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Saptarshi Sinha, Rajdeep K Grewal, Soumen Roy
Bacteriophages are more abundant than any other organism on our planet. The interaction of bacteriophages and bacteria and their coevolution is well known. In this chapter, we describe various aspects of modeling such systems and their dynamics. We explore their interaction in: (i) liquid media, which leads to well-mixed populations and (ii) solid media, where their interaction is spatially restricted. Such modeling, when used in conjunction with experiments would not only shed deep insight into the underlying dynamics but also provide useful clues toward potential therapeutic applications...
2018: Advances in Applied Microbiology
Luisa De Sordi, Marta Lourenço, Laurent Debarbieux
Viruses that infect bacteria, or bacteriophages, are among the most abundant entities in the gut microbiome. However, their role and the mechanisms by which they infect bacteria in the intestinal tract remain poorly understood. We recently reported that intestinal bacteria are an evolutionary force, driving the expansion of the bacteriophage host range by boosting the genetic variability of these viruses. Here, we expand these observations by studying antagonistic bacteriophage-bacteria coevolution dynamics and revealing that bacterial genetic variability is also increased under the pressure of bacteriophage predation...
June 18, 2018: Gut Microbes
Shiraz A Shah, Omer S Alkhnbashi, Juliane Behler, Wenyuan Han, Qunxin She, Wolfgang R Hess, Roger A Garrett, Rolf Backofen
A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clusters of Regularly IntersSpaced Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families...
June 18, 2018: RNA Biology
Mohit Sharma, Shiwani Guleria, Kirti Singh, Anjali Chauhan, Saurabh Kulshrestha
Fusarium is a large genus of filamentous fungi belongs to the division Ascomycota and was first described as Fusisporium . Innumerable members of this genus act as pathogens, endophytes and saprophytes and can be recovered from plants and soils worldwide. Many of these members are known to be phytopathogens. It is among the most diverse and widely dispersed phyto-pathogenic fungi which cause economically important blights, rots, wilts and cankers of many ornamental, field, horticultural and forest crops both in agricultural commodities and natural ecosystems...
June 2018: Virusdisease
Korin Albert, Asha Rani, David A Sela
Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates...
June 15, 2018: Microbial Genomics
Eloy A Colell, Javier A Iserte, Franco L Simonetti, Cristina Marino-Buslje
Correlated mutations between residue pairs in evolutionarily related proteins arise from constraints needed to maintain a functional and stable protein. Identifying these inter-related positions narrows down the search for structurally or functionally important sites. MISTIC is a server designed to assist users to calculate covariation in protein families and provide them with an interactive tool to visualize the results. Here, we present MISTIC2, an update to the previous server, that allows to calculate four covariation methods (MIp, mfDCA, plmDCA and gaussianDCA)...
June 14, 2018: Nucleic Acids Research
Ezgi Özcan, David A Sela
Human milk contains a high concentration of indigestible oligosaccharides, which likely mediated the coevolution of the nursing infant with its gut microbiome. Specifically, Bifidobacterium longum subsp. infantis ( B. infantis ) often colonizes the infant gut and utilizes these human milk oligosaccharides (HMOs) to enrich their abundance. In this study, the physiology and mechanisms underlying B. infantis utilization of two HMO isomers lacto- N -tetraose (LNT) and lacto- N -neotetraose (LNnT) was investigated in addition to their carbohydrate constituents...
2018: Frontiers in Nutrition
Chen Shen, Chen Chu, Lei Shi, Matjaž Perc, Zhen Wang
In this article, we propose an aspiration-based coevolution of link weight, and explore how this set-up affects the evolution of cooperation in the spatial prisoner's dilemma game. In particular, an individual will increase the weight of its link to its neighbours only if the payoff received via this interaction exceeds a pre-defined aspiration. Conversely, if the received payoff is below this aspiration, the link weight with the corresponding neighbour will decrease. Our results show that an appropriate aspiration level leads to a high-cooperation plateau, whereas too high or too low aspiration will impede the evolution of cooperation...
May 2018: Royal Society Open Science
Ricardo Nascimento Dos Santos, Shahid Khan, Faruck Morcos
Bacterial flagellar motility, an important virulence factor, is energized by a rotary motor localized within the flagellar basal body. The rotor module consists of a large framework (the C-ring), composed of the FliG, FliM and FliN proteins. FliN and FliM contacts the FliG torque ring to control the direction of flagellar rotation. We report that structure-based models constrained only by residue coevolution can recover the binding interface of atomic X-ray dimer complexes with remarkable accuracy (approx. 1 Å RMSD)...
May 2018: Royal Society Open Science
Sanduo Zheng, Lok-To Sham, Frederick A Rubino, Kelly P Brock, William P Robins, John J Mekalanos, Debora S Marks, Thomas G Bernhardt, Andrew C Kruse
The peptidoglycan cell wall provides an essential protective barrier in almost all bacteria, defining cellular morphology and conferring resistance to osmotic stress and other environmental hazards. The precursor to peptidoglycan, lipid II, is assembled on the inner leaflet of the plasma membrane. However, peptidoglycan polymerization occurs on the outer face of the plasma membrane, and lipid II must be flipped across the membrane by the MurJ protein before its use in peptidoglycan synthesis. Due to its central role in cell wall assembly, MurJ is of fundamental importance in microbial cell biology and is a prime target for novel antibiotic development...
June 11, 2018: Proceedings of the National Academy of Sciences of the United States of America
P Praest, R D Luteijn, I G J Brak-Boer, J Lanfermeijer, H Hoelen, L Ijgosse, A I Costa, R D Gorham, R J Lebbink, E J H J Wiertz
Herpesviruses encode numerous immune evasion molecules that interfere with the immune system, particularly with certain stages in the MHC class I antigen presentation pathway. In this pathway, the transporter associated with antigen processing (TAP) is a frequent target of viral immune evasion strategies. This ER-resident transporter is composed of the proteins TAP1 and TAP2, and plays a crucial role in the loading of viral peptides onto MHC class I molecules. Several variants of TAP1 and TAP2 occur in the human population, some of which are linked to autoimmune disorders and susceptibility to infections...
June 4, 2018: Molecular Immunology
Helen M Southern, Mitchell A Berger, Philippe G Young, Rhonda R Snook
Sperm morphology is incredibly diverse, even among closely related species, yet the coevolution between males and females of fertilization recognition systems is necessary for successful karyogamy (male and female pronuclear fusion). In most species, the entire sperm enters the egg during fertilization so sperm morphological diversity may impact the intracellular sperm-egg interactions necessary for karyogamy. We quantified morphological variation of sperm inside eggs prior to and following karyogamy in several species of Drosophila to understand whether evolution of sperm morphology could influence intracellular sperm-egg interactions (ISEIs)...
May 2018: Ecology and Evolution
Abdelaziz Heddi, Anna Zaidman-Rémy
Some years ago, Lynn Margulis proposed to envision symbiosis as a source of evolutionary innovation. Here we revisit this concept in the context of insect nutritional endosymbiosis, and discuss recent data suggesting that host-endosymbiont coevolution has led to the selection of innovative strategies towards endosymbiont maintenance and control by the host immune system.
June 2, 2018: Comptes Rendus Biologies
Michał Rachalewski, Jarosław Kobak, Eliza Szczerkowska-Majchrzak, Karolina Bącela-Spychalska
Temperature is a crucial factor determining biology and ecology of poikilothermic animals. It often constitutes an important barrier for invasive species originating from different climate zones but, on the other hand, may facilitate the invasion process of animals with wide thermal preferences and high resistance to extreme temperatures. In our experimental study, we investigated the thermal behaviour of two Ponto-Caspian amphipod crustaceans- Dikerogammarus villosus and Dikerogammarus haemobaphes . Both species are known to live under a wide range of thermal conditions which may promote their invasion...
2018: PeerJ
Christoph Grüter, Evelien Jongepier, Susanne Foitzik
Insect societies face many social parasites that exploit their altruistic behaviours or their resources. Due to the fitness costs these social parasites incur, hosts have evolved various behavioural, chemical, architectural and morphological defence traits. Similar to bacteria infecting multicellular hosts, social parasites have to successfully go through several steps to exploit their hosts. Here, we review how social insects try to interrupt this sequence of events. They can avoid parasite contact by choosing to nest in parasite-free locales or evade attacks by adapting their colony structure...
July 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Chase G Mayers, Craig C Bateman, Thomas C Harrington
Meredithiella norrisii (Microascales, Ceratocystidaceae) is an ambrosia fungus carried in mycangia of the North American ambrosia beetle, Corthylus punctatissimus. Reports on the identity of the fungal symbionts of other species of Corthylus have been inconsistent. This study tested the hypothesis that Meredithiella spp. are the primary symbionts of Corthylus spp. Cultures and/or internal transcribed spacer (ITS) rDNA barcode sequences of Meredithiella spp. were obtained consistently from beetles and galleries of nine Corthylus spp...
January 2018: Mycologia
Michaela Drahosova, Lukas Sekanina, Michal Wiglasz
In genetic programming (GP), computer programs are often coevolved with training data subsets that are known as fitness predictors. In order to maximize performance of GP, it is important to find the most suitable parameters of coevolution, particularly the fitness predictor size. This is a very time consuming process as the predictor size depends on a given application and many experiments have to be performed to find its suitable size. A new method is proposed which enables us to automatically adapt the predictor and its size for a given problem and thus to reduce not only the time of evolution, but also the time needed to tune the evolutionary algorithm...
June 4, 2018: Evolutionary Computation
Sophie Sacquin-Mora
Protein function depends just as much on flexibility as on structure, and in numerous cases, a protein's biological activity involves transitions that will impact both its conformation and its mechanical properties. Here, we use a coarse-grain approach to investigate the impact of structural changes on protein flexibility. More particularly, we focus our study on proteins presenting large-scale motions. We show how calculating directional force constants within residue pairs, and investigating their variation upon protein closure, can lead to the detection of a limited set of residues that form a structural lock in the protein's closed conformation...
May 28, 2018: Journal of Structural Biology
Miguel Dos Santos, Stuart A West
Cooperative behaviours in archaic hunter-gatherers could have been maintained partly due to the gains from cooperation being shared with kin. However, the question arises as to how cooperation was maintained after early humans transitioned to larger groups of unrelated individuals. We hypothesize that after cooperation had evolved via benefits to kin, the consecutive evolution of cognition increased the returns from cooperating, to the point where benefits to self were sufficient for cooperation to remain stable when group size increased and relatedness decreased...
May 30, 2018: Proceedings. Biological Sciences
Maliheh Safari, Marilyn J Roossinck
There are many nonpathogenic viruses that are maintained in a persistent lifestyle in plants. Plant persistent viruses are widespread, replicating in their hosts for many generations. So far, Endornaviridae is the only family of plant persistent viruses with a single-stranded RNA genome, containing one large open reading frame. Bell pepper endornavirus (BPEV), Hot pepper endornavirus, Capsicum frutescens endornavirus 1 (CFEV 1) have been identified from peppers. Peppers are native to Central and South America and, as domesticated plants, human selection accelerated their evolution...
May 30, 2018: Molecular Plant-microbe Interactions: MPMI
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