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https://www.readbyqxmd.com/read/28742933/gene-expression-is-more-strongly-influenced-by-age-than-caste-in-the-ant-lasius-niger
#1
Eric R Lucas, Jonathan Romiguier, Laurent Keller
Phenotypic plasticity, where a single genome can give rise to different phenotypes, underlies many remarkable features of the natural world and occurs in a wide range of organisms. Understanding the transcriptional differences that underlie plastic phenotypes remains a major unsolved problem in biology. In many ants, females can develop into either queens or workers, two phenotypes with different morphology, behaviour and longevity. In comparison to workers, queens are larger, more fecund and longer-lived. Here, we study gene expression differences between queens and workers in the ant Lasius niger...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742346/molecular-dynamics-of-double-stranded-xylo-nucleic-acid-xylona
#2
Amutha Ramaswamy, Daryna Smyrnova, Mattheus Froeyen, Mohitosh Maiti, Piet Herdewijn, Arnout Ceulemans
Xylo-nucleic acid (XyloNA) is a synthetic analogue of ribo-nucleic acid (RNA), where the ribose sugar has been replaced by xylose. We present a Molecular Dynamics study of the conformational evolution of XyloNA double strand oligomers derived from A-RNA through the substitution of beta-ᴅ-ribofuranose by beta-ᴅ-xylofuranose and having lengths of 8, 16 and 29 base pairs, using a set of independent all-atom simulations performed at various time scales ranging from 55 to 100 ns, , with one long 500 ns simulation of the 29-mer...
July 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28742046/a-fast-algorithm-for-analysis-of-molecular-communication-in-artificial-synapse
#3
Bilgesu A Bilgin, Ozgur B Akan
In this paper we analyse molecular communications (MC) in a proposed artificial synapse (AS), whose main difference from biological synapses (BSs) is that it is closed, i.e., transmitter molecules cannot diffuse out from AS. Such a setup has both advantages and disadvantages. Besides higher structural stability, being closed, AS never runs out of transmitters. Thus, MC in AS is disconnected from outer environment, which is very desirable for possible intra-body applications. On the other hand, clearance of transmitters from AS has to be achieved by transporter molecules on the presynaptic membrane of AS...
July 21, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28741177/birth-birth-death-processes-and-their-computable-transition-probabilities-with-biological-applications
#4
Lam Si Tung Ho, Jason Xu, Forrest W Crawford, Vladimir N Minin, Marc A Suchard
Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for evaluating finite-time transition probabilities of bivariate processes, however, has restricted statistical inference in these models. Researchers rely on computationally expensive methods such as matrix exponentiation or Monte Carlo approximation, restricting likelihood-based inference to small systems, or indirect methods such as approximate Bayesian computation...
July 24, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28741165/history-and-conceptual-developments-in-vascular-biology-and-angiogenesis-research-a-personal-view
#5
REVIEW
Andreas Bikfalvi
Vascular biology is an important scientific domain that has gradually penetrated many medical and scientific fields. Scientists are most often focused on present problems in their daily scientific work and lack awareness regarding the evolution of their domain throughout history and of how philosophical issues are related to their research field. In this article, I provide a personal view with an attempt to conceptualize vascular development research that articulates lessons taken from history, philosophy, biology and medicine...
July 24, 2017: Angiogenesis
https://www.readbyqxmd.com/read/28740497/the-role-of-multiscale-protein-dynamics-in-antigen-presentation-and-t-lymphocyte-recognition
#6
R Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V Coveney
T lymphocytes are stimulated when they recognize short peptides bound to class I proteins of the major histocompatibility complex (MHC) protein, as peptide-MHC complexes. Due to the diversity in T-cell receptor (TCR) molecules together with both the peptides and MHC proteins they bind to, it has been difficult to design vaccines and treatments based on these interactions. Machine learning has made some progress in trying to predict the immunogenicity of peptide sequences in the context of specific MHC class I alleles but, as such approaches cannot integrate temporal information and lack explanatory power, their scope will always be limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28740486/evolution-of-acinetobacter-baumannii-in-vivo-international-clone-ii-more-resistance-to-ceftazidime-mutation-in-ptk
#7
Xiaoting Hua, Zhihui Zhou, Qing Yang, Qiucheng Shi, Qingye Xu, Jianfeng Wang, Keren Shi, Feng Zhao, Long Sun, Zhi Ruan, Yan Jiang, Yunsong Yu
Acinetobacter baumannii is an important nosocomial pathogen worldwide. A more comprehensive understanding of the within-host genomic evolution of A. baumannii would provide a molecule basis for improving treatment of A. baumannii infection. To understand the evolutionary mechanism facilitating A. baumannii survived in human body, we here reported the genomic analysis of A. baumannii isolated sampled from Chinese patients. We used whole-genome sequence of A. baumannii isolates from the same patient to determine single-nucleotide variants, insertion sequence mapping, and gene change...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28739370/molecular-systematics-species-delimitation-and-diversification-patterns-of-the-phyllodactylus-lanei-complex-gekkota-phyllodactylidae-in-mexico
#8
Tonatiuh Ramírez-Reyes, Daniel Piñero, Oscar Flores-Villela, Ella Vázquez-Domínguez
The description of cryptic gecko species worldwide has revealed both that many putative species are, in fact, conformed by a complex of morphologically conserved species that are genetically distinct and highly divergent, and that gecko species diversity could be underestimated. The taxonomy and species delimitation of geckos belonging to the genus Phyllodactylus is still controversial, 16 of which are distributed in Mexico and 13 are endemic. Although the large morphological variation shown by the Phyllodactylus species from Mexico has been amply documented, little is known about their genetic diversity and evolutionary relationships, and much less regarding cryptic speciation...
July 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28739369/genomic-regression-of-claw-keratin-taste-receptor-and-light-associated-genes-provides-insights-into-biology-and-evolutionary-origins-of-snakes
#9
Christopher A Emerling
Regressive evolution of anatomical traits often corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The evolutionary origins of snakes involved the regression of a number of anatomical traits, including limbs, taste buds and the visual system, and by analyzing serpent genomes, I was able to test three hypotheses associated with the regression of these features...
July 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28738772/molecular-docking-and-drug-discovery-in-%C3%AE-adrenergic-receptors
#10
Santiago Vilar, Eduardo Sobarzo-Sánchez, Lourdes Santana, Eugenio Uriarte
Evolution in computer engineering, availability of increasing amounts of data and the development of new and fast docking algorithms and software have led to improved molecular simulations with crucial applications in virtual high-throughput screening and drug discovery. Moreover, analysis of protein-ligand recognition through molecular docking has become a valuable tool in drug design. In this review, we focus on the applicability of molecular docking on a particular class of G protein-coupled receptors: the β-adrenergic receptors, which are relevant targets in clinic for the treatment of asthma and cardiovascular diseases...
July 24, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28737038/evolution-of-aggregate-structure-in-solutions-of-anionic-monorhamnolipids-experimental-and-computational-results
#11
Ryan J Eismin, Elango Munusamy, Laurel L Kegel, David E Hogan, Raina M Maier, Steven D Schwartz, Jeanne E Pemberton
The evolution of solution aggregates of the anionic form of the native monorhamnolipid (mRL) mixture produced by Pseudomonas aeruginosa ATCC 9027 is explored at pH 8.0 using both experimental and computational approaches. Experiments utilizing surface tension measurements, dynamic light scattering, and both steady-state and time-resolved fluorescence spectroscopy reveal solution aggregation properties. All-atom molecular dynamics simulations on self-assemblies of the most abundant monorhamnolipid molecule, l-rhamnosyl-β-hydroxydecanoyl-β-hydroxydecanoate (Rha-C10-C10), in its anionic state explore the formation of aggregates and the role of hydrogen bonding, substantiating the experimental results...
July 24, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28735504/low-genetic-diversity-and-functional-constraint-of-mirna-genes-participating-pollen-pistil-interaction-in-rice
#12
Kun Wang, Xin Wang, Ming Li, Tao Shi, Pingfang Yang
In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield. Pollen-pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen-pistil interaction in rice and how they evolve under this conserved process...
July 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28734070/genome-scans-on-experimentally-evolved-populations-reveal-candidate-regions-for-adaptation-to-plant-resistance-in-the-potato-cyst-nematode-globodera-pallida
#13
D Eoche-Bosy, M Gautier, M Esquibet, F Legeai, A Bretaudeau, O Bouchez, S Fournet, E Grenier, J Montarry
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of the present study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734049/development-of-aptamers-against-unpurified-proteins
#14
Shinichi Goto, Kaori Tsukakoshi, Kazunori Ikebukuro
SELEX (Systematic Evolution of Ligands by EXponential enrichment) has been widely used for the generation of aptamers against target proteins. However, its requirement for pure target proteins remains a major problem in aptamer selection, as procedures for protein purification from crude bio-samples are not only complicated but also time and labour consuming. This is because native proteins can be found in a large number of diverse forms because of posttranslational modifications and their complicated molecular conformations...
July 22, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28733783/perianth-organs-in-nymphaeaceae-comparative-study-on-epidermal-and-structural-characters
#15
Lucía Melisa Zini, Beatriz Gloria Galati, María Silvia Ferrucci
The perianth organs of six species of Nymphaeaceae, representing Euryale, Nymphaea and Victoria, were studied on the basis of macroscopical, micromorphological, and anatomical characters. The aims were to determine whether perianth is differentiated among tepal whorls considering the presence of sepaloid and petaloid characters, and to evaluate the occurrence of both features in individual tepals. Selected perianth series were examined macroscopically, with light microscopy, and scanning electron microscopy...
July 21, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28733625/electronic-structure-of-polyethylene-role-of-chemical-morphological-and-interfacial-complexity
#16
Lihua Chen, Tran Doan Huan, Rampi Ramprasad
The electronic structure of an insulator encodes essential signatures of its short-term electrical performance and long-term reliability. A critical long-standing challenge though is that key features of the electronic structure of an insulator (and its evolution) under realistic conditions have not been entirely accessible, either via experimental or computational approaches, due to the inherent complexities involved. In this comprehensive study, we reveal the role of chemical and morphological imperfections that inevitably exist within the technologically important prototypical and pervasive insulator, polyethylene (PE), and at electrode/PE interfaces...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733620/adaptive-evolution-of-a-hyperthermophilic-archaeon-pinpoints-a-formate-transporter-as-a-critical-factor-for-the-growth-enhancement-on-formate
#17
Hae-Chang Jung, Seong Hyuk Lee, Sung-Mok Lee, Young Jun An, Jung-Hyun Lee, Hyun Sook Lee, Sung Gyun Kang
Previously, we reported that the hyperthermophilic archaeon Thermococcus onnurineus NA1 could grow on formate and produce H2. Formate conversion to hydrogen was mediated by a formate-hydrogen lyase complex and was indeed a part of chemiosmotic coupling to ATP generation. In this study, we employed an adaptation approach to enhance the cell growth on formate and investigated molecular changes. As serial transfer continued on formate-containing medium at the serum vial, cell growth, H2 production and formate consumption increased remarkably...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733194/breast-cancer-molecular-stratification-from-intrinsic-subtypes-to-integrative-clusters
#18
REVIEW
Hege G Russnes, Ole Christian Lingjærde, Anne-Lise Børresen-Dale, Carlos Caldas
Breast carcinomas can be stratified into different entities based on clinical behavior, histological features and/or by biological properties. A classification of breast cancer should be based on underlying biology, which we know must be determined by the somatic genomic landscape of mutations. Moreover, as the latest generations of anti-cancer agents are founded on biological mechanisms, a detailed molecular stratification is a requirement for appropriate clinical management. Such stratification, based on genomic drivers, will be important for selecting patients for clinical trials...
July 18, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28731826/convergently-evolved-toxic-secondary-metabolites-in-plants-drive-the-parallel-molecular-evolution-of-insect-resistance
#19
Georg Petschenka, Vera Wagschal, Michael von Tschirnhaus, Alexander Donath, Susanne Dobler
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae)...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731798/most-colorful-example-of-genetic-assimilation-exploring-the-evolutionary-destiny-of-recurrent-phenotypic-accommodation
#20
Alexander V Badyaev, Ahva L Potticary, Erin S Morrison
Evolution of adaptation requires both generation of novel phenotypic variation and retention of a locally beneficial subset of this variation. Such retention can be facilitated by genetic assimilation, the accumulation of genetic and molecular mechanisms that stabilize induced phenotypes and assume progressively greater control over their reliable production. A particularly strong inference into genetic assimilation as an evolutionary process requires a system where it is possible to directly evaluate the extent to which an induced phenotype is progressively incorporated into preexisting developmental pathways...
August 2017: American Naturalist
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