scholarly journals Prediction of Structures and Interactions from Genome Information

2018 ◽  
pp. 123-152 ◽  
Author(s):  
Sanzo Miyazawa
Keyword(s):  
Genome Information

scholarly journals Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eleni Voukali ◽  
Nithya Kuttiyarthu Veetil ◽  
Pavel Němec ◽  
Pavel Stopka ◽  
Michal Vinkler
Keyword(s):  
Cerebrospinal Fluid ◽  
Adult Neurogenesis ◽  
Neural Development ◽  
Neural Differentiation ◽  
Csf Proteins ◽  
Nymphicus Hollandicus ◽  
Liquid Chromatography Tandem Mass ◽  
Genome Information ◽  
Insight Into ◽  
Brain Homeostasis

AbstractCerebrospinal fluid (CSF) proteins regulate neurogenesis, brain homeostasis and participate in signalling during neuroinflammation. Even though birds represent valuable models for constitutive adult neurogenesis, current proteomic studies of the avian CSF are limited to chicken embryos. Here we use liquid chromatography–tandem mass spectrometry (nLC-MS/MS) to explore the proteomic composition of CSF and plasma in adult chickens (Gallus gallus) and evolutionarily derived parrots: budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus). Because cockatiel lacks a complete genome information, we compared the cross-species protein identifications using the reference proteomes of three model avian species: chicken, budgerigar and zebra finch (Taeniopygia guttata) and found the highest identification rates when mapping against the phylogenetically closest species, the budgerigar. In total, we identified 483, 641 and 458 unique proteins consistently represented in the CSF and plasma of all chicken, budgerigar and cockatiel conspecifics, respectively. Comparative pathways analyses of CSF and blood plasma then indicated clusters of proteins involved in neurogenesis, neural development and neural differentiation overrepresented in CSF in each species. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel evidence supporting the adult neurogenesis in birds.

scholarly journals Molecular Pathotyping of Plasmodiophora brassicae—Genomes, Marker Genes, and Obstacles

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 259
Author(s):  
Arne Schwelm ◽  
Jutta Ludwig-Müller
Keyword(s):  
Molecular Identification ◽  
Plasmodiophora Brassicae ◽  
Marker Genes ◽  
Future Perspectives ◽  
Genomic Information ◽  
Practical Applications ◽  
Genome Information

Here we review the usefulness of the currently available genomic information for the molecular identification of pathotypes. We focused on effector candidates and genes implied to be pathotype specific and tried to connect reported marker genes to Plasmodiophora brassicae genome information. The potentials for practical applications, current obstacles and future perspectives are discussed.

scholarly journals Strain difference in transgene-induced tumorigenesis and suppressive effect of ionizing radiation

2020 ◽  
Vol 62 (1) ◽  
pp. 12-24
Author(s):  
Bibek Dutta ◽  
Taichi Asami ◽  
Tohru Imatomi ◽  
Kento Igarashi ◽  
Kento Nagata ◽  
...  
Keyword(s):  
Genetic Background ◽  
Malignant Tumors ◽  
Pigment Cell ◽  
Strain Difference ◽  
Inbred Strains ◽  
Suppressive Effect ◽  
Model System ◽  
Pigment Cells ◽  
Transgenic Expression ◽  
Genome Information

Abstract Transgenic expression in medaka of the Xiphophorus oncogene xmrk, under a pigment cell specific mitf promoter, induces hyperpigmentation and pigment cell tumors. In this study, we crossed the Hd-rR and HNI inbred strains because complete genome information is readily available for molecular and genetic analysis. We prepared an Hd-rR (p53+/−, p53−/−) and Hd-rR HNI hybrid (p53+/−) fish-based xmrk model system to study the progression of pigment cells from hyperpigmentation to malignant tumors on different genetic backgrounds. In all strains examined, most of the initial hyperpigmentation occurred in the posterior region. On the Hd-rR background, mitf:xmrk-induced tumorigenesis was less frequent in p53+/− fish than in p53−/− fish. The incidence of hyperpigmentation was more frequent in Hd-rR/HNI hybrids than in Hd-rR homozygotes; however, the frequency of malignant tumors was low, which suggested the presence of a tumor suppressor in HNI genetic background fish. The effects on tumorigenesis in xmrk-transgenic immature medaka of a single 1.3 Gy irradiation was assessed by quantifying tumor progression over 4 consecutive months. The results demonstrate that irradiation has a different level of suppressive effect on the frequency of hyperpigmentation in purebred Hd-rR compared with hybrids.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

Bacillus minimum genome factory: effective utilization of microbial genome information

2007 ◽  
Vol 46 (3) ◽  
pp. 169 ◽  
Author(s):  
Katsuya Ozaki ◽  
Katsutoshi Ara ◽  
Kouji Nakamura ◽  
Kunio Yamane ◽  
Junichi Sekiguchi ◽  
...  
Keyword(s):  
Microbial Genome ◽  
Effective Utilization ◽  
Genome Information

scholarly journals VaProS: a database-integration approach for protein/genome information retrieval

2016 ◽  
Vol 17 (4) ◽  
pp. 69-81 ◽  
Author(s):  
Takashi Gojobori ◽  
Kazuho Ikeo ◽  
Yukie Katayama ◽  
Takeshi Kawabata ◽  
Akira R. Kinjo ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Database Integration ◽  
Integration Approach ◽  
Genome Information

scholarly journals A critical and Integrated View of the Yeast Interactome

2004 ◽  
Vol 5 (5) ◽  
pp. 382-402 ◽  
Author(s):  
Michael Cornell ◽  
Norman W. Paton ◽  
Stephen G. Oliver
Keyword(s):  
High Throughput ◽  
Protein Interactions ◽  
False Positive ◽  
Affinity Purification ◽  
Information Management System ◽  
Positive Interactions ◽  
Global Studies ◽  
Protein Protein Interactions ◽  
Integrative Analyses ◽  
Genome Information

Global studies of protein–protein interactions are crucial to both elucidating gene function and producing an integrated view of the workings of living cells. High-throughput studies of the yeast interactome have been performed using both genetic and biochemical screens. Despite their size, the overlap between these experimental datasets is very limited. This could be due to each approach sampling only a small fraction of the total interactome. Alternatively, a large proportion of the data from these screens may represent false-positive interactions. We have used the Genome Information Management System (GIMS) to integrate interactome datasets with transcriptome and protein annotation data and have found significant evidence that the proportion of false-positive results is high. Not all high-throughput datasets are similarly contaminated, and the tandem affinity purification (TAP) approach appears to yield a high proportion of reliable interactions for which corroborating evidence is available. From our integrative analyses, we have generated a set of verified interactome data for yeast.

scholarly journals The Policy of Genome Information Use for Secondary Research Purposes. On the Example of Great Britain

JURIST ◽  
2020 ◽  
Vol 7 ◽  
pp. 56-61
Author(s):  
Anna K. Zharova ◽  
Keyword(s):  
Great Britain ◽  
Information Use ◽  
Secondary Research ◽  
Genome Information

scholarly journals SPDE: A Multi-functional Software for Sequence Processing and Data Extraction

2020 ◽  
Author(s):  
Dong Xu ◽  
Zhuchou Lu ◽  
Kangming Jin ◽  
Wenmin Qiu ◽  
Guirong Qiao ◽  
...  
Keyword(s):  
Data Extraction ◽  
Single Gene ◽  
Biological Data ◽  
Sequence Processing ◽  
Reverse Complement ◽  
Biological Data Analysis ◽  
Basic Functions ◽  
Functional Software ◽  
Genome Information ◽  
Ncbi Blast

AbstractEfficiently extracting information from biological big data can be a huge challenge for people (especially those who lack programming skills). We developed Sequence Processing and Data Extraction (SPDE) as an integrated tool for sequence processing and data extraction for gene family and omics analyses. Currently, SPDE has seven modules comprising 100 basic functions that range from single gene processing (e.g., translation, reverse complement, and primer design) to genome information extraction. All SPDE functions can be used without the need for programming or command lines. The SPDE interface has enough prompt information to help users run SPDE without barriers. In addition to its own functions, SPDE also incorporates the publicly available analyses tools (such as, NCBI-blast, HMMER, Primer3 and SAMtools), thereby making SPDE a comprehensive bioinformatics platform for big biological data analysis.AvailabilitySPDE was built using Python and can be run on 32-bit, 64-bit Windows and macOS systems. It is an open-source software that can be downloaded from https://github.com/simon19891216/[email protected]

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