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James Cooper

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https://www.readbyqxmd.com/read/27915232/quantitative-profiling-of-selective-sox-pou-pairing-on-hundreds-of-sequences-in-parallel-by-coop-seq
#1
Yiming K Chang, Yogesh Srivastava, Caizhen Hu, Adam Joyce, Xiaoxiao Yang, Zheng Zuo, James J Havranek, Gary D Stormo, Ralf Jauch
Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements...
December 2, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913600/the-evolution-of-jaw-protrusion-mechanics-has-been-tightly-coupled-to-bentho-pelagic-divergence-in-damselfishes-pomacentridae
#2
W James Cooper, Casey B Carter, Andrew J Conith, Aaron N Rice, Mark W Westneat
Most species-rich lineages of aquatic organisms have undergone divergence between forms that feed from the substrate (benthic feeding) and forms that feed from the water column (pelagic feeding). Changes in trophic niche are frequently accompanied by changes in skull mechanics, and multiple fish lineages have evolved highly specialized biomechanical configurations that allow them to protrude their upper jaws toward the prey during feeding. Damselfishes (family Pomacentridae) are an example of a species-rich lineage with multiple trophic morphologies and feeding ecologies...
December 2, 2016: Journal of Experimental Biology
https://www.readbyqxmd.com/read/27913054/development-of-a-multi-stakeholder-partnership-to-improve-access-to-and-delivery-of-neurosurgical-services-in-ontario
#3
Sunjay Sharma, Des Bohn, Iphigenia Mikroyiannakis, Joslyn Trowbridge, Donna Thompson, Robert Bell, James Rutka
Neurosurgical emergencies require expedient access to definitive care at neurosurgical centers. Neurosurgical resources in province of Ontario are highly centralized, and subsequently, most patients with neurosurgical emergencies will present to non-neurosurgical centers. From 2000-2010, metrics demonstrated the organization of neurosurgical resources might not be optimal. In response to this a program entitled Provincial Neurosurgery Ontario (PNO)- was formed to address these issues in cooperation with neurosurgeons, hospitals and the provincial government...
November 22, 2016: Health Policy
https://www.readbyqxmd.com/read/27912064/modular-assembly-of-the-bacterial-large-ribosomal-subunit
#4
Joseph H Davis, Yong Zi Tan, Bridget Carragher, Clinton S Potter, Dmitry Lyumkis, James R Williamson
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27899508/optimized-inducible-shrna-and-crispr-cas9-platforms-for-in-vitro-studies-of-human-development-using-hpscs
#5
Alessandro Bertero, Matthias Pawlowski, Daniel Ortmann, Kirsten Snijders, Loukia Yiangou, Miguel Cardoso de Brito, Stephanie Brown, William G Bernard, James D Cooper, Elisa Giacomelli, Laure Gambardella, Nicholas R F Hannan, Dharini Iyer, Fotios Sampaziotis, Felipe Serrano, Mariëlle C F Zonneveld, Sanjay Sinha, Mark Kotter, Ludovic Vallier
Inducible loss of gene function experiments are necessary to uncover mechanisms underlying development, physiology and disease. However, current methods are complex, lack robustness and do not work in multiple cell types. Here we address these limitations by developing single-step optimized inducible gene knockdown or knockout (sOPTiKD or sOPTiKO) platforms. These are based on genetic engineering of human genomic safe harbors combined with an improved tetracycline-inducible system and CRISPR/Cas9 technology...
December 1, 2016: Development
https://www.readbyqxmd.com/read/27895045/cardiorespiratory-fitness-and-highly-sensitive-cardiac-troponin-levels-in-a-preventive-medicine-cohort
#6
Laura F DeFina, Benjamin L Willis, Nina B Radford, Robert H Christenson, Christopher R deFilippi, James A de Lemos
BACKGROUND: Cardiorespiratory fitness (CRF) and highly sensitive cardiac troponin T (hs-cTnT) are associated with risk of all-cause and cardiovascular mortality as well as incident heart failure. A link of low CRF to subclinical cardiac injury may explain this association. We hypothesized that CRF would be inversely associated with hs-cTnT measured in healthy adults over age 50. METHODS AND RESULTS: We evaluated 2498 participants (24.7% female, mean age 58.7 years) from the Cooper Center Longitudinal Study between August 2008 and January 2012...
November 28, 2016: Journal of the American Heart Association
https://www.readbyqxmd.com/read/27889086/impacts-of-regional-transport-on-black-carbon-in-huairou-beijing-china
#7
Yuqin Wang, Benjamin de Foy, James J Schauer, Michael R Olson, Yang Zhang, Zhengqiang Li, Yuanxun Zhang
The 22(nd) Asia-Pacific Economic Cooperation (APEC) Conference was held near Yanqi Lake, Huairou, in Beijing, China during November 10-11, 2014. To guarantee haze-free days during the APEC Conference, the Beijing government and the governments of the surrounding provinces implemented a series of controls. Three months of Aethalometer 880 nm black carbon (BC) measurements were examined to understand the hourly fluctuations in BC concentrations that resulted from emission controls and meteorology changes. Measurements were collected at the University of Chinese Academy of Sciences near the APEC Conference site and in Central Beijing at the Institute of Remote Sensing and Digital Earth of the Chinese Academy of Sciences...
November 23, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27881143/weekly-versus-every-three-weeks-platinum-based-chemoradiation-regimens-for-head-and-neck-cancer
#8
James M Melotek, Benjamin T Cooper, Matthew Koshy, Joshua S Silverman, Michael T Spiotto
BACKGROUND: The majority of chemoradiation (CRT) trials for locally advanced head and neck squamous cell carcinoma (HNSCC) have relied on platinum-based chemotherapy regimens administered every-3-weeks. However, given the increased utilization of weekly platinum regimens, it remains unclear how different chemotherapy schedules compare regarding efficacy and toxicity. METHODS: We retrospectively identified 212 patients with HNSCC who were treated at a single academic medical center with concurrent platinum-based CRT given weekly (N = 68) or every-three-weeks (N = 144)...
November 24, 2016: Journal of Otolaryngology—Head & Neck Surgery
https://www.readbyqxmd.com/read/27880765/mechanisms-for-complex-chromosomal-insertions
#9
Shen Gu, Przemyslaw Szafranski, Zeynep Coban Akdemir, Bo Yuan, Mitchell L Cooper, Maria A Magriñá, Carlos A Bacino, Seema R Lalani, Amy M Breman, Janice L Smith, Ankita Patel, Rodger H Song, Weimin Bi, Sau Wai Cheung, Claudia M B Carvalho, Paweł Stankiewicz, James R Lupski
Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH)...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27879988/immune-thrombocytopenia-a-need-for-assisted-suicide
#10
EDITORIAL
James B Bussel, Nichola Cooper
No abstract text is available yet for this article.
November 23, 2016: British Journal of Haematology
https://www.readbyqxmd.com/read/27869472/patients-affective-processes-within-initial-experiential-dynamic-therapy-sessions
#11
Katie Aafjes-van Doorn, Peter Lilliengren, Angela Cooper, James Macdonald, Fredrik Falkenström
Research has indicated that patients' in-session experience of previously avoided affects may be important for effective psychotherapy. The aim of this study was to investigate patients' in-session levels of affect experiencing in relation to their corresponding levels of insight, motivation, and inhibitory affects in initial Experiential Dynamic Therapy (EDT) sessions. Four hundred sixty-six 10-min video segments from 31 initial sessions were rated using the Achievement of Therapeutic Objectives Scale. A series of multilevel growth models, controlling for between-therapist variability, were estimated to predict patients' adaptive affect experiencing (Activating Affects) across session segments...
November 21, 2016: Psychotherapy
https://www.readbyqxmd.com/read/27869080/the-effect-of-biologically-effective-dose-and-radiation-treatment-schedule-on-overall-survival-in-stage-i-non-small-cell-lung-cancer-patients-treated-with-stereotactic-body-radiation-therapy
#12
John M Stahl, Rudi Ross, Eileen M Harder, Brandon R Mancini, Pamela R Soulos, Steven E Finkelstein, Timothy D Shafman, Arie P Dosoretz, Suzanne B Evans, Zain A Husain, James B Yu, Cary P Gross, Roy H Decker
PURPOSE: To determine the effect of biologically effective dose (BED10) and radiation treatment schedule on overall survival (OS) in patients with early-stage non-small cell lung cancer (NSCLC) undergoing stereotactic body radiation therapy (SBRT). METHODS AND MATERIALS: Using data from 65 treatment centers in the United States, we retrospectively reviewed the records of T1-2 N0 NSCLC patients undergoing SBRT alone from 2006 to 2014. Biologically relevant covariates, including dose per fraction, number of fractions, and time between fractions, were used to quantify BED10 and radiation treatment schedule...
December 1, 2016: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/27866765/safety-tolerability-and-immunogenicity-of-a-single-dose-4-antigen-or-3-antigen-staphylococcus-aureus-vaccine-in-healthy-older-adults-results-of-a-randomised-trial
#13
C Buddy Creech, Robert W Frenck, Eric A Sheldon, David J Seiden, Martin K Kankam, Edward T Zito, Douglas Girgenti, Joseph M Severs, Frederick W Immermann, Lisa K McNeil, David Cooper, Kathrin U Jansen, William Gruber, Joseph Eiden, Annaliesa S Anderson, James Baber
BACKGROUND: The decline in immune function with age is a challenge to vaccine development. Following an initial study in adults aged 18-64years, this study evaluated the safety and immunogenicity of Staphylococcus aureus (S. aureus) 4-antigen (SA4Ag) and 3-antigen (SA3Ag) vaccine in older adults. SA3Ag included capsular polysaccharide serotypes 5 and 8 (CP5 and CP8) conjugated to the nontoxic mutant form of diphtheria toxin (CRM197) and a recombinant version of clumping factor A (ClfA)...
November 17, 2016: Vaccine
https://www.readbyqxmd.com/read/27856760/molecular-mechanisms-of-substrate-controlled-ring-dynamics-and-substepping-in-a-nucleic-acid-dependent-hexameric-motor
#14
Nathan D Thomsen, Michael R Lawson, Lea B Witkowsky, Song Qu, James M Berger
Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the Escherichia coli Rho transcription termination factor as a model system, we have used solution and crystallographic structural methods to delineate the range of conformational changes that accompany distinct substrate and nucleotide cofactor binding events...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27856720/non-destructive-cryo-micro-ct-imaging-enables-structural-and-molecular-analysis-of-human-lung-tissue
#15
Dragos Mihai Vasilescu, André B Phillion, Naoya Tanabe, Daisuke Kinose, David F Paige, Jacob J Kantrowitz, Gang Liu, Hanqiao Liu, Nick Fishbane, Stijn E Verleden, Bart M Vanaudenaerde, Marc E Lenburg, Christopher S Stevenson, Avrum Spira, Joel D Cooper, Tillie-Louise Hackett, James C Hogg
Micro Computed Tomography (CT) enables 3-dimensional (3D) imaging of complex soft tissue structures, but current protocols used to achieve this goal preclude cellular and molecular phenotyping of the tissue. Here we describe a radiolucent cryo stage that permits micro CT imaging of unfixed frozen human lung samples at a spatial resolution of 11 µm under conditions where the sample is maintained frozen at -30°C during imaging. The cryo stage was tested for thermal stability to maintain samples frozen up to 8 hours...
November 17, 2016: Journal of Applied Physiology
https://www.readbyqxmd.com/read/27851958/alternative-splicing-of-four-trafficking-genes-regulates-myofiber-structure-and-skeletal-muscle-physiology
#16
Jimena Giudice, James A Loehr, George G Rodney, Thomas A Cooper
During development, transcriptional and post-transcriptional networks are coordinately regulated to drive organ maturation. Alternative splicing contributes by producing temporal-specific protein isoforms. We previously found that genes undergoing splicing transitions during mouse postnatal heart development are enriched for vesicular trafficking and membrane dynamics functions. Here, we show that adult trafficking isoforms are also expressed in adult skeletal muscle and hypothesize that striated muscle utilizes alternative splicing to generate specific isoforms required for function of adult tissue...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27836480/training-and-retaining-community-pharmacy-leaders-career-pathways-after-completing-a-pgy1-community-pharmacy-residency-affiliated-with-a-large-supermarket-chain
#17
Kenneth C Hohmeier, Nancy Borja-Hart, Maureen Cooper, James Kirby, Cindy Fisher
OBJECTIVE: To determine pharmacist career paths and resident perceptions after completion of a PGY1 community pharmacy residency with a national supermarket pharmacy chain. METHODS: Cross-sectional nationwide survey. RESULTS: Overall, 65% (n = 24) of residents who responded accepted a position with Kroger immediately after graduation. When asked about the degree of value the residency had on obtaining the resident's ideal position, 29 (76%) reported that it was "very valuable" and the remaining 9 (24%) reported that it was "somewhat valuable...
November 7, 2016: Journal of the American Pharmacists Association: JAPhA
https://www.readbyqxmd.com/read/27822534/long-term-evolution-of-burkholderia-multivorans-during-a-chronic-cystic-fibrosis-infection-reveals-shifting-forces-of-selection
#18
Inês N Silva, Pedro M Santos, Mário R Santos, James E A Zlosnik, David P Speert, Sean W Buskirk, Eric L Bruger, Christopher M Waters, Vaughn S Cooper, Leonilde M Moreira
Burkholderia multivorans is an opportunistic pathogen capable of causing severe disease in patients with cystic fibrosis (CF). Patients may be chronically infected for years, during which the bacterial population evolves in response to unknown forces. Here we analyze the genomic and functional evolution of a B. multivorans infection that was sequentially sampled from a CF patient over 20 years. The population diversified into at least four primary, coexisting clades with distinct evolutionary dynamics. The average substitution rate was only 2...
May 2016: MSystems
https://www.readbyqxmd.com/read/27821050/stringent-comparative-sequence-analysis-reveals-sox10-as-a-putative-inhibitor-of-glial-cell-differentiation
#19
Chetna Gopinath, William D Law, José F Rodríguez-Molina, Arjun B Prasad, Lingyun Song, Gregory E Crawford, James C Mullikin, John Svaren, Anthony Antonellis
BACKGROUND: The transcription factor SOX10 is essential for all stages of Schwann cell development including myelination. SOX10 cooperates with other transcription factors to activate the expression of key myelin genes in Schwann cells and is therefore a context-dependent, pro-myelination transcription factor. As such, the identification of genes regulated by SOX10 will provide insight into Schwann cell biology and related diseases. While genome-wide studies have successfully revealed SOX10 target genes, these efforts mainly focused on myelinating stages of Schwann cell development...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27820860/structure-and-calcium-binding-properties-of-a-neuronal-calcium-myristoyl-switch-protein-visinin-like-protein-3
#20
Congmin Li, Sunghyuk Lim, Karl H Braunewell, James B Ames
Visinin-like protein 3 (VILIP-3) belongs to a family of Ca2+-myristoyl switch proteins that regulate signal transduction in the brain and retina. Here we analyze Ca2+ binding, characterize Ca2+-induced conformational changes, and determine the NMR structure of myristoylated VILIP-3. Three Ca2+ bind cooperatively to VILIP-3 at EF2, EF3 and EF4 (KD = 0.52 μM and Hill slope of 1.8). NMR assignments, mutagenesis and structural analysis indicate that the covalently attached myristoyl group is solvent exposed in Ca2+-bound VILIP-3, whereas Ca2+-free VILIP-3 contains a sequestered myristoyl group that interacts with protein residues (E26, Y64, V68), which are distinct from myristate contacts seen in other Ca2+-myristoyl switch proteins...
2016: PloS One
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