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https://www.readbyqxmd.com/read/29793052/title-lhp1-interacts-with-atrx-through-plant-specific-domains-at-specific-loci-targeted-by-prc2
#1
Haifeng Wang, Danhua Jiang, Elin Axelsson, Zdravko J Lorković, Sean Montgomery, Sarah Holec, Bas J G E Pieters, Abbas H K Al Temimi, Jasmin Mecinović, Frédéric Berger
Heterochromatin Protein 1 (HP1) is a major regulator of chromatin structure and function. In animals, the network of proteins interacting with HP1 is mainly associated with constitutive heterochromatin marked by H3K9me3. HP1 physically interacts with the putative orthologue of the SNF2 chromatin remodeler ATRX, which controls deposition of the histone variant H3.3 in mammals. In Arabidopsis thaliana, we show that the orthologue of ATRX participates in H3.3 deposition and characterize the function of conserved domains of plant ATRX...
May 21, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29792991/codon-adaptation-biases-among-sylvatic-and-urban-genotypes-of-dengue-virus-type-2
#2
Marielton Dos Passos Cunha, Ayda Susana Ortiz-Baez, Caio César de Melo Freire, Paolo Marinho de Andrade Zanotto
Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for fine-tuning in viral codon usage, possibly due to viral adaptation to human transmission. We compared the codon adaptation of DENV serotype 2 (DENV-2) genotypes from urban and sylvatic habitats and tried to correlate the findings with key evolutionary determinants...
May 21, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29792990/identification-of-group-a-rotaviruses-from-zambian-fruit-bats-provides-evidence-for-long-distance-dispersal-events-in-africa
#3
Michihito Sasaki, Masahiro Kajihara, Katendi Changula, Akina Mori-Kajihara, Hirohito Ogawa, Bernard M Hang'ombe, Aaron S Mweene, Martin Simuunza, Reiko Yoshida, Michael Carr, Yasuko Orba, Ayato Takada, Hirofumi Sawa
Group A rotavirus (RVA) is a major cause of diarrhea in children worldwide. Although RVA infects many animals, little is known about RVA in bats. The present study investigated the genetic diversity of RVA in Zambian bats. We identified RVA from two straw-colored fruit bats (Eidolon helvum) and an Egyptian fruit bat (Rousettus aegyptiacus), and analyzed the genome sequences of these strains. Genome segments of the RVA strains from Zambian E. helvum showed 97%-99% nucleotide sequence identity with those of other RVA strains from E...
May 21, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29792826/fast-evolving-human-specific-neural-enhancers-are-associated-with-aging-related-diseases
#4
Han Chen, Chunyan Li, Zhicheng Zhou, Han Liang
The antagonistic pleiotropy theory hypothesizes that evolutionary adaptations maximizing the fitness in early age increase disease burden after reproduction. This theory remains largely untested at the molecular level. Here, we analyzed enhancer evolution in primates to investigate the relationships between aging-related diseases and enhancers acquired after the human-chimpanzee divergence. We report a 5-fold increased evolutionary rate of enhancers that are activated in neural tissues, leading to fixation of ∼100 human-specific enhancers potentially under adaptation...
May 23, 2018: Cell Systems
https://www.readbyqxmd.com/read/29792817/macroscopic-theory-for-evolving-biological-systems-akin-to-thermodynamics
#5
Kunihiko Kaneko, Chikara Furusawa
We present a macroscopic theory to characterize the plasticity, robustness, and evolvability of biological responses and their fluctuations. First, linear approximation in intracellular reaction dynamics is used to demonstrate proportional changes in the expression of all cellular components in response to a given environmental stress, with the proportion coefficient determined by the change in growth rate as a consequence of the steady growth of cells. We further demonstrate that this relationship is supported through adaptation experiments of bacteria, perhaps too well as this proportionality is held even across cultures of different types of conditions...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792591/comprehensive-evolutionary-and-phylogenetic-analysis-of-hepacivirus-n-hnv
#6
M S da Silva, D M Junqueira, L F Baumbach, S P Cibulski, A C S Mósena, M N Weber, S Silveira, G M de Moraes, R D Maia, V C S Coimbra, C W Canal
Hepaciviruses (HVs) have been detected in several domestic and wild animals and present high genetic diversity. The actual classification divides the genus Hepacivirus into 14 species (A-N), according to their phylogenetic relationships, including the bovine hepacivirus [Hepacivirus N (HNV)]. In this study, we confirmed HNV circulation in Brazil and sequenced the whole genome of two strains. Based on the current classification of HCV, which is divided into genotypes and subtypes, we analysed all available bovine hepacivirus sequences in the GenBank database and proposed an HNV classification...
May 24, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29792572/galnac-sirna-conjugates-leading-the-way-for-delivery-of-rnai-therapeutics
#7
Aaron D Springer, Steven F Dowdy
Short-interfering RNA (siRNA)-induced RNAi responses have great potential to treat a wide variety of human diseases from cancer to pandemic viral outbreaks to Parkinson's Disease. However, before siRNAs can become drugs, they must overcome a billion years of evolutionary defenses designed to keep invading RNAs on the outside cells from getting to the inside of cells. Not surprisingly, significant effort has been placed in developing a wide array of delivery technologies. Foremost of these has been the development of N-acetylgalactosamine (GalNAc) siRNA conjugates for delivery to liver...
May 24, 2018: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29792566/clues-to-an-evolutionary-mystery-the-genes-for-t-toxin-enabler-of-the-devastating-1970-southern-corn-leaf-blight-epidemic-are-present-in-ancestral-species-suggesting-an-ancient-origin
#8
Bradford J Condon, Candace E Elliott, Jonathan Gonzalez, Sung-Hwan Yun, Yasunori Akagi, Tyr Wiesner-Hanks, Motoichiro Kodama, Gillian Turgeon
The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while P. zeae-maydis produces PM-toxin, both host selective polyketide toxins necessary for supervirulence. Present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species...
May 24, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29792446/an-expanded-theory-of-alzheimer-s-caregiving
#9
Samantha F Lang, Blaine J Fowers
The ancient and cross-culturally prevalent pattern of caregiving suggests that long-term caregiving is species characteristic for humans. If so, then an evolutionary account of the adaptation(s) that underwrite this caregiving is necessary, particularly for the one-sided and long-term nature of Alzheimer's caregiving. Four standard evolutionary explanations are evaluated: kin selection theory, the grandmother hypothesis, direct reciprocity, and indirect reciprocity. Each is found inadequate to explain caregiving because of the lack of reproductive benefits...
May 24, 2018: American Psychologist
https://www.readbyqxmd.com/read/29791715/genome-skimming-provides-new-insight-into-the-relationships-in-ludwigia-section-macrocarpon-a-polyploid-complex
#10
Shih-Hui Liu, Christine E Edwards, Peter C Hoch, Peter H Raven, Janet C Barber
PREMISE OF THE STUDY: Interpreting relationships within groups containing polyploids, which are frequent in angiosperms, can be greatly assisted by genomic techniques. In this study, we used a genome-skimming approach to investigate the evolutionary relationships and origins of polyploids in the monophyletic group, Ludwigia section Macrocarpon (Onagraceae), which includes diploid, tetraploid, and hexaploid taxa. METHODS: We sampled all known taxa and ploidy levels in the section and conducted shotgun sequencing...
May 23, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29791565/a-giant-on-the-ground-another-large-bodied-atractus-serpentes-dipsadinae-from-ecuadorian-andes-with-comments-on-the-dietary-specializations-of-the-goo-eaters-snakes
#11
Paulo Passos, Agustín Scanferla, Paulo R Melo-Sampaio, Jorge Brito, Ana Almendariz
Body-size is significantly correlated with the number of vertebrae (pleomerism) in multiple vertebrate lineages, indicating that somitogenesis process is an important factor dictating evolutionary change associated to phyletic allometry and, consequently, species fitness and diversification. However, the role of the evolution of extreme body sizes (dwarfism and gigantism) remains elusive in snakes, mainly with respect to postnatal ontogeny in dietary preferences associated with evolution of gigantism in many lineages...
May 17, 2018: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29791443/traceability-reproducibility-and-wiki-exploration-for-%C3%A3-la-carte-reconstructions-of-genome-scale-metabolic-models
#12
Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V Markov, Alejandro Maass, Anne Siegel
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction...
May 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29791319/malignancy-in-a-retrospective-cohort-of-17-patients-with-dermatomyositis-or-polymyositis-in-southern-tunisia
#13
Khadija Sellami, Madiha Mseddi, Mouna Snoussi, Hela Gharbi, Faten Frikha, Rayda Ben Salah, Moez Jallouli, Sameh Marzouk, Abderrahmen Masmoudi, Zouhir Bahloul, Hamida Turki
INTRODUCTION: The prognosis of dermatomyositis (DM)/polymyositis (PM) in adults is partly related to their association with neoplasia. The aim of our study was to report the epidemiologic, clinical, paraclinical, therapeutic and evolutionary aspects of DM associated with malignancy in patients from Sfax, south eastern of Tunisia. METHODS: A retrospective cohort study of patients with DM or PM admitted in Dermatology and Internal Medicine Departments of Hedi Chaker University Hospital of Sfax between 1996 and 2015...
May 21, 2018: Romanian Journal of Internal Medicine, Revue Roumaine de Médecine Interne
https://www.readbyqxmd.com/read/29790980/contrasting-patterns-of-genomic-diversity-reveal-accelerated-genetic-drift-but-reduced-directional-selection-on-x-chromosome-in-wild-and-domestic-sheep-species
#14
Ze-Hui Chen, Min Zhang, Feng-Hua Lv, Xue Ren, Wen-Rong Li, Ming-Jun Liu, Kiwoong Nam, Michael W Bruford, Meng-Hua Li
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29790964/evidence-of-evolutionary-history-and-selective-sweeps-in-the-genome-of-meishan-pig-reveals-its-genetic-and-phenotypic-characterization
#15
Pengju Zhao, Ying Yu, Wen Feng, Heng Du, Jian Yu, Huimin Kang, Xianrui Zheng, Zhiquan Wang, George E Liu, Catherine W Ernst, Xueqin Ran, Jiafu Wang, Jian-Feng Liu
Background: Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with the unique features are still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to phenotypic traits of Meishan by large-scale sequencing. Results: We found the unique domestication of Meishan pigs happened at the Taihu Basin area between the Majiabang and the Liangzhu culture, during which 300 protein-coding genes have undergone positive selection...
May 22, 2018: GigaScience
https://www.readbyqxmd.com/read/29790946/a-microbial-endocrinology-based-simulated-small-intestinal-medium-for-the-evaluation-of-neurochemical-production-by-gut-microbiota
#16
Daniel N Villageliú, Sharon Rasmussen, Mark Lyte
Microbial endocrinology represents the union of microbiology and neurobiology and is concerned with the ability of neurochemicals to serve as an evolutionary-based language between host and microbiota in health and disease. The recognition that microorganisms produce, modify and respond to the same neurochemicals utilized in the various signaling pathways of their mammalian hosts is increasingly being recognized as a mechanism by which the host and microbiota may interact to influence the progression of infectious disease as well as influence behavior through the microbiota-gut-brain axis...
May 21, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29790909/ebic-an-evolutionary-based-parallel-biclustering-algorithm-for-pattern-discovery
#17
Patryk Orzechowski, Moshe Sipper, Xiuzhen Huang, Jason H Moore
Motivation: Biclustering algorithms are commonly used for gene expression data analysis. However, accurate identification of meaningful structures is very challenging and state-of-the-art methods are incapable of discovering with high accuracy different patterns of high biological relevance. Results: In this paper a novel biclustering algorithm based on evolutionary computation, a subfield of artificial intelligence (AI), is introduced. The method called EBIC aims to detect order-preserving patterns in complex data...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790439/principles-of-evolutionary-medicine
#18
Sunjai Gupta
No abstract text is available yet for this article.
June 2018: Journal of Mental Health
https://www.readbyqxmd.com/read/29790280/cas9-versus-cas12a-cpf1-structure-function-comparisons-and-implications-for-genome-editing
#19
REVIEW
Daan C Swarts, Martin Jinek
Cas9 and Cas12a are multidomain CRISPR-associated nucleases that can be programmed with a guide RNA to bind and cleave complementary DNA targets. The guide RNA sequence can be varied, making these effector enzymes versatile tools for genome editing and gene regulation applications. While Cas9 is currently the best-characterized and most widely used nuclease for such purposes, Cas12a (previously named Cpf1) has recently emerged as an alternative for Cas9. Cas9 and Cas12a have distinct evolutionary origins and exhibit different structural architectures, resulting in distinct molecular mechanisms...
May 22, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29790263/herbicide-hormesis-can-act-as-a-driver-of-resistance-evolution-in-weeds-ps-ii-target-site-resistance-in-chenopodium-album-l-as-a-case-study
#20
Regina G Belz
BACKGROUND: Herbicide hormesis may play a role in weed resistance evolution by increasing resistance selection. A standard herbicide rate may be subtoxic to resistant plants and make them more fit than untreated plants. If this increase in fitness is ultimately expressed in reproductive traits, resistance genes can accumulate more rapidly and exacerbate resistance evolution by magnifying the selection differential between resistant and sensitive plants. The hypothesis of hormetically enhanced reproductive fitness was studied for a PSII target-site resistant (TSR) biotype of Chenopodium album exposed to the triazinone metamitron in comparison to its wild type...
May 23, 2018: Pest Management Science
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