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https://www.readbyqxmd.com/read/28545781/tests-for-serum-transglutaminase-and-endomysial-antibodies-do-not-detect-most-patients-with-celiac-disease-and-persistent-villous-atrophy-on-gluten-free-diets-a-meta-analysis
#1
Jocelyn A Silvester, Satya Kurada, Andrea Szwajcer, Ciarán P Kelly, Daniel A Leffler, Donald R Duerksen
BACKGROUND & AIMS: Tests to measure serum endomysial antibodies (EMA) and antibodies to tissue transglutaminase (tTG) were developed to screen for celiac disease in patients consuming gluten. However, they are commonly used to monitor patients on a gluten-free diet (GFD). We conducted a meta-analysis to assess the sensitivity and specificity of tTG IgA and EMA IgA assays in identifying patients with celiac disease who have persistent villous atrophy despite a GFD. METHODS: We searched PUBMED, EMBASE, BIOSIS, SCOPUS, clinicaltrials...
May 22, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28543736/a-rapid-expression-and-purification-condition-screening-protocol-for-membrane-protein-structural-biology
#2
Dan Sjöstrand, Riccardo Diamanti, Camilla A K Lundgren, Benjamin Wiseman, Martin Högbom
Membrane proteins control a large number of vital biological processes and are often medically important - not least as drug targets. However, membrane proteins are generally more difficult to work with than their globular counterparts, and as a consequence comparatively few high-resolution structures are available. In any membrane protein structure project, a lot of effort is usually spent on obtaining a pure and stable protein preparation. The process commonly involves the expression of several constructs and homologs, followed by extraction in various detergents...
May 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28542505/alzhcpi-a-knowledge-base-for-predicting-chemical-protein-interactions-towards-alzheimer-s-disease
#3
Jiansong Fang, Ling Wang, Yecheng Li, Wenwen Lian, Xiaocong Pang, Hong Wang, Dongsheng Yuan, Qi Wang, Ai-Lin Liu, Guan-Hua Du
Alzheimer's disease (AD) is a complicated progressive neurodegeneration disorder. To confront AD, scientists are searching for multi-target-directed ligands (MTDLs) to delay disease progression. The in silico prediction of chemical-protein interactions (CPI) can accelerate target identification and drug discovery. Previously, we developed 100 binary classifiers to predict the CPI for 25 key targets against AD using the multi-target quantitative structure-activity relationship (mt-QSAR) method. In this investigation, we aimed to apply the mt-QSAR method to enlarge the model library to predict CPI towards AD...
2017: PloS One
https://www.readbyqxmd.com/read/28541304/digital-logic-circuits-in-yeast-with-crispr-dcas9-nor-gates
#4
Miles W Gander, Justin D Vrana, William E Voje, James M Carothers, Eric Klavins
Natural genetic circuits enable cells to make sophisticated digital decisions. Building equally complex synthetic circuits in eukaryotes remains difficult, however, because commonly used components leak transcriptionally, do not arbitrarily interconnect or do not have digital responses. Here, we designed dCas9-Mxi1-based NOR gates in Saccharomyces cerevisiae that allow arbitrary connectivity and large genetic circuits. Because we used the chromatin remodeller Mxi1, our gates showed minimal leak and digital responses...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28538661/mass-spectrometry-based-profiling-and-imaging-of-various-ginsenosides-from-panax-ginseng-roots-at-different-ages
#5
Jae Won Lee, Seung-Heon Ji, Young-Seob Lee, Doo Jin Choi, Bo-Ram Choi, Geum-Soog Kim, Nam-In Baek, Dae Young Lee
(1) Background: Panax ginseng root is one of the most important herbal products, and the profiling of ginsenosides is critical for the quality control of ginseng roots at different ages in the herbal markets. Furthermore, interest in assessing the contents as well as the localization of biological compounds has been growing. The objective of this study is to carry out the mass spectrometry (MS)-based profiling and imaging of ginsenosides to assess ginseng roots at different ages; (2) Methods: Optimal ultra performance liquid chromatography coupled to quadrupole time of flight/MS (UPLC-QTOF/MS) was used to profile various ginsenosides from P...
May 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28534478/complementary-information-derived-from-crispr-cas9-mediated-gene-deletion-and-suppression
#6
Joseph Rosenbluh, Han Xu, William Harrington, Stanley Gill, Xiaoxing Wang, Francisca Vazquez, David E Root, Aviad Tsherniak, William C Hahn
CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28531346/projector-augmented-wave-method-incorporated-into-gauss-type-atomic-orbital-based-density-functional-theory
#7
Xiao-Gen Xiong, Takeshi Yanai
The Projector Augmented Wave (PAW) method developed by Blochl is well recognized as an efficient, accurate pseudopotential approach in solid-state density functional theory (DFT) calculations with plane-wave basis. Here we present an approach to incorporate the PAW method into the Gauss-type function (GTF) based DFT implementation, which is widely used for molecular quantum chemistry calculations. The nodal and high-exponent GTF components of valence molecular orbitals (MOs) are removed or pseudized by the ultrasoft PAW treatment, while there is elaborate transparency to construct accurate and well-controlled pseudopotential from all-electron atomic description and to reconstruct all-electron form of valence MOs from the pseudo MOs...
May 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28531338/placental-exosomes-as-early-biomarker-of-preeclampsia-potential-role-of-exosomal-micrornas-across-gestation
#8
Carlos Salomon, Dominic Guanzon, Katherin Scholz-Romero, Sherri Longo, Paula Correa, Sebastian E Illanes, Gregory E Rice
Context: There is a need to develop strategies for early prediction of patients who will develop preeclampsia (PE), in order to establish preventive strategies to reduce the prevalence and severity of the disease and their associated complications. Objective: The objective of this study was to investigate whether exosomes and their microRNA cargo present in maternal circulation can be used as early biomarker for PE. Design, Setting, Patients, and Interventions: A retrospective stratified study design was used to quantify total exosomes (EXO) and placenta-derived exosomes (PdE) present in maternal plasma of normal (n=32 per time point) and PE (n=15 per time point) pregnancies...
May 22, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#9
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28530391/single-bead-quantification-of-peptide-loading-distribution-for-one-bead-one-compound-library-synthesis-using-confocal-raman-spectroscopy
#10
Yuchen Tang, Yann Thillier, Ruiwu Liu, Xiaocen Li, Kit S Lam, Tingjuan Gao
We report an analytical method to determine peptide loading of "one-bead one-compound" (OBOC) combinatorial peptide libraries at single-bead level. The quantification is based on a linear relationship between the amount of N-terminal amino groups on individual peptide beads and the intensity of Raman signal obtained from a specifically designed reporter labeled on amino groups. Confocal Raman spectroscopy was employed to characterize peptide loading of beads with defined peptide sequences and from OBOC combinatorial peptide libraries...
May 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28529914/characteristics-of-postintensive-care-syndrome-in-survivors-of-pediatric-critical-illness-a-systematic-review
#11
Elizabeth A Herrup, Beth Wieczorek, Sapna R Kudchadkar
AIM: To synthesize the available evidence focusing on morbidities in pediatric survivors of critical illness that fall within the defined construct of postintensive care syndrome (PICS) in adults, including physical, neurocognitive and psychological morbidities. METHODS: A comprehensive search was conducted in MEDLINE, EMBASE, the Cochrane Library, PsycINFO, and CINAHL using controlled vocabulary and key word terms to identify studies reporting characteristics of PICS in pediatric intensive care unit (PICU) patients...
May 4, 2017: World Journal of Critical Care Medicine
https://www.readbyqxmd.com/read/28529835/a-new-set-of-microsatellite-primers-for-coelogyne-fimbriata-orchidaceae-and-cross-amplification-in-c-ovalis
#12
Wei-Chang Huang, Kai Jiang, Chao Hu, Yue-E Xiao, Barnabas C Seyler, Yuan-Yuan Li
PREMISE OF THE STUDY: Declining orchid populations have made it necessary to prioritize the study of population structure and genetic diversity for species including Coelogyne fimbriata (Orchidaceae). METHODS AND RESULTS: A biotin-streptavidin capture method was used to construct a microsatellite library for C. fimbriata. A total of 15 polymorphic nuclear microsatellite loci were isolated and characterized using 47 C. fimbriata individuals from two natural populations in China...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28528024/structure-diverse-phylomer-libraries-as-a-rich-source-of-bioactive-hits-from-phenotypic-and-target-directed-screens-against-intracellular-proteins
#13
REVIEW
Paul M Watt, Nadia Milech, Shane R Stone
Phylomers are peptides derived from biodiverse protein fragments. Genetically encoded Phylomer libraries have been constructed, containing hundreds of billions of peptides derived from virtually all of the few thousand fold families found in the protein universe. They offer a rich source of high quality hits against diverse target sequences and have been used for three main purposes: firstly, to identify and validate targets in phenotypic screens; secondly, to block protein interactions with nanomolar potency binding affinities; thirdly as a source of more efficient cell penetrating peptides for the delivery of a wide range of biologics...
May 18, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28527015/a-genome-wide-association-study-identifies-the-genomic-region-associated-with-shell-color-in-yesso-scallop-patinopecten-yessoensis
#14
Liang Zhao, Yangping Li, Yajuan Li, Jiachen Yu, Huan Liao, Shuyue Wang, Jia Lv, Jun Liang, Xiaoting Huang, Zhenmin Bao
The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform...
May 19, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28523377/mining-lipolytic-enzymes-in-community-dna-from-high-andean-soils-using-a-targeted-approach
#15
Daniel Borda-Molina, José Salvador Montaña, María Mercedes Zambrano, Sandra Baena
Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes...
May 18, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28520936/impacts-of-amino-acid-substitutions-in-fungal-cytochrome-p450-monooxygenase-cyp57b3-on-the-effective-production-of-3-hydroxygenistein
#16
Mayumi Hatakeyama, Takuya Kitaoka, Hirofumi Ichinose
Aspergillus oryzae cytochrome P450 monooxygenase (CYP57B3) is capable of catalyzing hydroxylation of genistein to produce 3΄-hydroxygenistein. Because hydroxylated derivatives of genistein, including 3΄-hydroxygenistein, exhibit various pharmacological activities, CYP57B3 would potentially be useful as a biocatalyst in the pharmaceutical field. We therefore performed random mutagenesis of CYP57B3 to improve its catalytic activities for genistein. Random mutations were introduced by error-prone PCR into CYP57B3, resulting in construction of a library of mutants...
May 18, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28520717/modular-protein-expression-toolbox-mopet-a-standardized-assembly-system-for-defined-expression-constructs-and-expression-optimization-libraries
#17
Ernst Weber, Jörg Birkenfeld, Jürgen Franz, Uwe Gritzan, Lars Linden, Mark Trautwein
The design and generation of an optimal expression construct is the first and essential step in in the characterization of a protein of interest. Besides evaluation and optimization of process parameters (e.g. selection of the best expression host or cell line and optimal induction conditions and time points), the design of the expression construct itself has a major impact. However, the path to this final expression construct is often not straight forward and includes multiple learning cycles accompanied by design variations and retesting of construct variants, since multiple, functional DNA sequences of the expression vector backbone, either coding or non-coding, can have a major impact on expression yields...
2017: PloS One
https://www.readbyqxmd.com/read/28515773/building-a-multipurpose-insertional-mutant-library-for-forward-and-reverse-genetics-in-chlamydomonas
#18
Xi Cheng, Gai Liu, Wenting Ke, Lijuan Zhao, Bo Lv, Xiaocui Ma, Nannan Xu, Xiaoling Xia, Xuan Deng, Chunlei Zheng, Kaiyao Huang
BACKGROUND: The unicellular green alga, Chlamydomonas reinhardtii, is a classic model for studying flagella and biofuel. However, precise gene editing, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas9) system, is not widely used in this organism. Screening of random insertional mutant libraries by polymerase chain reaction provides an alternate strategy to obtain null mutants of individual gene. But building, screening, and maintaining such a library was time-consuming and expensive...
2017: Plant Methods
https://www.readbyqxmd.com/read/28513744/high-affinity-recognition-of-the-human-c-reactive-protein-independent-of-phosphocholine
#19
Jie Yang, Anna-Lena Gustavsson, Martin Haraldsson, Göran Karlsson, Thomas Norberg, Lars Baltzer
A high-affinity polypeptide conjugate 4-C25L22-DQ, has been developed for the molecular recognition of the human C-reactive protein, CRP, a well-known inflammation biomarker. CRP is one of the most frequently quantified targets in diagnostic applications and a target in drug development. With the exception of antibodies, most molecular constructs take advantage of the known affinity for CRP of phosphocholine that depends on Ca(2+) for its ability to bind. 4-C25L22-DQ which is unrelated to phosphocholine binds in the absence of Ca(2+) with a dissociation constant of 760 nM, an order of magnitude lower than that of phosphocholine, the KD of which is 5 μM...
May 17, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28508774/arden-syntax-mlm-building-blocks-for-microbiological-concepts-and-their-application-in-infection-surveillance
#20
Jeroen S de Bruin, Walter Koller, Julia Zeckl, Alexander Blacky, Andrea Rappelsberger, Klaus-Peter Adlassnig
BACKGROUND: The diagnosis - and hence definitions - of healthcare-associated infections (HAIs) rely on microbiological laboratory test results in specific constellations. OBJECTIVES: To construct a library that provides interoperable building blocks for the analysis of microbiological laboratory test results. METHODS: We used Java for preprocessing raw microbiological laboratory test results and Arden Syntax for knowledge-based querying of data based on microbiology information elements used in European surveillance criteria for HAIs...
2017: Studies in Health Technology and Informatics
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