Open Access. Powered by Scholars. Published by Universities.®

Biochemistry Commons

Open Access. Powered by Scholars. Published by Universities.®

3923 Full-Text Articles 7803 Authors 442518 Downloads 144 Institutions

All Articles in Biochemistry

Faceted Search

3923 full-text articles. Page 1 of 108.

Therapeutic Targets For Alzheimer's Disease: Insights From In Vitro And In Vivo Models Of Inflammation, Magdalena J. Kiprowska 2016 The Graduate Center, City University of New York

Therapeutic Targets For Alzheimer's Disease: Insights From In Vitro And In Vivo Models Of Inflammation, Magdalena J. Kiprowska

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive neuronal loss that over the years spreads from the hippocampus to the neural cortex and impairs memory and cognitive functions. At the cellular level AD is linked to the presence of β-amyloid plaques and neurofibrillary tangles but despite decades of research little is known about their contribution to neurodegeneration and whether they are a cause or rather a result of the disease. It is well established that proteasome activity is impaired in AD brains and some studies suggest that this could be one of the initial factors leading to ...


Role Of Hnrnp A1 In The Regulation Of Hdm2 Gene Expression, Heriberto Moran 2016 The Graduate Center, City University of New York

Role Of Hnrnp A1 In The Regulation Of Hdm2 Gene Expression, Heriberto Moran

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

hnRNP A1 is one of the most abundant and ubiquitously expressed member of hnRNPs (Heterogenous Nuclear Ribonucleoproteins) family of proteins that play multiple roles in gene expression by participating in major steps in the processing of nascent RNA transcripts 1. It is involved in mRNA biogenesis mechanisms such as the transcription, splicing, stability, export and translation of cellular and viral transcripts. The functions of hnRNP A1 extend to the processing of microRNAs, telomere maintenance and DNA repair 1. Our previous studies have shown that hnRNPA1 had reduced protein level and increased cytoplasmic accumulation in senescent human diploid fibroblasts 2,10 ...


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.


Topographical Expression Of Class Ia And Class Ii Phosphoinositide 3-Kinase Enzymes In Normal Human Tissues Is Consistent With A Role In Differentiation, Soha Salama El Sheikh, Jan Domin, Prakitpunthu Tomtitchong, Paul Abel, Gordon Stamp, El-Nasir Lalani 2016 Imperial College School of Medicine

Topographical Expression Of Class Ia And Class Ii Phosphoinositide 3-Kinase Enzymes In Normal Human Tissues Is Consistent With A Role In Differentiation, Soha Salama El Sheikh, Jan Domin, Prakitpunthu Tomtitchong, Paul Abel, Gordon Stamp, El-Nasir Lalani

El Nasir Lalani

Background: Growth factor, cytokine and chemokine-induced activation of PI3K enzymes constitutes the start of a complex signalling cascade, which ultimately mediates cellular activities such as proliferation, differentiation, chemotaxis, survival, trafficking, and glucose homeostasis. The PI3K enzyme family is divided into 3 classes; class I (subdivided into IA and IB), class II (PI3K-C2α, PI3K-C2β and PI3K-C2γ) and class III PI3K. Expression of these enzymes in human tissue has not been clearly defined.

Methods: In this study, we analysed the immunohistochemical topographical expression profile of class IA (anti-p85 adaptor) and class II PI3K (PI3K-C2α and PI3K-C2β) enzymes in 104 formalin-fixed, paraffin embedded ...


Autophagic Turnover Of Inactive 26s Proteasomes In Yeast Is Directed By The Ubiquitin Receptor Cue5 And The Hsp42 Chaperone, Richard S. Marshall, Fionn McLoughlin, Richard D. Vierstra 2016 Washington University in St Louis

Autophagic Turnover Of Inactive 26s Proteasomes In Yeast Is Directed By The Ubiquitin Receptor Cue5 And The Hsp42 Chaperone, Richard S. Marshall, Fionn Mcloughlin, Richard D. Vierstra

Biology Faculty Publications & Presentations

Highlights

  • The yeast 26S proteasome is degraded by Atg8-mediated autophagy
  • Nitrogen starvation and inactivation stimulate proteaphagy via distinct pathways
  • Proteasome inhibition is accompanied by extensive ubiquitylation of the complex
  • Proteaphagy engages the Cue5 autophagy receptor and the Hsp42 chaperone

Summary

The autophagic clearance of 26S proteasomes (proteaphagy) is an important homeostatic mechanism within the ubiquitin system that modulates proteolytic capacity and eliminates damaged particles. Here, we define two proteaphagy routes in yeast that respond to either nitrogen starvation or particle inactivation. Whereas the core autophagic machineries required for Atg8 lipidation and vesiculation are essential for both routes, the upstream Atg1 ...


The Effect Of An Enhanced Isopentenyl Monophosphate Pool On Terpenoid Biosynthesis In Vivo, Evan T. Adams, Laura K. Henry, Dr. Natalia Dudareva 2016 Department of Biochemistry, Purdue University

The Effect Of An Enhanced Isopentenyl Monophosphate Pool On Terpenoid Biosynthesis In Vivo, Evan T. Adams, Laura K. Henry, Dr. Natalia Dudareva

The Summer Undergraduate Research Fellowship (SURF) Symposium

Found in all living organisms, terpenoids make up the largest group of natural products and are essential compounds for many major processes, including photosynthesis, respiration, hormone production, and electron transport. Additionally, they have commercial and medical value in products including fragrances, cosmetics, and medicines. Terpenoids originate from the five-carbon building blocks isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are synthesized by the mevalonic acid (MVA) and methylerithritol phosphate (MEP) pathways. An alternative MVA pathway was discovered in Archaea with the final two enzymes being phosphomevalonate decarboxylase (MPD) and isopentenyl phosphate kinase (IPK). Even though this alternative pathway is not ...


Mutational And Biochemical Analysis Of Isoprenylcysteine Carboxyl Methyltransferase, Sahej Bains, Amy L. Funk, Christine A. Hrycyna 2016 Purdue University

Mutational And Biochemical Analysis Of Isoprenylcysteine Carboxyl Methyltransferase, Sahej Bains, Amy L. Funk, Christine A. Hrycyna

The Summer Undergraduate Research Fellowship (SURF) Symposium

Ninety percent of pancreatic cancers are attributed to mutations in the Ras protein, making it paramount to concentrate on Ras activity. This study focuses on Ras activity by targeting a post-translational modifying enzyme of Ras called Isoprenylcysteine carboxyl methyltransferase (Icmt). Elucidation of the binding site of Icmt will allow the development of therapeutics that effectively inhibit Icmt causing the mislocalization of Ras, and in turn, aid in the treatment of Ras driven cancers. Currently, the hydrophobic substrate binding site of Icmt is unknown. In order to characterize the substrate binding site of Icmt, site-directed mutagenesis was used to design mutations ...


Nanobubbles Provide Theranostic Relief To Cancer Hypoxia, Christopher M. Long, Pushpak N. Bhandari, Joseph Irudayaraj 2016 Purdue University

Nanobubbles Provide Theranostic Relief To Cancer Hypoxia, Christopher M. Long, Pushpak N. Bhandari, Joseph Irudayaraj

The Summer Undergraduate Research Fellowship (SURF) Symposium

Hypoxia is a common motif among tumors, contributing to metastasis, angiogenesis, cellular epigenetic abnormality, and resistance to cancer therapy. Hypoxia also plays a pivotal role in oncological studies, where it can be used as a principal target for new anti-cancer therapeutic methods. Oxygen nanobubbles were designed in an effort to target the hypoxic tumor regions, thus interrupting the hypoxia-inducible factor-1α (HIF-1α) regulatory pathway and inhibiting tumor progression. At less than 100nm, oxygen nanobubbles act as a vehicle for site-specific oxygen delivery, while also serving as an ultrasound contrast agent for advanced imaging purposes. Through in vitro and in vivo studies ...


Role Of Sumoylation In Mitochondrial Division In Tetrahymena Thermophila, Ramya Modi, James Forney 2016 Purdue University

Role Of Sumoylation In Mitochondrial Division In Tetrahymena Thermophila, Ramya Modi, James Forney

The Summer Undergraduate Research Fellowship (SURF) Symposium

SUMOylation is a post translation modification that involves the addition of a small protein called SUMO, Small Ubiquitin-like MOdifier to a target protein. It is an important mechanism for the regulation of gene expression, the maintenance of genomic stability and in modifying nuclear proteins. More recently evidence has emerged for its importance in regulating mitochondrial fission and fusion in mammalian cells. This study evaluates the parameters for optimal staining of Tetrahymena thermophila mitochondria using two different dyes and then examines different cell lines with defects in the SUMOylation pathway. The first staining method uses Mitotracker Green, a vital stain that ...


In Vitro Motility Of Actin Filaments Powered By Plant Myosins Xi, Cesar A. Quintana-Cataño, Christopher J. Staiger, Weiwei Zhang 2016 Universidad de Los Andes - Colombia

In Vitro Motility Of Actin Filaments Powered By Plant Myosins Xi, Cesar A. Quintana-Cataño, Christopher J. Staiger, Weiwei Zhang

The Summer Undergraduate Research Fellowship (SURF) Symposium

The actomyosin network is thought to support fundamental processes of plant development and cell expansion such as polarized elongation of root hairs and the diffuse growth of epidermal and mesophyll cells. Inhibition of myosins via pharmacological treatments represents one of the key approaches for understanding of their roles in different cellular processes. However, the use of the standard plant myosin inhibitor, 2,3-butanedionemonoxime (BDM), is questioned as it requires a high concentration and may not be as specific as desired. By testing drugs that inhibit animal and yeast myosins V, the Staiger laboratory previously found pentabromopseudilin (PBP) as a potential ...


Expression And Site-Directed Mutagenesis Of Type Iii Polyketide Synthases, Logan R. Richards, Odessa Goudy, Lee M. Stunkard, Aaron B. Benjamin, Bethany P. Manning, Jeremy Lohman 2016 Purdue University

Expression And Site-Directed Mutagenesis Of Type Iii Polyketide Synthases, Logan R. Richards, Odessa Goudy, Lee M. Stunkard, Aaron B. Benjamin, Bethany P. Manning, Jeremy Lohman

The Summer Undergraduate Research Fellowship (SURF) Symposium

Natural products are a well-established source of drugs, and evolution has yielded polyketides such as leinamycin and iso-migrastatin that have demonstrated anti-tumor activity. Polyketides are large metabolites with a high degree of chemical variability and are commonly produced by soil bacteria. Polyketide synthases (PKS) exist as three different archetypes, and the reaction mechanisms of ketosynthases from all archetypes is not understood. Type III PKSs exist as an independently functioning ketosynthase (KS), which primarily use coenzyme A (CoA), with some exceptions, for the biosynthesis of polyketides. We elected to focus our studies on ketosynthases, because they are responsible for forming the ...


Biochemical And Structural Characterization Of Cdc14 Phosphatases From Pathogenic Fungi, John Whitney, Kyle Wettschurack, Mark Hall, Jeremy Lohman, Aaron Benjamin, Lee M. Stunkard 2016 Purdue University- West Lafayette

Biochemical And Structural Characterization Of Cdc14 Phosphatases From Pathogenic Fungi, John Whitney, Kyle Wettschurack, Mark Hall, Jeremy Lohman, Aaron Benjamin, Lee M. Stunkard

The Summer Undergraduate Research Fellowship (SURF) Symposium

Cyclin-dependent kinases (Cdk) drive cell cycle progression and reversal of Cdk phosphorylation is essential for mitotic exit. Cdc14 is a widely conserved family of protein phosphatases that reverse Cdk phosphorylation. Recently, Cdc14 was also found to be essential for pathogenicity of some fungal plant pathogens. Fungal pathogens, like Ustilago maydis, decrease agricultural crop yield costing global agriculture by some accounts $60 billion per year. Since Cdc14 is absent in plants, a fungi specific Cdc14 inhibitor could be made to reduce the pathogenicity of U. maydis and other fungal plant pathogens to increase crop yields. To guide inhibitor development, a three-dimensional ...


Investigating The Roles Of Δnp63 As A Suppressor Of Migration, Invasion, And Metastasis, Ramon E. Flores Gonzalez 2016 The University of Texas Graduate School of Biomedical Sciences at Houston

Investigating The Roles Of Δnp63 As A Suppressor Of Migration, Invasion, And Metastasis, Ramon E. Flores Gonzalez

UT GSBS Dissertations and Theses (Open Access)

Cancer is one of the leading causes of death and disease in the world. Considerable resources are spent to study and understand cancer, with the hope of developing new treatments and eventually cures that will help millions of people. Efforts to understand cancer are hindered by its inherent complexity and instability. Nonetheless, understanding the basics of tumor development and progression are the key to focused on studying the role of ΔNp63 in cancer, a p53 family member known to be involved in epithelial development, microRNA biogenesis, and stem cell maintenance. Using the strength of in vivo mouse models, we found ...


Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu 2016 Pacific Northwest National Laboratory

Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu

STAR (STEM Teacher and Researcher) Program Posters

Fibronectin is an important biomolecule due to its role in cell differentiation, growth, kinesis, and adhesion. Such biological responses are mediated through membrane recognition and signaling; where fibronectin is found. Studying the outer molecular surface of fibronectin allows deeper insight into the microbiological reactions that occur during these processes. In situ mass spectrometry analysis in aqueous solution accurately represents fibronectin’s chemical components, made possible by a vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface). SALVI was paired with the analytical tools: time-of-flight secondary ion mass spectrometer (ToF-SIMS), single photon ionization mass spectrometer (SPI-MS) and ...


Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci 2016 University of Tennessee, Knoxville

Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci

Doctoral Dissertations

Plasminogen activator inhibitor type-1 (PAI-1) specifically inhibits the proteases tissue type plasminogen activator and urokinase plasminogen activator to control the activation of fibrinolysis. Vitronectin interacts with PAI-1 primarily through the somatomedin B (SMB) domain to stabilize and localize PAI-1 to sites of injury. Our laboratory observed that transition metals such as copper2+ have VN dependent, reciprocal effects on how long PAI-1 remains active. We aim to determine the molecular basis for effects of copper2+ on PAI-1 activity. We employed a computational algorithm (MUG) to predict metal binding clusters, and introduced mutations hypothesized to create metal binding deficiency. We ...


New Insights Into An Old Interaction: Developing A Model For Pai-1:Vn Interactions, Letitia Nichole Puster 2016 University of Tennessee, Knoxville

New Insights Into An Old Interaction: Developing A Model For Pai-1:Vn Interactions, Letitia Nichole Puster

Doctoral Dissertations

Active human Plasminogen Activator Inhibitor 1 (PAI-1) is most often found in complex with Vitronectin (VN), an ~62kDa glycoprotein. Research has shown PAI-1 and VN form higher order complexes in tissues, and our work indicates a 2:1 (PAI-1:VN) stoichiometry for these complexes. A logical model for PAI-1:VN interaction proposes that two PAI-1 molecules bind VN at separate sites. However, our small-angle neutron scattering (SANS) data suggest that there is a PAI-1: PAI-1:VN interaction, in which PAI-1 forms a dimer when in complex with VN. We tested this novel arrangement of PAI-1 within the complex by using ...


Protein Kinase Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (Map4k4) Promotes Obesity-Induced Hyperinsulinemia, Rachel J. Roth Flach, Laura V. Danai, Marina DiStefano, Mark Kelly, Lorena Garcia Menendez, Agata Jurczyk, Rohit B. Sharma, Dae Young Jung, Jong Hun Kim, Jason K. Kim, Rita Bortell, Laura C. Alonso, Michael P. Czech 2016 University of Massachusetts Medical School

Protein Kinase Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (Map4k4) Promotes Obesity-Induced Hyperinsulinemia, Rachel J. Roth Flach, Laura V. Danai, Marina Distefano, Mark Kelly, Lorena Garcia Menendez, Agata Jurczyk, Rohit B. Sharma, Dae Young Jung, Jong Hun Kim, Jason K. Kim, Rita Bortell, Laura C. Alonso, Michael P. Czech

Open Access Articles

Previous studies revealed a paradox whereby mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4) acted as a negative regulator of insulin sensitivity in chronically obese mice, yet systemic deletion of Map4k4 did not improve glucose tolerance. Here, we report markedly reduced glucose-responsive plasma insulin and C-peptide levels in whole body Map4k4-depleted mice (M4K4 iKO) as well as an impaired first phase of insulin secretion from islets derived from M4K4 iKO mice ex vivo After long-term high fat diet (HFD), M4K4 iKO mice pancreata also displayed reduced beta cell mass, fewer proliferating beta cells and reduced islet-specific gene mRNA expression compared ...


Tumor Necrosis Factor Alpha, Citrullination, And Peptidylarginine Deiminase 4 In Lung And Joint Inflammation, Mandar Bawadekar, Annette Gendron-Fitzpatrick, Ryan Rebernick, Daeun Shim, Thomas F. Warner, Anthony P. Nicholas, Lennart K. Lundblad A, Paul R. Thompson, Miriam A. Shelef 2016 University of Wisconsin - Madison

Tumor Necrosis Factor Alpha, Citrullination, And Peptidylarginine Deiminase 4 In Lung And Joint Inflammation, Mandar Bawadekar, Annette Gendron-Fitzpatrick, Ryan Rebernick, Daeun Shim, Thomas F. Warner, Anthony P. Nicholas, Lennart K. Lundblad A, Paul R. Thompson, Miriam A. Shelef

Open Access Articles

BACKGROUND: The relationship between lung and joint inflammation in rheumatoid arthritis is poorly understood. Lung inflammation with resultant protein citrullination may trigger anti-citrullinated protein antibodies, inflammation, and arthritis. Alternatively, lung and joint inflammation may be two manifestations of a single underlying pathology. The lung has increased citrullination and TNF-alpha levels are high in rheumatoid arthritis; however, it is unknown if TNF-alpha can induce lung protein citrullination. The citrullinating enzyme peptidylarginine deiminase 4 (PAD4) exacerbates TNF-alpha-induced arthritis, but a role for PAD4 in lung citrullination and TNF-alpha-induced lung inflammation has not been explored. Our aim was to use TNF-alpha-overexpressing mice to ...


Isotopic Abundance Ratio Analysis Of 1,2,3-Trimethoxybenzene (Tmb) After Biofield Energy Treatment (The Trivedi Effect®) Using Gas Chromatography-Mass Spectrometry, Mahendra Trivedi 2016 Trivedi Global Inc.

Isotopic Abundance Ratio Analysis Of 1,2,3-Trimethoxybenzene (Tmb) After Biofield Energy Treatment (The Trivedi Effect®) Using Gas Chromatography-Mass Spectrometry, Mahendra Trivedi

Mahendra Kumar Trivedi

1,2,3-Trimethoxybenzene (TMB) is one of the most versatile chemical used for the synthesis of several pharmaceuticals, dyes, polymers, organic compounds, etc. The stable isotope ratio analysis has increased attention day-by-days in several fields such as agricultural, food authenticity, biochemistry, medical research, etc. The current study was aimed to evaluate the effect of the biofield energy treatment on the isotopic abundance ratios of 13C/12C or 2H/1H or 17O/16O (PM+1/PM) and 18O/16O (PM+2/PM) in TMB using Gas chromatography - mass spectrometry (GC-MS) technique. TMB was divided into two parts - one part was denoted ...


Determination Of Isotopic Abundance Ratio Of Biofield Energy Treated 1,4-Dichlorobenzene Using Gas Chromatography-Mass Spectrometry (Gc-Ms), Mahendra Trivedi 2016 Trivedi Global Inc.

Determination Of Isotopic Abundance Ratio Of Biofield Energy Treated 1,4-Dichlorobenzene Using Gas Chromatography-Mass Spectrometry (Gc-Ms), Mahendra Trivedi

Mahendra Kumar Trivedi

The objective of the current study was to evaluate the effect of biofield energy treatment on the isotopic abundance ratios of P M+1/PM, PM+2/PM, PM+3/PMand PM+4/PM in p-DCB using gas chromatography-mass spectrometry (GC-MS). The p-DCB was divided into two parts - one part was control sample, and another part was considered as the treated sample which was subjected to biofield energy treatment (The Trivedi Effect®). T1, T2, T3, and T4 were referred the biofield treated p-DCB having analyzed at different time intervals. The GC-MS analysis of both the control and ...


Digital Commons powered by bepress