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in vitro evolution

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https://www.readbyqxmd.com/read/28645146/analysis-of-in-vitro-evolution-reveals-the-underlying-distribution-of-catalytic-activity-among-random-sequences
#1
Abe Pressman, Janina E Moretti, Gregory W Campbell, Ulrich F Müller, Irene A Chen
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645099/harnessing-the-natural-diversity-and-in-vitro-evolution-of-cas9-to-expand-the-genome-editing-toolbox
#2
REVIEW
Tautvydas Karvelis, Giedrius Gasiunas, Virginijus Siksnys
In the past few years, the Cas9 endonuclease from the type II CRISPR-Cas bacterial antiviral defense system has revolutionized the genome editing field. Guided by an RNA molecule, Cas9 can be reprogrammed to target almost any DNA sequence: the only limitation being the short nucleotide sequence in the vicinity of the target, termed the PAM, which is characteristic for each Cas9 protein. Streptococcus pyogenes Cas9 which recognizes the NGG PAM is currently most widely used for genome manipulation. However, Cas9 orthologues and engineered Cas9 variants offer expanded genome targeting capabilities, improved specificity and biochemical properties...
June 20, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28642484/mir-100-5p-inhibition-induces-apoptosis-in-dormant-prostate-cancer-cells-and-prevents-the-emergence-of-castration-resistant-prostate-cancer
#3
Noushin Nabavi, Nur Ridzwan Nur Saidy, Erik Venalainen, Anne Haegert, Abhijit Parolia, Hui Xue, Yuwei Wang, Rebecca Wu, Xin Dong, Colin Collins, Francesco Crea, Yuzhuo Wang
Carcinoma of the prostate is the most common cancer in men. Treatment of aggressive prostate cancer involves a regiment of radical prostectomy, radiation therapy, chemotherapy and hormonal therapy. Despite significant improvements in the last decade, the treatment of prostate cancer remains unsatisfactory, because a significant fraction of prostate cancers develop resistance to multiple treatments and become incurable. This prompts an urgent need to investigate the molecular mechanisms underlying the evolution of therapy-induced resistance of prostate cancer either in the form of castration-resistant prostate cancer (CRPC) or transdifferentiated neuroendocrine prostate cancer (NEPC)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28632925/a-kallikrein-targeting-rna-aptamer-inhibits-the-intrinsic-pathway-of-coagulation-and-reduces-bradykinin-release
#4
K-A Steen-Burrell, J Layzer, B A Sullenger
BACKGROUND: Plasma kallikrein is a serine protease that plays an integral role in many biological processes including coagulation, inflammation, and fibrinolysis. The main function of kallikrein in coagulation is the amplification of activated factor XIIa (FXIIa) generation which ultimately leads to thrombin generation and fibrin clot formation. Kallikrein is generated by FXIIa-mediated cleavage of the zymogen, prekallikrein which is usually complexed with the nonenzymatic cofactor, high-molecular-weight kininogen (HK)...
June 20, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28629043/carbon-quantum-dots-from-carbonized-walnut-shells-structural-evolution-fluorescence-characteristics-and-intracellular-bioimaging
#5
Chaoge Cheng, Yanni Shi, Min Li, Malcolm Xing, Qilin Wu
Carbon quantum dots (CQDs) have attracted tremendous attention for their prominent fluorescence, excellent stability, and outstanding biocompatibility. Herein, we report a facile method to prepare CQDs from walnut shells, which mainly consist of natural cellulose. After carbonization of the walnut shells and acid treatments, zigzag and armchair edges of CQDs with an average size of 3.4nm were revealed by the high-resolution transmission electron microscopy. Consistent with the (100) planes of graphitic carbon, the lattice spacing distance of these CQDs was 0...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28628615/flipping-chromosomes-in-deep-sea-archaea
#6
Matteo Cossu, Catherine Badel, Ryan Catchpole, Danièle Gadelle, Evelyne Marguet, Valérie Barbe, Patrick Forterre, Jacques Oberto
One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements...
June 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28622386/alpha-defensin-dependent-enhancement-of-enteric-viral-infection
#7
Sarah S Wilson, Beth A Bromme, Mayumi K Holly, Mayim E Wiens, Anshu P Gounder, Youngmee Sul, Jason G Smith
The small intestinal epithelium produces numerous antimicrobial peptides and proteins, including abundant enteric α-defensins. Although they most commonly function as potent antivirals in cell culture, enteric α-defensins have also been shown to enhance some viral infections in vitro. Efforts to determine the physiologic relevance of enhanced infection have been limited by the absence of a suitable cell culture system. To address this issue, here we use primary stem cell-derived small intestinal enteroids to examine the impact of naturally secreted α-defensins on infection by the enteric mouse pathogen, mouse adenovirus 2 (MAdV-2)...
June 16, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28616970/the-structure-and-biocompabibility-of-bioabsorbable-nanocomposites-of-aliphatic-aromatic-co-polyester-and-cellulose-nanocrystals
#8
Shahab Kashani Rahimi, Robabeh Aeinehvand, Kyoungtae Kim, Joshua U Otaigbe
Poly(butylene adipate-co-terephthalate) (PBAT) was first chemically modified via free radical grafting with maleic anhydride (MA) and the MA-g-PBAT graft copolymer was then used as a matrix material to obtain cellulose nanocrystal (CNC)-reinforced MA-g-PBAT bio-nanocomposites via reactive extrusion process to accelerate efforts to develop functional bioabsorbable polymer nanocomposites with improved properties. The molecular structure of the PBAT after chemical modification with maleic anhydride was confirmed by 1H NMR and FTIR spectroscopy...
June 15, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28609429/reciprocal-evolution-of-opiate-science-from-medical-and-cultural-perspectives
#9
George B Stefano, Nastazja Pilonis, Radek Ptacek, Richard M Kream
Over the course of human history, it has been common to use plants for medicinal purposes, such as for providing relief from particular maladies and self-medication. Opium represents one longstanding remedy that has been used to address a range of medical conditions, alleviating discomfort often in ways that have proven pleasurable. Opium is a combination of compounds obtained from the mature fruit of opium poppy, papaver somniferum. Morphine and its biosynthetic precursors thebaine and codeine constitute the main bioactive opiate alkaloids contained in opium...
June 13, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28608421/polydopamine-mediated-assembly-of-hydroxyapatite-nanoparticles-and-bone-morphogenetic-protein-2-on-magnesium-alloys-for-enhanced-corrosion-resistance-and-bone-regeneration
#10
Yanan Jiang, Bi Wang, Zhanrong Jia, Xiong Lu, Liming Fang, Kefeng Wang, Fuzeng Ren
Magnesium alloys have the great potential to be used as orthopaedic implants due to their biodegradability and mechanical resemblance to human cortical bone. However, the rapid degradation in physiological environment with the evolution of hydrogen gas release hinders their clinical applications. In this study, we developed a novel functional and biocompatible coating strategy through polydopamine mediated assembly of hydroxyapatite nanoparticles and growth factor, bone morphogenetic protein-2 (BMP-2), onto the surface of AZ31 Mg alloys...
June 12, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28597984/dual-inhibition-of-bdnf-trkb-and-autophagy-a-promising-therapeutic-approach-for-colorectal-cancer
#11
Clément Mazouffre, Sophie Geyl, Aurélie Perraud, Sabrina Blondy, Marie-Odile Jauberteau, Muriel Mathonnet, Mireille Verdier
Colorectal cancer (CRC) is the most common digestive cancer in the Western world. Despite effective therapies, resistance and/or recurrence frequently occur. The present study investigated the impact of two survival pathways-neurotrophic factors (TrkB/BDNF) and autophagy-on cell fate and tumour evolution. In vitro studies were performed on two CRC cell lines, SW480 (primary tumour) and SW620 (lymph node invasion), which were also used for subcutaneous xenografts on a nude mouse model. In addition, the presence of neurotrophic factors (NTs) and autophagy markers were assessed in tissue samples representative of different stages...
June 9, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28596102/evolution-of-the-fusogenic-activity-of-the-receptor-fgfrl1
#12
Lei Zhuang, Beat Trueb
FGFRL1 is a transmembrane receptor that can induce the fusion of CHO cells to multinucleated syncytia. This cell fusion activity has been attributed to the extracellular Ig3 domain of the receptor. We investigated how the fusogenic activity evolved during the evolution of animals. We found that the Ig3 domain from humans, mice, chicken and fish stimulates fusion of CHO cells, while the Ig3 domain from lancelet and sea urchin does not. It is therefore conceivable that the fusogenic activity of FGFRL1 developed during the evolution of vertebrates...
June 5, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28593940/time-programmable-drug-dosing-allows-the-manipulation-suppression-and-reversal-of-antibiotic-drug-resistance-in-vitro
#13
Mari Yoshida, Sabrina Galiñanes Reyes, Soichiro Tsuda, Takaaki Horinouchi, Chikara Furusawa, Leroy Cronin
Multi-drug strategies have been attempted to prolong the efficacy of existing antibiotics, but with limited success. Here we show that the evolution of multi-drug-resistant Escherichia coli can be manipulated in vitro by administering pairs of antibiotics and switching between them in ON/OFF manner. Using a multiplexed cell culture system, we find that switching between certain combinations of antibiotics completely suppresses the development of resistance to one of the antibiotics. Using this data, we develop a simple deterministic model, which allows us to predict the fate of multi-drug evolution in this system...
June 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28592438/cd14-cd15-hla-dr-myeloid-derived-suppressor-cells-impair-antimicrobial-responses-in-patients-with-acute-on-chronic-liver-failure
#14
Christine Bernsmeier, Evangelos Triantafyllou, Robert Brenig, Fanny J Lebosse, Arjuna Singanayagam, Vishal C Patel, Oltin T Pop, Wafa Khamri, Rooshi Nathwani, Robert Tidswell, Christopher J Weston, David H Adams, Mark R Thursz, Julia A Wendon, Charalambos Gustav Antoniades
OBJECTIVE: Immune paresis in patients with acute-on-chronic liver failure (ACLF) accounts for infection susceptibility and increased mortality. Immunosuppressive mononuclear CD14(+)HLA-DR(-) myeloid-derived suppressor cells (M-MDSCs) have recently been identified to quell antimicrobial responses in immune-mediated diseases. We sought to delineate the function and derivation of M-MDSC in patients with ACLF, and explore potential targets to augment antimicrobial responses. DESIGN: Patients with ACLF (n=41) were compared with healthy subjects (n=25) and patients with cirrhosis (n=22) or acute liver failure (n=30)...
June 7, 2017: Gut
https://www.readbyqxmd.com/read/28589190/cholesteric-liquid-crystals-in-living-matter
#15
REVIEW
Michel Mitov
Liquid crystals play an important role in biology because the combination of order and mobility is a basic requirement for self-organisation and structure formation in living systems. Cholesteric liquid crystals are omnipresent in living matter under both in vivo and in vitro conditions and address the major types of molecules essential to life. In the animal and plant kingdoms, the cholesteric structure is a recurring design, suggesting a convergent evolution to an optimised left-handed helix. Herein, we review the recent advances in the cholesteric organisation of DNA, chromatin, chitin, cellulose, collagen, viruses, silk and cholesterol ester deposition in atherosclerosis...
June 14, 2017: Soft Matter
https://www.readbyqxmd.com/read/28588068/comprehensive-global-genome-dynamics-of-chlamydia-trachomatis-show-ancient-diversification-followed-by-contemporary-mixing-and-recent-lineage-expansion
#16
James Hadfield, Simon R Harris, Helena M B Seth-Smith, Surendra Parmar, Patiyan Andersson, Philip M Giffard, Julius Schachter, Jeanne Moncada, Louise Ellison, María Lucía Gallo Vaulet, Marcelo Rodríguez Fermepin, Frans Radebe, Suyapa Mendoza, Sander Ouburg, Servaas A Morré, Konrad Sachse, Mirja Puolakkainen, Suvi J Korhonen, Chris Sonnex, Rebecca Wiggins, Hamid Jalal, Tamara Brunelli, Patrizia Casprini, Rachel Pitt, Cathy Ison, Alevtina Savicheva, Elena Shipitsyna, Ronza Hadad, Laszlo Kari, Matthew J Burton, David Mabey, Anthony W Solomon, David Lewis, Peter Marsh, Magnus Unemo, Ian N Clarke, Julian Parkhill, Nicholas R Thomson
Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes...
June 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28586547/pcl-ha-microscaffolds-for-in-vitro-modular-bone-tissue-engineering
#17
Alessandra Totaro, Aurelio Salerno, Giorgia Imparato, Concepción Domingo, Francesco Urciuolo, Paolo Antonio Netti
The evolution of microscaffolds and bone-bioactive surfaces is a pivotal point in modular bone tissue engineering. In this study, the design and fabrication of porous polycaprolactone (PCL) microscaffolds functionalized with hydroxyapatite (HA) nanoparticles by means of a bio-safe and versatile thermally-induced phase separation process is reported. The ability of the as-prepared nanocomposite microscaffolds to support the adhesion, growth and osteogenic differentiation of human mesenchymal stem cells (hMSCs) in standard and osteogenic media and using dynamic seeding/culture conditions was investigated...
June 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28581516/pancreatic-cancer-heterogeneity-and-response-to-mek-inhibition
#18
K Pedersen, F Bilal, C Bernadó Morales, M T Salcedo, T Macarulla, D Massó-Vallés, V Mohan, A Vivancos, M-J Carreras, X Serres, M Abu-Suboh, J Balsells, E Allende, I Sagi, L Soucek, J Tabernero, J Arribas
Our increasing knowledge of the mechanisms behind the progression of pancreatic cancer (PC) has not yet translated into effective treatments. Many promising drugs have failed in the clinic, highlighting the need for better preclinical models to assess drug efficacy and characterize mechanisms of resistance. Using different experimental models, including patient-derived xenografts (PDXs), we gauged the efficacy of therapies aimed at two hallmark lesions of PCs: activation of signaling pathways by oncogenic KRAS and inactivation of tumor-suppressor genes...
June 5, 2017: Oncogene
https://www.readbyqxmd.com/read/28581455/attenuation-of-rna-viruses-by-redirecting-their-evolution-in-sequence-space
#19
Gonzalo Moratorio, Rasmus Henningsson, Cyril Barbezange, Lucia Carrau, Antonio V Bordería, Hervé Blanc, Stephanie Beaucourt, Enzo Z Poirier, Thomas Vallet, Jeremy Boussier, Bryan C Mounce, Magnus Fontes, Marco Vignuzzi
RNA viruses pose serious threats to human health. Their success relies on their capacity to generate genetic variability and, consequently, on their adaptive potential. We describe a strategy to attenuate RNA viruses by altering their evolutionary potential. We rationally altered the genomes of Coxsackie B3 and influenza A viruses to redirect their evolutionary trajectories towards detrimental regions in sequence space. Specifically, viral genomes were engineered to harbour more serine and leucine codons with nonsense mutation targets: codons that could generate Stop mutations after a single nucleotide substitution...
June 5, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28576863/evolving-mistranslating-trnas-through-a-phenotypically-ambivalent-intermediate-in-saccharomyces-cerevisiae
#20
Matthew D Berg, Kyle S Hoffman, Julie Genereaux, Safee Mian, Ryan S Trussler, David B Haniford, Patrick O'Donoghue, Christopher J Brandl
The genetic code converts information from nucleic acid into protein. The genetic code was thought to be immutable, yet many examples in nature indicate that variations to the code provide a selective advantage. We used a sensitive selection system involving suppression of a deleterious allele (tti2-L187P) in Saccharomyces cerevisiae to detect mistranslation and identify mechanisms that allow genetic code evolution. Though tRNA(Ser) containing a proline anticodon (UGG) is toxic, using our selection system, we identified four tRNA(Ser)UGG variants, each with a single mutation, that mistranslate at a tolerable level...
June 2, 2017: Genetics
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