Tag: Chemistry

From the very beginning of my academic journey, the intersection of chemistry and biology has thrilled me, as it embodies the essence of interdisciplinary challenges that encourage innovative thinking. Having BS and MS in biochemistry, I joined the Chemistry Department at Michigan Technological University in August 2018 as a Fulbright Graduate Student from Ukraine. Under the mentorship of Dr. Marina Tanasova, I pursued chemical biology research to utilize small molecules produced through synthetic chemistry for the study of complex biological systems.
My Ph.D. research focuses on the development of tools for the targeted detection of disease-relevant sugar transporters (GLUTs) to advance diagnostic and imaging capabilities. Working in Dr. Tanasova’s lab has been an incredibly rich research experience, allowing me to master a diverse set of skills and carry out the whole research project from the beginning to the end. I truly enjoy the process of designing molecules, synthesizing them, and validating their properties through a range of analytical techniques. Witnessing the colorful array of fluorescent probes we have developed and applying them for cancer research has evoked excitement in me. I am genuinely excited about the potential outcomes of my research, as they contribute to the advancement of novel strategies for targeting cancers in both diagnostic and therapeutic applications. Collaborating with other researchers and students, sharing my research, and promoting a safety culture within my department and on the national level have been rewarding and enriching experiences for me during my Ph.D. I am grateful for the opportunities I have had during my graduate program. I am confident that the training I received at MTU has provided me with a solid foundation to realize my research aspirations.
I am honored to be selected as one of the recipients of the Doctoral Finishing Fellowship. I would like to thank the Graduate Dean Awards Advisory Panel and Dean for granting the fellowship to me during this crucial phase of my Ph.D. journey. It is indeed an invaluable opportunity to dedicate my time and efforts to writing my dissertation, preparing for the defense, and embarking on the next chapter of my scientific career. I would like to thank my research advisor Dr. Marina Tanasova for the support and guidance she provided over the last 5 years. Her belief in my potential paved the way for me to transition from a Master’s student to a doctoral candidate, and I am truly grateful for the mentorship and encouragement she has provided. Moreover, I wish to express my gratitude to the Chemistry Department, Dr. Sarah Green, my committee members, and all the individuals who have played a role in shaping me into an independent research scientist.

I began my Ph.D. journey in Chemistry in the Fall 2019 under the guidance of Dr. Tatyana G. Karabencheva-Christova. Prior to joining MTU, I earned a master’s degree in Applied Chemistry from Mahatma Gandhi University and a bachelor’s degree in Chemistry from Calicut University, India. It was during my master’s program that I developed a profound interest in computational chemistry, which ultimately led me to pursue advanced studies in this fascinating field.

My research primarily focuses on exploring enzyme characteristics and mechanisms through the application of multilevel computational methods, including Molecular Dynamics (MD), Quantum Mechanics (QM), and combined Quantum mechanics/Molecular mechanics (QM/MM). During my Ph.D., I had the opportunity to contribute to NIH-funded projects on the non-heme Fe(II) and 2-oxoglutarate dependent oxygenase, Fat mass and Obesity Associated Protein (FTO), and the Zn(II) dependent metalloprotease, Matrix metalloproteinase-1 (MMP-1), both of which have crucial implications in various types of cancers. In the former project, I investigated the enzymatic mechanism of FTO with its major substrate, N6-methyladenine in single-stranded RNA, and explored the influence of clinically relevant mutations Arg316Gln and Ser319Phe on different stages of the catalytic cycle. In the latter, I unraveled the water-mediated catalytic mechanism of MMP-1, conformational dynamics and long-range correlated motions assisting in catalysis and the role of the catalytic and structural Zn(II) ions in the overall stability of enzyme.

I am immensely grateful to the Graduate Dean Awards Advisory Panel and the Dean for recognizing my efforts and awarding me the Doctoral Finishing Fellowship. I extend my heartfelt gratitude to my advisor, Dr. Tatyana G. Karabencheva-Christova, whose guidance and support have been invaluable throughout my Ph.D. journey. I also extend my thanks to all the faculty and staff in the Chemistry department for their encouragement and assistance.

I joined the Ph.D.in Chemistry program at Michigan Tech in Fall 2018. Prior to this, I obtained a Bachelor’s degree in Chemistry from Miranda House, University of Delhi, New Delhi, India in 2016 and Master’s in Organic Chemistry from Maharshi Dayanand University, Rohtak, India in 2018. During the course of my Ph.D., I honed multiple skills needed for the organic laboratory work, and developed various interpersonal skills including communication, presentation, critical thinking, problem-solving, collaboration, leadership qualities and many more. These skills have not only contributed to my research success but have also shaped me into a confident and capable professional.

As an organic chemist, to accomplish the research objectives, I successfully synthesized various small and macromolecules that served as a monomer for oligodeoxynucleotides. This process involved the utilization of various instrumental analysis techniques. During my research, I focused on the synthesis of sensitive oligodeoxynucleotides under mild deprotection and cleavage conditions. Sensitive oligodeoxynucleotides are the DNA nucleosides that are unstable to harsh deprotection and cleavage conditions. The results of my work have been published in the New Journal of Chemistry in 2023. Furthermore, I developed a method for the direct quantification of the oligodeoxynucleotides using the HPLC peak area. This method not only eliminated the need for additional steps in quantification and purification but also saved valuable time for the researchers. The details of this method were published in PeerJ Analytical Chemistry in 2022. Additionally, I was able to achieve the 49 bases long oligodeoxynucleotides which could retain the sensitive groups under mild deprotection and cleavage conditions. These sensitive groups are believed to be the modifications present in the human genome resulting in disease-cause. The manuscript on this accomplishment is under review in a prestigious Peer-Reviewed Journal.

I would also like to express my sincere gratitude towards the Graduate Dean Awards Advisory Panel and the Dean for providing me the Doctoral Finishing Fellowship for Fall 2023. This fellowship will help me to focus on my research goals while accomplishing all the degree completion timelines, including writing and defending my dissertation to graduate timely. Finally, I would like to sincerely thank my advisor Dr. Shiyue Fang whose unwavering support, guidance, and mentorship have been invaluable throughout my Ph.D. journey to help me to expand my knowledge and professional growth in the field.

I completed my bachelor’s and master’s degrees at the University of Peradeniya in Sri Lanka. In the fall of 2018, I started my PhD in chemistry at Michigan Tech and joined the research group of Dr. Lynn Mazzoleni. The group’s primary research focuses on using ultrahigh-resolution mass spectrometry to study the chemistry of organic aerosols in the atmosphere.

In my research, I have developed a new post-data processing approach for liquid chromatographic high-resolution mass spectrometric data. The need for this approach arose from the requirement to effectively analyze complex mixtures in the environment. Mimicking ambient BBOA is one of the significant challenges scientists face in atmospheric research. Therefore, I improved liquid smoke to simulate the ambient BBOA by mixing them with different environmental species. This significantly impacts aerosol research as it provides an option for environmentally relevant lab studies.

I would like to thank my advisor Dr. Lynn Mazzoleni for her guidance, support, and encouragement during my research journey. Her mentorship has been invaluable to me and has played an integral role in helping me with my accomplishment. Also, I sincerely thank the Graduate Dean Awards Advisory Panel for selecting me as a recipient of the finishing fellowship, which will allow me to focus on finishing my dissertation and publishing my work.

I came to Michigan Technological University in August 2018 to pursue a PhD degree in chemistry. I became interested in analytical chemistry during my undergraduate studies in polymer engineering and color science at the Amir Kabir University of Tehran, where I trained to design, synthesize, and analyze various materials such as polymers and pigments with industrial applications. Currently, my research focuses on using analytical techniques such as fluorescence spectroscopy and mass spectrometry to elucidate the origins of fluorescence in complex organic mixtures such as dissolved organic matter (DOM). DOM is one of the largest carbon reservoirs in soil and water, which plays a major role in global climate change and significantly impacts nutrient cycling for different ecosystems and their living organisms. 

During my journey as a PhD student, I have had many excellent learning opportunities while working as a teaching and research assistant. I collaborated on a research project with the department of natural resources and published a research paper titled “Insights on Dissolved Organic Matter Production Revealed by Removal of Charge-Transfer Interactions in Senescent Leaf Leachates” in the Water journal in August 2020. Also, I was fortunate to complete a 12-week co-op opportunity last summer, which helped me gain expertise in analytical techniques such as mass spectrometry, chromatography, and their applications in manufacturing and environmental studies. One of our most recent projects focuses on developing extraction methods and characterizing fluorescent compounds in animals to help us understand these species and their ecosystems more deeply. These natural fluorescent compounds can have various biological, medicinal, and industrial applications. 

I am immensely grateful to the Graduate Dean Awards Advisory Panel and the Dean for granting me this finishing fellowship award. I would like to thank my advisor, Dr. Sarah Green for being a great mentor and offering her continuous support and encouragement throughout my journey.

I commenced my PhD program in Chemistry here at Michigan Tech in the Fall of 2018 under the direction of Dr. Christo Z. Christov and Dr. Tatyana G. Karabencheva-Christova. Before joining Michigan Tech, I obtained bachelor’s and master’s degrees in Industrial Chemistry and Physical Chemistry, respectively, from the University of Ibadan, Nigeria. Also, I received the Erasmus Mundus Joint Master’s Degree (EMJMD) in Theoretical Chemistry and Computational Modelling (TCCM) from the University of Porto, Portugal, and the University of Valencia, Spain, in summer 2018.

My doctoral research focuses on the use of computational modeling approaches to understand the structure-function relationships, conformational flexibility, collective motions, catalytic mechanisms, and the electronic structures of non-heme Fe(II) and 2-oxoglutarate dependent enzymes, such as AlkB, AlkBH2, TET2 and KDM4E that are involved in DNA repair, epigenetic regulation, and histone demethylation. 

During my PhD program, I worked on an NIH-funded project on matrix metalloproteinase-1 (MMP-1) enzyme, where I explored the early catalytic events of the enzyme necessary for its collagenolytic activity. In this project, I studied the processes of formation of the catalytically productive enzyme-substrate complex of MMP-1 and the associated changes in the coordination states of the catalytic Zn(II) site during the conformational transition to the productive complex. Moreover, I have worked on applying external electric fields (EEFs) to enhance the specificity of KDM4E enzyme for C—H activation over N—H activation during the histone N-methyl arginine demethylation. I was also involved in a collaborative project on artificial metalloenzyme with experimental groups at the University of Michigan, Ann Arbor, and Martin-Luther University Halle-Wittenberg, Germany, where we studied the use of YfeX hemoprotein, naturally a peroxidase, as a carbene transferase to mediate some organic reactions.   

I would like to extend my sincere gratitude to my co-advisors, Dr. Christo Z. Christov and Dr. Tatyana G. Karabencheva-Christova, PhD committee members (Dr. Tarun Dam, Dr. Haiying Liu, and Dr. Stephen Techtmann), and the Department of Chemistry for their continuous support. I am grateful to the Graduate Dean Awards Advisory Panel and the Dean for awarding me the Doctoral Finishing Fellowship. This fellowship will afford me the opportunity to focus on completing my PhD dissertation and preparing for my defense.