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Directed Evolution

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https://www.readbyqxmd.com/read/28634300/understanding-the-mechanical-response-of-double-stranded-dna-and-rna-under-constant-stretching-forces-using-all-atom-molecular-dynamics
#1
Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633937/our-teacher-likes-you-so-i-like-you-a-social-network-approach-to-social-referencing
#2
Marloes M H G Hendrickx, Tim Mainhard, Henrike J Boor-Klip, Mieke Brekelmans
A teacher is a social referent for peer liking and disliking when students adjust their evaluations of a peer based on their perceptions of teacher liking and disliking for this peer. The present study investigated social referencing as an intra-individual process that occurs over time, using stochastic actor-oriented modeling with RSiena. The co-evolution of peer-perceived teacher liking and disliking networks with peer liking and disliking networks was analyzed in 52 fifth-grade classes in the Netherlands, with 1370 students (Mage=10...
August 2017: Journal of School Psychology
https://www.readbyqxmd.com/read/28633473/experimental-evolution-and-the-adjustment-of-metabolic-strategies-in-lactic-acid-bacteria
#3
Herwig Bachmann, Douwe Molenaar, Filipe Branco Dos Santos, Bas Teusink
Experimental evolution of microbes has gained lots of interest in recent years, mainly due to the ease of strain characterisation through next-generation sequencing. While evolutionary and systems biologists use experimental evolution to address fundamental questions in their respective fields, studies with lactic acid bacteria are often more directed by applied questions. Insight into population and genome dynamics are valuable for experimental design and data interpretation, and it is becoming increasingly apparent how different constraints limit and govern the outcome of microbial adaptation to a selective environment...
June 19, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28633349/colchicine-application-significantly-affects-plant-performance-in-the-second-generation-of-synthetic-polyploids-and-its-effects-vary-between-populations
#4
Zuzana Münzbergová
Background and Aims: Understanding the direct consequences of polyploidization is necessary for assessing the evolutionary significance of this mode of speciation. Previous studies have not studied the degree of between-population variation that occurs due to these effects. Although it is assumed that the effects of the substances that create synthetic polyploids disappear in second-generation synthetic polyploids, this has not been tested. Methods: The direct consequences of polyploidization were assessed and separated from the effects of subsequent evolution in Vicia cracca , a naturally occurring species with diploid and autotetraploid cytotypes...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28632147/crossover-iliofemoral-bypass-graft-through-tension-free-abdominal-wall-repair-mesh
#5
Mircea Muresan, Ovidiu Jimborean, Gabriela Jimborean, Radu Neagoe, Serban Bancu, Muresan Simona, Cristian Borz
INTRODUCTION: In vascular surgery the crossover iliofemoral bypass grafting is a well-known surgical technique. In general surgery the repair of an abdominal defect using a Polypropylene mesh is also a standard procedure. A particular technique is defined by the performance of these 2 separate procedures inside a single operation in which the crossover arterial graft is directed from the retroperitoneal space toward the contra-lateral femoral bifurcation through a Polypropylene mesh which closes the musculoaponeurotic layers of the abdominal wall...
June 8, 2017: Annali Italiani di Chirurgia
https://www.readbyqxmd.com/read/28631535/high-resolution-magnetic-resonance-imaging-for-exposing-facial-nerve-zonal-vulnerability-to-microbleeds-a-rare-cause-of-facial-palsy
#6
Charlie Chia-Tsong Hsu, Dalveer Singh, Trevor William Watkins, Gigi Nga Chi Kwan, Sachintha Hapugoda
Background We report a case of hypertensive microbleeds strategically located at the attached segment (AS) and root entry zone (REZ) at the left facial nerve causing facial paralysis. Case Report A 60-year-old woman presented with sudden onset left facial paralysis. Medical history was significant for poorly controlled hypertension secondary to bilateral adrenal hyperplasia (primary hyperaldosteronism). The patient was initially treated for presumptive Bell's palsy. Subsequent magnetic resonance imaging of the brain and internal auditory canal showed two microbleeds at the left cerebellopontine angle...
January 1, 2017: Neuroradiology Journal
https://www.readbyqxmd.com/read/28630909/dynamic-fracture-of-tantalum-under-extreme-tensile-stress
#7
Bruno Albertazzi, Norimasa Ozaki, Vasily Zhakhovsky, Anatoly Faenov, Hideaki Habara, Marion Harmand, Nicholas Hartley, Denis Ilnitsky, Nail Inogamov, Yuichi Inubushi, Tetsuya Ishikawa, Tetsuo Katayama, Takahisa Koyama, Michel Koenig, Andrew Krygier, Takeshi Matsuoka, Satoshi Matsuyama, Emma McBride, Kirill Petrovich Migdal, Guillaume Morard, Haruhiko Ohashi, Takuo Okuchi, Tatiana Pikuz, Narangoo Purevjav, Osami Sakata, Yasuhisa Sano, Tomoko Sato, Toshimori Sekine, Yusuke Seto, Kenjiro Takahashi, Kazuo Tanaka, Yoshinori Tange, Tadashi Togashi, Kensuke Tono, Yuhei Umeda, Tommaso Vinci, Makina Yabashi, Toshinori Yabuuchi, Kazuto Yamauchi, Hirokatsu Yumoto, Ryosuke Kodama
The understanding of fracture phenomena of a material at extremely high strain rates is a key issue for a wide variety of scientific research ranging from applied science and technological developments to fundamental science such as laser-matter interaction and geology. Despite its interest, its study relies on a fine multiscale description, in between the atomic scale and macroscopic processes, so far only achievable by large-scale atomic simulations. Direct ultrafast real-time monitoring of dynamic fracture (spallation) at the atomic lattice scale with picosecond time resolution was beyond the reach of experimental techniques...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630465/changes-in-pore-structure-of-coal-caused-by-coal-to-gas-bioconversion
#8
Rui Zhang, Shimin Liu, Jitendra Bahadur, Derek Elsworth, Yi Wang, Guanglong Hu, Yanna Liang
Microbial enhanced coalbed methane (ME-CBM) recovery is critically examined as a viable technology for natural gas recovery from coalbed methane (CBM) reservoirs. Since the majority of gas-in-place (GIP) is stored as an adsorbed phase in fine pores of coal matrix, the nano-pore structure directly influences gas storage and transport properties. Only limited studies have quantified the alteration of the nano-pore structure due to ME-CBM treatment. This study examines the evolution of the pore structure using a combination of small angle X-ray scattering (SAXS), low-pressure N2 and CO2 adsorption (LPGA) and high-pressure methane adsorption methods...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628526/determinants-of-hiv-1-cd4-independent-brain-adaptation
#9
Madina Shakirzyanova, Xiang-Peng Kong, Cecilia Cheng-Mayer
BACKGROUND: HIV-1 is known to adapt to the local environment in its usage of receptors and it can become CD4 independent in the brain where the receptor is scarce. This adaptation is through amino acid variations, but the patterns of such variation are not yet well understood. Given that infection of long-lived CD4-low and CD4-negative cells in anatomic compartments such as the brain expand cell tropism in vivo and may serve as potential viral reservoirs that pose challenge for HIV eradication, understanding the evolution to CD4-independence and envelope conformation associated with infection in the absence of CD4 will not only broaden our insights into HIV pathogenesis, but may guide functional cure strategies as well...
June 15, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28628253/3d-atomic-scale-insights-into-anisotropic-core-shell-structured-ingaas-nanowires-grown-by-metal-organic-chemical-vapor-deposition
#10
Jiangtao Qu, Sichao Du, Tim Burgess, Changhong Wang, Xiangyuan Cui, Qiang Gao, Weichao Wang, Hark Hoe Tan, Hui Liu, Chennupati Jagadish, Yingjie Zhang, Hansheng Chen, Mansoor Khan, Simon Ringer, Rongkun Zheng
III-V ternary InGaAs nanowires have great potential for electronic and optoelectronic device applications; however, the 3D structure and chemistry at the atomic-scale inside the nanowires remain unclear, which hinders tailoring the nanowires for specific applications. Here, atom probe tomography is used in conjunction with a first-principles simulation to investigate the 3D structure and chemistry of InGaAs nanowires, and reveals i) the nanowires form a spontaneous core-shell structure with a Ga-enriched core and an In-enriched shell, due to different growth mechanisms in the axial and lateral directions; ii) the shape of the core evolves from hexagon into Reuleaux triangle and grows larger, which results from In outward and Ga inward interdiffusion occurring at the core-shell interface; and iii) the irregular hexagonal shell manifests an anisotropic growth rate on {112}A and {112}B facets...
June 19, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28627786/the-north-african-middle-stone-age-and-its-place-in-recent-human-evolution
#11
Eleanor M L Scerri
The North African Middle Stone Age (NAMSA, ∼300-24 thousand years ago, or ka) features what may be the oldest fossils of our species as well as extremely early examples of technological regionalization and 'symbolic' material culture (d'Errico, Vanhaeren, Barton, Bouzouggar, Mienis, Richter, Hublin, McPherron, Louzouet, & Klein, ; Scerri, ; Richter, Grün, Joannes-Boyau, Steele, Amani, Rué, Fernandes, Raynal, Geraads, Ben-Ncer Hublin, McPherron, ). The geographic situation of North Africa and an increased understanding of the wet-dry climatic pulses of the Sahara Desert also show that North Africa played a strategic role in continental-scale evolutionary processes by modulating human dispersal and demographic structure (Drake, Blench, Armitage, Bristow, & White, ; Blome, Cohen, Tryon, Brooks, & Russell, )...
May 2017: Evolutionary Anthropology
https://www.readbyqxmd.com/read/28627727/development-of-hgf-binding-aptamers-with-the-combination-of-g4-promoter-derived-aptamer-selection-and-in-silico-maturation
#12
Tomomi Yokoyama, Kaori Tsukakoshi, Wataru Yoshida, Taiki Saito, Kentaro Teramoto, Nasa Savory, Koichi Abe, Kazunori Ikebukuro
We describe the selection of aptamers based on bioinformatics-based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR-amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer-screening method, G4 promoter-derived aptamer selection (G4PAS), and an aptamer-improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively...
June 19, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28627135/in-situ-electrochemistry-of-rechargeable-battery-materials-status-report-and-perspectives
#13
REVIEW
Yijun Yang, Xizheng Liu, Zhonghua Dai, Fangli Yuan, Yoshio Bando, Dmitri Golberg, Xi Wang
The development of rechargeable batteries with high performance is considered to be a feasible way to satisfy the increasing needs of electric vehicles and portable devices. It is of vital importance to design electrodes with high electrochemical performance and to understand the nature of the electrode/electrolyte interfaces during battery operation, which allows a direct observation of the complicated chemical and physical processes within the electrodes and electrolyte, and thus provides real-time information for further design and optimization of the battery performance...
June 19, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28626973/role-of-parasite-transmission-in-promoting-inbreeding-ii-pedigree-reconstruction-reveals-sib-transmission-and-consequent-kin-mating
#14
Jillian T Detwiler, Charles D Criscione
Even though parasitic flatworms are one of the most species rich groups of hermaphroditic organisms, we know virtually nothing of their mating systems (selfing or kin-mating rates) in nature. Hence, we lack an understanding of the role of inbreeding in parasite evolution. The natural mating systems of parasitic flatworms have remained elusive due to the inherent difficulty in generating progeny-array data in many parasite systems. New developments in pedigree reconstruction allow direct inference of realized selfing rates in nature by simply using a sample of genotyped individuals...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626938/role-of-parasite-transmission-in-promoting-inbreeding-i-infection-intensities-drive-individual-parasite-selfing-rates
#15
Jillian T Detwiler, Isabel C Caballero, Charles D Criscione
Among parasitic organisms, inbreeding has been implicated as a potential driver of host-parasite coevolution, drug-resistance evolution, and parasite diversification. Yet, fundamental topics about how parasite life histories impact inbreeding remain to be addressed. In particular, there are no direct selfing-rate estimates for hermaphroditic parasites in nature. Our objectives were to elucidate the mating system of a parasitic flatworm in nature and to understand how aspects of parasite transmission could influence the selfing rates of individual parasites...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28625482/equalizing-the-information-amounts-of-protein-and-mrna-by-information-theory
#16
Y Adiguzel
Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein...
June 15, 2017: Bio Systems
https://www.readbyqxmd.com/read/28624475/oxidoreductases-on-their-way-to-industrial-biotransformations
#17
REVIEW
Angel T Martínez, Francisco J Ruiz-Dueñas, Susana Camarero, Ana Serrano, Dolores Linde, Henrik Lund, Jesper Vind, Morten Tovborg, Owik M Herold-Majumdar, Martin Hofrichter, Christiane Liers, René Ullrich, Katrin Scheibner, Giovanni Sannia, Alessandra Piscitelli, Cinzia Pezzella, Mehmet E Sener, Sibel Kılıç, Willem J H van Berkel, Victor Guallar, Maria Fátima Lucas, Ralf Zuhse, Roland Ludwig, Frank Hollmann, Elena Fernández-Fueyo, Eric Record, Craig B Faulds, Marta Tortajada, Ib Winckelmann, Jo-Anne Rasmussen, Mirjana Gelo-Pujic, Ana Gutiérrez, José C Del Río, Jorge Rencoret, Miguel Alcalde
Fungi produce heme-containing peroxidases and peroxygenases, flavin-containing oxidases and dehydrogenases, and different copper-containing oxidoreductases involved in the biodegradation of lignin and other recalcitrant compounds. Heme peroxidases comprise the classical ligninolytic peroxidases and the new dye-decolorizing peroxidases, while heme peroxygenases belong to a still largely unexplored superfamily of heme-thiolate proteins. Nevertheless, basidiomycete unspecific peroxygenases have the highest biotechnological interest due to their ability to catalyze a variety of regio- and stereo-selective monooxygenation reactions with H2O2 as the source of oxygen and final electron acceptor...
June 14, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28623609/administration-of-direct-oral-anticoagulants-in-patients-with-myeloproliferative-neoplasms
#18
Jean-Christophe Ianotto, Marie-Anne Couturier, Hubert Galinat, Dominique Mottier, Christian Berthou, Gaëlle Guillerm, Eric Lippert, Aurélien Delluc
Direct oral anticoagulants (DOACs) have been approved to treat and prevent thrombotic events. However, they are not yet labeled for use in patients with active cancers. Myeloproliferative neoplasms (MPNs) are clonal chronic disorders with a high incidence of thrombotic events, for which low-dose aspirin (LDA) is the standard drug treatment. We analyzed efficacy and safety of DOACs prescription in patients treated for MPNs. An MPN database, the OBENE registry, was established at our institution. We collected biological and clinical data from diagnosis to last follow-up for every patient included in this study...
June 16, 2017: International Journal of Hematology
https://www.readbyqxmd.com/read/28623580/selex-seq-a-method-to-determine-dna-binding-specificities-of-plant-transcription-factors
#19
Cezary Smaczniak, Gerco C Angenent, Kerstin Kaufmann
Systematic evolution of ligands by exponential enrichment (SELEX) is a method that allows isolating specific nucleotide sequences that interact with a DNA binding protein of choice. By using a transcription factor (TF) and a randomized pool of double-stranded DNA, this technique can be used to characterize TF DNA binding specificities and affinities. The method is based on protein-DNA complex immunoprecipitation with protein-specific antibodies and subsequent DNA selection and amplification. Application of massively parallel sequencing (-seq) at each cycle of SELEX allows determining the relative affinities to any DNA sequence for any transcription factor or TF complex...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623234/a-ciliary-opsin-in-the-brain-of-a-marine-annelid-zooplankton-is-uv-sensitive-and-the-sensitivity-is-tuned-by-a-single-amino-acid-residue
#20
Hisao Tsukamoto, I-Shan Chen, Yoshihiro Kubo, Yuji Furutani
Ciliary opsins were classically thought to function only in vertebrates for vision, but they have been recently identified also in invertebrates for non-visual photoreception. Larvae of the annelid Platynereis dumerilii are used as a zooplankton model, and this zooplankton species possesses a "vertebrate-type" ciliary opsin (named c-opsin) in the brain. Platynereis c-opsin is suggested to relay light signals to melatonin production and circadian behaviors. Thus, the spectral and biochemical characteristics of this c-opsin would be directly related to non-visual photoreception in this zooplankton model...
June 16, 2017: Journal of Biological Chemistry
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