keyword
MENU ▼
Read by QxMD icon Read
search

Evolutionary dynamics

keyword
https://www.readbyqxmd.com/read/27913680/new-nuclear-and-perinuclear-functions-of-formins
#1
REVIEW
Tadamoto Isogai, Metello Innocenti
Formin family proteins (formins) represent an evolutionary conserved protein family encoded in the genome of a wide range of eukaryotes. Formins are hallmarked by a formin homology 1 (FH1) domain juxtaposed to an FH2 domain whereby they control actin and microtubule dynamics. Not surprisingly, formins are best known as key regulators of the cytoskeleton in a variety of morphogenetic processes. However, mounting evidence implicates several formins in the assembly and organization of actin within and around the nucleus...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27912243/vomeronasal-receptors-in-vertebrates-and-the-evolution-of-pheromone-detection
#2
Liliana Silva, Agostinho Antunes
Pheromones were identified as chemical signals used for intraspecific communication in insects (e.g., sexual attraction) in the 1950s. However, only almost 40 years later the vomeronasal receptors type-1 (V1R) and type-2 (V2R) were identified, usually associated with the presence of a vomeronasal organ (VNO). VRs are widespread in amphibians, reptiles, and mammals, but birds lost the VNO. Similarly, fishes lack VRs and a VNO but can still detect pheromones, instead using the olfactory receptors related to class A and class C G protein-coupled receptors...
November 28, 2016: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/27907076/clinical-determinants-of-hiv-1b-between-host-evolution-and-their-association-with-drug-resistance-in-pediatric-patients
#3
Israel Pagán, Patricia Rojas, José Tomás Ramos, África Holguín
Understanding the factors that modulate the evolution of virus populations is essential to design efficient control strategies. Mathematical models predict that factors affecting viral within-host evolution may also determine that at the between-host level. Although HIV-1 within-host evolution has been associated with clinical factors used to monitor AIDS progression, such as patient age, CD4 cells count, viral load, and antiretroviral experience, little is known about the role of these clinical factors in determining between-host HIV-1 evolution...
2016: PloS One
https://www.readbyqxmd.com/read/27907061/tracking-the-evolution-of-infrastructure-systems-and-mass-responses-using-publically-available-data
#4
Xiangyang Guan, Cynthia Chen, Dan Work
Networks can evolve even on a short-term basis. This phenomenon is well understood by network scientists, but receive little attention in empirical literature involving real-world networks. On one hand, this is due to the deceitfully fixed topology of some networks such as many physical infrastructures, whose evolution is often deemed unlikely to occur in short term; on the other hand, the lack of data prohibits scientists from studying subjects such as social networks that seem likely to evolve on a short-term basis...
2016: PloS One
https://www.readbyqxmd.com/read/27906523/developmental-evolution
#5
REVIEW
Robert Lickliter
Biologists and psychologists are re-thinking the long-standing premise of genes as the primary cause of development, a view widely embraced in 20th-century biology. This shift in thinking is based in large part on: (1) the growing appreciation of the complex, distributed regulatory dynamics of gene expression; and (2) the growing appreciation of the probabilistic, contingent, and situated nature of development. We now appreciate that what actually unfolds during individual development represents only one of many possibilities...
December 1, 2016: Wiley Interdisciplinary Reviews. Cognitive Science
https://www.readbyqxmd.com/read/27905065/spatial-measures-of-genetic-heterogeneity-during-carcinogenesis
#6
K Storey, M D Ryser, K Leder, J Foo
In this work we explore the temporal dynamics of spatial heterogeneity during the process of tumorigenesis from healthy tissue. We utilize a spatial stochastic model of mutation accumulation and clonal expansion in a structured tissue to describe this process. Under a two-step tumorigenesis model, we first derive estimates of a non-spatial measure of diversity: Simpson's Index, which is the probability that two individuals sampled at random from the population are identical, in the premalignant population. We next analyze two new measures of spatial population heterogeneity...
November 30, 2016: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/27900364/analysis-of-intrapatient-heterogeneity-uncovers-the-microevolution-of-middle-east-respiratory-syndrome-coronavirus
#7
Donghyun Park, Hee Jae Huh, Yeon Jeong Kim, Dae-Soon Son, Hyo-Jeong Jeon, Eu-Hyun Im, Jong-Won Kim, Nam Yong Lee, Eun-Suk Kang, Cheol In Kang, Doo Ryeon Chung, Jin-Hyun Ahn, Kyong Ran Peck, Sun Shim Choi, Yae-Jean Kim, Chang-Seok Ki, Woong-Yang Park
Genome sequence analysis of Middle East respiratory syndrome coronavirus (MERS-CoV) variants from patient specimens has revealed the evolutionary dynamics and mechanisms of pathogenesis of the virus. However, most studies have analyzed the consensus sequences of MERS-CoVs, precluding an investigation of intrapatient heterogeneity. Here, we analyzed non-consensus sequences to characterize intrapatient heterogeneity in cases associated with the 2015 outbreak of MERS in South Korea. Deep-sequencing analysis of MERS-CoV genomes performed on specimens from eight patients revealed significant intrapatient variation; therefore, sequence heterogeneity was further analyzed using targeted deep sequencing...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27898037/analyses-of-evolutionary-characteristics-of-the-hemagglutinin-esterase-gene-of-influenza-c-virus-during-a-period-of-68-years-reveals-evolutionary-patterns-different-from-influenza-a-and-b-viruses
#8
Yuki Furuse, Yoko Matsuzaki, Hidekazu Nishimura, Hitoshi Oshitani
Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses...
November 26, 2016: Viruses
https://www.readbyqxmd.com/read/27896736/structural-and-functional-annotation-of-long-noncoding-rnas
#9
Martin A Smith, John S Mattick
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896030/historical-reconstruction-of-climatic-and-elevation-preferences-and-the-evolution-of-cloud-forest-adapted-tree-ferns-in-mesoamerica
#10
Victoria Sosa, Juan Francisco Ornelas, Santiago Ramírez-Barahona, Etelvina Gándara
BACKGROUND: Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials...
2016: PeerJ
https://www.readbyqxmd.com/read/27894997/structural-and-evolutionary-analyses-reveal-determinants-of-dna-binding-specificities-of-nucleoid-associated-proteins-hu-and-ihf
#11
Debayan Dey, Valakunja Nagaraja, Suryanarayanarao Ramakumar
Nucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins...
November 25, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27892853/structure-of-the-germline-genome-of-tetrahymenathermophila-and-relationship-to-the-massively-rearranged-somatic-genome
#12
Eileen P Hamilton, Aurélie Kapusta, Piroska E Huvos, Shelby L Bidwell, Nikhat Zafar, Haibao Tang, Michalis Hadjithomas, Vivek Krishnakumar, Jonathan H Badger, Elisabet V Caler, Carsten Russ, Qiandong Zeng, Lin Fan, Joshua Z Levin, Terrance Shea, Sarah K Young, Ryan Hegarty, Riza Daza, Sharvari Gujja, Jennifer R Wortman, Bruce W Birren, Chad Nusbaum, Jainy Thomas, Clayton M Carey, Ellen J Pritham, Cédric Feschotte, Tomoko Noto, Kazufumi Mochizuki, Romeo Papazyan, Sean D Taverna, Paul H Dear, Donna M Cassidy-Hanley, Jie Xiong, Wei Miao, Eduardo Orias, Robert S Coyne
The germline genome of the binucleated ciliate Tetrahymenathermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally...
November 28, 2016: ELife
https://www.readbyqxmd.com/read/27892509/evolution-of-cooperation-under-indirect-reciprocity-and-arbitrary-exploration-rates
#13
Fernando P Santos, Jorge M Pacheco, Francisco C Santos
Cooperation has been recognized as an evolutionary puzzle since Darwin, and remains identified as one of the biggest challenges of the XXIst century. Indirect Reciprocity (IR), a key mechanism that humans employ to cooperate with each other, establishes that individual behaviour depends on reputations, which in turn evolve depending on social norms that classify behaviours as good or bad. While it is well known that different social norms give rise to distinct cooperation levels, it remains unclear how the performance of each norm is influenced by the random exploration of new behaviours, often a key component of social dynamics where a plethora of stimuli may compel individuals to deviate from pre-defined behaviours...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27891618/co2-studies-remain-key-to-understanding-a-future-world
#14
REVIEW
Katie M Becklin, S Michael Walker, Danielle A Way, Joy K Ward
I. II. III. IV. V. References SUMMARY: Characterizing plant responses to past, present and future changes in atmospheric carbon dioxide concentration ([CO2 ]) is critical for understanding and predicting the consequences of global change over evolutionary and ecological timescales. Previous CO2 studies have provided great insights into the effects of rising [CO2 ] on leaf-level gas exchange, carbohydrate dynamics and plant growth. However, scaling CO2 effects across biological levels, especially in field settings, has proved challenging...
November 28, 2016: New Phytologist
https://www.readbyqxmd.com/read/27891142/genetic-structure-and-evolutionary-history-of-three-alpine-sclerophyllous-oaks-in-east-himalaya-hengduan-mountains-and-adjacent-regions
#15
Li Feng, Qi-Jian Zheng, Zeng-Qiang Qian, Jia Yang, Yan-Ping Zhang, Zhong-Hu Li, Gui-Fang Zhao
The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27890449/independent-evolution-of-genomic-characters-during-major-metazoan-transitions
#16
REVIEW
Oleg Simakov, Takeshi Kawashima
Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages...
November 24, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27888126/understanding-the-complex-evolution-of-rapidly-mutating-viruses-with-deep-sequencing-beyond-the-analysis-of-viral-diversity
#17
REVIEW
Preston Leung, Auda A Eltahla, Andrew R Lloyd, Rowena A Bull, Fabio Luciani
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts...
November 22, 2016: Virus Research
https://www.readbyqxmd.com/read/27887566/the-common-redstart-as-a-suitable-model-to-study-cuckoo-host-coevolution-in-a-unique-ecological-context
#18
Peter Samaš, Jarkko Rutila, Tomáš Grim
BACKGROUND: Co-evolutionary arms-races result in spatio-temporally dynamic relationships between interacting species, e.g., brood parasites and their avian hosts. However, majority of avian co-evolutionary studies are limited to "snap-shots" of a single breeding season in an open-nesting host. In a long-term study (11 breeding seasons), we explored a unique system between the brood parasitic common cuckoo (Cuculus canorus) and its host, the common redstart (Phoenicurus phoenicurus) which is exceptional among all cuckoo hosts due to being a cavity nester...
November 25, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27886244/reconstructing-networks-from-profit-sequences-in-evolutionary-games-via-a-multiobjective-optimization-approach-with-lasso-initialization
#19
Kai Wu, Jing Liu, Shuai Wang
Evolutionary games (EG) model a common type of interactions in various complex, networked, natural and social systems. Given such a system with only profit sequences being available, reconstructing the interacting structure of EG networks is fundamental to understand and control its collective dynamics. Existing approaches used to handle this problem, such as the lasso, a convex optimization method, need a user-defined constant to control the tradeoff between the natural sparsity of networks and measurement error (the difference between observed data and simulated data)...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27886243/creating-new-layered-structures-at-high-pressures-sis2
#20
Dušan Plašienka, Roman Martoňák, Erio Tosatti
Old and novel layered structures are attracting increasing attention for their physical, electronic, and frictional properties. SiS2, isoelectronic to SiO2, CO2 and CS2, is a material whose phases known experimentally up to 6 GPa exhibit 1D chain-like, 2D layered and 3D tetrahedral structures. We present highly predictive ab initio calculations combined with evolutionary structure search and molecular dynamics simulations of the structural and electronic evolution of SiS2 up to 100 GPa. A highly stable CdI2-type layered structure, which is octahedrally coordinated with space group surprisingly appears between 4 and up to at least 100 GPa...
November 25, 2016: Scientific Reports
keyword
keyword
62259
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"