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Tingting Wang, Yi-Ping Phoebe Chen, Iona M MacLeod, Jennie E Pryce, Michael E Goddard, Ben J Hayes
BACKGROUND: Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some traits, the most accurate genomic predictions are achieved with non-linear Bayesian methods. However, as the number of variants and the size of the reference population increase, the computational time required to implement these Bayesian methods (typically with Monte Carlo Markov Chain sampling) becomes unfeasibly long...
August 15, 2017: BMC Genomics
Malvina Kadlec, Dirk U Bellstedt, Nicholas C Le Maitre, Michael D Pirie
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae)...
2017: PeerJ
Doris E Braun, Ulrich J Griesser
The complex interplay of temperature and water activity (aw) / relative humidity (RH) on the solid form stability and transformation pathways of three hydrates (HyA, HyB and HyC), an isostructural dehydrate (HyAdehy ), an anhydrate (AH) and amorphous brucine has been elucidated and the transformation enthalpies quantified. The dihydrate (HyA) shows a non-stoichimetric (de)hydration behavior at RH < 40% at 25 °C and the removal of the water molecules results in an isomorphic dehydrate structure. The metastable dehydration product converts to AH upon storage at driest conditions or to HyA if exposed to moisture...
October 5, 2016: Crystal Growth & Design
Aurélie Periat, Davy Guillarme, Jean-Luc Veuthey, Julien Boccard, Sofia Moco, Denis Barron, Alexandre Grand-Guillaume Perrenoud
Plant secondary metabolites are an almost unlimited reservoir of potential bioactive compounds. In view of the wide chemical space covered by natural compounds, their comprehensive analysis requires multiple and complementary approaches. In this study, numerous chromatographic conditions were tested for the analysis of a set of 120 representative natural compounds covering a wide polarity range (18 log P units). The experiments were performed on 59 different conditions involving 29 RPLC and HILIC dedicated stationary phases, as well as more exotic mixed mode columns...
May 10, 2017: Journal of Chromatography. A
Amanda He, Stephanie R Penix, Preston J Basting, Jessie M Griffith, Kaitlin E Creamer, Dominic Camperchioli, Michelle W Clark, Alexandra S Gonzales, Jorge Sebastian Chávez Erazo, Nadja S George, Arvind A Bhagwat, Joan L Slonczewski
Acid-adapted strains of Escherichia coli K-12 W3110 were obtained by serial culture in medium buffered at pH 4.6 (M. M. Harden, A. He, K. Creamer, M. W. Clark, I. Hamdallah, K. A. Martinez, R. L. Kresslein, S. P. Bush, and J. L. Slonczewski, Appl Environ Microbiol 81:1932-1941, 2015, Revised genomic analysis of these strains revealed insertion sequence (IS)-driven insertions and deletions that knocked out regulators CadC (acid induction of lysine decarboxylase), GadX (acid induction of glutamate decarboxylase), and FNR (anaerobic regulator)...
June 15, 2017: Applied and Environmental Microbiology
Koji Shindo, Jun Yu, Masaya Suenaga, Shahriar Fesharakizadeh, Koji Tamura, Jose Alejandro Navarro Almario, Aaron Brant, Michael Borges, Abdulrehman Siddiqui, Lisa Datta, Christopher L Wolfgang, Ralph H Hruban, Alison Patricia Klein, Michael Goggins
CEL-HYB is a hybrid allele that arose from a crossover between the 3' end of the Carboxyl ester lipase (CEL) gene and the nearby CEL pseudogene (CELP) and was recently identified as a risk factor for chronic pancreatitis. Since chronic pancreatitis is a risk factor for the development of pancreatic cancer, we compared the prevalence of the CEL-HYB allele in patients with pancreatic ductal adenocarcinoma to spousal controls and disease controls. The CEL-HYB allele was detected using Sanger and next generation sequencing...
February 7, 2017: Oncotarget
Kouichi Mizuno, Tetsuo Tokiwano, Yuko Yoshizawa
β-cryptoxanthin (β-Cry), a xanthophyll, is unlike other abundant carotenoids, such as α-carotene, β-carotene, lycopene, lutein, and zeaxanthin. It is not found in most fruits or vegetables but is found only in specific fruits, such as hot chili pepper, persimmon, and citrus fruits. Because recent reports suggest that β-Cry intake is beneficial to human health, the xanthophyll requires further investigation. Although β-Cry accumulates in the fruit of wild raspberry, Rubus palmatus, it is not present in cultivated raspberry...
March 18, 2017: Biochemical and Biophysical Research Communications
Ying Sun, Yu Huang, Guojun Hu, Xinhui Zhang, Zhiqiang Ruan, Xiaomeng Zhao, Chuanyu Guo, Zhujing Tang, Xiaofeng Li, Xinxin You, Haoran Lin, Yong Zhang, Qiong Shi
Grouper (Epinephelus spp.) is a group of fish species with great economic importance in Asian countries. A novel hybrid grouper, generated by us and called the Hulong grouper (Hyb), has better growth performance than its parents, E. fuscoguttatus (Efu, ♀) and E. lanceolatus (Ela, ♂). We previously reported that the GH/IGF (growth hormone/insulin-like growth factor) system in the brain and liver contributed to the superior growth of the Hyb. In this study, using transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR), we analyzed RNA expression levels of comprehensive genes in the muscle of the hybrid and its parents...
2016: PloS One
Sheng Zhong, Afsar Naqvi, Eric Bair, Salvador Nares, Asma A Khan
INTRODUCTION: MicroRNAs (miRs) are a family of noncoding RNAs that regulate gene expression. They are ubiquitous among multicellular eukaryotes and are also encoded by some viruses. Upon infection, viral miRs (vmiRs) can potentially target gene expression in the host and alter the immune response. Although prior studies have reported viral infections in human pulp, the role of vmiRs in pulpal disease is yet to be explored. The purpose of this study was to examine the expression of vmiRs in normal and diseased pulps and to identify potential target genes...
January 2017: Journal of Endodontics
Andreas M Schneider, Ralph W Aye, Candice L Wilshire, Alexander S Farivar, Brian E Louie
BACKGROUND: A randomized controlled trial (RCT) showed that laparoscopic Nissen fundoplication (LNF) and Hill (LHR) repairs are equivalent in treating uncomplicated GERD. We combined both repairs to create a laparoscopic Nissen-Hill Hybrid repair (HYB). The purpose of this study is to compare clinical and objective outcomes of a matched group of HYB to the two cohorts of the RCT. METHODS: A retrospective analysis of prospectively collected data from the RCT and a prospectively collected data base was performed...
March 2017: Journal of Gastrointestinal Surgery: Official Journal of the Society for Surgery of the Alimentary Tract
Monica Dalva, Khadija El Jellas, Solrun J Steine, Bente B Johansson, Monika Ringdal, Janniche Torsvik, Heike Immervoll, Dag Hoem, Felix Laemmerhirt, Peter Simon, Markus M Lerch, Stefan Johansson, Pål R Njølstad, Frank U Weiss, Karianne Fjeld, Anders Molven
BACKGROUND/OBJECTIVES: We have recently described copy number variants (CNVs) of the human carboxyl-ester lipase (CEL) gene, including a recombined deletion allele (CEL-HYB) that is a genetic risk factor for chronic pancreatitis. Associations with pancreatic disease have also been reported for the variable number of tandem repeat (VNTR) region located in CEL exon 11. Here, we examined if CEL CNVs and VNTR length polymorphisms affect the risk for developing pancreatic cancer. METHODS: CEL CNVs and VNTR were genotyped in a German family with non-alcoholic chronic pancreatitis and pancreatic cancer, in 265 German and 197 Norwegian patients diagnosed with pancreatic adenocarcinoma, and in 882 controls...
January 2017: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
E Cabanelas, C M López, P Díaz, A Pérez-Creo, P Morrondo, P Díez-Baños, R Panadero
This study investigates the in vitro modulatory effects of interferon-γ (IFN-γ) and interleukin-4 (IL-4) on both proliferative bovine T cell responses and IL-10 production induced by different antigens [crude larval extract and the purified fractions hypodermin A, B and C (HyA, HyB, HyC)] obtained from first instars of Hypoderma lineatum (Diptera: Oestridae), alone or in the presence of the mitogen concanavalin A. Incubation with the different parasitic antigens resulted in significant inhibition of T cell proliferation and IL-10 production, which, in general, did not revert after the addition of IFN-γ and IL-4...
September 9, 2016: Medical and Veterinary Entomology
Chenghao Su, Yong Lin, Lin Cai, Qianguo Mao, Jianjun Niu
The innate immunity gene mannose-binding lectin2 (MBL2) has played an important role in hepatitis B virus (HBV) infection, and the relationship between MBL2 variants and hepatocellular carcinoma (HCC) risk has not yet been identified. In total, 315 HCC cases and 315 healthy controls were enrolled and blood samples were acquired. High resolution melt analysis (HRM) was employed to genotype 6 polymorphisms in MBL2 gene. Increased HCC risk in carriers of LL genotype of -550 polymorphism with an adjusted OR (AOR) of 1...
2016: Scientific Reports
Amanda E Fisher, Kristen M Hasenstab, Hester L Bell, Ellen Blaine, Amanda L Ingram, J Travis Columbus
Chloridoideae (chloridoid grasses) are a subfamily of ca. 1700 species with high diversity in arid habitats. Until now, their evolutionary relationships have primarily been studied with DNA sequences from the chloroplast, a maternally inherited organelle. Next-generation sequencing is able to efficiently recover large numbers of nuclear loci that can then be used to estimate the species phylogeny based upon bi-parentally inherited data. We sought to test our chloroplast-based hypotheses of relationships among chloridoid species with 122 nuclear loci generated through targeted-enrichment next-generation sequencing, sometimes referred to as hyb-seq...
December 2016: Molecular Phylogenetics and Evolution
Gal Levy, Ralph W Aye, Alexander S Farivar, Brian E Louie
INTRODUCTION: We compared clinical and objective outcomes of combined Nissen-Hill hybrid (HYB) to Nissen fundoplication (LNF) for repair of paraesophageal hernia (PEH). METHODS: This study is a single-institution retrospective chart review of prospectively collected data for consecutive patients undergoing PEH repair from 2006 to 2015 with at least 6 months of follow-up. Quality of life metrics (QOLRAD, HRQL, and dysphagia), manometry, radiographic imaging, and pH testing were administered pre- and postoperatively...
January 2017: Journal of Gastrointestinal Surgery: Official Journal of the Society for Surgery of the Alimentary Tract
Khoi Duc Than, Stacie Nguyen, Paul Park, Dean Chou, Frank La Marca, Juan S Uribe, Todd Douglas Vogel, Pierce D Nunley, Robert Eastlack, Neel Anand, Adam S Kanter, Praveen V Mummaneni, Gregory M Mundis
INTRODUCTION: This study aims to compare differences in incidence and type of complications (COMP) between circumferential minimally invasive surgery (cMIS, ie MIS transforaminal lumbar interbody fusion [TLIF] and/or lumbar lateral interbody fusion [LLIF] with MIS screws) and hybrid approaches (HYB, ie MIS LLIF ± with open screws). METHODS: A retrospective review of a multicenter MIS deformity database was performed. Inclusion criteria for this database: age >18 years, and at least one of the following: coronal Cobb angle (CCA) >20, SVA >5 cm, PI-LL >10, and PT > 20...
August 2016: Neurosurgery
Charles R Hatt, Michael A Speidel, Amish N Raval
In recent years, registration between x-ray fluoroscopy (XRF) and transesophageal echocardiography (TEE) has been rapidly developed, validated, and translated to the clinic as a tool for advanced image guidance of structural heart interventions. This technology relies on accurate pose-estimation of the TEE probe via standard 2D/3D registration methods. It has been shown that latencies caused by slow registrations can result in errors during untracked frames, and a real-time ( > 15 hz) tracking algorithm is needed to minimize these errors...
December 2016: Medical Image Analysis
Krystel El Hage, Tristan Bereau, Sofie Jakobsen, Markus Meuwly
Halogenation is one of the cases for which advanced molecular simulation methods are mandatory for quantitative and predictive studies. The present work provides a systematic investigation of the importance of higher-order multipoles on specific sites of halobenzenes, other than the halogen, for static and dynamic properties in condensed-phase simulations. For that purpose, solute-solvent interactions using point charge (PC), multipole (MTP), and hybrid point charge/multipole (HYB) electrostatic models are analyzed in regions of halogen bonding and extended to regions of π orbitals of phenyl carbons...
July 12, 2016: Journal of Chemical Theory and Computation
Muhammad Iqbal, Maqsood Hayat
BACKGROUND AND OBJECTIVES: Gene splicing is a vital source of protein diversity. Perfectly eradication of introns and joining exons is the prominent task in eukaryotic gene expression, as exons are usually interrupted by introns. Identification of splicing sites through experimental techniques is complicated and time-consuming task. With the avalanche of genome sequences generated in the post genomic age, it remains a complicated and challenging task to develop an automatic, robust and reliable computational method for fast and effective identification of splicing sites...
May 2016: Computer Methods and Programs in Biomedicine
Wen-Bin Zou, Arnaud Boulling, Atsushi Masamune, Prachand Issarapu, Emmanuelle Masson, Hao Wu, Xiao-Tian Sun, Liang-Hao Hu, Dai-Zhan Zhou, Lin He, Yann Fichou, Eriko Nakano, Shin Hamada, Yoichi Kakuta, Kiyoshi Kume, Hiroyuki Isayama, Sumit Paliwal, K Radha Mani, Seema Bhaskar, David N Cooper, Claude Férec, Tooru Shimosegawa, Giriraj R Chandak, Jian-Min Chen, Zhao-Shen Li, Zhuan Liao
A hybrid allele between the carboxyl ester lipase gene (CEL) and its pseudogene, CELP (called CEL-HYB), generated by nonallelic homologous recombination between CEL intron 10 and CELP intron 10', was found to increase susceptibility to chronic pancreatitis in a case-control study of patients of European ancestry. We attempted to replicate this finding in 3 independent cohorts from China, Japan, and India, but failed to detect the CEL-HYB allele in any of these populations. The CEL-HYB allele might therefore be an ethnic-specific risk factor for chronic pancreatitis...
June 2016: Gastroenterology
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