scholarly journals Selective modes determine evolutionary rates, gene compactness and expression patterns inBrassica

2017 ◽  
Vol 91 (1) ◽  
pp. 34-44 ◽  
Author(s):  
Yue Guo ◽  
Jing Liu ◽  
Jiefu Zhang ◽  
Shengyi Liu ◽  
Jianchang Du
Keyword(s):  
Expression Patterns ◽  
Evolutionary Rates ◽  
Gene Compactness

scholarly journals Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

PLoS ONE ◽  
2008 ◽  
Vol 3 (10) ◽  
pp. e3599 ◽  
Author(s):  
Aleksey Y. Ogurtsov ◽  
Leonardo Mariño-Ramírez ◽  
Gibbes R. Johnson ◽  
David Landsman ◽  
Svetlana A. Shabalina ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Expression Patterns ◽  
Evolutionary Rates ◽  
Gene Architecture

scholarly journals Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 490 ◽  
Author(s):  
Yunpeng Cao ◽  
Lan Jiang ◽  
Lihu Wang ◽  
Yongping Cai
Keyword(s):  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Different Types ◽  
Synonymous Substitution Rates ◽  
Gene Structures

Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.

scholarly journals The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences

2020 ◽  
Vol 12 (8) ◽  
pp. 1444-1458
Author(s):  
Isaac Adeyemi Babarinde ◽  
Naruya Saitou
Keyword(s):  
Litter Size ◽  
Evolutionary Rate ◽  
Expression Patterns ◽  
Draft Genome ◽  
Evolutionary Rates ◽  
Gestation Length ◽  
Generation Interval ◽  
Rate Acceleration ◽  
Mammalian Genomes ◽  
Taxonomic Order

Abstract Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae–Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.

scholarly journals Non-canonical expression patterns and evolutionary rates of sex-biased genes in a seasonal fish

2016 ◽  
Vol 83 (12) ◽  
pp. 1102-1115 ◽  
Author(s):  
Miguel P. Machado ◽  
Isa Matos ◽  
Ana R. Grosso ◽  
Manfred Schartl ◽  
Maria M. Coelho
Keyword(s):  
Expression Patterns ◽  
Evolutionary Rates

378: 14-3-3 Expression Patterns in the Human Kidney: From Fetal Development to the Adult State to Malignant Transformation

2005 ◽  
Vol 173 (4S) ◽  
pp. 103-103
Author(s):  
Adam G. Baseman ◽  
Andrew J. Kirsch ◽  
Fray F. Marshall ◽  
Haiyen E. Zhau ◽  
Leland W.K. Chung ◽  
...  
Keyword(s):  
Malignant Transformation ◽  
Fetal Development ◽  
Expression Patterns ◽  
Human Kidney

Gene expression patterns in blood predict future severe endpoints in community acquired pneumonia

Pneumologie ◽  
2018 ◽  
Vol 72 (S 01) ◽  
pp. S8-S9
Author(s):  
M Bauer ◽  
H Kirsten ◽  
E Grunow ◽  
P Ahnert ◽  
M Kiehntopf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Community Acquired Pneumonia ◽  
Gene Expression Patterns

Analysis of expression patterns in the brains of tet-off promoter mice

2004 ◽  
Vol 31 (S 1) ◽  
Author(s):  
J Boy ◽  
TB Leergaard ◽  
T Schmidt ◽  
C Holzmann ◽  
M Niwar ◽  
...  
Keyword(s):  
Expression Patterns

C-fos, ERK1/2, MAP2, NOTCH1 Proteins Expression Patterns in Human Cerebral Cortex Neurons after Ischemic Stroke

2020 ◽  
Vol 75 (3) ◽  
pp. 226-233
Author(s):  
Svetlana P. Sergeeva ◽  
Aleksey V. Lyundup ◽  
Valery V. Beregovykh ◽  
Petr F. Litvitskiy ◽  
Aleksey A. Savin ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
Ischemic Stroke ◽  
Expression Patterns ◽  
Immunohistochemical Method ◽  
Left Middle Cerebral Artery ◽  
Contralateral Hemisphere ◽  
Human Cerebral Cortex ◽  
Fos Protein ◽  
Urgent Task ◽  
Indirect Immunoperoxidase

Background. The search for protein (these include c-fos, ERK1/2, MAP2, NOTCH1) expression that provide neuroplasticity mechanisms of the cerebral cortex after ischemic stroke (IS) patterns is an urgent task. Aims to reveal c-fos, ERK1/2, MAP2, NOTCH1 proteins expression patterns in human cerebral cortex neurons after IS. Materials and methods. We studied 9 left middle cerebral artery (LMCA) IS patients cerebral cortex samples from 3 zones: 1 the zone adjacent to the necrotic tissue focus; 2 zone remote from the previous one by 47 cm; 3 zone of the contralateral hemisphere, symmetric to the IS focus. Control samples were obtained from 3 accident died people. Identification of targeted proteins NSE, c-fos, ERK1/2, MAP2, NOTCH1 was performed by indirect immunoperoxidase immunohistochemical method. Results. Moving away from the ischemic focus, there is an increase in the density of neurons and a decrease in the damaged neurons proportion, the largest share of c-fos protein positive neurons in zone 2, NOTCH1 positive neurons in zone 1, smaller fractions of ERK1/2 and MAP2 positive neurons compared to the control only in samples of zone 1. Conclusions. With the IS development, the contralateral hemisphere is intact tissue increased activation zone, while the zones 1 and 2 have pathological activation signs. In zone 1 of the range, the adaptive response of the tissue decreases, and in zone 2 it expands. Therefore, a key target for therapeutic intervention is zone 2.

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