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Other Biochemistry, Biophysics, and Structural Biology Commons

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453 full-text articles. Page 5 of 18.

Stability Of Peatland Carbon To Rising Temperatures, R. M. Wilson, A. M. Hopple, M. M. Tfaily, S. D. Sebestyen, C. W. Schadt, L. Pfeifer-Meister, Cassandra Medvedeff, K. J. McFarlane, J. E. Kostka, M. Kolton, R. K. Kolka, L. A. Kluber, Jason K. Keller, T. P. Guilderson, N. A. Griffiths, J. P. Chanton, S. D. Brigham, P. J. Hanson 2016 Florida State University

Stability Of Peatland Carbon To Rising Temperatures, R. M. Wilson, A. M. Hopple, M. M. Tfaily, S. D. Sebestyen, C. W. Schadt, L. Pfeifer-Meister, Cassandra Medvedeff, K. J. Mcfarlane, J. E. Kostka, M. Kolton, R. K. Kolka, L. A. Kluber, Jason K. Keller, T. P. Guilderson, N. A. Griffiths, J. P. Chanton, S. D. Brigham, P. J. Hanson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20–30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily ...


Expression Of Glycine-Rich Proteins Found In Salivary Glands Of The Lone Star Tick (Amblyomma Americanum) Using A Mammalian Cell Line, Annabelle Clark 2016 The University of Southern Mississippi

Expression Of Glycine-Rich Proteins Found In Salivary Glands Of The Lone Star Tick (Amblyomma Americanum) Using A Mammalian Cell Line, Annabelle Clark

Honors Theses

Ticks play an important ecological role as well as a growing role in human health and veterinary care. Ticks are hosts to a plethora of microbial pathogens that can be transferred during feeding to cause tick-borne diseases in humans and many animals. Ticks may in large part owe the success of the transfer of these pathogens between hosts to their complex saliva. The saliva secreted upon a tick’s attachment to a host serves the following, among other, functions: anti-hemostasis of the blood pool, preventing an inflammatory response at the bite site, and serving as a natural anti-microbial substance. An ...


The Intestinal Copper Exporter Cua-1 Is Required For Systemic Copper Homeostasis In Caenorhabditis Elegans, Haarin Chun, Anuj Kumar Sharma, Jaekwon Lee, Jefferson Chan, Shang Jia, Byung-Eun Kim 2016 University of California at Berkeley

The Intestinal Copper Exporter Cua-1 Is Required For Systemic Copper Homeostasis In Caenorhabditis Elegans, Haarin Chun, Anuj Kumar Sharma, Jaekwon Lee, Jefferson Chan, Shang Jia, Byung-Eun Kim

Biochemistry -- Faculty Publications

Copper plays key catalytic and regulatory roles in biochemical processes essential for normal growth, development, and health. Defects in copper metabolism cause Menkes and Wilson’s disease, myeloneuropathy, and cardiovascular disease and are associated with other pathophysiological states. Consequently, it is critical to understand the mechanisms by which organisms control the acquisition, distribution, and utilization of copper. The intestinal enterocyte is a key regulatory point for copper absorption into the body; however, the mechanisms by which intestinal cells transport copper to maintain organismal copper homeostasis are poorly understood. Here, we identify a mechanism by which organismal copper homeostasis is maintained ...


Maintenance Of The Ph Gradient In The Gastric Mucus Layer., Owen Lewis 2016 The University Of Utah

Maintenance Of The Ph Gradient In The Gastric Mucus Layer., Owen Lewis

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Microfluidic Cantilever Detects Bacteria And Measures Their Susceptibility To Antibiotics In Small Confined Volumes, Hashem Etayash, M. F. Khan, Kamaljit Kaur, Thomas Thundat 2016 University of Alberta

Microfluidic Cantilever Detects Bacteria And Measures Their Susceptibility To Antibiotics In Small Confined Volumes, Hashem Etayash, M. F. Khan, Kamaljit Kaur, Thomas Thundat

Pharmacy Faculty Articles and Research

In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a ...


Structural Determinants Allowing Transferase Activity In Sensitive To Freezing 2, Classified As A Family I Glycosyl Hydrolase, Rebecca Roston, Kun Wang, Leslie A. Kuhn, Christoph Benning 2016 University of Nebraska- Lincoln

Structural Determinants Allowing Transferase Activity In Sensitive To Freezing 2, Classified As A Family I Glycosyl Hydrolase, Rebecca Roston, Kun Wang, Leslie A. Kuhn, Christoph Benning

Biochemistry -- Faculty Publications

Background: SENSITIVE TO FREEZING 2 (SFR2) is classified as a glycosyl hydrolase, and by using glycosyltransferase activity, it modifies membrane lipids to promote freeze tolerance.

Results: Although the active site of SFR2 is identical to hydrolases, adjacent loop regions contribute to its transferase activity.

Conclusion: Transferase activity evolved by modifications external to the core catalytic site.

Significance: Defined structure-function relationships will inform engineering of transferases and freeze tolerance.


Sending Out An Sos: Mitochondria As A Signaling Hub, Iryna Bohovych, Oleh Khalimonchuk 2016 University of Nebraska- Lincoln

Sending Out An Sos: Mitochondria As A Signaling Hub, Iryna Bohovych, Oleh Khalimonchuk

Biochemistry -- Faculty Publications

Normal cellular physiology is critically dependent on numerous mitochondrial activities including energy conversion, cofactor and precursor metabolite synthesis, and regulation of ion and redox homeostasis. Advances in mitochondrial research during the last two decades provide solid evidence that these organelles are deeply integrated with the rest of the cell and multiple mechanisms are in place to monitor and communicate functional states of mitochondria. In many cases, however, the exact molecular nature of various mitochondria-to-cell communication pathways is only beginning to emerge. Here, we review various signals emitted by distressed or dysfunctional mitochondria and the stress-responsive pathways activated in response to ...


Electron Transport To Photosystem I By Soluble Carriers: Evolution Of The Interacting Pair, Khoa Dang Nguyen 2016 University of Tennessee, Knoxville

Electron Transport To Photosystem I By Soluble Carriers: Evolution Of The Interacting Pair, Khoa Dang Nguyen

Doctoral Dissertations

Oxygenic photosynthesis is driven via sequential action of Photosystem II (PSII) and (PSI) reaction centers via the Z-­‐scheme. Both of these pigment– membrane protein complexes are found in cyanobacteria, algae, and plants. PSI, unlike PSII, is remarkably stable and does not undergo limiting photo-­‐damage. This stability, as well as other fundamental structural differences, makes PSI the most attractive reaction centers for applied photosynthetic applications. These applied applications exploit the efficient light harvesting and high quantum yield of PSI where the isolated PSI particles are redeployed providing electrons directly as a photocurrent or, via a coupled catalyst to yield ...


In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne 2016 Dublin Institute of Technology

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.


Spectroscopic Studies Of Anthracyclines: Structural Characterization And In Vitro Tracking, Zeineb Farhane, Hugh Byrne, Malgorzata Baranska 2016 Dublin Institute of Technology

Spectroscopic Studies Of Anthracyclines: Structural Characterization And In Vitro Tracking, Zeineb Farhane, Hugh Byrne, Malgorzata Baranska

Articles

A broad spectroscopic characterization, using ultraviolet-visible (UV-vis) and Fourier transform infrared absorption as well as Raman scattering, of two commonly used anthracyclines antibiotics (DOX) daunorubicin (DNR), their epimers (EDOX, EDNR) and ten selected analogs is presented. The paper serves as a comprehensive spectral library of UV-vis, IR and Raman spectra of anthracyclines in the solid state and in solution. The particular advantage of Raman spectroscopy for the measurement and analysis of individual antibiotics is demonstrated. Raman spectroscopy can be used to monitor the in vitro uptake and distribution of the drug in cells, using both 488 nm and 785 nm ...


Small-Angle X-Ray Scattering Studies Of The Oligomeric State And Quaternary Structure Of The Trifunctional Proline Utilization A (Puta) Flavoprotein From Escherichia Coli, Ranjan K. Singh, John D. Larson, Weidong Zhu, Robert P. Rambo, Greg L. Hura, Donald F. Becker, John J. Tanner 2016 University of Missouri-Columbia

Small-Angle X-Ray Scattering Studies Of The Oligomeric State And Quaternary Structure Of The Trifunctional Proline Utilization A (Puta) Flavoprotein From Escherichia Coli, Ranjan K. Singh, John D. Larson, Weidong Zhu, Robert P. Rambo, Greg L. Hura, Donald F. Becker, John J. Tanner

Biochemistry -- Faculty Publications

Background: Trifunctional proline utilization A (PutA) proteins are multifunctional flavoproteins that catalyze two reactions and repress transcription of the put regulon.

Results: PutA from Escherichia coli is a V-shaped dimer, with the DNA-binding domain mediating dimerization.

Conclusion: Oligomeric state and quaternary structures are not conserved by PutAs.

Significance: The first three-dimensional structural information for any trifunctional PutA is reported.


A Comparison Of Catabolic Pathways Induced In Primary Macrophages By Pristine Single Walled Carbon Nanotubes And Pristine Graphene, Caroline More, Jennifer McIntyre, Luke O'Neill, Hugh Byrne 2016 Dublin Institute of Technology

A Comparison Of Catabolic Pathways Induced In Primary Macrophages By Pristine Single Walled Carbon Nanotubes And Pristine Graphene, Caroline More, Jennifer Mcintyre, Luke O'Neill, Hugh Byrne

Articles

Understanding the correlation between the physico-chemical properties of carbonaceous nanomaterials and how these properties impact on cells and subcelluar mechanisms is critical to their risk assessment and safe translation into newly engineered devices. Here the toxicity, uptake and catabolic response of primary human macrophages to pristine graphene (PG) and pristine single walled carbon nanotubes (pSWCNT) are explored, compared and contrasted. The nanomaterial toxicity was assessed using three complementary techniques (live-dead assay, real time impedance technique and confocal microscopic analysis), all of which indicated no signs of acute cytotoxicity in response to PG or pSWCNT. Transmission electron microscopy (TEM) demonstrated that ...


Modification Of The In Vitro Uptake Mechanism And Anti-Oxidant Levels In Hacat Cells And Resultant Changes To Toxicity And Oxidative Stress Of G4 And G6 Poly (Amido Amine) Dendrimer Nanoparticles., Marcus Maher, Hugh J. Byrne 2016 Dublin Institute of Technology

Modification Of The In Vitro Uptake Mechanism And Anti-Oxidant Levels In Hacat Cells And Resultant Changes To Toxicity And Oxidative Stress Of G4 And G6 Poly (Amido Amine) Dendrimer Nanoparticles., Marcus Maher, Hugh J. Byrne

Articles

The mechanism of cellular uptake by endocytosis and subsequent oxidative stress has been identified as the paradigm for the toxic response of cationically surface charged nanoparticles. In an attempt to circumvent the process, the effect of increased cellular membrane permeability on the uptake mechanisms of poly (amidoamine) dendrimers generation 4 (G4) and 6 (G6) in vitro was investigated. Immortalised, non-cancerous human keratinocyte (HaCaT) cells were treated with DL-Buthionine-(S,R)-sulfoximine (BSO). Active uptake of the particles was monitored using fluorescence microscopy to identify and quantify endosomal activity and resultant oxidative stress, manifest as increased levels of reactive oxygen species ...


Computational Investigations Into The Molecular Underpinnings Of Eyesight Signaling Pathways, Shaan Kamal 2016 University of Connecticut

Computational Investigations Into The Molecular Underpinnings Of Eyesight Signaling Pathways, Shaan Kamal

University Scholar Projects

Phosphodiesterase 6 (PDE6) is a critical enzyme in the eyesight-signaling pathway. When activated, PDE6 hydrolyzes cGMP to GMP, which deactivates cGMP- gated ion channels, causing hyperpolarization of the cell and activating the sensory neurons responsible for vision. Within the PDE family, PDE6 is the only enzyme known to have an inhibitory subunit (PDE6-γ), which allows for the regulation of cGMP levels. When PDE6-γ is bound to PDE6, the enzyme is turned “off” and cannot catalyze cGMP. The α subunit of the G-protein transducin removes PDE6-γ and activates PDE6. PDE6 has proven problematic to isolate, making it difficult to study experimentally ...


Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel 2016 University of Arkansas, Fayetteville

Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel

Chemistry & Biochemistry Undergraduate Honors Theses

Fibroblast growth factors (FGFs) are family of proteins that belong to a group of growth factors that are found in mammals and play an important role in angiogenesis, differentiation, organogenesis, and tissue repair. In summary, their main functionality is involved in cell division and proliferation. Because FGFs plays such a vital role in cell proliferation, they are mainly involved in the process of wound healing and injuries. FGF binds to its ligand, heparin—a heavily sulfated glycosaminoglycan. The binding of heparin to FGF occurs through electrostatic interactions, specifically between the negatively charged sulfate groups on heparin and positively charged residues ...


Modulation Of Cell Death Signaling And Cell Proliferation By The Interaction Of Homoserine Lactones And Paraoxonase 2., Aaron Mackallan Neely 2016 University of Louisville

Modulation Of Cell Death Signaling And Cell Proliferation By The Interaction Of Homoserine Lactones And Paraoxonase 2., Aaron Mackallan Neely

Electronic Theses and Dissertations

Pseudomonas aeruginosa produces N-(3-oxododecanoyl)-homoserine lactone (C12) as a quorum-sensing molecule that functions to facilitate bacteria-bacteria communication. C12 has also been reported to affect many aspects of human host cell physiology, including evoking cell death in various types of cells. However, the signaling pathway(s) leading to C12-triggerred cell death remains unclear. To clarify cell death signaling induced by C12, we examined mouse embryonic fibroblasts (MEFs) deficient in one or more caspases. Our data indicate that, unlike most apoptotic inducers, C12 evokes a novel form of apoptosis in cells, probably through the direct induction of mitochondrial membrane permeabilization. Previous ...


Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu 2016 University of Tennessee - Knoxville

Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu

Doctoral Dissertations

Internal structural motions in proteins are essential to their functions. In this present dissertation, we present the results from an extensive set of molecular dynamics simulations of three very different globular proteins and demonstrate that the structural fluctuations observed are highly complex, manifesting in non-ergodic and self-similar subdiffusive dynamics with non-exponential relaxation behavior. The characteristic time of the motion observed at a given timescale is dependent on the length of the observation time, indicating an aging effect. By comparing the simulation results to the existing single-molecule fluorescence spectroscopic data on other globular proteins, we found the characteristic relaxation time for ...


Effects Of Creatine, Leucine, And Ethanol On Glial Cell Line-Derived Neurotrophic Factor In C2c12 Skeletal Muscle Cells, Daniel Waters 2016 Western Michigan University

Effects Of Creatine, Leucine, And Ethanol On Glial Cell Line-Derived Neurotrophic Factor In C2c12 Skeletal Muscle Cells, Daniel Waters

Honors Theses

Glial Cell Line-Derived Neurotrophic Factor (GDNF) is a protein expressed throughout the mammalian nervous system that serves several protective functions. Originally discovered in the brain, where it supports the survival of dopaminergic neurons, GDNF has since been shown to be expressed in skeletal muscle and is vital for the maintenance of motor neurons. The relationship between muscle hypertrophy, and GDNF is not well understood. The purpose of this study was to examine the relationship between hypertrophy and GDNF by inducing hypertrophy in C2C12 skeletal muscle cells using leucine and creatine, inhibiting hypertrophy using ethanol and measuring GDNF content. As measured ...


The Hmut Protein In The Heme Uptake Pathway Of Corynebacterium Diphtheriae, Cyrianne Sonia Keutcha 2016 Georgia State University

The Hmut Protein In The Heme Uptake Pathway Of Corynebacterium Diphtheriae, Cyrianne Sonia Keutcha

Georgia State Undergraduate Research Conference

No abstract provided.


Methods For Detecting Microbial Methane Production And Consumption By Gas Chromatography, Jared T. Aldridge, Jennie L. Catlett, Megan L. Smith, Nicole R. Buan 2016 University of Nebraska-Lincoln

Methods For Detecting Microbial Methane Production And Consumption By Gas Chromatography, Jared T. Aldridge, Jennie L. Catlett, Megan L. Smith, Nicole R. Buan

Biochemistry -- Faculty Publications

Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO2. Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al., 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al., 2002). Methanogens are anaerobic archaea that grow by producing methane gas as a metabolic byproduct (Wolfe, 1982; Thauer, 1998). Our lab has developed and optimized three different gas chromatograph-utilizing assays to characterize methanogen metabolism (Catlett et al., 2015). Here we describe the end point and kinetic ...


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