Digital Commons Network^™

Genome Announcement For E Cluster Phage Tarkin, Katherine Cleary

Chemistry & Biochemistry Student Scholarship

Katherine Cleary ’23
Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Methods For Increasing The Electron Richness Of Iron Tricarbonyl Diimine Complexes, Francesca Lombardi, Joseph Maher, Sean Peloquin

Chemistry & Biochemistry Student Scholarship

Francesca Lombardi ’24, Major: Chemistry

Joseph Maher ’25, Major: Chemistry

Sean Peloquin ’26, Major: Biochemistry

Faculty Mentor: Dr. Maria Carroll, Chemistry and Biochemistry

The goal of our research is to synthesize new iron complexes that can reduce carbon dioxide. Increasing the electron richness of iron tricarbonyl diimine complexes, which have been synthesized previously in the Carroll research group, will increase the likelihood of a reaction with carbon dioxide occurring. We have taken two approaches to changing the electron density in the complexes. First, we reacted the complex Fe((CF3)2ArDABMe)(CO)¬3 with the reducing agent potassium on graphite, in order to reduce either …

Kinetic Analysis Of Glu115ala Cytosolic Human Malate Dehydrogenase Mutation Shows A Change In Activity On Non-Native Substrate Phenylpyruvate, Kailey Paar

Chemistry & Biochemistry Student Scholarship

The cytosolic human enzyme, malate dehydrogenase (MDH1), is believed to have a significant effect on the proliferation of cancerous cells. This enzyme oxidizes NADH to NAD+ as it converts oxaloacetate (OAA) to malate. This oxidation of NADH provides the needed NAD+ to cancer cells, which require NAD+ as they upregulate glycolysis in aerobic conditions. Targeting MDH1 can reveal new therapeutic treatments for cancer by preventing the conversion of OAA to malate and depleting NAD+ stores in cancer cells, which can be done by mutating residues in the enzyme and assessing the change in activity. Here we show the replacement of …

Purification And Kinetic Characterization Of Mutant R111v Human Cytosolic Malate Dehydrogenase, Jackson Demartino

Chemistry & Biochemistry Student Scholarship

Metabolic profiling for a variety of cancerous cells indicate significant increases in the levels of glucose consumption. To support uncontrolled cell division, cancer cells also present an uncoupling of glycolysis from the citric acid cycle to promote glucose carbons to the synthesis of biomass, therefore, requiring a constant supply of NAD⁺. Recent studies indicate that cancer cells exhibit upregulated cytosolic malate dehydrogenase (MDH1) activity, which catalyzes the conversion of oxaloacetate to malate with the oxidation of NADH, generating NAD⁺. Given its increased activity, MDH1 may serve as a valuable target for treating cancer. Here we report …

Exploring Indicator Displacement Assays For Phosphate Detection In Seawater, Francis Radics

Chemistry & Biochemistry Student Scholarship

Francis Radics ’22
Major: Biochemistry
Faculty Mentor: Dr. John Breen, Chemistry and Biochemistry

Indicator displacement assays are based on the optical signal modulation of a noncovalently bound indicator upon dissociation by an analyte species. Our work has focused on exploring the lower detection limits for luminescent displacement assays for inorganic phosphate in seawater using complex ions containing two di(2-picolyl)amine ligands (also called DPA or bis(2-pyridylmethyl)amine), each coordinating a zinc cation. Following the work of B.D. Smith and coworkers, we have prepared three ligands by covalently attaching two DPA moieties, 2,6-bis(chloromethyl) benzene, and 2,6-bis(chloromethyl)-4-methylphenol, and 1,2-phenylenedimethylamine, for assays with 6,7-dihydroxy-4-methanesulfonic acid …

The Discovery And Analysis Of Mycobacteriophage “Rita”, Anna Fakhri

Chemistry & Biochemistry Student Scholarship

Anna Fakhri ’24
Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Mycobacteriophage “Rita” was isolated on Mycobacterium smegmatis mc2155 from an enriched soil sample from North Easton, Massachusetts. As Rita infects Mycobacterium smegmatis, further study of the phage was completed in order to determine its ability to be utilized in phage therapy for infections caused by pathogenic Mycobacterium, such as Mycobacterium tuberculosis and Mycobacterium abscessus. Once isolated, the phage DNA was analyzed through PCR to determine the phage belonged to cluster F and subcluster F1. The phage DNA was sequenced, and a genome annotation was completed. The annotation …

Characterization Of Immunity Systems In A Cluster Phages, Katherine Cleary

Chemistry & Biochemistry Student Scholarship

Katherine Cleary ’23
Major: Biochemistry
Faculty Mentor: Dr. Kathleen A. Cornely, Chemistry and Biochemistry

Bacteriophages are viruses that infect bacteria. Bacteriophages may use two different cycles to infect their hosts, which are the lytic cycle and the lysogenic cycle. During the lysogenic cycle, the phage genome integrates into the bacteria chromosome and becomes a part of the host. If a phage remains in the lysogenic cycle, the host is susceptible to infection from other bacteriophages. This process is known as superinfection and it can have a variety of outcomes. Homoimmunity occurs when the phages have similar repressor proteins. Heteroimmunity occurs …

Metal Complexes Of Redox Active Ligands, Alexandra Chaparro, Parker Keller

Chemistry & Biochemistry Student Scholarship

Alexandra Chaparro ’22, Major: Biochemistry

Parker Keller ’24, Major: Chemistry

Mentor: Dr. Maria Carroll, Chemistry and Biochemistry

Our research focuses on synthesizing and studying the properties of metal complexes that contain redox active ligands. Ligands are molecules or ions that can bind to a metal ion, and this particular class of ligands is interesting because they can either accept or lose electrons. We synthesized zinc complexes, in order to measure the reduction potentials of the ligands, which provide information about the ease with which they accept electrons. We then synthesized iron complexes and determined their structures. These complexes are potentially …

Development And Kinetic Survey Of A G148t Mutant Human Cytosolic Malate Dehydrogenase Isoform 3 Enzyme With Oxaloacetate And A-Ketoglutarate, Ethan N. Dionne

Chemistry & Biochemistry Student Scholarship

Cancer cells often use an altered metabolic pathway in which glycolysis, uncoupled from the citric acid cycle, serves as the primary source of ATP. To support cancer cell proliferation and growth, the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) must have a constant source of NAD. While lactate dehydrogenase (LDH) in its conversion of pyruvate to lactate is a well-known source of cytosolic NAD for GAPDH activity, cytosolic malate dehydrogenase (MDH1) also plays a role in cell proliferation through its generation of cytosolic NAD by the conversion of OAA to malate. This development has implicated MDH1 in cancer cell metabolism and characterizing …

Proline To Serine Mutation In The Active Site Loop Of Malate Dehydrogenase Alters Substrate Specificity, Olivia J. Schmitt

Chemistry & Biochemistry Student Scholarship

Cancer cells preferentially undergo glycolysis in aerobic environments, a phenomenon termed the Warburg effect. Malate dehydrogenase (MDH) catalyzes the reversible interconversion of malate and oxaloacetate. Human cytosolic malate dehydrogenase (hMDH1) isoform 3 is involved in the malate-aspartate shuttle (MAS), which oxidizes cytosolic NADH. hMDH1 is implicated in high aerobic glycolysis in cancer cells because NAD is a necessary cofactor for glycolysis. Thus, hMDH1 is a promising molecular target for cancer treatment. A single proline residue at position 110 in the mobile active site loop of hMDH1 was mutated to a serine with the intention of altering the enzyme’s substrate specificity. …

A Damaged Reputation: Nuclear Depictions In Entertainment Media, Alexander Cannon

Chemistry & Biochemistry Student Scholarship

This paper, originally written for Dr. Adamus Liotta in an honors chemistry class, explores the possibility of a significant influence over public common sense found in the depictions of entertainment media. Through careful analysis and interpretation of Godzilla, The Simpsons, Fallout, and Call of Duty, this paper finds a synergy throughout this diverse range of audience, medium and historical origin, which culminates in an effect much greater than the sum of its parts. This effect frames nuclear science, of any kind, in a hyperbolically catastrophic and horrific light, reinforcing an excessively cautious, pessimistic public perspective on nuclear technology …

Computational Modeling, Energy State Calculations, And Determination Of The Barriers To Rotation Of Atropisomeric Β-Carbolines, Lorenzo Battistoni

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry
Faculty Mentor: Dr. Seann Mulcahy

Axially chiral molecules that have high barriers to rotation about a single bond are called atropisomers. This project aims to expand information on atropisomeric β-carbolines by utilizing computational chemistry to generate energy profiles and determine the barriers to rotation of a library of atropisomeric β-carboline compounds using the program Spartan. Various substituents on the atropisomeric β-carboline scaffold can impact steric strain, electronic effects, and intramolecular hydrogen bonding in the molecule. These factors can impede bond rotation. We will be able to determine which atropisomeric β-carbolines are the best suited to synthesize experimentally using …

An Investigation Of K2 Mycobacteriophage Lysin A Proteins, Ethan Dionne

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Development Of New Methodology Towards Accessing 2-Imidazoline Scaffolds For Combatting Tuberculosis And Multiple Myeloma By Proteasome Modulation, Karen Saldarriaga, Victoria Rasmussen

Chemistry & Biochemistry Student Scholarship

Karen Saldarriaga ’20
Major: Biochemistry

Victoria Rasmussen '20
Major: Biology and Psychology

Faculty Mentor: Dr. Travis K. Bethel, Chemistry and Biochemistry

Multiple Myeloma (MM) is a disorder of differentiated B cells in which the inhibition of the proteasome is standard care. The current drug, bortezomib, used to treat MM is ineffective against drug tolerance where 97% of all patients become intolerant within a few years. Imidazoline scaffolds are capable of overcoming that resistance and delaying MM tumor growth. We believe we will be able to effectively yield imidazolines. Synthesis will occur with commercially available starting materials, making the process less …

Towards The Development Of Low-Cost And Easily-Deployable Sensing Platforms For Phosphate, Maureen Pontarelli, Thomas Koch

Chemistry & Biochemistry Student Scholarship

Maureen Pontarelli ’20
Major: Chemistry

Thomas Koch '20
Major: Biochemistry

Faculty Mentor: Dr. John Breen, Chemistry and Biochemistry

Surface Mutations Promote Metal Ion Affinity In Haemophilus Influenzae Carbonic Anhydrase, Ella Sheehan

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

αβ-Carbonic anhydrases are metalloenzymes that are essential to the growth of bacteria, making them a target for antibiotic research in the drug industry. These enzymes contain zinc ions that catalyze the hydration of carbon dioxide to bicarbonate for homeostatic balance. To enhance isolation, surface mutations were completed to introduce histidine residues because they demonstrate affinity for Ni-NTA resin in a column chromatography procedure. After generation and isolation of these mutants, the mutant HICA proteins can be used in a kinetic assay to observe the effect of mutation on the rate …

Exploration Of K2 Mycobacteriophages With Bred​, Colby Agostino, Olivia Schmitt

Chemistry & Biochemistry Student Scholarship

Colby Agostino ’22
Major: Biochemistry and Computer Science

Olivia Schmitt ’22
Major: Biochemistry

Faculty Mentor: Dr. Kathleen A. Cornely, Chemistry and Biochemistry

ZoeJ and Marcoliusprime are mycobacteriophage capable of infecting tuberculosis causing bacteria via the lytic and lysogenic cycles. The lytic cycle is the form of viral replication that results in cell death. Lysogeny involves phage DNA being integrated with the DNA of the host cell and preserved through binary fission. However, the bacteria causing tuberculosis do not die in the lysogenic phase. This research project will involve creating mutants of ZoeJ and Marcoliusprime that will not contain the genes …

Mycobacteriophage Morphology As A Diagnostic For Cluster Assignment, Ethan Dionne

Chemistry & Biochemistry Student Scholarship

Major: Biochemistry

Faculty Mentor: Dr. Kathleen A. Cornely, Chemistry and Biochemistry

Phages are viral bodies that infect bacterial hosts, and have shown promising applications as alternatives to antibiotics for the treatment of bacterial infections. This project examines the morphology of siphoviridae mycobacteriophage, which have long, flexible, non-contractile tails as well as the characteristic head, called a capsid. Using electron microscopy photos of sequenced phages, tail length and capsid diameter were measured and compared to further characterize morphological relationships between genetically distinct phages. The data presented has the potential to work as a diagnostic tool to classify unsequenced phages to genetically …

Ile126his And Lys129his Surface Mutations Aid In Purification Of Haemophilus Influenzae Carbonic Anhydrase Through Increased Metal Ion Affinity, Timothy Rigdon, Kathleen Cornely

Chemistry & Biochemistry Student Scholarship

Carbonic anhydrase (CA) is an enzyme that plays a major role in the survival of many bacterial, chiefly Haemophilus influenzae. Because of its crucial role in bacteria, recent research has turned to CA as a possible target for drug development to kill bacteria and possibly cure different bacterial diseases. While research has focused on this drug target, the isolation and purification of specific types of CA has remained a major obstacle for further research. The current method of immobilized metal affinity chromatography (IMAC) with a Ni-NTA column is used widely for CA purification; however, the H. influenzae carbonic anhydrase …

Surface Mutation Thr34his Facilitates Purification Of Haemophilus Influenza Carbonic Anhydrase Via Metal Affinity Chromatography, Caroline Foley, Dr. Kathleen Cornely

Chemistry & Biochemistry Student Scholarship

In order to pursue Haemophilus influenza carbonic anhydrase (HICA) as a potential drug target, easy and efficient purification methods must be developed. While immobilized metal affinity chromatography (IMAC) may be used, complications with polyhistidine tags is a concern. Inspired by the endogenous metal affinity of Escherichia coli β-carbonic anhydrase (ECCA), we suggest that the generation of histidine clusters on HICA’s surface will facilitate its purification by metal affinity chromatography without the potential interference of His-tags. Here we investigate the Thr34His mutation as a method to generate metal affinity in HICA. Since Thr34His is located only 5.3 Å away from His32, …

E56h + E59h Mutation Affects Binding Of The Recombinant Haemphilus Influenza Carbonic Anhydrase To A Ni-Nta Column, Eric D. Lebel, Kathleen Cornely

Chemistry & Biochemistry Student Scholarship

The Haemophilus influenzae carbonic anhy- drase (HICA) is important in converting carbon dioxide to bicarbonate in bacteria. Endogenous cellular proteins, like Escherichia coli carbonic anhydrase (ECCA), have been observed to bind to a Ni-NTA column, which can be used as a means of protein purification. The possibility ex- ists that proteins that do not normally bind to Ni-NTA, like HICA, can be engineered using site directed mutagenesis to introduce histidine resi- dues that would give the protein the capability to bind, allowing for a one-step purification method. Site-directed mutagenesis was used to introduce the double mutation of E56H + E59H …

Mutation Of Surface Histidines In Haemophilus Influenzae Carbonic Anhydrase To Enable Purification By Metal Affinity Chromatography, Shelby E. Scola, Kathleen Cornely

Chemistry & Biochemistry Student Scholarship

No abstract provided.

Characterization Of A Reductively-Activated Elimination Pathway Relevant To The Biological Chemistry Of The Kinamycins And Lomaiviticins, Seann P. Mulcahy, Christina M. Woo, Weidong Ding, George A. Ellestad, Seth B. Herzon

Chemistry & Biochemistry Faculty Publications

The lomaiviticins (1 and 2) and kinamycins (3–5) are bacterial metabolites with potent antimicrobial and antiproliferative activities. Herein we establish that 1–5 are capable of generating electrophilic acylfulvene intermediates (6) under mildly reducing conditions. These acylfulvenes 6 are formed by a multistep process comprising two-electron reduction and loss of dinitrogen to form an ortho-quinone methide, followed by elimination. Based on these studies, the structure of the product formed from 1 in DNA-cleavage assays is proposed (26). We also show that the bis(hydroxynaphthoquinone) substructures of the lomaiviticins activate the metabolites toward reduction. Finally, based on COMPARE and time-dependent cell response profiling …

Hepatic Lipase Treatment Of Chylomicron Remnants Increases Exposure Of Apolipoprotein E, Dawn L. Brasaemle, Kathleen Cornely-Moss, André Bensadoun

Chemistry & Biochemistry Faculty Publications

The consequences of hepatic lipase treatment of chylomicron remnants were studied. Rats were fed corn oil to induce production and secretion of chylomicrons and were then injected with polyclonal antiserum raised against hepatic lipase to specifically and quantitatively inhibit hepatic lipase activity in vivo. A fraction enriched in chylomicron remnants was isolated from rat plasma by a brief centrifugation step that preferentially isolates triglyceride-rich apolipoprotein (apo) B-48-containing lipoproteins. The chylomicron remnants were then treated with hepatic lipase in vitro, or incubated under identical conditions in the absence of enzyme (control incubations). Hepatic lipase-treated and control chylomicron remnants were isolated by …

Volume 3, Number 1 - May 1957

The Entropy

The Entropy (also published as the Providence College Journal of Physics and Chemistry) was an undergraduate scholarship journal published by the Phi Chi Club of Providence College. (Volume 3, Number 1 - May 1957 - 19 pages in total.)

Volume 2, Number 1 - May 1956

The Entropy

The Entropy (also published as the Providence College Journal of Physics and Chemistry) was an undergraduate scholarship journal published by the Phi Chi Club of Providence College. (Volume 2, Number 1 - May 1956 - 16 pages in total.)

Volume 1, Number 2 - May 1954

The Entropy

The Entropy (also published as the Providence College Journal of Physics and Chemistry) was an undergraduate scholarship journal published by the Phi Chi Club of Providence College. (Volume 1, Number 2 - May 1954 - 10 pages in total.)

Volume 1, Number 1 - January 1954

The Entropy

The Entropy (also published as the Providence College Journal of Physics and Chemistry) was an undergraduate scholarship journal published by the Phi Chi Club of Providence College. (Volume 1, Number 1 - January 1954 - 22 pages in total.)