Life Sciences Commons^™

The Pathological Effects Of Ccr2+ Inflammatory Monocytes Are Amplified By An Ifnar1-Triggered Chemokine Feedback Loop In Highly Pathogenic Influenza Infection, Sue-Jane Lin, Ming Lo, Rei-Lin Kuo, Shin-Ru Shih, David M. Ojcius, Jean Lu, Chien-Kuo Lee, Hui-Chen Chen, Meei Yun Lin, Chuen-Miin Leu, Chia-Ni Lin, Ching-Hwa Tsai

All Dugoni School of Dentistry Faculty Articles

Background: Highly pathogenic influenza viruses cause high levels of morbidity, including excessive infiltration of leukocytes into the lungs, high viral loads and a cytokine storm. However, the details of how these pathological features unfold in severe influenza infections remain unclear. Accumulation of Gr1 + CD11b + myeloid cells has been observed in highly pathogenic influenza infections but it is not clear how and why they accumulate in the severely inflamed lung. In this study, we selected this cell population as a target to investigate the extreme inflammatory response during severe influenza infection.

Results: We established H1N1 IAV-infected mouse models using …

A Novel Role For Nf-Κb In Proximal T Cell Signaling, Crystina Bronk Watson

USF Tampa Graduate Theses and Dissertations

The interrogation of T cell signaling over the past fifty years has led to the discovery of amazingly intricate cascade networks and elaborate descriptions of individual proteins' domains and functions. A complex landscape has been rendered in which proteins relay messages from the extracellular ligation of the TCR by a cognate peptide loaded MHC via changes in sub-cellular location, phosphorylation, and binding affinities and partners to enact nuclear localization of three key transcription factors required for cellular effector function and proliferation: AP-1, NF-AT, and NF-κB. Dogma has favored activation of each of these transcription regulating elements to be a linear …

Nuclear Transport Of Single Molecules: Dwell Times At The Nuclear Pore Complex, Ulrich Kubitscheck, David Grunwald, Andreas Hoekstra, Daniel Rohleder, Thorsten Kues, Jan Peter Siebrasse, Reiner Peters

David Grünwald

The mechanism by which macromolecules are selectively translocated through the nuclear pore complex (NPC) is still essentially unresolved. Single molecule methods can provide unique information on topographic properties and kinetic processes of asynchronous supramolecular assemblies with excellent spatial and time resolution. Here, single-molecule far-field fluorescence microscopy was applied to the NPC of permeabilized cells. The nucleoporin Nup358 could be localized at a distance of 70 nm from POM121-GFP along the NPC axis. Binding sites of NTF2, the transport receptor of RanGDP, were observed in cytoplasmic filaments and central framework, but not nucleoplasmic filaments of the NPC. The dwell times of …

Intranuclear Binding Kinetics And Mobility Of Single Native U1 Snrnp Particles In Living Cells, David Grunwald, Beatrice Spottke, Volker Buschmann, Ulrich Kubitscheck

David Grünwald

Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are splicing factors, which are diffusely distributed in the nucleoplasm and also concentrated in nuclear speckles. Fluorescently labeled, native U1 snRNPs were microinjected into the cytoplasm of living HeLa cells. After nuclear import single U1 snRNPs could be visualized and tracked at a spatial precision of 30 nm at a frame rate of 200 Hz employing a custom-built microscope with single-molecule sensitivity. The single-particle tracks revealed that most U1 snRNPs were bound to specific intranuclear sites, many of those presumably representing pre-mRNA splicing sites. The dissociation kinetics from these sites showed a multiexponential decay …

Conversion Of Red Fluorescent Protein Into A Bright Blue Probe, Oksana M. Subach, Illia S. Gundorov, Masami Yoshimura, Fedor V. Subach, Jinghang Zhang, David Grunwald, Ekaterina A. Souslova, Dmitriy M. Chudakov, Vladislav V. Verkhusha

David Grünwald

We used a red chromophore formation pathway, in which the anionic red chromophore is formed from the neutral blue intermediate, to suggest a rational design strategy to develop blue fluorescent proteins with a tyrosine-based chromophore. The strategy was applied to red fluorescent proteins of the different genetic backgrounds, such as TagRFP, mCherry, HcRed1, M355NA, and mKeima, which all were converted into blue probes. Further improvement of the blue variant of TagRFP by random mutagenesis resulted in an enhanced monomeric protein, mTagBFP, characterized by the substantially higher brightness, the faster chromophore maturation, and the higher pH stability than blue fluorescent proteins …

Autonomy And Robustness Of Translocation Through The Nuclear Pore Complex: A Single-Molecule Study, Thomas Dange, David Grunwald, Antje Grunwald, Reiner Peters, Ulrich Kubitscheck

David Grünwald

All molecular traffic between nucleus and cytoplasm occurs via the nuclear pore complex (NPC) within the nuclear envelope. In this study we analyzed the interactions of the nuclear transport receptors kapalpha2, kapbeta1, kapbeta1DeltaN44, and kapbeta2, and the model transport substrate, BSA-NLS, with NPCs to determine binding sites and kinetics using single-molecule microscopy in living cells. Recombinant transport receptors and BSA-NLS were fluorescently labeled by AlexaFluor 488, and microinjected into the cytoplasm of living HeLa cells expressing POM121-GFP as a nuclear pore marker. After bleaching the dominant GFP fluorescence the interactions of the microinjected molecules could be studied using video microscopy …

Nuclear Pore Component Nup98 Is A Potential Tumor Suppressor And Regulates Posttranscriptional Expression Of Select P53 Target Genes, Stephan Singer, Ruiying Zhao, Anthony M. Barsotti, Anette Ouwehand, Mina Fazollahi, Elias Coutavas, Kai Breuhahn, Olaf Neumann, Thomas Longerich, Tobias Pusterla, Maureen A. Powers, Keith M. Giles, Peter J. Leedman, Jochen Hess, David Grunwald, Harmen J. Bussemaker, Robert H. Singer, Peter Schirmacher, Carol Prives

David Grünwald

The p53 tumor suppressor utilizes multiple mechanisms to selectively regulate its myriad target genes, which in turn mediate diverse cellular processes. Here, using conventional and single-molecule mRNA analyses, we demonstrate that the nucleoporin Nup98 is required for full expression of p21, a key effector of the p53 pathway, but not several other p53 target genes. Nup98 regulates p21 mRNA levels by a posttranscriptional mechanism in which a complex containing Nup98 and the p21 mRNA 3'UTR protects p21 mRNA from degradation by the exosome. An in silico approach revealed another p53 target (14-3-3sigma) to be similarly regulated by Nup98. The expression …

The Complexity Of Molecular Interactions And Bindings Between Cyclic Peptide And Inhibit Polymerase A And B1 (Pac-Pb1n) H1n1, Arli A. Parikesit, Harry Noviardi Hn, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft

Arli A Parikesit

The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus was devised. The polymerase pac-pb1n enzyme is responsible for the replication of H1N1 virus. Thus, novel inhibitors were developed to ward off the functionality of the enzyme. In this research, cyclic peptides has been chosen to inhibit PAc-PB1n due to its proven stability in reaching the drug target. Thus, computational method for elucidating the molecular interaction between cyclic peptides …

The In Silico Molecular Interaction Of Organoboron Compounds As Curative Measure Toward Cervical Cancer, Ridla Bakri Rb, Arli A. Parikesit, Cipta Prio Satryanto Cps, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft

Arli A Parikesit

No abstract provided.

Nanoparticle Building Blocks For Functional Structures, Youngdo Jeong

Doctoral Dissertations

A major goal in material science is achieving a desired function using structures fabricated with designed building blocks. Advanced synthetic and self-assembly techniques allow various nanomaterials to become promising building blocks, providing the control of the interaction between building blocks. The unique properties of nanomaterials can be transferred to structured systems. Among nanomaterials, inorganic nanoparticles such as gold nanoparticles (AuNPs), magnetic particles, and quantum dots (QDs) provide useful physical properties stemming from their inorganic core, large surface areas, and oriented surface functionalities. My research has focused on fabricating functional systems using gold nanoparticles (AuNPs), manipulating the interaction between AuNPs, bio-entities, …

Properties Of Potential Substrates Of A Cyanobacterial Small Heat Shock Protein, Yichen Zhang

Masters Theses

Most proteins must fold into native three-dimensional structures to be functional. But, newly synthesized proteins are at high risk of misfolding and aggregating in the cell. Stress, disease or mutations can also cause protein aggregation. A cyanobacterial small heat shock protein, Hsp16.6, can act as a chaperone to prevent irreversible protein aggregation during heat stress. This thesis is focused on the properties of proteins that were associated with Hsp16.6 during heat stress, and which therefore may be “substrates” of Hsp16.6. Bioinformatics were used to determine if Hsp16.6 preferentially binds to proteins with certain properties, and biochemical studies were performed to …

Expression And Purification Of Human Lysosomal Β-Galactosidase From Pichia Pastoris, Sarah E. Tarullo

Masters Theses

Lysosomal storage diseases are genetically inherited diseases caused by the dysfunction of lysosomal enzymes. In a normal cell, lysosomal enzymes cleave specific macromolecules as they are transported to the lysosome. However, in diseased cells, these lysosomal enzymes are either absent or malfunctioning, causing macromolecular substrates to accumulate, becoming toxic to the cell. Over fifty lysosomal storage diseases have been identified, collectively occurring in one out of 7,700 live births. We investigated the lysosomal enzyme β-galactosidase (β-gal). In order to study the biochemistry and enzymology of this protein a robust expression system was needed. The GLB1 gene has been inserted into …

Kynurenine Aminotransferase Iii And Glutamine Transaminase L Are Identical Enzymes That Have Cysteine S-Conjugate Beta-Lyase Activity And Can Transaminate L-Selenomethionine, John T. Pinto, Boris F. Krasnikov, Steven Alcutt, Melanie E. Jones, Thambi Dorai, Arthur J L Cooper

NYMC Faculty Publications

Three of the four kynurenine aminotransferases (KAT I, II, and IV) that synthesize kynurenic acid, a neuromodulator, are identical to glutamine transaminase K (GTK), α-aminoadipate aminotransferase, and mitochondrial aspartate aminotransferase, respectively. GTK/KAT I and aspartate aminotransferase/KAT IV possess cysteine S-conjugate β-lyase activity. The gene for the former enzyme, GTK/KAT I, is listed in mammalian genome data banks as CCBL1 (cysteine conjugate beta-lyase 1). Also listed, despite the fact that no β-lyase activity has been assigned to the encoded protein in the genome data bank, is a CCBL2 (synonym KAT III). We show that human KAT III/CCBL2 possesses cysteine S-conjugate β-lyase …

Ribosomes Left In The Dust: Diverse Strategies For Peptide-Mediated Translation Stalling, Benjamin H. Hudson, Hani S. Zaher

Biology Faculty Publications & Presentations

In two recent papers, Arenz et al. (2014a) and Bischoff et al. (2014) provide structural insights into drug-induced, peptide-mediated stalling of the ribosome.

Cold Magnetically Trapped 2DG Scandium Atoms. I. Interaction Potential, Tijs Karman, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

We present a first principles description of the interaction of two ground-state scandium atoms. Scandium has a ²D_g ground state. Thirty molecular states correlate to the lowest dissociation limit of the dimer. In the short range, potential energy curves are calculated using second-order n-electron valence state perturbation theory. The first-order long-range interaction is calculated at the complete active space self-consistent field level. We determine the second-order long-range dispersion interaction from atomic dynamic polarizabilities at imaginary frequencies. These polarizabilities are calculated using time-dependent density functional theory. We merge the short-range approach with the long-range model to obtain a physical …

Anticancer Drug Delivery Via Unique Properties Of Gold Nanoparticles, Sam Lohmar, Jeffrey Schulte, Daniel Scott

Annual Student Research Poster Session

No abstract provided.

Semi-Synthetic Development Of Mithramycin Analogues, Sterling Brooks, Allison Foster, Daniel Scott

Annual Student Research Poster Session

No abstract provided.

Helping Families With Rare Diseases: Finding Disease-Causing Variants In A Wealth Of Genomic Data, Tyler Huff

Annual Student Research Poster Session

No abstract provided.

Tandem Cancer Drug Delivery Via Gold Nanoparticle Targeting Platforms, Jeffrey Schulte, Sam Lohmar, Daniel Scott

Annual Student Research Poster Session

No abstract provided.

Automatic Animation Of Molecular Motion Using Python And Cinema 4d, Diana Zajac, Nathaniel Smith, Dan Gurnon

Annual Student Research Poster Session

No abstract provided.

Er-Associated Degradation And Cadmium Dependent Rescue Of Pca1, Nathan Smith

Department of Biochemistry: Dissertations, Theses, and Student Research

Protein synthesis and proper folding is an essential process for all organisms. In eukaryotes proteins of the secretory pathway are synthesized and inserted into the lumen or membrane of the endoplasmic reticulum. Eukaryotic cells maintain a mechanism for removal of proteins unable to fold properly. This process is known as ER-associated degradation (ERAD). A poorly functioning ERAD can lead to a build-up of misfolded proteins which has been implicated in several degenerative diseases such as Alzheimer’s, Amyotrophic lateral sclerosis, and Parkinson’s. Thus, the study of how proteins are recognized, extracted from the ER, and degraded is essential for determining methods …

Cross-Disciplinary Sciences At Gettysburg College: Second Annual Poster Presentation, X-Sig

Student Publications

This booklet includes Biology student presentations by: Taylor Bury, Abigail Dworkin-Brodsky, Mary Pearce, Jasper Leavitt, Morgan Panzer, Ellen Petley, Kalli Qutub, Taylor Randell, Samantha Eck, Lana McDowell, Jenn Soroka, Celina Harris, Natalie Tanke, Alexandra Turano, and Caroline Garliss.

This booklet includes Biochemistry & Molecular Biology student presentations by: Matthew Dunworth, Andrew Sydenstricker, Brianne Tomko, Albert Vill, Warren Campbell, David Van Doren, Kevin Mrugalski, Stacey Heaver, Alecia Achimovich, and Katherine Boas.

This booklet includes Chemistry student presentations by: Kristen Baker, Laura Lee, Kathryn Fodale, Daniel Ruff, Michael Counihan, Ida DiMucci, Joshua Sgroi, Celina Harris, and Natalie Tanke.

This booklet include Health …

Characterization Of Severe Fever With Thrombocytopenia Syndrome In Rural Regions Of Zhejiang, China, Lei Zhang, Ling Ye, David M. Ojcius, Xiuyu Lou, Chengwei Wang, Cen Feng, Yi Sun, Zhongfa Wang, Shibo Li, Yanjun Zhang

All Dugoni School of Dentistry Faculty Articles

Severe fever with thrombocytopenia syndrome virus (SFTSV) infections have recently been found in rural regions of Zhejiang. A severe fever with thrombocytopenia syndrome (SFTS) surveillance and sero-epidemiological investigation was conducted in the districts with outbreaks. During the study period of 2011–2014, a total of 51 SFTSV infection cases were identified and the case fatality rate was 12% (6/51). Ninety two percent of the patients (47/51) were over 50 years of age, and 63% (32/51) of laboratory confirmed cases occurred from May to July. Nine percent (11/120) of the serum samples from local healthy people without symptoms were found to be …

A Cytoplasmic Rna Virus Generates Functional Viral Small Rnas And Regulates Viral Ires Activity In Mammalian Cells, Kuo-Feng Weng, Chuan-Tien Hung, Po-Ting Hsieh, Mei-Ling L. Li, Guang-Wu Chen, Yu-An Kung, Peng-Nien Huang, Rei-Lin Kuo, Li-Lien Chen, Jing-Yi Lin, Robert Yung-Liang Wang, Shu-Jen Chen, Petrus Tang, Jim-Tong Horng, Hsing-I Huang, Jen-Ren Wang, David M. Ojcius, Gary Brewer, Shin-Ru Shih

All Dugoni School of Dentistry Faculty Articles

The roles of virus-derived small RNAs (vsRNAs) have been studied in plants and insects. However, the generation and function of small RNAs from cytoplasmic RNA viruses in mammalian cells remain unexplored. This study describes four vsRNAs that were detected in enterovirus 71-infected cells using next-generation sequencing and northern blots. Viral infection produced substantial levels (>10⁵ copy numbers per cell) of vsRNA1, one of the four vsRNAs. We also demonstrated that Dicer is involved in vsRNA1 generation in infected cells. vsRNA1 overexpression inhibited viral translation and internal ribosomal entry site (IRES) activity in infected cells. Conversely, blocking vsRNA1 enhanced …

Hydroxamic Acid-Based Histone Deacetylase (Hdac) Inhibitors Can Mediate Neuroprotection Independent Of Hdac Inhibition, Sama Sleiman, Yan-Ling Zhang, Jennifer Gale, Manuela Basso, Giovanni Coppola, John T. Pinto, Rajiv Ratan

NYMC Faculty Publications

Histone deacetylase (HDAC) inhibition improves function and extends survival in rodent models of a host of neurological conditions, including stroke, and neurodegenerative diseases. Our understanding, however, of the contribution of individual HDAC isoforms to neuronal death is limited. In this study, we used selective chemical probes to assess the individual roles of the Class I HDAC isoforms in protecting Mus musculus primary cortical neurons from oxidative death. We demonstrated that the selective HDAC8 inhibitor PCI-34051 is a potent neuroprotective agent; and by taking advantage of both pharmacological and genetic tools, we established that HDAC8 is not critically involved in PCI-34051's …

Hdac8 And Stat3 Repress Bmf Gene Activity In Colon Cancer Cells, Y Kang, Hui Nian, P Rajendran, W Dashwood, John T. Pinto, E Ho, R Dashwood

NYMC Faculty Publications

Histone deacetylase (HDAC) inhibitors are undergoing clinical trials as anticancer agents, but some exhibit resistance mechanisms linked to anti-apoptotic Bcl-2 functions, such as BH3-only protein silencing. HDAC inhibitors that reactivate BH3-only family members might offer an improved therapeutic approach. We show here that a novel seleno-α-keto acid triggers global histone acetylation in human colon cancer cells and activates apoptosis in a p21-independent manner. Profiling of multiple survival factors identified a critical role for the BH3-only member Bcl-2-modifying factor (Bmf). On the corresponding BMF gene promoter, loss of HDAC8 was associated with signal transducer and activator of transcription 3 (STAT3)/specificity protein …

Aerosol Emissions From Prescribed Fires In The United States: A Synthesis Of Laboratory And Aircraft Measurements, A. A. May, G. R. Mcmeeking, T. Lee, J. W. Taylor, J. S. Craven, I. R. Burling, A. P. Sullivan, Sheryl Kashi Akagi, J. L. Collett Jr., M. Flynn, H. Coe, S. P. Urbanski, J. H. Seinfeld, Robert Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Aerosol emissions from prescribed fires can affect air quality on regional scales. Accurate representation of these emissions in models requires information regarding the amount and composition of the emitted species.Wemeasured a suite of submicron particulatematter species in young plumes emitted from prescribed fires (chaparral and montane ecosystems in California; coastal plain ecosystem in South Carolina) and from open burning of over 15 individual plant species in the laboratory. We report emission ratios and emission factors for refractory black carbon (rBC) and submicron nonrefractory aerosol and compare field and laboratory measurements to assess the representativeness of our laboratory-measured emissions. Laboratory measurements …

Regulation Of Igfbp-1 Phosphorylation In Hypoxia Via Mtor Signaling, Ian Damerill

Electronic Thesis and Dissertation Repository

In this study, we provide novel evidence for a role of fetal liver mTOR signaling in regulating IGF-I bioavailability by modulating IGFBP-1 phosphorylation due to hypoxia – a key factor in the development of reduced fetal growth in utero. We utilized HepG2 cells in vitro and demonstrated a link between mTOR inhibition and hypoxia-induced IGFBP-1 phosphorylation. Using a biological assay for IGF-I receptor autophosphorylation, we demonstrated a functional significance for hypoxia-induced IGFBP-1 phosphorylation in reducing IGF-I bioactivity in vitro. Further, we have implicated a mechanistic link to increased CK2 activity within this regulation. We demonstrate that mTOR inhibition …

Overexpression Of Patatin-Related Phospholipase Aiiiβ Altered The Content And Composition Of Sphingolipids In Arabidopsis, Maoyin Li, Jennifer E. Markham, Xuemin Wang

Department of Biochemistry: Faculty Publications

In plants, fatty acids are primarily synthesized in plastids and then transported to the endoplasmic reticulum (ER) for synthesis of most of the complex membrane lipids, including glycerolipids and sphingolipids. The first step of sphingolipid synthesis, which uses a fatty acid and a serine as substrates, is critical for sphingolipid homeostasis; its disruption leads to an altered plant growth. Phospholipase As have been implicated in the trafficking of fatty acids from plastids to the ER. Previously, we found that overexpression of a patatin-related phospholipase, pPLAIIIβ, resulted in a smaller plant size and altered anisotropic cell expansion. Here, we determined the …

Airborne Characterization Of Smoke Marker Ratios From Prescribed Burning, A. P. Sullivan, A. A. May, T. Lee, G. R. Mcmeeking, S. M. Kreidenweis, S. K. Akagi, Robert Yokelson, S. P. Urbanski, J. L. Collett Jr.

Chemistry and Biochemistry Faculty Publications

A Particle-Into-Liquid Sampler – Total Organic Carbon (PILS-TOC) and fraction collector system was flown aboard a Twin Otter aircraft sampling prescribed burning emissions in South Carolina in November 2011 to obtain smoke marker measurements. The fraction collector provided 2 min time-integrated offline samples for carbohydrate (i.e., smoke markers levoglucosan, mannosan, and galactosan) analysis by high-performance anion-exchange chromatography with pulsed amperometric detection. Each fire location appeared to have a unique 1levoglucosan /1water-soluble organic carbon (WSOC) ratio (RF01/RF02/RF03/RF05 = 0.163± 0.007 μg C μg−1 C, RF08 = 0.115 ± 0.011 μg C μg−1 C, RF09A = 0.072 ± 0.028 μgC μg−1 C, …