Read by QxMD icon Read

in vitro evolution

Hui Mei, Jen-Yu Liao, Randi M Jimenez, Yajun Wang, Saikat Bala, Cailen McCloskey, Christopher Switzer, John C Chaput
In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection...
April 18, 2018: Journal of the American Chemical Society
Kirstin Gutekunst, Dörte Hoffmann, Ulrike Westernströer, Rüdiger Schulz, Dieter Garbe-Schönberg, Jens Appel
Cyanobacteria provide all components for sunlight driven biohydrogen production. Their bidirectional NiFe-hydrogenase is resistant against low levels of oxygen with a preference for hydrogen evolution. However, until now it was unclear if its catalytic efficiency can keep pace with the photosynthetic electron transfer rate. We identified NikKLMQO (sll0381-sll0385) as a nickel transporter, which is required for hydrogen production. ICP-MS measurements were used to quantify hydrogenase molecules per cell. We found 400 to 2000 hydrogenase molecules per cell depending on the conditions...
April 17, 2018: Scientific Reports
Sourav Dutta, K Bavya Devi, Sanjay Gupta, Biswanath Kundu, Vamsi Krishna Balla, Mangal Roy
In order to make magnesium (Mg) a successful candidate for fracture fixation devices, it is imperative to control the corrosion rate and enhance its elastic modulus. In the present work, we have prepared bioactive glass (BG) reinforced magnesium composite using spark plasma sintering (SPS). Simultaneous application of heat and pressure during SPS decreased the softening point of BG (600°C), allowing it to coat the Mg particles partially. As a result, BG was found along the Mg particle boundaries, which was confirmed by elemental mapping...
April 15, 2018: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Lyulin Hu, Sijie Ren, Qing Shen, Xingqian Ye, Jianchu Chen, Jiangang Ling
BACKGROUND: Roasted fish enjoys great popularity in Asia, but how roasting and subsequent digestion influence the oxidation and proteolysis of fish meat is unknown. This paper is aimed to investigate the effect of roasting time on lipid and protein oxidation and their evolution and consequence on proteolysis during simulated digestion of fish fillets. RESULTS: Several oxidation markers (TBARS, free thiols, total carbonyls and Schiff bases) were employed to assess the oxidation of fish...
April 15, 2018: Journal of the Science of Food and Agriculture
Julien Bernaud, Axel Rossi, Anny Fis, Lara Gardette, Ludovic Aillot, Hildegard Büning, Martin Castelnovo, Anna Salvetti, Cendrine Faivre-Moskalenko
Virus families have evolved different strategies for genome uncoating, which are also followed by recombinant vectors. Vectors derived from adeno-associated viruses (AAV) are considered as leading delivery tools for in vivo gene transfer, and in particular gene therapy. Using a combination of atomic force microscopy (AFM), biochemical experiments, and physical modeling, we investigated here the physical properties and stability of AAV vector particles. We first compared the morphological properties of AAV vectors derived from two different serotypes (AAV8 and AAV9)...
April 14, 2018: Journal of Biological Physics
Vojtech Hudzieczek, Radim Cegan, Tomas Cermak, Nela Bacovska, Zuzana Machalkova, Karel Dolezal, Lucie Plihalova, Daniel Voytas, Roman Hobza, Boris Vyskot
Silene latifolia serves as a model species to study dioecy, the evolution of sex chromosomes, dosage compensation and sex-determination systems in plants. Currently, no protocol for genetic transformation is available for this species, mainly because S. latifolia is considered recalcitrant to in vitro regeneration and infection with Agrobacterium tumefaciens. Using cytokinins and their synthetic derivatives, we markedly improved the efficiency of regeneration. Several agrobacterial strains were tested for their ability to deliver DNA into S...
April 12, 2018: New Biotechnology
Katja B Schilling, Jeffrey DeGrasse, Jacquelina W Woods
This study investigates the enrichment of aptamers targeting the norovirus protruding domain in the presence of foods often associated with norovirus outbreaks. The goal is to explore if and how the presence of food alters in vitro selection of aptamers and target binding of the enriched oligonucleotides. Our study demonstrates that the introduction of food to SELEX (systematic evolution of ligands by exponential enrichment) is either detrimental to enrichment of oligonucleotides with target-specific binding, or facilitates enrichment of non-target-specific oligonucleotides...
August 30, 2018: Food Chemistry
Chong-Yu Liao, Ying-Cai Feng, Gang Li, Xiao-Min Shen, Shi-Huo Liu, Wei Dou, Jin-Jun Wang
The citrus red mite, Panonychus citri , a major citrus pest distributed worldwide, has evolved severe resistance to various classes of chemical acaricides/insecticides including pyrethroids. It is well known that the resistance to pyrethroids is mainly caused by point mutations of voltage-gated sodium channel gene in a wide range of pests. However, increasing number of evidences support that pyrethroids resistance might also be resulted from the integrated mechanisms including metabolic mechanisms. In this study, firstly, comparative analysis of RNA-seq data showed that multiple detoxification genes, including a GSTs gene PcGSTd1 , were up-regulated in a fenpropathrin-resistant population compared with the susceptible strain (SS)...
2018: Frontiers in Physiology
Mario Mergelsberg, Valentin Egle, Matthias Boll
Xenobiotic phthalates are industrially produced on the annual million ton scale. The oxygen-independent enzymatic reactions involved in anaerobic phthalate degradation have only recently been elucidated. In vitro assays suggested that phthalate is first activated to phthaloyl-CoA followed by decarboxylation to benzoyl-CoA. Here, we report the heterologous production and characterization of the enzyme initiating anaerobic phthalate degradation from 'Aromatoleum aromaticum': a highly specific succinyl-CoA:phthalate CoA transferase (SPT, class III CoA transferase)...
April 12, 2018: Molecular Microbiology
Dalia Halawani, Valentin Gogonea, Joseph A DiDonato, Vitaliy Pipich, Peng Yao, Arnab China, Celalettin Topbas, Kommireddy Vasu, Abul Arif, Stanley L Hazen, Paul L Fox
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation...
April 11, 2018: Journal of Biological Chemistry
Honghu Sun, Jumei Zeng, Song Li, Pengkuan Liang, Chao Zheng, Yong Liu, Tao Luo, Nalin Rastogi, Qun Sun
Background: The interaction between different drug-resistant mutations is important to the development of drug resistance and its evolution. In this study, we aimed to reveal the potential relationships between mutations conferring resistance to two important antituberculosis drugs streptomycin (STR) and fluoroquinolones (FLQ). Materials and methods: We used an in vitro competitive fitness assay to reveal the interactions between different mutations of rpsL and gyrA in drug-resistant Mycobacterium smegmatis , followed by the analysis of the frequency of rpsL and gyrA mutation combinations in 213 STR-FLQ dual-resistant clinical Mycobacterium tuberculosis isolates from Sichuan region, which was also investigated by the whole genome data from 3,056 global clinical M...
2018: Infection and Drug Resistance
Pascal Röthlisberger, Marcel Hollenstein
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification...
April 4, 2018: Advanced Drug Delivery Reviews
S Papa, I Vismara, A Mariani, M Barilani, S Rimondo, M De Paola, N Panini, E Erba, E Mauri, F Rossi, G Forloni, L Lazzari, P Veglianese
Spinal cord injury (SCI) is an acute neurodegenerative disorder caused by traumatic damage of the spinal cord. The neuropathological evolution of the primary trauma involves multifactorial processes that exacerbate the pathology, worsening the neurodegeneration and limiting neuroregeneration. This complexity suggests that multi-therapeutic approaches, rather than any single treatment, might be more effective. Encouraging preclinical results indicate that stem cell-based treatments may improve the disease outcome due to their multi-therapeutic ability...
April 2, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
Eveline Staub, Hanna Marti, Roberta Biondi, Aurora Levi, Manuela Donati, Cory Ann Leonard, Serej D Ley, Trestan Pillonel, Gilbert Greub, Helena M B Seth-Smith, Nicole Borel
Chlamydia species have recently been recognized as emerging pathogens in snakes. However, isolation of novel snake chlamydiae is critical and their growth characteristics are largely unknown. In this study, two novel chlamydial species are described: Chlamydia serpentis and Chlamydia poikilothermis, isolated after attempts on 23 cloacal and choanal swabs from 18 PCR-positive captive snakes originating from different Swiss snake collections. Isolation success, growth curve and infectivity rates over a 48-hour time period were dependent on temperature (37 °C for C...
April 4, 2018: Scientific Reports
Daniel C Bailey, Evan Alexander, Matthew R Rice, Eric J Drake, Lisa S Mydy, Courtney C Aldrich, Andrew M Gulick
Aerobactin, a citryl-hydroxamate siderophore, is produced by a number of pathogenic Gram-negative bacteria to aid in iron assimilation. Interest in this well-known siderophore was reignited by recent investigations suggesting that it plays a key role in mediating the enhanced virulence of a hypervirulent pathotype of Klebsiella pneumoniae (hvKP). In contrast to classical opportunistic strains of Klebsiella pneumoniae, hvKP causes serious life-threatening infections in previously healthy individuals in the community...
April 4, 2018: Journal of Biological Chemistry
Huai Yao, Jiu-Ba Wen, Yi Xiong, Yan Lu, Marko Huttula
Being a biocompatible metal with similar mechanical properties as bones, magnesium bears both biodegradability suitable for bone substitution and chemical reactivity detrimental in bio-ambiences. To benefit its biomaterial applications, we developed Mg-2.0Zn-0.5Zr-3.0Gd (wt%) alloy through hot extrusion and tailored its biodegradability by just varying the extrusion temperatures during alloy preparations. The as-cast alloy is composed of the α-Mg matrix, a network of the fish-bone shaped and ellipsoidal (Mg, Zn)3 Gd phase, and a lamellar long period stacking ordered phase...
2018: Frontiers in Chemistry
Bernardo J Gomez-Fernandez, Eva Garcia-Ruiz, Javier Martin-Diaz, Patricia Gomez de Santos, Paloma Santos-Moriano, Francisco J Plou, Antonio Ballesteros, Monica Garcia, Marisa Rodriguez, Valeria A Risso, Jose M Sanchez-Ruiz, Spencer M Whitney, Miguel Alcalde
Rubisco is an ancient, catalytically conserved yet slow enzyme, which plays a central role in the biosphere's carbon cycle. The design of Rubiscos to increase agricultural productivity has hitherto relied on the use of in vivo selection systems, precluding the exploration of biochemical traits that are not wired to cell survival. We present a directed -in vitro- evolution platform that extracts the enzyme from its biological context to provide a new avenue for Rubisco engineering. Precambrian and extant form II Rubiscos were subjected to an ensemble of directed evolution strategies aimed at improving thermostability...
April 3, 2018: Scientific Reports
Mona Abed, Eliya Bitman-Lotan, Amir Orian
The ubiquitin and SUMO (small ubiquitin-like modifier) pathways modify proteins that in turn regulate diverse cellular processes, embryonic development, and adult tissue physiology. These pathways were originally discovered biochemically in vitro, leading to a long-standing challenge of elucidating both the molecular cross-talk between these pathways and their biological importance. Recent discoveries in Drosophila established that ubiquitin and SUMO pathways are interconnected via evolutionally conserved SUMO-targeted ubiquitin ligase (STUbL) proteins...
January 1, 2018: Journal of Developmental Biology
Nikita Pozdeyev, Laurie Gay, Ethan S Sokol, Ryan J Hartmaier, Kelsi E Deaver, Stephanie N Davis, Jena D French, Pierre Vanden Borre, Daniel V LaBarbera, Aik-Choon Tan, Rebecca E Schweppe, Lauren Fishbein, Jeffrey S Ross, Bryan R Haugen, Daniel W Bowles
PURPOSE: To define the genetic landscape of advanced differentiated and anaplastic thyroid cancer and identify genetic alterations of potential diagnostic, prognostic and therapeutic significance. EXPERIMENTAL DESIGN: The genetic profiles of 583 advanced differentiated and 196 anaplastic thyroid cancers (ATC) generated with targeted next-generation sequencing cancer-associated gene panels MSK-IMPACT and FoundationOne were analyzed. RESULTS: ATC had more genetic alterations per tumor, and pediatric papillary thyroid cancer had fewer genetic alterations per tumor when compared to other thyroid cancer types...
April 3, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Marco Werner, Thorsten Auth, Paul A Beales, Jean Baptiste Fleury, Fredrik Höök, Holger Kress, Reid C Van Lehn, Marcus Müller, Eugene P Petrov, Lev Sarkisov, Jens-Uwe Sommer, Vladimir A Baulin
Synthetic polymers, nanoparticles, and carbon-based materials have great potential in applications including drug delivery, gene transfection, in vitro and in vivo imaging, and the alteration of biological function. Nature and humans use different design strategies to create nanomaterials: biological objects have emerged from billions of years of evolution and from adaptation to their environment resulting in high levels of structural complexity; in contrast, synthetic nanomaterials result from minimalistic but controlled design options limited by the authors' current understanding of the biological world...
April 3, 2018: Biointerphases
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"