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https://www.readbyqxmd.com/read/27911825/elucidating-the-druggable-interface-of-protein-protein-interactions-using-fragment-docking-and-coevolutionary-analysis
#1
Fang Bai, Faruck Morcos, Ryan R Cheng, Hualiang Jiang, José N Onuchic
Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27903799/cxcr6-mediated-sivagmsab-entry-into-sabaeus-african-green-monkey-lymphocytes-implicates-widespread-use-of-non-ccr5-pathways-in-natural-host-infections
#2
Katherine S Wetzel, Yanjie Yi, Sarah T C Elliott, Dino Romero, Beatrice Jacquelin, Beatrice H Hahn, Michaela Muller-Trutwin, Cristian Apetrei, Ivona Pandrea, Ronald G Collman
: African green monkeys (AGM) and sooty mangabeys (SM) are well-studied natural hosts of SIV, which do not progress to AIDS when infected with their species-specific viruses. SIV natural hosts express very low levels of the canonical entry coreceptor CCR5, and recent studies have shown that CCR5 is dispensable for SIV infection of SM in vivo, and blocking CCR5 does not prevent ex vivo infection of PBMC from SM or vervet AGM. In both hosts, CXCR6 is an efficient entry pathway in vitro...
November 30, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27888301/the-genome-sequence-and-insights-into-the-immunogenetics-of-the-bananaquit-passeriformes-coereba-flaveola
#3
Jennifer Antonides, Robert Ricklefs, J Andrew DeWoody
Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of immunogenetic loci within the host genome...
November 25, 2016: Immunogenetics
https://www.readbyqxmd.com/read/27887566/the-common-redstart-as-a-suitable-model-to-study-cuckoo-host-coevolution-in-a-unique-ecological-context
#4
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/27871852/some-pungent-arguments-against-the-physico-chemical-theories-of-the-origin-of-the-genetic-code-and-corroborating-the-coevolution-theory
#5
Massimo Di Giulio
Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code"...
November 19, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27870263/coevolution-local-adaptation-and-ecological-speciation
#6
John N Thompson
Coevolution is one of the major processes organizing the earth's biodiversity, but it remains unclear when and how it may generate species diversity. The study by Parchman et al. () in this issue of Molecular Ecology provides the clearest evidence to date that divergent local adaptation in a coevolving interaction may lead to speciation on one side of an interaction but not necessarily on the other side. Red crossbills in North America have diversified into ecotypes that specialize on different conifer species, use different calls and vary in the extent to which they are nomadic or sedentary...
November 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27869203/no-effect-of-natural-transformation-on-the-evolution-of-resistance-to-bacteriophages-in-the-acinetobacter-baylyi-model-system
#7
Amy McLeman, Pawel Sierocinski, Elze Hesse, Angus Buckling, Gabriel Perron, Nils Hülter, Pål Jarle Johnsen, Michiel Vos
The adaptive benefits of natural transformation, the active uptake of free DNA molecules from the environment followed by incorporation of this DNA into the genome, may be the improved response to selection resulting from increased genetic variation. Drawing analogies with sexual reproduction, transformation may be particularly beneficial when selection rapidly fluctuates during coevolution with virulent parasites ('the Red Queen Hypothesis'). Here we test this hypothesis by experimentally evolving the naturally transformable and recombinogenic species Acinetobacter baylyi with a cocktail of lytic phages...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27867147/evolution-of-krab-containing-zinc-finger-proteins-and-their-roles-in-species-evolution
#8
Wang Jinlong, Wang Jian, Tian Chunyan
The C2H2 zinc finger protein family, one of the largest families of transcription factor/transcriptional regulator in mammal, arose from a small ancestral group of eukaryotic zinc finger transcription factors through many repeated gene duplications accompanied by functional divergence. As the biggest subfamily of C2H2 zinc finger protein family, Kruppel-associated box-containing zinc finger proteins (KRAB-ZFPs) appeared at the period oftetrapod, expand rapidly along with species evolution, and take about 60% of the total C2H2 zinc finger proteins in human...
November 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27864137/intergenomic-evolution-and-metabolic-cross-talk-between-rumen-and-thermophilic-autotrophic-methanogenic-archaea
#9
M Bharathi, P Chellapandi
Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter...
November 15, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27862515/coevolutionary-dynamics-between-a-defensive-microbe-and-a-pathogen-driven-by-fluctuating-selection
#10
Suzanne A Ford, David Williams, Steve Paterson, Kayla C King
Microbes that protect their hosts from pathogenic infection are widespread components of the microbiota of both plants and animals. It has been found that interactions between 'defensive' microbes and pathogens can be genotype-specific and even underlie the variation in host resistance to pathogenic infection. These observations suggest a dynamic coevolutionary association between pathogens and defensive microbes, but direct evidence of coevolution is lacking. We tested the hypothesis that defensive microbes and pathogens could coevolve within host populations by co-passaging a microbe with host-defensive properties (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within Caenorhabditis elegans nematodes...
November 8, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27856145/sequence-specific-sensing-of-nucleic-acids
#11
REVIEW
Nicolas Vabret, Nina Bhardwaj, Benjamin D Greenbaum
Innate immune cells are endowed with many nucleic acid receptors, but the role of sequence in the detection of foreign organisms remains unclear. Can sequence patterns influence recognition? In addition, how can we infer those patterns from sequence data? Here, we detail recent computational and experimental evidence associated with sequence-specific sensing. We review the mechanisms underlying the detection and discrimination of foreign sequences from self. We also describe quantitative approaches used to infer the stimulatory capacity of a given pathogen nucleic acid species, and the influence of sequence-specific sensing on host-pathogen coevolution, including endogenous sequences of foreign origin...
November 14, 2016: Trends in Immunology
https://www.readbyqxmd.com/read/27852220/coevolution-of-paired-receptors-in-xenopus-carcinoembryonic-antigen-related-cell-adhesion-molecule-families-suggests-appropriation-as-pathogen-receptors
#12
Wolfgang Zimmermann, Robert Kammerer
BACKGROUND: In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions are such paired receptors. Various bacterial pathogens bind to CEACAM1 on epithelial and immune cells facilitating both entry into the host and down-regulation of the immune response whereas interaction with granulocyte-specific CEACAM3 leads to their uptake and destruction...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27848978/the-impact-of-heterogeneity-and-awareness-in-modeling-epidemic-spreading-on-multiplex-networks
#13
Marialisa Scatà, Alessandro Di Stefano, Pietro Liò, Aurelio La Corte
In the real world, dynamic processes involving human beings are not disjoint. To capture the real complexity of such dynamics, we propose a novel model of the coevolution of epidemic and awareness spreading processes on a multiplex network, also introducing a preventive isolation strategy. Our aim is to evaluate and quantify the joint impact of heterogeneity and awareness, under different socioeconomic conditions. Considering, as case study, an emerging public health threat, Zika virus, we introduce a data-driven analysis by exploiting multiple sources and different types of data, ranging from Big Five personality traits to Google Trends, related to different world countries where there is an ongoing epidemic outbreak...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27836928/the-common-mouse-protozoa-tritrichomonas-muris-alters-mucosal-t-cell-homeostasis-and-colitis-susceptibility
#14
Nichole K Escalante, Paul Lemire, Mayra Cruz Tleugabulova, David Prescott, Arthur Mortha, Catherine J Streutker, Stephen E Girardin, Dana J Philpott, Thierry Mallevaey
The mammalian gastrointestinal tract hosts a diverse community of microbes including bacteria, fungi, protozoa, helminths, and viruses. Through coevolution, mammals and these microbes have developed a symbiosis that is sustained through the host's continuous sensing of microbial factors and the generation of a tolerant or pro-inflammatory response. While analyzing T cell-driven colitis in nonlittermate mouse strains, we serendipitously identified that a nongenetic transmissible factor dramatically increased disease susceptibility...
November 11, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27825220/direct-coevolutionary-couplings-reflect-biophysical-residue-interactions-in-proteins
#15
Alice Coucke, Guido Uguzzoni, Francesco Oteri, Simona Cocco, Remi Monasson, Martin Weigt
Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 × 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost...
November 7, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27824149/coevolution-of-cooperation-and-partner-rewiring-range-in-spatial-social-networks
#16
Tommy Khoo, Feng Fu, Scott Pauls
In recent years, there has been growing interest in the study of coevolutionary games on networks. Despite much progress, little attention has been paid to spatially embedded networks, where the underlying geographic distance, rather than the graph distance, is an important and relevant aspect of the partner rewiring process. It thus remains largely unclear how individual partner rewiring range preference, local vs. global, emerges and affects cooperation. Here we explicitly address this issue using a coevolutionary model of cooperation and partner rewiring range preference in spatially embedded social networks...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27822520/getting-the-hologenome-concept-right-an-eco-evolutionary-framework-for-hosts-and-their-microbiomes
#17
Kevin R Theis, Nolwenn M Dheilly, Jonathan L Klassen, Robert M Brucker, John F Baines, Thomas C G Bosch, John F Cryan, Scott F Gilbert, Charles J Goodnight, Elisabeth A Lloyd, Jan Sapp, Philippe Vandenkoornhuyse, Ilana Zilber-Rosenberg, Eugene Rosenberg, Seth R Bordenstein
Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon...
March 2016: MSystems
https://www.readbyqxmd.com/read/27821530/the-evolution-of-asymmetric-genitalia-in-coleoptera
#18
Menno Schilthuizen, Paulien de Jong, Rick van Beek, Tamara Hoogenboom, Melanie Meijer Zu Schlochtern
The evolution of asymmetry in male genitalia is a pervasive and recurrent phenomenon across almost the entire animal kingdom. Although in some taxa the asymmetry may be a response to the evolution of one-sided, male-above copulation from a more ancestral female-above condition, in other taxa, such as Mammalia and Coleoptera, this explanation appears insufficient. We carried out an informal assessment of genital asymmetry across the Coleoptera and found that male genital asymmetry is present in 43% of all beetle families, and at all within-family taxonomic levels...
December 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27813668/learning-in-insect-pollinators-and-herbivores
#19
Patricia L Jones, Anurag A Agrawal
The relationship between plants and insects is influenced by insects' behavioral decisions during foraging and oviposition. In mutualistic pollinators and antagonistic herbivores, past experience (learning) affects such decisions, which ultimately can impact plant fitness. The higher levels of dietary generalism in pollinators than in herbivores may be an explanation for the differences in learning seen between these two groups. Generalist pollinators experience a high level of environmental variation, which we suggest favors associative learning...
October 28, 2016: Annual Review of Entomology
https://www.readbyqxmd.com/read/27798309/evidence-for-parasite-mediated-selection-during-short-lasting-toxic-algal-blooms
#20
François Blanquart, Myriam Valero, Catharina Alves-de-Souza, Aliou Dia, Frédéric Lepelletier, Estelle Bigeard, Christian Jeanthon, Christophe Destombe, Laure Guillou
Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A...
October 26, 2016: Proceedings. Biological Sciences
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