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https://www.readbyqxmd.com/read/28109393/a-modified-and-less-invasive-procedure-in-aortic-arch-replacement
#1
Feng Gao, Jing Chen, Qian Zeng, Fangming Lin
Circulation arrest is widely used during total aortic arch replacement. However, the conventional procedures have high morbidity and mortality. We modified the hybrid procedure by optimizing the sequence of anastomosis between the graft and aorta. As a result, the time of extracorporeal circulation was obviously shortened, and cardiac arrest was needed only during the two anastomoses of the aorta with aorta graft main body. In addition, both circulation arrest and deep hypothermia were avoided. Leakage was also prevented by creating a lengthened sealing zone for stent graft deployment...
February 2017: Annals of Thoracic Surgery
https://www.readbyqxmd.com/read/28108520/rna-binding-specificity-landscape-of-the-pentatricopeptide-repeat-protein-ppr10
#2
Rafael G Miranda, Margarita Rojas, Michael P Montgomery, Kyle P Gribbin, Alice Barkan
Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that influence gene expression in mitochondria and chloroplasts. PPR tracts can bind RNA via a modular one repeat-one nucleotide mechanism in which the nucleotide is specified by the identities of several amino acids in each repeat. This mode of recognition, the so-called PPR code, offers opportunities for the prediction of native PPR binding sites and the design of proteins to bind specified RNAs. However, a deep understanding of the parameters that dictate the affinity and specificity of PPR-RNA interactions is necessary to realize these goals...
January 20, 2017: RNA
https://www.readbyqxmd.com/read/28108232/ns5a-resistance-associated-substitutions-in-patients-with-genotype-1-hepatitis-c-virus-prevalence-and-effect-on-treatment-outcome
#3
Stefan Zeuzem, Masashi Mizokami, Stephen Pianko, Alessandra Mangia, Kwang-Hyub Han, Ross Martin, Evguenia Svarovskaia, Hadas Dvory-Sobol, Brian Doehle, Charlotte Hedskog, Chohee Yun, Diana M Brainard, Steven Knox, John G McHutchison, Michael D Miller, Hongmei Mo, Wan-Long Chuang, Ira Jacobson, Gregory J Dore, Mark Sulkowski
BACKGROUND: The efficacy of NS5A inhibitors for the treatment of patients chronically infected with hepatitis C virus (HCV) can be affected by the presence of NS5A resistance-associated substitutions (RASs). We analyzed data from 35 phase 1, 2, and 3 studies in 22 countries to determine the pretreatment prevalence of various NS5A RASs, and their effect on outcomes of treatment with ledipasvir-sofosbuvir in patients with genotype 1 HCV. METHODS: NS5A gene deep sequencing analysis was performed on samples from 5,397 patients in Gilead clinical trials...
January 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28107423/characterization-of-the-drug-resistance-profiles-of-patients-infected-with-crf07_bc-using-phenotypic-assay-and-ultra-deep-pyrosequencing
#4
Szu-Wei Huang, Wei-You Li, Wen-Hung Wang, Yu-Ting Lin, Chih-Hung Chou, Marcelo Chen, Hsien-Da Huang, Yen-Hsu Chen, Po-Liang Lu, Sheng-Fan Wang, Shinichi Oka, Yi-Ming Arthur Chen
The usefulness of ultra-deep pyrosequencing (UDPS) for the diagnosis of HIV-1 drug resistance (DR) remains to be determined. Previously, we reported an explosive outbreak of HIV-1 circulating recombinant form (CRF) 07_BC among injection drug users (IDUs) in Taiwan in 2004. The goal of this study was to characterize the DR of CRF07_BC strains using different assays including UDPS. Seven CRF07_BC isolates including 4 from early epidemic (collected in 2004-2005) and 3 from late epidemic (collected in 2008) were obtained from treatment-naïve patient's peripheral blood mononuclear cells...
2017: PloS One
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#5
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106726/discrepancy-between-hepatitis-c-virus-genotypes-and-ns4-based-serotypes-association-with-their-subgenomic-sequences
#6
Nan Nwe Win, Shingo Nakamoto, Tatsuo Kanda, Hiroki Takahashi, Azusa Takahashi-Nakaguchi, Shin Yasui, Masato Nakamura, Shuang Wu, Fumio Imazeki, Shigeru Mikami, Osamu Yokosuka, Tohru Gonoi, Hiroshi Shirasawa
Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5'-untranslated region (5'-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results...
January 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106209/sub-100-nm-wrinkling-of-polydimethylsiloxane-by-double-frontal-oxidation
#7
Manuela Nania, Fabrizia Foglia, Omar K Matar, João T Cabral
We demonstrate nanoscale wrinkling on polydimethylsiloxane (PDMS) at sub-100 nm length scales via a (double) frontal surface oxidation coupled with a mechanical compression. The kinetics of the glassy skin propagation is resolved by neutron and X-ray reflectivity, and atomic force microscopy, combined with mechanical wrinkling experiments to evaluate the resulting pattern formation. In conventional PDMS surface oxidation, the smallest wrinkling patterns attainable have an intrinsic lower wavelength limit due to the coupling of skin formation and front propagation at fixed strain εprestrain, whose maximum is, in turn, set by material failure...
January 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28105939/evolution-of-mitochondrial-genomes-in-baikalian-amphipods
#8
Elena V Romanova, Vladimir V Aleoshin, Ravil M Kamaltynov, Kirill V Mikhailov, Maria D Logacheva, Elena A Sirotinina, Alexander Yu Gornov, Anton S Anikin, Dmitry Yu Sherbakov
BACKGROUND: Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105525/characterization-of-the-cell-polarity-gene-crumbs-during-the-early-development-and-maintenance-of-the-squid-vibrio-light-organ-symbiosis
#9
Suzanne M Peyer, Elizabeth A C Heath-Heckman, Margaret J McFall-Ngai
The protein Crumbs is a determinant of apical-basal cell polarity and plays a role in apoptosis of epithelial cells and their protection against photodamage. Using the squid-vibrio system, a model for development of symbiotic partnerships, we examined the modulation of the crumbs gene in host epithelial tissues during initiation and maintenance of the association. The extracellular luminous symbiont Vibrio fischeri colonizes the apical surfaces of polarized epithelia in deep crypts of the Euprymna scolopes light organ...
January 20, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28104644/draft-genome-sequence-of-hydrogenibacillus-schlegelii-ma48-a-deep-branching-member-of-the-bacilli-class-of-firmicutes
#10
Allison Maker, James Hemp, Laura A Pace, Lewis M Ward, Woodward W Fischer
We report here the draft genome sequence of Hydrogenibacillus schlegelii MA48, a thermophilic facultative anaerobe that can oxidize hydrogen aerobically. H. schlegelii MA48 belongs to a deep-branching clade of the Bacilli class and provides important insight into the acquisition of aerobic respiration within the Firmicutes phylum.
January 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#11
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28102337/deep-brain-stimulation-for-myoclonus-dystonia-syndrome-with-double-mutations-in-dyt1-and-dyt11
#12
Jia-Wei Wang, Ji-Ping Li, Yun-Peng Wang, Xiao-Hua Zhang, Yu-Qing Zhang
Myoclonus-dystonia syndrome (MDS) is a rare autosomal dominant inherited disorder characterized by the presentation of both myoclonic jerks and dystonia. Evidence is emerging that deep brain stimulation (DBS) may be a promising treatment for MDS. However, there are no studies reporting the effects of DBS on MDS with double mutations in DYT1 and DYT11. Two refractory MDS patients with double mutations were treated between 2011 and 2015 in our center. Genetic testing for DYT1 and DYT11 was performed through polymerase chain reaction amplification and direct sequencing of the specific exons of genes...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101858/coiled-coil-design-updated-and-upgraded
#13
Derek N Woolfson
α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101583/integrated-analysis-of-microrna-and-transcription-factor-reveals-important-regulators-and-regulatory-motifs-in-adult-b-cell-acute-lymphoblastic-leukemia
#14
Xiao-Cong Lin, Xin-Guang Liu, Yu-Ming Zhang, Ning Li, Zhi-Gang Yang, Wei-Yu Fu, Liu-Bo Lan, Hai-Tao Zhang, Yong Dai
B-cell acute lymphoblastic leukemia (B‑ALL) is an aggressive hematological malignancy and a leading cause of cancer-related mortality in children and young adults. The molecular mechanisms involved in the regulation of its gene expression has yet to be fully elucidated. In the present study, we performed large scale expression profiling of microRNA (miRNA) and transcription factor (TF) by Illumina deep‑sequencing and TF array technology, respectively, and identified 291 differentially expressed miRNAs and 201 differentially expressed TFs in adult B‑ALL samples relative to their controls...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28100596/genomic-epidemiology-of-penicillin-non-susceptible-pneumococci-with-non-vaccine-serotypes-causing-invasive-disease-in-the-usa
#15
Cheryl P Andam, Patrick K Mitchell, Alanna Callendrello, Qiuzhi Chang, Jukka Corander, Chrispin Chaguza, Lesley McGee, Bernard W Beall, William P Hanage
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic resistant strains throughout the 2000s; however, disease caused by resistant non-vaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with 581 isolates from 2012-2013, collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC)...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28099855/primary-cell-culture-of-live-neurosurgically-resected-aged-adult-human-brain-cells-and-single-cell-transcriptomics
#16
Jennifer M Spaethling, Young-Ji Na, Jaehee Lee, Alexandra V Ulyanova, Gordon H Baltuch, Thomas J Bell, Steven Brem, H Isaac Chen, Hannah Dueck, Stephen A Fisher, Marcela P Garcia, Mugdha Khaladkar, David K Kung, Timothy H Lucas, Donald M O'Rourke, Derek Stefanik, Jinhui Wang, John A Wolf, Tamas Bartfai, M Sean Grady, Jai-Yoon Sul, Junhyong Kim, James H Eberwine
Investigation of human CNS disease and drug effects has been hampered by the lack of a system that enables single-cell analysis of live adult patient brain cells. We developed a culturing system, based on a papain-aided procedure, for resected adult human brain tissue removed during neurosurgery. We performed single-cell transcriptomics on over 300 cells, permitting identification of oligodendrocytes, microglia, neurons, endothelial cells, and astrocytes after 3 weeks in culture. Using deep sequencing, we detected over 12,000 expressed genes, including hundreds of cell-type-enriched mRNAs, lncRNAs and pri-miRNAs...
January 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/28099251/utility-of-assessing-the-number-of-mutated-kras-cdkn2a-tp53-and-smad4-genes-using-a-targeted-deep-sequencing-assay-as-a-prognostic-biomarker-for-pancreatic-cancer
#17
Hideyuki Hayashi, Takashi Kohno, Hideki Ueno, Nobuyoshi Hiraoka, Shunsuke Kondo, Motonobu Saito, Yoko Shimada, Hitoshi Ichikawa, Mamoru Kato, Tatsuhiro Shibata, Chigusa Morizane, Yasunari Sakamoto, Kazuaki Shimada, Yoshito Komatsu, Naoya Sakamoto, Takuji Okusaka
OBJECTIVES: KRAS, CDKN2A, TP53, and SMAD4 have been recognized as major driver genes in pancreatic carcinogenesis. We examined somatic mutations in 50 cancer-related genes, including the four above-mentioned driver genes, to identify genomic biomarkers for predicting the outcome of patients with pancreatic cancer. METHODS: Genomic DNA was extracted from fresh-frozen specimens obtained from 100 patients with pancreatic cancer who had undergone a pancreatectomy with curative intent...
January 18, 2017: Pancreas
https://www.readbyqxmd.com/read/28098351/the-elicitation-of-steady-state-visual-evoked-potentials-during-sleep
#18
James J S Norton, Stephen Umunna, Timothy Bretl
This study confirmed the hypothesis that it is possible to elicit SSVEPs through closed eyelids during NREM sleep. To test this hypothesis, SSVEP amplitudes were measured in eight subjects across two conditions of stimulation (stimulation on and stimulation off) and three brain states (waking, light sleep, and deep sleep). Results showed a significant interaction between stimulation and brain state. In particular, EEG activity at the frequency of stimulation was higher during both light sleep and deep sleep in the stimulation on condition than in the stimulation off condition...
January 18, 2017: Psychophysiology
https://www.readbyqxmd.com/read/28098143/efficient-dna-free-genome-editing-of-bread-wheat-using-crispr-cas9-ribonucleoprotein-complexes
#19
Zhen Liang, Kunling Chen, Tingdong Li, Yi Zhang, Yanpeng Wang, Qian Zhao, Jinxing Liu, Huawei Zhang, Cuimin Liu, Yidong Ran, Caixia Gao
Substantial efforts are being made to optimize the CRISPR/Cas9 system for precision crop breeding. The avoidance of transgene integration and reduction of off-target mutations are the most important targets for optimization. Here, we describe an efficient genome editing method for bread wheat using CRISPR/Cas9 ribonucleoproteins (RNPs). Starting from RNP preparation, the whole protocol takes only seven to nine weeks, with four to five independent mutants produced from 100 immature wheat embryos. Deep sequencing reveals that the chance of off-target mutations in wheat cells is much lower in RNP mediated genome editing than in editing with CRISPR/Cas9 DNA...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097865/molecular-requirements-of-high-fidelity-replication-competent-dna-backbones-for-orthogonal-chemical-ligation
#20
Arun Shivalingam, Agnes E S Tyburn, Afaf H El-Sagheer, Tom Brown
The molecular properties of the phosphodiester backbone that made it the evolutionary choice for the enzymatic replication of genetic information are not well understood. To address this, and to develop new chemical ligation strategies for assembly of biocompatible modified DNA, we have synthesized oligonucleotides containing several structurally and electronically varied artificial linkages. This has yielded a new highly promising ligation method based on amide backbone formation that is chemically orthogonal to CuAAC "click" ligation...
January 18, 2017: Journal of the American Chemical Society
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