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in vitro evolution

Yasuhiro Kyono, Laurent M Sachs, Patrice Bilesimo, Luan Wen, Robert J Denver
Thyroid hormone (TH) is essential for normal development in vertebrates. In amphibians, TH controls metamorphosis by inducing tissue-specific gene regulation programs. A hallmark of TH action is the modification of chromatin structure, which underlies changes in gene transcription. We found that mRNA for the de novo DNA methyltransferase (DNMT) dnmt3a, but not dnmt1, increased in the brain of Xenopus tadpoles during metamorphosis in parallel with plasma [TH]. Addition of 3,5,3`-triiodothyronine (T3) to the rearing water caused a time-dependent increase in dnmt3a mRNA in tadpole brain, tail and hind limb...
October 25, 2016: Endocrinology
Jie Li, He Huang, Yingguang Li, Li Li, Wenhui Hou, Zeshan You
Long non-coding RNA growth arrest-specific 5 (GAS5) was reported to be aberrantly expressed in various types of cancers. However, the role of GAS5 in the evolution and progression of ovarian cancer remains elusive. In the present study, we aimed to investigate the cellular function and clinical significance of GAS5 in ovarian cancer. GAS5 expression levels in 63 ovarian cancer tissues were detected by quantitative real-time PCR. Cell Counting Kit-8 (CCK-8) assay was performed to analyze the effect of GAS5 on cell proliferation...
October 24, 2016: Oncology Reports
Vishvanath Tiwari
Enzymes catalyze various biochemical functions with high efficiency and specificity. In vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. Similarly, combined computational and in vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme...
2016: Frontiers in Chemistry
Jinhu Huang, Jiale Ma, Kexin Shang, Xiao Hu, Yuan Liang, Daiwei Li, Zuowei Wu, Lei Dai, Li Chen, Liping Wang
Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S...
2016: Frontiers in Cellular and Infection Microbiology
Michelangela Barbieri, Raffaele Marfella, Antonietta Esposito, Maria Rosaria Rizzo, Edith Angellotti, Ciro Mauro, Mario Siniscalchi, Fabio Chirico, Pasquale Caiazzo, Fulvio Furbatto, Alessandro Bellis, Nunzia D'Onofrio, Milena Vitiello, Franca Ferraraccio, Giuseppe Paolisso, Maria Luisa Balestrieri
AIMS: Glucagon like peptide 1 (GLP-1) analogues and dipeptidyl peptidase IV (DPP-4) inhibitors reduce atherosclerosis progression in type 2 diabetes mellitus (T2DM) patients and are associated with morphological and compositional characteristics of stable plaque phenotype. GLP-1 promotes the secretion of adiponectin which exerts anti-inflammatory effects through the adaptor protein PH domain and leucine zipper containing 1 (APPL1). The potential role of APPL1 expression in the evolution of atherosclerotic plaque in TDM2 patients has not previously evaluated...
October 5, 2016: Journal of Diabetes and its Complications
Ching-Feng Yang, Wan-Yu Tsai, Wei-An Chen, Kai-Wen Liang, Cheng-Ju Pan, Pei-Lun Lai, Pan-Chyr Yang, Hsiao-Chun Huang
During natural evolution, the spindles often scale with cell sizes to orchestrate accurate chromosome segregation. Whether in cancer evolution, when the constraints on genome integrity are relaxed, cancer cells may evolve the spindle to confer other advantages has not been investigated. Using invasion as a selective pressure in vitro, we found that a highly metastatic cancer clone displays a lengthened metaphase spindle, with faster spindle elongation that correlates with transiently elevated speed of cell migration...
October 21, 2016: Scientific Reports
Lêniféré Chantal Soro, Sylvie Munier, Yves Pelissier, Lidwine Grosmaire, Rickey Yada, David Kitts, Anin Louise Ocho-Anin Atchibri, Caroline Guzman, Frédéric Boudard, Chantal Menut, Jean Charles Robinson, Patrick Poucheret
ETHNOPHARMACOLOGICAL RELEVANCE: Lippia multiflora is a plant with nutritional and pharmaco-therapeutic properties that is native to central and occidental Africa. The potential effects of plants on health are associated with their chemical composition. Therefore, the present study aimed to identify chemical variations in essential oils of Lippia multiflora as a function of geographic origin and time of annual harvest to determine optimal chemical profiles for ethno-pharmacotherapeutic applications...
October 17, 2016: Journal of Ethnopharmacology
Nathan Crook, Joseph Abatemarco, Jie Sun, James M Wagner, Alexander Schmitz, Hal S Alper
Directed evolution remains a powerful, highly generalizable approach for improving the performance of biological systems. However, implementations in eukaryotes rely either on in vitro diversity generation or limited mutational capacities. Here we synthetically optimize the retrotransposon Ty1 to enable in vivo generation of mutant libraries up to 1.6 × 10(7) l(-1) per round, which is the highest of any in vivo mutational generation approach in yeast. We demonstrate this approach by using in vivo-generated libraries to evolve single enzymes, global transcriptional regulators and multi-gene pathways...
October 17, 2016: Nature Communications
Arianna Pompilio, Valentina Crocetta, Dipankar Ghosh, Malabika Chakrabarti, Giovanni Gherardi, Luca Agostino Vitali, Ersilia Fiscarelli, Giovanni Di Bonaventura
The present study was carried out to understand the adaptive strategies developed by Stenotrophomonas maltophilia for chronic colonization of the cystic fibrosis (CF) lung. For this purpose, 13 temporally isolated strains from a single CF patient chronically infected over a 10-year period were systematically characterized for growth rate, biofilm formation, motility, mutation frequencies, antibiotic resistance, and pathogenicity. Pulsed-field gel electrophoresis (PFGE) showed over time the presence of two distinct groups, each consisting of two different pulsotypes...
2016: Frontiers in Microbiology
Christiane Gebhardt
This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. Species from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL)...
October 15, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Pauline D Scanlan, Anna M Bischofberger, Alex R Hall
Although experiments indicate that the abiotic environment plays an important role in bacterial interactions with their parasitic viruses (bacteriophages or phages), it is not yet clear how exposure to compounds present in nature alters the impact of phages on bacterial growth and evolution. To address this question we exposed Escherichia coli K12 MG1655, in combination with three lytic phages, to various substances that natural and clinical microbial populations are likely to encounter: bile salts (present in mammalian gastrointestinal tracts), sodium dodecyl sulfate (SDS, a common surfactant in cleaning and hygiene products), and four antibiotics (present at variable concentrations in natural and clinical environments)...
October 12, 2016: FEMS Microbiology Ecology
Marta Cavo, Marco Fato, Leonardo Peñuela, Francesco Beltrame, Roberto Raiteri, Silvia Scaglione
Three-dimensional (3D) cell cultures represent fundamental tools for the comprehension of cellular phenomena both in normal and in pathological conditions. In particular, mechanical and chemical stimuli play a relevant role on cell fate, cancer onset and malignant evolution. Here, we use mechanically-tuned alginate hydrogels to study the role of substrate elasticity on breast adenocarcinoma cell activity. The hydrogel elastic modulus (E) was measured via atomic force microscopy (AFM) and a remarkable range (150-4000 kPa) was obtained...
October 13, 2016: Scientific Reports
Eric R Weiss, Galit Alter, Javier Gordon Ogembo, Jennifer L Henderson, Barbara Tabak, Yasin Bakiş, Mohan Somasundaran, Manuel Garber, Liisa Selin, Katherine Luzuriaga
: The Epstein Barr virus (EBV) gp350 glycoprotein interacts with the cellular receptor to mediate viral entry and is thought to be the major target for neutralizing antibodies. To better understand the role of EBV-specific antibodies in the control of viral replication and evolution of sequence diversity, we measured EBV gp350-specific antibody responses and sequenced the gp350 gene in samples obtained from individuals experiencing primary EBV infection (acute infectious mononucleosis; AIM) and again 6 months later (convalescence, CONV)...
October 12, 2016: Journal of Virology
Cristina J Wittkopp, Madison B Adolph, Lily I Wu, Linda Chelico, Michael Emerman
Humans express seven human APOBEC3 proteins, which can inhibit viruses and endogenous retroelements through cytidine deaminase activity. The seven paralogs differ in the potency of their antiviral effects, as well as in their antiviral targets. One APOBEC3, APOBEC3C, is exceptional as it has been found to only weakly block viruses and endogenous retroelements compared to other APOBEC3s. However, our positive selection analyses suggest that APOBEC3C has played a role in pathogen defense during primate evolution...
October 2016: PLoS Pathogens
H P Gajera, Darshna G Hirpara, Zinkal A Katakpara, S V Patel, B A Golakiya
The biocontrol agent Trichoderma (T. harzianum, T. viride, T. virens, T. hamantum, T. koningii, T. pseudokoningii and Trichoderma species) inhibited variably (15.32 - 88.12%) the in vitro growth of Rhizoctonia solani causing root rot in cotton. The T. koningii MTCC 796 evidenced highest (88.12%) growth inhibition of test pathogen followed by T. viride NBAII Tv23 (85.34%). Scanning electron microscopic study confirmed mycoparasitism for MTCC 796 and Tv23 which were capable of completely overgrowing on R. solani by degrading mycelia, coiling around the hyphae with hook-like structures...
October 5, 2016: Infection, Genetics and Evolution
Farhana Lipi, Suxiang Chen, Madhuri Chakravarthy, Shilpa Rakesh, Rakesh N Veedu
Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt three-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamics properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX)...
October 7, 2016: RNA Biology
M Sierra, J Grasa, M J Muñoz, F J Miana-Mena, D González
A novel technique is proposed to predict force reduction in skeletal muscle due to fatigue under the influence of electrical stimulus parameters and muscle physiological characteristics. Twelve New Zealand white rabbits were divided in four groups ([Formula: see text]) to obtain the active force evolution of in vitro Extensor Digitorum Longus muscles for an hour of repeated contractions under different electrical stimulation patterns. Left and right muscles were tested, and a total of 24 samples were used to construct a response surface based in the proper generalized decomposition...
October 6, 2016: Biomechanics and Modeling in Mechanobiology
Hirak K Patra, Yashpal Sharma, Mohammad Mirazul Islam, Mohammad Javad Jafari, N Arul Murugan, Hisatoshi Kobayashi, Anthony P F Turner, Ashutosh Tiwari
To cope with the rapid evolution of the tissue engineering field, it is now essential to incorporate the use of on-site responsive scaffolds. Therefore, it is of utmost importance to find new 'Intelligent' biomaterials that can respond to the physicochemical changes in the microenvironment. In this present report, we have developed biocompatible stimuli responsive polyaniline-multiwalled carbon nanotube/poly(N-isopropylacrylamide), (PANI-MWCNT/PNIPAm) composite nanofiber networks and demonstrated the physiological temperature coordinated cell grafting phenomenon on its surface...
October 6, 2016: Nanoscale
Kelei Zhao, Xikun Zhou, Wujiao Li, Xiuyue Zhang, Bisong Yue
Bacteria use a cell-cell communication system termed quorum-sensing (QS) to adjust population size by coordinating the costly but beneficial cooperative behaviors. It has long been suggested that bacterial social conflict for expensive extracellular products may drive QS divergence and cause the "tragedy of the commons". However, the underlying molecular mechanism of social divergence and its evolutionary consequences for the bacterial ecology still remain largely unknown. By using the model bacterium Pseudomonas aeruginosa PAO1, here we show that nutrient reduction can promote QS divergence for population fitness during evolution but requiring adequate cell density...
October 7, 2016: Scientific Reports
Kei Matsumoto, Sandhya Xavier, Jun Chen, Yujiro Kida, Mark Lipphardt, Reina Ikeda, Annie Gevertz, Mario Caviris, Antonis K Hatzopoulos, Ivo Kalajzic, James Dutton, Brian B Ratliff, Hong Zhao, Zbygniew Darzynkiewicz, Stefan Rose-John, Michael S Goligorsky
: : Accumulation of myofibroblasts is a hallmark of renal fibrosis. A significant proportion of myofibroblasts has been reported to originate via endothelial-mesenchymal transition. We initially hypothesized that exposing myofibroblasts to the extract of endothelial progenitor cells (EPCs) could reverse this transition. Indeed, in vitro treatment of transforming growth factor-β1 (TGF-β1)-activated fibroblasts with EPC extract prevented expression of α-smooth muscle actin (α-SMA); however, it did not enhance expression of endothelial markers...
October 5, 2016: Stem Cells Translational Medicine
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