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71.
The role of mutation rate in optimizing key features of evolutionary dynamics has recently been investigated in various computational models. Here, we address the related question of how maximum mutation size affects the formation of species in a simple computational evolutionary model. We find that the number of species is maximized for intermediate values of a mutation size parameter μ; the result is observed for evolving organisms on a randomly changing landscape as well as in a version of the model where negative feedback exists between the local population size and the fitness provided by the landscape. The same result is observed for various distributions of mutation values within the limits set by μ. When organisms with various values of μ compete against each other, those with intermediate μ values are found to survive. The surviving values of μ from these competition simulations, however, do not necessarily coincide with the values that maximize the number of species. These results suggest that various complex factors are involved in determining optimal mutation parameters for any population, and may also suggest approaches for building a computational bridge between the (micro) dynamics of mutations at the level of individual organisms and (macro) evolutionary dynamics at the species level. 相似文献
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74.
Tumor necrosis factor-alpha (TNF-α) and interleukin 1 beta (IL-1β) genetic variants which resulting in TNF-α and IL-1 overproduction
may increase susceptibility to autoimmune diseases such as atherosclerosis. We have studied the association of TNF-α G308A
and IL-1β (+3953) C/T polymorphism with myocardial infarction in Turkish population. 143 patients with myocardial infarction
and 213 age-matched healthy controls were included in the study. In univariant analysis, the frequencies of IL-1β, TNF-α genotype
or allele, and haplotype of C:A and T:A were significantly elevated in patients when compared with those of controls. GA genotype
of TNF-α, T allele of IL-1β and A of TNF-α allele seem to be risk factors for myocardial infarction. In contrast, CC genotype
of IL-1β and GG genotype of TNF-α have protective effect against myocardial infarction. In multivariate logistic regression
analysis, TNF-α A allele, gender and smoking were associated with myocardial infarction. In conclusion, we can state that
TNF-α A allele might be associated with myocardial infarction. 相似文献
75.
Ignacio J. General Ying Liu Mandy E. Blackburn Wenzhi Mao Lila M. Gierasch Ivet Bahar 《PLoS computational biology》2014,10(5)
The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70 domains regulate each other''s activity remains elusive. Covariance data from experiments and computations emerged in recent years as valuable sources of information towards gaining insights into the molecular events that mediate allostery. In the present study, conservation and covariance properties derived from both sequence and structural dynamics data are integrated with results from Perturbation Response Scanning and in vivo functional assays, so as to establish the dynamical basis of interdomain signal transduction in Hsp70s. Our study highlights the critical roles of SBD residues D481 and T417 in mediating the coupled motions of the two domains, as well as that of G506 in enabling the movements of the α-helical lid with respect to the β-sandwich. It also draws attention to the distinctive role of the NBD subdomains: Subdomain IA acts as a key mediator of signal transduction between the ATP- and substrate-binding sites, this function being achieved by a cascade of interactions predominantly involving conserved residues such as V139, D148, R167 and K155. Subdomain IIA, on the other hand, is distinguished by strong coevolutionary signals (with the SBD) exhibited by a series of residues (D211, E217, L219, T383) implicated in DnaJ recognition. The occurrence of coevolving residues at the DnaJ recognition region parallels the behavior recently observed at the nucleotide-exchange-factor recognition region of subdomain IIB. These findings suggest that Hsp70 tends to adapt to co-chaperone recognition and activity via coevolving residues, whereas interdomain allostery, critical to chaperoning, is robustly enabled by conserved interactions. 相似文献
76.
Thermal sensitivity is a crucial determinant of insect abundance and distribution. The way it is measured can have a critical influence on the conclusions made. Diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae) is an important insect pest of cruciferous crops around the world and the thermal responses of polyphagous species are critical to understand the influences of a rapidly changing climate on their distribution and abundance. Experiments were carried out to the lethal temperature limits (ULT0 and LLT0: temperatures where there is no survival) as well as Upper and Lower Lethal Temperature (ULT25 and LLT25) (temperature where 25% DBM survived) of lab-reared adult DBM population to extreme temperatures attained by either two-way ramping (ramping temperatures from baseline to LT25 and ramping back again) or sudden plunging method. In this study the ULT0 for DBM was recorded as 42.6°C and LLT0 was recorded as −16.5°C. DBM had an ULT25 of 41.8°C and LLT25 of −15.2°C. The duration of exposure to extreme temperatures had significant impacts on survival of DBM, with extreme temperatures and/or longer durations contributing to higher lethality. Comparing the two-way ramping temperature treatment to that of direct plunging temperature treatment, our study clearly demonstrated that DBM was more tolerant to temperature in the two-way ramping assay than that of the plunging assay for cold temperatures, but at warmer temperatures survival exhibited no differences between ramping and plunging. These results suggest that DBM will not be put under physiological stress from a rapidly changing climate, rather access to host plants in marginal habitats has enabled them to expand their distribution. Two-way temperature ramping enhances survival of DBM at cold temperatures, and this needs to be examined across a range of taxa and life stages to determine if enhanced survival is widespread incorporating a ramping recovery method. 相似文献
77.
Gustavo Glusman Anita Bahar Dror Sharon Yitzhak Pilpel Julia White Doron Lancet 《Mammalian genome》2000,11(11):1016-1023
The vertebrate olfactory receptor (OR) subgenome harbors the largest known gene family, which has been expanded by the need
to provide recognition capacity for millions of potential odorants. We implemented an automated procedure to identify all
OR coding regions from published sequences. This led us to the identification of 831 OR coding regions (including pseudogenes)
from 24 vertebrate species. The resulting dataset was subjected to neighbor-joining phylogenetic analysis and classified into
32 distinct families, 14 of which include only genes from tetrapodan species (Class II ORs). We also report here the first
identification of OR sequences from a marsupial (koala) and a monotreme (platypus). Analysis of these OR sequences suggests
that the ancestral mammal had a small OR repertoire, which expanded independently in all three mammalian subclasses. Classification
of ``fish-like' (Class I) ORs indicates that some of these ancient ORs were maintained and even expanded in mammals.
A nomenclature system for the OR gene superfamily is proposed, based on a divergence evolutionary model. The nomenclature
consists of the root symbol `OR', followed by a family numeral, subfamily letter(s), and a numeral representing the individual
gene within the subfamily. For example, OR3A1 is an OR gene of family 3, subfamily A, and OR7E12P is an OR pseudogene of family
7, subfamily E. The symbol is to be preceded by a species indicator. We have assigned the proposed nomenclature symbols for
all 330 human OR genes in the database. A WWW tool for automated name assignment is provided.
Received: / Accepted: 相似文献
78.
Figen Seymen Youn Jung Kim Ye Ji Lee Jenny Kang Tak-Heun Kim Hwajung Choi Mine Koruyucu Yelda Kasimoglu Elif Bahar Tuna Koray Gencay Teo Jeon Shin Hong-Keun Hyun Young-Jae Kim Sang-Hoon Lee Zang Hee Lee Hong Zhang Jan C-C. Hu James P. Simmer Eui-Sic Cho Jung-Wook Kim 《American journal of human genetics》2016,99(5):1199-1205
79.
Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores 总被引:11,自引:0,他引:11
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We propose a mathematical model for mitochondria-dependent apoptosis, in which kinetic cooperativity in formation of the apoptosome is a key element ensuring bistability. We examine the role of Bax and Bcl-2 synthesis and degradation rates, as well as the number of mitochondrial permeability transition pores (MPTPs), on the cell response to apoptotic stimuli. Our analysis suggests that cooperative apoptosome formation is a mechanism for inducing bistability, much more robust than that induced by other mechanisms, such as inhibition of caspase-3 by the inhibitor of apoptosis (IAP). Simulations predict a pathological state in which cells will exhibit a monostable cell survival if Bax degradation rate is above a threshold value, or if Bax expression rate is below a threshold value. Otherwise, cell death or survival occur depending on initial caspase-3 levels. We show that high expression rates of Bcl-2 can counteract the effects of Bax. Our simulations also demonstrate a monostable (pathological) apoptotic response if the number of MPTPs exceeds a threshold value. This study supports our contention, based on mathematical modeling, that cooperativity in apoptosome formation is critically important for determining the healthy responses to apoptotic stimuli, and helps define the roles of Bax, Bcl-2, and MPTP vis-à-vis apoptosome formation. 相似文献
80.
Tehmina Bahar Adeeba Mahboob Qureshi Fasiha Qurashi Muniba Abid Misbah Batool Zahra Muhammad Saleem Haider 《Phyton》2021,90(1):75-86
Most damaging plant diseases have been caused by viruses in the entire world. In tropical and subtropical areas, the damage caused by plant virus leads to great economic and agricultural losses. Single stranded DNA viruses (geminiviruses) are the most perilous pathogens which are responsible for major diseases in agronomic and horticultural crops. Significantly begomoviruses and mastreviruses are the biggest genus of plant infecting viruses, transmitted though Bemisia tabaci and members of Cicadellidae respectively. Plants possesses some naturally existing chemicals term as phyto-chemicals which perform important functions in the plant. Some antioxidant enzymes are used by plants for self-defense upon foreign invasion of infection. This review explains the present perceptive of influence of viral infections on phyto-chemicals, oxidative enzymes and biochemical changes occurring in the plant. Viral infection mediated phyto-chemical changes in plants mainly includes: up and down regulation of photosynthetic pigment, increase in the concentration of phenolic compounds, elevation of starch content in the leaf and up & down regulation of anti-oxidative enzymes including (GPX) guaiacol peroxidase, (PPO) polyphenol oxidase, (APX) ascorbate peroxidase, (SOD) superoxide dismutase and (CTA) catalase. These changes lead to initiation of hypersensitive response, by thicken of the leaf lamina, lignification under the leaf surface, blocking to stomatal openings, systematic cell death, generation of reactive oxidative species (ROS), activation of pathogen mediated resistance pathways i.e., production of salicylic acid and jasmonic acid. Collectively all the physiological changes in the plant due to viral infection supports the activation of defense mechanism of the plant to combat against viral infection by limiting virus in specific area, followed with the production of barriers for pathogen, accumulation of starch in the leaf and excess production of (ROS). These strategies used by the plant to prevent the spread of virus in whole plant and to minimize the risk of severe yield loss. 相似文献