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https://www.readbyqxmd.com/read/28335400/online-classification-of-contaminants-based-on-multi-classification-support-vector-machine-using-conventional-water-quality-sensors
#1
Pingjie Huang, Yu Jin, Dibo Hou, Jie Yu, Dezhan Tu, Yitong Cao, Guangxin Zhang
Water quality early warning system is mainly used to detect deliberate or accidental water pollution events in water distribution systems. Identifying the types of pollutants is necessary after detecting the presence of pollutants to provide warning information about pollutant characteristics and emergency solutions. Thus, a real-time contaminant classification methodology, which uses the multi-classification support vector machine (SVM), is proposed in this study to obtain the probability for contaminants belonging to a category...
March 13, 2017: Sensors
https://www.readbyqxmd.com/read/28334828/flexible-crispr-library-construction-using-parallel-oligonucleotide-retrieval
#2
Abigail Read, Shaojian Gao, Eric Batchelor, Ji Luo
CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#3
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28333914/genome-scale-crispr-cas9-knockout-and-transcriptional-activation-screening
#4
Julia Joung, Silvana Konermann, Jonathan S Gootenberg, Omar O Abudayyeh, Randall J Platt, Mark D Brigham, Neville E Sanjana, Feng Zhang
Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28332627/cross-neutralizing-anti-hiv-1-human-single-chain-variable-fragments-scfvs-against-cd4-binding-site-and-n332-glycan-identified-from-a-recombinant-phage-library
#5
Lubina Khan, Rajesh Kumar, Ramachandran Thiruvengadam, Hilal Ahmad Parray, Muzamil Ashraf Makhdoomi, Sanjeev Kumar, Heena Aggarwal, Madhav Mohata, Abdul Wahid Hussain, Raksha Das, Raghavan Varadarajan, Jayanta Bhattacharya, Madhu Vajpayee, K G Murugavel, Suniti Solomon, Subrata Sinha, Kalpana Luthra
More than 50% of HIV-1 infection globally is caused by subtype_C viruses. Majority of the broadly neutralizing antibodies (bnAbs) targeting HIV-1 have been isolated from non-subtype_C infected donors. Mapping the epitope specificities of bnAbs provides useful information for vaccine design. Recombinant antibody technology enables generation of a large repertoire of monoclonals with diverse specificities. We constructed a phage recombinant single chain variable fragment (scFv) library with a diversity of 7.8 × 10(8) clones, using a novel strategy of pooling peripheral blood mononuclear cells (PBMCs) of six select HIV-1 chronically infected Indian donors whose plasma antibodies exhibited potent cross neutralization efficiency...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330315/characterization-and-development-of-est-ssr-markers-in-sweet-potato-ipomoea-batatas-l-lam
#6
Jin-Hee Kim, Jun-Hoi Kim, Won-Sam Jo, Jeong-Gwan Ham, Il Kyung Chung, Kyung-Min Kim
In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330232/high-quality-metagenomic-dna-from-marine-sediment-samples-for-genomic-studies-through-a-preprocessing-approach
#7
Solly Solomon, Bhavya Kachiprath, G Jayanath, T P Sajeevan, I S Bright Singh, Rosamma Philip
Recent advances in culture-independent studies of microbes had proved to be more reliable and efficient than the conventional ones. The isolation of good quality and quantity of total community DNA are one of the major hurdles in this endeavour. Shearing of DNA during the extraction process and the co-extraction of inhibitory compounds reduce the quality of the isolated nucleic acids making it unsuitable for the construction of large insert metagenomic libraries. In the present study, a multi-level filtration step was brought in which efficiently isolated total bacterial DNA from three different environment samples...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330093/exploration-of-nifh-gene-through-soil-metagenomes-of-the-western-indian-himalayas
#8
Ravindra Soni, Deep Chandra Suyal, Santosh Sai, Reeta Goel
This group has previously highlighted the prevalence of Csp genes from cold Himalayan environments. However, this study has explored the uncultured diazotrophs from metagenomes of western Indian Himalayas. The metagenomic nifH gene clone library was constructed from the Temperate, Subtropical and Tarai soils of Western Himalaya, India followed by polymerase chain reaction (PCR) amplification. After preliminary screening, selected clones were sequenced. In silico analysis of the clones was done, which documented 83...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28326786/solvent-free-mechanosynthesis-of-composition-tunable-cesium-lead-halide-perovskite-quantum-dots
#9
Zhi-Yuan Zhu, Qi-Qi Yang, Lin-Feng Gao, Lei Zhang, An-Ye Shi, Chun-Lin Sun, Qiang Wang, Hao-Li Zhang
A facile and green mechanosynthesis strategy free of solvent and high reaction temperature was developed to fabricate highly emissive cesium lead halide perovskite (CsPbX3) quantum dots (QDs). Their composition can be adjusted conveniently simply through mechanically milling/grinding stoichiometric combinations of raw reagents, thereby introducing a broad luminescence tunability of the product with adjustable wavelength, linewidth and photoluminescence quantum yield. Desired CsPbX3 QDs "library" can thus be readily constructed in a way like assembling Lego building blocks...
March 22, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28323250/the-atomic-simulation-environment-a-python-library-for-working-with-atoms
#10
Ask Larsen, Jens Mortensen, Jakob Blomqvist, Ivano Castelli, Rune Christensen, Marcin Dulak, Jesper Friis, Michael Groves, Bjork Hammer, Cory Hargus, Eric Hermes, Paul Jennings, Peter Jensen, James Kermode, John Kitchin, Esben Kolsbjerg, Joseph Kubal, Kristen Kaasbjerg, Steen Lysgaard, Jon Maronsson, Tristan Maxson, Thomas Olsen, Lars Pastewka, Andrew Peterson, Carsten Rostgaard, Jakob Schiøtz, Ole Schütt, Mikkel Strange, Kristian Thygesen, Tejs Vegge, Lasse Vilhelmsen, Michael Walter, Zhenhua Zeng, Karsten Wedel Jacobsen
The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface...
March 21, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28322330/distribution-of-bathyarchaeota-communities-across-different-terrestrial-settings-and-their-potential-ecological-functions
#11
Xing Xiang, Ruicheng Wang, Hongmei Wang, Linfeng Gong, Baiying Man, Ying Xu
High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321208/detection-of-a-putative-tetr-like-gene-related-to-mycobacterium-bovis-bcg-growth-in-cholesterol-using-a-gfp-transposon-mutagenesis-system
#12
Isabel Otal, Esther Pérez-Herrán, Lazaro Garcia-Morales, María C Menéndez, Jorge A Gonzalez-Y-Merchand, Carlos Martín, María J García
In vitro transposition is a powerful genetic tool for identifying mycobacterial virulence genes and studying virulence factors in relation to the host. Transposon shuttle mutagenesis is a method for constructing stable insertions in the genome of different microorganisms including mycobacteria. Using an IS1096 derivative, we have constructed the Tngfp, a transposon containing a promoterless green fluorescent protein (gfp) gene. This transposon was able to transpose randomly in Mycobacterium bovis BCG. Bacteria with a single copy of the gfp gene per chromosome from an M...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28319021/engineering-a-growth-sensor-to-select-intracellular-antibodies-in-the-cytosol-of-mammalian-cells
#13
Thuy Duong Nguyen, Hitoshi Takasuka, Yoshihiro Kaku, Satoshi Inoue, Teruyuki Nagamune, Masahiro Kawahara
Intracellular antibodies (intrabodies) are expected to function as therapeutics as well as tools for elucidating in vivo function of proteins. In this study, we propose a novel intrabody selection method in the cytosol of mammalian cells by utilizing a growth signal, induced by the interaction of the target antigen and an scFv-c-kit growth sensor. Here, we challenge this method to select specific intrabodies against rabies virus nucleoprotein (RV-N) for the first time. As a result, we successfully select antigen-specific intrabodies from a naïve synthetic library using phage panning followed by our growth sensor-based intracellular selection method, demonstrating the feasibility of the method...
March 16, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28317060/prognostic-factors-for-mortality-in-patients-with-bullous-pemphigoid-a-meta-analysis
#14
Yi-Di Liu, Yan-Hong Wang, Yi-Cong Ye, Wen-Ling Zhao, Li Li
Bullous pemphigoid (BP) is a chronic debilitating autoimmune blistering disease that frequently occurs in the elderly population. Previous studies have suggested a high morbidity and mortality associated with BP. However, relatively few studies have investigated prognostic factors of BP mortality, and they showed considerably various results. This meta-analysis aimed to quantitatively assess the association between several potential prognostic factors and risk of mortality in bullous pemphigoid. A comprehensive search was performed using Pubmed, Embase, and Cochrane Library...
March 19, 2017: Archives of Dermatological Research
https://www.readbyqxmd.com/read/28316652/a-novel-descriptor-based-on-atom-pair-properties
#15
Masataka Kuroda
BACKGROUND: Molecular descriptors have been widely used to predict biological activities and physicochemical properties or to analyze chemical libraries on the basis of similarity. Although fingerprints and properties are generally used as descriptors, neither is perfect for these purposes. A fingerprint can distinguish between molecules, whereas a property may not do the same in certain cases, and vice versa. When the number of the training set is especially small, the construction of good predictive models is difficult...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28316049/structure-and-function-of-the-bacterial-communities-during-rhizoremediation-of-hexachlorobenzene-in-constructed-wetlands
#16
Cuiping Zhang, Bei Wang, Xiaoyan Dai, Shuying Li, Guangqiu Lu, Yuanqing Zhou
Vertical flow constructed wetlands (VF CWs) are considered to be effective for treating organic pollutants. The rhizosphere of macrophytes such as Phragmites sp., Typha sp. serves as an active and dynamic zone for the microbial degradation of organic pollutants. However, it is still not clear how soil bacterial communities respond to macrophytes and pollutants during the process. For this purpose, the seedlings of Phragmites australis and Typha angustifolia were planted respectively in the VF CWs added with HCB at a dose of 2 mg/kg...
March 18, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28315364/genome-guided-transcriptome-analysis-of-miiuy-croaker-provides-insights-into-pattern-recognition-receptors-and-cytokines-in-response-to-vibrio-anguillarum
#17
Qing Chu, Weihua Song, Junxia Cui, Tianjun Xu
Miiuy croaker (Miichthys miiuy), as an economically important marine fish is affected by numerous bacterial diseases. Infection by bacterial pathogen Vibrio anguillarum causes high mortality and great economic loss in aquaculture. To understand the immune response of the miiuy croaker to V. anguillarum infection, we analyzed the transcriptomic profile of V. anguillarum-challenged M. miiuy, and two cDNA libraries, namely, the normal library (Ctrl) and V. anguillarum challenged library (Van) were constructed...
March 14, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28315209/recombinant-allergen-production-in-e-coli
#18
Changqi Liu, LeAnna N Willison, Shridhar K Sathe
Recombinant protein allergens have been used in allergy studies, allergy diagnosis, and epitope mapping. Messenger RNAs (mRNAs) are isolated from tissues of interest for complementary DNA (cDNA) library construction. Subsequently, the allergen gene is amplified by polymerase chain reaction (PCR) and sequenced. The amplified gene is then cloned into an expression vector, expressed in Escherichia coli cells, and purified from the cell lysate. This chapter describes the protocols for recombinant allergen production...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315069/toolkits-and-libraries-for-deep-learning
#19
REVIEW
Bradley J Erickson, Panagiotis Korfiatis, Zeynettin Akkus, Timothy Kline, Kenneth Philbrick
Deep learning is an important new area of machine learning which encompasses a wide range of neural network architectures designed to complete various tasks. In the medical imaging domain, example tasks include organ segmentation, lesion detection, and tumor classification. The most popular network architecture for deep learning for images is the convolutional neural network (CNN). Whereas traditional machine learning requires determination and calculation of features from which the algorithm learns, deep learning approaches learn the important features as well as the proper weighting of those features to make predictions for new data...
March 17, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28314725/a-genome-survey-and-postharvest-transcriptome-analysis-in-lentinula-edodes
#20
Yuichi Sakamoto, Keiko Nakade, Shiho Sato, Kentaro Yoshida, Kazuhiro Miyazaki, Satoshi Natsume, Naotake Konno
Lentinula edodes is a popular cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction of Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and long reads by PacBio, resulting in a contig number of 1951 and an N50 of 1 Mb. Further, we predicted genes by Augustus using RNA-seq data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes...
March 17, 2017: Applied and Environmental Microbiology
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