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Parallel evolution

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https://www.readbyqxmd.com/read/28714990/an-approach-to-suppress-the-evolution-of-resistance-in-braf-v600e-mutant-cancer
#1
Yaohua Xue, Luciano Martelotto, Timour Baslan, Alberto Vides, Martha Solomon, Trang Thi Mai, Neelam Chaudhary, Greg J Riely, Bob T Li, Kerry Scott, Fabiola Cechhi, Ulrika Stierner, Kalyani Chadalavada, Elisa de Stanchina, Sarit Schwartz, Todd Hembrough, Gouri Nanjangud, Michael F Berger, Jonas Nilsson, Scott W Lowe, Jorge S Reis-Filho, Neal Rosen, Piro Lito
The principles that govern the evolution of tumors exposed to targeted therapy are poorly understood. Here we modeled the selection and propagation of an amplification in the BRAF oncogene (BRAF(amp)) in patient-derived tumor xenografts (PDXs) that were treated with a direct inhibitor of the kinase ERK, either alone or in combination with other ERK signaling inhibitors. Single-cell sequencing and multiplex fluorescence in situ hybridization analyses mapped the emergence of extra-chromosomal amplification in parallel evolutionary trajectories that arose in the same tumor shortly after treatment...
July 17, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28709327/spatially-periodic-deformations-in-planar-and-twisted-flexoelectric-nematic-layers
#2
M Buczkowska, G Derfel
Electric field induced deformations in twisted and untwisted planar layers of nematic liquid crystals possessing flexoelectric properties were investigated numerically. The spatially periodic deformations, taking the form of parallel stripes, were found to have smaller free energy than the homogeneous deformations. The structures of distorted layers as well as the evolution of deformations during changes of bias voltage were recognized. The role of flexoelectric properties was analyzed. Calculations taking into account the peculiar elastic properties of the bent-core nematics were also performed...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28706072/ravens-parallel-great-apes-in-flexible-planning-for-tool-use-and-bartering
#3
Can Kabadayi, Mathias Osvath
The ability to flexibly plan for events outside of the current sensory scope is at the core of being human and is crucial to our everyday lives and society. Studies on apes have shaped a belief that this ability evolved within the hominid lineage. Corvids, however, have shown evidence of planning their food hoarding, although this has been suggested to reflect a specific caching adaptation rather than domain-general planning. Here, we show that ravens plan for events unrelated to caching-tool-use and bartering-with delays of up to 17 hours, exert self-control, and consider temporal distance to future events...
July 14, 2017: Science
https://www.readbyqxmd.com/read/28702971/history-of-venous-leg-ulcers
#4
S Gianfaldoni, U Wollina, J Lotti, R Gianfaldoni, T Lotti, M G Roccia
To retrieve the history of venous ulcers and of skin lesions in general, we must go back to the appearance of human beings on earth. It is interesting to note that cutaneous injuries evolved parallel to human society. An essential first step in the pathogenesis of ulcers was represented by the transition of the quadruped man to Homo Erectus. This condition was characterized by a greater gravitational pressure on the lower limbs, with consequences on the peripheral venous system. Furthermore, human evolution was characterized by an increased risk of traumatic injuries, secondary to his natural need to create fire and hunt (e...
July 13, 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28702542/methanol-oxidation-on-stoichiometric-and-oxygen-rich-ruo2-110
#5
Rahul Rai, Jason F Weaver
We used temperature-programmed reaction spectroscopy (TPRS) to investigate the adsorption and oxidation of methanol on stoichiometric and O-rich RuO2(110) surfaces. We find that the complete oxidation of CH3OH is strongly preferred on stoichiometric RuO2(110) during TPRS for initial CH3OH coverages below ∼0.33 ML (monolayer), and that partial oxidation to mainly CH2O becomes increasingly favored with increasing CH3OH coverage from 0.33 to 1.0 ML. We present evidence that an adsorbed CH2O2 species serves as the key intermediate to complete oxidation and that CH2O2 formation is intrinsically facile but becomes limited by the availability of bridging O-atoms on stoichiometric RuO2(110) at initial CH3OH coverages above 0...
July 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28698367/structure-of-the-arabidopsis-topless-corepressor-provides-insight-into-the-evolution-of-transcriptional-repression
#6
Raquel Martin-Arevalillo, Max H Nanao, Antoine Larrieu, Thomas Vinos-Poyo, David Mast, Carlos Galvan-Ampudia, Géraldine Brunoud, Teva Vernoux, Renaud Dumas, François Parcy
Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as Arabidopsis thaliana, the most prominent corepressor is TOPLESS (TPL), which plays a key role in hormone signaling and development. Here we present the crystallographic structure of the Arabidopsis TPL N-terminal region comprising the LisH and CTLH (C-terminal to LisH) domains and a newly identified third region, which corresponds to a CRA domain. Comparing the structure of TPL with the mammalian TBL1, which shares a similar domain structure and performs a parallel corepressor function, revealed that the plant TPLs have evolved a new tetramerization interface and unique and highly conserved surface for interaction with repressors...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28696285/early-paleocene-landbird-supports-rapid-phylogenetic-and-morphological-diversification-of-crown-birds-after-the-k-pg-mass-extinction
#7
Daniel T Ksepka, Thomas A Stidham, Thomas E Williamson
Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known...
July 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28692677/fux-sim-implementation-of-a-fast-universal-simulation-reconstruction-framework-for-x-ray-systems
#8
Monica Abella, Estefania Serrano, Javier Garcia-Blas, Ines García, Claudia de Molina, Jesus Carretero, Manuel Desco
The availability of digital X-ray detectors, together with advances in reconstruction algorithms, creates an opportunity for bringing 3D capabilities to conventional radiology systems. The downside is that reconstruction algorithms for non-standard acquisition protocols are generally based on iterative approaches that involve a high computational burden. The development of new flexible X-ray systems could benefit from computer simulations, which may enable performance to be checked before expensive real systems are implemented...
2017: PloS One
https://www.readbyqxmd.com/read/28687650/parallel-evolution-of-two-clades-of-a-major-atlantic-endemic-vibrio-parahaemolyticus-pathogen-lineage-by-independent-acquisition-of-related-pathogenicity-islands
#9
Feng Xu, Narjol Gonzalez-Escalona, Kevin P Drees, Robert P Sebra, Vaughn S Cooper, Stephen H Jones, Cheryl A Whistler
Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased from locations with historically low disease incidence, such as the Northeast United States (US). This change coincided with a bacterial population shift towards human pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43 and ST636) to near-shore areas off the Atlantic coast of the Northeast US. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human pathogenic variant evolved independently through acquisition of distinct Vibrio pathogenicity islands (VPaI)...
July 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28687596/expression-and-light-dependent-translocation-of-%C3%AE-arrestin-in-the-visual-system-of-the-terrestrial-slug-limax-valentianus
#10
Ryota Matsuo, Yuka Takatori, Shun Hamada, Mitsumasa Koyanagi, Yuko Matsuo
Vertebrates, cephalopods, and arthropods are equipped with eyes having the highest spatiotemporal resolution among the animal phyla. In parallel, it is only the animals in these three phyla that have visual arrestin specialized for the termination of visual signaling triggered by opsin, in addition to ubiquitously expressed β-arrestin that serves in terminating general G protein-coupled receptor signaling. Indeed, visual arrestin in Drosophila and rodents translocates to the opsin-rich subcellular region in response to light to reduce the overall sensitivity of photoreceptors in an illuminated environment (i...
July 7, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28685945/evolutionary-changes-of-hox-genes-and-relevant-regulatory-factors-provide-novel-insights-into-mammalian-morphological-modifications
#11
Kui Li, Xiaohui Sun, Meixiu Chen, Yingying Sun, Ran Tian, Zhengfei Wang, Shixia Xu, Guang Yang
The diversity of body plan of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial, and aquatic habitats. However, the genetic basis of those phenotypic modifications, which occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head-tail axis of animal embryos and main regulatory factors (Mll, Bmi1, and E2f6) that control the expression of Hox genes...
July 7, 2017: Integrative Zoology
https://www.readbyqxmd.com/read/28679357/genome-scale-analysis-of-regulatory-protein-acetylation-enzymes-from-photosynthetic-eukaryotes
#12
R Glen Uhrig, Pascal Schläpfer, Devang Mehta, Matthias Hirsch-Hoffmann, Wilhelm Gruissem
BACKGROUND: Reversible protein acetylation occurring on Lys-N(e) has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) that catalyze the addition and removal of acetyl groups from target proteins. Estimates indicate that protein acetylation is second to protein phosphorylation in abundance, with thousands of acetylated sites now identified in different subcellular compartments...
July 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28675202/natural-product-analogues-towards-a-blueprint-for-analogue-focused-synthesis
#13
REVIEW
Magnus W P Bebbington
For the first time a general overview of approaches to the synthesis of natural product analogues is presented. This reflects a process of evolution of natural product synthesis which has accelerated in the years since the implementation of diversity-oriented synthesis, which has emerged in parallel with collective synthesis, diverted total synthesis and the preparation of truncated natural products optimised for biological activity. A method involving computational assessment for the validation of core-modified natural product analogues is discussed...
July 4, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28665809/the-rapid-evolution-of-molecular-genetic-diagnostics-in-neuromuscular-diseases
#14
Alexander E Volk, Christian Kubisch
PURPOSE OF REVIEW: The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. RECENT FINDINGS: MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs...
June 29, 2017: Current Opinion in Neurology
https://www.readbyqxmd.com/read/28665405/damage-tolerance-of-nuclear-graphite-at-elevated-temperatures
#15
Dong Liu, Bernd Gludovatz, Harold S Barnard, Martin Kuball, Robert O Ritchie
Nuclear-grade graphite is a critically important high-temperature structural material for current and potentially next generation of fission reactors worldwide. It is imperative to understand its damage-tolerant behaviour and to discern the mechanisms of damage evolution under in-service conditions. Here we perform in situ mechanical testing with synchrotron X-ray computed micro-tomography at temperatures between ambient and 1,000 °C on a nuclear-grade Gilsocarbon graphite. We find that both the strength and fracture toughness of this graphite are improved at elevated temperature...
June 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28660593/is-obesity-the-new-hypertension-parallels-in-the-evolution-of-obesity-and-hypertension-as-recognized-disease-states
#16
REVIEW
Devika Umashanker, Alpana P Shukla, Katherine H Saunders, Louis J Aronne
Obesity and hypertension are recognized disease states that share many similarities including complex physiology, therapeutic response to both lifestyle modification and pharmacotherapy, and the need for long-term management. Both were initially believed to be disorders of lifestyle rather than true disease entities, and initial efforts at developing medical and surgical therapies were criticized. Ultimately, both have proven to be amenable to treatments that control their underlying physiology. Both hypertension and obesity have complex pathophysiology involving multiple regulatory pathways that may require combination therapies in addition to lifestyle modification to reach therapeutic goals...
August 2017: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/28653624/parallel-evolution-of-influenza-across-multiple-spatiotemporal-scales
#17
Katherine S Xue, Terry Stevens-Ayers, Angela P Campbell, Janet A Englund, Steven A Pergam, Michael Boeckh, Jesse D Bloom
Viral variants that arise in the global influenza population begin as de novo mutations in single infected hosts, but the evolutionary dynamics that transform within-host variation to global genetic diversity are poorly understood. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population...
June 27, 2017: ELife
https://www.readbyqxmd.com/read/28649268/muscle-development-in-the-shark-scyliorhinus-canicula-implications-for-the-evolution-of-the-gnathostome-head-and-paired-appendage-musculature
#18
Janine M Ziermann, Renata Freitas, Rui Diogo
BACKGROUND: The origin of jawed vertebrates was marked by profound reconfigurations of the skeleton and muscles of the head and by the acquisition of two sets of paired appendages. Extant cartilaginous fish retained numerous plesiomorphic characters of jawed vertebrates, which include several aspects of their musculature. Therefore, myogenic studies on sharks are essential in yielding clues on the developmental processes involved in the origin of the muscular anatomy. RESULTS: Here we provide a detailed description of the development of specific muscular units integrating the cephalic and appendicular musculature of the shark model, Scyliorhinus canicula...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28646506/three-lessons-for-genetic-toxicology-from-baseball-analytics
#19
EDITORIAL
Stephen D Dertinger
In many respects the evolution of baseball statistics mirrors advances made in the field of genetic toxicology. From its inception, baseball and statistics have been inextricably linked. Generations of players and fans have used a number of relatively simple measurements to describe team and individual player's current performance, as well as for historical record-keeping purposes. Over the years, baseball analytics has progressed in several important ways. Early advances were based on deriving more meaningful metrics from simpler forerunners...
June 24, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28646326/transposable-elements-mediate-adaptive-debilitation-of-flagella-in-experimental-escherichia-coli-populations
#20
Gordon R Plague, Krystal S Boodram, Kevin M Dougherty, Sandar Bregg, Daniel P Gilbert, Hira Bakshi, Daniel Costa
Although insertion sequence (IS) elements are generally considered genomic parasites, they can mediate adaptive genetic changes in bacterial genomes. We discovered that among 12 laboratory-evolved Escherichia coli populations, three had experienced at least six different IS1-mediated deletions of flagellar genes. These deletions all involved the master flagellar regulator flhDC, and as such completely incapacitate motility. Two lines of evidence strongly suggest that these deletions were adaptive in our evolution experiment: (1) parallel evolution in three independent populations is highly unlikely just by chance, and (2) one of these deletion mutations swept to fixation within ~1000 generations, which is over two million times faster than expected if this deletion was instead selectively neutral and thus evolving by genetic drift...
June 2017: Journal of Molecular Evolution
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