In Situ Measurements And Modeling Of Reactive Trace Gases In A Small Biomass Burning Plume, 2015 University of Innsbruck
In Situ Measurements And Modeling Of Reactive Trace Gases In A Small Biomass Burning Plume, M. Muller, B. Anderson, A. Beyersdorf, J. H. Crawford, G. Diskin, P. Eichler, A. Fried, F. N. Keutsch, T. Mikoviny, K. L. Thornhill, J. G. Walega, A. J. Weinheimer, M. Yang, Robert Yokelson, A. Wisthaler
Chemistry and Biochemistry Faculty Publications
An instrumented NASA P-3B aircraft was used for airborne sampling of trace gases in a plume that had emanated from a small forest understory fire in Georgia, USA. The plume was sampled at its origin for deriving emission factors and followed ~ 13.6 km downwind for observing chemical changes during the first hour of atmospheric aging. The P-3B payload included a proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS), which measured non-methane organic gases (NMOGs) at unprecidented spatio-temporal resolution (10m/0.1 s). Quantitative emission data are reported for CO2, CO, NO, NO2, HONO, NH3 and 16 NMOGs (formaldehyde, methanol ...
Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20151027 - Please Download "75" Instead, 2015 M.D. Anderson Cancer Center
Mcnamara 201412 Nih Scap Innocentive Challenge Solution - T-Bow Rainbow T-Cells And Tumor Cells Spatial Multiplexing Gene Expression Reporter System – Plus Supplement Plus Posters - 20151027 - Please Download "75" Instead, George Mcnamara
McNamara 201412 NIH SCAP InnoCentive Challenge Solution - T-Bow Rainbow T-cells and Tumor Cells Spatial Multiplexing Gene Expression Reporter System – plus supplement plus posters - 20151027.
Please download the current 20151027 (October 27, 2015) Tattletales and T-Bow update from
The bepress web site is not letting me replace the old pdf here at "65" with the additional 10 pages update.
The download is my/Cooper lab solution (submission) to the 2014 NIH Single Cell Analysis Program (SCAP) InnoCentive Challenge, "Follow That Cell". I submitted the Solution on 20141215Mon (with 20 minutes to spare). The Challenge web ...
Tattletales And T-Bow Update 20151027tue, 2015 M.D. Anderson Cancer Center
Tattletales And T-Bow Update 20151027tue, George Mcnamara
20151027Tue this "75"
is my update of "65" posting
See text at
for text summary. The PDf here in "75" supersedes "65".
The PDF here has 10 pages added to the end from the "65" version (pages 40-49 of PDF when including the bepress cover page)..
here is the text in my cover page (bepress may add its own cover):
20151027Tue: added 10 page e-poster at bottom explaining Binary Tattletales and T-Bow. That is, binary with respect to protein components. For one color (number of repeats, epitope tags ...
Interdomain Interactions Of The Transactive Response Dna Binding Protein 43 Kda (Tdp-43), 2015 The University of Western Ontario
Interdomain Interactions Of The Transactive Response Dna Binding Protein 43 Kda (Tdp-43), Karen M. Dunkerley
Electronic Thesis and Dissertation Repository
Transactive response DNA binding protein, 43 kDa (TDP-43) is 416-residue RNA processing and transport protein, observed in insoluble cytoplasmic aggregates within affected neurons in neurodegenerative diseases. TDP-43 has three domains: the N-terminal (N), RNA-binding (R) and unstructured C-terminal domains (G). Unstructured domains often form intramolecular interactions regulating other domains; our goal was to determine if such an interaction occurs in TDP-43. In Far Western blots, tagged NR was observed to bind to G. A 10 residue C-terminal truncation of G virtually abolished binding and introduction of phosphomimetics at Ser409/Ser410 also reduced binding. Sedimentation velocity ultracentrifugation with tagged NR and ...
Feasibility Study Of Inversely-Optimized Intensity Modulated Grid-Therapy For Bulky Lung Tumors, 2015 Western University
Feasibility Study Of Inversely-Optimized Intensity Modulated Grid-Therapy For Bulky Lung Tumors, M Macfarlane, J Lam, R Dar, E Yu, K Jordan, Jz Chen
Purpose/Objective(s): Grid therapy with megavoltage photon beams has been clinically shown to improve local control of bulky tumors. The purpose of this study is to develop intensity modulated grid therapy (IMGT) with multiple beams. We hypothesize that when compared to conventional single-field grid therapy, IMGT will provide lower spatially fractionated doses to the surrounding organs at risk (OAR) while increasing the minimum dose to the whole tumor volume and thus improve tumor control probability as supported by conventionalradiobiology. Materials/Methods: IMGT was developed with multiple photon beams using dynamic MLC segments and orthogonal blocks. Spatially fractionated fluence patterns ...
The Generation, Exploitation And Future Of Induced Pluripotent Stem Cells, 2015 Clark University
The Generation, Exploitation And Future Of Induced Pluripotent Stem Cells, Jacob Steenwyk
Scholarly Undergraduate Research Journal at Clark
The foundational advancements of John Gurdon and Shinya Yamanaka have improved understanding of dedifferen- tiation of cells to a pluripotent state. The seminal discovery established a novel system to study disease pathogenesis, drug screening, and toxicity, as well as sprouted the new field of regenerative medicine. In this article, the method- ology to obtain dedifferentiated cells, known as induced pluripotent stem (iPS) cells, subsequent validation, and application of which are reviewed. The experiments investigated here aim to demonstrate the capacity of iPS cells to replace the ethically-gray human embryonic cells by developing human livers and viable, healthy animals. It is ...
Biochemical Effects Of Meditation: A Literature Review, 2015 Clark University
Biochemical Effects Of Meditation: A Literature Review, William C. Daube, Charles E. Jakobsche
Scholarly Undergraduate Research Journal at Clark
Meditation is an activity that can help reduce stress and anxiety from daily life as well as help cultivate overall feel- ings of peacefulness, relaxation, and contentment. This review describes several studies that have been used to assess how meditation can influence the body at the molecular level. The presented results focus on small-molecule metab- olites, which are broadly defined as naturally-produced molecules that weigh less than approximately 1000 Da. The results show that meditation can significantly affect hormones and neurotransmitters such as cortisol, dehydroepi- androstrone, serotonin, melatonin, and epinephrine. Some common and modern experimental techniques that are relevant to ...
Hyperpolarized 129xe Magnetic Resonance Imaging Of Radiation-Induced Lung Injury, 2015 The University of Western Ontario
Hyperpolarized 129xe Magnetic Resonance Imaging Of Radiation-Induced Lung Injury, Ozkan Doganay
Electronic Thesis and Dissertation Repository
Lung cancer is the largest contributor to cancer-related mortality worldwide. Only 20% of stage III non-small cell lung cancer patients survive after 5-years post radiation therapy (RT). Although RT is an important treatment modality for lung cancer, it is limited by Radiation-Induced Lung Injury (RILI). RILI develops in two phases: (i) the early phase (days-weeks) referred to radiation pneumonitis (RP), and (ii) the late phase (months). There is a strong interest in early detection of RP using imaging to improve outcomes of RT for lung cancer. This thesis describes a promising approach based on 129Xe gas as a contrast ...
Isotopic Discrimination In The Double-Crested Cormorant (Phalacrocorax Auritus), 2015 Cornell University
Isotopic Discrimination In The Double-Crested Cormorant (Phalacrocorax Auritus), Elizabeth C. Craig, Brian S. Dorr, Katie C. Hanson-Dorr, Jed P. Sparks, Paul D. Curtis
Brian S Dorr
The diet-tissue discrimination factor is the amount by which a consumer’s tissue varies isotopically from its diet, and is therefore a key element in models that use stable isotopes to estimate diet composition. In this study we measured discrimination factors in blood (whole blood, red blood cells and plasma), liver, muscle and feathers of Double- crested Cormorants (Phalacrocorax auritus) for stable isotope ratios of carbon, nitrogen and sulfur. Cormorants exhibited discrimination factors that differed significantly among tissue types (for carbon and nitrogen), and differed substantially (in the context of the isotopic variation among relevant prey species) from those observed ...
Incorporation Of Fibrin Into A Collagen–Glycosaminoglycan Matrix Results In A Scaffold With Improved Mechanical Properties And Enhanced Capacity To Resist Cell-Mediated Contraction, 2015 Dublin Institute of Technology
Incorporation Of Fibrin Into A Collagen–Glycosaminoglycan Matrix Results In A Scaffold With Improved Mechanical Properties And Enhanced Capacity To Resist Cell-Mediated Contraction, Claire Brougham, Tanya J. Levingstone, Stefan Jockenhoevel, Thomas C. Flanagan, Fergal J. O'Brien
Fibrin has many uses as a tissue engineering scaffold, however many in vivo studies have shown a reduction in function resulting from the susceptibility of fibrin to cell-mediated contraction. The overall aim of the present study was to develop and characterise a reinforced natural scaffold using fibrin, collagen and glycosaminoglycan (FCG), and to examine the cell-mediated contraction of this scaffold in comparison to fibrin gels. Through the use of an injection loading technique, a homogenous FCG scaffold was developed. Mechanical testing showed a sixfold increase in compressive modulus and a thirtyfold increase in tensile modulus of fibrin when reinforced with ...
Evaluation Of Effective Operational Cycle Time And Bioprocess Parameters In A Sequential Batch Reactor For Efficient Organic And Nutrient Removal From Domestic Sewage, Sandip S. Magdum, Siva Kumar Varigala, Yogesh N. Patil, Gauri P. Minde, Janardhan B. Bornare, V. Kalyanraman
Sandip S. Magdum
Anaerobic, anoxic and aerobic environment can be simulated in the single stage sequential batch reactor (SBR) . Various design conditions viz., combinations of different phase time and different cycle time, hydraulic residence time (HRT), substrate loading rate, sludge age (SRT) and aeration time were analyzed for optimum biological treatment. The pilot runs were evaluated with the design conditions of food/microbe ratio (F/M) 0.2 per day and MLSS of 4950 mg/L. For the given design conditions 4, 5 and 6 hours cycle lengths were analyzed for their efficient performance with 30-33% of decant volume for sewage containing C ...
Reactive Oxygen Species-Mediated Neurodegeneration Is Independent Of The Ryanodine Receptor In Caenorhabditis Elegans, 2015 Coastal Carolina University
Reactive Oxygen Species-Mediated Neurodegeneration Is Independent Of The Ryanodine Receptor In Caenorhabditis Elegans, Lyndsay E.A. Young, Daniel C. Williams
Journal of the South Carolina Academy of Science
Despite the significant impacts on human health caused by neurodegeneration, our understanding of the degeneration process is incomplete. The nematode Caenorhabditis elegans is emerging as a genetic model organism well suited for identification of conserved cellular mechanisms and molecular pathways of neurodegeneration. Studies in the worm have identified factors that contribute to neurodegeneration, including excitotoxicity and stress due to reactive oxygen species (ROS). Disruption of the gene unc-68, which encodes the ryanodine receptor, abolishes excitotoxic cell death, indicating a role for calcium (Ca2+) signaling in neurodegeneration. We tested the requirement for unc-68 in ROS-mediated neurodegeneration using the genetically encoded ...
Characterization Of Inhibitors Of Fatty Acid Transport Protein-2 In Cell And Animal Models, 2015 University of Nebraska-Lincoln
Characterization Of Inhibitors Of Fatty Acid Transport Protein-2 In Cell And Animal Models, Nipun Saini
Theses and Dissertations in Biochemistry
Obesity is correlated with insulin resistance and elevated levels of glucose, triglycerides and free fatty acids in blood. This affects overall metabolism and leads to disease. In the obese state, fat also accumulates in non-adipose tissue including liver, muscle and pancreas, where it can lead to cellular dysfunction and death. Currently, only a limited number of drugs are available to combat obesity and it is clear that new drugs, which more narrowly target the metabolic pathways involved, are required. Fatty Acid Transport Proteins (FATPs) are bifunctional proteins involved in the uptake and activation of fatty acids by esterification with coenzyme ...
Molecular Targeting Of Protein Arginine Deiminases To Suppress Colitis And Prevent Colon Cancer, 2015 South Carolina College of Pharmacy
Molecular Targeting Of Protein Arginine Deiminases To Suppress Colitis And Prevent Colon Cancer, Erin E. Witalison, Xiangli Cui, Corey P. Causey, Paul R. Thompson, Lorne J. Hofseth
Thompson Lab Publications
Ulcerative colitis (UC) is a chronic disease, in which the lining of the colon becomes inflamed and develops ulcers leading to abdominal pain, diarrhea, and rectal bleeding. The extent of these symptoms depends on disease severity. The protein arginine deiminase (PAD) family of enzymes converts peptidyl-Arginine to peptidyl-Citrulline through citrullination. PADs are dysregulated, with abnormal citrullination in many diseases, including UC and colorectal cancer (CRC). We have developed the small molecule, pan-PAD inhibitor, Chlor-amidine (Cl-amidine), with multiple goals, including treating UC and preventing CRC. Building off our recent results showing that: 1) Cl-amidine suppresses colitis in vivo in a dextran ...
Chromatin Interaction Analysis Reveals Changes In Small Chromosome And Telomere Clustering Between Epithelial And Breast Cancer Cells, 2015 University of Massachusetts Medical School
Chromatin Interaction Analysis Reveals Changes In Small Chromosome And Telomere Clustering Between Epithelial And Breast Cancer Cells, Ahmet Rasim Barutcu, Bryan R. Lajoie, Rachel Patton Mccord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, Andre J. Van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano, Gary S. Stein
Program in Systems Biology Publications and Presentations
BACKGROUND: Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines.
RESULTS: Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency ...
Heterogeneous Oxidation Of Catechol, 2015 University of Kentucky
Heterogeneous Oxidation Of Catechol, Elizabeth A. Pillar, Ruixin Zhou, Marcelo I. Guzman
Chemistry Faculty Publications
Natural and anthropogenic emissions of aromatic hydrocarbons from biomass burning, agro-industrial settings, and fossil fuel combustion contribute precursors to secondary aerosol formation (SOA). How these compounds are processed under humid tropospheric conditions is the focus of current attention to understand their environmental fate. This work shows how catechol thin films, a model for oxygenated aromatic hydrocarbons present in biomass burning and combustion aerosols, undergo heterogeneous oxidation at the air–solid interface under variable relative humidity (RH = 0–90%). The maximum reactive uptake coefficient of O3(g) by catechol γO3 = (7.49 ± 0.35) × 10–6 occurs for ...
Caenorhabditis Elegans Alg-1 Antimorphic Mutations Uncover Functions For Argonaute In Microrna Guide Strand Selection And Passenger Strand Disposal, 2015 University of Massachusetts Medical School
Caenorhabditis Elegans Alg-1 Antimorphic Mutations Uncover Functions For Argonaute In Microrna Guide Strand Selection And Passenger Strand Disposal, Anna Y. Zinovyeva, Isana Veksler-Lublinsky, Ajay A. Vashisht, James A. Wohlschlegel, Victor R. Ambros
Program in Molecular Medicine Publications and Presentations
MicroRNAs are regulators of gene expression whose functions are critical for normal development and physiology. We have previously characterized mutations in a Caenorhabditis elegans microRNA-specific Argonaute ALG-1 (Argonaute-like gene) that are antimorphic [alg-1(anti)]. alg-1(anti) mutants have dramatically stronger microRNA-related phenotypes than animals with a complete loss of ALG-1. ALG-1(anti) miRISC (microRNA induced silencing complex) fails to undergo a functional transition from microRNA processing to target repression. To better understand this transition, we characterized the small RNA and protein populations associated with ALG-1(anti) complexes in vivo. We extensively characterized proteins associated with wild-type and mutant ALG-1 and ...
Transcriptional And Post-Transcriptional Control Of Adipocyte Differentiation By Jumonji Domain-Containing Protein 6, 2015 University of Massachusetts Medical School
Transcriptional And Post-Transcriptional Control Of Adipocyte Differentiation By Jumonji Domain-Containing Protein 6, Yu-Jie Hu, Houda Belaghzal, Wen-Yu Hsiao, Jun Qi, James E. Bradner, David A. Guertin, Said Sif, Anthony N. Imbalzano
Cell and Developmental Biology Publications and Presentations
Jumonji domain-containing protein 6 (JMJD6) is a nuclear protein involved in histone modification, transcription and RNA processing. Although JMJD6 is crucial for tissue development, the link between its molecular functions and its roles in any given differentiation process is unknown. We report that JMJD6 is required for adipogenic gene expression and differentiation in a manner independent of Jumonji C domain catalytic activity. JMJD6 knockdown led to a reduction of C/EBPbeta and C/EBPdelta protein expression without affecting mRNA levels in the early phase of differentiation. However, ectopic expression of C/EBPbeta and C/EBPdelta did not rescue differentiation. Further ...
Cfap54 Is Required For Proper Ciliary Motility And Assembly Of The Central Pair Apparatus In Mice, Casey W. Mckenzie, Branch Craige, Tiffany V. Kroeger, Rozzy Finn, Todd A. Wyatt, Joseph H. Sisson, Jacqueline A. Pavlik, Lara Strittmatter, Gregory M. Hendricks, George B. Witman, Lance Lee
Cell and Developmental Biology Publications and Presentations
Motile cilia and flagella play critical roles in fluid clearance and cell motility, and dysfunction commonly results in the pediatric syndrome primary ciliary dyskinesia (PCD). CFAP221, also known as PCDP1, is required for ciliary and flagellar function in mice and Chlamydomonas reinhardtii, where it localizes to the C1d projection of the central microtubule apparatus and functions in a complex that regulates flagellar motility in a calcium-dependent manner. We demonstrate that the genes encoding the mouse homologues of the other C. reinhardtii C1d complex members are primarily expressed in motile ciliated tissues, suggesting a conserved function in mammalian motile cilia. The ...
Quinone Reductase 2 Is A Flavin Redox Switch, 2015 The University of Western Ontario
Quinone Reductase 2 Is A Flavin Redox Switch, Kevin Ka Ki Leung
Electronic Thesis and Dissertation Repository
Quinone reductase 2 (NQO2) is a mammalian enzyme that catalyzes the reduction of quinone using an unusual co-substrate, dihydronicotinamide riboside (NRH). In addition, NQO2 has a secondary function, which is to modulate the 20S proteasomal degradation of p53 in a redox-dependent manner. This alternate function has been characterized in its sister enzyme quinone reductase 1 (NQO1) and yeast quinone reductase Lot6p, but relatively few studies have investigated the role of NQO2 beyond quinone catalysis. From studies of Lot6p, it was proposed that quinone reductases could be categorized as flavin redox switches. In this thesis, the how NQO2 functions as a ...