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https://www.readbyqxmd.com/read/28231512/the-impact-of-third-generation-genomic-technologies-on-plant-genome-assembly
#1
REVIEW
Wen-Biao Jiao, Korbinian Schneeberger
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies...
February 20, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28231340/the-widely-used-nicotiana-benthamiana-16c-line-has-an-unusual-t-dna-integration-pattern-including-a-transposon-sequence
#2
Joshua G Philips, Fatima Naim, Michał T Lorenc, Kevin J Dudley, Roger P Hellens, Peter M Waterhouse
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site...
2017: PloS One
https://www.readbyqxmd.com/read/28231257/targeted-sequencing-identifies-a-novel-sh2d1a-pathogenic-variant-in-a-chinese-family-carrier-screening-and-prenatal-genetic-testing
#3
Jun-Yu Zhang, Song-Chang Chen, Yi-Yao Chen, Shu-Yuan Li, Lan-Lan Zhang, Ying-Hua Shen, Chun-Xin Chang, Yu-Qian Xiang, He-Feng Huang, Chen-Ming Xu
X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family...
2017: PloS One
https://www.readbyqxmd.com/read/28231255/confidence-and-self-attribution-bias-in-an-artificial-stock-market
#4
Mario A Bertella, Felipe R Pires, Henio H A Rego, Jonathas N Silva, Irena Vodenska, H Eugene Stanley
Using an agent-based model we examine the dynamics of stock price fluctuations and their rates of return in an artificial financial market composed of fundamentalist and chartist agents with and without confidence. We find that chartist agents who are confident generate higher price and rate of return volatilities than those who are not. We also find that kurtosis and skewness are lower in our simulation study of agents who are not confident. We show that the stock price and confidence index-both generated by our model-are cointegrated and that stock price affects confidence index but confidence index does not affect stock price...
2017: PloS One
https://www.readbyqxmd.com/read/28231017/boosting-hole-mobility-in-coherently-strained-110-oriented-ge-si-core-shell-nanowires
#5
Sonia Conesa-Boj, Ang Li, Sebastian Koelling, Matthias Brauns, Joost Ridderbos, Ton T Nguyen, Marcel A Verheijen, Paul M Koenraad, Floris Arnoud Zwanenburg, Erik P A M Bakkers
The ability of core-shell nanowires to overcome existing limitations of heterostructures is one of the key ingredients for the design of next generation devices. This requires a detailed understanding of the mechanism for strain relaxation in these systems, in order to eliminate strain-induced defect formation and thus to boost important electronic properties such as carrier mobility. Here we demonstrate how the hole mobility of [110]-oriented Ge-Si core-shell nanowires can be substantially enhanced thanks to the realization of large band offset and coherent strain in the system, reaching values as high as 4200 cm(2)/(Vs) at 4K and 1600 cm(2)/(Vs) at room temperature for high hole densities of 1019 cm(-3)...
February 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28230858/ngs-based-transcriptome-profiling-reveals-biomarkers-for-companion-diagnostics-of-the-tgf-%C3%AE-receptor-blocker-galunisertib-in-hcc
#6
Yuan Cao, Rahul Agarwal, Francesco Dituri, Luigi Lupo, Paolo Trerotoli, Serena Mancarella, Peter Winter, Gianluigi Giannelli
Transforming growth factor-beta (TGF-β) signaling has gained extensive interest in hepatocellular carcinoma (HCC). The small molecule kinase inhibitor galunisertib, targeting the TGF-β receptor I (TGF-βRI), blocks HCC progression in preclinical models and shows promising effects in ongoing clinical trials. As the drug is not similarly effective in all patients, this study was aimed at identifying new companion diagnostics biomarkers for patient stratification. Next-generation sequencing-based massive analysis of cDNA ends was used to investigate the transcriptome of an invasive HCC cell line responses to TGF-β1 and galunisertib...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230760/bioinformatics-approaches-for-fetal-dna-fraction-estimation-in-noninvasive-prenatal-testing
#7
REVIEW
Xianlu Laura Peng, Peiyong Jiang
The discovery of cell-free fetal DNA molecules in plasma of pregnant women has created a paradigm shift in noninvasive prenatal testing (NIPT). Circulating cell-free DNA in maternal plasma has been increasingly recognized as an important proxy to detect fetal abnormalities in a noninvasive manner. A variety of approaches for NIPT using next-generation sequencing have been developed, which have been rapidly transforming clinical practices nowadays. In such approaches, the fetal DNA fraction is a pivotal parameter governing the overall performance and guaranteeing the proper clinical interpretation of testing results...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28230656/role-of-nonneutralizing-antibodies-in-vaccines-and-or-hiv-infected-individuals
#8
Luzia Mayr, Bin Su, Christiane Moog
PURPOSE OF REVIEW: Increased body of evidence gathered over time indicate that antibodies are capable of many inhibitory mechanisms, virus neutralization being just one of them. Nonneutralizing antibodyactivities interfering with HIV replication can also lead to a decrease in viral load and even in-vivo protection. RECENT FINDINGS: It was previously believed that neutralizing antibodies can achieve sterilizing protection mainly by using their neutralization capacities against the infecting virus directly at the portal of virus entry...
February 21, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28230645/clinical-scale-rapid-autologous-bk-virus-specific-t-cell-line-generation-from-kidney-transplant-recipients-with-active-viremia-for-adoptive-immunotherapy
#9
Caroline Lamarche, Julie Orio, Victoria Georges-Tobar, Thomas Pincez, Mathieu Goupil, Amina Dahmani, Cedric Carli C, Ann Brasey, Lambert Busque, Jean-Sébastien Delisle
BACKGROUND: Polyomavirus-associated nephropathy (PVAN) following BK virus reactivation in kidney transplant recipients (KTR) can compromise graft survival. Lowering immunosuppression is the only established approach to prevent or treat PVAN but nonspecifically increasing host immune competence also augments rejection risk. Ex vivo T cell stimulation/expansion offers the possibility to generate BK-specific T cell lines for adoptive immunotherapy. The objective of this study was to develop and characterize a clinical scale protocol to generate BK-specific T cell lines from viremic KTR...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28230642/strategies-to-obtain-diverse-and-specific-human-monoclonal-antibodies-from-transgenic-animals
#10
Marianne Brüggemann, Michael J Osborn, Biao Ma, Roland Buelow
Techniques to obtain large quantities of antigen-specific monoclonal antibodies, mAbs, were first established in the 1970s when Georges Köhler and César Milstein immortalized antibody-producing mouse B-lymphocytes by fusion with myeloma cells (http://www.whatisbiotechnology.org/exhibitions/milstein). Combined with the expression of human antibodies in transgenic animals, this technique allowed upon immunization the generation of highly specific fully human mAbs for therapeutic applications. Apart from being extremely beneficial, mAbs are a huge success commercially...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28230599/a-targeted-next-generation-genetic-sequencing-study-on-tetralogy-of-fallot-combined-with-cleft-lip-and-palate
#11
Lin Liu, Haisong Bu, Yifeng Yang, Zhiping Tan, Fei Zhang, Shijun Hu, Tianli Zhao
BACKGROUND: Congenital heart disease (CHD), plus cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Many genes have been investigated for their involvement in CHD with CLP. Targeted next-generation sequencing can analyze large amounts of genetic information rapidly, and thus address this question. METHODS: The authors designed a targeted, next-generation sequencing gene panel for 455 genes previously implicated in CHD or CLP...
February 22, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28230377/tailoring-anisotropic-li-ion-transport-tunnels-on-orthogonally-arranged-li-rich-layered-oxide-nanoplates-towards-high-performance-li-ion-batteries
#12
Ming Xu, Linfeng Fei, Wei-Bing Zhang, Tao Li, Wei Lu, Nian Zhang, Yanqing Lai, Zhian Zhang, Jing Fang, Kai Zhang, Jie Li, Haitao Huang
High-performance Li-rich layered oxide (LRLO) cathode material is appealing for next-generation Li-ion batteries owing to its high specific capacity (>300 mAh g-1). Despite intense studies in past decade, the low initial Coulombic efficiency and unsatisfactory cycling stability of LRLO still remain great challenges for its practical application. Here, we report a rational design of the orthogonally arranged {010}-oriented LRLO nanoplates with built-in anisotropic Li+ ion transport tunnels. Such a novel structure enables fast Li+ ion intercalation and deintercalation kinetics and enhanced structure stability for LRLO...
February 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28230180/assessment-of-chicken-carcass-microbiome-responses-during-processing-in-the-presence-of-commercial-antimicrobials-using-a-next-generation-sequencing-approach
#13
Sun Ae Kim, Si Hong Park, Sang In Lee, Casey M Owens, Steven C Ricke
The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230084/highly-potent-antimicrobial-peptides-from-n-terminal-membrane-binding-region-of-e-coli-mreb
#14
Karabi Saikia, Yalavarthi Durga Sravani, Vibin Ramakrishnan, Nitin Chaudhary
Microbial pathogenesis is a serious health concern. The threat escalates as the existing conventional antimicrobials are losing their efficacy against the evolving pathogens. Peptides hold promise to be developed into next-generation antibiotics. Antimicrobial peptides adopt amphipathic structures that could selectively bind to and disrupt the microbial membranes. Interaction of proteins with membranes is central to all living systems and we reasoned that the membrane-binding domains in microbial proteins could be developed into efficient antimicrobials...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230064/direct-observation-of-intrinsic-twin-domains-in-tetragonal-ch3nh3pbi3
#15
Mathias Uller Rothmann, Wei Li, Ye Zhu, Udo Bach, Leone Spiccia, Joanne Etheridge, Yi-Bing Cheng
Organic-inorganic hybrid perovskites are exciting candidates for next-generation solar cells, with CH3NH3PbI3 being one of the most widely studied. While there have been intense efforts to fabricate and optimize photovoltaic devices using CH3NH3PbI3, critical questions remain regarding the crystal structure that governs its unique properties of the hybrid perovskite material. Here we report unambiguous evidence for crystallographic twin domains in tetragonal CH3NH3PbI3, observed using low-dose transmission electron microscopy and selected area electron diffraction...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28230015/screening-of-gene-mutations-associated-with-bone-metastasis-in-nonsmall-cell-lung-cancer
#16
Kun Zhang, Min Zhang, Jinlong Zhu, Wang Hong
OBJECTIVE: The objective of this study is to assess the gene mutation of advanced nonsmall cell lung cancer (NSCLC) patients with bone metastasis using next-generation sequencing (NGS), and screen for the driver genes which are associated with bone metastasis of lung cancer. MATERIALS AND METHODS: Eight clinicopathologic samples from advanced NSCLC combined with bone metastasis patients were collected. Exome sequencing was conducted within 483 tumor-associated genes using Hiseq 2000_PE75 NGS platform...
December 2016: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#17
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28229402/next-generation-sequencing-to-guide-treatment-of-advanced-melanoma
#18
Klaus G Griewank, Bastian Schilling
Next-generation sequencing (NGS) has provided significant insights into the pathogenesis of human malignancies. In advanced melanoma, two therapeutic avenues have appeared and have immediately become the standard of care, i.e. targeted therapy with small molecule inhibitors, and immune checkpoint blockade. Sequencing has always been essential for determining which patients may benefit from targeted therapies (e.g. the presence of BRAF mutations). While sequencing does not currently help recognize which patients might benefit from immune checkpoint blockade, recent data suggest that this may change...
February 22, 2017: American Journal of Clinical Dermatology
https://www.readbyqxmd.com/read/28229383/mirna-based-heavy-metal-homeostasis-and-plant-growth
#19
Ali Noman, Muhammad Aqeel
Plants have been naturally gifted with mechanisms to adjust under very high or low nutrient concentrations. Heavy metal toxicity is considered as a major growth and yield-limiting factor for plants. This stress includes essential as well as non-essential metals. MicroRNAs (miRNAs) are known for mediating post-transcriptional regulation by cleaving transcripts or translational inhibition. It is commonly agreed that an extensive understanding of plant miRNAs will significantly help in the induction of tolerance against environmental stresses...
February 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#20
Thomas Milan, Brian T Wilhelm
The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them...
February 22, 2017: Molecular Diagnosis & Therapy
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