Skip header and navigation

Refine By

598 records – page 1 of 60.

[Genetic control of isozymes in European spruces (Picea abies (L) Karst) of the Ukrainian Carpathian mountains]

https://arctichealth.org/en/permalink/ahliterature81333
Source
Tsitol Genet. 2006 Mar-Apr;40(2):20-6
Publication Type
Article
Author
Privalikhin S N
Korshikov I I
Pirko N N
Velikorid'ko T I
Pirko Ia V
Source
Tsitol Genet. 2006 Mar-Apr;40(2):20-6
Language
Russian
Publication Type
Article
Keywords
Alleles
Electrophoresis, Polyacrylamide Gel
Gene Expression Regulation, Enzymologic
Gene Expression Regulation, Plant
Genotype
Isoenzymes - genetics
Picea - enzymology - genetics
Ukraine
Variation (Genetics)
Abstract
Genetical control of the enzymes GOT, GDH, DIA, MDH, SOD, FDH, ADH, ACP and LAP has been studied in nine natural Carpathian populations of Norway spruce (Picea abies (L.) Karst.) using polyacrylamide gel elecrophoresis and analysis of isozyme variability in 346 trees. Seventy one allel products of 20 gene loci have been clearly established. Segregation analysis of the revealed allele variants confirms their monogenic inheritance.
PubMed ID
16865984 View in PubMed
Less detail

17 beta-hydroxysteroid dehydrogenases--their role in pathophysiology.

https://arctichealth.org/en/permalink/ahliterature17852
Source
Mol Cell Endocrinol. 2004 Feb 27;215(1-2):83-8
Publication Type
Article
Date
Feb-27-2004
Author
P. Vihko
P. Härkönen
P. Soronen
S. Törn
A. Herrala
R. Kurkela
A. Pulkka
O. Oduwole
V. Isomaa
Author Affiliation
Biocenter Oulu and Research Center for Molecular Endocrinology, University of Oulu, P.O. Box 5000, FIN-90014, Oulu, Finland. pvihko@whoccr.oulu.fi
Source
Mol Cell Endocrinol. 2004 Feb 27;215(1-2):83-8
Date
Feb-27-2004
Language
English
Publication Type
Article
Keywords
17-Hydroxysteroid Dehydrogenases - metabolism
Gene Expression Regulation, Enzymologic
Gene Expression Regulation, Neoplastic
Gonadal Steroid Hormones - metabolism
Humans
Neoplasms - enzymology
Oxygen - metabolism
Research Support, Non-U.S. Gov't
Abstract
17 beta-Hydroxysteroid dehydrogenases (17HSDs) regulate the biological activity of sex steroid hormones in a variety of tissues by catalyzing the interconversions between highly active steroid hormones, e.g. estradiol and testosterone, and corresponding less active hormones, estrone and androstenedione. Epidemiological and endocrine evidence indicates that estrogens play a role in the etiology of breast cancer, while androgens are involved in mechanisms controlling the growth of normal and malignant prostatic cells. Using LNCaP prostate cancer cell lines, we have developed a cell model to study the progression of prostate cancer. In the model LNCaP cells are transformed in culture condition into more aggressive cells. Our data suggest that substantial changes in androgen and estrogen metabolism occur in the cells, leading to increased production of active estrogens during the process. In breast cancer, the reductive 17HSD type 1 activity is predominant in malignant cells, while the oxidative 17HSD type 2 mainly seems to be present in non-malignant breast epithelial cells. Deprivation of an estrogen response by using specific 17HSD type 1 inhibitors is a tempting approach in treating estrogen-dependent breast cancer. Our recent studies demonstrate that in addition to sex hormone target tissues, estrogens may be important in the development of cancer in some other tissues previously not considered to be estrogen target tissues, such as the gastrointestinal tract.
PubMed ID
15026178 View in PubMed
Less detail

Expression genetics and the phenotype revolution.

https://arctichealth.org/en/permalink/ahliterature81815
Source
Mamm Genome. 2006 Jun;17(6):496-502
Publication Type
Article
Date
Jun-2006
Author
Williams Robert W
Author Affiliation
Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA. rwilliam@nb.utmem.edu
Source
Mamm Genome. 2006 Jun;17(6):496-502
Date
Jun-2006
Language
English
Publication Type
Article
Keywords
Animals
Gene Expression Profiling
Gene Expression Regulation - genetics
Humans
Phenotype
Abstract
Genetic analysis of variation demands large numbers of individuals and even larger numbers of genotypes. The identification of alleles associated with Mendelian disorders has involved sample sizes of a thousand or more. Pervasive and common diseases that afflict human populations--cancer, heart disease, diabetes, neurodegeneration, addiction--are all polygenic and are even more demanding of large numbers. DeCode Genetics (http://www.decode.com) has harnessed the human resources of Iceland to unravel genetic and molecular causes of complex disease. The UK BioBank project (http://www.ukbiobank.ac.uk/) will incorporate 500,000 adult volunteers. The murine Collaborative Cross is the experimental equivalent of these human populations and will consist of a panel of approximately 1000 recombinant strains, expandable by intercrossing to much larger numbers of isogenic but heterozygous F(1)s. Massive projects of these types require efficient technologies. We have made enormous progress on the genotyping front, and it is now important to focus energy on devising ultrahigh-throughput methods to phenotype. Molecular phenotyping of the transcriptome has matured, and it is now possible to acquire hundreds of thousands of mRNA phenotypes at a cost matching those of SNPs. Proteomic and cell-based assays are also maturing rapidly. The acquisition of a personal genome along with a personal molecular phenome will provide an effective foundation for personalized medicine. Rodent models will be essential to test our ability to predict susceptibility and disease outcome using SNP data, molecular phenomes, and environmental exposures. These models will also be essential to test new treatments in a robust systems context that accounts for genetic variation.
PubMed ID
16783631 View in PubMed
Less detail

Comparative proteomic responses of two bermudagrass (Cynodon dactylon (L). Pers.) varieties contrasting in drought stress resistance.

https://arctichealth.org/en/permalink/ahliterature261345
Source
Plant Physiol Biochem. 2014 Sep;82:218-28
Publication Type
Article
Date
Sep-2014
Author
Haitao Shi
Tiantian Ye
Zhulong Chan
Source
Plant Physiol Biochem. 2014 Sep;82:218-28
Date
Sep-2014
Language
English
Publication Type
Article
Keywords
Cynodon - metabolism - physiology
Droughts
Gene Expression Regulation, Plant
Proteomics - methods
Abstract
Drought (water-deficit) stress is a serious environmental problem in plant growth and cultivation. As one of widely cultivated warm-season turfgrass, bermudagrass (Cynodon dactylon (L). Pers.) exhibits drastic natural variation in the drought stress resistance in leaves and stems of different varieties. In this study, proteomic analysis was performed to identify drought-responsive proteins in both leaves and stems of two bermudagrass varieties contrasting in drought stress resistance, including drought sensitive variety (Yukon) and drought tolerant variety (Tifgreen). Through comparative proteomic analysis, 39 proteins with significantly changed abundance were identified, including 3 commonly increased and 2 decreased proteins by drought stress in leaves and stems of Yukon and Tifgreen varieties, 2 differentially regulated proteins in leaves and stems of two varieties after drought treatment, 23 proteins increased by drought stress in Yukon variety and constitutively expressed in Tifgreen variety, and other 3 differentially expressed proteins under control and drought stress conditions. Among them, proteins involved in photosynthesis (PS), glycolysis, N-metabolism, tricarboxylicacid (TCA) and redox pathways were largely enriched, which might be contributed to the natural variation of drought resistance between Yukon and Tifgreen varieties. These studies provide new insights to understand the molecular mechanism underlying bermudagrass response to drought stress.
PubMed ID
24992888 View in PubMed
Less detail

Genetic control of methanol utilization in yeasts.

https://arctichealth.org/en/permalink/ahliterature12529
Source
J Basic Microbiol. 1988;28(5):293-319
Publication Type
Article
Date
1988
Author
A A Sibirny
V I Titorenko
M V Gonchar
V M Ubiyvovk
G P Ksheminskaya
O P Vitvitskaya
Author Affiliation
Academy of Sciences of Ukrainian SSR, Lvov Branch of A. V. Palladin Institute of Biochemistry, USSR.
Source
J Basic Microbiol. 1988;28(5):293-319
Date
1988
Language
English
Publication Type
Article
Keywords
Biotechnology
Gene Expression Regulation
Methanol - metabolism
Mutation
Yeasts - genetics - metabolism - ultrastructure
Abstract
Considered are our own data and those found in literature on the properties of yeast mutants impaired in their ability to utilize methanol as sole carbon and energy source; hypotheses about the role of alcohol oxidase and citrate synthase in biogenesis of peroxisomes are proposed. It has been proved that formaldehyde reductase participates in the control of the formaldehyde level in the cell. Properties of mutants defective in the catabolite repression and inactivation of enzymes of methanol metabolism are described. The existence of several autonomous mechanisms of the catabolite repression of alcohol oxidase has been shown. It has been found, that the induction of glyoxysomal enzymes of C2-metabolism is repressed by methanol in the ecr1 mutant of Pichia pinus with the affected repression of alcohol oxidase by ethanol. Data are presented on the regulatory properties of the recently discovered acidification system of the medium induced by methanol. Such acidification occurs due to symport extrusion of protons and formate anions from the cells.
Notes
Erratum In: J Basic Microbiol 1989;29(7):462
PubMed ID
3068350 View in PubMed
Less detail

Cloning, characterization and localization of three novel class III peroxidases in lignifying xylem of Norway spruce (Picea abies).

https://arctichealth.org/en/permalink/ahliterature81153
Source
Plant Mol Biol. 2006 Jul;61(4-5):719-32
Publication Type
Article
Date
Jul-2006
Author
Marjamaa Kaisa
Hildén Kristiina
Kukkola Eija
Lehtonen Mikko
Holkeri Heidi
Haapaniemi Pekka
Koutaniemi Sanna
Teeri Teemu H
Fagerstedt Kurt
Lundell Taina
Author Affiliation
Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland. kaisa.marjamaa@helsinki.fi
Source
Plant Mol Biol. 2006 Jul;61(4-5):719-32
Date
Jul-2006
Language
English
Publication Type
Article
Keywords
Amino Acid Sequence
Catharanthus
Cloning, Molecular
Gene Expression Regulation, Enzymologic
Gene Expression Regulation, Plant
Molecular Sequence Data
Peroxidases - chemistry - genetics - metabolism
Phylogeny
Picea - classification - enzymology - genetics
Plant Stems
Protein Transport
Tobacco - cytology
Abstract
Plant class III peroxidases (POXs) take part in the formation of lignin and maturation of plant cell walls. However, only a few examples of such peroxidases from gymnosperm tree species with highly lignified xylem tracheids have been implicated so far. We report here cDNA cloning of three xylem-expressed class III peroxidase encoding genes from Norway spruce (Picea abies). The translated proteins, PX1, PX2 and PX3, contain the conserved amino acids required for heme-binding and peroxidase catalysis. They all begin with putative secretion signal propeptide sequences but diverge substantially at phylogenetic level, grouping to two subclusters when aligned with other class III plant peroxidases. In situ hybridization analysis on expression of the three POXs in Norway spruce seedlings showed that mRNA coding for PX1 and PX2 accumulated in the cytoplasm of young, developing tracheids within the current growth ring where lignification is occurring. Function of the putative N-terminal secretion signal peptides for PX1, PX2 and PX3 was confirmed by constructing chimeric fusions with EGFP (enhanced green fluorescent protein) and expressing them in tobacco protoplasts. Full-length coding region of px1 was also heterologously expressed in Catharanthus roseus hairy root cultures. Thus, at least the spruce PX1 peroxidase is processed via the endoplasmic reticulum (ER) most likely for secretion to the cell wall. Thereby, PX1 displays correct spatiotemporal localization for participation in the maturation of the spruce tracheid secondary cell wall.
PubMed ID
16897487 View in PubMed
Less detail

The use of third and fourth generation cephalosporins affects the occurrence of extended-spectrum cephalosporinase-producing Escherichia coli in Danish pig herds.

https://arctichealth.org/en/permalink/ahliterature277707
Source
Vet J. 2015 Jun;204(3):345-50
Publication Type
Article
Date
Jun-2015
Author
V D Andersen
V F Jensen
H. Vigre
M. Andreasen
Y. Agersø
Source
Vet J. 2015 Jun;204(3):345-50
Date
Jun-2015
Language
English
Publication Type
Article
Keywords
Animals
Cephalosporinase - classification - genetics - metabolism
Cephalosporins - administration & dosage - pharmacology
Denmark - epidemiology
Drug Resistance, Multiple, Bacterial
Escherichia coli - drug effects - enzymology - metabolism
Escherichia coli Infections
Gene Expression Regulation, Bacterial
Gene Expression Regulation, Enzymologic
Swine
Swine Diseases - epidemiology - microbiology
Abstract
Extended-spectrum cephalosporinase resistance is currently the fastest emerging antimicrobial resistance problem worldwide; however, evidence documenting the effect of potential risk factors is limited. The main objective of this study was to investigate the effect of using third and fourth generation cephalosporins on the occurrence of extended-spectrum cephalosporinase-producing Escherichia coli (ESC-Ec) in Danish pig herds. Conventional, integrated, medium to large herds were selected based on information from the Danish Central Husbandry Register and two groups were formed based on the use of third and fourth generation cephalosporins within a specified period, namely, 20 herds with no cephalosporin use (non-exposed) and 19 herds with frequent use (exposed). Data on prescribed antimicrobials were obtained from the National database (VetStat). Management data were obtained through a questionnaire. At the herd level, three pooled faecal samples were collected from sows with their piglets (farrowing pens), weaners, and finishers. ESC-Ec were then identified using selective enrichment. Because several of the herds only had a low number of weaners and/or finishers, analysis was only performed on samples from the farrowing pens. Logistic regression showed a significant effect of using cephalosporins-III/IV on the occurrence of ESC-Ec in the farrowing pens, even when adjusted for use of other antimicrobials 1 year prior to sampling. No confounding effect was identified in relation to management data. The relative risk ESC-Ec in exposed compared to non-exposed was 4.7 (95% confidence interval 2.0-11.5), confirming that regular use of cephalosporins-III/IV was a significant risk factor for the occurrence of ESC-Ec.
PubMed ID
25935558 View in PubMed
Less detail

Transcriptional Responses Associated with Virulence and Defence in the Interaction between Heterobasidion annosum s.s. and Norway Spruce.

https://arctichealth.org/en/permalink/ahliterature272021
Source
PLoS One. 2015;10(7):e0131182
Publication Type
Article
Date
2015
Author
Karl Lundén
Marie Danielsson
Mikael Brandström Durling
Katarina Ihrmark
Miguel Nemesio Gorriz
Jan Stenlid
Frederick O Asiegbu
Malin Elfstrand
Source
PLoS One. 2015;10(7):e0131182
Date
2015
Language
English
Publication Type
Article
Keywords
Basidiomycota - genetics - pathogenicity
Cluster analysis
Disease Resistance - genetics
Gene Expression Regulation, Fungal
Gene Expression Regulation, Plant
Gene Ontology
Host-Pathogen Interactions - genetics
Norway
Picea - genetics - microbiology
Plant Diseases - genetics - microbiology
Reverse Transcriptase Polymerase Chain Reaction
Transcriptome
Virulence - genetics
Abstract
Heterobasidion annosum sensu lato is a serious pathogen causing root and stem rot to conifers in the northern hemisphere and rendering the timber defective for sawing and pulping. In this study we applied next-generation sequencing to i) identify transcriptional responses unique to Heterobasidion-inoculated Norway spruce and ii) investigate the H. annosum transcripts to identify putative virulence factors. To address these objectives we wounded or inoculated 30-year-old Norway spruce clones with H. annosum and 454-sequenced the transcriptome of the interaction at 0, 5 and 15 days post inoculation. The 491,860 high-quality reads were de novo assembled and the relative expression was analysed. Overall, very few H. annosum transcripts were represented in our dataset. Three delta-12 fatty acid desaturase transcripts and one Clavaminate synthase-like transcript, both associated with virulence in other pathosystems, were found among the significantly induced transcripts. The analysis of the Norway spruce transcriptional responses produced a handful of differentially expressed transcripts. Most of these transcripts originated from genes known to respond to H. annosum. However, three genes that had not previously been reported to respond to H. annosum showed specific induction to inoculation: an oxophytodienoic acid-reductase (OPR), a beta-glucosidase and a germin-like protein (GLP2) gene. Even in a small data set like ours, five novel highly expressed Norway spruce transcripts without significant alignment to any previously annotated protein in Genbank but present in the P. abies (v1.0) gene catalogue were identified. Their expression pattern suggests a role in defence. Therefore a more complete survey of the transcriptional responses in the interactions between Norway spruce and its major pathogen H. annosum would probably provide a better understanding of gymnosperm defence than accumulated until now.
Notes
Cites: Tree Physiol. 2012 Sep;32(9):1137-4722899808
Cites: BMC Genomics. 2012;13:73423270466
Cites: Planta. 2013 Apr;237(4):1037-4523223898
Cites: Nature. 2013 May 30;497(7451):579-8423698360
Cites: Plant Mol Biol. 2000 May;43(1):1-1010949369
Cites: Nat Struct Biol. 2000 Feb;7(2):127-3310655615
Cites: Annu Rev Plant Biol. 2014;65:365-8424313842
Cites: J Biol Chem. 2001 Jul 13;276(28):25766-7411352908
Cites: Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12837-4211592974
Cites: Nucleic Acids Res. 2002 May 1;30(9):e3611972351
Cites: Fungal Genet Biol. 2003 Jun;39(1):51-912742063
Cites: Tree Physiol. 2003 Oct;23(14):977-8612952784
Cites: Appl Environ Microbiol. 2004 Jul;70(7):3948-5315240268
Cites: Microbiology. 2004 Sep;150(Pt 9):2881-815347747
Cites: J Bacteriol. 1995 Mar;177(5):1307-147868606
Cites: Plant Physiol. 1995 Feb;107(2):331-97724669
Cites: Nucleic Acids Res. 1997 Sep 1;25(17):3389-4029254694
Cites: Eur J Biochem. 1999 May;261(3):812-2010215899
Cites: Lipids. 1999 Jul;34(7):649-5910478922
Cites: New Phytol. 2005 Aug;167(2):353-7515998390
Cites: Bioinformatics. 2005 Sep 15;21(18):3674-616081474
Cites: Tree Physiol. 2005 Dec;25(12):1533-4316137939
Cites: Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9446-5116763049
Cites: FEBS Lett. 2007 Jan 23;581(2):315-917208234
Cites: Phytochemistry. 2007 Jul;68(14):1975-9117590394
Cites: Plant Mol Biol. 2007 Oct;65(3):311-2817764001
Cites: Plant Mol Biol. 2008 Mar;66(5):533-4918209956
Cites: Planta. 2008 Aug;228(3):459-7218493789
Cites: Appl Environ Microbiol. 2009 Feb;75(4):1156-6419088315
Cites: FEBS J. 2009 Sep;276(17):4693-70419663904
Cites: Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-5120460310
Cites: Fungal Biol. 2010 Jan;114(1):16-2520965057
Cites: BMC Genomics. 2010;11:57120950480
Cites: Mol Ecol. 2010 Nov;19(22):4979-9320964759
Cites: Genome Biol. 2010;11(10):R10620979621
Cites: Genome Res. 2011 Sep;21(9):1552-6021690186
Cites: Tree Physiol. 2011 Nov;31(11):1262-7222084022
Cites: BMC Plant Biol. 2011;11:15422067529
Cites: Plant Signal Behav. 2011 Oct;6(10):1503-921897131
Cites: New Phytol. 2012 Jun;194(4):1001-1322463738
PubMed ID
26151363 View in PubMed
Less detail

Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression.

https://arctichealth.org/en/permalink/ahliterature271800
Source
Mol Biol Evol. 2015 Aug;32(8):2036-47
Publication Type
Article
Date
Aug-2015
Author
Mandy Menzel
Nina Sletvold
Jon Ågren
Bengt Hansson
Source
Mol Biol Evol. 2015 Aug;32(8):2036-47
Date
Aug-2015
Language
English
Publication Type
Article
Keywords
Arabidopsis - genetics
Gene Expression Regulation, Plant
Genes, Plant
Inbreeding
Norway
Photosynthesis
Reproduction
Selection, Genetic
Sweden
Abstract
Knowledge of which genes and pathways are affected by inbreeding may help understanding the genetic basis of inbreeding depression, the potential for purging (selection against deleterious recessive alleles), and the transition from outcrossing to selfing. Arabidopsis lyrata is a predominantly self-incompatible perennial plant, closely related to the selfing model species A. thaliana. To examine how inbreeding affects gene expression, we compared the transcriptome of experimentally selfed and outcrossed A. lyrata originating from two Scandinavian populations that express similar inbreeding depression for fitness (? ˜ 0.80). The number of genes significantly differentially expressed between selfed and outcrossed individuals were 2.5 times higher in the Norwegian population (˜ 500 genes) than in the Swedish population (˜ 200 genes). In both populations, a majority of genes were upregulated on selfing (˜ 80%). Functional annotation analysis of the differentially expressed genes showed that selfed offspring were characterized by 1) upregulation of stress-related genes in both populations and 2) upregulation of photosynthesis-related genes in Sweden but downregulation in Norway. Moreover, we found that reproduction- and pollination-related genes were affected by inbreeding only in Norway. We conclude that inbreeding causes both general and population-specific effects. The observed common effects suggest that inbreeding generally upregulates rather than downregulates gene expression and affects genes associated with stress response and general metabolic activity. Population differences in the number of affected genes and in effects on the expression of photosynthesis-related genes show that the genetic basis of inbreeding depression can differ between populations with very similar levels of inbreeding depression.
Notes
Cites: Nature. 1992 Jan 2;355(6355):33-451731198
Cites: Biol Lett. 2014 Sep;10(9). pii: 20140648. doi: 10.1098/rsbl.2014.064825232028
Cites: J Evol Biol. 2005 Jul;18(4):789-80316033550
Cites: Bioinformatics. 2005 Aug 15;21(16):3448-915972284
Cites: Bioinformatics. 2005 Sep 15;21(18):3674-616081474
Cites: Genetics. 2005 Sep;171(1):157-6715944359
Cites: Genetics. 2006 Jul;173(3):1329-3616624914
Cites: Trends Plant Sci. 2006 Sep;11(9):449-5916893672
Cites: Genetics. 2006 Dec;174(4):1811-2417028338
Cites: J Evol Biol. 2007 Mar;20(2):558-6717305822
Cites: Nucleic Acids Res. 2014 Jan;42(Database issue):D191-824253303
Cites: Conserv Biol. 2009 Aug;23(4):920-3019627320
Cites: Genome Res. 2009 Sep;19(9):1639-4519541911
Cites: Nat Rev Genet. 2009 Nov;10(11):783-9619834483
Cites: Trends Ecol Evol. 2010 Jan;25(1):44-5219733933
Cites: PLoS One. 2010;5(11):e1398421085593
Cites: Genome Biol. 2010;11(10):R10620979621
Cites: Genet Res (Camb). 2011 Feb;93(1):47-6421226974
Cites: Nat Methods. 2011 Jul;8(7):528-921716279
Cites: Evolution. 2011 Dec;65(12):3339-5922133210
Cites: Nucleic Acids Res. 2012 Jan;40(Database issue):D857-6122096227
Cites: Nucleic Acids Res. 2012 Jan;40(Database issue):D26-3222110030
Cites: Nucleic Acids Res. 2012 Jan;40(Database issue):D841-622121220
Cites: PLoS One. 2012;7(8):e4232622879940
Cites: Genetics. 2012 Dec;192(4):1477-8223051641
Cites: Evolution. 2013 Oct;67(10):2876-8824094340
Cites: Bioinformatics. 2001 Sep;17(9):847-811590104
Cites: Gene. 2002 Jan 9;282(1-2):215-2511814694
Cites: Mol Ecol. 2002 Mar;11(3):591-60111918792
Cites: Plant Cell. 2002;14 Suppl:S227-3812045279
Cites: Plant J. 2002 Aug;31(3):279-9212164808
Cites: Nucleic Acids Res. 2003 Jan 1;31(1):248-5012519993
Cites: Nature. 2003 May 1;423(6935):74-712721627
Cites: Genome Res. 2003 Nov;13(11):2498-50414597658
Cites: Plant J. 2004 Mar;37(6):914-3914996223
Cites: Proc Natl Acad Sci U S A. 2004 May 18;101(20):7663-815136717
Cites: Nature. 1991 Aug 8;352(6335):522-41865906
Cites: Mol Ecol. 2007 Sep;16(17):3565-8017845431
Cites: New Phytol. 2008;178(3):503-1418346103
Cites: BMC Genomics. 2009;10:2219144180
Cites: Bioinformatics. 2009 May 1;25(9):1105-1119289445
Cites: Plant Cell. 1997 Jan;9(1):49-609014364
PubMed ID
25855783 View in PubMed
Less detail

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus.

https://arctichealth.org/en/permalink/ahliterature291124
Source
BMC Evol Biol. 2017 12 28; 17(Suppl 2):258
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
12-28-2017
Author
Alexey ? Moskalev
Anna V Kudryavtseva
Alexander S Graphodatsky
Violetta R Beklemisheva
Natalya A Serdyukova
Konstantin V Krutovsky
Vadim V Sharov
Ivan V Kulakovskiy
Andrey S Lando
Artem S Kasianov
Dmitry A Kuzmin
Yuliya A Putintseva
Sergey I Feranchuk
Mikhail V Shaposhnikov
Vadim E Fraifeld
Dmitri Toren
Anastasia V Snezhkina
Vasily V Sitnik
Author Affiliation
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation. amoskalev@list.ru.
Source
BMC Evol Biol. 2017 12 28; 17(Suppl 2):258
Date
12-28-2017
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Gene Expression Regulation
Gene Library
Genome
Molecular Sequence Annotation
Phylogeny
Transcriptome - genetics
Whales - genetics
Abstract
Gray whale, Eschrichtius robustus (E. robustus), is a single member of the family Eschrichtiidae, which is considered to be the most primitive in the class Cetacea. Gray whale is often described as a "living fossil". It is adapted to extreme marine conditions and has a high life expectancy (77 years). The assembly of a gray whale genome and transcriptome will allow to carry out further studies of whale evolution, longevity, and resistance to extreme environment.
In this work, we report the first de novo assembly and primary analysis of the E. robustus genome and transcriptome based on kidney and liver samples. The presented draft genome assembly is complete by 55% in terms of a total genome length, but only by 24% in terms of the BUSCO complete gene groups, although 10,895 genes were identified. Transcriptome annotation and comparison with other whale species revealed robust expression of DNA repair and hypoxia-response genes, which is expected for whales.
This preliminary study of the gray whale genome and transcriptome provides new data to better understand the whale evolution and the mechanisms of their adaptation to the hypoxic conditions.
Notes
Cites: Bioinformatics. 2015 Jan 15;31(2):166-9 PMID 25260700
Cites: Nat Genet. 2015 Mar;47(3):272-5 PMID 25621460
Cites: Science. 2017 Apr 21;356(6335):307-311 PMID 28428423
Cites: Ageing Res Rev. 2013 Mar;12(2):661-84 PMID 22353384
Cites: Genome Res. 2002 Apr;12(4):656-64 PMID 11932250
Cites: Nat Methods. 2012 Mar 04;9(4):357-9 PMID 22388286
Cites: Bioinformatics. 2010 Jan 1;26(1):139-40 PMID 19910308
Cites: Database (Oxford). 2016 Mar 19;2016:null PMID 26994912
Cites: Mol Biol Evol. 2017 Jul 1;34(7):1812-1819 PMID 28387841
Cites: Nucleic Acids Res. 2016 Jan 4;44(D1):D710-6 PMID 26687719
Cites: Nat Genet. 2014 Jan;46(1):88-92 PMID 24270359
Cites: Bioinformatics. 2015 Oct 1;31(19):3210-2 PMID 26059717
Cites: Baillieres Clin Endocrinol Metab. 1989 Aug;3(2):249-311 PMID 2698139
Cites: Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85 PMID 26673716
Cites: Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9 PMID 26612867
Cites: Bioinformatics. 2011 Mar 15;27(6):757-63 PMID 21216780
Cites: Nucleic Acids Res. 1997 Mar 1;25(5):955-64 PMID 9023104
Cites: Cytogenet Genome Res. 2016;148(1):25-34 PMID 27088853
Cites: Bioinformatics. 2014 Aug 1;30(15):2114-20 PMID 24695404
Cites: Front Zool. 2017 Aug 2;14 :41 PMID 28785294
Cites: BMC Genomics. 2014 Jul 07;15:570 PMID 25001289
Cites: BMC Genomics. 2015 Jan 22;16:13 PMID 25609461
Cites: Nat Protoc. 2013 Aug;8(8):1494-512 PMID 23845962
Cites: Aging (Albany NY). 2014 Oct;6(10):879-99 PMID 25411232
Cites: Mol Biol Evol. 2012 Aug;29(8):1969-73 PMID 22367748
Cites: J Exp Biol. 2014 Apr 1;217(Pt 7):1024-39 PMID 24671961
Cites: Genome Biol. 2008 Jan 11;9(1):R7 PMID 18190707
Cites: Toxicol Pathol. 2005;33(1):136-45 PMID 15805065
Cites: Bioinformatics. 2014 May 1;30(9):1312-3 PMID 24451623
Cites: Am J Med Sci. 2007 Jul;334(1):65-71 PMID 17630596
Cites: Nat Commun. 2013;4:2212 PMID 23962925
Cites: Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199 PMID 27899635
Cites: Cell Rep. 2015 Jan 6;10(1):112-22 PMID 25565328
Cites: Bioinformatics. 2016 Jul 1;32(13):1933-42 PMID 27153688
Cites: Anat Rec (Hoboken). 2007 Jun;290(6):514-22 PMID 17516441
Cites: PLoS One. 2014 Jan 24;9(1):e86051 PMID 24475070
Cites: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W20-5 PMID 15215342
Cites: Integr Comp Biol. 2016 Dec;56(6):1103-1112 PMID 27549198
Cites: Mob DNA. 2015 Jun 02;6:11 PMID 26045719
Cites: Nucleic Acids Res. 2012 Jan;40(Database issue):D343-50 PMID 22086950
Cites: PLoS One. 2015 Aug 26;10(8):e0134655 PMID 26309028
Cites: Genomics. 2010 Nov;96(5):281-9 PMID 20800674
Cites: Genome Biol Evol. 2014 Feb;6(2):433-50 PMID 24504087
Cites: BMC Bioinformatics. 2005 Feb 15;6:31 PMID 15713233
Cites: Syst Biol. 2007 Aug;56(4):564-77 PMID 17654362
Cites: Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12 PMID 25348405
Cites: Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93 PMID 26582926
PubMed ID
29297306 View in PubMed
Less detail

598 records – page 1 of 60.