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https://www.readbyqxmd.com/read/28538097/biochemical-characterization-of-the-functional-roles-of-residues-in-the-active-site-of-the-%C3%AE-galactosidase-from-bacillus-circulans-atcc-31382
#1
Huifang Yin, Tjaard Pijning, Xiangfeng Meng, Lubbert Dijkhuizen, Sander Sebastiaan van Leeuwen
The β-galactosidase enzyme from Bacillus circulans ATCC 31382 BgaD is widely used in the food industry to produce prebiotic galactooligosaccharides (GOS). Recently, the crystal structure of a C-terminally truncated version of the enzyme (BgaD-D) has been elucidated. The roles of active site amino acid residues in β-galactosidase enzyme reaction and product specificity have remained unknown. Based on a structural alignment of the β-galactosidase enzymes BgaD-D from Bacillus circulans and BgaA from Streptococcus pneumoniae, and the complex of BgaA with LacNAc, we identified 8 active site amino acid residues (Arg185, Asp481, Lys487, Tyr511, Trp570, Trp593, Glu601, and Phe616) in BgaD-D...
May 24, 2017: Biochemistry
https://www.readbyqxmd.com/read/28537729/stretching-induced-conductance-variations-as-fingerprints-of-contact-configurations-in-single-molecule-junctions
#2
Yong-Hoon Kim, Hu Sung Kim, Juho Lee, Makusu Tsutsui, Tomoji Kawai
Molecule-electrode contact atomic structures are a critical factor that characterizes molecular devices, but their precise understanding and control still remain elusive. Based on combined first-principles calculations and single-molecule break junction experiments, we herein establish that the conductance of alkanedithiolate junctions can both increase and decrease with mechanical stretching and the specific trend is determined by the S-Au linkage coordination number (CN) or the molecule-electrode contact atomic structure...
May 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28535423/chromatographic-separation-and-detection-methods-of-aloe-arborescens-miller-constituents-a-systematic-review
#3
REVIEW
Jilan A Nazeam, Haidy A Gad, Hala M El-Hefnawy, Abdel-Naser B Singab
Aloe arborescens Miller (Family Asphodelaceae) is a member of genus Aloe, which is used in traditional medicine to cure various diseases. The extracts of the plant have been reported to possess anticancer, immunomodulator, antidiabetic, anti-inflammatory and antioxidant activities. The phytochemical investigations have revealed diverse chemical constituents, including phenolics [anthraquinones, anthrones, pyrones, chromones and coumarins], polysaccharides [arborans [(1-4) linked glucomannans, polysaccharide (A, B and C): (A: a linear (1-6)-O-α-glucan, B: a branching (1-2)-O-l-arabinose with (1-2)-O-d-galactose linkages and C: (1-4)-O-β-mannan with 18% acetyl group)]], glycoproteins and carboxypeptidase enzyme...
April 29, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28535339/ecophysiological-examination-of-the-lake-erie-microcystis-bloom-in-2014-linkages-between-biology-and-the-water-supply-shutdown-of-toledo-ohio
#4
Morgan Michelle Steffen, Timothy W Davis, Robert Michael McKay, George S Bullerjahn, Lauren E Krausfeldt, Joshua M A Stough, Michelle L Neitzey, Naomi E Gilbert, Gregory L Boyer, Thomas H Johengen, Duane C Gossiaux, Ashley M Burtner, Danna Palladino, Mark Rowe, Gregory J Dick, Kevin Meyer, Shawn Levy, Braden Boone, Richard Stumpf, Timothy Wynne, Paul V Zimba, Danielle B Gutierrez, Steven W Wilhelm
Annual cyanobacterial blooms dominated by Microcystis have occurred in western Lake Erie (USA/Canada) during summer months since 1995. The production of toxins by bloom-forming cyanobacteria can lead to drinking water crises, such as the one experienced by the city of Toledo in August of 2014, when the city was rendered without drinking water for > 2 days. It is important to understand the conditions and environmental cues that were driving this specific bloom to provide a scientific framework for management of future bloom events...
May 23, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28535200/the-draft-genome-of-blunt-snout-bream-megalobrama-amblycephala-reveals-the-development-of-intermuscular-bone-and-adaptation-to-herbivorous-diet
#5
Han Liu, Chunhai Chen, Zexia Gao, Jiumeng Min, Yongming Gu, Jianbo Jian, Xiewu Jiang, Huimin Cai, Ingo Ebersberger, Meng Xu, Xinhui Zhang, Jianwei Chen, Wei Luo, Boxiang Chen, Junhui Chen, Hong Liu, Jiang Li, Ruifang Lai, Mingzhou Bai, Jin Wei, Shaokui Yi, Huanling Wang, Xiaojuan Cao, Xiaoyun Zhou, Yuhua Zhao, Kaijian Wei, Ruibin Yang, Bingnan Liu, Shancen Zhao, Xiaodong Fang, Manfred Schartl, Xueqiao Qian, Weimin Wang
Background: The blunt snout bream, Megalobrama amblycephala , is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. Results: As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala , with 779.54 Mb anchored on 24 linkage groups...
May 23, 2017: GigaScience
https://www.readbyqxmd.com/read/28534793/an-information-theoretic-cluster-visualization-for-self-organizing-maps
#6
Leonardo Enzo Brito da Silva, Donald C Wunsch
Improved data visualization will be a significant tool to enhance cluster analysis. In this paper, an information-theoretic-based method for cluster visualization using self-organizing maps (SOMs) is presented. The information-theoretic visualization (IT-vis) has the same structure as the unified distance matrix, but instead of depicting Euclidean distances between adjacent neurons, it displays the similarity between the distributions associated with adjacent neurons. Each SOM neuron has an associated subset of the data set whose cardinality controls the granularity of the IT-vis and with which the first- and second-order statistics are computed and used to estimate their probability density functions...
May 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28534210/association-study-of-estrogen-receptor-alpha-gene-polymorphisms-with-bone-mass-assessed-by-quantitative-ultrasound-in-young-adults
#7
María Correa-Rodriguez, Jacqueline Schmidt-RioValle, Blanca Rueda-Medina
Different genetic variants in estrogen receptor alpha (ESR1) have been shown to influence bone phenotypes including quantitative bone ultrasound in elderly. We aimed to investigate the role of ESR1 polymorphisms in bone mass assessed by calcaneal quantitative ultrasound (QUS) in a population of young adults. The study sample consisted of 466 healthy individuals of Caucasian ancestry (315 females and 152 males) aged 18 and 25 years (median age 20.39 ± 2.70). Six ESR1 polymorphisms (rs302033, rs2982552, rs2982575, rs2504063, rs2234693-PvuII and rs9340799-XbaI) were selected as genetic markers and genotyped...
May 22, 2017: Rheumatology International
https://www.readbyqxmd.com/read/28534096/genomic-prediction-ability-for-yield-related-traits-in-german-winter-barley-elite-material
#8
Patrick Thorwarth, Jutta Ahlemeyer, Anne-Marie Bochard, Kerstin Krumnacker, Hubert Blümel, Eberhard Laubach, Nadine Knöchel, László Cselényi, Frank Ordon, Karl J Schmid
Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material. To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L...
May 22, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28533786/high-density-linkage-map-construction-and-mapping-of-yield-trait-qtls-in-maize-zea-mays-using-the-genotyping-by-sequencing-gbs-technology
#9
Chengfu Su, Wei Wang, Shunliang Gong, Jinghui Zuo, Shujiang Li, Shizhong Xu
Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28532305/production-and-use-of-estimates-for-monitoring-progress-in-the-health-sector-the-case-of-bangladesh
#10
Karar Zunaid Ahsan, Tazeen Tahsina, Afrin Iqbal, Nazia Binte Ali, Suman Kanti Chowdhury, Tanvir M Huda, Shams El Arifeen
BACKGROUND:  In order to support the progress towards the post-2015 development agenda for the health sector, the importance of high-quality and timely estimates has become evident both globally and at the country level. OBJECTIVE AND METHODS: Based on desk review, key informant interviews and expert panel discussions, the paper critically reviews health estimates from both the local (i.e. nationally generated information by the government and other agencies) and the global sources (which are mostly modeled or interpolated estimates developed by international organizations based on different sources of information), and assesses the country capacity and monitoring strategies to meet the increasing data demand in the coming years...
January 2017: Global Health Action
https://www.readbyqxmd.com/read/28531190/real-time-cell-toxicity-profiling-of-tox21-10k-compounds-reveals-cytotoxicity-dependent-toxicity-pathway-linkage
#11
Jui-Hua Hsieh, Ruili Huang, Ja-An Lin, Alexander Sedykh, Jinghua Zhao, Raymond R Tice, Richard S Paules, Menghang Xia, Scott S Auerbach
Cytotoxicity is a commonly used in vitro endpoint for evaluating chemical toxicity. In support of the U.S. Tox21 screening program, the cytotoxicity of ~10K chemicals was interrogated at 0, 8, 16, 24, 32, & 40 hours of exposure in a concentration dependent fashion in two cell lines (HEK293, HepG2) using two multiplexed, real-time assay technologies. One technology measures the metabolic activity of cells (i.e., cell viability, glo) while the other evaluates cell membrane integrity (i.e., cell death, flor). Using glo technology, more actives and greater temporal variations were seen in HEK293 cells, while results for the flor technology were more similar across the two cell types...
2017: PloS One
https://www.readbyqxmd.com/read/28530812/probing-the-binding-modes-of-a-multi-domain-protein-to-lipid-based-nanoparticles-by-relaxation-based-nmr
#12
Alberto Ceccon, Vitali Tugarinov, Andrew J Boughton, David Fushman, G Marius Clore
The interactions of two model multi-domain proteins - covalently linked di-ubiquitins, Ub2 - with lipid-based nanoparticles have been quantitatively probed by the measurements of NMR lifetime line broadening, ΔR2. By combined analysis of ΔR2 profiles arising from interactions with liposomes of varying sizes, an approach recently developed for the characterization of interactions of mono-ubiquitin with liposomes, we determine how the parameters of exchange (liposome binding) and dynamics of each individual domain of Ub2 on the surface of liposomes change when the domains are covalently attached to one another by a flexible linker...
May 22, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28530388/microfluidic-capillary-electrophoresis-mass-spectrometry-for-analysis-of-monosaccharides-oligosaccharides-and-glycopeptides
#13
Kshitij Khatri, Joshua A Klein, John Haserick, Deborah R Leon, Catherine E Costello, Mark E McComb, Joseph Zaia
Glycomics and glycoproteomics analyses by mass spectrometry require efficient front-end separation methods to enable deep characterization of heterogeneous glycoform populations. Chromatography methods are generally limited in their ability to resolve glycoforms using mobile phases that are compatible with online liquid chromatography-mass spectrometry (LC-MS). The adoption of capillary electrophoresis-mass spectrometry methods (CE-MS) for glycomics and glycoproteomics is limited by the lack of convenient interfaces for coupling the CE devices to mass spectrometers...
May 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28530049/examining-the-effects-of-hiv-self-testing-compared-to-standard-hiv-testing-services-a-systematic-review-and-meta-analysis
#14
Cheryl C Johnson, Caitlin Kennedy, Virginia Fonner, Nandi Siegfried, Carmen Figueroa, Shona Dalal, Anita Sands, Rachel Baggaley
INTRODUCTION: HIV self-testing (HIVST) is a discreet and convenient way to reach people with HIV who do not know their status, including many who may not otherwise test. To inform World Health Organization (WHO) guidance, we assessed the effect of HIVST on uptake and frequency of testing, as well as identification of HIV-positive persons, linkage to care, social harm, and risk behaviour. METHODS: We systematically searched for studies comparing HIVST to standard HIV testing until 1 June 2016...
May 15, 2017: Journal of the International AIDS Society
https://www.readbyqxmd.com/read/28529714/recent-advances-in-predicting-gene-disease-associations
#15
REVIEW
Kenneth Opap, Nicola Mulder
Deciphering gene-disease association is a crucial step in designing therapeutic strategies against diseases. There are experimental methods for identifying gene-disease associations, such as genome-wide association studies and linkage analysis, but these can be expensive and time consuming. As a result, various in silico methods for predicting associations from these and other data have been developed using different approaches. In this article, we review some of the recent approaches to the computational prediction of gene-disease association...
2017: F1000Research
https://www.readbyqxmd.com/read/28528802/symptomatic-dengue-infection-during-pregnancy-and-livebirth-outcomes-in-brazil-2007-13-a-retrospective-observational-cohort-study
#16
Laura B Nascimento, Cláudio M Siqueira, Giovanini E Coelho, João B Siqueira
BACKGROUND: Dengue is a major public health challenge in Brazil. We assessed the relationship between symptomatic dengue infection during pregnancy and adverse birth outcomes in the country between 2007 and 2013. METHODS: We did a retrospective observational cohort study using information reported in the Brazilian national reportable disease information system (SINAN) and the livebirth information system (SINASC) databases. We probabilistically linked confirmed dengue-positive and dengue-negative pregnancies with live childbirths using Fine-Grained Record Integration and Linkage (FRIL) software...
May 18, 2017: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/28528003/acinetobacter-baumannii-k11-and-k83-capsular-polysaccharides-have-the-same-6-deoxy-l-talose-containing-pentasaccharide-k-units-but-different-linkages-between-the-k-units
#17
Johanna J Kenyon, Alexander S Shashkov, Sof'ya N Senchenkova, Mikhail M Shneider, Bin Liu, Anastasiya V Popova, Nikolay P Arbatsky, Konstantin A Miroshnikov, Lei Wang, Yuriy A Knirel, Ruth M Hall
Acinetobacter baumannii produces a variety of capsular polysaccharides (CPS) via genes located at the chromosomal K locus and some KL gene clusters include genes for the synthesis of specific sugars. The structures of K11 and K83 CPS produced by isolates LUH5545 and LUH5538, which carry related KL11a and KL83 gene clusters, respectively, were established by sugar analysis and one- and two-dimensional (1)H and (13)C NMR spectroscopy. Both CPS contain L-rhamnose (L-Rha) and 6-deoxy-L-talose (L-6dTal), and both KL gene clusters include genes for dTDP-L-Rhap synthesis and a tle (talose epimerase) gene encoding an epimerase that converts dTDP-L-Rhap to dTDP-L-6dTalp...
May 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28526932/inpatient-addiction-consultation-for-hospitalized-patients-increases-post-discharge-abstinence-and-reduces-addiction-severity
#18
Sarah E Wakeman, Joshua P Metlay, Yuchiao Chang, Grace E Herman, Nancy A Rigotti
BACKGROUND: Alcohol and drug use results in substantial morbidity, mortality, and cost. Individuals with alcohol and drug use disorders are overrepresented in general medical settings. Hospital-based interventions offer an opportunity to engage with a vulnerable population that may not otherwise seek treatment. OBJECTIVE: To determine whether inpatient addiction consultation improves substance use outcomes 1 month after discharge. DESIGN: Prospective quasi-experimental evaluation comparing 30-day post-discharge outcomes between participants who were and were not seen by an addiction consult team during hospitalization at an urban academic hospital...
May 19, 2017: Journal of General Internal Medicine
https://www.readbyqxmd.com/read/28526836/characterisation-of-antibiotic-prescriptions-for-acute-respiratory-tract-infections-in-danish-general-practice-a-retrospective-registry-based-cohort-study
#19
Rune Aabenhus, Malene Plejdrup Hansen, Laura Trolle Saust, Lars Bjerrum
Inappropriate use of antibiotics is contributing to the increasing rates of antimicrobial resistance. Several Danish guidelines on antibiotic prescribing for acute respiratory tract infections in general practice have been issued to promote rational prescribing of antibiotics, however it is unclear if these recommendations are followed. We aimed to characterise the pattern of antibiotic prescriptions for patients diagnosed with acute respiratory tract infections, by means of electronic prescriptions, labeled with clinical indications, from Danish general practice...
May 19, 2017: NPJ Primary Care Respiratory Medicine
https://www.readbyqxmd.com/read/28526730/a-targeted-capture-linkage-map-anchors-the-genome-of-the-schistosomiasis-vector-snail-biomphalaria-glabrata
#20
Jacob A Tennessen, Stephanie R Bollmann, Michael S Blouin
The aquatic planorbid snail Biomphalaria glabrate is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here we used targeted capture markers to map over 10,000 B. glabrate scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups. We added additional scaffolds to these linkage groups based on linkage disequilibrium analysis of targeted capture and whole-genome sequences of 96 unrelated snails...
May 19, 2017: G3: Genes—Genomes—Genetics
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