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• Thesis Guidelines

A thesis for Distinction in Biology is a wonderful way for you to close the loop on your undergraduate research experience and showcase your scientific scholarship. Your thesis will be evaluated by the Faculty in Biology and answers the following questions: What did you do? Why did you do it? What is the significance of your results? What else would you do, were you to continue the project?

In answering the above questions, you have an opportunity to demonstrate your understanding and intellectual ownership of a project; not simply your productivity in the lab. The volume of results or completeness of the study is not critical for a successful thesis. Instead, we will be looking for the following:

• An argument for the significance of your research, contextualized within the scientific literature;
• A review of appropriate literature as evidence in support of claims you make in your argument;
• A statement of your research goals, i.e., a meaningful question of biological importance;
• A description of experimental approaches and methods ;
• Appropriate presentation of results through tables, figures, and images;
• A discussion of the meaning and significance of your results;
• A description of limitations and future directions for the project.

Expanded guidelines can be found in the Biology Thesis Assessment Protocol (BioTAP):

Format of the Thesis

The basic format of the thesis should resemble that of any scientific journal article that is common in your subdiscipline. It generally includes the following sections: Introduction & Background; Methods; Results; Discussion; Acknowledgements; and References. In some instances, it may be useful to sub-divide the Methods & Results section to correspond to multiple aims. However, if you chose to take this route, remember that there should still be a general Introduction and Discussion sections that address the project as a whole. The thesis should not consist of several "mini-papers" that are unconnected.  

Submission Guidelines

The format of the final copy should follow these guidelines:

• Cover Page ( sample ): Title; student's name; supervisor's name; date of submission; 3 signature lines at bottom right (Research Supervisor, DUS, Reader). Please follow the format and language of the sample.
• Abstract Page: single-spaced, roughly 250 words.
• Thesis should be double-spaced
• Pages should be numbered at the top right corner of the page
• It is preferred that figures are embedded within the document instead of all at the end
• There is no minimum page requirement or limit, although most are approximately 25 pages. 

Sample Theses

Examples of Distinction papers from previous years are available for examination in the Undergraduate Studies Office (Rm 135 BioSci).  Several samples are also available below as PDF files.

• Tracing the origins of antimalarial resistance in Plasmodium vivax
• Interaction network optimization improves the antimicrobial efficacy of phage cocktails
• Identifying how ufmylation of RAB1B regulates IFN-β signaling

Additional Resources

• Library Resources for Students Writing Theses
• How to write and publish a scientific paper by Barbara Gastel and Robert A. Day
• Biology 495(S): Scientific Argument in Writing . This course is particularly appropriate for seniors working on an undergraduate thesis or major research paper and is recommended, although not required, for all candidates for Graduation with Distinction in biology. The course is writing intensive and carries a “W” designation and, in the fall semester only, is a seminar and carries an “S” designation.
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BIOLOGICAL SCIENCES MAJOR

Senior thesis examples.

Graduating seniors in Biological Sciences have the option of submitting a senior thesis for consideration for Honors and Research Prizes .  Below are some examples of particularly outstanding theses from recent years (pdf):

Sledd Thesis

ScholarWorks@UMass Amherst

Home > CNS > BIOCHEM > MCB > MCB_THESES

Molecular and Cellular Biology Masters Theses Collection

Theses from 2024 2024.

The Impact of a Non-ionic Adjuvant to the Persistence of Pesticides on Produce Surfaces , Daniel Barnes, Molecular & Cellular Biology

Investigating the Role of Got2 in Murine Organogenesis and Placenta Development , Olivia Macrorie, Molecular & Cellular Biology

Chromatin Accessibility Impacts Knockout of Mt-Bell4 Transcription Factor , Thomas Redden, Molecular & Cellular Biology

UNDERSTANDING THE FUNCTIONAL IMPACT OF DISEASE-ASSOCIATED PHOSPHORYLATION SITES ON THE NEURODEGENERATIVE PROTEIN TAU , Navya T. Sebastian, Molecular & Cellular Biology

Theses from 2023 2023

Elucidating the Priming Mechanism of ClpXP Protease by Single-Domain Response Regulator CpdR in Caulobacter crescentus , Kimberly E. Barker, Molecular & Cellular Biology

The Discovery of a Novel Bacteria from a Large Co-assembly of Metagenomes , Matthew Finkelberg, Molecular & Cellular Biology

Investigating Diterpene Biosynthesis in Medicago Truncatula , Sungwoo Hwang, Molecular & Cellular Biology

Combining Simulation and the MspA Nanopore to Study p53 Dynamics and Interactions , Samantha A. Schultz, Molecular & Cellular Biology

Caulobacter ClpXP Adaptor PopA’s Domain Interactions in the Adaptor Hierarchy of CtrA Degradation , Thomas P. Scudder, Molecular & Cellular Biology

Climate Change, Giant Viruses and Their Putative Hosts , Sarah K. Tucker, Molecular & Cellular Biology

Theses from 2022 2022

Changes in Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping to FAC-Sorted Bacteria , Christopher A. Colvin, Molecular & Cellular Biology

Determining CaMKII Variant Activities and Their Roles in Human Disease , Matthew J. Dunn, Molecular & Cellular Biology

Developmental Exposures to PFAS Mixtures Impair Elongation of the Exocrine Pancreas in Zebrafish (Danio rerio) , Emily M. Formato, Molecular & Cellular Biology

A Metatranscriptomic Analysis of the Long-Term Effects of Warming on the Harvard Forest Soil Microbiome , Brooke A. Linnehan, Molecular & Cellular Biology

Characterization of the Poly (ADP-Ribose) Polymerase Family in the Fusarium oxysporum Species Complex , Daniel Norment, Molecular & Cellular Biology

Theses from 2021 2021

Exploring Knockdown Phenotypes and Interactions between ATAD3 Proteins in Arabidopsis thaliana , Eli S. Gordon, Molecular & Cellular Biology

Development of a Site-Specific Labeling Assay to Study the Pseudomonas aeruginosa Type III Secretion Translocon in Native Membranes , Kyle A. Mahan, Molecular & Cellular Biology

Liposomal Nanoparticles Target TLR7/8-SHP2 to Repolarize Macrophages to Aid in Cancer Immunotherapy , Vaishali Malik, Molecular & Cellular Biology

Hsp70 Phosphorylation: A Case Study of Serine Residues 385 and 400 , Sashrika Saini, Molecular & Cellular Biology

Activation of Nrf2 at Critical Windows of Development Alters Protein S-Glutathionylation in the Zebrafish Embryo (Danio rerio) , Emily G. Severance, Molecular & Cellular Biology

Utilizing Fluorescence Microscopy to Characterize the Subcellular Distribution of the Novel Protein Acheron , Varun Sheel, Molecular & Cellular Biology

Theses from 2020 2020

The Association Between Sperm DNA Methylation and Sperm Mitochondrial DNA Copy Number , Emily Houle, Molecular & Cellular Biology

Gene Expression Regulation in the Mouse Liver by Mechanistic Target Of Rapamycin Complexes I and II , Anthony Poluyanoff, Molecular & Cellular Biology

Sperm Mitochondrial DNA Biomarkers as a Measure of Male Fecundity and Overall Sperm Quality , Allyson Rosati, Molecular & Cellular Biology

Exploration of the Association between Muscle Volume and Bone Geometry Reveals Surprising Relationship at the Genetic Level , Prakrit Subba, Molecular & Cellular Biology

Theses from 2019 2019

Studies on the Interaction and Organization of Bacterial Proteins on Membranes , Mariana Brena, Molecular & Cellular Biology

Investigating The Role Of LBH During Early Embryonic Development In Xenopus Laevis , Emma Weir, Molecular & Cellular Biology

Theses from 2018 2018

Exploring the Influence of PKC-theta Phosphorylation on Notch1 Activation and T Helper Cell Differentiation , Grace Trombley, Molecular & Cellular Biology

Theses from 2017 2017

Partial Craniofacial Cartilage Rescue in ace/fgf8 Mutants from Compensatory Signaling From the Ventricle of Danio Rerio , Douglas A. Calenda II, Molecular & Cellular Biology

THE FAR C-TERMINUS OF TPX2 CONTRIBUTES TO SPINDLE MORPHOGENESIS , Brett Estes, Molecular & Cellular Biology

Characterization of Calcium Homeostasis Parameters in TRPV3 and CaV3.2 Double Null Mice , Aujan Mehregan, Molecular & Cellular Biology

Microtransplantation of Rat Brain Neurolemma into Xenopus Laevis Oocytes to Study the Effect of Environmental Toxicants on Endogenous Voltage-Sensitive Ion Channels , Edwin Murenzi, Molecular & Cellular Biology

Regulation of Katanin Activity on Microtubules , Madison A. Tyler, Molecular & Cellular Biology

Theses from 2016 2016

The Role of MicroRNAs in Regulating the Translatability and Stability of Target Messenger RNAs During the Atrophy and Programmed Cell Death of the Intersegmental Muscles of the Tobacco Hawkmoth Manduca sexta. , Elizabeth Chan, Molecular & Cellular Biology

An in Vivo Study of Cortical Dynein Dynamics and its Contribution to Microtubule Sliding in the Midzone , Heather M. Jordan, Molecular & Cellular Biology

A Genetic Analysis of Cichlid Scale Morphology , Kenta C. Kawasaki, Molecular & Cellular Biology

Modulation of Notch in an Animal Model of Multiple Sclerosis , Manit Nikhil Munshi, Molecular & Cellular Biology

One-Carbon Metabolism Related B-Vitamins Alter The Expression Of MicroRNAS And Target Genes Within The Wnt Signaling Pathway In Mouse Colonic Epithelium , Riccardo Racicot, Molecular & Cellular Biology

Characterizing the Inhibition of Katanin Using Tubulin Carboxy-Terminal Tail Constructs , Corey E. Reed, Molecular & Cellular Biology

The Identification of Notch1 Functional Domains Responsible for its Physical Interaction with PKCθ , Wesley D. Rossiter, Molecular & Cellular Biology

Dynamics of Microtubule Networks with Antiparallel Crosslinkers , Kasimira T. Stanhope, Molecular & Cellular Biology

Modifications of Myofilament Structure and Function During Global Myocardial Ischemia , Mike K. Woodward, Molecular & Cellular Biology

Theses from 2015 2015

Regulation of Jak1 and Jak2 Synthesis through Non-Classical Progestin Receptors , Hillary Adams, Molecular & Cellular Biology

Antineoplastic Effects of Rhodiola Crenulata on B16-F10 Melanoma , Maxine Dudek, Molecular & Cellular Biology

RNAi Validation of Resistance Genes and Their Interactions in the Highly DDT-Resistant 91-R Strain of Drosophila Melanogaster , Kyle Gellatly, Molecular & Cellular Biology

Characterization of Protein-Protein Interactions for Therapeutic Drug Design Utilizing Mass Spectrometry , Alex J. Johnson, Molecular & Cellular Biology

Promoting Extracellular Matrix Crosslinking in Synthetic Hydrogels , Marcos M. Manganare, Molecular & Cellular Biology

Characterization of the Reconstituted and Native Pseudomonas aeruginosa Type III Secretion System Translocon , Kathryn R. Monopoli, Molecular & Cellular Biology

Thermocycle-regulated WALL REGULATOR INTERACTING bHLH Encodes a Protein That Interacts with Secondary-Cell-Wall-Associated Transcription Factors , Ian P. Whitney, Molecular & Cellular Biology

Theses from 2014 2014

Engineering Camelina sativa for Biofuel Production via increasing oil yield and tolerance to abiotic stresses , Kenny Ablordeppey, Molecular & Cellular Biology

Designing a Pore-Forming Toxin Cytolysin A (ClyA) Specific to Target Cancer Cells , Alzira Rocheteau Avelino, Molecular & Cellular Biology

The Role of the Novel Lupus Antigen, Acheron, in Moderating Life and Death Decisions , Ankur Sheel, Molecular & Cellular Biology

Expression and Purification of Human Lysosomal β-galactosidase from Pichia Pastoris , Sarah E. Tarullo, Molecular & Cellular Biology

Properties of Potential Substrates of a Cyanobacterial Small Heat Shock Protein , Yichen Zhang, Molecular & Cellular Biology

Theses from 2013 2013

Characterizing the Heavy Metal Chelator, Tpen, as a Ca2+ Tool in the Mammalian Oocyte , Robert A. Agreda Mccaughin, Molecular & Cellular Biology

Sustainable Biofuels Production Through Understanding Fundamental Bacterial Pathways Involved in Biomass Degradation and Sugar Utilization , James CM Hayes, Molecular & Cellular Biology

Stiffness and Modulus and Independent Controllers of Breast Cancer Metastasis , Dannielle Ryman, Molecular & Cellular Biology

Theses from 2012 2012

The Pyrethroid Deltamethrin, Which Causes Choreoathetosis with Salivation (CS-Syndrome), Enhances Calcium Ion Influx via Phosphorylated CaV2.2 expresssed in Xenopus laevis oocytes , Anna-maria Alves, Molecular & Cellular Biology

A Test of the Hypothesis That Environmental Chemicals Interfere With Thyroid Hormone Action in Human Placenta , Katherine Geromini, Molecular & Cellular Biology

Analyzing the Role of Reactive Oxygen Species in Male-Female Interactions in Arabidopsis thaliana. , Eric A. Johnson, Molecular & Cellular Biology

Rhythmic Growth And Vascular Development In Brachypodium Distachyon , Dominick A. Matos, Molecular & Cellular Biology

Polymer Prodrug Conjugation to Tumor Homing Mesenchymal Stem Cells , Nick Panzarino, Molecular & Cellular Biology

Investigation of Differential Vector Competence of Bartonella quintana in Human Head and Body Lice , Domenic j. Previte, Molecular & Cellular Biology

Downregulation of Cinnamyl Alcohol Dehydrogenase or Caffeic Acid O-Methyltransferase Leads to Improved Biological Conversion Efficiency in Brachypodium distachyon , Gina M. Trabucco, Molecular & Cellular Biology

Theses from 2011 2011

Evolutionary Relationship of the ampC Resistance Gene In E. cloacae , Shanika S. Collins, Molecular & Cellular Biology

Sex Difference in Calbindin Cell Number in the Mouse Preoptic Area: Effects of Neonatal Estradiol and Bax Gene Deletion , Richard F. Gilmore III, Molecular & Cellular Biology

In Vivo Investigations of Polymer Conjugates as Therapeutics , Elizabeth M. Henchey, Molecular & Cellular Biology

Examination of Sexually Dimorphic Cell Death in the Pubertal Mouse Brain , Amanda Holley, Molecular & Cellular Biology

Human Niemann-Pick Type C2 Disease Protein Expression, Purification and Crystallization , Yurie T. Kim, Molecular & Cellular Biology

Revealing the Localization of the Class I Formin Family in the Moss Physcomitrella patens Using Gene Targeting Strategies , Kelli Pattavina, Molecular & Cellular Biology

Connecting Motors and Membranes: A Quantitative Investigation of Dynein Pathway Components and in vitro Characterization of the Num1 Coiled Coil Domain , Bryan J. St. Germain, Molecular & Cellular Biology

Theses from 2010 2010

The Protective Effects A Full-term Pregnancy Plays Against Mammary Carcinoma , Matthew p. Carter, Molecular & Cellular Biology

Analysis Of An Actin Binding Guanine Exchange Factor, Gef8, And Actin Depolymerizing Factor In Arabidopsis Thaliana. , Aleksey Chudnovskiy, Molecular & Cellular Biology

The Role of Ykl-40, a Secreted Heparin-Binding Glycoprotein, in Tumor Angiogenesis, Metastasis, and Progression: a Potential Therapeutic Target , Michael Faibish, Molecular & Cellular Biology

In Vivo Visualization of Hedgehog Signaling in Zebrafish , Christopher J. Ferreira, Molecular & Cellular Biology

An In Vivo Study of the Mammalian Mitotic Kinesin Eg5 , Alyssa D. Gable, Molecular & Cellular Biology

Identification of Dynein Binding Sites in Budding Yeast Pac1/LIS1 , Christopher W. Meaden, Molecular & Cellular Biology

Functional Characterization of Arabidopsis Formin Homologues Afh1, Afh5, Afh6, Afh7 and Afh8 , Shahriar Niroomand, Molecular & Cellular Biology

Regulation of Crbp1 In Mammary Epithelial Cells , Stacy L. Pease, Molecular & Cellular Biology

In Vivo Labeling Of A Model β-Clam Protein With A Fluorescent Amino Acid , Mangayarkarasi Periasamy, Molecular & Cellular Biology

In Vivo Characterization of Interactions Among Dynein Complex Components at Microtubule Plus Ends , Karen M. Plevock, Molecular & Cellular Biology

Anti-Diabetic Potentials of Phenolic Enriched Chilean Potato and Select Herbs of Apiaceae and Lamiaceae Families , Fahad Saleem, Molecular & Cellular Biology

Interconversion of the Specificities of Human Lysosomal Enzymes , Ivan B. Tomasic, Molecular & Cellular Biology

Deletions of Fstl3 and/or Fst Isoforms 303 and 315 Results in Hepatic Steatosis , Nathan A. Ungerleider, Molecular & Cellular Biology

Theses from 2009 2009

A New Laser Pointer Driven Optical Microheater for Precise Local Heat Shock , Mike Placinta, Molecular & Cellular Biology

Theses from 2008 2008

Cysteine Dioxygenase: The Importance of Key Residues and Insight into the Mechanism of the Metal Center , Jonathan H. Leung, Molecular & Cellular Biology

Invertebrate Phenology and Prey Selection of Three Sympatric Species of Salmonids; Implications for Individual Fish Growth , Jeffrey V. Ojala, Wildlife & Fisheries Conservation

Paralemmin Splice Variants and mRNA and Protein Expression in Breast Cancer , Casey M. Turk, Molecular & Cellular Biology

Stability of the frog motor nerve terminal: roles of perisynaptic Schwann cells and muscle fibers , Ling Xin, Molecular & Cellular Biology

Theses from 2007 2007

Antioxidant Response Mechanism in Apples during Post-Harvest Storage and Implications for Human Health Benefits , Ishan Adyanthaya, Molecular & Cellular Biology

Progress Towards A Model Flavoenzyme System , Kevin M. Bardon, Molecular & Cellular Biology

The effect of Rhodiola crenulata on a highly metastatic murine mammary carcinoma , Jessica L. Doerner, Molecular & Cellular Biology

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Biological Sciences thesis and dissertation collection

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Super-resolution imaging of proteins in live cells using reversibly interacting peptide pairs , understanding the role and function of spocd1 in pirna-directed de novo dna methylation , sequencing b cell receptor repertoires in human disease: applications in myalgic encephalomyelitis/chronic fatigue syndrome and in experimental malaria infection , role of tyrosine phosphatase ptpn22 in ctl responses to tumours and t cell exhaustion , rna editing ligases as novel drug targets in trypanosomatid parasites , pifs as a novel target in soybean to modulate the shade avoidance syndrome , structure and function of microtubule nucleation proteins , evaluation of the structural, functional, cellular and molecular basis of heart pathophysiology in mouse models of spinal muscular atrophy , understanding and utilising bacterial growth rate changes at high external osmolarities , origin and maintenance of diversity in british euphrasia (orobanchaceae) , single-cell time-series analysis of metabolic rhythms in yeast , ectopic heterochromatin provides an alternative route to fungal resistance , understanding adaptive immunity using immune receptor repertoire sequencing , mapping inbreeding depression in wild red deer (cervus elaphus) , transcription-only cell-free systems and their application in biosensing , encapsulin engineering for metal nanoparticle production , adaptive genomics and phylogeography of guazuma ulmifolia (malvaceae) , structural and functional characterization of cenp-v: a novel glutathione-binding protein , chromosome rearrangements and population genomics , quantitative genetics of gene expression: regulatory complexity and patterns of variation .

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Digital Commons @ USF > College of Arts and Sciences > Molecular Biosciences > Theses and Dissertations

Molecular Biosciences Theses and Dissertations

Theses/dissertations from 2023 2023.

Exploring strain variation and bacteriophage predation in the gut microbiome of Ciona robusta , Celine Grace F. Atkinson

Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression , Janine M. DeBlasi

Thermodynamic frustration of TAD2 and PRR contribute to autoinhibition of p53 , Emily Gregory

Utilization of Detonation Nanodiamonds: Nanocarrier for Gene Therapy in Non-Small Cell Lung Cancer , Allan E. Gutierrez

Role of HLA-DRB1 Fucosylation in Anti-Melanoma Immunity , Daniel K. Lester

Targeting BET Proteins Downregulates miR-33a To Promote Synergy with PIM Inhibitors in CMML , Christopher T. Letson

Regulated Intramembrane Proteolysis by M82 Peptidases: The Role of PrsS in the Staphylococcus aureus Stress Response , Baylie M. Schott

Histone Deacetylase 8 is a Novel Therapeutic Target for Mantle Cell Lymphoma and Preserves Natural Killer Cell Cytotoxic Function , January M. Watters

Theses/Dissertations from 2022 2022

Regulation of the Heat Shock Response via Lysine Acetyltransferase CBP-1 and in Neurodegenerative Disease in Caenorhabditis elegans , Lindsey N. Barrett

Determining the Role of Dendritic Cells During Response to Treatment with Paclitaxel/Anti-TIM-3 , Alycia Gardner

Cell-free DNA Methylation Signatures in Cancer Detection and Classification , Jinyong Huang

The Role Of Eicosanoid Metabolism in Mammalian Wound Healing and Inflammation , Kenneth D. Maus

A Holistic Investigation of Acidosis in Breast Cancer , Bryce Ordway

Characterizing the Impact of Postharvest Temperature Stress on Polyphenol Profiles of Red and White-Fruited Strawberry Cultivars , Alyssa N. Smith

Theses/Dissertations from 2021 2021

Multifaceted Approach to Understanding Acinetobacter baumannii Biofilm Formation and Drug Resistance , Jessie L. Allen

Cellular And Molecular Alterations Associated with Ovarian and Renal Cancer Pathophysiology , Ravneet Kaur Chhabra

Ecology and diversity of boletes of the southeastern United States , Arian Farid

CircREV1 Expression in Triple-Negative Breast Cancer , Meagan P. Horton

Microbial Dark Matter: Culturing the Uncultured in Search of Novel Chemotaxonomy , Sarah J. Kennedy

The Multifaceted Role of CCAR-1 in the Alternative Splicing and Germline Regulation in Caenorhabditis elegans , Doreen Ikhuva Lugano

Unraveling the Role of Novel G5 Peptidase Family Proteins in Virulence and Cell Envelope Biogenesis of Staphylococcus aureus , Stephanie M. Marroquin

Cytoplasmic Polyadenylation Element Binding Protein 2 Alternative Splicing Regulates HIF1α During Chronic Hypoxia , Emily M. Mayo

Transcriptomic and Functional Investigation of Bacterial Biofilm Formation , Brooke R. Nemec

A Functional Characterization of the Omega (ω) subunit of RNA Polymerase in Staphylococcus aureus , Shrushti B. Patil

The Role Of Cpeb2 Alternative Splicing In TNBC Metastasis , Shaun C. Stevens

Screening Next-generation Fluorine-19 Probe and Preparation of Yeast-derived G Proteins for GPCR Conformation and Dynamics Study , Wenjie Zhao

Theses/Dissertations from 2020 2020

Understanding the Role of Cereblon in Hematopoiesis Through Structural and Functional Analyses , Afua Adutwumwa Akuffo

To Mid-cell and Beyond: Characterizing the Roles of GpsB and YpsA in Cell Division Regulation in Gram-positive Bacteria , Robert S. Brzozowski

Spatiotemporal Changes of Microbial Community Assemblages and Functions in the Subsurface , Madison C. Davis

New Mechanisms That Regulate DNA Double-Strand Break-Induced Gene Silencing and Genome Integrity , Dante Francis DeAscanis

Regulation of the Heat Shock Response and HSF-1 Nuclear Stress Bodies in C. elegans , Andrew Deonarine

New Mechanisms that Control FACT Histone Chaperone and Transcription-mediated Genome Stability , Angelo Vincenzo de Vivo Diaz

Targeting the ESKAPE Pathogens by Botanical and Microbial Approaches , Emily Dilandro

Succession in native groundwater microbial communities in response to effluent wastewater , Chelsea M. Dinon

Role of ceramide-1 phosphate in regulation of sphingolipid and eicosanoid metabolism in lung epithelial cells , Brittany A. Dudley

Allosteric Control of Proteins: New Methods and Mechanisms , Nalvi Duro

Microbial Community Structures in Three Bahamian Blue Holes , Meghan J. Gordon

A Novel Intramolecular Interaction in P53 , Fan He

The Impact of Myeloid-Mediated Co-Stimulation and Immunosuppression on the Anti-Tumor Efficacy of Adoptive T cell Therapy , Pasquale Patrick Innamarato

Investigating Mechanisms of Immune Suppression Secondary to an Inflammatory Microenvironment , Wendy Michelle Kandell

Posttranslational Modification and Protein Disorder Regulate Protein-Protein Interactions and DNA Binding Specificity of p53 , Robin Levy

Mechanistic and Translational Studies on Skeletal Malignancies , Jeremy McGuire

Novel Long Non-Coding RNA CDLINC Promotes NSCLC Progression , Christina J. Moss

Genome Maintenance Roles of Polycomb Transcriptional Repressors BMI1 and RNF2 , Anthony Richard Sanchez IV

The Ecology and Conservation of an Urban Karst Subterranean Estuary , Robert J. Scharping

Biological and Proteomic Characterization of Cornus officinalis on Human 1.1B4 Pancreatic β Cells: Exploring Use for T1D Interventional Application , Arielle E. Tawfik

Evaluation of Aging and Genetic Mutation Variants on Tauopathy , Amber M. Tetlow

Theses/Dissertations from 2019 2019

Investigating the Proteinaceous Regulome of the Acinetobacter baumannii , Leila G. Casella

Functional Characterization of the Ovarian Tumor Domain Deubiquitinating Enzyme 6B , Jasmin M. D'Andrea

Integrated Molecular Characterization of Lung Adenocarcinoma with Implications for Immunotherapy , Nicholas T. Gimbrone

The Role of Secreted Proteases in Regulating Disease Progression in Staphylococcus aureus , Brittney D. Gimza

Advanced Proteomic and Epigenetic Characterization of Ethanol-Induced Microglial Activation , Jennifer Guergues Guergues

Understanding immunometabolic and suppressive factors that impact cancer development , Rebecca Swearingen Hesterberg

Biochemical and Proteomic Approaches to Determine the Impact Level of Each Step of the Supply Chain on Tomato Fruit Quality , Robert T. Madden

Enhancing Immunotherapeutic Interventions for Treatment of Chronic Lymphocytic Leukemia , Kamira K. Maharaj

Characterization of the Autophagic-Iron Axis in the Pathophysiology of Endometriosis and Epithelial Ovarian Cancers , Stephanie Rockfield

Understanding the Influence of the Cancer Microenvironment on Metabolism and Metastasis , Shonagh Russell

Modeling of Interaction of Ions with Ether- and Ester-linked Phospholipids , Matthew W. Saunders

Novel Insights into the Multifaceted Roles of BLM in the Maintenance of Genome Stability , Vivek M. Shastri

Conserved glycine residues control transient helicity and disorder in the cold regulated protein, Cor15a , Oluwakemi Sowemimo

A Novel Cytokine Response Modulatory Function of MEK Inhibitors Mediates Therapeutic Efficacy , Mengyu Xie

Novel Strategies on Characterizing Biologically Specific Protein-protein Interaction Networks , Bi Zhao

Theses/Dissertations from 2018 2018

Characterization of the Transcriptional Elongation Factor ELL3 in B cells and Its Role in B-cell Lymphoma Proliferation and Survival , Lou-Ella M.m. Alexander

Identification of Regulatory miRNAs Associated with Ethanol-Induced Microglial Activation Using Integrated Proteomic and Transcriptomic Approaches , Brandi Jo Cook

Molecular Phylogenetics of Floridian Boletes , Arian Farid

MYC Distant Enhancers Underlie Ovarian Cancer Susceptibility at the 8q24.21 Locus , Anxhela Gjyshi Gustafson

Quantitative Proteomics to Support Translational Cancer Research , Melissa Hoffman

A Systems Chemical Biology Approach for Dissecting Differential Molecular Mechanisms of Action of Clinical Kinase Inhibitors in Lung Cancer , Natalia Junqueira Sumi

Investigating the Roles of Fucosylation and Calcium Signaling in Melanoma Invasion , Tyler S. Keeley

Synthesis, Oxidation, and Distribution of Polyphenols in Strawberry Fruit During Cold Storage , Katrina E. Kelly

Investigation of Alcohol-Induced Changes in Hepatic Histone Modifications Using Mass Spectrometry Based Proteomics , Crystina Leah Kriss

Off-Target Based Drug Repurposing Using Systems Pharmacology , Brent M. Kuenzi

Investigation of Anemarrhena asphodeloides and its Constituent Timosaponin-AIII as Novel, Naturally Derived Adjunctive Therapeutics for the Treatment of Advanced Pancreatic Cancer , Catherine B. MarElia

The Role of Phosphohistidine Phosphatase 1 in Ethanol-induced Liver Injury , Daniel Richard Martin

Theses/Dissertations from 2017 2017

Changing the Pathobiological Paradigm in Myelodysplastic Syndromes: The NLRP3 Inflammasome Drives the MDS Phenotype , Ashley Basiorka

Modeling of Dynamic Allostery in Proteins Enabled by Machine Learning , Mohsen Botlani-Esfahani

Uncovering Transcriptional Activators and Targets of HSF-1 in Caenorhabditis elegans , Jessica Brunquell

The Role of Sgs1 and Exo1 in the Maintenance of Genome Stability. , Lillian Campos-Doerfler

Mechanisms of IKBKE Activation in Cancer , Sridevi Challa

Discovering Antibacterial and Anti-Resistance Agents Targeting Multi-Drug Resistant ESKAPE Pathogens , Renee Fleeman

Functional Roles of Matrix Metalloproteinases in Bone Metastatic Prostate Cancer , Jeremy S. Frieling

Disorder Levels of c-Myb Transactivation Domain Regulate its Binding Affinity to the KIX Domain of CREB Binding Protein , Anusha Poosapati

Role of Heat Shock Transcription Factor 1 in Ovarian Cancer Epithelial-Mesenchymal Transition and Drug Sensitivity , Chase David Powell

Cell Division Regulation in Staphylococcus aureus , Catherine M. Spanoudis

A Novel Approach to the Discovery of Natural Products From Actinobacteria , Rahmy Tawfik

Non-classical regulators in Staphylococcus aureus , Andy Weiss

Theses/Dissertations from 2016 2016

In Vitro and In Vivo Antioxidant Capacity of Synthetic and Natural Polyphenolic Compounds Identified from Strawberry and Fruit Juices , Marvin Abountiolas

Quantitative Proteomic Investigation of Disease Models of Type 2 Diabetes , Mark Gabriel Athanason

CMG Helicase Assembly and Activation: Regulation by c-Myc through Chromatin Decondensation and Novel Therapeutic Avenues for Cancer Treatment , Victoria Bryant

Computational Modeling of Allosteric Stimulation of Nipah Virus Host Binding Protein , Priyanka Dutta

Cell Cycle Arrest by TGFß1 is Dependent on the Inhibition of CMG Helicase Assembly and Activation , Brook Samuel Nepon-Sixt

Gene Expression Profiling and the Role of HSF1 in Ovarian Cancer in 3D Spheroid Models , Trillitye Paullin

VDR-RIPK1 Interaction and its Implications in Cell Death and Cancer Intervention , Waise Quarni

Regulation of nAChRs and Stemness by Nicotine and E-cigarettes in NSCLC , Courtney Schaal

Targeting Histone Deacetylases in Melanoma and T-cells to Improve Cancer Immunotherapy , Andressa Sodre De Castro Laino

Nonreplicative DNA Helicases Involved in Maintaining Genome Stability , Salahuddin Syed

Theses/Dissertations from 2015 2015

Functional Analysis of the Ovarian Cancer Susceptibility Locus at 9p22.2 Reveals a Transcription Regulatory Network Mediated by BNC2 in Ovarian Cells , Melissa Buckley

Exploring the Pathogenic and Drug Resistance Mechanisms of Staphylococcus aureus , Whittney Burda

Regulation and Targeting of the FANCD2 Activation in DNA Repair , Valentina Celeste Caceres

Mass Spectrometry-Based Investigation of APP-Dependent Mechanisms in Neurodegeneration , Dale Chaput

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Undergraduate Theses, Department of Biology, 2022-2023

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Current results range from 2022 to 2023

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23 catalog results, online 1. a predictive model of human transcriptional activators and repressors [2023].

• Liongson, Ivan (Author)
• May 4, 2023

Online 2. A Representative Role for the Alternative Splicing of Synaptic Genes [2023]

• Choeb, Reyan (Author)

Online 3. Building a B Cell Differentiation Model for X-Linked Agammaglobulinemia Using Pluripotent Stem Cells [2023]

• Hernández González, Elaine (Author)
• May 5, 2023

Online 4. Dissecting the Parasympathetic Neural Circuits of the Heart [2023]

• Nguyen, Annie (Author)

Online 5. Early Life Stress Moderates the Relation Between Inflammation and Nucleus Accumbens Gray Matter Volume in Adolescents [2023]

• Jaeger, Emma L. (Author)

Online 6. Identification of DNA Termini in Sequencing Data through Combined Analysis of End Capture and Local Strand Bias [2023]

• Wang, William (Author)

Online 7. Identifying Endocrine Bases of Parental Neglect and Infanticide in the Mimic Poison Frog [2023]

• Lewis, Amaris (Author)

Online 8. Injectable Biomimetic Hydrogels Providing Prolonged Delivery of GLP-1 Analogues for Enhanced Diabetes Treatment [2023]

• Lu, Katie (Author)

Online 9. Internalization of anti-GD2 antibodies as a key component of the antibody-induced cell death mechanism in pediatric neuroblastoma [2023]

• Wang, Alice (Author)

Online 10. Investigating impacts of heat stress on symbiosis in cnidarian larvae using high-throughput fluorescence-based quantification [2023]

• Paul, Maitri (Author)

Online 11. Mechanisms of Ferroptosis Evasion Promoted by Extracellular Metabolites [2023]

• Alchemy, Grace (Author)

Online 12. Morphological Analysis of Axo-Axonic Cell Variability [2023]

• Linker, Lexi (Author)

Online 13. Mosquitoes in the Anthropocene: A Multi-Decade Study at Jasper Ridge Biological Preserve [2023]

• Dutta Gupta, Tanvi (Author)

Online 14. Propagule size has context-dependent effects on colonization success in mixtures of gut microbial communities [2023]

• Goldman, Doran (Author)

Online 15. Spatiotemporal gene expression mapping of brain aging in mice [2023]

• Kedir, Blen (Author)

Online 16. Specific extrusion of Enterovirus-A71-infected cells from human colonoids and consequences for viral spread [2023]

• Craven, Ailsa (Author)

Online 17. Stuck in the Matrix- Patch Matrix Dynamics in Florida Scrub [2023]

• Narasimhan, Sriram (Author)

Online 18. The Junctional Epithelium Organoid: A Novel System for Periodontitis Research [2023]

• Dawid, Isaiah (Author)

Online 19. Using inducible signaling receptors for in vivo fate determination of hematopoietic stem cells to erythroid-specific lineages [2023]

• Majeti, Kiran (Author)

Online 20. We Are What We Eat: The Impact of Agricultural Intensity on the Microbiome of Honeybee Guts [2023]

• Murran, Aisling (Author)
• May 17, 2023

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Current Masters Students

• Masters Thesis Standards

Successfully defending a thesis requires that the student has obtained sufficient data to make a significant contribution to a research paper that could be published in a peer-reviewed journal. Such contribution could consist of one or more of the following:

• The student produces at least one figure or a table that could be included in a peer-reviewed research paper.
• The student's work lays a significant foundation for further research (for example, the student conducted a genetic screen).
• The student develops a new technique or improves an existing method, producing a significant, applicable technical advance.

Thesis Assessment Criteria

The Master’s Thesis should contain the following components. Please be sure that the thesis addresses each of the bullet points within. The thesis may address more points than listed below. The following general criteria should be applied when assessing the overall quality of a Master’s thesis:

• Does the student briefly and clearly state the focus of the described research, experimental design and methods of data collection?
• Does the abstract provide a summary of the most important findings and conclusion?

Introduction

• Does the student provide the background information for understanding the problem, its significance, and how it fits in biology at large?
• Does the student support the background information, ideas, and hypotheses with citations of the appropriate scientific sources?
• Does the student identify the gap of knowledge and clearly state the questions being answered/hypotheses being tested?

Materials & Methods

• Are the experimental or analytical/modeling approaches appropriate to tackle the specific biological question?
• Are the methodologies described in sufficient detail for another researcher to be able to repeat the experiments?
• Are the experiments clearly described, and their results presented in the appropriate visual formats (graphs, tables)?
• Are the figures and tables of sufficiently high quality and well labeled? Are figure legends concise and informative? Are the figures and tables appropriately referred to and described in the text of the thesis?
• Were the appropriate control experiments carried out?
• Were the appropriate statistical analyses employed?
• Are the interpretations of the experiments supported by the data?
• Are the data collected adequate for the solution of the problem?
• Has the student obtained sufficient data to make a significant contribution to a research paper that could be published in a peer-reviewed journal?
• Does the discussion provide a thoughtful summary of the data and draw the appropriate conclusions?
• Does the student discuss whether the questions posed at the beginning of the study have been answered, and address the adequacy of the obtained data in answering these questions?
• Are there any discrepancies/unexpected results and, if such were encountered, addressed?
• Does the student discuss how her/his findings contribute to our understanding of the area of study?
• Does the student cite relevant literature sources?
• Does the student identify questions that remain unanswered and suggest possible follow-up directions?
• Does the student use a sufficient number of primary and secondary, peer-reviewed literature sources?
• Are all citations in a uniform, accepted reference format?

Updated Thesis and Graduation Requirements

The following includes updated requirements for Biology Master's students in light of the COVID-19 pandemic.

Changes to the original requirements are italicized.

The research requirements of the program can be accomplished either as bench- or field-based research, data analysis, a literature-based research, or co-writing a research proposal with the PI. Students must complete at least 24 units of research over a two years period that includes both the BS and the MS parts of the program (BISP193/196/199 and BGGN 271). This research needs to span six consecutive quarters, with at least three quarters at the graduate level. The student's faculty advisor will determine the need for modifications in the original research plan and the specific way in which a student will complete his or her research requirements (e.g., decrease in bench research and increase in data analysis or literature research).

The total number of units students must take in their graduate year is 36, including research (BGGN 271). The number of coursework units (not BGGN 271 course) should be no less than 12, but can be increased, as long as the total number of research units (BISP193/196/199 and BGGN 271) is no less than 24. The course of study must be approved by the faculty advisor.

Thesis preparation and defense

In addition to completing the required coursework, students will write and defend their thesis. In lieu of completing their experiments and obtaining sufficient data to make a significant contribution to a research paper, students can provide a more extensive literature review in the Introduction section of the thesis or a more extensive and detailed proposal of future experiments in the Discussion section of the thesis. The student's faculty advisor, in consultation with the student's thesis committee, will determine the appropriate way for the student to complete his or her thesis if the completion of experiments is not feasible.

Questions? Current UCSD students: Please submit your questions via the VAC . An advisor will respond in 1-3 business days. Drop-in Advising times are posted on the Advising Calendar .

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Master's Thesis

Writing, defending and filing your master's thesis.

Your thesis is based on original research. The subject, format and all other aspects of the research are guided by the students thesis committee.

During the semester in which you intend to complete and file your thesis, you will enroll in Biology 898 (Thesis Research) — except when the thesis is filed during summer (see below). To register in Biology 898 a student must be fully classified and have: filed an approved ATC Form, a Thesis Prospectus and a Proposal for Culminating Experience Form. Students generally will have completed 3 - 6 units of research course work prior to registering for Biology 898. This course is completed when the Master's Thesis has been approved by the student's graduate committee and by the University Graduate Office.

Summer Filing. If you intend to file your thesis in the summer, you must enroll in Biology 898 in the spring semester — not during the summer. This means that your GAP, etc. must be filed in the previous fall semester.

Master's Applied Research Project

 In lieu of a thesis, Biology graduate students may elect to undertake an Applied Research Project. This option is nearly identical to the thesis option, with similar requirements. The differences are:

• The Culminating Experience course is Biology 895 (3 units)
• The final research project does not go forth to the Division of Graduate Studies

Thesis/Project Committee

You must arrange for three faculty members to be on your thesis committee. At least two of these members must be tenured or tenure-track faculty of Biology at SF State.

Your major advisor must be a regular faculty member of the Biology Department at SF State, Research Faculty at the California Academy of Sciences or graduate faculty at the Romberg Tiburon Center.

Occasionally the third reader on a committee will be outside of the Biology Department. Outside readers must hold a Ph.D. degree or equivalent.

It is your responsibility to confer with the committee about your research program.

All members of the committee will read your thesis/project prior to your preparing the final copy. The major advisor has the principal responsibility for approving the thesis and adjudicating disagreements.

All members of the committee must sign the Proposal for Culminating Experience Requirement and the Approval Page in the written thesis/project.

Oral Defense of the Thesis/Project

All Biology graduate students are required to present an Oral Defense of Thesis/Project at about the same time that they file their thesis/project.

All defenses are to be held on the SF State campus or at the Romberg Tiburon Center and are open to the public.

At least two of the three committee members must be present at the defense. The major professor is required to be in attendance.

The format of the defense should be decided by the committee.

Fliers announcing the defense must be posted in Hensill Hall at least one week prior to the defense. You should also request the Graduate Secretary to send an email announcement of your defense to the faculty and graduate students in Biology.

Take to your defense a  Report of Completion of Requirements  form (not downloadable — get the form from the Biology Office), have it signed and return it to the graduate secretary.

Filing the Thesis

Once your committee has approved your thesis you must file it with Graduate Studies. Guidelines for formatting the thesis are detailed on the  Graduate Studies  website. Follow their guidelines precisely.

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Home > Life Sciences > Microbiology and Molecular Biology > Theses and Dissertations

Microbiology and Molecular Biology Theses and Dissertations

Theses/dissertations from 2023 2023.

Elucidating the Architecture of the TclIJN Complex that Converts Cysteine to Thiazoles in the Biosynthesis of Micrococcin , Diana G. Calvopina Chavez

Manipulating and Assaying Chromatin Architecture Around Enhancer Elements in vivo , John Lawrence Carter

Halophilic Genes that Impact Plant Growth in Saline Soils , Mckay A. Meinzer

Characterizing Stress Granule Regulation by PAS Kinase, Ataxin-2 and Ptc6 and Investigating the Lifespan of Covid-19 Virus on Currency , Colleen R. Newey

Changes in RNA Expression of HuT78 Cells Resulting From the HIV-1 Viral Protein R R77Q Mutation , Joshua S. Ramsey

Theses/Dissertations from 2022 2022

Biofilm Characterization and the Potential Role of eDNA in Horizontal Gene Transfer in Hospital and Meat Isolates of Staphylococcus aureus and Their Biofilms , Ashley Lynne Ball

Novel Patterns for Nucleosome Positioning: From in vitro to in vivo , David Andrew Bates

The Effects of Polymorphisms of Viral Protein R of HIV-1 on the Induction of Apoptosis in Primary Cells and the Characterization of Twelve Novel Bacillus anthracis Bacteriophage , Jacob D. Fairholm

Analysis of the Cytopathogenic Effect of Different HIV-1 Vpr Isoforms on Primary Human CD4+ T Cells and a Model Cell Line , Jonatan Josue Fierro Nieves

The Role of Chitinase A in Mastitis-Associated Escherichia coli Pathogenesis , Weston D. Hutchison

Big Data Meta-Analyses of Transcriptional Responses of Human Samples to Orthohantavirus Infection and Shotgun Metagenomics From Crohn's Disease Patients. , John L. Krapohl

An Exploration of Factors that Impact Uptake of Human Papillomavirus Vaccines , David Samuel Redd

Genomic Analysis and Therapeutic Development of Bacteriophages to Treat Bacterial Infections and Parasitic Infestations , Daniel W. Thompson

The Use of Nucleotide Salvage Pathway Enzymes as Suitable Tumor Targets for Antibody-Based and Adoptive Cell Therapies , Edwin J. Velazquez

Comparative Sequence Analysis Elucidates the Evolutionary Patterns of Yersinia pestis in New Mexico over Thirty-Two Years , M. Elizabeth Warren

Regulation of T Cell Activation by the CD5 Co-Receptor and Altered Peptides, Characterization of Thymidine Kinase-Specific Antibodies, and Integrating Genomics Education in Society , Kiara Vaden Whitley

Theses/Dissertations from 2021 2021

Evolution and Selection: From Suppression of Metabolic Deficiencies to Bacteriophage Host Range and Resistance , Daniel Kurt Arens

Identifying Sinorhizobium meliloti Genes that Determine Fitness Outcomes , Alexander B. Benedict

Pushing the Limits of SARS-CoV-2 Survival: How SARS-CoV-2 Responds to Quaternary Ammonium Compounds and Wastewater , Benjamin Hawthorne Ogilvie

Mutations in HIV-1 Vpr Affect Pathogenesis in T-Lymphocytes and Novel Strategies to Contain the Current COVID-19 Pandemic , Antonio Solis Leal

Theses/Dissertations from 2020 2020

Staphylococcus aureus Metal Acquisition in Milk and Mammary Gland Tissue , Shalee Killpack Carlson

Antimicrobial Peptide Development: From Massively Parallel Peptide Sequencing to Bioinformatic Motif Identification , Alexander K. Erikson

A Comparison of Chikungunya Virus Infection, Dissemination, and Cytokine Induction in Human and Murine Macrophages and Characterization of RAG2-/-γc-/- Mice as an Animal Model to Study Neurotropic Chikungunya Disease , Israel Guerrero

The Effects of Immune Regulation and Dysregulation: Helper T Cell Receptor Affinity, Systemic Lupus Erythematosus and Cancer Risk, and Vaccine Hesitancy , Deborah K. Johnson

Identification of Genes that Determine Fitness, Virulence, and Disease Outcomes in Mastitis Associated Eschericia coli , Michael Andrew Olson

Theses/Dissertations from 2019 2019

Investigation of Thymidine Kinase 1 in Cancer Progression , Eliza Esther King Bitter

Ribosomally Synthesized and Post-Translationally Modified Peptides as Potential Scaffolds for Peptide Engineering , Devan Bursey

Bioaerosols Associated with Evaporative Cooler Use in Low-Income Homes in Semi-Arid Climates , Ashlin Elaine Cowger

PAS Kinase and TOR, Controllers of Cell Growth and Proliferation , Brooke Jasmyn Cozzens

Regulation of Immune Cell Activation and Functionby the nBMPp2 Protein andthe CD5 Co-Receptor , Claudia Mercedes Freitas

Characterizing Novel Pathways for Regulation and Function of Ataxin-2 , Elise Spencer Melhado

Interactions Between the Organellar Pol1A, Pol1B, and Twinkle DNA Replication Proteins and Their Role in Plant Organelle DNA Replication , Stewart Anthony Morley

SNFing Glucose to PASs Mitochondrial Dysfunction: The Role of Two Sensory Protein Kinases in Metabolic Diseases , Kai Li Ong

Characterizing the Function of PAS kinase in Cellular Metabolism and Neurodegenerative Disease , Jenny Adele Pape

Isolation, Characterization, and Genomic Comparison of Bacteriophages of Enterobacteriales Order , Ruchira Sharma

Isolation, Genetic Characterization and Clinical Application of Bacteriophages of Pathogenic Bacterial Species , Trever Leon Thurgood

Investigation of Therapeutic Immune Cell Metabolism , Josephine Anna Tueller

Theses/Dissertations from 2018 2018

Innate Immune Cell Phenotypes Are Dictated by Distinct Epigenetic Reprogramming , Kevin Douglas Adams

Bacteriophages for Treating American Foulbrood and the Neutralization of Paenibacillus larvae Spores , Thomas Scott Brady

Methods for Detection of and Therapy for Carbapenem-Resistant Enterobacteriaceae , Olivia Tateoka Brown

The Diversity Found Among Carbapenem-Resistant Bacteria , Galen Edward Card

Exploration of Antimicrobial Activity in Natural Peptides and High-Throughput Discovery of Synthetic Peptides , Emma Kay Dallon

Gut Microbiota Regulates the Interplay Between Diet and Genetics to Influence Insulin Resistance , Jeralyn Jones Franson

The Antimicrobial Properties of Honey and Their Effect on Pathogenic Bacteria , Shreena Himanshu Mody

The Ability of Novel Phage to Infect Virulent Bacillus anthracis Isolates , Hyrum Smith Shumway

Galleria Mellonella as an Alternate Infection Model for Burkholderia Species and a Comparison of Suspension and Surface Test Methods for Evaluating Sporicidal Efficacy , Joseph D. Thiriot

The Clinical Significance of HPRT as a Diagnostic and Therapeutic Biomarker for Hematological and Solid Malignancies , Michelle Hannah Townsend

Biomarker Analysis and Clinical Relevance of Thymidine Kinase 1 in Solid and Hematological Malignancies , Evita Giraldez Weagel

Hospital and meat associated Staphylococcus aureus and Their Biofilm Characteristics , Trevor Michael Wienclaw

Theses/Dissertations from 2017 2017

Comparison of Cytokine Expression and Bacterial Growth During Periparturient and Mid Lactation Mastitis in a Mouse Model , Rhonda Nicole Chronis

Influence of Epstein-Barr Virus on Systemic Lupus Erythematosus Disease Development and the Role of Depression on Disease Progression , Caleb Cornaby

The Effects of Nucleosome Positioning and Chromatin Architecture on Transgene Expression , Colton E. Kempton

Phosphate Signaling Through Alternate Conformations of the PstSCAB Phosphate Transporter , Ramesh Krishna Vuppada

Acetobacter fabarum Genes Influencing Drosophila melanogaster Phenotypes , Kylie MaKay White

Theses/Dissertations from 2016 2016

The Path to Understanding Salt Tolerance: Global Profiling of Genes Using Transcriptomics of the Halophyte Suaeda fruticosa , Joann Diray Arce

Genetic and Biochemical Analysis of the Micrococcin Biosynthetic Pathway , Philip Ross Bennallack

Characterizing Interaction Between PASK and PBP1/ ATXN2 to Regulate Cell Growth and Proliferation , Nidhi Rajan Choksi

The Activity of Alkaline Glutaraldehyde Against Bacterial Endospores and Select Non-Enveloped Viruses , Justen Thalmus Despain

The Role of Viral Interleukin-6 in Tumor Development of Kaposi's Sarcoma-Associated Herpesvirus Lymphomas , Rebecca A. Fullwood

The Role of the Transcriptional Antiterminator RfaH in Lipopolysaccharide Synthesis, Resistance to Antimicrobial Peptides, and Virulence of Yersinia pseudotuberculosis and Yersinia pestis , Jared Michael Hoffman

A CryAB Interactome Reveals Clientele Specificity and Dysfunction of Mutants Associated with Human Disease , Whitney Katherine Hoopes

The pmrHFIJKLM Operon in Yersinia pseudotuberculosis Enhances Resistance to CCL28 and Promotes Phagocytic Engulfment by Neutrophils , Lauren Elizabeth Johnson

Characterization of Five Brevibacillus Bacteriophages and Their Genomes , Michael Allen Sheflo

Analysis of Nucleosome Isolation and Recovery: From In Silico Invitrosomes to In Vivo Nucleosomes , Collin Brendan Skousen

Human Herpesvirus 6A Infection and Immunopathogenesis in Humanized Rag2 -/-γc-/- Mice and Relevance to HIV/AIDS and Autoimmunity , Anne Tanner

Theses/Dissertations from 2015 2015

Identifying and Characterizing Yeast PAS Kinase 1 Substrates Reveals Regulation of Mitochondrial and Cell Growth Pathways , Desiree DeMille

The Detection and Molecular Evolution of Francisella tularensis Subspecies , Mark K. Gunnell

Isolation and Host Range of Staphylococcus aureus Bacteriophages and Use for Decontamination of Fomites , Kyle C. Jensen

The Antioxidant and DNA Repair Capacities of Resveratrol, Piceatannol, and Pterostilbene , Justin Ryan Livingston

High Salinity Stabilizes Bacterial Community Composition and Activity Through Time , Tylan Wayne Magnusson

Advancing Phage Genomics and Honeybee Health Through Discovery and Characterization of Paenibacillaceae Bacteriophages , Bryan Douglas Merrill

Specialized Replication Operons Control Rhizobial Plasmid Copy Number in Developing Symbiotic Cells , Clarice Lorraine Perry

Gene Networks Involved in Competitive Root Colonization and Nodulation in the Sinorhizobium meliloti-Medicago truncatula Symbiosis , Ryan D. VanYperen

Theses/Dissertations from 2014 2014

Snf1 Mediated Phosphorylation and Activation of PAS Kinase , Bryan D. Badal

Studies of PhoU in Escherichia coli: Metal Binding, Dimerization,Protein/Protein Interactions, and a Signaling Complex Model , Stewart G. Gardner

Pharmacologic Immunomodulation of Macrophage Activation by Caffeine , Ryan Perry Steck

Analysis of Nucleosome Mobility, Fragility, and Recovery: From Embryonic Stem Cells to Invitrosomes , Ashley Nicolle Wright

Enhancing Protein and Enzyme Stability Through Rationally Engineered Site-Specific Immobilization Utilizing Non-Canonical Amino Acids , Jeffrey Chun Wu

Theses/Dissertations from 2013 2013

Thymidine Kinase 1: Diagnostic and Prognostic Significance in Malignancy , Melissa Marie Alegre

Promoter Polymorphisms in Interferon Regulatory Factor 5 , Daniel N. Clark

Modulators of Symbiotic Outcome in Sinorhizobium meliloti , Matthew B. Crook

Evidences for Protein-Protein Interactions Between PstB and PhoU in the Phosphate Signaling Complex of Escherichia coli , Kristine Dawn Johns

Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins , Kelsey Murphey Langston

A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Burkholderia pseudomallei Complex: B. mallei , B. pseudomallei , and B. thailandensis , Chinn-woan Lowe

The Role of Nuclear BMP2 in the Cell Cycle and Tumorigenesis , Brandt Alan Nichols

Nuclear BMP2 and the Immune Response , Daniel S. Olsen

Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy , Joshua Christopher Vert

Theses/Dissertations from 2012 2012

Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated , John D. Cupp

Effect of Antioxidants and Oxidative Stress on Different Cancer Cell Types , Gaytri Devi Gupta Elera

Effects of Chemical Stimulation and Tumor Co-Incubation on Macrophage Activation and Aggressiveness, Measured Through Phagocytosis and Respiratory Burst , Bo Marcus Gustafsson

Loss of the Lipopolysaccharide Core Biosynthesis rfaD Gene Increases Antimicrobial Chemokine Binding and Bacterial Susceptibility to CCL28 and Polymyxin: A Model for Understanding the Interface of Antimicrobial Chemokines and Bacterial Host Defense Avoidance Mechanisms , Cynthia S. Lew

Partial Characterization of the Antimicrobial Activity of CCL28 , Bin Liu

Characterizing the Role of HspB2 in Cardiac Metabolism and Muscle Structure Using Yeast and Mammalian Systems , Jonathan Paul Neubert

Humanized Mice as a Model to Study Human Viral Pathogenesis and Novel Antiviral Drugs , Freddy Mauricio Sanchez Tumbaco

Transgene Delivery via Microelectromechanical Systems , Aubrey Marie Mueller Wilson

Theses/Dissertations from 2011 2011

Antioxidants in Cancer Research and Prevention: Assay Comparison, Structure-Function Analysis, and Food Product Analysis , Andrew Robert Garrett

Characterization of the Role Nuclear Bmp2 (nBmp2) Plays in Regulating Gene Expression , Fialka Grigorova

Theses/Dissertations from 2010 2010

Effects of Diabetic State and Gender on Pro-Inflammatory Cytokine Secretion by Human Macrophages Infected with Burkholderia pseudomallei , Annette J. Blam

Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana , Jeffrey M. Brammer

Determining the Function of Nuclear Bmp4 , Trina Jane Loos

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Home > FACULTIES > Biology > BIOLOGY-ETD

Biology Theses and Dissertations

This collection contains theses and dissertations from the Department of Biology, collected from the Scholarship@Western Electronic Thesis and Dissertation Repository

Theses/Dissertations from 2024 2024

Biosynthesis of a Novel O-methylhydroxy Isoflavone in Soybean: Expression Analysis and Identification of Isoflavone O-methyltransferases , Elizabeth Copley

The role of fruitless P3 and P4 transcripts in Drosophila melanogaster , Sara A. Kulinski

Theses/Dissertations from 2023 2023

SUFU in SHH signalling mediated myogenesis , Suleyman Abdullah

Effect of rearing conditions on the allocation of larval and adult acquired essential and nonessential fatty acids to flight in two adult Lepidoptera: Danaus plexippus and Mythimna unipuncta , Libesha Anparasan

The effect of dietary thiaminase on cardiac function and morphology in lake trout (Salvelinus namaycush) , Peter Baker

The introduction of nursery seedlings and their fungi to a spruce-fir forest in Newfoundland , Alicia G. Banwell

Evaluating Phosphorylation as a Potential Regulator of ADT5 in Arabidopsis thaliana , Eileen Barac

Elucidating the neural circuitry underlying social spacing in Drosophila melanogaster through the lens of neuroligin 3 , Abigail T. Bechard

Development of reverse genetics tools in the two-spotted spider mite Tetranychus urticae , Nivitha Bhaskar

Post-breeding survival of adult and hatch-year Bank Swallows (Riparia riparia) in the Great Lakes region: a radio telemetry study , Christian M.M Buchanan-Fraser

Effects of 11-KT and Prolactin on Gene Expression, Parental Care Behaviour and Immune Response in Male Bluegill Sunfish. , Adriano A P da Cunha

Differential Migration Timing and the Form and Function of Avian Wings , Jessica E. Deakin

Unraveling The Evolution And Diversity Of Giant Plastid Genomes In Chlamydomonadalean Green Algae , Hager Gaouda

Elucidating the Relationships Between Spider Size, Joint Stiffness, and the Mechanical Frequency Response of the Body , Reese L. Gartly

The effects of elevated carbon dioxide and warming on photosynthesis and growth in five boreal tree species , Julia M. Hammer

Molecular Characterization of Osmotin and Four Plasmodesmata Callose Binding Protein Homologs from Arabidopsis in Turnip Mosaic Virus Infection , Rongrong He

The effects of warming on floral traits , Kiana J. Lee Ms.

The Adaptor Protein p66Shc Governs Central Nervous System Cell Metabolism and Resistance to Aβ Toxicity , Asad Lone

The detectability of Atlantic salmon (Salmo salar) microsatellite and mitochondrial environmental DNA , Simone N. Miklosi

Changes in peatland soil fauna biomass alter food web structure and function under warming and hydrological changes , Trevor L. Pettit

Mouse Genotyping Array-Based Analysis of Variation at Single Nucleotide Polymorphic Loci in the Context of Macro- and Micro-environments , Freda Qi

Investigating the Soil Mycobiome of American Ginseng , Rachel Amelia Rajsp

Age and Sex Differences in Stopover Behaviours and Flight Performance in Black-throated Blue Warblers , Patricia Rokitnicki

Freezing tolerance of herbaceous legumes within southwestern Ontario: evidence of disproportionate freezing sensitivity , Samuel L. Rycroft

Short-term versus long-term effects of nitrogen addition and warming on ecosystem N dynamics in a grass-dominated temperate old field , Benjamin F. A. Souriol

Characterization of Etoxazole Resistance in Tetranychus urticae Populations Collected from Commercial Greenhouses & Fields in Ontario , Jeremy Spenler

Molecular identification and characterization of Heat shock protein 70 family proteins essential for Turnip mosaic virus infection in Arabidopsis thaliana , Ziwei Tang

Role and regulation of galectin-12 in the context of cellular differentiation , Rada Tazhitdinova

Random Mating in the Face of Balancing Selection at the Major Histocompatibility Complex Class I in Song Sparrows (Melospiza melodia) , Scout R.L Thompson

Investigating soil microbiome changes during Panax quinquefolius cultivation in new gardens , Pok Man Paul Wan

Recovery from social isolation in Drosophila: The role of dopamine and the autism-related gene nlg3. , Ryley T. Yost

Theses/Dissertations from 2022 2022

Effects of the Brain Nonapeptides Arginine-Vasotocin and Isotocin on Shoaling Behaviour in the Guppy (Poecilia reticulata) , Babak Ataei Mehr

Effects of methylmercury and unpredictable food stress exposure on songbirds’ physiology and seasonal transition , Claire L.J. Bottini

Gene Regulatory Context of Honey Bee Worker Sterility , Rahul Choorakkat Unnikrishnan

The Sequence-Function Relationship of Arabidopsis AROGENATE DEHYDRATASES , Emily J. Clayton

Characterization of SPL4's role in drought stress and trichome development in alfalfa , Matei A. Dan-Dobre

Cadmium Uptake in Plants as Influenced by Selenium Uptake and Sulphate Availability , Marnie J. Demand

Nitrogen transfer from cover crops to the subsequent grain crop and the influence of variability in winter conditions , Spencer Heuchan

Effects of Experimental Malaria Infection On Migration of Yellow-rumped Warblers (Setophaga coronata) , Rebecca J. Howe

Understanding the molecular mechanism of postharvest seed coat darkening in pinto beans , Nishat Shayala Islam

Characterization of galectin-16 expression and function in placental cells , Jennifer Kaminker

Using conservation genetics to inform reintroduction of the endangered Mottled Duskywing (Erynnis martialis) , Shayla Kroeze

Mechanisms of Diapause and Cold Tolerance in the Colorado Potato Beetle , Jacqueline E. Lebenzon

Effects of spatial and temporal heterogeneity on the genetic diversity of the alpine butterfly Parnassius smintheus , Mel Lucas

The Biosynthesis of Non-protein Sulfur Amino Acid in Developing Seeds of Common Bean , Zixuan Lu

Additional Sulfur Does Not Alleviate Cadmium Toxicity In Soybean , Spencer Matt

From Individuals To Communities: The Effect Of Climate Change On Ectothermic Predators , Matthew Lawrence Meehan

Temperature-Dependent Developmental Plasticity in the Cardiorespiratory System of Atlantic Salmon , Carlie A. Muir

Characterization of the Role of miR156-SPL12 Regulatory Module in Root Architecture and Stress Response in Medicago sativa (alfalfa) , Vida Nasrollahi

The impact of long-term artificial removal experiment and natural local extinctions on the genetics of an alpine butterfly , Keon Young Park

Role of HXXXD-motif acyltransferases in suberin biosynthesis , Yudelkis Indira Queralta Castillo

Spatiotemporal characterization of the prr12 paralogues in zebrafish , Renee Jeannine Resendes

Manipulating the root mycobiome to improve plant performance and reduce pathogen pressure in corn (Zea mays) , Noor F. Saeed Cheema

The role of galectins in differentiation of acute myeloid leukemia cells , Jolaine Smith

Regulation of Hedgehog and Wnt Signaling in Neural Differentiation of P19 Embryonal Carcinoma Cells , Danielle Margaret Spice

Biochemistry of trehalose accumulation in the spring field cricket, Gryllus veletis , Alyssa R. Stephens

Investigation of HD2 family histone deacetylases relationship in drought stress response and root growth in Arabidopsis thaliana , Muhammad Sufyan Tahir

Western diet-like culture conditions and oxidative stress on a cell model of non-alcoholic fatty liver disease , Celina M. Valvano

Root-Inhabiting and Rhizosphere Mycobiomes and Crop Yield of Corn and Wheat , Marianna E. Wallace

MT1-MMP enhances cell survival and proliferation via roles unrelated to metabolic transcript levels in MCF7 breast cancer cells , Rachel A. Wise

Using Stable Isotope Techniques To Complement Existing Northern Pintail Management. , Dariusz Wojtaszek

Theses/Dissertations from 2021 2021

The Effects of Silver Nanoparticles on Soybean (Glycine max) Growth and Nodulation , Paul J. Boersma

Response of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Macrolide Antibiotic Contamination , Liam Paul Brown

Screens for Phenotypic Non-Specificity of Transcription Factor Function in Drosophila melanogaster , Sheng Cheng

A genetic perspective on social insect castes: A synthetic review and empirical study , Anna M. Chernyshova

Investigating social dynamics using automated radiotracking of winter flocks of Black-capped chickadees (Poecile atricapillus) , Christopher J. Course

Long-term vs. Short-term Plant Responses to Warming and Nitrogen Addition in a Temperate Old Field , Breanna Craig

Diversity and drivers of oribatid mites (Acari: Oribatida) in boreal peatlands , Carlos Rafael de Araujo Barreto

Effects of Gene-Environment Interactions on the Evolution of Social Behaviours , Vonica J. Flear

Fear of the Human "Super-Predator" In African Mammals , Nikita R. Frizzelle

Metabolic regulation during extraembryonic endoderm differentiation , Mohamed Gatie

Hibernation is super complex: dynamics of electron transport system supercomplexes , Amalie J. Hutchinson

The Analysis of Ginsenosides in Ginseng Garden Soil , Karina Marie Kaberi

Dynamics of the Soil Microbiome in Ginseng Gardens , Megan E. Lambert

Metschnikowia mitochondria , Dong Kyung Lee

Food Caching Decisions in Canada Jays (Perisoreus canadensis) , Robert J. Martin

Insights into O-GlcNAc-mediated regulation of galectin expression and secretion in promyelocytic HL-60 cells , Adam J. McTague

Developing a toolbox to engineer quantitative trait variation in legume species using CRISPR/Cas technologies. , Petar Miletic

Kindlin-1 is involved in spreading, migration, and protein regulation in epidermal SCC-13 cells , Naomi Mishan

Evaluation of two mouse models of high genetic variation for suitability to test a heterozygote instability hypothesis , Hailie Pavanel

Evaluation of the Bioactive Properties of Peptides Derived From the Common Bean (Phaseolus vulgaris L.) , Zhujun Qiu

Mitigation of Replant Disease using Solarization in American Ginseng (Panex quinquefolius) , Andrew G. Rabas

Functional Characterization of Arogenate Dehydratase Isoforms in Soybean , Ramtin Sirjani

Short-term vs. Long-term Warming and Nitrogen Treatment Effects on Soil Carbon and Microbial Activity in a Temperate Old Field , Erica Stroud

Production of self-assembling protein nanocages and virus-like particles displaying porcine reproductive and respiratory syndrome virus epitopes in Nicotiana benthamiana , Jordan T. VanderBurgt

Establishment of a pesticide resistance monitoring tool for the two-spotted spider mite, Tetranychus urticae , Hanna Varonina

Microplastics in White Sucker (Catostomus commersonii) and Common Carp (Cyprinus carpio) from the Upper Thames River, Ontario. , Colleen Wardlaw

Investigating mycelial-crop residue mat application to reduce early-colonizing weeds in row-crop agriculture , Donald T. Watson

Sequencing and Assembling the Nuclear Genome of the Antarctic Psychrophilic Green Alga Chlamydomonas sp. UWO241: Unravelling the Evolution of Cold Adaptation , Xi Zhang

Theses/Dissertations from 2020 2020

Behavioural And Molecular Consequences Of Postnatal Stress In A Mouse Model Of Fetal Alcohol Spectrum Disorder , Bonnie Alberry

Foliage Type Controls Mercury Input, Storage, and Release in the Boreal Forest , Madelaine J R Anderson

The effects of legacy sulphur deposition on methylmercury production in northern peatlands; geochemical and biological considerations , Jennifer L. Blythe

Heterozygosity: An Inconspicuous Meiosis-Linked Intrinsic Mutagen in Mice , Nicholas A. Boehler

Mass spectrometry identification of membrane-type 1 matrix metalloproteinase (MT1-MMP) binding partners following co-immunoprecipitation in MCF-7 cells , Bradley Bork

Niche segregation among three sympatric species of swallows in southern Ontario , Kaelyn H. Bumelis

Yield improvement of a plant-made antibody against Enterohemorrhagic E. coli , Adam S. Chin-Fatt

The Role of V-ATPase in Regulating pH in the Digestive Tract of Tetranychus urticae Koch , Zoran Culo

Reactive oxygen species damage and consequences for mitochondrial function in the hibernating thirteen-lined ground squirrel, Ictidomys tridecemlineatus , Brynne Duffy

microRNA156: A Short RNA with a Major Role in Abiotic Stress Tolerance in Alfalfa , Biruk Ayenew Feyissa

Chemical Communication in Songbirds , Leanne A. Grieves

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M.s. biology.

The School of Biological Sciences offers two distinct programs leading to the M.S. in Biology degree. The M.S. in Biology (non-thesis) is intended for students who need advanced training in some aspect of modern biology but do not intend to pursue a career in research. The M.S. in Biology (with thesis) is intended for students wishing to obtain a strong background in modern biology and independent research experience in preparation for a technician-level job or further training leading to the PhD in biology.

Quick Facts

• Masters with Thesis offers research without full commitment to PhD program.
• Masters students do not receive stipends or tuition waivers.

General Inquiries

• Chung Kim Academic Program Coordinator Email  | 404.385.4240 | EBB2009

Areas of concentration:

• Ecology, Evolution, and Behavior   including population and evolutionary ecology; community ecology; aquatic chemical ecology; ecological genomics; sensory ecology; evolution of development, behavior, and sociality; biological oceanography; environmental microbiology; theoretical ecology.
• Molecular and Cell Biology   including eukaryotic and prokaryotic cell biology; molecular physiology; molecular biophysics and structural biology; animal, plant, and microbial molecular genetics; human genomics; molecular evolution.
• Computational Biology and Bioinformatics   (with available   M.S.   and interdepartmental PhD   programs in Bioinformatics) focusing on DNA and protein sequence analysis; comparative genomic analysis; macromolecular structure modeling including protein-protein, protein-nucleic acid, and protein-small molecule interactions; molecular evolution.

Masters (non-thesis) Program Overview:

Masters with thesis program overview:.

The Masters with Thesis in Biology requires 36 credit hours(for students starting their MS in Summer 2018) consisting of 12 hours of graduate-level coursework and thesis research hours performed under the mentorship of a faculty advisor and thesis committee. Up to 6 credit hours of coursework can be transferred from another institution, by negotiation upon entrance to the program. In order to be accepted into this program, a student must have the prior agreement of a faculty member in the School of Biological Sciences who will act as thesis advisor. Students who enter the M.S. (non-thesis) in Biology program can transfer to the M.S. with thesis program upon agreement from such an advisor and the graduate committee. It is possible, although challenging, to maintain part-time employment elsewhere while pursuing the M.S. with thesis degree in Biology.

Choosing between the Ph.D. and Masters Programs

Our graduate program is primarily focused on the PhD which prepares students for careers in scientific research and employment in academia, industry, or government. Students who are not yet sure of their interest in scientific research or are interested in other kinds of professional development should consider the M.S. degree in Biology or   Bioinformatics .

Georgia Tech provides application fee waivers to advance diversity, recognize outstanding undergraduate achievement, and engage prospective students in recruitment events where Georgia Tech is affiliated. Such fee waivers are currently available only to domestic applicants.

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Biology related research centers.

• Aquatic Chemical Ecology Center
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• Center for NanoMAD
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BIOL Senior Honors Thesis

To graduate with Highest Honors or Honors in Biology, Bio majors/2nd majors must meet the following requirements:

GPA requirement. Biology majors/2nd majors must be in the last semester of their senior year at UNC.  You don’t have to be a student in the honors program to take BIOL 692H. You must have an overall CUM GPA of at least 3.300   and a BIO GPA of at least 3.300 as posted by the end of the application semester (5:00 p.m. on the last day all grades are due as set by the Registrar).  GPAs must meet the minimum 3.300 and won’t be rounded up.  The Bio GPA must include all cross-listed BIOL courses and one semester of BIOL 395 (your most recent 395 grade); however, do NOT count BIOL 101 and BIOL 101L in calculating your Bio GPA.  All candidates must be approved by the Biology Honors Chair, Dr Amy Shaub Maddox ( [email protected] ).

bio-gpa-calculation-in-connect-carolina

gpa-manual-calculation

Research requirement. Students must have completed at least 3 credit hours of BIOL 395.

Thesis statement requirement.   On a separate sheet of paper to be submitted with your BIOL 692H application, answer ALL of the following (typewritten, please):

1. Proposed thesis title

2. Rationale for your research in the form of background on the subject and  “but it is not known whether . . .” (1-2 sentences)

3. Central hypothesis (1 sentence)

4. Methods including level of experience and availability of reagents and equipment (3-4 sentences)

5. Predicted relevance to ecology or human health or other broader impacts (1 sentence)

6. Relevance to long-term goals (1 sentence)

Senior Honors thesis expectations :  The honors thesis is the culmination of high quality research performed in the preceding semester(s) of undergraduate study.  The products of BIOL 692H are a written thesis (minimum of 10 pages) and an oral presentation.  Your BIOL 395 paper or poster will serve as a first draft for the honors thesis.  Beginning early in the semester, the class will work in teams to refine each written thesis and prepare oral presentations.  Thus, new results should not be counted on to go into the honors thesis.  Instead, the research findings that comprise the written and oral theses should be completed before the start of the last semester of undergraduate coursework.  However, extension of that research can and should be going on in parallel to the preparation of the written and oral presentations in BIOL 692H.  Research should continue in the same lab as for BIOL 395.

Senior Honors thesis course (BIOL 692H). BIOL majors/2nd majors can BIOL 692H in their final semester at UNC.  In addition to doing your research, presenting your research in an oral talk and writing a senior honors thesis paper, you also need to attend the BIOL 692H class.  Students receive a letter grade for BIOL 692H and also will get the designation of Highest Honors or Honors added to their transcript.

Enrollment. Only electronic applications will be accepted. Please go to this webpage for the link to the application: https://bio.unc.edu/undergraduate/research/honors-info/ If you are graduating in December, your application is due April 15 (usually around fall semester pre-registration).  If you are graduating in May, your application is due November 15 (usually around spring semester pre-registration). After your CUM & BIOL GPAs have been verified and your application has been approved, the Biology Registrar will register you. If your grades don’t make the minimums, you can continue doing research in BIOL 395 or 495.  If you decide  you want to drop BIOL 692H, please email Dr Maddox by the end of the first week of classes.

Written work. BIOL 692H students must write an Senior Honors Thesis (minimum of 10 pages) based on the independent research project.  Your thesis will be stored electronically in the Wilson Library repository.

Symposium presentation. BIOL 692H students must present and defend their thesis research during the John K. Koeppe Biology Undergraduate Research Symposium.  The exact day/time  you will give your presentation will be assigned within the first 4 weeks of class.  Two graders will independently evaluate the content and presentation of your work.

Koeppe Symposium

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• University Courses

The Biology Department considers a basic understanding of biological systems to be an essential skill in our increasingly technological society and offers a range of courses for both biology majors and non-majors. Courses are designed to promote scientific literacy and a sophisticated understanding of complex biological systems. Our courses introduce students to life at various levels of organization, with topics ranging from the molecular basis of cellular function, to the coordination of organ systems in the physiology of organisms, to the interactions of organisms with each other and the environment. The importance of research and experimentation in biology is stressed throughout the curriculum, which includes both lab courses and research experiences.

The Biology Department offers the following degrees:

Bachelor of Science (B.S.) in Biology  is a structured program for biology majors who are interested in pursuing those aspects of the field that require a strong background knowledge in physics, chemistry, and mathematics and for students who want to fulfill premedical/predental requirements.

Bachelor of Arts (B.A.) in Biology  is a flexible program that can prepare students for graduate school in the life sciences or can be integrated with other areas, including law, ethics, history, sociology, computer science, and management. The B.A. provides a solid foundation in biology but allows more flexibility in course selection by removing some of the chemistry and quantitative requirements that characterize the B.S. program. Thus, students in the B.A. program can either add more depth and focus around a sub-discipline or have more breadth, either within the biology curriculum or by taking advantage of the B.A. elective options. Students should note that, unlike the B.S. program, the B.A. program does not fulfill medical school admission requirements.

The Biology Department offers a  minor in Biology, a concentration in Bioinformatics , and also co-sponsors a  Bachelor of Science (B.S.) in Biochemistry  together with the Chemistry Department. The Biochemistry degree is described separately in this Catalog. Requirements for the Biology minor and bioinformatics concentration can be found on the Biology Department website.

Biology Courses

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Bachelor of Science (B.S.) and Bachelor of Arts (B.A.) Program Requirements

• BIOL2000 Molecules and Cells
• BIOL2010 Ecology and Evolution
• BIOL2040 Investigations in Molecular Cell Biology
• BIOL3050 Genetics                          
• BIOL3060 Introduction to Genetics ( summer only )                        
• BIOL3150 Introduction to Genomics
• BIOL3030 Introduction to Physiology
• BIOL4110 Ornithology
• BIOL4320 Developmental Biology
• BIOL4330 Human Physiology with Lab
• BIOL4450 Behavioral Ecology
• BIOL4540 Neuroscience
• One course from the Advanced Experience list—a minimum of 2 credits
• Microbiology
• Cell Biology and Development
• Genetics and Genomics
• Physiology and Organismal Biology
• A complete listing of Biology courses is available on the departmental website.
• For the B.A.: Additional electives numbered 3000 and above to reach a minimum of  33 credits for ALL Biology courses . (9 credits can be from the B.A. elective list available on the departmental website or pre-approval from the department).

Advanced Experience courses include undergraduate research, research lab courses, and smaller classes involving the primary literature and data analysis. Courses fulfilling this requirement are available on the Biology Department website. Note: While independent undergraduate research courses can be taken over several semesters for credit, only 3 of these credits can be applied toward the 30 required credits for the Biology major (B.A. or B.S.). Students using undergraduate research to fulfill the Advanced Experience requirement and/or to have the 3 credits applied to the Biology major must complete at least two semesters.

Students wishing to focus their studies on biology subdisciplines, can choose biology electives from the following concentrations: Microbiology, Cell Biology and Development, Genetics and Genomics, and Physiology/Organismal Biology. A list of elective courses and directions for completing a concentration are found on the departmental website.

Corequisite Courses for the Bachelor of Science (B.S.) Program

Chemistry (15–16 credits).

• General Chemistry I and II with Labs (CHEM1109–1110, CHEM1111–1112)
• Organic Chemistry I with Lab (CHEM2231–2232)
• Organic Chemistry II with Lab (CHEM2233–2234)  or  Biological Chemistry (BIOL4350) or Biochemistry I (CHEM4461)*

Quantitative Requirements: Mathematics, Physics, and Computer Science

• Calculus I (MATH1100)
• PHYS2100 Physics I (calculus) with Lab
• PHYS2101 Physics II (calculus) with Lab
• BIOL2300 Biostatistics (or EC1151 or MATH3353)
• BIOL3140 Experimental Methods in Organismal Biology
• BIOL4250 Population Genetics*
• CSCI1101 Computer Science I
• CSCI1102 Computer Science II
• CSCI2291 Topics: Data Science
• CSCI2257 Database Systems and Application
• MATH1101 Calculus II
• Mathematics courses numbered 2000 or higher

Additional options are noted on the  Biology Department  website.

*BIOL3140, BIOL4350, BIOL4250, and CHEM4461 cannot be used to satisfy both a corequisite and a biology elective.

Calculus Placement

• Calculus I requirement is satisfied by completing MATH1100 or with an AP score of 4 or 5 on the AB exam or a score of 3 on the BC exam
• Calculus I and II can be satisfied by completing MATH1101 or with an AP score of 4 or 5 on the BC exam

Corequisite Courses for the Bachelor of Arts (B.A.) Program (8–12 Credits)

Advanced placement programs for the b.a. and b.s. degrees.

Students who received a score of 5 on the AP exam in their senior year of high school and wish to consider advanced placement may enroll in BIOL3040 in place of BIOL2000. Freshmen should enroll in BIOL2010 first semester (there is no AP substitution for BIOL2010), and take BIOL3040 in the second semester, if they wish to continue with the AP substitution for BIOL2000. The AP substitution does not reduce the total number of credits for the major; students will still need a total of 30 credits in biology courses.

Information for First Year Students: Biology Majors and Others Considering a Major in Biology

Biology majors in the regular B.A. and B.S. programs are advised to enroll in BIOL2000 Molecules and Cells and BIOL2010 Ecology and Evolution their freshman year. Freshmen are also advised to enroll in CHEM1109/CHEM1110 General Chemistry (with corequisite Labs) and Calculus I or II, depending on their AP scores. First-term AP students should enroll in BIOL2010 Ecology and Evolution. Second term, students using the AP option will enroll directly in BIOL3040, or they can continue with the regular program by enrolling in BIOL2000 Molecules and Cells. Calculus need not be taken in the freshman year.

Information for Study Abroad and Summer Programs

With Department approval, students may apply ONE course taken either abroad or during an off-campus summer session to their biology elective requirements. To be considered as a possible substitute for a biology elective, a course must be a second level course with published biology prerequisites and not be an introductory level course or a course intended for professional study or for non-biology majors. As an exception, students studying abroad for two full academic semesters may apply two courses taken abroad to the biology elective requirement.

This policy does not apply to Biology Department major elective courses offered through the Boston College Summer School; such courses are applied to the Biology major as regular academic-year electives.

Research Opportunities for Undergraduates

Research is a fundamental aspect of undergraduate training in the sciences, and the Biology Department actively encourages interested majors to take advantage of the undergraduate research programs that are available. There are two distinct options for engaging in research activity.

Option 1: Students do research in the laboratory of a Biology Department faculty member or at an off-site laboratory with departmental approval. Undergraduate research can be taken for course credit over multiple semesters. Two semesters must be completed to fulfill a Biology elective requirement. Only 3 credits of the undergraduate research are applied to the Biology major; all credits are applied to the 120 credits for graduation

Option 2: The Department offers a number of research lab courses where students build technical skills in the context of an ongoing research project. These one-semester courses are taught by Biology faculty and focus on their current area of research. Students have full access to dedicated lab space throughout the semester and present their data at the departmental Undergraduate Research Day.

Biology Senior Thesis

Students doing undergraduate research may elect to write a Senior Thesis with the approval and support of their faculty research adviser. Students writing a thesis are recognized at Undergraduate Research Day. The student producing the “Best Senior Thesis,” as judged by a faculty committee, is awarded the Balkema Prize.

Information for Non-majors

Non-majors may fulfill their Natural Science Core requirements through the introductory major courses (BIOL2000 or BIOL2010) or one of several university Core courses offered for non-majors by the Department. Information about preparation for the allied health professions is available online at  bc.edu/premed .

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Honors Thesis

General information about honors in biology.

Rebecca Dobbins ’16 studied fin regeneration in zebra fish using the Leica scanning confocal microscope for her senior thesis research.

In contrast to Latin honors ( cum laude , magna cum laude , summa cum laude ), which are based solely on overall GPA, achieving honors in one’s major is determined by a rigorous thesis process. This achievement appears on a graduate’s transcript as, for example, Honors in Biology. In Biology, any student may apply to conduct an Honors Thesis.

The Honors Thesis differs from a regular senior thesis in several key regards, all detailed below. (1) The research and writing are expected to meet a higher standard for rigor and scope. (2) The Honors candidate defends the thesis orally in front of a panel of examiners. (3) The deadline for thesis submission is earlier than for non-honors theses; this may seem trivial now but can become more important as the deadline approaches!  Although the details of achieving Honors in the major are somewhat specific to each department and program, there are some commonalities to the Honors Program as described here: https://www.bates.edu/honors/ .

Because of the high expectations for Honors Theses, and because of the relatively early deadline for submission of Honors Theses, an early start is crucial. The actual research project can begin during the junior year as an independent study, during the summer between the junior and senior years, or during the senior year itself. Honors Thesis work must extend over at least two semesters, by registering for Bio 457 & 458. Proposals for collaborative work may be considered by the department.

An Honors Thesis must be presented and defended orally at the end of the final semester. This oral examination covers the thesis and topics related to the thesis, including biology in general. For the oral defense, an Honors Panel is assigned specifically for each student and comprises one faculty member from the Biology Department, one Bates faculty member outside Biology, and one outside examiner from off campus (who has expertise in the relevant field but has not had input into the project). The student’s research advisor will also be present to ask questions but cannot vote on the outcome. The Honors Panel determines whether Honors is awarded, based on a combination of the written work (60%) and the oral defense (40%).

TIMETABLE FOR HONORS IN BIOLOGY

Winter Semester of the Junior Year

Meet with potential advisors to discuss summer plans and the possibility of doing Honors; it doesn’t hurt to start these conversations in the fall of the junior year.

Summer between Junior and Senior Years

Spend the summer either conducting research with your advisor or reading and planning in preparation for a full-speed start in the fall semester.

Fall of Senior Year

Submit a written proposal to your biology thesis advisor by the 10th day of classes in the first

Research posters and publications produced by Larissa Williams and her Bates students.

semester of the senior year. Students whose proposals are approved by the department then can begin (or continue) an in-depth research project under the guidance of the individual faculty advisor.

Winter of Senior Year

At the first Biology faculty meeting of the winter semester, the department will discuss each Honors candidate’s progress and decide whether the student should proceed with the official Honors nomination process.

Details for the remaining steps of the process, including exact deadlines for the current academic year, are available at https://www.bates.edu/honors/ .

• Work with faculty mentor to submit an Honors Nomination Form to the Honors Program by the Program’s January deadline of the student’s final semester.
• Submit a thesis abstract to the Honors Program by the late-January deadline.
• Upload the completed thesis to SCARAB by the late-March deadline.
• Conduct an oral defense of the thesis by the late-April deadline.
• Upload a revised thesis, if necessary, by the early-May deadline.

Honors candidates are also encouraged to present their work at the Mount David Summit in late April and/or at a regional or national conference.

Withdrawing from Honors Consideration

If, at any time prior to the submission of the written thesis, the thesis advisor feels that the student is not meeting the department’s expectations for a satisfactory Honors Thesis, the advisor has the authority to withdraw the student from the Honors Program.  Likewise, withdrawal may be initiated by the student, at any time prior to the thesis submission deadline or oral exam date.  Withdrawal forms are available on the Honors Program website.

STANDARDS AND EXPECTATIONS FOR HONORS IN BIOLOGY

Receipt of Honors in Biology is a special distinction awarded to those students who have excelled in their academic accomplishments at Bates and have completed a rigorous and substantive thesis project.  The distinction of Honors requires that the student and the thesis meet all of the criteria specified below.  An outstanding performance in several of the expectations for Honors may offset a less than exemplary performance in another area, but a significant deficiency in any one expectation is sufficient grounds to deny Honors. The Honors Panel, who may consult with the advisor, has final authority for judging whether the student has satisfactorily met the criteria for receipt of Honors.

The thesis must explore a novel question or topic, with creative and independent intellectual work by the student.

The thesis should describe a project that, if brought to completion, would be suitable for publication in the peer-reviewed literature, either as a stand-alone item or as part of a larger project.  The department recognizes that two semesters of work is seldom sufficient to complete a project to the point of a peer-reviewed publication, but the project should be on a trajectory for such an outcome.

In the written thesis and oral defense, the student must demonstrate a thorough understanding of the theoretical and methodological underpinnings of the project.  The thesis must develop the necessary background, theory and/or methodology via a thorough discussion and citation of relevant primary literature.

The student must demonstrate a high level of self-motivation, independence, and continuous engagement over the duration of the project.

The student must demonstrate that considerable progress has been made in the actual execution of the project. The student must have advanced the project to the stage where defensible conclusions can be drawn.

The thesis must be well written and accessible to expert and non-expert audiences.  A high quality thesis is well organized, concise, grammatically and mechanistically correct, and coherent and logical in its arguments and development of ideas.  The written thesis must cite appropriate sources that inform the project.  Data must be clearly presented.  Language must be precise and sophisticated, with terminology appropriate for the topic of the thesis.

In the oral exam, the student must demonstrate both a mastery of the field and an understanding of the limitations of the research project and the limitations of the student’s own knowledge.  The student must be able to answer questions posed by the Honors Panel and engage with members of the Panel in a scholarly discussion of all facets of the project, including relevant background and supporting coursework.

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Thesis Seminar: Characterization of Phytohormone Signaling in Ceratopteris richardii: Reproductive Transition and Meristematic Activity

Kelley Renninger (Cheng Lab), a PhD candidate in the Integrated Biology (iBio) Graduate Program , will be defending her thesis on Thursday, April 11 at 2 p.m. in Room 106, Biology Building East (BBE) and via Zoom:  https://uiowa.zoom.us/j/97188093099?pwd=Zk8vdU1ZeUVlbmpReXJpTzdoRUdrdz09 (Meeting ID: 971 8809 3099; Passcode: ferns).

Office of Neuroscience Research

Thesis Defense: Ellie Gaylord (Molecular Microbiology and Microbial Pathogenesis Program) – “The Cell Biology of Cryptococcal Capsule Production”

“The Cell Biology of Cryptococcal Capsule Production”

Thesis lab: Tamara Doering (WashU Molecular Microbiology)

For inquiries contact Ellie at [email protected] .

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Michelle Deprenger-Levin Ph.D. Thesis Defense

Congratulations michelle deprenger-levin for successfully defending your ph.d. degree thesis, michelle deprenger-levin.

Ph.D. Degree Candidate CU Denver Department of Integrative Biology

When: Friday, March 15th, 2024, 12:00pm Where: Science Building, Room 2001

Using demography to inform plant conservation: an examination of uses and pitfalls of conventional population models.

Demography is used to detect and predict population trends and assess the impact of management actions. Demographic data is lacking for many rare and threatened or potentially invasive species. To assess the risk of extinction or potential of establishment for species lacking demographic data, this work sets expectations for near-term dynamics by population structure, population size, and life history. Empirical data can be tested against these expectations. However, population models often fail to predict future dynamics. One cause of error that is rarely addressed in plant populations is imperfect detection. There are extensive models to address imperfect detection for mobile organisms but little attention on which models are appropriate for plant populations. I developed a guide to apply statistical models and field methods to address plant population dynamics while accounting for imperfect detection. I then apply these models to a long-term demographic study of a perennial herb to quantify the impact of ignoring imperfect detection.

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