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https://www.readbyqxmd.com/read/29165665/novel-structural-features-drive-dna-binding-properties-of-cmr-a-crp-family-protein-in-tb-complex-mycobacteria
#1
Sridevi Ranganathan, Jonah Cheung, Michael Cassidy, Christopher Ginter, Janice D Pata, Kathleen A McDonough
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr's DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29161242/cadherin-1-and-cadherin-3-cooperation-determines-the-aggressiveness-of-pancreatic-ductal-adenocarcinoma
#2
Carole Siret, Aurélie Dobric, Anna Martirosyan, Chloé Terciolo, Sébastien Germain, Renaté Bonier, Thassadite Dirami, Nelson Dusetti, Richard Tomasini, Marion Rubis, Stéphane Garcia, Juan Iovanna, Dominique Lombardo, Véronique Rigot, Frédéric André
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is characterised by an extensive tissue invasion and an early formation of metastasis. Alterations in the expression of cadherins have been reported in PDAC. Yet, how these changes contribute to tumour progression is poorly understood. Here, we investigated the relationship between cadherins expression and PDAC development. METHODS: Cadherins expression was assessed by immunostaining in both human and murine tissue specimens...
November 21, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29160793/a-gal-m%C3%A2%C2%B5s-device-to-evaluate-cell-migratory-response-to-combined-galvano-chemotactic-fields
#3
Shawn Mishra, Maribel Vazquez
Electric fields have been studied extensively in biomedical engineering (BME) for numerous regenerative therapies. Recent studies have begun to examine the biological effects of electric fields in combination with other environmental cues, such as tissue-engineered extracellular matrices (ECM), chemical gradient profiles, and time-dependent temperature gradients. In the nervous system, cell migration driven by electrical fields, or galvanotaxis, has been most recently studied in transcranial direct stimulation (TCDS), spinal cord repair and tumor treating fields (TTF)...
November 21, 2017: Biosensors
https://www.readbyqxmd.com/read/29158239/comparative-genomics-of-myxobacterial-chemosensory-systems
#4
Gaurav Sharma, Indu Khatri, Srikrishna Subramanian
The chemosensory system (CSS) is amongst the most complex organizations of proteins functioning cooperatively to regulate bacterial motility and other cellular activities. These systems have been studied extensively in bacteria and usually, they are present as a single system. Eight CSS, the highest number in bacteria, have been reported in Myxococcus xanthus DK1622 which are involved in coordinating diverse functions. Here, we have explored and compared the CSS in all available genomes of order Myxococcales...
November 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29156593/site-directed-mutagenesis-of-the-fibronectin-domains-in-insulin-receptor-related-receptor
#5
Igor E Deyev, Natalia A Chachina, Egor S Zhevlenev, Alexander G Petrenko
The orphan insulin receptor-related receptor (IRR), in contrast to its close homologs, the insulin receptor (IR) and insulin-like growth factor receptor (IGF-IR) can be activated by mildly alkaline extracellular medium. We have previously demonstrated that IRR activation is defined by its extracellular region, involves multiple domains, and shows positive cooperativity with two synergistic sites. By the analyses of point mutants and chimeras of IRR with IR in, we now address the role of the fibronectin type III (FnIII) repeats in the IRR pH-sensing...
November 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29148741/controlling-association-and-separation-of-gold-nanoparticles-with-computationally-designed-zinc-coordinating-proteins
#6
Matthew J Eibling, Christopher M MacDermaid, Zhaoxia Qian, Christopher J Lanci, So-Jung Park, Jeffery G Saven
Functionalization of nanoparticles with biopolymers has yielded a wide range of structured and responsive hybrid materials. DNA provides the ability to program length and recognition using complementary oligonucleotide sequences. Nature more often leverages the versatility of proteins, however, where structure, assembly, and recognition are more subtle to engineer. Herein, a protein was computationally designed to present multiple Zn(2+) coordination sites and cooperatively self-associate to form an antiparallel helical homodimer...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29147538/scaling-behaviour-and-rate-determining-steps-in-filamentous-self-assembly
#7
Georg Meisl, Luke Rajah, Samuel A I Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K Buell, Adriano Aguzzi, Sara Linse, Michele Vendruscolo, Christopher M Dobson, Tuomas P J Knowles
The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29141911/transcriptional-integration-of-mitogenic-and-mechanical-signals-by-myc-and-yap
#8
Ottavio Croci, Serena De Fazio, Francesca Biagioni, Elisa Donato, Marieta Caganova, Laura Curti, Mirko Doni, Silvia Sberna, Deborah Aldeghi, Chiara Biancotto, Alessandro Verrecchia, Daniela Olivero, Bruno Amati, Stefano Campaner
Mammalian cells must integrate environmental cues to determine coherent physiological responses. The transcription factors Myc and YAP-TEAD act downstream from mitogenic signals, with the latter responding also to mechanical cues. Here, we show that these factors coordinately regulate genes required for cell proliferation. Activation of Myc led to extensive association with its genomic targets, most of which were prebound by TEAD. At these loci, recruitment of YAP was Myc-dependent and led to full transcriptional activation...
October 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/29141440/explaining-the-t-v-dependent-dynamics-of-glass-forming-liquids-the-cooperative-free-volume-model-tested-against-new-simulation-results
#9
Ronald P White, Jane E G Lipson
In this article, we derive a rate model, the "cooperative free volume" (CFV) model, to explain relaxation dynamics in terms of a system's free volume, Vfree, and its temperature, T, over widely varied pressure dependent conditions. In the CFV model, the rate a molecule moves a distance on the order of its own size is dependent on the cooperation of surrounding molecules to open up enough free space. To test CFV, we have generated extensive T,V dependent simulation data for structural relaxation times, τ, on a Kob and Andersen type Lennard-Jones (KA-LJ) fluid...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29140767/genomic-medicine-without-borders-which-strategies-should-developing-countries-employ-to-invest-in-precision-medicine-a-new-fast-second-winner-strategy
#10
Konstantinos Mitropoulos, David N Cooper, Christina Mitropoulou, Spiros Agathos, Jürgen K V Reichardt, Fatima Al-Maskari, Wasun Chantratita, Ambroise Wonkam, Collet Dandara, Theodora Katsila, Catalina Lopez-Correa, Bassam R Ali, George P Patrinos
Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29140462/data-portal-for-the-library-of-integrated-network-based-cellular-signatures-lincs-program-integrated-access-to-diverse-large-scale-cellular-perturbation-response-data
#11
Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J Cooper, John P Turner, Dušica Vidovic, Michele Forlin, Tanya T Kelley, Alessandro D'Urso, Bryce K Allen, Denis Torre, Kathleen M Jagodnik, Lily Wang, Sherry L Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Mahi, Marcin Pilarczyk, Nicholas Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C Schürer
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138443/local-reasons-to-give-globally-identity-extension-and-global-cooperation
#12
Nancy R Buchan, Sophia Soyoung Jeong, A K Ward
Recent political events across the world suggest a retrenchment from globalization and a possible increase in parochialism. This inward-looking threat from parochialism occurs just as the global community faces growing challenges that require trans-national cooperation. In this research, we question if strong identification with an in-group necessarily leads to parochialism and ultimately is detrimental to global cooperation. Building on research on global social identification, we explore whether strong local identification can expand in inclusiveness to global identification, and among whom this is likely to happen...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138411/divide-and-conquer-tournament-on-social-networks
#13
Jiasheng Wang, Yichao Zhang, Jihong Guan, Shuigeng Zhou
In social gaming networks, previous studies extensively investigated the influence of a variety of strategies on reciprocal behaviors in the prisoner's dilemma game. The studied frameworks range from the case that an individual uniformly cooperates or defects with all social contacts, to the recently reported divide-and-conquer games, where an individual can choose a particular move to play with each neighbor. In this paper, we investigate a divide-and-conquer tournament among 14 well-known strategies on social gaming networks...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136196/analysis-of-the-natively-unstructured-rna-protein-recognition-core-in-the-escherichia-coli-rna-degradosome-and-its-interactions-with-regulatory-rna-hfq-complexes
#14
Heather A Bruce, Dijun Du, Dijana Matak-Vinkovic, Katarzyna J Bandyra, R William Broadhurst, Esther Martin, Frank Sobott, Alexander V Shkumatov, Ben F Luisi
The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29131503/association-between-plasma-fibrinogen-and-survival-in-patients-with-small-cell-lung-carcinoma
#15
Shanshan Fan, Yin Guan, Guanfei Zhao, Guangyu An
BACKGROUND: Elevated plasma fibrinogen (Fbg) levels contribute to tumor progression and metastasis; however, limited research on Fbg in small cell lung cancer (SCLC) has been conducted. This study evaluated the prognostic value of Fbg levels in patients with SCLC. METHODS: Data on plasma Fbg level, clinical features, and overall survival were retrospectively collected. Kaplan-Meier estimates and log-rank tests were used to analyze the relationship between Fbg level and survival...
November 13, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/29125535/an-intelligent-cooperative-visual-sensor-network-for-urban-mobility
#16
Giuseppe Riccardo Leone, Davide Moroni, Gabriele Pieri, Matteo Petracca, Ovidio Salvetti, Andrea Azzarà, Francesco Marino
Smart cities are demanding solutions for improved traffic efficiency, in order to guarantee optimal access to mobility resources available in urban areas. Intelligent video analytics deployed directly on board embedded sensors offers great opportunities to gather highly informative data about traffic and transport, allowing reconstruction of a real-time neat picture of urban mobility patterns. In this paper, we present a visual sensor network in which each node embeds computer vision logics for analyzing in real time urban traffic...
November 10, 2017: Sensors
https://www.readbyqxmd.com/read/29121805/prostate-cancer-xenograft-inhibitory-activity-and-pharmacokinetics-of-decursinol-a-metabolite-of-angelica-gigas-pyranocoumarins-in-mouse-models
#17
Wei Wu, Su-Ni Tang, Yong Zhang, Manohar Puppala, Timothy K Cooper, Chengguo Xing, Cheng Jiang, Junxuan Lü
We have previously shown that the ethanol extract of dried Angelica gigas Nakai (AGN) root exerts anticancer activity against androgen receptor (AR)-negative human DU145 and PC-3 prostate cancer xenografts and primary carcinogenesis in the transgenic adenocarcinoma of mouse prostate (TRAMP) model. The major pyranocoumarin isomers decursin (D) and decursinol angelate (DA), when provided at equi-molar intake to that provided by AGN extract, accounted for the inhibitory efficacy against precancerous epithelial lesions in TRAMP mice...
November 9, 2017: American Journal of Chinese Medicine
https://www.readbyqxmd.com/read/29109425/landscape-scale-conservation-design-across-biotic-realms-sequential-integration-of-aquatic-and-terrestrial-landscapes
#18
Paul B Leonard, Robert F Baldwin, R Daniel Hanks
Systematic conservation planning has been used extensively throughout the world to identify important areas for maintaining biodiversity and functional ecosystems, and is well suited to address large-scale biodiversity conservation challenges of the twenty-first century. Systematic planning is necessary to bridge implementation, scale, and data gaps in a collaborative effort that recognizes competing land uses. Here, we developed a conservation planning process to identify and unify conservation priorities around the central and southern Appalachian Mountains as part of the Appalachian Landscape Conservation Cooperative (App LCC)...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29109077/safety-and-efficacy-of-intratumoral-injections-of-chimeric-antigen-receptor-car-t-cells-in-metastatic-breast-cancer
#19
Julia Tchou, Yangbing Zhao, Bruce L Levine, Paul J Zhang, Megan M Davis, Jan Joseph Melenhorst, Irina Kulikovskaya, Andrea L Brennan, Xiajun Liu, Simon F Lacey, Avery Posey, Austin D Williams, Alycia So, Jose R Conejo-Garcia, Gabriela Plesa, Regina M Young, Shannon McGettigan, Jean Campbell, Robert H Pierce, Jennifer M Matro, Angela M DeMichele, Amy S Clark, Laurence J N Cooper, Lynn M Schuchter, Robert H Vonderheide, Carl H June
Chimeric antigen receptors (CARs) are synthetic molecules that provide new specificities to T cells. Although successful in treatment of hematologic malignancies, CAR T cells are ineffective for solid tumors to date. We found that the cell-surface molecule c-Met was expressed in ~50% of breast tumors, prompting the construction of a CAR T cell specific for c-Met, which halted tumor growth in immune-incompetent mice with tumor xenografts. We then evaluated the safety and feasibility of treating metastatic breast cancer with intratumoral administration of mRNA-transfected c-Met-CAR T cells in a phase 0 clinical trial (NCT01837602)...
November 6, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/29108020/post-conflict-opponent-affiliation-reduces-victim-re-aggression-in-a-family-group-of-captive-arctic-wolves-canis-lupus-arctos
#20
Martina Lazzaroni, Sarah Marshall-Pescini, Simona Cafazzo
Post-conflict affiliative interactions have been widely investigated in primates but not extensively in other species. Using the Post Conflict-Matched Control (PC-MC) comparison method, this study investigated the patterns of post-conflict opponent affiliation (POA) of a captive family group of 19 arctic wolves (Canis lupus arctos), investigating the correlation with various factors. We found that POAs occurred mainly in the non-feeding context and more often when the victim was dominant and the aggressor subordinate...
2017: PloS One
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