Use Of Clustering Techniques For Protein Domain Analysis,
2016
University of Nebraska - Lincoln
Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene
Department of Computer Science and Engineering: Dissertations, Theses, and Student Research
Next-generation sequencing has allowed many new protein sequences to be identified. However, this expansion of sequence data limits the ability to determine the structure and function of most of these newly-identified proteins. Inferring the function and relationships between proteins is possible with traditional alignment-based phylogeny. However, this requires at least one shared subsequence. Without such a subsequence, no meaningful alignments between the protein sequences are possible. The entire protein set (or proteome) of an organism contains many unrelated proteins. At this level, the necessary similarity does not occur. Therefore, an alternative method of understanding relationships within diverse sets of proteins …
Structural Analysis Of Tpr Ligand Complexes Of Stip1 Implicated In Alzheimer's Disease,
2016
The University of Western Ontario
Structural Analysis Of Tpr Ligand Complexes Of Stip1 Implicated In Alzheimer's Disease, Andrzej Maciejewski
Electronic Thesis and Dissertation Repository
Amyloid-beta oligomers (AbOs) induce neurological dysfunction in part through the cellular prion protein (PrPC) resulting in deregulation of Ca2+ homeostasis in Alzheimer’s disease (AD). Stress inducible phosphoprotein 1 (STIP1), a cochaperone of Hsp70 and Hsp90, protects neurons from AbO-induced cell death. As well, STIP1 interacts with the Ca2+ sensor S100A1, which is an important biomarker upregulated in AD and regulates STIP1 and other cochaperone association with Hsp70 and Hsp90. While the molecular details of STIP1-Hsp complexes are well studied, little information is available concerning alternate STIP1 binding partners. Here, we investigated the structural details of STIP1 …
Competent Overall Water-Splitting Electrocatalysts Derived From Zif-67 Grown On Carbon Cloth,
2016
Utah State University
Competent Overall Water-Splitting Electrocatalysts Derived From Zif-67 Grown On Carbon Cloth, Xin Liu, Jinmei Dong, Bo You, Yujie Sun
Chemistry and Biochemistry Faculty Publications
The design of nonprecious, bifunctional, and highly competent electrocatalysts for both H2 and O2evolution reactions (HER and OER) has attracted increasing interest recently. Herein, we report a cobalt-based electrocatalyst derived from ZIF-67 grown on carbon cloth (Co–P/NC/CC) for overall water splitting electrocatalysis. The as-prepared Co–P/NC/CC catalyst exhibited remarkable catalytic performance in 1 M KOH with Tafel slopes of 52 and 61 mV dec−1 for HER and OER, respectively. When serving as catalysts for both the cathode and anode, our Co–P/NC/CC demonstrated high efficiency and strong robustness. A thorough comparison with other control samples and detailed characterization …
Nmrfx Processor: A Cross-Platform Nmr Data Processing Program,
2016
One Moon Scientific
Nmrfx Processor: A Cross-Platform Nmr Data Processing Program, Michael Norris, Bayard Fetler, Jan Marchant, Bruce A. Johnson
Advanced Science Research Center
NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with multiple cores or CPUs. Processing scripts can be generated automatically from the parameters of NMR experiments or interactively constructed in the GUI. …
Fulleretic Well-Defined Scaffolds: Donor–Fullerene Alignment Through Metal Coordination And Its Effect On Photophysics,
2016
University of South Carolina
Fulleretic Well-Defined Scaffolds: Donor–Fullerene Alignment Through Metal Coordination And Its Effect On Photophysics, Derek E. Williams, Ekaterina A. Dolgopolova, Danielle C. Godfrey, Evgeniya D. Ermolaeva, Perry J. Pellechia Dr., Andrew B. Greytak Prof. Dr., Mark Smith Dr., Stanislav M. Avdoshenko, Dr., Alexey A. Popov Dr., Natalia B. Shustova Prof. Dr.
Faculty Publications
Herein, we report the first example of a crystalline metal–donor–fullerene framework, in which control of the donor–fullerene mutual orientation was achieved through chemical bond formation, in particular, by metal coordination. The 13C cross-polarization magic-angle spinning NMR spectroscopy, X-ray diffraction, and time-resolved fluorescence spectroscopy were performed for comprehensive structural analysis and energy-transfer (ET) studies of the fulleretic donor–acceptor scaffold. Furthermore, in combination with photoluminescence measurements, the theoretical calculations of the spectral overlap function, Förster radius, excitation energies, and band structure were employed to elucidate the photophysical and ET processes in the prepared fulleretic material. We envision that the well-defined fulleretic donor–acceptor …
Long-Range Acoustic Interactions In Insect Swarms: An Adaptive Gravity Model,
2016
Weizmann Institute of Science
Long-Range Acoustic Interactions In Insect Swarms: An Adaptive Gravity Model, Dan Gorbonos, Reuven Ianconescu, James G. Puckett, Rui Ni, Nicholas T. Ouellette, Nir S. Gov
Physics and Astronomy Faculty Publications
The collective motion of groups of animals emerges from the net effect of the interactions between individual members of the group. In many cases, such as birds, fish, or ungulates, these interactions are mediated by sensory stimuli that predominantly arise from nearby neighbors. But not all stimuli in animal groups are short range. Here, we consider mating swarms of midges, which are thought to interact primarily via long-range acoustic stimuli. We exploit the similarity in form between the decay of acoustic and gravitational sources to build a model for swarm behavior. By accounting for the adaptive nature of the midges' …
The Confounding Effects Of Particle Size And Substrate Bulk Density On Phanerochaete Chrysosporium Pretreatment On Panicum Virgatum,
2016
University of Kentucky
The Confounding Effects Of Particle Size And Substrate Bulk Density On Phanerochaete Chrysosporium Pretreatment On Panicum Virgatum, Amanda N. Hickman, Sue E. Nokes, William S. Sympson, Mathew J. Ruwaya, Michael D. Montross, Barbara L. Knutson
Biosystems and Agricultural Engineering Faculty Publications
Phanerochaete chrysosporium treatment is less effective as a biological pretreatment on feedstock with larger particle sizes. We hypothesized that the improved effectiveness of the pretreatment when smaller particle sizes are used may be due to the inherently higher bulk density with smaller particle sizes. The effects of substrate bulk density and particle size on the efficacy of P. chrysosporium pretreatment of switchgrass (Panicum virgatum) was tested experimentally. Phanerochaete chrysosporium was grown on senesced switchgrass (2 different particle sizes) with various bulk densities. In all treatments, the fungal-pretreated samples released more glucose during enzymatic saccharification than the control sample. …
Identification Of Preferred Dna-Binding Sites For The Thermus Thermophilus Transcriptional Regulator Sbtr By The Combinatorial Approach Repsa,
2016
Kennesaw State University
Identification Of Preferred Dna-Binding Sites For The Thermus Thermophilus Transcriptional Regulator Sbtr By The Combinatorial Approach Repsa, Michael W. Van Dyke, Matthew D. Beyer, Emily Clay, Jonathan L. Mcmurry
Faculty and Research Publications
One of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred DNA-binding sequences. This may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. Previously, we had developed the novel combinatorial approach Restriction Endonuclease Protection, Selection and Amplification (REPSA), which relies not on the physical separation of ligand-nucleic acid complexes but instead selects on the basis of ligand-dependent inhibition of enzymatic template inactivation, specifically cleavage by type …
In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy,
2016
Technological University Dublin
In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne
Articles
No abstract provided.
Polyisobutylene-Paclitaxel Conjugates With Pendant Carboxylic Acids And Polystyrene Chains: Towards Multifunctional Stent Coatings With Slow Drug Release,
2016
The University of Western Ontario
Polyisobutylene-Paclitaxel Conjugates With Pendant Carboxylic Acids And Polystyrene Chains: Towards Multifunctional Stent Coatings With Slow Drug Release, John F. Trant, Mahmoud M. Abd Rabo Moustafa, Inderpreet Sran, Elizabeth R. Gillies
Chemistry and Biochemistry Publications
Drug-eluting stents are used in the treatment of atherosclerosis, where the incorporation of anti-proliferative or anti-inflammatory drugs decreases the rate of restenosis, the recurrence of artery narrowing. However, these stents can suffer from limitations such as drug depletion and delamination of the drug-eluting coating from the stent surface. Described here is an approach aimed at addressing these issues. Starting from a maleic anhydride adduct of polyisobutylene (PIB) prepared from butyl rubber, ring opening using paclitaxel (PTX) or a combination of PTX and polystyrene (PS) afforded covalent conjugates of PTX and PIB or PIB-PS graft copolymers bearing pendant carboxylic acids. When …
Domains Of Stip1 Responsible For Regulating Prpc-Dependent Amyloid-Β Oligomer Toxicity.,
2016
Western University
Domains Of Stip1 Responsible For Regulating Prpc-Dependent Amyloid-Β Oligomer Toxicity., Andrzej Maciejewski, Valeriy G Ostapchenko, Flavio H Beraldo, Vania F Prado, Marco A M Prado, Wing-Yiu Choy
Biochemistry Publications
Soluble oligomers of amyloid-beta peptide (AβO) transmit neurotoxic signals through the cellular prion protein (PrP(C)) in Alzheimer's disease (AD). Secreted stress-inducible phosphoprotein 1 (STIP1), an Hsp70 and Hsp90 cochaperone, inhibits AβO binding to PrP(C) and protects neurons from AβO-induced cell death. Here, we investigated the molecular interactions between AβO and STIP1 binding to PrP(C) and their effect on neuronal cell death. We showed that residues located in a short region of PrP (90-110) mediate AβO binding and we narrowed the major interaction in this site to amino acids 91-100. In contrast, multiple binding sites on STIP1 (DP1, TPR1 and TPR2A) …
Ten Simple Rules For Taking Advantage Of Git And Github,
2016
European Bioinformatics Institute (EMBL-EBI), UK
Ten Simple Rules For Taking Advantage Of Git And Github, Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe Da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno
Molecular and Cellular Biochemistry Faculty Publications
No abstract provided.
Morphological And Material Effects In Van Der Waals Interactions,
2016
University of Massachusetts Amherst
Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins
Doctoral Dissertations
Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions. In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these …
Control Of Proteolysis During The Caulobacter Cell Cycle,
2016
University of Massachusetts Amherst
Control Of Proteolysis During The Caulobacter Cell Cycle, Joanne Lau
Doctoral Dissertations
Intracellular protein destruction is a carefully coordinated and timed regulatory mechanism that cells utilize to modulate growth, adaptation to environmental cues, and survival. In Caulobacter crescentus, a bacterium known for studies of bacterial cell division cycle, the response regulator CpdR couples phosphorylation events with the AAA+ protease ClpXP to provide punctuated degradation of crucial substrates involved in cell cycle regulation. CpdR functions like an adaptor to alter substrate choice by ClpXP, however it remains unclear how CpdR influences its multiple targets. In this thesis, we show that, unlike canonical ClpXP adaptors, CpdR alone does not strongly bind its substrate. …
Novel Advancements For Improving Sprout Safety,
2016
University of Massachusetts Amherst
Novel Advancements For Improving Sprout Safety, Kyle S. Landry
Doctoral Dissertations
All varieties of bean sprouts (mung bean, alfalfa, broccoli, and radish) are classified as a “super-food” and are common staples for health conscious consumers. Along with the proposed health benefits, there is also an inherent risk of foodborne illness. When sprouts are cooked, there is little risk of illness. The purpose of this dissertation was to explore novel techniques to minimize or prevent the incidence of foodborne illness associated with the consumption of sprouts. Three areas were investigated: 1) the use of a biocontrol organism, 2) the use of a novel spontaneous carvacrol nanoemulsion, and 3) the influence of the …
Photolysis Of Triazenylbenzoic Acids For Click Chemistry,
2016
University of Massachusetts Amherst
Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann
Doctoral Dissertations
Copper catalyzed cycloaddition of terminal alkynes and azides has revolutionized the field of bioconjugate chemistry. Unfortunately, typical copper catalysts are known to disrupt relevant biological systems, so it has become necessary to develop new, copper-free methods that are less cytotoxic. particular interest are "click" probes which can be activated with an outside light source, giving the user spatial and temporal control over the system being investigated. We have developed a method in which an aryl diazonium salt is rapidly generated using photolysis of the triazene functional group, and subsequently coupled with an electron rich aromatic nucleophile to yield an azobenzene. …
Kinetic And Dynamic Insights Into The Substrate Interactions And Catalysis Of Factor Inhibiting Hif-1 (Fih-1),
2016
University of Massachusetts Amherst
Kinetic And Dynamic Insights Into The Substrate Interactions And Catalysis Of Factor Inhibiting Hif-1 (Fih-1), Cristina B. Martin
Doctoral Dissertations
inhibiting HIF-1 (FIH-1) modulates the master regulator of hypoxia sensing, hypoxia inducible factor-1 (HIF-1), by transcriptional repression making it an attractive potential target for treatment of hypoxia-related diseases. Given that similar enzymes are present within the cell and that they have other important physiological roles, defining the therapeutic window by which it can be selectively targeted becomes an issue. Consequently, it’s necessary to have a deeper understanding of the substrate interactions in FIH-1 that contributes to catalysis as this is one avenue that can be explored for future therapeutic investigations. The overall goal of this dissertation is to gain kinetic …
Dynamics Of Microtubule Networks With Antiparallel Crosslinkers,
2016
University of Massachusetts Amherst
Dynamics Of Microtubule Networks With Antiparallel Crosslinkers, Kasimira T. Stanhope
Masters Theses
Microtubules are the most rigid element of the cytoskeleton. They are responsible for the structure of cells and make up the tracks for intracellular cargo transport. Interactions between microtubules, motor proteins, and microtubule-associated proteins drive important mechanisms in the cell, such as cell division, cell motility, cell homeostasis, and cell signaling. I seek to understand how such complex, energy-consuming non-equilibrium biological networks self-organize by studying in vitro microtubules bundled by microtubule-associated protein 65 (MAP65), in kinesin-1 gliding assays. I found that large networks can break into smaller, cell-like networks that can mimic types of cell motility. Dynamics of these networks …
Chemical Stability Of Curcumin: Structure And Activity Relationship (Sar) Study,
2016
University of Massachusetts Amherst
Chemical Stability Of Curcumin: Structure And Activity Relationship (Sar) Study, Zheyuan Du
Masters Theses
Over the past decades, numerous studies have shown that curcumin has potent biological activities. As a potential chemopreventing agent, curcumin was demonstrated to exert anti-cancer effects in both in vitro and in vivo studies. However, low bioavailability of curcumin limited human clinical trials and its application to be formulated as therapeutics. In this thesis, we will summarize the anti-cancer effects of curcumin in animal studies and clinical trials. In addition, an SAR study will be introduced to elucidate the mechanism of curcumin degradation at physiological pH. We synthesized various curcumin analogues and compared their stability in phosphate buffer using HPLC …
Assessment Of Post-Treatment Imaging Changes Following Radiotherapy Using Magnetic Susceptibility Techniques,
2016
The University of Western Ontario
Assessment Of Post-Treatment Imaging Changes Following Radiotherapy Using Magnetic Susceptibility Techniques, Jean-Guy Belliveau
Electronic Thesis and Dissertation Repository
Radiation therapy (RT) is a common treatment for brain neoplasms and is used alone or in combination with other therapies. The use of RT has been found to be successful in controlling tumors and extending the overall survival of patients; however, there are many unanswered questions regarding radiotherapy effects in the normal brain surrounding or infiltrated by tumor. Changes to the vascular and parenchyma have been documented, and more recently inflammatory mechanisms have been postulated to play a role in radiation injury. Traditional imaging techniques used within the clinic (CT and MRI) are often lacking in their ability to differentiate …
