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Parallel evolution

James J Hsieh, Emily H Cheng
With the ever-increasing complexity of tumor heterogeneity (TH) discovered through cancer genome sequencing, it is apparent that TH has become the biggest hurdle for precision cancer therapeutics. Through studying the genomics of exceptional responders to targeted therapeutic agents in kidney cancer, we demonstrated parallel convergent gene/pathway/capability/function evolution of kidney cancer in the context of TH, which prompted us to propose a new cancer evolution model "the braided cancer river model". Based on this model, we might be able to outsmart a given cancer type within an individual patient through simultaneously inhibiting preferred parallel pathways or sequential nodes...
December 2016: Clinical and Translational Medicine
Xiaoyuan Du, Xia Wang, Su Wang, Yang Zhou, Yu Zhang, Shicui Zhang
Our understanding of the function of vitellogenin (Vg) in reproduction has undergone a transformation over the past decade in parallel with new insights into the role of Vg in immunity. However, the time when Vg was endowed with immunological activities during animal evolution remains elusive. Here we demonstrate for the first time that the recombinant proteins rVitellogenin_N, rDUF1943, and rVWD from Vg of the basal metazoan coral Euphyllia ancora not only interact with Gram-positive and negative bacteria as well as their conserved surface components LTA and LPS but also enhance phagocytosis of bacteria by macrophages...
October 17, 2016: Developmental and Comparative Immunology
Elisabeth Wiig, Janne E Reseland, Kjartan Østbye, Håvard J Haugen, Leif A Vøllestad
INTRODUCTION: It is important to understand the drivers leading to adaptive phenotypic diversity within and among species. The threespine stickleback (Gasterosteus aculeatus) has become a model system for investigating the genetic and phenotypic responses during repeated colonization of fresh waters from the original marine habitat. During the freshwater colonization process there has been a recurrent and parallel reduction in the number of lateral bone plates, making it a suitable system for studying adaptability and parallel evolution...
2016: PloS One
Cristina M Crava, Sukania Ramasamy, Lino Ometto, Gianfranco Anfora, Omar Rota-Stabelli
Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D...
October 19, 2016: G3: Genes—Genomes—Genetics
Maria Zhivagui, Michael Korenjak, Jiri Zavadil
Mutation spectra in cancer genomes provide information on the disease aetiology and the causality underlying the evolution and progression of cancer. Genome-wide mutation patterns reflect the effects of mutagenic insults and can thus reveal past carcinogen-specific exposures and inform hypotheses on the causative factors for specific cancer types. In order to identify mutation profiles in human cancers, single genes studies were first employed, focusing mainly on the tumour suppressor gene TP53. Furthermore, experimental studies had been developed in model organisms...
October 18, 2016: Basic & Clinical Pharmacology & Toxicology
Sumul A Gandhi, Jeremy T Kampp
BACKGROUND: Dermatologic surgery requires precision and accuracy given the delicate nature of procedures performed. The use of the most appropriate instrument for each action helps optimize both functionality and cosmetic outcome. OBJECTIVE: To review the history of surgical instruments used in dermatology, with a focus on mechanism and evolution to the instruments that are used in current practice. MATERIALS AND METHODS: A comprehensive literature search was conducted via textbook and journal research for historic references while review of current references was conducted online using multiple search engines and PubMed...
October 4, 2016: Dermatologic Surgery: Official Publication for American Society for Dermatologic Surgery [et Al.]
Yuan-Yuan Li, Zhen Liu, Fei-Yan Qi, Xin Zhou, Peng Shi
Molecular basis for mammalian echolocation has been receiving much concerns. Recent findings on the parallel evolution of prestin sequences among echolocating bats and toothed whales suggest that adaptations for high-frequency hearing have occurred during the evolution of echolocation. Here, we report that although the species tree for echolocating bats emitting echolocation calls with frequency modulated (FM) sweeps is paraphyletic, prestin exhibits similar functional changes between FM bats. Site-directed mutagenesis shows that the amino acid 308S in FM bats is responsible for the similar functional changes of prestin We strongly support that the occurrence of serine at position 308 is a case of hemiplasy, caused by incomplete lineage sorting of an ancestral polymorphism...
October 15, 2016: Molecular Biology and Evolution
Majid Ahmadlouydarab, Chuanjin Lan, Arup Kumar Das, Yanbao Ma
While there are intensive studies on the coalescence of sessile macroscale droplets, there is little study on the coalescence of sessile microdroplets. In this paper, the coalescence process of two sessile microdroplets is studied by using a many-body dissipative particle dynamics numerical method. A comprehensive parametric study is conducted to investigate the effects on the coalescence process from the wettability gradient, hydrophilicity of the solid surface, and symmetric or asymmetric configurations. A water bridge is formed after two microdroplets contact...
September 2016: Physical Review. E
Mikko Pentinsaari, Heli Salmela, Marko Mutanen, Tomas Roslin
DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function...
October 13, 2016: Scientific Reports
Nathalie Feiner
Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes...
October 12, 2016: Proceedings. Biological Sciences
David T Tzou, Manint Usawachintachit, Kazumi Taguchi, Thomas Chi
Ultrasound has become a mainstay tool in urologists' armamentarium for the diagnosis and management of nephrolithiasis. From starting as a rudimentary form of imaging, it has come to play a more prominent role over time, paralleling evolution in ultrasound technology. Throughout the medical community there is a growing emphasis on reducing the amount of ionizing radiation delivered to patients during routine imaging. As such there has been a resurgence of interest in ultrasound given its lack of associated radiation exposure and proven effectiveness as a diagnostic and therapeutic imaging modality...
October 12, 2016: Journal of Endourology
Zhun Liu, Ru-Zhi Wang, Peter Zapol
Elucidation of homoepitaxial growth mechanisms on vicinal non-polar surfaces of GaN is highly important for gaining an understanding of and control thin film surface morphology and properties. Using first-principles calculations, we study the step-flow growth in m-plane GaN based on atomic row nucleation and kink propagation kinetics. Ga-N dimer adsorption onto the m-plane is energetically more favorable than that of Ga and N isolated adatoms. Therefore, we have treated the dimers as the dominant growth species attached to the step edges...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
Carlos Montemuiño, Antonio Espinosa, Juan C Moure, Gonzalo Vera, Porfidio Hernández, Sebastián Ramos-Onsins
The msParSm application is an evolution of msPar, the parallel version of the coalescent simulation program ms, which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, without compromising the accuracy of the standard coalescence. This work introduces msParSm, describes its significant performance improvements over msPar and its shared memory parallelization details, and shows how it can get better, if not similar, execution times than MaCS. Two case studies with different mutation rates were analyzed, one approximating the human average and the other approximating the Drosophila melanogaster average...
2016: Evolutionary Bioinformatics Online
Subhash Rajpurohit, Robert Hanus, Vladimír Vrkoslav, Emily L Behrman, Alan O Bergland, Dmitri Petrov, Josef Cvačka, Paul S Schmidt
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field...
October 8, 2016: Journal of Evolutionary Biology
Zofia M Sikorska-Piwowska, Antoni L Dawidowicz
The authors examined a large random sample of skulls from two species of macaques: rhesus monkeys and cynomolgus monkeys. The skulls were measured, divided into age and sex groups and thoroughly analysed using statistical methods. The analysis shows that skulls of young rhesuses are considerably more domed, i.e. have better-developed neurocrania, than their adult counterparts. Male and female skulls, on the other hand, were found to be very similar, which means that sexual dimorphism of the rhesus macaque was suppressed...
October 7, 2016: Folia Morphologica (Warsz)
S García Ballesteros, M Costante, R Vicente, M Mora, A M Amat, A Arques, L Carlos, F S García Einschlag
In this work, analysis of excitation-emission-matrices (EEM) has been employed to gain further insight into the characterization of humic like substances (HLS) obtained from urban wastes (soluble bio-organic substances, SBOs). In particular, complexation of these substances with iron and changes along a photo-Fenton process have been studied. Recorded EEMs were decomposed by using parallel factor analysis (PARAFAC). Three fluorescent components were identified by PARAFAC modeling of the entire set of SBO solutions studied...
September 29, 2016: Photochemical & Photobiological Sciences
Santiago Jose Cartamil-Bueno, Peter Gerard Steeneken, Alba Centeno, Amaia Zurutuza, Herre S J van der Zant, Samer Houri
Previous statistical studies on the mechanical properties of chemical-vapor-deposited (CVD) suspended graphene membranes have been performed by means of measuring individual devices or with techniques that affect the material. Here, we present a colorimetry technique as a parallel, non-invasive, and affordable way of characterizing suspended graphene devices. We exploit Newton's rings interference patterns to study the deformation of a double-layer graphene drum 13.2 μm in diameter when a pressure step is applied...
October 6, 2016: Nano Letters
Marie-Therese Nödl, Alexandra Kerbl, Manfred G Walzl, Gerd B Müller, Heinz Gert de Couet
BACKGROUND: Cephalopods are a highly derived class of molluscs that adapted their body plan to a more active and predatory lifestyle. One intriguing adaptation is the modification of the ventral foot to form a bilaterally symmetric arm crown, which constitutes a true morphological novelty in evolution. In addition, this structure shows many diversifications within the class of cephalopods and therefore offers an interesting opportunity to study the molecular underpinnings of the emergence of phenotypic novelties and their diversification...
2016: Frontiers in Zoology
Jasper J Koehorst, Edoardo Saccenti, Peter J Schaap, Vitor A P Martins Dos Santos, Maria Suarez-Diez
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method...
2016: F1000Research
Bryan D Clifton, Pablo Librado, Shu-Dan Yeh, Edwin Solares, Daphne Real, Suvini Jayasekera, Wanting Zhang, Mijuan Shi, Ronni Park, Robert Magie, Hsiu-Ching Ma, Xiao-Qin Xia, Antonio Marco, Julio Rozas, José M Ranz
Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition...
October 3, 2016: Molecular Biology and Evolution
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