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Directed Evolution

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https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#1
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538630/the-evolution-of-care-improves-outcome-in-blunt-thoracic-aortic-injury-a-western-trauma-association-multicenter-study
#2
Steven R Shackford, Casey E Dunne, Riyad Karmy-Jones, William Long, Desarom Teso, Martin A Schreiber, Justin Watson, Cheri Watson, Robert C McIntyre, Lisa Ferrigno, Mark L Shapiro, Kevin Southerland, Julie A Dunn, Paul Reckard, Thomas M Scalea, Megan Brenner, William A Teeter
BACKGROUND: The management of blunt thoracic aortic injury (BTAI) has evolved radically in the last decade with changes in the processes of care and the introduction of thoracic endovascular repair (TEVAR). These changes have wrought improved outcome, but the direct effect of TEVAR on outcome remains in question as previous studies have lacked vigorous risk adjustment and long-term follow-up. To address these knowledge gaps, we compared the outcomes of TEVAR, open surgical repair, and nonoperative management for BTAI...
May 22, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28535344/clarifying-the-controversial-catalytic-performance-of-co-oh-2-and-co3o4-for-oxygen-reduction-evolution-reactions-toward-efficient-zn-air-batteries
#3
Zhishuang Song, Xiaopeng Han, Yida Deng, Naiqin Zhao, Wenbin Hu, Cheng Zhong
Cobalt-based nanomaterials have been widely studied as catalysts for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) due to their remarkable bifunctional catalytic activity, low cost and easy available. However, controversial results concerning OER/ORR performance exist between different types of cobalt-based catalysts, especially for Co(OH)2 and Co3O4. To address this issue, we develop a facile electrochemical deposition method to grow Co(OH)2 directly on the skeleton of carbon cloth, and further Co3O4 was obtained by post thermal treatment...
May 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28535168/invited-commentary-evolution-of-social-networks-health-and-the-role-of-epidemiology
#4
Allison E Aiello
Almost 40 years ago, Berkman and Syme demonstrated that social networks were related to the risk of early mortality (Am J Epidemiol. 1979;109(2):186-204). Their study was highly innovative because they directly measured and quantified social networks in a large prospective population-based survey with mortality follow-up. The results of the study showed robust network gradients, whereby those with fewer networks and weaker social ties had significantly higher mortality rates. The important influence of social networks that Berkman and Syme noted many years ago is likely to heighten in the future, as demographic characteristics shift and individuals become more inclined to socialize through online platforms instead of real-world interactions...
May 23, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28534501/electronic-evidence-of-temperature-induced-lifshitz-transition-and-topological-nature-in-zrte5
#5
Yan Zhang, Chenlu Wang, Li Yu, Guodong Liu, Aiji Liang, Jianwei Huang, Simin Nie, Xuan Sun, Yuxiao Zhang, Bing Shen, Jing Liu, Hongming Weng, Lingxiao Zhao, Genfu Chen, Xiaowen Jia, Cheng Hu, Ying Ding, Wenjuan Zhao, Qiang Gao, Cong Li, Shaolong He, Lin Zhao, Fengfeng Zhang, Shenjin Zhang, Feng Yang, Zhimin Wang, Qinjun Peng, Xi Dai, Zhong Fang, Zuyan Xu, Chuangtian Chen, X J Zhou
The topological materials have attracted much attention for their unique electronic structure and peculiar physical properties. ZrTe5 has host a long-standing puzzle on its anomalous transport properties manifested by its unusual resistivity peak and the reversal of the charge carrier type. It is also predicted that single-layer ZrTe5 is a two-dimensional topological insulator and there is possibly a topological phase transition in bulk ZrTe5. Here we report high-resolution laser-based angle-resolved photoemission measurements on the electronic structure and its detailed temperature evolution of ZrTe5...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28534475/strain-engineering-of-monoclinic-domains-in-k-x-na1-x-nbo3-epitaxial-layers-a-pathway-to-enhanced-piezoelectric-properties
#6
Martin Schmidbauer, Dorothee Braun, Toni Markurt, Michael Hanke, Jutta Schwarzkopf
A novel concept to obtain a ferroelectric material with enhanced piezoelectric properties is proposed. This approach is based on the combination of two pathways: (i) the evolution of a ferroelectric monoclinic phase and, (ii) the coexistence of different types of ferroelectric domains leading to polarization discontinuities at the domain walls. Each of these pathways enables polarization rotation in the material which is responsible for giant piezoelectricity. Targeted incorporation of anisotropic epitaxial lattice strain is used to implement this approach...
May 23, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28533859/-a-particular-type-of-cicatricial-pemphigoid-with-unique-iga-deposit
#7
Amina Aounallah, Mariem Jrad, Mehdi Ksiaa, Sana Mokni, Wafa Saidi, Lobna Boussofara, Badreddine Sriha, Mohamed Denguezli, Najet Ghariani, Colandane Belajouza, Rafia Nouira
Cicatricial Pemphigoid is a subepithelial bullous dermatosis which essentially involves the mucous membranes with cicatricial evolution We report the case of a 66-year old patient hospitalized with erosive gingivitis associated with dysphagia, dyspnea and blurred vision. Dermatologic examination showed erosive lesions involving the palate and the pharynx. Ophthalmologic examination showed symblepharons, ectropion and bilateral cataract. Gingival biopsy revealed a necrotic detachment of the buccal epithelium...
2017: Pan African Medical Journal
https://www.readbyqxmd.com/read/28533467/the-current-and-future-state-of-animal-coloration-research
#8
REVIEW
John A Endler, Johanna Mappes
Animal colour patterns are a model system for understanding evolution because they are unusually accessible for study and experimental manipulation. This is possible because their functions are readily identifiable. In this final paper of the symposium we provide a diagram of the processes affecting colour patterns and use this to summarize their functions and put the other papers in a broad context. This allows us to identify significant 'holes' in the field that only become obvious when we see the processes affecting colour patterns, and their interactions, as a whole...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533068/in-vivo-kinetics-of-lipids-and-astaxanthin-evolution-in-haematococcus-pluvialis-mutant-under-15-co2-using-raman-microspectroscopy
#9
Ke Li, Jun Cheng, Qing Ye, Yong He, Junhu Zhou, Kefa Cen
In vivo spatiotemporal dynamics of lipids and astaxanthin evolution in Haematococcus pluvialis mutant induced with 15% CO2 and high light intensity were monitored with high spatial resolution in a non-destructive and label-free manner using single-cell Raman imaging. Astaxanthin intensity increased by 3.5 times within 12h under 15% CO2, and the accumulation rate was 5.8 times higher than that under air. Lipids intensity under 15% CO2 was 27% higher than that under air. The lipids initially concentrated in chloroplast under 15% CO2 due to an increase of directly photosynthetic fatty acid, which was different from the whole-cell dispersed lipids under air...
May 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28533064/strategies-for-design-of-improved-biocatalysts-for-industrial-applications
#10
REVIEW
Aravind Madhavan, Raveendran Sindhu, Parameswaran Binod, Rajeev K Sukumaran, Ashok Pandey
Biocatalysts are creating increased interest among researchers due to their unique properties. Several enzymes are efficiently produced by microorganisms. However, the use of natural enzymes as biocatalysts is hindered by low catalytic efficiency and stability during various industrial processes. Many advanced enzyme technologies have been developed to reshape the existing natural enzymes to reduce these limitations and prospecting of novel enzymes. Frequently used enzyme technologies include protein engineering by directed evolution, immobilisation techniques, metagenomics etc...
May 8, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28532521/animal-board-invited-review-sheep-birth-distribution-in-past-herds-a-review-for-prehistoric-europe-6th-to-3rd-millennia-bc
#11
M Balasse, A Tresset, A Bălăşescu, E Blaise, C Tornero, H Gandois, D Fiorillo, É Á Nyerges, D Frémondeau, E Banffy, M Ivanova
In temperate latitudes sheep have a seasonal reproductive behaviour, which imposes strong constraints on husbandry in terms of work organization and availability of animal products. During the last 50 years, researchers have focused on understanding the mechanisms driving small ruminants' reproduction cycles and finding ways to control them. This characteristic is inherited from their wild ancestor. However, the history of its evolution over the 10 millennia that separates present day European sheep from their Near Eastern ancestors' remains to be written...
May 23, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28531958/unique-postglacial-evolution-of-the-hornbeam-carpinus-betulus-l-in-the-carpathians-and-the-balkan-peninsula-revealed-by-chloroplast-dna
#12
Dragoş Postolache, Flaviu Popescu, Ladislav Paule, Dalibor Ballian, Peter Zhelev, Sorina Fărcaş, Juraj Paule, Ovidiu Badea
The Balkan Peninsula is one of the largest and most important European glacial refugia. However, the evolutionary history and phylogeographic pattern of temperate tree species that survived in the Balkans glacial refugia and their contribution to the genetic structure of the current population in the Carpathian Mountains remains poorly understood. Using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP), and extensive population sampling, we explored the phylogeographic pattern of Carpinus betulus in both the Balkan Peninsula and the Carpathian region...
May 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28531298/evolution-of-bacterial-virulence
#13
Médéric Diard, Wolf-Dietrich Hardt
Bacterial virulence is highly dynamic and context-dependent. For this reason, it is challenging to predict how molecular changes affect the growth of a pathogen in a host and its spread in host population. Two schools of thought have taken quite different directions to decipher the underlying principles of bacterial virulence. While molecular infection biology is focusing on the basic mechanisms of the pathogen-host interaction, evolution biology takes virulence as one of several parameters affecting pathogen spread in a host population...
May 22, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28531234/directed-evolution-to-improve-the-catalytic-efficiency-of-urate-oxidase-from-bacillus-subtilis
#14
Wenjie Li, Shouteng Xu, Biao Zhang, Yelin Zhu, Yan Hua, Xin Kong, Lianhong Sun, Jiong Hong
Urate oxidase is a key enzyme in purine metabolism and catalyzes the oxidation of uric acid to allantoin. It is used to treat hyperuricemia and gout, and also in a diagnostic kit. In this study, error-prone polymerase chain reaction and staggered extension process was used to generate a mutant urate oxidase with improved enzyme activity from Bacillus subtilis. After several rounds of mutagenesis and screening, two mutants 6E9 and 8E279 were obtained which exhibited 2.99 and 3.43 times higher catalytic efficiency, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28529469/a-comparative-genomics-approach-revealed-evolutionary-dynamics-of-microsatellite-imperfection-and-conservation-in-genus-gossypium
#15
Muhammad Mahmood Ahmed, Chao Shen, Anam Qadir Khan, Muhammad Atif Wahid, Muhammad Shaban, Zhongxu Lin
BACKGROUND: Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood. RESULTS: Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites...
2017: Hereditas
https://www.readbyqxmd.com/read/28528777/fcab-her2-interaction-a-m%C3%A3-nage-%C3%A3-trois-lessons-from-x-ray-and-solution-studies
#16
Elisabeth Lobner, Anne-Sophie Humm, Kathrin Göritzer, Georg Mlynek, Martin G Puchinger, Christoph Hasenhindl, Florian Rüker, Michael W Traxlmayr, Kristina Djinović-Carugo, Christian Obinger
The crystallizable fragment (Fc) of the immunoglobulin class G (IgG) is an attractive scaffold for the design of novel therapeutics. Upon engineering the C-terminal loops in the CH3 domains, Fcabs (Fc domain with antigen-binding sites) can be designed. We present the first crystal structures of Fcabs, i.e., of the HER2-binding clone H10-03-6 having the AB and EF loop engineered and the stabilized version STAB19 derived by directed evolution. Comparison with the crystal structure of the Fc wild-type protein reveals conservation of the overall domain structures but significant differences in EF-loop conformations...
May 18, 2017: Structure
https://www.readbyqxmd.com/read/28528702/detailed-characterization-of-mesenchymal-stem-stromal-cells-from-a-large-cohort-of-aml-patients-demonstrates-a-definitive-link-to-treatment-outcomes
#17
Rafael Diaz de la Guardia, Belen Lopez-Millan, Jessie R Lavoie, Clara Bueno, Julio Castaño, Maite Gómez-Casares, Susana Vives, Laura Palomo, Manel Juan, Julio Delgado, Maria L Blanco, Josep Nomdedeu, Alberto Chaparro, Jose Luis Fuster, Eduardo Anguita, Michael Rosu-Myles, Pablo Menéndez
Bone marrow mesenchymal stem/stromal cells (BM-MSCs) are key components of the hematopoietic niche thought to have a direct role in leukemia pathogenesis. BM-MSCs from patients with acute myeloid leukemia (AML) have been poorly characterized due to disease heterogeneity. We report a functional, genetic, and immunological characterization of BM-MSC cultures from 46 AML patients, stratified by molecular/cytogenetics into low-risk (LR), intermediate-risk (IR), and high-risk (HR) subgroups. Stable MSC cultures were successfully established and characterized from 40 of 46 AML patients irrespective of the risk subgroup...
May 18, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28527568/evolution-of-nuclear-receptors-and-ligand-signaling-toward-a-soft-key-lock-model
#18
Guillaume Holzer, Gabriel V Markov, Vincent Laudet
Nuclear receptors (NRs) are a family of ligand-regulated transcription factors that modulate a wide variety of physiological functions in a ligand-dependent manner. The first NRs were discovered as receptors of well-known hormones such as 17β-estradiol, corticosteroids, or thyroid hormones. In these cases a direct activation of the receptor transcriptional activity by a very specific ligand, with nanomolar affinity, was demonstrated, providing a strong conceptual framework to understand the mechanism of action of these hormones...
2017: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/28527465/super-and-sub-lorentzian-effects-in-the-ar-broadened-line-wings-of-hcl-gas
#19
Ha Tran, Gang Li, Volker Ebert, Jean-Michel Hartmann
Using previously recorded spectra of HCl diluted in Ar gas at room temperature for several pressure conditions, we show that the absorptions in between successive P and R transitions are significantly different from those predicted using purely Lorentzian line shapes. Direct theoretical predictions of the spectra are also made using requantized classical molecular dynamics simulations and an input HCl-Ar interaction potential. They provide the time evolution of the dipole auto-correlation function (DAF) whose Fourier-Laplace transform yields the absorption spectrum...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527415/trace-bromide-ion-impurity-leads-to-formation-of-chlorobromoaromatic-by-products-in-peroxymonosulfate-based-oxidation-of-chlorophenols
#20
Changling Fang, Zhaohui Wang, Min Feng, Ying Huang, Fei Yang, Jianshe Liu
Trace bromide (Br(-)) released from industrial effluents or brominated compounds is able to directly react with peroxymonosulfate (PMS) to generate a series of reactive oxidants which can oxidize and also halogenate organics. We report the identification and evolution of by-products during 2,4,6-trichlorophenol (TCP) degradation in the presence of PMS and trace Br(-). The influencing factors, including Br(-) concentration and pH, were investigated. The depletion of TCP was accelerated with increasing trace Br(-) concentration (0-0...
May 15, 2017: Chemosphere
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