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https://www.readbyqxmd.com/read/28724074/high-resolution-genetic-and-physical-mapping-of-the-eastern-filbert-blight-resistance-region-in-jefferson-hazelnut-corylus-avellana-l
#1
Vidyasagar Sathuvalli, Shawn A Mehlenbacher, David C Smith
Eastern filbert blight (EFB), caused by the pyrenomycete (Peck) E. Müller, is a devastating disease of European hazelnut ( L) in the US Pacific Northwest. A dominant allele at a single locus from the obsolete pollenizer 'Gasaway' confers a high level of resistance to EFB. To identify the gene responsible for resistance, we initiated map-based cloning efforts in a population of 1488 seedlings that segregated for resistance. Chromosome walking was initiated using primers designed from eight previously identified random amplified polymorphic DNA markers linked to resistance...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723968/new-library-construction-method-for-single-cell-genomes
#2
Larry Xi, Alexander Belyaev, Sandra Spurgeon, Xiaohui Wang, Haibiao Gong, Robert Aboukhalil, Richard Fekete
A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments...
2017: PloS One
https://www.readbyqxmd.com/read/28721670/extending-a-tandem-mass-spectral-library-to-include-ms-2-spectra-of-fragment-ions-produced-in-source-and-ms-n-spectra
#3
Xiaoyu Yang, Pedatsur Neta, Stephen E Stein
Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS(2) spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS(3) and MS(4) spectra. These can assist the chemical identification process...
July 18, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28719724/synthesis-and-properties-of-new-n-heteroheptacenes-for-solution-based-organic-field-effect-transistors
#4
Fei Zhou, Sheng Liu, Bernard D Santarsiero, Donald J Wink, Damien Boudinet, Antonio Facchetti, Tom G Driver
A series of N-heteroheptacenes was synthesized from ortho-thiophene-substituted aryl azides using a Rh2(II)-catalyzed C-H bond amination reaction to construct the thienoindole moieties. This reaction tolerated the presence of electron-donating or withdrawing groups on the aryl azide without adversely affecting the yield of the amination reaction. The central thiophene ring was created from two thienoindole pieces through a Pd-catalyzed Stille reaction to install the thioether followed by a Cu-mediated Ullman reaction to trigger the cyclization...
July 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28719653/isolation-of-a-monoclonal-antibody-from-a-phage-display-library-binding-the-rhesus-macaque-mhc-class-i-allomorph-mamu-a1-001
#5
Nathan Holman, Jason T Weinfurter, Trevor R Harsla, Roger W Wiseman, Aaron J Belli, Anthony J Michaels, Keith A Reimann, Robert I DeMars, Matthew R Reynolds
Monoclonal antibodies that bind to human leukocyte antigen (HLA) are useful tools for HLA-typing, tracking donor-recipient chimerisms after bone marrow transplants, and characterizing specific major histocompatibility complexes (MHC) on cell surfaces. Unfortunately, equivalent reagents are not available for rhesus macaques, which are commonly used animal as models in organ transplant and infectious disease research. To address this deficiency, we isolated an antibody that recognizes the common Indian rhesus macaque MHC class I molecule, Mamu-A1*001...
2017: PloS One
https://www.readbyqxmd.com/read/28716994/diagnosis-and-management-of-perinatal-depression-and-anxiety-in-general-practice-a-meta-synthesis-of-qualitative-studies
#6
Elizabeth Ford, Suzanne Lee, Judy Shakespeare, Susan Ayers
BACKGROUND: Up to 20% of women experience anxiety and depression during the perinatal period. In the UK, management of perinatal mental health falls under the remit of GPs. AIM: This review aimed at synthesising the available information from qualitative studies on GPs' attitudes, recognition, and management of perinatal anxiety and depression. DESIGN AND SETTING: Meta-synthesis of the available published qualitative evidence on GPs' recognition and management of perinatal anxiety and depression...
July 17, 2017: British Journal of General Practice: the Journal of the Royal College of General Practitioners
https://www.readbyqxmd.com/read/28714399/design-synthesis-and-antibacterial-evaluation-of-compounds-based-on-new-benzoxepine-oxime-1-2-3-triazole-hybrid
#7
Naveen Kuntala, Jhonsee Rani Telu, Venkanna Banothu, Sridhar Balasubramanian, Jaya Shree Anireddy, Sarbani Pal
A library of small molecules based on the new benzoxepine-oxime-1,2,3-triazole hybrid was initially designed as potential antibacterial agents. These compounds were synthesized using a Cu-catalyzed azide-alkyne cycloaddition (CuAAC) as a key step to construct the desired 1,2,3-triazole ring. Thus the click reaction between the appropriate alkyne containing the benzoxepine-oxime framework with aryl azides afforded the target compounds in good yields. To assess their antibacterial properties all the synthesized compounds were tested against four strains of bacterial microorganisms including one Gram-positive and three Gram-negative species...
July 17, 2017: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/28713847/next-generation-sequencing-of-the-dna-virome-from-fecal-samples
#8
Cynthia L Monaco, Douglas S Kwon
Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent...
March 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28712705/engineering-of-global-regulators-and-cell-surface-properties-toward-enhancing-stress-tolerance-in-saccharomyces-cerevisiae
#9
REVIEW
Kouichi Kuroda, Mitsuyoshi Ueda
Microbial cell factories are subject to various stresses, leading to the reductions of metabolic activity and bioproduction efficiency. Therefore, the development of stress-tolerant microorganisms is important for improving bio-production efficiency. Recently, modifications of cell surface properties and master regulators have been shown to be effective approaches for enhancing stress tolerance. The cell surface is an attractive target owing to its interactions with the environment and its role in transmitting environmental information...
July 13, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28710267/increased-processivity-misincorporation-and-nucleotide-incorporation-efficiency-in-sulfolobus-solfataricus-dpo4-thumb-domain-mutations
#10
Li Wang, Chenchen Liang, Jing Wu, Liming Liu, Keith E J Tyo
The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4...
July 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28707884/rapid-and-programmable-protein-mutagenesis-using-plasmid-recombineering
#11
Sean Andrew Higgins, Sorel Ounkap, David F Savage
Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. However, current techniques enabling comprehensive protein mutagenesis are based on PCR and require in vitro reactions involving specialized protocols and reagents. This has complicated efforts to rapidly and reliably produce desired comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space...
July 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28705785/determination-of-certain-bacterial-groups-in-gut-microbiota-and-endotoxin-levels-in-patients-with-nonalcoholic-steatohepatitis
#12
Ceren Özkul, Meltem Yalınay, Tarkan Karakan, Güldal Yılmaz
BACKGROUND/AIMS: In recent years, the role of the gut microbiota has emerged in several diseases. Herein we aimed to determine the fecal microbiota, endotoxin levels, and inflammation markers in patients with nonalcoholic steatohepatitis (NASH) and healthy controls. MATERIALS AND METHODS: A total of 46 NASH patients and 38 healthy controls were included. NASH patients were diagnosed according to the steatosis, activity, and fibrosis score/fatty liver inhibition of progression algorithm...
July 13, 2017: Turkish Journal of Gastroenterology: the Official Journal of Turkish Society of Gastroenterology
https://www.readbyqxmd.com/read/28700485/value-of-contrast-enhanced-ultrasound-in-differential-diagnosis-of-solid-lesions-of-pancreas-slp-a-systematic-review-and-a-meta-analysis
#13
Li Ran, Wenli Zhao, Ye Zhao, Huaien Bu
BACKGROUND: Contrast-enhanced ultrasound (CEUS) is considered a novel method for diagnosing pancreatic cancer, but currently, there is no conclusive evidence of its accuracy. Using CEUS in discriminating between pancreatic carcinoma and other pancreatic lesions, we aimed to evaluate the diagnostic accuracy of CEUS in predicting pancreatic tumours. METHODS: Relevant studies were selected from the PubMed, Cochrane Library, Elsevier, CNKI, VIP, and WANFANG databases dating from January 2006 to May 2017...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28698098/development-of-a-single-cell-glxr-based-camp-biosensor-for-corynebacterium-glutamicum
#14
Julia Schulte, Meike Baumgart, Michael Bott
Cyclic adenosine monophosphate (cAMP) plays a regulatory role as second messenger in many species. In the industrial model organism Corynebacterium glutamicum, cAMP acts as effector of the global transcriptional regulator GlxR, a homolog of enterobacterial Crp. The cAMP-GlxR complex activates or represses the expression of about 200 target genes. CyaB, a membrane-bound class III adenylate cyclase, synthesizes cAMP from ATP, but another yet unknown cAMP-forming enzyme is likely present in C. glutamicum. Recently, we identified the cAMP phosphodiesterase CpdA, which catalyzes the conversion of cAMP to AMP...
July 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28697453/electricity-production-and-microbial-characterization-of-thermophilic-microbial-fuel-cells
#15
Kun Dai, Jun-Li Wen, Fang Zhang, Xi-Wen Ma, Xiang-Yu Cui, Qi Zhang, Ting-Jia Zhao, Raymond J Zeng
Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m(2), and the columbic efficiency in this work was 20...
July 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28695927/a-3d-printed-mini-hydrocyclone-for-high-throughput-particle-separation-application-to-primary-harvesting-of-microalgae
#16
Maira Shakeel Syed, Mehdi Rafeie, Rita Henderson, Dries Vandamme, Mohsen Asadnia, Majid Ebrahimi Warkiani
The separation of micro-sized particles in a continuous flow is crucial part of many industrial processes, from biopharmaceutical manufacturing to water treatment. Conventional separation techniques such as centrifugation and membrane filtration are largely limited by factors such as clogging, processing time and operation efficiency. Microfluidic based techniques have been gaining great attention in recent years as efficient and powerful approaches for particle-liquid separation. Yet the production of such systems using standard micro-fabrication techniques is proven to be tedious, costly and have cumbersome user interfaces, which all render commercialization difficult...
July 11, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28693420/differential-proteomic-analysis-of-replanted-rehmannia-glutinosa-roots-by-itraq-reveals-molecular-mechanisms-for-formation-of-replant-disease
#17
Mingjie Li, Yanhui Yang, Fajie Feng, Bao Zhang, Shuqiang Chen, Chuyun Yang, Li Gu, Fengqing Wang, Junyi Zhang, Aiguo Chen, Wenxiong Lin, Xinjian Chen, Zhongyi Zhang
BACKGROUND: The normal growth of Rehmannia glutinosa, a widely used medicinal plant in China, is severely disturbed by replant disease. The formation of replant disease commonly involves interactions among plants, allelochemicals and microbes; however, these relationships remain largely unclear. As a result, no effective measures are currently available to treat replant disease. RESULTS: In this study, an integrated R. glutinosa transcriptome was constructed, from which an R...
July 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28689267/the-novel-srna-s015-improves-nisin-yield-by-increasing-acid-tolerance-of-lactococcus-lactis-f44
#18
Jiakun Qi, Qinggele Caiyin, Hao Wu, Kairen Tian, Binbin Wang, Yanni Li, Jianjun Qiao
Nisin, a polycyclic antibacterial peptide produced by Lactococcus lactis, is stable at low pH. Improving the acid tolerance of L. lactis could thus enhance nisin yield. Small non-coding RNAs (sRNAs) play essential roles in acid tolerance by regulating their target mRNAs at the post-transcriptional level. In this study, a novel sRNA, s015, was identified in L. lactis F44 via the use of RNA sequencing, qRT-PCR analysis, and Northern blotting. s015 improved the acid tolerance of L. lactis and boosted nisin yield at low pH...
July 9, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28687989/screening-novel-autoantigens-targeted-by-serum-igg-autoantibodies-in-immunorelated-pancytopenia-by-serex
#19
Shanfeng Hao, Rong Fu, Huaquan Wang, Zonghong Shao
Immunorelated pancytopenia (IRP) is characterized by pancytopenia caused by autoantibody-mediated destruction or suppression of bone marrow. However, the autoantigens targeted by autoantibodies in IRP remain unclear. In the present study, we screened novel autoantigens in IRP by serological analysis of recombinant cDNA expression libraries and compared anti-UQCR10 antibody levels between IRP and normal controls detected by immunoblotting. Our results indicate that we successfully constructed the K562 cDNA library, which we used to screen seven candidate autoantigens expressed in haematopoietic cells of IRP: ferritin, light polypeptide, ubiquinol-cytochrome c reductase, complex III subunit X (UQCR10), multifunctional methyl-transferase subunit TRM112-like protein isoform 1 (TRMT112), hemoglobin gamma-G, stathmin 1 (STMN1), transcript variant 3, phosphoglycerate kinase 1 (PGK1), and trafficking protein particle complex subunit 4 (TRAPPC4)...
July 7, 2017: International Journal of Hematology
https://www.readbyqxmd.com/read/28686569/spatio-temporal-variations-in-the-abundance-and-structure-of-denitrifier-communities-in-sediments-differing-in-nitrate-content
#20
David Correa-Galeote, Germán Tortosa, Silvia Moreno, David Bru, Laurent Philippot, Eulogio J Bedmar
Spatial and temporal variations related to hydric seasonality in abundance and diversity of denitrifier communities were examined in sediments taken from two sites differing in nitrate concentration along a stream Doñana National Park during a 3-year study. We found a positive relationship between the relative abundance of denitrifiers, determined as narG, napA, nirK, nirS and nosZ denitrification genes, and sediment nitrate content, with similar spatial and seasonal variations. However, we did not find association between denitrification activity and the community structure of denitrifiers...
July 6, 2017: Current Issues in Molecular Biology
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