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Directed Evolution

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https://www.readbyqxmd.com/read/29155921/aridification-as-a-driver-of-biodiversity-a-case-study-for-the-cycad-genus-dioon-zamiaceae
#1
José Said Gutiérrez-Ortega, Takashi Yamamoto, Andrew P Vovides, Miguel Angel Pérez-Farrera, José F Martínez, Francisco Molina-Freaner, Yasuyuki Watano, Tadashi Kajita
Background and Aims: Aridification is considered a selective pressure that might have influenced plant diversification. It is suggested that plants adapted to aridity diversified during the Miocene, an epoch of global aridification (≈15 million years ago). However, evidence supporting diversification being a direct response to aridity is scarce, and multidisciplinary evidence, besides just phylogenetic estimations, is necessary to support the idea that aridification has driven diversification...
November 16, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29155461/nanoscale-trimetallic-metal-organic-frameworks-enable-efficient-oxygen-evolution-electrocatalysis
#2
Xiaoqing Huang
Metal-organic frameworks (MOFs) are a class of promising materials for diverse catalysis, but they are usually not directly employed for oxygen evolution electrocatalysis. Most reports focus on using MOFs as templates to in-situ create efficient electrocatalysts via annealing. Herein, we prepared a series of Fe/Ni/-based trimetallic MOFs (Fe/Ni/Co(Mn)-Material of Institute Lavoisier (MIL-53)) by solvothermal synthesis, which can be directly adopted as electrocatalysts. It was revealed that the Fe/Ni/Co(Mn)-MIL-53 exhibited volcano-type oxygen evolution reaction (OER) activity as a function of compositions...
November 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29154459/additive-genetic-variation-in-the-craniofacial-skeleton-of-baboons-genus-papio-and-its-relationship-to-body-and-cranial-size
#3
Jessica L Joganic, Katherine E Willmore, Joan T Richtsmeier, Kenneth M Weiss, Michael C Mahaney, Jeffrey Rogers, James M Cheverud
OBJECTIVES: Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (VP ) and additive genetic (VA ) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution? MATERIALS AND METHODS: We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs)...
November 20, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29153875/the-role-of-operating-parameters-and-oxidative-damage-mechanisms-of-advanced-chemical-oxidation-processes-in-the-combat-against-antibiotic-resistant-bacteria-and-resistance-genes-present-in-urban-wastewater
#4
REVIEW
I Michael-Kordatou, P Karaolia, D Fatta-Kassinos
An upsurge in the study of antibiotic resistance in the environment has been observed in the last decade. Nowadays, it is becoming increasingly clear that urban wastewater is a key source of antibiotic resistance determinants, i.e. antibiotic-resistant bacteria and antibiotic resistance genes (ARB&ARGs). Urban wastewater reuse has arisen as an important component of water resources management in the European Union and worldwide to address prolonged water scarcity issues. Especially, biological wastewater treatment processes (i...
October 27, 2017: Water Research
https://www.readbyqxmd.com/read/29151855/toward-a-mechanistic-understanding-of-vulnerability-to-hook-and-line-fishing-boldness-as-the-basic-target-of-angling-induced-selection
#5
Thomas Klefoth, Christian Skov, Anna Kuparinen, Robert Arlinghaus
In passively operated fishing gear, boldness-related behaviors should fundamentally affect the vulnerability of individual fish and thus be under fisheries selection. To test this hypothesis, we used juvenile common-garden reared carp (Cyprinus carpio) within a narrow size range to investigate the mechanistic basis of behavioral selection caused by angling. We focused on one key personality trait (i.e., boldness), measured in groups within ponds, two morphological traits (body shape and head shape), and one life-history trait (juvenile growth capacity) and studied mean standardized selection gradients caused by angling...
December 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29150706/application-of-directed-evolution-to-develop-ethanol-tolerant-oenococcus-oeni-for-more-efficient-malolactic-fermentation
#6
Alice L Betteridge, Krista M Sumby, Joanna F Sundstrom, Paul R Grbin, Vladimir Jiranek
Malolactic fermentation (MLF) is an important step in winemaking, which can be notoriously unreliable due to the fastidious nature of Oenococcus oeni. This study aimed to use directed evolution (DE) to produce a more robust strain of O. oeni having the ability to withstand high ethanol concentrations. DE involves an organism mutating and potentially adapting to a high stress environment over the course of extended cultivation. A continuous culture of O. oeni was established and exposed to progressively increasing ethanol content such that after approximately 330 generations, an isolate from this culture was able to complete MLF in high ethanol content medium earlier than its parent...
November 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29150513/high-prevalence-and-genetic-diversity-of-large-phicd211-phicdif1296t-like-prophages-in-clostridioides-difficile
#7
Julian R Garneau, Ognjen Sekulovic, Bruno Dupuy, Olga Soutourina, Marc Monot, Louis-Charles Fortier
Clostridioides difficile (formerly Clostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified in C. difficile so far, with a genome of 131-kbp. It shares morphological and genomic similarity with other large siphophages like phage 949 infecting Lactococcus lactis and phage c-st infecting Clostridium botulinum...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150502/hyperthermophilic-carbamate-kinase-stability-and-anabolic-in-vitro-activity-at-alkaline-ph
#8
James E Hennessy, Melissa J Latter, Somayeh Fazelinejad, Amy Philbrook, Daniel M Bartkus, Hye-Kyung Kim, Hideki Onagi, John G Oakeshott, Colin Scott, Apostolos Alissandratos, Christopher J Easton
Carbamate kinases catalyze the conversion of carbamate to carbamoyl phosphate, which is readily transformed into other compounds. Carbamate forms spontaneously from ammonia and carbon dioxide in aqueous solutions, so the kinases have potential for sequestrative utilization of the latter compounds. Here, we compare seven carbamate kinases from mesophilic, thermophilic and hyperthermophilic sources. In addition to the known enzymes from Enterococcus faecalis and Pyrococcus furiosus, the previously unreported enzymes from the hyperthermophiles Thermococcus sibiricus and Thermococcus barophilus, the thermophiles Fervidobacterium nodosum and Thermosipho melanesiensis, and the mesophile Clostridium tetani, were all expressed recombinantly, each in high yield...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149287/genomic-and-epigenomic-immunity-in-common-bean-the-unusual-features-of-nb-lrr-gene-family
#9
Manon M S Richard, Ariane Gratias, Vincent Thareau, Kyung Do Kim, Sandrine Balzergue, Johann Joets, Scott A Jackson, Valérie Geffroy
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149207/evolution-of-the-metabolome-in-response-to-selection-for-increased-immunity-in-populations-of-drosophila-melanogaster
#10
Navdeep Gogna, Rakesh Sharma, Vanika Gupta, Kavita Dorai, N G Prasad
We used NMR-based metabolomics to test two hypotheses-(i) there will be evolved differences in the metabolome of selected and control populations even under un-infected conditions and (ii) post infection, the metabolomes of the selected and control populations will respond differently. We selected replicate populations of Drosophila melanogaster for increased survivorship (I) against a gram-negative pathogen. We subjected the selected (I) and their control populations (S) to three different treatments: (1) infected with heat-killed bacteria (i), (2) sham infected (s), and (3) untreated (u)...
2017: PloS One
https://www.readbyqxmd.com/read/29148784/multistage-transformation-and-lattice-fluctuation-at-agcl-ag-interface
#11
Jingshan S Du, Jungwon Park, QHwan Kim, Wonho Jhe, Vinayak P Dravid, Deren Yang, David A Weitz
Solid-state transformation between different materials is often accompanied by mechanical expansion and compression due to their volume change and structural evolution at interfaces. However, these two types of dynamics are usually difficult to monitor in the same time. In this work, we use in situ transmission electron microscopy to directly study the reduction transformation at the AgCl-Ag interface. Three stages of lattice fluctuations were identified and correlated to the structural evolution. During the steady state, a quasi-layered growth mode of Ag in both vertical and lateral directions were observed due to the confinement of AgCl lattices...
November 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29148711/rational-manipulation-of-iro2-lattice-strain-on-%C3%AE-mno2-nanorods-as-a-highly-efficient-water-splitting-catalyst
#12
Wei Sun, Zhenhua Zhou, Waqas Qamar Zaman, Li-Mei Cao, Ji Yang
Developing more efficient and stable oxygen evolution reaction (OER) catalysts is critical for future energy conversion and storage technologies. We demonstrate that inducing a lattice strain in IrO2 crystal structure due to interface lattice mismatch enables an enhancement of the OER catalytic activity. The lattice strain is obtained by the direct growth of IrO2 nanoparticles on a specially exposed surface of α-MnO2 nanorods via a simple two-step hydrothermal synthesis. Interestingly, the prepared hydride OER activity increases with a lower IrO2 grown mass, which offers an opportunity to reduce the usage of precious iridium and ultimately obtains a specific mass activity of 3...
November 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29148703/bond-energy-driven-low-high-angle-grain-boundary-movement-mediated-porous-se-te-synthesis-for-water-splitting-reaction
#13
Anup Kumar Sasmal, Arpan Kumar Nayak, Prashant Kartikeya, Debabrata Pradhan, Tarasankar Pal
Herein, for the first time we applied metal-metal bond energy factor for the evolution of porous Se-Te alloy. Porous Se-Te material has been prepared from their elemental states only through heating-cooling process in silicone oil without using any reagent, surfactant or capping agent. Surprisingly the reaction occurred at much lower temperature (240 °C) than the m.p. (450 °C) of Te0. The nucleation and growth have been clarified by means of varied bond energy for the first time. Difference in bond energy between hetero metal-metal bond (Se-Te) and homo metal-metal (Se-Se) directs nucleation and growth towards the fabrication of porous structure even from their elemental state where low angle grain boundary (LAGB) and high angle grain boundary (HAGB) movements play their governing roles...
November 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29148573/phenotypic-and-genetic-integration-of-personality-and-growth-under-competition-in-the-sheepshead-swordtail-xiphophorus-birchmanni
#14
K Boulton, C A Walling, A J Grimmer, G G Rosenthal, A J Wilson
Competition for resources including food, physical space, and potential mates is a fundamental ecological process shaping variation in individual phenotype and fitness. The evolution of competitive ability, in particular social dominance, depends on genetic (co)variation among traits causal (e.g., behaviour) or consequent (e.g. growth) to competitive outcomes. If dominance is heritable, it will generate both direct and indirect genetic effects (IGE) on resource dependent traits. The latter are expected to impose evolutionary constraint because winners necessarily gain resources at the expense of losers...
November 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29146727/primary-intraventricular-haemorrhage-due-to-rupture-of-giant-varix-of-the-basal-vein-of-rosenthal-in-a-patient-with-long-standing-direct-ccf-angiographic-features-and-treatment-considerations
#15
Chinmay P Nagesh, Aneesh Mohimen, Santhosh K Kannath, Jayadevan E Rajan
Direct carotid cavernous fistulae (CCF) are often detected early and treated promptly resulting in a paucity of literature regarding its long-term evolution. We present a case of high flow post-traumatic direct CCF that was neglected for over 6 years and presented with a rare manifestation of primary intraventricular haemorrhage. Occlusions of the primary venous outlets likely resulted in engorgement of the deep venous system. The segmental anatomy of the shunting basal vein is critical to the clinical presentation and may range from basal ganglia or brainstem oedema/infarctions to uniquely, as in our case, isolated intraventricular haemorrhage secondary to variceal rupture...
November 16, 2017: BMJ Case Reports
https://www.readbyqxmd.com/read/29146397/temporal-evolution-of-the-environmental-performance-of-implementing-selective-collection-in-municipal-waste-management-systems-in-developing-countries-a-brazilian-case-study
#16
Valeria Ibáñez-Forés, María D Bovea, Claudia Coutinho-Nóbrega, Hozana R de Medeiros-García, Raissa Barreto-Lins
The aim of this study is to analyse the evolution of the municipal solid waste management system of João Pessoa (Brazil), which was one of the Brazilian pioneers cities in implementing door-to-door selective collection programmes, in order to analyse the effect of policy decisions adopted in last decade with regard to selective collection. To do it, this study focuses on analysing the evolution, from 2005 to 2015, of the environmental performance of the municipal solid waste management (MSWM) system implemented in different sorting units with selective collection programmes by applying the Life Cycle Assessment (LCA) methodology and using as a starting point data collected directly from the different stakeholders involved in the MSWM system...
November 13, 2017: Waste Management
https://www.readbyqxmd.com/read/29146250/revitalization-of-plant-growth-promoting-rhizobacteria-for-sustainable-development-in-agriculture
#17
REVIEW
Sushanto Gouda, Rout George Kerry, Gitishree Das, Spiros Paramithiotis, Han-Seung Shin, Jayanta Kumar Patra
The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29145803/unraveling-the-evolution-and-coevolution-of-small-regulatory-rnas-and-coding-genes-in-listeria
#18
Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145727/directly-observing-micelle-fusion-and-growth-in-solution-by-liquid-cell-transmission-electron-microscopy
#19
Lucas R Parent, Evangelos Bakalis, Abelardo Ramírez-Hernández, Jacquelin K Kammeyer, Chiwoo Park, Juan de Pablo, Francesco Zerbetto, Joseph P Patterson, Nathan C Gianneschi
Amphiphilic small molecules and polymers form commonplace nanoscale macromolecular compartments and bilayers, and as such are truly essential components in all cells and in many cellular processes. The nature of these architectures, including their formation, phase changes, and stimuli-response behaviors, is necessary for the most basic functions of life, and over the past half-century, these natural micellar structures have inspired a vast diversity of industrial products, from biomedicines to detergents, lubricants, and coatings...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29145480/engineering-the-gh1-%C3%AE-glucosidase-from-humicola-insolens-insights-on-the-stimulation-of-activity-by-glucose-and-xylose
#20
Luana Parras Meleiro, José Carlos Santos Salgado, Raquel Fonseca Maldonado, Sibeli Carli, Luiz Alberto Beraldo Moraes, Richard John Ward, João Atílio Jorge, Rosa Prazeres Melo Furriel
The activity of the GH1 β-glucosidase from Humicola insolens (Bglhi) against p-nitrophenyl-β-D-glucopyranoside (pNP-Glc) and cellobiose is enhanced 2-fold by glucose and/or xylose. Kinetic and transglycosylation data showed that hydrolysis is preferred in the absence of monosaccharides. Stimulation involves allosteric interactions, increased transglycosylation and competition of the substrate and monosaccharides for the -1 glycone and the +1/+2 aglycone binding sites. Protein directed evolution has been used to generate 6 mutants of Bglhi with altered stimulation patterns...
2017: PloS One
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