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Library construction

Hyun-Jeong Ryu, Seung-Ju Yang, Gee-Hyung Lee, Young-Dae Gong
A 2-amido benzo[d]imidazole library has been constructed on solid-phase synthesis. The key step of this solid-phase synthesis involves the preparation of polymer-bound 2-amino benzo[d]imidazole resin through desulfurative cyclization of thiourea resin by using DMC and DIPEA in DCM, and the resin is then functionalized by acylation at the 2-amine position, to afford 2-amido benzo[d]imidazole resin. In the case of 2-amido benzo[d]imidazole resin having p-I, and m-NO2, the resin was further functionalized by Suzuki/Sonogashira-coupling (p-I), and was reduced to primary amine (m-NO2), followed by acylation...
March 20, 2018: ACS Combinatorial Science
Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F Chen, Dong-Sheng Cao
BACKGROUND: With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important...
March 20, 2018: Journal of Cheminformatics
Haitao Huang, Huaqiang Tan, Dongmei Xu, Yi Tang, Yisong Niu, Yunsong Lai, Manman Tie, Huanxiu Li
Genetic maps are a prerequisite for quantitative trait locus (QTL) analysis, marker-assisted selection (MAS), fine gene mapping, and assembly of genome sequences. So far, several asparagus bean linkage maps have been established using various kinds of molecular markers. However, these maps were all constructed by gel- or array-based markers. No maps based on sequencing method have been reported. In this study, an NGS-based strategy, SLAF-seq, was applied to create a high-density genetic map for asparagus bean...
March 19, 2018: Scientific Reports
Michal M Dykas, Stuti K Desai, Abhijeet Patra, Mallikarjuna Rao Motapothula, Kingshuk Poddar, Linda J Kenney, Thirumalai Venkatesan
With the rise in nosocomial infections worldwide, research on materials with an intrinsic ability to inhibit biofilm formation has been generating a great deal of interest. In the present work, we describe how thin film material libraries generated by pulsed laser deposition can be used for simultaneously screening several novel metal oxide mixtures that inhibit biofilm formation in a common human pathogen, Salmonella enterica serovar Typhimurium. We discovered that in a material library constructed using two metal oxides, the net effect on biofilm formation can be modelled as an addition of the activities of the individual oxides weighted to their relative composition at that particular point on the library...
March 19, 2018: ACS Applied Materials & Interfaces
Vid Leko, Smitha Sripathy, Robin L Adrianse, Taylor Loe, Angela Park, Uyen Lao, Eric J Foss, Marisa S Bartolomei, Antonio Bedalov
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi)...
March 2, 2018: Journal of Visualized Experiments: JoVE
Erqing Jin, Lynn Wong, Yun Jiao, Jake Engel, Benjamin Holdridge, Peng Xu
Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements...
December 2017: Synthetic and Systems Biotechnology
Xinjian Yin, Jianping Wu, Lirong Yang
The objective of this study was to identify and exploit a robust biocatalyst that can be applied in reductive amination for enantioselective synthesis of the competitive herbicide L-phosphinothricin. Applying a genome mining-based library construction strategy, eight NADPH-specific glutamate dehydrogenases (GluDHs) were identified for reductively aminating 2-oxo-4-[(hydroxy)(methyl)phosphinoyl]butyric acid (PPO) to L-phosphinothricin. Among them, the glutamate dehydrogenase cloned from Pseudomonas putida (PpGluDH) exhibited relatively high catalytic activity and favorable soluble expression...
March 16, 2018: Applied Microbiology and Biotechnology
Paula Nahuelhual, Carolina Giaconi, M Alejandra Machuca
INTRODUCTION: According to the International Classification of Functioning, Disability and Health (ICF), participation is defined as "the involvement of the subject in situations of life" and is fun damental in the development of children and adolescents. In case of children with disabilities, participation allows a better understanding of the possible impact of deficiencies in daily life. OBJECTIVE: To evaluate measurement scales of participation in children and adolescents with and without disabilities...
December 2017: Revista Chilena de Pediatría
Yan Yang, Zhongyin Zhou, Rong Liu, Lu Chen, Hongyu Xiang, Na Chen
Endoscopic retrograde cholangiopancreatography (ERCP) is an important treatment for inoperable hilar cholangiocarcinoma (HCC). The aim of the present study as to evaluate the clinical value of three-dimensional visualization (3DV) and 3D printing (3DP) technologies for ERCP in patients with HCC. The clinical data of 15 patients with HCC admitted for ERCP were analyzed retrospectively, including 9 males and 6 females. Thin-sliced data of computed tomography and magnetic resonance cholangiopancreatography (MRCP) were acquired and imported into Mimics Innovation Suite v17...
April 2018: Experimental and Therapeutic Medicine
Seung Yub Han, Alesia Antoine, David Howard, Bryant Chang, Woo Sung Chang, Matthew Slein, Gintaras Deikus, Sofia Kossida, Patrice Duroux, Marie-Paule Lefranc, Robert P Sebra, Melissa L Smith, Ismael Ben F Fofana
The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque ( Macaca mulatta ) using oligonucleotide primers based on human IG gene sequences...
2018: Frontiers in Immunology
Joo Yeon Seok, Jina Yang, Sang Jin Choi, Hyun Gyu Lim, Un Jong Choi, Kyung-Jin Kim, Sunghoon Park, Tae Hyeon Yoo, Gyoo Yeol Jung
3-Hydroxypropionic acid (3-HP) is an important platform chemical, and biological production of 3-HP from glycerol as a carbon source using glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) has been revealed to be effective because it involves a relatively simple metabolic pathway and exhibits higher yield and productivity than other biosynthetic pathways. Despite the successful attempts of 3-HP production from glycerol, the biological process suffers from problems arising from low activity and inactivation of the two enzymes...
March 12, 2018: Metabolic Engineering
Qian-Wen Deng, Xiang-Dong Luo, Ya-Ling Chen, Yi Zhou, Fan-Tao Zhang, Biao-Lin Hu, Jian-Kun Xie
BACKGROUND: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. RESULTS: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response...
March 15, 2018: Biological Research
Joshua D Sackett, Desiree C Huerta, Brittany R Kruger, Scott D Hamilton-Brehm, Duane P Moser
Devils Hole is the sole natural habitat of the critically endangered Devils Hole pupfish (Cyprinodon diabolis). To establish a backup population, the Ash Meadows Fish Conservation Facility (AMFCF), a full-scale replica of the uppermost 6.7 m of Devils Hole, was constructed by management agencies in the mid-2010s. Despite rigorous efforts to mimic the bathymetric and physical details of the Devils Hole environment, the biogeochemistry and microbiology of the AMFCF refuge tank remain largely unaddressed. We evaluated water physicochemistry and employed Illumina DNA sequencing of 16S rRNA gene libraries to evaluate planktonic and benthic bacterial and archaeal community composition within their respective physicochemical contexts in Devils Hole and AMFCF on the same day...
2018: PloS One
He Chen, Jiacheng Yao, Yusi Fu, Yuhong Pang, Jianbin Wang, Yanyi Huang
The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically labeling adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing...
March 15, 2018: ACS Applied Materials & Interfaces
Ya-Dong Gao, Ya-Wei Qu, Hai-Feng Liu
OBJECTIVE: The accurate diagnosis of undetermined pancreaticobiliary strictures remains challenging. Current ERCP-guided tissue sampling methods are of low sensitivity. Confocal laser endomicroscopy (CLE) is a new procedure and allows real optical biopsies that may improve the diagnosis of undetermined pancreaticobiliary strictures. The aim of this meta-analysis was to determine the diagnostic yield of CLE, tissue sampling, and CLE combined with tissue sampling for undetermined pancreaticobiliary strictures...
March 15, 2018: Scandinavian Journal of Gastroenterology
Masatoshi Matsunami, Daiji Endo, Naruya Saitou, Hitoshi Suzuki, Manabu Onuma
The wood mouse (genus Apodemus ) is one of the most common rodents in broad-leaf forests in the temperate zone of the Palaearctic region. Molecular studies of wood mice have critically enhanced the understanding of their evolution and ancestral biogeographic events. However, their molecular data are currently only limited to partial mitochondrial sequences and a few genes. Therefore, we sequenced the wood mouse genome to facilitate the acquisition of useful resources for inferring their molecular evolution...
February 2018: Data in Brief
Fei Tao, Junjuan Wang, Zhongfeng Guo, Jingjing Hu, Xiangming Xu, Jiarong Yang, Xianming Chen, Xiaoping Hu
Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is a destructive disease of wheat worldwide. The disease is preferably controlled by growing resistant cultivars. Wheat cultivar Xiaoyan 6 (XY 6) has been resistant to stripe rust since its release. In the previous studies, XY 6 was found to have higher-temperature seedling-plant (HTSP) resistance. However, the molecular mechanisms of HTSP resistance were not clear. To identify differentially expressed genes (DEGs) involved in HTSP resistance, we sequenced 30 cDNA libraries constructed from XY 6 seedlings exposed to several temperature treatments...
2018: Frontiers in Plant Science
Mei Wang, Vijayasankar Raman, Jianping Zhao, Bharathi Avula, Yan-Hong Wang, Philip L Wylie, Ikhlas A Khan
Correct identification of the true bay leaf ( Laurus nobilis ) and its substitutes is important not only for the quality control of the products, but also for the safety of the consumers. L. nobilis is often substituted or confused with other species, such as Cinnamomum tamala, Pimenta racemosa, Syzygium polyanthum , and Umbellularia californica. In the present study, the potential of gas chromatography combined with quadrupole time-of-flight mass spectrometry for the profiling of various bay leaf products was evaluated for the first time...
March 14, 2018: Planta Medica
Tiandong Che, Diyan Li, Long Jin, Yuhua Fu, Yingkai Liu, Pengliang Liu, Yixin Wang, Qianzi Tang, Jideng Ma, Xun Wang, Anan Jiang, Xuewei Li, Mingzhou Li
Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar...
2018: PloS One
Katia Tarasava, Rongming Liu, Andrew Garst, Ryan T Gill
Optimization of metabolic flux is a difficult and time-consuming process that often involves changing the expression levels of multiple genes simultaneously. While some pathways have a known rate limiting step, more complex metabolic networks can require a trial-and-error approach of tuning the expression of multiple genes to achieve a desired distribution of metabolic resources. Here we present an efficient method for generating expression diversity on a combinatorial scale using CRISPR interference. We use a modified native Escherichia coli Type I-E CRISPR-Cas system and an iterative cloning strategy for construction of guide RNA arrays...
March 14, 2018: Biotechnology and Bioengineering
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