scholarly journals III-2. Microbial genome information for biofuels

2011 ◽  
Vol 77 (2) ◽  
pp. 255
Author(s):  
SHIGEKI SAWAYAMA
Keyword(s):  
Microbial Genome ◽  
Genome Information

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

Energy Department Expanding Microbial Genome Efforts

2007 ◽  
Vol 2 (4) ◽  
pp. 169-170
Author(s):  
Jeffrey L. Fox
Keyword(s):  
Microbial Genome

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.

scholarly journals Development of Microbial Genome-Probing Microarrays using Digital Multiple Displacement Amplification of Uncultivated Microbial Single Cells

2008 ◽  
Vol 42 (22) ◽  
pp. 8614-8614
Author(s):  
Ho-Won Chang ◽  
Youboong Sung ◽  
Kyoung-Ho Kim ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Microbial Genome

scholarly journals The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcel Huntemann ◽  
Natalia N. Ivanova ◽  
Konstantinos Mavromatis ◽  
H. James Tripp ◽  
David Paez-Espino ◽  
...  
Keyword(s):  
Operating Procedure ◽  
Genome Annotation ◽  
Standard Operating Procedure ◽  
Microbial Genome ◽  
Annotation Pipeline ◽  
Standard Operating
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