Biochemistry Commons^™

Hare-Mediated Endocytosis Of Hyaluronan And Heparin Is Targeted By Different Subsets Of Three Endocytic Motifs, Madhu S. Pandey, Edward N. Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

The hyaluronan (HA) receptor for endocytosis (HARE) is a multifunctional recycling clearance receptor for 14 different ligands, including HA and heparin (Hep), which bind to discrete nonoverlapping sites. Four different functional endocytic motifs (M) in the cytoplasmic domain (CD) target coated pit mediated uptake: (YSYFRI²⁴⁸⁵ (M1), FQHF²⁴⁹⁵ (M2), NPLY²⁵¹⁹ (M3), and DPF²⁵³⁴ (M4)). We previously found (Pandey et al. J. Biol. Chem. 283, 21453, 2008) that M1, M2, and M3 mediate endocytosis of HA. Here we assessed the ability of HARE variants with a single-motif deletion …

Advances In Hyaluronan Biology: Signaling, Regulation, And Disease Mechanisms, Melanie A. Simpson, Carol De La Motte, Larry S. Sherman, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Hyaluronan is an extracellular glycosaminoglycan polymer consisting of linear disaccharide units containing alternating glucuronate and N-acetylglucosamine.Many cell types make hyaluronan, which unlike most other macromolecules is assembled at the plasmamembrane and concurrently translocated through the hyaluronan synthase enzyme. The normal function of large hyaluronan polymers (>1MDa) in tissue cushioning, hydration, and lubrication is well established. The aberrant accumulation and degradation of hyaluronan and the receptor-mediated signaling of smaller hyaluronan fragments have also been extensively implicated in a variety of pathological states including inflammation and cancer. More recently, the discovery that hyaluronan can either be a structural matrix component or …

Salivary Gland Structure Of Ctenarytaina Eucalypti (Maskell, 1890) (Hemiptera) And Phloem Exudate In Eucalyptus Globulus Labillarière, 1799 (Myrtaceae), Anamika Sharma, Soundararajan Madhavan, Anantanarayanan Raman, Gary S. Taylor, Murray J. Fletcher

Department of Biochemistry: Faculty Publications

The structure of the salivary glands of the free-living aphalarid Ctenarytaina eucalypti, which infests multiple species of Eucalyptus in Australasia and has been introduced into many other regions of the world, is described and illustrated. The principal salivary gland is multilobed whereas the accessory gland is tubular. 1-D electrophoresis revealed proteins of approximately 58 and 64 kDa in the salivary gland extracts and proteins of similar molecular weights in the extracted plant exudates, including phloem, from infested leaves and tender shoots of E. globulus. Proteins that could fall within this range include, but are not limited to, …

Janus-Faced Sestrin2 Controls Ros And Mtor Signalling Through Two Separate Functional Domains, Hanseong Kim, Sojin An, Seung-Hyun Ro, Filipa Teixeira, Gyeong Jin Park, Cheal Kim, Chun-Seok Cho, Jeong-Sig Kim, Ursula Jakob, Jun Hee Lee, Uhn-Soo Cho

Department of Biochemistry: Faculty Publications

Sestrins are stress-inducible metabolic regulators with two seemingly unrelated but physiologically important functions: reduction of reactive oxygen species (ROS) and inhibition of the mechanistic target of rapamycin complex 1 (mTORC1). How Sestrins fulfil this dual role has remained elusive so far. Here we report the crystal structure of human Sestrin2 (hSesn2), and show that hSesn2 is twofold pseudo-symmetric with two globular subdomains, which are structurally similar but functionally distinct from each other. While the N-terminal domain (Sesn-A) reduces alkylhydroperoxide radicals through its helix–turn–helix oxidoreductase motif, the C-terminal domain (Sesn-C) modified this motif to accommodate physical interaction with GATOR2 and subsequent …

Genetic Variation In Miscanthus X Giganteus And The Importance Of Estimating Genetic Distance Thresholds For Differentiating Clones, Katarzyna Glowacka, Lindsay V. Clark, Shivani Adhikari, Junhua Peng, J. Ryan Stewart, Aya Nishiwaki, Toshihiko Yamada, Uffe Jorgensen, Trevor R. Hodkinson, Justin Gifford, John A. Juvik, Erik J. Sacks

Department of Biochemistry: Faculty Publications

Miscanthus x giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type-specimen. A subset of …

Use Of Designer Nucleases For Targeted Gene And Genome Editing In Plants, Donald P. Weeks, Martin H. Spalding, Bing Yang

Department of Biochemistry: Faculty Publications

The ability to efficiently inactivate or replace genes in model organisms allowed a rapid expansion of our understanding of many of the genetic, biochemical, molecular and cellular mechanisms that support life. With the advent of new techniques for manipulating genes and genomes that are applicable not only to single-celled organisms, but also to more complex organisms such as animals and plants, the speed with which scientists and biotechnologists can expand fundamental knowledge and apply that knowledge to improvements in medicine, industry and agriculture is set to expand in an exponential fashion. At the heart of these advancements will be the …

Secretoglobin And Transferrin Expression In Bronchoalveolar Lavage Fluid Of Horses With Chronic Respiratory Disease, M. Miskovic Feutz, Laurent Couetil, C.P. Riley, X. Zhang, J. Adamec, R.E. Raskin

Department of Biochemistry: Faculty Publications

Background: Lower expression of secretoglobin and transferrin has been found in the bronchoalveolar lavage fluid (BALF) of a small number of horses with experimentally induced signs of recurrent airway obstruction (RAO) compared to healthy controls.

Hypothesis/Objectives: Secretoglobin and transferrin BALF expression will be similarly decreased in horses with naturally occurring clinical signs of RAO and in horses with experimentally induced clinical signs of RAO as compared to healthy controls and intermediate in horses with inflammatory airway disease (IAD).

Animals: Recurrent airway obstruction-affected and control horses were subjected to an experimental hay exposure trial to induce signs of RAO. Client-owned horses …

Divergent Responses Of Atlantic Coastal And Oceanic Synechococcus To Iron Limitation, Katherine R. M. Mackey, Anton F. Post, Matthew R. Mcilvin, Gregory A. Cutter, Seth G. John, Mak A. Saito

OES Faculty Publications

Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet used few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multitiered, hierarchical cascade …

The Relative Importance Of Methanogenesis In The Decomposition Of Organic Matter In Northern Peatlands, J. Elizabeth Corbett, Malak M. Tfaily, David J. Burdige, Paul H. Glaser, Jeffrey P. Chanton

OES Faculty Publications

Using an isotope-mass balance approach and assuming the equimolar production of CO₂ and CH₄ from methanogenesis (e.g., anaerobic decomposition of cellulose), we calculate that the proportion of total CO₂ production from methanogenesis varies from 37 to 83% across a variety of northern peatlands. In a relative sense, methanogenesis was a more important pathway for decomposition in bogs (80 ± 13% of CO₂ production) than in fens (64 ± 5.7% of CO₂ production), but because fens contain more labile substrates they may support higher CH4 production overall. The concentration of CO₂ produced from methanogenesis (CO …

Alternate Germinants Of C. Difficile, A Leading Hospital Pathogen, Sean Tanzey, Ernesto Abel-Santos

McNair Poster Presentations

Clostridium difficile infections (CDI) are the leading nosocomial infections worldwide. Humans are asymptomatic carriers of C. difficile spores in the intestinal tract. The process known as germination occurs when otherwise harmless C. difficile spores are converted to toxin-producing cells upon recognition of bile salts in humans. This distinctive transition ultimately leads to the onset of disease and recurrent CDI. Germination profiles will be characterized in response to peptidoglycan (PG) fragments isolated from various bacterial species. These specific peptidoglycan fragments contain different amino acid residues that may induce different germination responses. Purification and structural determination of the peptidoglycan fragments will be …

Dysregulation Of Micrornas In Blood As Biomarkers For Diagnosing Prostate Cancer, Rhonda W. Daniel

Theses and Dissertations

Prostate cancer is the most common noncutaneous cancer among men, yet current diagnostic methods are insufficient and more reliable diagnostic markers need to be developed. The answer that can bridge this gap and enable more efficient diagnoses may lie in microRNAs. These small, single stranded RNA molecules impact protein expression at the translational level and regulate important cellular pathways. Dysregulation of these small RNA molecules can have tumorigenic effects on cells and lead to many types of cancers.

Currently the Prostate-Stimulating Antigen (PSA) is used as a diagnostic marker for prostate cancer. However, many factors can elevate PSA levels such …

Bacterial Expression Of Plant Pyruvate Kinase, Kristina Fuller

STAR Program Research Presentations

Pyruvate kinases serve an important role in regulating glycolysis pathways. Different pyruvate kinase isozymes can dictate which of several different products will be formed during the final step of glycolysis. Being able to reliably copy active pyruvate kinases (PK) would allow study of the different isozymes, with the goal of eventually creating plants that are more nutritionally beneficial for humans. This study focused on improving the protocol for replicating each of two isolated PK isozymes from the model plant Arabidopsis thaliana. Previous attempts had resulted in the PK denaturing and consequently precipitating out of solution and so we manipulated the …

Nanoparticle Behavior In Biological Gels And Biofluids: The Impact Of Interactions With Charged Biogels And The Formation Of Protein Coronas On Nanoparticles, Xiaolu Zhang

Theses and Dissertations--Chemistry

With the rapid growth of nanotechnology, situations where nanomaterials will interact with biological systems will unquestionably grow. Therefore, it is increasingly understood that interactions between nanomaterials and biological environments will play an essential role in nanomedicine. Biological polymer networks, including mucus and the extracellular matrix, serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate transport processes through finely tuned particle-network interactions. In chapters 3 and 4, we investigate the role of electrostatics on the basic mechanisms governing the diffusion of charged molecules inside model polymer networks by …

Fors 401: Forensic Biochemistry—A Peer Review Of Teaching Project Inquiry Portfolio, Ashley Hall

UNL Faculty Course Portfolios

Students who participate in active and experiential learning activities develop a better understanding of basic scientific principles and are also more likely to be retained in a STEM discipline. Developing such activities, however, can be difficult. In the present study, we sought to develop classroom activities to engage university students and increase understanding of the theory and practice of forensic science. One common accessory amongst the target audience was the ever-present media, both social and popular (entertainment). In fact, a majority of students report watching at least one of the many popular forensic science shows on TV. Therefore, we hypothesized …

A Comparison Of Whole Body Mercury Concentrations Of Mummichogs (Fundulus Heteroclitus) And Atlantic Silversides (Menidia Menidia), Daniel P. Ferons

Electronic Theses and Dissertations

Few studies have focused on mercury cycling within salt marsh estuaries. Mummichogs (Fundulus heteroclitus) and Atlantic silversides (Menidia menidia) are two species of forage fish that live year round in South Carolina salt marshes. During high tide, mummichogs feed from the water column, sediment, and off of smooth cordgrass while Atlantic silversides prey upon zooplankton. In this study, total and methyl mercury within mummichogs and Atlantic silversides from Dunn Sound, SC were quantified and compared over four seasons throughout 2014. Gut contents were also quantified and compared to determine if there was a dietary impact on the concentrations of total …

Constitutive Activity In Orphan G Protein Coupled Receptors, Adam Lee Martin

Doctoral Dissertations

"The goal of this research was to use a distal signaling pathway analysis to evaluate the extent of agonist independent constitutive signaling among orphan class-A G protein coupled receptors (GPCRs). These receptors translate extracellular signals via conformational change into intracellular activation of different G proteins and subsequent second messenger synthesis. These small molecules regulate cellular biochemistry, eventually leading to nuclear signaling that results in changes in gene expression. Some GPCRs are capable of signaling in the absence of an activating ligand, a phenomenon called constitutive activity that is inhibited via an "inverse-agonist". The use of cAMP dependent Luciferase expression is …

Effects Of N-Acetylcysteine Amide In Preventing/Treating Cataracts, Sri Krishna Yasaswi Maddirala

Doctoral Dissertations

"Cataract, the opacification of an eye lens, is a common pathological abnormality of the lens accounting for approximately 50% of all blindness. The only effective treatment currently available for a cataract is the surgical removal of the affected lens and replacement with an artificial lens for the restoration of vision. Although, cataract surgery is considered to be a very successful procedure in terms of visual outcome, the cost of surgery, need for trained personnel and surgeons, and postsurgical complications, limit the worldwide availability and accessibility of this procedure. Hence, alternative preventive and treatment procedures are worthy of investigation. The lens …

The Effects Of Hibernation On The Hemostatic Properties Of The American Bullfrog, Rana Catesbeiana, Kiana Cullinan

Honors Program Theses

It is known that hibernating animals display a drastic reduction in metabolic rate, accompanied by reduced heart rate and rate of blood flow through vessels. Sluggish blood flow increases the risk for developing clots, yet it has been observed that hibernators conclusively display elongated clotting times. This observed impairment may be caused by the decrease in body temperature, due to a negative impact on the functioning of the enzymes involved in coagulation. Some hibernating endotherms, or “warm-blooded” animals, employ biological mechanisms as preventative means to prevent clotting during hibernation, such as the down-regulation of certain clotting factors or the production …

Primer Efficacy In The Dna Barcoding Of Spiders, Rhennetta Jo Bork

Honors Program Theses

DNA barcoding is the process of amplifying a 650 base pair segment of the sequence of the mitochondrial gene cytochrome c oxidase (COI), and amplifying this gene with a polymerase chain reaction (PCR). It is used to help identify and distinguish animal species and also to help determine genetic differences in species. DNA barcoding can be especially useful when working with spiders since they tend to be very small and hard to distinguish. However, achieving a DNA barcode can be difficult and thus techniques to improve the method of DNA barcoding can be helpful. This research looked into the different …

Characterization Of The Sufc Atpase During Fe-S Cluster Assembly By The Suf Pathway In Escherichia Coli, Khaleh Mykel Thomas

Theses and Dissertations

The gram-negative bacterium E. coli encodes the Suf pathway to assemble iron-sulfur (Fe-S) clusters under iron starvation and oxidative stress conditions. The ATPase activity of SufC is critical for in vivo Fe-S cluster assembly by the Suf pathway. SufC shares homology with the nucleotide binding domain (NBD) of ATP-binding cassette (ABC) transporters and belongs to the AAA+ (ATPases Associated with diverse cellular Activities) ATPase superfamily, a family of proteins that utilizes energy from ATP hydrolysis to perform a variety of cellular functions. SufC forms a stable SufBC2D complex with partner proteins SufB and SufD. The SufBC2D complex serves as a …

Study Of Escherichia Coli Adp-Glucose Pyrophosphorylase Catalysis: Investigating Critical Roles Of Conserved Arg32 And Lys42 Residues, Angela Lynn Mahaffey

Dissertations

Carbohydrates have been most notable as energy sources for mammals, bacteria (glycogen) and plants (starch) – and in many other species. As such the biosynthesis of carbohydrates is essential to the sustainability of many forms of life, on earth. Adenosine-‘5-diphosphate glucose pyrophosphate (ADP-Glc pyrophosphorylase; ADP-Glc PPase) is the allosterically controlled “first committed step” in both the biosynthetic pathways of starch (~25% amylose and ~75% amylopectin, in plants and algae) and glycogen (in bacteria), preceding the starch/glycogen synthase reaction. By catalyzing the following reaction, ATP + α –D-Glc-1P ADP-Glc + PPi , ADP-Glc PPase functions as the primary enzyme in the …

Structure And Molecular Mechanism Of A Plp/Gaba Dependent Transcription Regulator Gabr, Rui Wu

Dissertations

GabR is a member of the MocR/GabR subfamily of the GntR family of bacterial transcription regulators. It regulates the metabolism of γ-aminobutyric acid (GABA), an important nitrogen and carbon source in many bacteria. The crystal structures reported here show that this protein has evolved from the fusion of a type I aminotransferase and a winged helix-turn-helix (wHTH) DNA binding protein to form a chimeric protein that adopts a dimeric head-to-tail configuration. The pyridoxal 5′-phosphate (PLP)-binding regulatory domain of GabR is therefore an example of a coenzyme playing a role in transcription regulation rather than in enzymatic catalysis. Our structural and …

Genetic Indicators Of Iron Limitation In Wild Populations Of Thalassiosira Oceanica From The Northeast Pacific Ocean, P. Dreux Chappell, Leann P. Whitney, Joselynn R. Wallace, Adam I. Darer, Samua Jean-Charles, Bethany D. Jenkins

OES Faculty Publications

Assessing the iron (Fe) nutritional status of natural diatom populations has proven challenging as physiological and molecular responses can differ in diatoms of the same genus. We evaluated expression of genes encoding flavodoxin (FLDA1) and an Fe-starvation induced protein (ISIP3) as indicators of Fe limitation in the marine diatom Thalassiosira oceanica. The specificity of the response to Fe limitation was tested in cultures grown under Fe-and macronutrient-deficient conditions, as well as throughout the diurnal light cycle. Both genes showed a robust and specific response to Fe limitation in laboratory cultures and were detected in small volume samples collected from …

The Geotraces Intermediate Data Product 2014, Edward Mawji, Reiner Schlitzer, Elena M. Dodas, Cyril Abadie, Wafa Abouchami, Robert F. Anderson, Gregory A. Cutter

OES Faculty Publications

The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEls) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in …

The Role Of Srsf3 In Control Of Alternative Splicing Of Cpeb2 In Triple Negative Breast Cancer, Brian P. Griffin

Theses and Dissertations

In the presented study, we identified that SRSF3 controls the alternative splicing of CPEB2 and consequently promotes a metastatic phenotype in triple negative breast cancer (TNBC). TNBC causes thousands of deaths annually, frequently due to a lack of effective treatments and a high rate of metastasis in patients. Alternative splicing has been found to be dysregulated in numerous cancers, while splicing factors such as SRSF3 are variably expressed. In this study we performed a siRNA panel to screen potential splicing factors, then used specific siRNA to study the effect of its knockdown on cellular function. These results showed that SRSF3 …

Pemetrexed, A Modulator Of Amp-Activated Kinase Signaling And An Inhibitor Of Wild Type And Mutant P53, Stuti Agarwal

Theses and Dissertations

New drug discoveries and new approaches towards diagnosis and treatment have improved cancer therapeutics remarkably. One of the most influential and effective discoveries in the field of cancer therapeutics was antimetabolites, such as the antifolates. The interest in antifolates increased as some of the antifolates showed responses in cancers, such as mesothelioma, leukemia, and breast cancers. When pemetrexed (PTX) was discovered, our laboratory had established that the primary mechanism of action of pemetrexed is to inhibit thymidylate 22 synthase (TS) (E. Taylor et al., 1992). Preclinical studies have shown that PTX has a broad range of antitumor activity in human …

Interaction Between Atm Kinase And P53 In Determining Glioma Radiosensitivity, Syed F. Ahmad

Theses and Dissertations

Glioblastoma multiforme (GBM) is the most common primary brain tumor. Studies have shown that targeting the DNA damage response can sensitize cancer cells to DNA damaging agents. Ataxia telangiectasia mutated (ATM) is involved in signaling DNA double strand breaks. Our group has previously shown that ATM inhibitors (ATMi) sensitize GBM cells and tumors to ionizing radiation. This effect is greater when the tumor suppressor p53 is mutated.

The goals of this work include validation of a new ATM inhibitor, AZ32, and elucidation of how ATMi and p53 status interact to promote cell death after radiation. We propose that ATMi and …

Nitric Oxide Synthase Activity And Its Modulation In The Treatment Of Colorectal Cancer, Asim Alam

Theses and Dissertations

The American Cancer Society estimates more than 141,000 new cases of and about 50,000 deaths from colorectal cancer every year. Treatment options include surgery, radiation therapy and targeted therapies such as anti-angiogenics. However, no therapies address the key driving factor of colorectal cancer: inflammation. It is well known that chronic inflammatory conditions such as Crohn’s Disease, ulcerative colitis, diabetes, obesity and cigarette smoking all elevate the risk of developing colorectal cancer. One of the hallmarks of chronic inflammation is the elevated levels of reactive oxygen/nitrogen species (ROS/RNS). A primary source of these ROS/RNS is uncoupled Nitric Oxide Synthase (NOS). Under …

Non-Destructive Dna Extraction Methods That Yield Dna Barcodes In Spiders, Reva Ann Bork

Honors Program Theses

DNA barcodes are short sequences of nucleotides that differ from species to species (Hebert et al., 2003; Hebert & Gregory, 2005). DNA barcoding is very important in helping to reconstruct phylogenetic trees and to confirm the identity of threatened or endangered species in the wild. Additionally, it has become increasingly popular in the food industry to test the accuracy of the food being sold in fast food chains (Wong and Hanner, 2008). For scientific purposes, nondestructive DNA extraction techniques need to be explored because they allow for preservation of the voucher specimen, which is particularly important for rare or extinct …

Characterization Of The Trans-Plasma Membrane Electron Transport System In The Myelin Membrane, Afshan Sohail

Theses and Dissertations (Comprehensive)

Myelination is the key feature of evolution in the nervous system of vertebrates. Myelin is the protrusion of glial cells. More specifically, "oligodendrocytes" in the central nervous system (CNS), and "Schwann" cells in the peripheral nervous system (PNS) form myelin membranes. Myelin remarkably, enhances the propagation of nerve impulses. However, myelin restricts the access of extracellular metabolites to the axons. A pathology called "demyelination" is associated with myelin. The myelin sheath is not only an insulator, but it is itself metabolically active. In this study it is hypothesized that the ratio of NAD(P)⁺/NAD(P)H and the glycolytic pathway of …