mechanisms
#19
Danny Spampinato, Pablo Celnik
Acquiring complex motor skills involves learning a number of distinct motor components. Two fundamental elements that constitute a skill are the internal representation (i.e., the calibration of a sensorimotor map) and the sequence of movements needed to execute the task. Learning each of these likely rely on different neural substrates such as the cerebellum and primary motor cortex (M1), and physiological mechanisms. However, the specific neurophysiological processes underlying the acquisition of these components remains poorly understood...
March 27, 2018: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/29775785/integration-of-mirna-weighted-gene-co-expression-network-and-mirna-mrna-co-expression-analyses-reveals-potential-regulatory-functions-of-mirnas-in-calf-rumen-development
#20
Duy N Do, Pier-Luc Dudemaine, Bridget E Fomenky, Eveline M Ibeagha-Awemu
This study aimed to explore the roles of microRNAs (miRNAs) in calf rumen development during early life. Rumen tissues were collected from 16 calves (8 at pre-weaning and 8 at post-weaning) for miRNA-sequencing, differential expression (DE), miRNA weighted gene co-expression network (WGCNA) and miRNA-mRNA co-expression analyses. 295 miRNAs were identified. Bta-miR-143, miR-26a, miR-145 and miR-27b were the most abundantly expressed. 122 miRNAs were significantly DE between the pre- and post-weaning periods and the most up- and down-regulated miRNAs were bta-miR-29b and bta-miR-493, respectively...
May 15, 2018: Genomics
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