Biochemistry Commons^™

Design, Synthesis, Application Of Biodegradable Polymers, Mussie Gide

USF Tampa Graduate Theses and Dissertations

Bacterial infections have posed a serious threat to the public health due to the significant rise of the infections caused by antibiotic-resistant bacteria. There has been considerable interest in the development of antimicrobial agents which mimic the natural HDPs, and among them biodegradable polymers are newly discovered drug candidates with ease of synthesis and low manufacture cost compared to synthetic host defense peptides. Herein, we present the synthesis of biocompatible and biodegradable polymers including polycarbonate polymers, unimolecular micelle hyperbranched polymers and dendrimers that mimic the antibacterial mechanism of HDPs by compromising bacterial cell membranes. The developed amphiphilic polycarbonates are highly …

Investigating The Synthesis Of 1,3,4-Oxadiazoles Via A Novel Two-Step-One-Pot Cyclodehydration Reaction, Brittney Sowers

Undergraduate Honors Thesis Projects

The given research will investigate synthetic strategies and differential functionalization of 1,3,4- oxadiazoles in hopes of obtaining moderate to high yields. Particularly, the effects of electron withdrawing on oxadiazoles will reveal more information about possible mechanistic details and reaction optimization.

The research in this report is a part of a lager research effort being investigated by Dr. Robin Grote. This research is ongoing and has evolved from its start in the Grote Lab. Previously, the Grote Lab has focused on the formation of a patented heterocycle that contained an amino-pyrazine functional group. Currently, our research has shifted focus to the …

A Chimeric Nucleobase - Phenylazo Derivative As An Intrinsic Nucleobase Quencher, Gyeongsu Park, Timothy Martin-Chan, Amer El Samm, Robert H.E. Hudson

Western Research Forum

Molecular beacons are important bioanalytical probes which are most often

constructed from a single-stranded oligonucleotide which has been labeled at

opposite termini with a fluorophore and a quencher. When the fluorophore and

quencher are in close proximity, no fluorescence is observed due to FRET

(Fluorescence Resonance Energy Transfer). DABCYL (4-dimethylaminoazobenzene-

4'-carboxylic acid) has been used as a quencher in the molecular beacon to absorbs

excitation energy from a fluorophore and to dissipate the energy as heat. However,

DABCYL is unable to form a base-pair and is conventionally placed as an overhanging

residue. This produces a derivative wherein the chromophore has …

Developing Novel Therapeutics For Bacterial Lung Infections, Brandon J. Baer, Ruud Veldhuizen, Cory Yamashita

Western Research Forum

Background: Bacterial lung infections are leading causes of death worldwide. Unfortunately, increasing resistance to antibiotics and the inflammation often accompanying these infections are leading to poor outcomes despite antibiotic intervention. Complicating treatment further, the tree-like branching structure of the lung makes drug delivery to distal sites of infection difficult. Our research aims to address these challenges by developing new therapeutics and new tools to improve and assess drug delivery, bacterial killing and inflammation. Our therapy combines host defense peptides, which have been shown to kill antibiotic-resistant bacteria and down regulate inflammation, with a pulmonary vehicle, exogenous surfactant, that can improve …

Maternal Protein Restriction (Mpr): A Risk Factor For Acute Respiratory Distress Syndrome (Ards), Reza Khazaee

Western Research Forum

Background: Acute respiratory distress syndrome (ARDS) is defined as severe lung dysfunction. The lung impairments in ARDS result from alterations to pulmonary surfactant; a lipid-protein mixture coating the inside of the lung and maintains the lungs’ ability to expand easily. Due to a lack of effective pharmacological therapies mortality associated with ARDS is over 30%. Our research focuses on risk factors that indicate a susceptibility to the disease, which could provide new and early therapeutic options. One such potential risk factor is Maternal Protein Restriction (MPR). MPR is defined by low birth weight and contributes to a variety of adult-onset …

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot …

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the Next …

Killi-Data News (Summer), Tyrone Genade

Killifish Research Review

Over the last three months several interesting and exciting pa- pers have been published. By now most of you have heard the Nothobranchius fish poo news emanating from the Valenzano lab. That paper is reviewed and certainly has repercussions for the health of our captive fish. Polaçik et al have published interesting data with ramifications as to how we breed and incubate annual killifish. The big news in this issue is the paper from the Reznick lab which Jean Huber reviews. The contents of that paper goes to the heart of the question of just what a killifish is. The …

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

This is the fourth edition, and concluding issue of the first volume, of Killi-Data News and I am happy that it has been well received by readers. At 25 pages this issue is a bit thin- ner than the last but this is because we agreed to make the cut-off for submissions the 1 st of December so we could get this edition out by the New Year. This is an exciting edition full of new species descrip- tions and analyses that will keep taxonomists busy for years to come. Costa has given us two molecular phylogenies on Melanorivulus as …

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don’t know everything …

Characterization Of Metabolic Networks In Differentiated Cd4+ T Cells, Bailee Lichter

Honors Program: Senior Projects (Public)

CD4+ T cells play a critical role in the immune system and protecting the body from infection. Cell differentiation of T-cells leads to the specialization of the immune system and has been determined to have plasticity. Differentiation of the CD4+ T cells depends on cytokines present in the environment, concentration of antigens, types of antigen – presenting cells (APCs), and costimulatory molecules (Luckheeram, 2012). Commonly known differentiated T-cells include the T-helper 1 (Th1) and the T-helper 2 (Th2) cells. Upon CD4+ T cell activation, the cells undergo metabolic changes that allow for cell growth and division. By characterizing the metabolic …

Thermodynamics In Large Hairpin Polyamide-Dna Interactions, Yang Song

Dissertations

Human papillomavirus (HPV) is a common sexually transmitted virus responsible for cervical cancers, and its infection is currently incurable. Only a few vaccines against high-risk HPV strains are available. Hairpin polyamides (PAs) in different sizes (8-20 units long) bind DNA in different lengths. They have been shown to have different anti-HPV activities in cell culture.

The interaction between PA and DNA is stabilized by two types of molecular forces: attractive and repulsive forces. Attractive forces include hydrogen bonds, van der Waals contacts and electrostatic forces between PA and DNA. Repulsive forces include the hydrophobic effect, which forces the PA out …

Non-Methane Organic Gas Emissions From Biomass Burning: Identification, Quantification, And Emission Factors From Ptr-Tof During The Firex 2016 Laboratory Experiment, Abigail R. Koss, Kanako Sekimoto, Jessica B. Gilman, Vanessa Selimovic, Matthew M. Coggon, Kyle J. Zarzana, Bin Yuan, Brian M. Lerner, Steven S. Brown, Jose L. Jimenez, Jordan Krechmer, James M. Roberts, Carsten Warneke, Robert J. Yokelson, Joost De Gouw

Chemistry and Biochemistry Faculty Publications

Volatile and intermediate-volatility non-methane organic gases (NMOGs) released from biomass burning were measured during laboratory-simulated wildfires by proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF). We identified NMOG contributors to more than 150 PTR ion masses using gas chromatography (GC) pre-separation with electron ionization, H3O+ chemical ionization, and NO+ chemical ionization, an extensive literature review, and time series correlation, providing higher certainty for ion identifications than has been previously available. Our interpretation of the PTR-ToF mass spectrum accounts for nearly 90ĝ€-% of NMOG mass detected by PTR-ToF across all fuel types. The relative contributions of different NMOGs to individual exact ion masses are …

Studies Of Amino Acid Mutations In Drug Resistance Of The Smo Protein, Eunice Wintona

UNO Student Research and Creative Activity Fair

Smoothened receptor (SMO) is a protein that in humans, is encoded by the SMO gene. A systemic mutation in its binding pocket helps predict the sensitivity of mutant proteins to different drugs. Known as a GPCR-like receptor, it is a component of the hedgehog signaling pathway; a pathway involved in body patterning and the regulation of adult stem cells. An uncontrolled or inappropriate activation of the Hedgehog pathway drives tumor progression in cancers and a number of birth defects. To achieve these goals, the molecular modeling software MOE was used to build small molecules and drug molecules like Vismodegib and …

Aerosol Optical Properties And Trace Gas Emissions By Pax And Op-Ftir For Laboratory-Simulated Western Us Wildfires During Firex, Vanessa Selimovic, Robert J. Yokelson, Carsten Warneke, James M. Roberts, Joost De Gouw, James Reardon, David W.T. Griffith

Chemistry and Biochemistry Faculty Publications

Western wildfires have a major impact on air quality in the US. In the fall of 2016, 107 test fires were burned in the large-scale combustion facility at the US Forest Service Missoula Fire Sciences Laboratory as part of the Fire Influence on Regional and Global Environments Experiment (FIREX). Canopy, litter, duff, dead wood, and other fuel components were burned in combinations that represented realistic fuel complexes for several important western US coniferous and chaparral ecosystems including ponderosa pine, Douglas fir, Engelmann spruce, lodgepole pine, subalpine fir, chamise, and manzanita. In addition, dung, Indonesian peat, and individual coniferous ecosystem fuel …

A Gender-Based Comparison In Health Behaviors And State Of Happiness Among University Students, Rehana Rehman, Amara Zafar, Aleena Mohib, Mukhtiar Baig

Department of Biological & Biomedical Sciences

Objective: The presence of good healthy behaviors among university students is imperative for their future life. This study aimed to compare positive health behaviors and state of happiness between the two genders of Bahria University (BU), Karachi, Pakistan.
Subjects and methods: This cross-sectional study was conducted at BU, Karachi, Pakistan. A total 813 students participated in this study. The healthquestionnaire, adapted from Health and Behavior Survey and the Subjective Happiness Scale, was used to assess self-reported happiness. The data were analyzed using IBM SPSS version 22.
Results: Overall self-reported health behaviors were found to be more prevalent in females as …

In Vitro Label Free Screening Of Chemotherapeutic Drugs Using Raman Micro-Spectroscopy: Towards A New Paradigm Of Spectralomics., Zeineb Farhane, Haq Nawaz, Franck Bonnier, Hugh Byrne

Articles

This overview groups some of the recent studies highlighting the potential application of Raman micro-spectroscopy as an analytical technique in preclinical development to predict drug mechanism of action and in clinical application as a companion diagnostic and in personalised therapy due to its capacity to predict cellular resistance and therefore to optimise chemotherapeutic treatment efficacy.

Notably, the anthracyclines, Doxorubicin and Actinomycin D, elicit similar spectroscopic signatures of subcellular interaction characteristic of the mode of action of intercalation. Although Cisplatin and Vincristine show markedly different signatures, at low exposure doses, their signatures at higher doses show marked similarities to those elicited …

Rescue Of Neocortical Circuit Deficits With Modified Bone Marrow-Derived Mesenchymal Stem Cells, Sb623, In A Rat Model Of Photothrombotic Stroke, Alexander Urry

Yale Day of Data

The following poster characterizes the effects of a novel stem cell line on treating the neural circuit deficits resulting from stroke.

Electron Transfer To Nitrogenase In Different Genomic And Metabolic Backgrounds, Saroj Poudel, Daniel R. Colman, Kathryn R. Fixen, Rhesa N. Ledbetter, Yanning Zheng, Natasha Pence, Lance C. Seefeldt, John W. Peters, Caroline S. Harwood, Eric S. Boyd

Chemistry and Biochemistry Faculty Publications

Nitrogenase catalyzes the reduction of dinitrogen (N₂) using low-potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP-dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O₂)-sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds, including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd-/Fld-reducing enzymes in 359 genomes of putative N₂ fixers (diazotrophs). Six distinct lineages …

Implications Of Monomer Deformation For Tetrel And Pnicogen Bonds, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A series of TF₄ and ZF₅ molecules (T = Si, Ge, Sn and Z = P, As, Sb) were allowed to engage in tetrel and pnicogen bonds, respectively, with NH₃, pyrazine, and HCN. The interaction energies are quite large, approaching 50 kcal mol^-1 in some cases. The formation of each complex is accompanied by substantial geometrical deformation of the Lewis acid to accommodate the approaching base. The energy associated with this monomer rearrangement is the largest for the smaller central atoms Si and P, where it exceeds 20 kcal mol^-1. The total reaction …

Chemical Characterization Of Fine Particulate Matter Emitted By Peat Fires In Central Kalimantan, Indonesia, During The 2015 El Niño, Thilina Jayarathne, Chelsea E. Stockwell, Ashley A. Gilbert, Kaitlyn Daugherty, Mark A. Cochrane, Kevin C. Ryan, Erianto I. Putra, Bambang H. Saharjo, Ati D. Nurhayati, Israr Albar, Robert J. Yokelson, Elizabeth A. Stone

Chemistry and Biochemistry Faculty Publications

Fine particulate matter (PM2:5) was collected in situ from peat smoke during the 2015 El Niño peat fire episode in Central Kalimantan, Indonesia. Twenty-one PM samples were collected from 18 peat fire plumes that were primarily smoldering with modified combustion efficiency (MCE) values of 0.725-0.833. PM emissions were determined and chemically characterized for elemental carbon (EC), organic carbon (OC), water-soluble OC, water-soluble ions, metals, and organic species. Fuel-based PM2:5 mass emission factors (EFs) ranged from 6.0 to 29.6 g kg1 with an average of 17:36:0 g kg1. EC was detected only in 15 plumes and comprised 1% of PM mass. …

Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter From Wood-And Dung-Fueled Cooking Fires, Garbage And Crop Residue Burning, Brick Kilns, And Other Sources, Thilina Jayarathne, Chelsea E. Stockwell, Prakash V. Bhave, Puppala S. Praveen, Chathurika M. Rathnayake, Robiul Md Islam, Arnico K. Panday, Sagar Adhikari, Rashmi Maharjan, J. Douglas Goetz, Peter F. Decarlo, Eri Saikawa, Robert J. Yokelson, Elizabeth A. Stone

Chemistry and Biochemistry Faculty Publications

The Nepal Ambient Monitoring and Source Testing Experiment (NAMaSTE) characterized widespread and under-sampled combustion sources common to South Asia, including brick kilns, garbage burning, diesel and gasoline generators, diesel groundwater pumps, idling motorcycles, traditional and modern cooking stoves and fires, crop residue burning, and heating fire. Fuel-based emission factors (EFs; with units of pollutant mass emitted per kilogram of fuel combusted) were determined for fine particulate matter (PM2.5), organic carbon (OC), elemental carbon (EC), inorganic ions, trace metals, and organic species. For the forced-draft zigzag brick kiln, EFPM2.5 ranged from 12 to 19gkg-1 with major contributions from OC (7%), sulfate …

Distinct Properties Underlie Flavin-Based Electron Bifurcation In A Novel Electron Transfer Flavoprotein Fixab From Rhodopseudomonas Palustris, H. Diessel Duan, Carolyn E. Lubner, Monika Tokmina-Lukaszewska, George H. Gauss, Brian Bothner, Paul W. King, John W. Peters, Anne-Frances Miller

Chemistry Faculty Publications

A newly recognized third fundamental mechanism of energy conservation in biology, electron bifurcation, uses free energy from exergonic redox reactions to drive endergonic redox reactions. Flavin-based electron bifurcation furnishes low-potential electrons to demanding chemical reactions, such as reduction of dinitrogen to ammonia. We employed the heterodimeric flavoenzyme FixAB from the diazotrophic bacterium Rhodopseudomonas palustris to elucidate unique properties that underpin flavin-based electron bifurcation. FixAB is distinguished from canonical electron transfer flavoproteins (ETFs) by a second FAD that replaces the AMP of canonical ETF. We exploited near-UV–visible CD spectroscopy to resolve signals from the different flavin sites in FixAB and to …

Investigating Biomass Burning Aerosol Morphology Using A Laser Imaging Nephelometer, Katherine M. Manfred, Rebecca A. Washenfelder, Nicholas L. Wagner, Gabriela Adler, Frank Erdesz, Caroline C. Womack, Kara D. Lamb, Joshua P. Schwarz, Alessandro Franchin, Vanessa Selimovic, Robert J. Yokelson, Daniel M. Murphy

Chemistry and Biochemistry Faculty Publications

Particle morphology is an important parameter affecting aerosol optical properties that are relevant to climate and air quality, yet it is poorly constrained due to sparse in situ measurements. Biomass burning is a large source of aerosol that generates particles with different morphologies. Quantifying the optical contributions of non-spherical aerosol populations is critical for accurate radiative transfer models, and for correctly interpreting remote sensing data. We deployed a laser imaging nephelometer at the Missoula Fire Sciences Laboratory to sample biomass burning aerosol from controlled fires during the FIREX intensive laboratory study. The laser imaging nephelometer measures the unpolarized scattering phase …

Pi Tetrel Bonds, And Their Influence On Hydrogen Bonds And Proton Transfers, Yuanxin Wei, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The positive region that lies above the plane of F2TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H‐bond. The T atom of F2TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F2TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F2SiO engages in a much stronger interaction than does F2CO, reaching nearly 200 kJ mol−1. The π‐tetrel bond strengthens/weakens the MDA H‐bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an …

Expansion Of The (Bb)>Ru Metallacycle With Coinage Metal Cations: Formation Of B-M-Ru-B (M= Cu, Ag, Au) Dimetalacyclodiboryls†, Bennett J. Eleazer, Mark D. Smith, Alexey A. Popov, Dmitry V. Peryshkov

Faculty Publications

In this work, we introduce a novel approach for the selective assembly of heterometallic complexes by unprecedented coordination of coinage metal cations to strained single ruthenium–boron bonds on a surface of icosahedral boron clusters. M(I) cations (M ¼ Cu, Ag, and Au) insert into B–Ru bonds of the (BB)–carboryne complex of ruthenium with the formation of four-membered B–M–Ru–B metalacycles. Results of theoretical calculations suggest that bonding within these metalacycles can be best described as unusual three-center-two-electron B–M/Ru interactions that are isolobal to B–H/Ru borane coordination for M ¼ Cu and Ag, or the pairs of two-center-two electron B–Au and Au–Ru …

Lack Of Association Of Statin Use With Vitamin D Levels In A Hospital Based Population Of Type 2 Diabetes Mellitus Patients, Khalida Iqbal, Najmul Islam, Iqbal Azam Syed, Naseema Mehboobali, Mohammad Perwaiz Iqbal

Department of Biological & Biomedical Sciences

Objective: To investigate the relationship of statins (drug given to reduce serum levels of LDL-cholesterol) on vitamin D levels of Pakistani type 2 diabetes mellitus (DM) patients in a hospital in Karachi.
Methods: In a cross-sectional survey, 312 consecutive patients with type 2 DM (219 males and 93 females, age 22-70 years) were recruited with informed consent. A questionnaire was administered to find out whether they were statin users or non-users. Serum was analyzed for concentrations of 25(OH) vitamin D [25(OH)D] and other related biomarkers such as serum cholesterol, triglycerides, HDL-cholesterol, LDL-cholesterol, phosphate and calcium using kit methods. Multiple Linear …

Functional Interactions Of Tau, Pin1, P53 And Mrna 3′ Processing Factors In Non-Neuronal Cells, Jorge E. Baquero

Dissertations, Theses, and Capstone Projects

ABSTRACT

mRNA 3’ end processing, an essential step in eukaryotic RNA metabolism, regulates the steady-state levels of different mRNAs and contributes to the cells rapid response to stress. Studies have described potential contributions of mRNA 3’ end processing to numerous human diseases, including cancer and Alzheimer’s disease (AD). Therefore, the main purpose of this dissertation is to further elucidate some of the roles of disease-related factors Pin1, p53 and tau in the regulation mRNA 3’ end processing in non-neuronal cells under different cellular conditions, including during the DNA damage response (DDR).

The results from Chapter II show that the prolyl …

Mechanisms For Survival And Drug Resistance In Cancer Cells, Matthew B. Utter

Dissertations, Theses, and Capstone Projects

PART I

Prostate cells are hormonally driven to grow and divide. Typical treatments for prostate cancer involve blocking the hormone androgen from activating the androgen receptor (AR) and thus inhibit growth and proliferation of the cancer. Androgen deprivation therapy (ADT) can lead to the selection of cancer cells that grow and divide independently of androgen receptor activation. Prostate cancer cells that are insensitive to androgens commonly display metastatic phenotypes and reduced long-term survival of patients. In this study, we provide evidence that androgen-insensitive prostate cancer cells have elevated phospholipase D (PLD) activity relative to the androgen-sensitive prostate cancer cells. PLD …