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https://www.readbyqxmd.com/read/28931053/identification-and-molecular-characterization-of-a-metagenome-derived-l-lysine-decarboxylase-gene-from-subtropical-soil-microorganisms
#1
Jie Deng, Hua Gao, Zhen Gao, Huaxian Zhao, Ying Yang, Qiaofen Wu, Bo Wu, Chengjian Jiang
L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs...
2017: PloS One
https://www.readbyqxmd.com/read/28930546/tick-host-pathogen-systems-immunobiology-an-interactive-trio
#2
Stephen K Wikel
Significant new insights are being made into tick modulation of host immune defenses and the implications of those host defense changes on tick-borne pathogen transmission and establishment of infection. Understanding tick saliva complexity increased with construction and analyses of salivary gland cDNA libraries. High throughput next generation sequencing and advances in proteomics are revealing greater complexity of saliva, nature of gene families and differential gene expression patterns not previously attainable...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929370/a-termite-symbiotic-mushroom-maximizing-sexual-activity-at-growing-tips-of-vegetative-hyphae
#3
Huei-Mei Hsieh, Mei-Chu Chung, Pao-Yang Chen, Fei-Man Hsu, Wen-Wei Liao, Ai-Ning Sung, Chun-Ru Lin, Chung-Ju Rachel Wang, Yu-Hsin Kao, Mei-Jane Fang, Chi-Yung Lai, Chieh-Chen Huang, Jyh-Ching Chou, Wen-Neng Chou, Bill Chia-Han Chang, Yu-Ming Ju
BACKGROUND: Termitomyces mushrooms are mutualistically associated with fungus-growing termites, which are widely considered to cultivate a monogenotypic Termitomyces symbiont within a colony. Termitomyces cultures isolated directly from termite colonies are heterokaryotic, likely through mating between compatible homokaryons. RESULTS: After pairing homokaryons carrying different haplotypes at marker gene loci MIP and RCB from a Termitomyces fruiting body associated with Odontotermes formosanus, we observed nuclear fusion and division, which greatly resembled meiosis, during each hyphal cell division and conidial formation in the resulting heterokaryons...
September 19, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28928718/analysing-microbial-community-composition-through-amplicon-sequencing-from-sampling-to-hypothesis-testing
#4
REVIEW
Luisa W Hugerth, Anders F Andersson
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28927259/generation-diversity-determination-and-application-to-antibody-selection-of-a-human-na%C3%A3-ve-fab-library
#5
Sangkyu Kim, Insoo Park, Seung Gu Park, Seulki Cho, Jin Hong Kim, Nagesh S Ipper, Sun Shim Choi, Eung Suk Lee, Hyo Jeong Hong
We constructed a large naïve human Fab library (3 x 1010 colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and κ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries...
September 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28926980/indexing-natural-products-for-their-potential-anti-diabetic-activity-filtering-and-mapping-discriminative-physicochemical-properties
#6
Mouhammad Zeidan, Mahmoud Rayan, Nuha Zeidan, Mizied Falah, Anwar Rayan
Diabetes mellitus (DM) poses a major health problem, for which there is an unmet need to develop novel drugs. The application of in silico techniques and optimization algorithms is instrumental to achieving this goal. A set of 97 approved anti-diabetic drugs, representing the active domain, and a set of 2892 natural products, representing the inactive domain, were used to construct predictive models and to index anti-diabetic bioactivity. Our recently-developed approach of 'iterative stochastic elimination' was utilized...
September 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28926213/whole-genome-amplification-and-sequencing-of-a-daphnia-resting-egg
#7
Justin B Lack, Lawrence J Weider, Punidan D Jeyasingh
Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Although a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA...
September 19, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28925699/ab-initio-computation-of-energy-deposition-during-electron-ionization-of-molecules
#8
Karl K Irikura
The dissociative ionization of molecules under electron impact forms the basis for analytical mass spectrometry of volatile compounds. It is also important in other situations, notably plasmas. Although qualitative theory for mass spectrometry was developed long ago, progress toward predictive theory has been slow. A major obstacle has been ignorance of the amount of energy deposited in the molecular ion, prior to its fragmentation. Here, we consider the Binary-Encounter Bethe (BEB) theory, which was originally developed for predicting total ionization cross sections...
September 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28924030/altered-regulation-of-the-diguanylate-cyclase-yaic-reduces-production-of-type-1-fimbriae-in-a-pst-mutant-of-uropathogenic-e-coli-cft073
#9
Sébastien Crépin, Gaëlle Porcheron, Sébastien Houle, Josée Harel, Charles M Dozois
The pst gene cluster encodes the phosphate specific transport system (Pst). Inactivation of the Pst system constitutively activates the two-component regulatory system PhoBR and attenuates virulence of pathogenic bacteria. In uropathogenic E. coli strain CFT073, attenuation by inactivation of pst is predominantly attributed to the decreased expression of type 1 fimbriae. However, the molecular mechanisms connecting the Pst system and type 1 fimbriae are unknown. To address this, a transposon library was constructed in the pst mutant, and clones were tested for a regain in type 1 fimbriae production...
September 18, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28924003/learning-the-high-dimensional-immunogenomic-features-that-predict-public-and-private-antibody-repertoires
#10
Victor Greiff, Cédric R Weber, Johannes Palme, Ulrich Bodenhofer, Enkelejda Miho, Ulrike Menzel, Sai T Reddy
Recent studies have revealed that immune repertoires contain a substantial fraction of public clones, which may be defined as Ab or TCR clonal sequences shared across individuals. It has remained unclear whether public clones possess predictable sequence features that differentiate them from private clones, which are believed to be generated largely stochastically. This knowledge gap represents a lack of insight into the shaping of immune repertoire diversity. Leveraging a machine learning approach capable of capturing the high-dimensional compositional information of each clonal sequence (defined by CDR3), we detected predictive public clone and private clone-specific immunogenomic differences concentrated in CDR3's N1-D-N2 region, which allowed the prediction of public and private status with 80% accuracy in humans and mice...
September 18, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28923591/transcriptome-profiling-based-on-protein-protein-interaction-networks-provides-a-core-set-of-genes-for-understanding-blood-immune-response-mechanisms-against-edwardsiella-tarda-infection-in-japanese-flounder-paralichthys-olivaceus
#11
Zan Li, Xiumei Liu, Jinxiang Liu, Kai Zhang, Haiyang Yu, Yan He, Xubo Wang, Jie Qi, Zhigang Wang, Quanqi Zhang
Marine organisms are commonly under threat from various pathogens. Edwardsiella tarda is one of the fish pathogens that can infect both cultured and wild fish species. E. tarda can also infect other vertebrates, including amphibians, reptiles, and mammals. Bacteremia caused by E. tarda can be a fatal disease in humans. Blood acts as a pipeline for the fish immune system. Generating blood transcriptomic resources from fish challenged by E. tarda is crucial for understanding molecular mechanisms underlying blood immune response process...
September 15, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28922416/multi-level-computational-methods-for-interdisciplinary-research-in-the-hathitrust-digital-library
#12
Jaimie Murdock, Colin Allen, Katy Börner, Robert Light, Simon McAlister, Andrew Ravenscroft, Robert Rose, Doori Rose, Jun Otsuka, David Bourget, John Lawrence, Chris Reed
We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We provide a case study for the application of the methods to the problem of identifying and extracting arguments about anthropomorphism during a critical period in the development of comparative psychology...
2017: PloS One
https://www.readbyqxmd.com/read/28921549/%C3%AE-flucs-brighter-photinus-pyralis-firefly-luciferases-identified-by-surveying-consecutive-single-amino-acid-deletion-mutations-in-a-thermostable-variant
#13
Lisa M Halliwell, Amit P Jathoul, Jack P Bate, Harley L Worthy, James C Anderson, Dafydd D Jones, James A H Murray
The bright bioluminescence catalysed by Photinus pyralis firefly luciferase (Fluc) enables a vast array of life science research such as bioimaging in live animals and sensitive in vitro diagnostics. The effectiveness of such applications is improved using engineered enzymes that to date have been constructed using amino acid substitutions. We describe ΔFlucs: consecutive single amino acid deletion mutants within 6 loop structures of the bright and thermostable x11 Fluc. Deletion mutations are a promising avenue to explore new sequence and functional space and isolate novel mutant phenotypes...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28916961/practical-computational-toolkits-for-dendrimers-and-dendrons-structure-design
#14
Nuno Martinho, Liana C Silva, Helena F Florindo, Steve Brocchini, Teresa Barata, Mire Zloh
Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures...
September 15, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28916650/differential-expression-of-mirnas-in-the-respiratory-tree-of-the-sea-cucumber-apostichopus-japonicus-under-hypoxia-stress
#15
Da Huo, Lina Sun, Xiaoni Li, Xiaoshang Ru, Shilin Liu, Libin Zhang, Lili Xing, Hongsheng Yang
Sea cucumber, an important economic species, has encountered high mortality since 2013 in northern China because of seasonal environmental stress such as hypoxia, high temperature, and low salinity. MicroRNAs (miRNAs) are important in regulating gene expression in marine organisms in response to environmental change. In the present study, high-throughput sequencing was used to investigate alterations in miRNA expression in the sea cucumber under different levels of dissolved oxygen (DO). Nine small RNA libraries were constructed from the sea cucumber respiratory trees...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28912799/triportheus-albus-cope-1872-in-the-blackwater-clearwater-and-whitewater-of-the-amazon-a-case-of-phenotypic-plasticity
#16
José D A Araújo, Andrea Ghelfi, Adalberto L Val
The Amazon basin includes 1000s of bodies of water, that are sorted according to their color in three types: blackwater, clearwater, and whitewater, which significantly differ in terms of their physicochemical parameters. More than 3,000 species of fish live in the rivers of the Amazon, among them, the sardine, Triportheus albus, which is one of the few species that inhabit all three types of water. The purpose of our study was to analyze if the gene expression of T. albus is determined by the different types of water, that is, if the species presents phenotypic plasticity to live in blackwater, clearwater, and whitewater...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28911314/construction-of-a-combinatorial-library-of-chimeric-tumor-specific-promoters
#17
Kirill N Kashkin, Igor P Chernov, Dmitry A Didych, Eugene D Sverdlov
Gene therapy is a fast-developing field of molecular medicine. New, effective, and cancer-specific promoters are in high demand by researchers seeking to treat cancer through expression of therapeutic genes. Here, we created a combinatorial library of tumor-specific chimeric promoter modules for identifying new promoters with desired functions. The library was constructed by randomly combining promoter fragments from eight human genes involved in cell proliferation control. The pool of chimeric promoters was inserted into a lentiviral expression vector upstream of the CopGFP reporter gene, transduced into A431 cells, and enriched for active promoters by cell sorting...
September 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28911121/engineering-human-primpol-into-an-efficient-rna-dependent-dna-primase-polymerase
#18
Rubén Agudo, Patricia A Calvo, María I Martínez-Jiménez, Luis Blanco
We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28906599/dual-extrusion-3d-printing-of-anatomical-models-for-education
#19
Michelle L Smith, James F X Jones
Two material 3D printing is becoming increasingly popular, inexpensive and accessible. In this paper, freely available printable files and dual extrusion fused deposition modelling were combined to create a number of functional anatomical models. To represent muscle and bone FilaFlex(3D) flexible filament and polylactic acid (PLA) filament were extruded respectively via a single 0.4 mm nozzle using a Big Builder printer. For each filament, cubes (5 mm(3) ) were printed and analyzed for X, Y, and Z accuracy...
September 14, 2017: Anatomical Sciences Education
https://www.readbyqxmd.com/read/28906455/deep-circular-rna-sequencing-provides-insights-into-the-mechanism-underlying-grass-carp-reovirus-infection
#20
Libo He, Aidi Zhang, Lv Xiong, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu, And Yaping Wang
Grass carp hemorrhagic disease, caused by the grass carp reovirus (GCRV), is a major disease that hampers the development of grass carp aquaculture in China. The mechanism underlying GCRV infection is still largely unknown. Circular RNAs (circRNAs) are important regulators involved in various biological processes. In the present study, grass carp were infected with GCRV, and spleen samples were collected at 0 (control), 1, 3, 5, and 7 days post-infection (dpi). Samples were used to construct and sequence circRNA libraries, and a total of 5052 circRNAs were identified before and after GCRV infection, of which 41 exhibited differential expression compared with controls...
September 14, 2017: International Journal of Molecular Sciences
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