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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):

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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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Prize-Winning Thesis and Dissertation Examples

Published on September 9, 2022 by Tegan George . Revised on July 18, 2023.

It can be difficult to know where to start when writing your thesis or dissertation . One way to come up with some ideas or maybe even combat writer’s block is to check out previous work done by other students on a similar thesis or dissertation topic to yours.

This article collects a list of undergraduate, master’s, and PhD theses and dissertations that have won prizes for their high-quality research.

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Table of contents

Award-winning undergraduate theses, award-winning master’s theses, award-winning ph.d. dissertations, other interesting articles.

University : University of Pennsylvania Faculty : History Author : Suchait Kahlon Award : 2021 Hilary Conroy Prize for Best Honors Thesis in World History Title : “Abolition, Africans, and Abstraction: the Influence of the “Noble Savage” on British and French Antislavery Thought, 1787-1807”

University : Columbia University Faculty : History Author : Julien Saint Reiman Award : 2018 Charles A. Beard Senior Thesis Prize Title : “A Starving Man Helping Another Starving Man”: UNRRA, India, and the Genesis of Global Relief, 1943-1947

University: University College London Faculty: Geography Author: Anna Knowles-Smith Award:  2017 Royal Geographical Society Undergraduate Dissertation Prize Title:  Refugees and theatre: an exploration of the basis of self-representation

University: University of Washington Faculty:  Computer Science & Engineering Author: Nick J. Martindell Award: 2014 Best Senior Thesis Award Title:  DCDN: Distributed content delivery for the modern web

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University:  University of Edinburgh Faculty:  Informatics Author:  Christopher Sipola Award:  2018 Social Responsibility & Sustainability Dissertation Prize Title:  Summarizing electricity usage with a neural network

University:  University of Ottawa Faculty:  Education Author:  Matthew Brillinger Award:  2017 Commission on Graduate Studies in the Humanities Prize Title:  Educational Park Planning in Berkeley, California, 1965-1968

University:  University of Ottawa Faculty: Social Sciences Author:  Heather Martin Award:  2015 Joseph De Koninck Prize Title:  An Analysis of Sexual Assault Support Services for Women who have a Developmental Disability

University : University of Ottawa Faculty : Physics Author : Guillaume Thekkadath Award : 2017 Commission on Graduate Studies in the Sciences Prize Title : Joint measurements of complementary properties of quantum systems

University:  London School of Economics Faculty: International Development Author: Lajos Kossuth Award:  2016 Winner of the Prize for Best Overall Performance Title:  Shiny Happy People: A study of the effects income relative to a reference group exerts on life satisfaction

University : Stanford University Faculty : English Author : Nathan Wainstein Award : 2021 Alden Prize Title : “Unformed Art: Bad Writing in the Modernist Novel”

University : University of Massachusetts at Amherst Faculty : Molecular and Cellular Biology Author : Nils Pilotte Award : 2021 Byron Prize for Best Ph.D. Dissertation Title : “Improved Molecular Diagnostics for Soil-Transmitted Molecular Diagnostics for Soil-Transmitted Helminths”

University:  Utrecht University Faculty:  Linguistics Author:  Hans Rutger Bosker Award: 2014 AVT/Anéla Dissertation Prize Title:  The processing and evaluation of fluency in native and non-native speech

University: California Institute of Technology Faculty: Physics Author: Michael P. Mendenhall Award: 2015 Dissertation Award in Nuclear Physics Title: Measurement of the neutron beta decay asymmetry using ultracold neutrons

University:  Stanford University Faculty: Management Science and Engineering Author:  Shayan O. Gharan Award:  Doctoral Dissertation Award 2013 Title:   New Rounding Techniques for the Design and Analysis of Approximation Algorithms

University: University of Minnesota Faculty: Chemical Engineering Author: Eric A. Vandre Award:  2014 Andreas Acrivos Dissertation Award in Fluid Dynamics Title: Onset of Dynamics Wetting Failure: The Mechanics of High-speed Fluid Displacement

University: Erasmus University Rotterdam Faculty: Marketing Author: Ezgi Akpinar Award: McKinsey Marketing Dissertation Award 2014 Title: Consumer Information Sharing: Understanding Psychological Drivers of Social Transmission

University: University of Washington Faculty: Computer Science & Engineering Author: Keith N. Snavely Award:  2009 Doctoral Dissertation Award Title: Scene Reconstruction and Visualization from Internet Photo Collections

University:  University of Ottawa Faculty:  Social Work Author:  Susannah Taylor Award: 2018 Joseph De Koninck Prize Title:  Effacing and Obscuring Autonomy: the Effects of Structural Violence on the Transition to Adulthood of Street Involved Youth

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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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Undergraduate Theses, Department of Biology, 2022-2023

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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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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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• 1 Introduction
• 1.1 Current year deadlines
• 2 Guidelines for the dissertation
• 2.1 Proposing a dissertation
• 2.2 Preparing to submit
• 2.2.1 Formatting requirements
• 2.2.2 What to include
• 2.3 Extensions to dissertation deadlines
• 2.3.1 Penalties for late submission:
• 2.4 Plagiarism
• 3 Advice on preparing your dissertation
• 3.1 Supplementary information to assist in the preparation of dissertations
• 3.1.1 Latin, generic and vernacular names
• 3.1.2 Figures and tables
• 3.1.3 References
• 3.1.4 Notes on literature retrieval

Introduction

Examples of dissertations topics offered in the past are available here .

You can expect to receive a maximum of four supervisions with your dissertation supervisor. You are expected to meet with your supervisor at least twice during the preparation of your dissertation. Supervisors are only permitted to view a single draft of your dissertation prior to submission.

Course Organisers will tell you when and how dissertation titles will be released; and you will be required to have your title approved by Division of Michaelmas term.

Your dissertation should be prepared in accordance with the dissertation guidelines shown below, which have been issued by the Faculty Board. Please consult these guidelines at an early stage and pay particular attention to the appropriate closing dates.

Current year deadlines

Division of Michaelmas term: 9th November 2023, 4pm - Title/proposal approved Friday 15th March 2024 - Last day to change title of dissertation Friday 26th April 2024, 12:30pm - Dissertation must be submitted electronically

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Guidelines for the dissertation

Proposing a dissertation.

All NST Part II BBS students should take note of the following regulations and guidelines for their dissertation.

The dissertation topic may be proposed by the candidate or chosen from one offered by the relevant Department and should be not more than 6,000 words, on a subject associated with either the Major or Minor subject . You must complete the form available on the BBS Moodle site, following the instructions stated there. This must be done no later than Division of Michaelmas term, that is 4.00 pm on Thursday, 9 November 2023 .

You must notify the Faculty Office of any subsequent changes to either the title or the subject of your dissertation. In order to change your title, please fill in the required form available on the BBS Moodle site so an update can be made with Student Registry. The latest date by which you can change the title of your dissertation is the last day of Lent Term, that is Friday, 15th March 2024 .

Please note that you are free to do a dissertation in your minor subject, but you should inform your major subject Course Organiser if you take this option.

Preparing to submit

Your dissertation, in its complete form, must be submitted in electronic form via Moodle, in accordance with the guidance provided by the department you have written your dissertation in, by the deadline of 12.30 pm on Friday 26th April 2024 . Please click here for instructions on how to do this.

The marking scheme for dissertations can be found here .

The electronic version of your dissertation may be run through a plagiarism-detection software program. For information, please see the Faculty Board's statement on plagiarism.

You will not examined by viva voce examination for your dissertation.

Formatting requirements

Your dissertation must not exceed 6,000 words, excluding the cover sheet, title page, summary, appendices, contents page, tables (and table legends), figures (and figure legends), footnotes, bibliography and acknowledgements. References and citations within the text count towards the word total. Students can submit the electronic version of their dissertation in either PDF or Word format. Please contact the Faculty Office if submitting in the above formats is undesirable.

Your dissertation must be typewritten or word-processed, double spaced, with 2.5 cm margins, a font size for main body text no larger than 12pt and no smaller than 10pt. 

Please remember it is your responsibility to write and submit your dissertation on time.

What to include

Please note that you should follow Departmental guidelines for BBS students if these are different from those below

Your dissertation must be accompanied by an A4 cover page (a sample form is available by clicking here ) , and must include:

• the full title (as approved)
• your full name
• your supervisor's name
• your college
• a signed declaration that it is your own original work, and that it does not contain material that has already been used to any substantial extent for a comparable purpose
• a statement that this is a dissertation submitted in partial fulfillment of the Regulations for NST Part II Biological and Biomedical Sciences.
• a statement saying " I have read and understood the Faculty of Biology statement on plagiarism found here:  https://www.biology.cam.ac.uk/exams/AllExams/plagiarism "

You should include a title page, which should include the title of your dissertation, the name of your supervisor, the word count and your examination candidate number – please do not include your name on the title page, or any page other than the cover sheet referred to above . If you have not yet received your examination candidate number (BGN), please contact the teaching administrator of your major subject Department.

The dissertation must include a summary of not more than 300 words. The summary must be immediately after the title page.

Due to copyright/intellectual property issues, please do not include the University logo anywhere on your dissertation.

Extensions to dissertation deadlines

In line with the University's Dissertation and Coursework extensions policy , students can self-certify for extensions to coursework for up to a maximum of 7 days. Extensions can be requested for any reason (medical or non-medical) and students are not required to provide evidence of their reasoning. However, students will be required to confirm that they have informed their Tutor of the extension. If departments have concerns about additional support needs or a student’s wellbeing resulting from a student self-certifying for numerous pieces of coursework, they may contact the student’s Tutor directly to notify them further. If you require an extension longer than 7 days, you need to apply, with the support of your college, for a further extension through the EAMC.

To self-certify and provide the evidence needed students should fill out this form .

Where coursework extensions are applied there are likely to be delays to feedback.

Students are reminded that time management within the NST is important, and it can be easy to fall behind with work and deadlines. This policy should not be relied on to meet those deadlines as this simply pushes the workload to one week later. Please speak with your Director of Studies or Tutor if you are struggling to meet these deadlines.

Penalties for late submission:

You are required to self-certify prior to the original submission date (or at the point of submission at the very latest). Retrospective requests will not be accepted.

Where a student does not self-certify and does not submit their coursework by the original submission date, zero marks will be awarded.

Where a student has self-certified and does not submit their work by the revised submission date, zero marks will be awarded, unless a further extension has been granted by the department or EAMC (see below).

Where a student has applied for a further extension via the department (for Parts IA and IB) or  EAMC  (for Parts II and III) and does not submit their work by the agreed submission date, zero marks will be awarded.

If you have any concerns about the supervision you are receiving please contact the Course Organiser/dissertation organiser as soon as possible.

The Faculty Board has issued a statement on plagiarism , and you should read this carefully before preparing your dissertation. For information on plagiarism issued by the Board of Examinations, please click here. In addition your work may be submitted to the Turnitin plagiarism software program.  The BBS Turnitin policy is as follows:

"Work submitted for assessment as a component of Part II BBS (i.e. Dissertations) may be submitted to Turnitin UK software according to the policy of the examiners within the relevant department. Some departments may choose to submit all work to the software; other departments may choose to submit work if and only if the examiners have specific concerns regarding the originality of the particular piece of work. Please consult with the relevant Department on what their specific policy is for use of Turnitin. If the relevant Department does not use Turnitin, the BBS examiners reserve the right to utilise Turnitin in cases where they suspect plagiarism has taken place. Students are required to submit an electronic copy of their dissertation at the same time as a hard copy of their dissertation

If Turnitin UK detects matches between your work and another source, the Examiners will review the resulting originality report to judge whether the matches are innocent, or whether you have appropriately referenced these matches (if not, this may constitute plagiarism), and/or whether you have made excessive use of material from other sources (which may be poor academic practice).

The Examiners will mark your work purely on the basis of its academic merit. However, depending on the extent and context of the matches, your work may be referred to the Proctors for further investigation. In such cases the Turnitin UK originality report may be used as evidence. If you are found to have plagiarised, the penalty may be severe and your degree may be withheld. "

Advice on preparing your dissertation

The purpose of the dissertation is to give you an opportunity to produce a substantial piece of original work, which will form part of the assessment on which your class in the Tripos will be based. The advice that follows relates particularly to dissertations on scientific subjects; if you are doing a dissertation in a discipline which is not, in the narrow sense, scientific, you should listen particularly carefully to the advice of your supervisor and model your work on well-written reviews in the field in which you are working. Nevertheless, much of the advice that follows is applicable to all writing - scientific or otherwise.

• Define your topic: The dissertation must not exceed 6000 words. It is an extended account of a topic or question that lies broadly within the field of one of the courses you are taking. Before you begin, you should spend time defining your topic, discussing this with your supervisor, other members of staff and your colleagues. If you can define your objectives clearly, you will find that the rest of the process is much easier.
• Focus on the essential question: Beware of trying to do too much. You will find that you will need to refine your initial topic to make your dissertation manageable. Remember that, if you try to cover too wide a canvas you will not be able to do your topic justice in the space you are allowed. For example, "The role of genes in cancer" would be too wide but, "Is the xxx gene implicated in cancer of the lung?", would be manageable. Focusing on the essential question is a critical first step; be prepared to spend time on this and interact with your supervisor during this process.
• Writing Style: The dissertation is a scholarly piece of work. That means that you should write it in the style of a scientific document. The exact form depends on what you do, but your dissertation should be divided into sections, reflecting the nature of the evidence that you are reviewing and the arguments should be backed by references, where appropriate. The overall objective is a critical assessment of a restricted topic. This means that part of your dissertation will be devoted to presenting the evidence or data which forms the topic (hence the need for references), and part will be your own assessment of what you have read or otherwise found out. You should make sure that a reader can distinguish which is which.

Sources: The sources of your material can be various. Reading the relevant literature is essential and, at the end of your text, you must provide a list of the references you have quoted. If you quote a reference, it will be assumed you have read it. If you have not, you should refer to the source in which it was cited. Your supervisor will help you with the literature and also point you in the direction of other people who have knowledge in the area you have chosen. The task of locating the relevant literature is made much easier these days by the use of computerised literature searches; if there is a particular key paper in your field of interest, a computer (using Web of Science, for example) can tell you all the more recent scientific papers that have cited it - a particularly useful method for tracking the development of a subject following a key contribution. Resist the temptation to include every paper you have seen or can think of. Most dissertations contain about 20 to 40 references. Do not exceed the latter figure without very careful thought and consultation with your supervisor.

• Hint toward future research: It will often be a good idea to include a separate section setting out promising lines of future research. This could, in some cases, represent a substantial part of your dissertation, and you might approach the writing of this section as if you were preparing a research proposal for a grant-giving body. It is an opportunity for you to display real originality and creativity. You may even lay the foundations for your future research career!
• Proofread multiple times: Short sentences are better than long sentences! Try to be entertaining without being either facetious or colloquial. Remember that a good critic justifies his/her criticism by careful argument. A good critical assessment is a creative process. Do not be afraid of uncertainty. Prune the first version of your dissertation mercilessly.
• Final product: The final product should look like an extended, balanced, informative critique. You should have assessed the various categories of evidence and weighed them. You should point to gaps in the knowledge (see paragraph 7), or to flaws in the evidence. You should say why your topic is important. Beware of starting the work for your dissertation with your mind already made up.

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Supplementary information to assist in the preparation of dissertations

Latin, generic and vernacular names.

Latin names of the genera and species in the text etc should be underlined or written in italics. Where a generic name is the same as the last mentioned it may be abbreviated as the initial letter with full stop, eg Agrostis canina and A. tenuis . If in doubt, use the full generic name throughout. Vernacular names of organisms can be used without capital letters unless a proper name is involved eg 'bottle-nosed dolphins', but 'Mediterranean seals'. The Latin name should accompany the first mention of the vernacular name and subsequently either may be used. Anglicised names of higher taxa should not have initial capital letters eg 'carabids'; but not 'Carabidae'.

Figures and tables

Figures and tables can be used to illustrate the essay, compiled or copied complete from original papers or books. Each should be numbered, eg Figure 1, and provided with a caption. They must be referred to in the text, eg 'Table 2 shows ...'.

References should be given in the text by using the author's name with year of publication in brackets - Smith (1992). No comma is required between name and date when the whole reference is in brackets (Smith 1992), but use (Smith 1992; White 1971), (Black, 1972, 1975). If the reference has three or more authors use (Smith et al 1992) or (Smith et al 1992). Place the list of references at the end, in alphabetical order by first author and then date order, with the journal name preferably in full, eg Smith, A., Black, B. & White, E.J. (1967). The ecology of natural communities. Journal of Ecology, 42, 460-53. Or if a book: Smith, A. (1976) Mountains and Moorlands. Collins, London . (Italics for journal and book titles and bold for volume number may be excused for essay purposes). All the references should be accurate and cited by author and date in the text as above - be consistent in using (ed), pp, etc. Please also consult your home Department's guidelines for citation of references.

Notes on literature retrieval

Literature retrieval is more of an art than a science and there are many ways of achieving your goal of finding all/most of the relevant literature on your chosen subject. Experts working in the same field often provide a helpful start, especially if approached in person!

are usually out of date when published, but may provide a useful starting point (eg The Handbook of British Mammals ). Look for authors or titles in Books in Print .

'Trends in';, 'Advances in', 'Progress in', 'Annual Review of',

etc, as well as symposium articles and recent reviews of your subject are also useful, but beware of imitation! The review journals mentioned above are useful as well as the review articles in many ecological journals such as Oikos and Ecology.

Computerised or printed indexing or abstracting services

(including the Internet) may provide lists of references/abstracts from recent journals and earlier literature may be found from Zoological Record (ceased 198?) (Balfour), Biological Abstracts (1926-, SPL), Science Citation Index (1964-, SPL - including papers referring to a particular author), Excerpta Medica (1947 - Medical Library), and bibliographies in papers, etc.

Online services

in Cambridge are available via ISI Web of Science or ATHENS National authentication system, which provide access to MIMAS, EDINA and NISS.

Specialist abstracting services

are also available in print such as Key-word Index of Wildlife Research (Swiss Information Service) and Wildlife Review (North American literature), but these are difficult to find outside personal subscriptions (ask your Supervisor).

Alerting systems

such as Current Contents (SPL and available on the Internet) and even the index to New Scientist (SPL) may help in bringing the review right up to date.

The Internet

gives summaries of research in progress and details of research workers' interests as well as much, much more.

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Home > Biological Sciences > Dissertations, Theses, and Student Research

Biological Sciences, School of

School of biological sciences: dissertations, theses, and student research.

The Developmental Process for Adenoviral Vectored Canine Influenza Vaccines , Nicholas Jeanjaquet

Exploring The Interactions Between SARS-CoV-2 and Host Proteins. , Sojan Shrestha

Evaluating Assessment Score Validity and Characterizing Undergraduate Biology Exam Content , Crystal Uminski

Discovering Novel Polyextremotolerant Fungi, and Determining their Ecological Role Within the Biological Soil Crust Consortium , Erin Carr

METHANOGEN METABOLIC FLEXIBILITY , Sean Carr

A Tale of Two Genomes: The Complex Interplay Between the Mitochondrial and the Nuclear Genomes , Abhilesh S. Dhawanjewar

Transcriptome Assembly and Characterization of Chemoreceptors for Corn Rootworms , Bailee Egan

Mitochondrial Functions are Major Targets of Isocyanide Activity in Saccharomyces cerevisiae , Morgan A. Siemek

Access to Online Formative Assessments in Introductory Biology Courses: Investigating Barriers to Student Engagement , Allison Upchurch

Characterization of a novel glycerol-3-phosphate dehydrogenase (GPD2) in the alga Chlamydomonas reinhardtii , Itzela A. Cruz Powell

Mitochondrial Genome Structure and Double Strand Break Repair in Arabidopsis thaliana , Sterling Ericsson

Characterization of Novel Chlorovirus Glycosyltransferases That Synthesize Atypical Glycans , Eric Noel

Studies of the dUTPase of the Western Corn Rootworm , Carlos Riera-Ruiz

BIOINFORMATIC ANALYSIS OF THE GUT MICROBIOTA DERIVED FROM THE OIL FLY HELAEOMYIA PETROLEI FROM THE LA BREA TAR PITS , Brian Dillard

Functions of Vocal Mimicry in the Complex Song of the European Starling, Sturnus vulgaris , Maria Goller

POLEROVIRUS GENOMIC VARIATION AND MECHANISMS OF SILENCING SUPPRESSION BY P0 PROTEIN , Natalie Holste

The Relationship Between the Cervical Microbiome and Cervical Cancer Risk in Sub-Saharan Africa , Cameron Klein

Identification of the Kaposi's Sarcoma-associated Herpesvirus (KSHV) Surface Glycoprotein Targets of Human KSHV-specific Neutralizing Antibody Responses , Yasaman Mortazavi

Prey Selection by Birds of Prey , Anisha Pokharel

Metagenomic, Viral and Host Genetic Analyses of Congenital Tremor in Pigs , Kylee Sutton

DGTS Production as a Phosphate Starvation Response in the Human Fungal Pathogen Candida albicans , Caleb Wehling

Regulation of Vaccinia Virus Replication: a Story of Viral Mimicry and a Novel Antagonistic Relationship Between Vaccinia Kinase and Pseudokinase , Annabel T. Olson

Plant mitochondrial genome evolution and structure has been shaped by double-strand break repair and recombination , Emily Wynn

Contributions of the gp120 Variable Loops to Envelope Glycoprotein Trimer Stability in Primate Lentiviruses , Dane Bowder

CONDITION-DEPENDENT LIFE HISTORY STRATEGIES , Shivani V. Jadeja

EVALUATION OF A HUMAN PAPILLOMAVIRUS GENOTYPING ASSAY FOR CERVICAL CANCER SCREENING IN TANZANIA , kandali kapie

Influenza D Virus M2 Protein Exhibits Ion Channel Activity in Xenopus laevis Oocytes , Evan Daniel Kesinger

Establishing Benchmark Criteria for Single Chromosome Bacterial Genome Assembly , Timothy Krause

Behavioral Plasticity Across Non-Social Contexts in Female Green Swordtails, Xiphophorus Hellerii , Lindsey M. Coit

Resource allocation for acorn production: A comparison across species pairs of oaks with contrasting acorn production patterns and water use strategies , Kyle A. Funk

Variation in Density Dependent Seedling Survival Across Forests of Different Successional Age and Hunting Protection Status , Nohemi Huanca-Nunez

Phytohormone signaling in Chlorella sorokiniana: perspectives on the evolution of plant cell-to-cell signaling , Maya Khasin

Small RNA-Dependent Gene Silencing in the Green Alga Chlamydomonas reinhardtii : Functions and Mechanisms , EUN JEONG KIM

Nitrogen Addition and Ecosystem Functioning: Changes in Species Composition Leaf Traits Amplify Increases in Leaf Area Index and Canopy Chlorophyll , Anna R. Tatarko

Examination of Contribution of Pentose Catabolism to Molecular Hydrogen Formation by Targeted Disruption of Arabinose Isomerase ( araA ) in the Hyperthermophilic Bacterium, Thermotoga maritima , Derrick White

The Roles of Biotin in Candida Albicans Physiology , Nur Ras Aini Ahmad Hussin

The Plasticity of Functional Traits in the Dipterocarps of Borneo , Ju Ping Chan

Proximate and Evolutionary Causes of Sexual Size Dimorphism in the Crab Spider Mecaphesa celer , Marie Claire Chelini

Inter- and Intra-individual Variation in Predator-related Behavioral Plasticity Expressed by Female Green Swordtails ( Xiphophorus hellerii ) , Rachael A. DiSciullo

POPULATION AND MORPHOLOGICAL CHANGES IN AMERICAN KESTRELS THROUGH SPACE AND TIME , Teresa E. Ely

Evaluation of the Effects of Radiation on the Positioning of Histones and Other Proteins , Ashley Elizabeth Foster

THE JOINT EFFECT OF PHENOTYPIC VARIATION AND TEMPERATURE ON PREDATOR-PREY INTERACTIONS , Jean P. Gibert

Sequencing and Comparative Analysis of de novo Genome Assemblies of Streptomyces aureofaciens ATCC 10762 , Julien S. Gradnigo

Investigation of Lipid Profile Patterns Along Latitude in an Eastern Australian Cline and After Stress Selection in the Laboratory, and Experiments on Stress Tolerance with RNAi Knockdown of Lipid Biosynthesis Genes , Li Ko

Characterization of the Role of Host and Dietary Factors in the Establishment of Bacteria in the Gastrointestinal Tract , Janina A. Krumbeck

Identification and Characterization of Ion Channel Activity of the M2 Protein from Influenza Virus D (DM2) , Jianing Liu

No Nonsense: The Protection of Wild-Type mRNAs From Nonsense-Mediated mRNA Decay in Saccharomyces cerevisiae , Krista Patefield

RELATIONSHIP BETWEEN MORPHOGENESIS AND SECRETION IN THE FILAMENTOUS FUNGUS ASPERGILLUS NIDULANS , Lakshmi Preethi Yerra

Observational Learning in the Jumping Spider Phidippus audax , Robert M. Adams

Kaposi’s Sarcoma-Associated Herpesvirus Transmission and Infection among Young Zambian Children , Landon Olp

Expansion of the Chlorovirus Genus by Studies on Virus Natural History and Chlorella Host Metabolism , Cristian F. Quispe

A Lipidomics Approach to the Viral-Host Dynamics of the Unicellular, Eukaryotic Alga Chlorella variabilis and its Viral Pathogen, PBCV-1 , Suzanne Rose

Plasticity in Female Mate Choosiness: A Result of Variation in Perceived Predation Risk and the Interaction of Female Age and Male Density , Ashley Atwell

Placental HPV Infection in HIV Positive and HIV Negative Zambian Women , Chrispin Chisanga

Stress Responses and Energy Storage in Drosophila melanogaster Selected for Resistance to a Gram-Positive Bacillus cereus Spores , Zhen Hu

FUNCTIONAL IMPLICATIONS OF THE BAF-B1 AXIS DURING THE VACCINIA VIRUS LIFE CYCLE , Nouhou Ibrahim

Costs of Female Mating Behavior in the Variable Field Cricket, Gryllus lineaticeps , Cassandra M. Martin

Chlorovirus Skp1 and Core Ankyrin-Repeat Protein Interplay and Mimicry of Cellular Ubiquitin Ligase Machinery , Eric Andrew Noel

The equitable contributions of environment, management and restoration status on grassland diversity and composition , RaeAnn C. Powers

Investigations into Sensory Ecology and Gene Evolution of the pea aphid ( Acyrthosiphon pisum ) , Swapna R. Purandare

Biosorption of Heavy Metals onto the Surface of Bacteriophage T4 , Zheng Huan Tan

THE ROLE OF THE N-TERMINUS ON THE ENZYMATIC ACTIVITY OF dUTPase FROM DICTYOSTELIUM DISCOIDEUM , Kyle C. Varon

Investigating the Role of MicroRNAs in the Response to Nitrogen Deprivation in the Green Alga Chlamydomonas reinhardtii , Adam Voshall

The Mechanism of Small RNA Biogenesis, Degradation, and Function in Arabidopsis , Meng Xie

THE PREDICTION OF B-CELL EPITOPE VIA BIOSTATISTICAL AND BIOINFORMATIC METHODOLOGY AND APPLICATIONS , Bo Yao

Regulation of Phialide Morphogenesis in Aspergillus nidulans , Hu Yin

Trade-offs in Male Lek Behavior , Sarah A. Cowles

THE EPIDEMIOLOGY OF HUMAN HERPESVIRUS-8: TRANSMISSION OF INFECTION TO CHILDREN IN ZAMBIAN HOUSEHOLDS , Kay L. Crabtree

THE ORIGIN AND MOLECULAR EVOLUTION OF TWO MULTIGENE FAMILIES: G-PROTEIN COUPLED RECEPTORS AND GLYCOSIDE HYDROLASE FAMILIES , Seong-il Eyun

Analysis of Human Papillomavirus Capsid Proteins: Insights into Capsid Assembly , Willie A. Hughes

Coccidia of Gerbils from Mongolia , Ethan T. Jensen

Investigation of the life history and lipid content consequences of reduced abundance of delta-9 Desaturases in Drosophila melanogaster , Li Ko

Small Interfering RNA-Mediated Translation Repression Alters Ribosome Sensitivity to Inhibition by Cycloheximide in Chlamydomonas reinhardtii , Xinrong Ma

PREDATION AND BEHAVIORAL PLASTICITY IN GREEN SWORDTAILS: MATE CHOICE IN FEMALES AND EXPLORATORY BEHAVIOR IN MALES , Andrew J. Melie

Telomere-Related Factors and Human Papillomavirus Genome Maintenance , Adam Rogers

Spontaneous male death and monogyny in the dark fishing spider Dolomedes tenebrosus Hentz, 1843 (Araneae, Pisauridae) , Steven K. Schwartz

EVOLUTION OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CLADE C ENVELOPE V1-V5 REGION DURING DISEASE PROGRESSION IN NON-HUMAN PRIMATE MODEL , For Yue Tso

The Roles of Phenotypic Plasticity and Genotypic Specialization in High Altitude Adaptation , Danielle M. Tufts

Transcriptional analysis of cervical epithelial cell responses to HIV-1 , Andrew A. Block

THE PSEUDOMONAS SYRINGAE TYPE III SECRETION SYSTEM: THE TRANSLOCATOR PROTEINS, THEIR SECRETION, AND THE RESTRICTION OF TRANSLOCATION BY THE PLANT IMMUNE SYSTEM , Emerson Crabill

Gene Duplication and the Evolution of Hemoglobin Isoform Differentiation in Birds , Michael T. Grispo

Foraging Challenges: Unsuitable Prey and Limited Information , Travis M. Hinkelman

ASSESSING PATTERNS OF HYBRIDIZATION AND MULTIPLE MECHANISMS OF REPRODUCTIVE ISOLATION BETWEEN ERYTHRONIUM ALBIDUM AND ITS CONGENER E. MESOCHOREUM , Kathy Roccaforte

Characterization of Binding and Fusion Efficiencies Mediated by the V1-V5 Env Derived from Transmitted and Non-transmitted Viruses Isolated from a Perinatal Transmission Cohort from Zambia , Mackenzie Waltke

Herbivory affects patterns of plant reproductive effort and seed production , Natalie M. West

COMPARATIVE STUDIES OF DIFFERENTIAL GENE CALLING METHODS FOR RNA-SEQ DATA , Ximeng Zheng

Population Genetics of Cell to Cell Movement of Wheat Streak Mosaic Virus , Melissa S. Bartels

EXPLORING SOURCES OF SELECTION ON THE MULTIMODAL COURTSHIP DISPLAYS OF TWO SISTER SPECIES OF WOLF SPIDERS: SCHIZOCOSA CRASSIPALPATA AND SCHIZOCOSA BILINEATA , Mitch Bern

The Role of Human Ubc9 During the Human Immunodeficiency Virus Replication Cycle , Christopher R. Bohl

EFFECT OF DIET QUANITITY AND QUALITY ON FEMALE SAMPLING BEHAVIOUR AND MATING PREFERENCES IN A FIELD CRICKET , Heidi L. Bulfer

ANALYSIS OF TURNIP CRINKLE VIRUS EFFECTS ON THE INNATE AND ADAPTIVE IMMUNITY IN ARABIDOPSIS THALIANA , Teresa J. Donze

Investigation of Bovine Herpesvirus 1 (BHV-1) Encoded Infected Cell Protein 0 (bICP0) , Natasha N. Gaudreault

Characterization of RNAi-defective mutants -- Mut13-2 and Mut20 -- in Chlamydomonas reinhardtii , Arit Ghosh

THE EFFECTS OF SOCIAL CONTEXT & CACHE SURVIVAL ON PINYON JAY CACHING BEHAVIOR , Christine L. Keefe

HUMAN PAPILLOMAVIRUS GENOTYPE CONCORDANCE WITHIN ZAMBIAN COUPLES , Kgomotso Makhaola

Life history tradeoffs and phenotypic plasticity: The tale of a flight polyphenic field cricket , Chandreyee Mitra

Truncated dUTPase of Dictyostelium discoideum is active and likely to form trimers , Phuoc V. Nguyen

Functional Classification of Divergent Protein Sequences and Molecular Evolution of Multi-Domain Proteins , Pooja K. Strope

MSH1 INFLUENCE ON PLANT MITOCHONDRIAL GENOME RECOMBINATION AND PHENOTYPE IN TOBACCO , Peibei Sun

The Complexities of Wolf Spider Communication Exploring Courtship Signal Function in Rabidosa rabida , Dustin J. Wilgers

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• Undergraduate
• Honors Thesis Examples

EBIO student's Honors Thesis submissions from past years are archived here with abstracts from the student's respective papers. Peruse several of the submissions to get a sense of the area's of study our students delve into for their Honors Thesis projects.

Landscape Patterns of Litter Decomposition in Alpine Tundra - H. A. O'Lear and T. R. Seastedt - 1994

Effects of Mobile Tree Islands on Soil Carbon Storage in Tundra Ecosystems - Sheridan J. Pauker and T. R. Seastedt - 1996

Effects of Sequestered Iridoid Glycosides on Prey Choice of the Prairie Wolf Spider,  Lycosa carolinensis  - Demetri Hilario Theodoratus and M. Deane Bowers - 1998

Effects of Soil Nitrogen Reduction on Nonnative Plants in Restored Grasslands - K.J. Reever Morghan & T. R. Seastedt - 1999

Phylogeny of hammerhead sharks (Family Sphyrnidae) inferred from mitochondrial and nuclear genes -  Douglas D. Lim, Philip Motta, Kyle Mara, Andrew P. Martin - 2010

Beyond immunity: quantifying the efects of host anti-parasite behavior on parasite transmission -  Elizabeth W. Daly & Pieter T. J. Johnson - 2011

Land Use and Wetland Spatial Position Jointly Determine Amphibian Parasite Communities - Richard B. Hartson,  Sarah A. Orlofske,  Vanessa E. Melin,  Robert T. Dillon Jr., and Pieter T. J. Johnson - 2011

Effects of fuels reductions on plant communities and soils in a Piñon-juniper woodland - M.R. Ross, S.C. Castle, N.N. Barger - 2012

Investigating the dispersal routes used by an invasive amphibian, Lithobates catesbeianus , in human-dominated landscapes - Anna C. Peterson & Katherine L. D. Richgels & Pieter T. J. Johnson & Valerie J. McKenzie - 2012

Incorporation of an Introduced Weed into the Diet of a Native Butterfly: Consequences for Preference, Performance and Chemical Defense - Angela Knerl & M. Deane Bowers 

Quantifying the biomass of parasites to understand their role in aquatic communities - Jason Lambden & Pieter T. J. Johnson - 2013

Conceptual Revision and Synthesis of Proximate Factors Associated with Age-Related Improvement in Reproduction - Rachel J Bradley & Rebecca J. Safran - 2014

Patterns and ecological predictors of age-related performance in female North American barn swallows,  Hirundo rustica erythrogaster    -  R. J. Bradley & J. K. Hubbard & B. R. Jenkins & R. J. Safran - 2014

Assessing The Harmful Impacts Of Increased Commercial Shipping On Arctic Marine Mammals: A Systematic Literature Review - Hayley Wuestenberg - 2021

June 27, 2021

Read more about Assessing The Harmful Impacts Of Increased Commercial Shipping On Arctic Marine Mammals: A Systematic Literature Review - Hayley Wuestenberg - 2021

Harmful Algal Blooms As A Possible Cause Of Late Cretaceous Vertebrate Mortality Events In Northwestern Madagascar - Christopher Mulligan - 2021

Read more about Harmful Algal Blooms As A Possible Cause Of Late Cretaceous Vertebrate Mortality Events In Northwestern Madagascar - Christopher Mulligan - 2021

Population Structure Of The Endangered Mud Shrimp Upogebia Pugettensis - Madeleine Horan - 2021

Read more about Population Structure Of The Endangered Mud Shrimp Upogebia Pugettensis - Madeleine Horan - 2021

Exploring The Biogeographic Relationship Between Variation In Parasites And Pathogens And Host Plant Dispersal Traits - Patrick Heffernan - 2021

Read more about Exploring The Biogeographic Relationship Between Variation In Parasites And Pathogens And Host Plant Dispersal Traits - Patrick Heffernan - 2021

Flowering Time And Related Genes In Cannabis - Zachary Girard - 2021

Read more about Flowering Time And Related Genes In Cannabis - Zachary Girard - 2021

May Physical Activity Ameliorate Symptoms And Comorbidities Associated With Human Immunodeficiency Virus (Hiv) Infection? - Elizabeth Enichen - 2021

Read more about May Physical Activity Ameliorate Symptoms And Comorbidities Associated With Human Immunodeficiency Virus (Hiv) Infection? - Elizabeth Enichen - 2021

Nest Insulative Capacity Varies Between Chickadee Species But Not Along An Elevation Gradient - Shay Ding - 2021

Read more about Nest Insulative Capacity Varies Between Chickadee Species But Not Along An Elevation Gradient - Shay Ding - 2021

The Impact Of Early Snowmelt, Warming, And Microtopography On In Situ Geum Rossii Germination Rates In The Alpine - Nyika Campbell - 2021

Read more about The Impact Of Early Snowmelt, Warming, And Microtopography On In Situ Geum Rossii Germination Rates In The Alpine - Nyika Campbell - 2021

Entomology Education Since 2000: Methods, Outcomes, Challenges, and Suggestions for Practice - Elizabeth Woolner - 2020

Dec. 3, 2020

Read more about Entomology Education Since 2000: Methods, Outcomes, Challenges, and Suggestions for Practice - Elizabeth Woolner - 2020

Loss of Microbial Biodiversity: Implications for Human Health and Food Security - Shannon Ross - 2020

Dec. 2, 2020

Read more about Loss of Microbial Biodiversity: Implications for Human Health and Food Security - Shannon Ross - 2020

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Undergraduate Thesis

The School of Biological Sciences offers a senior thesis option that is available for all students. As part of this experience, students will learn about the proper way to conduct research in a classroom setting, conduct an independent research project, and communicate their results. The thesis, a written description of your work, includes the normal parts of a research paper (introduction, methods, results, figures, discussion and literature references). If you are going on to graduate school, a Senior Thesis is strongly recommended. For students applying to professional schools or even applying for a job, completing a Senior Thesis shows hard work and dedication as it's not required for graduation, but an extra effort you put into your education.

Students would generally complete BSC 196 and 197 during their freshman year, and BSC 204 in their sophomore year prior to registering for BSC 290 or 299 (Research in Biological Sciences, at least 3 hours) in their sophomore or junior years. BSC 303 (Senior Thesis) is taken in the senior year.

Completion of the thesis option is indicated on your transcripts.

A checklist of requirements is available.

Need more information? Contact Dr. Andres Vidal-Gadea

Want to see what a Senior Thesis looks like?  Copies available for viewing in the School of Biological Sciences Office in 210 Julian Hall.

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• Knowledge Base
• Dissertation

Prize-Winning Thesis and Dissertation Examples

Published on 9 September 2022 by Tegan George . Revised on 6 April 2023.

It can be difficult to know where to start when writing your thesis or dissertation . One way to come up with some ideas or maybe even combat writer’s block is to check out previous work done by other students.

This article collects a list of undergraduate, master’s, and PhD theses and dissertations that have won prizes for their high-quality research.

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Table of contents

Award-winning undergraduate theses, award-winning master’s theses, award-winning ph.d. dissertations.

University : University of Pennsylvania Faculty : History Author : Suchait Kahlon Award : 2021 Hilary Conroy Prize for Best Honors Thesis in World History Title : “Abolition, Africans, and Abstraction: the Influence of the “Noble Savage” on British and French Antislavery Thought, 1787-1807”

University : Columbia University Faculty : History Author : Julien Saint Reiman Award : 2018 Charles A. Beard Senior Thesis Prize Title : “A Starving Man Helping Another Starving Man”: UNRRA, India, and the Genesis of Global Relief, 1943-1947

University: University College London Faculty: Geography Author: Anna Knowles-Smith Award:  2017 Royal Geographical Society Undergraduate Dissertation Prize Title:  Refugees and theatre: an exploration of the basis of self-representation

University: University of Washington Faculty:  Computer Science & Engineering Author: Nick J. Martindell Award: 2014 Best Senior Thesis Award Title:  DCDN: Distributed content delivery for the modern web

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University:  University of Edinburgh Faculty:  Informatics Author:  Christopher Sipola Award:  2018 Social Responsibility & Sustainability Dissertation Prize Title:  Summarizing electricity usage with a neural network

University:  University of Ottawa Faculty:  Education Author:  Matthew Brillinger Award:  2017 Commission on Graduate Studies in the Humanities Prize Title:  Educational Park Planning in Berkeley, California, 1965-1968

University:  University of Ottawa Faculty: Social Sciences Author:  Heather Martin Award:  2015 Joseph De Koninck Prize Title:  An Analysis of Sexual Assault Support Services for Women who have a Developmental Disability

University : University of Ottawa Faculty : Physics Author : Guillaume Thekkadath Award : 2017 Commission on Graduate Studies in the Sciences Prize Title : Joint measurements of complementary properties of quantum systems

University:  London School of Economics Faculty: International Development Author: Lajos Kossuth Award:  2016 Winner of the Prize for Best Overall Performance Title:  Shiny Happy People: A study of the effects income relative to a reference group exerts on life satisfaction

University : Stanford University Faculty : English Author : Nathan Wainstein Award : 2021 Alden Prize Title : “Unformed Art: Bad Writing in the Modernist Novel”

University : University of Massachusetts at Amherst Faculty : Molecular and Cellular Biology Author : Nils Pilotte Award : 2021 Byron Prize for Best Ph.D. Dissertation Title : “Improved Molecular Diagnostics for Soil-Transmitted Molecular Diagnostics for Soil-Transmitted Helminths”

University:  Utrecht University Faculty:  Linguistics Author:  Hans Rutger Bosker Award: 2014 AVT/Anéla Dissertation Prize Title:  The processing and evaluation of fluency in native and non-native speech

University: California Institute of Technology Faculty: Physics Author: Michael P. Mendenhall Award: 2015 Dissertation Award in Nuclear Physics Title: Measurement of the neutron beta decay asymmetry using ultracold neutrons

University:  Stanford University Faculty: Management Science and Engineering Author:  Shayan O. Gharan Award:  Doctoral Dissertation Award 2013 Title:   New Rounding Techniques for the Design and Analysis of Approximation Algorithms

University: University of Minnesota Faculty: Chemical Engineering Author: Eric A. Vandre Award:  2014 Andreas Acrivos Dissertation Award in Fluid Dynamics Title: Onset of Dynamics Wetting Failure: The Mechanics of High-speed Fluid Displacement

University: Erasmus University Rotterdam Faculty: Marketing Author: Ezgi Akpinar Award: McKinsey Marketing Dissertation Award 2014 Title: Consumer Information Sharing: Understanding Psychological Drivers of Social Transmission

University: University of Washington Faculty: Computer Science & Engineering Author: Keith N. Snavely Award:  2009 Doctoral Dissertation Award Title: Scene Reconstruction and Visualization from Internet Photo Collections

University:  University of Ottawa Faculty:  Social Work Author:  Susannah Taylor Award: 2018 Joseph De Koninck Prize Title:  Effacing and Obscuring Autonomy: the Effects of Structural Violence on the Transition to Adulthood of Street Involved Youth

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Thesis proposal example 2

Senior Honors Thesis Research Proposal

Albert B. Ulrich III Thesis Advisor: Dr. Wayne Leibel 11 September 1998

Introduction:

Neotropical fish of the family Cichlidae are a widespread and diverse group of freshwater fish which, through adaptive radiation, have exploited various niches in freshwater ecosystems. One such evolutionary adaptation employed by numerous taxa is miniaturization, an evolutionary process in which a large ancestral form becomes reduced in size to exploit alternative niches. A considerable amount of research has been conducted on the effects of miniaturization on amphibians (Hanken 1983), but although miniaturization has been found to occur in 85 species of freshwater South American fish, little has been done to investigate the effects which miniaturization imposes on the anatomy of the fish (Hanken and Wake 1993).

Background:

Evolution is the process by which species adapt to environmental stresses over time. Nature imposes various selective pressures on ecosystems causing adaptive radiation, where species expand and fill new niches. One such adaptation for a new niche is miniaturization. Miniaturization can be defined as “the evolution of extremely small adult body size within a lineage” (Hanken and Wake 1993). Miniaturization is observed in a variety of taxa, and evolutionary size decreases are observed in mammals and higher vertebrates, but it is more common and more pronounced in reptiles, amphibians and fish (Hanken and Wake 1993). Miniaturization evolved as a specialization which allowed the organisms to avoid selective pressures and occupy a new niche. Miniaturization as a concept is dependent on the phylogenetic assumption that the organism evolved from a larger predecessor. Over time, the miniature organism had to adapt to the new conditions as a tiny species. All of the same basic needs had to be met, but with a smaller body.

In miniature species there is a critical relationship between structure of the body and body size, and frequently this downsizing results in structural and functional changes within the animal (Harrison 1996). Within the concept of miniaturization is the assumption that the species evolved from a larger progenitor. It is necessary then to explore the effects of the miniaturization process. “Miniaturization involves not only small body size per se, but also the consequent and often dramatic effects of extreme size reduction on anatomy, physiology, ecology, life history, and behavior” (Hanken and Wake 1993).

Hanken and Wake 1993 found that the adult skulls of the salamander Thorius were lacking several bones, others were highly underdeveloped, and many species within the genus were toothless. Several invertebrate species display the wholesale loss of major organs systems as a result of the drastic reduction in body size (Hanken and Wake 1993). Hanken and Wake also have shown that morphological novelty is a common result of miniaturization. Morphological novelty, in essence, is the development of new structures in the miniature organism. For example, as body size decreases, certain vital organs will only be able to be reduced by a certain amount and still function. As a result organs such as the inner ear remain large relative to the size of the miniature skull, and structural innovations have to occur in order to support the proportionately large inner ear.

In 1983, James Hanken, at the University of Colorado determined that the adult skull of the Plethodontid salamanders could be characterized by three observations: 1) there was a limited development or even an absence of several ossified elements such as dentition and other bones; 2) there was interspecific and intraspecific variability; 3) there were novel mophological configurations of the braincase and jaw (Hanken 1983).

In his experiments, Hanken found that cranial miniaturization of the Thorius skull was achieved at the expense of ossification. Much of the ossified skeleton was lost or reduced, especially in the anterior elements, which are seen typically in larger adult salamanders (Hanken 1983). In contrast to this ossified downsizing, many of the sensory organs were not diminished in size — therefore present in greater proportion to the rest of the reduced head. He also reported that due to the geometrical space availability, there is a competition for space in reduced sized skulls, and the “predominant brain, otic capsules, and eyes have imposed structural rearrangements on much of the skull that remains” (Hanken 1983).

Hanken proposed that paedomorphosis was the mode of evolution of the plethodontid salamanders (Hanken 1983). Paedomorphosis is the state where the miniaturized structures of the adult salamanders can be described as arrested juvenile states. To support this theory, Hanken showed data where cranial skeletal reduction was less extreme in the posterior regions of the skull. One of the hallmarks of paedamorphosis is the lack of conservation in structures derived late in development. Early developed structures are highly conserved, and the latter derivations become either lost, or greatly reduced. Again, Hanken has shown that elements appearing late in development exhibit greater variation among species than do elements appearing earlier in ontogeny (Hanken 1983). But the presence of novel morphological features cannot be accounted for merely by truncated development and the retention of juvenile traits. Miniature Plethodontid salamanders display features that are not present in other species, juvenile or adult. These novel morphological features are associated with the evolution of decreased size and are postulated to compensate for the reductions occurring in other areas (Hanken 1983).

In 1985, Trueb and Alberch published a paper presenting similar results in their experiments with frogs. They explored the “relationships between body sizes of anurans and their cranial configurations with respect to the degree of ossification of the skull and two ontogenetic variables‹shape and number of differentiation events” (Trueb and Alberch 1985). Trueb and Alberch examined three morphological variables: size, sequence of differentiation events, and shape changes in individual structures. Size and snout length were measured, and the data showed that the more heavily ossified frogs tended to be smaller, whereas the less-ossified species were of average size, contrary to what was hypothesized. But Trueb and Alberch also attributed the diminution in size to paedomorphosis, citing that the smaller frogs lacked one or more of the elements typically associated with anuran skulls‹these missing elements were typically late in the developmental sequence. It is significant to note, however, that although there was an apparent paedomorphic trend, it could not be “applied unequivocally to all anuans” (Trueb and Alberch 1985). Very little research has been done on the effects of miniaturization on fish. In 1993, Buckup published a paper discussing the phylogeny of newly found minature species of Characidiin fish, but the extent of the examination was merely an acknowledgment that the species were indeed miniatures so that they could be taxonomically reclassified ( Buckup 1993). It is this deficit of knowledge with regard to miniaturization in fish that prompts this research.

Statement of the Problem:

How does miniaturization affect other vertebrates, such as fish? There are over 85 species of freshwater South American fish which are regarded as miniature, spanning 5 orders, 11 families and 40 genera (Hanken and Wake 1993). One such species, Apistogramma cacatuoides, is a South American Cichlid native to Peru. It lives in shallow water bodies in the rainforests, where miniature size is necessary. Males in this species reach approximately 8cm, and females only 5cm. This makes A. cacatuoides an ideal specimen for examination. In this senior honors thesis, I intend to examine the effects of miniaturization on cranial morphology of A. cacatuoides.

Plan of Research:

In this thesis, I will compare the cranial anatomy of A. cacatuoides to that of “Cichlasoma” (Archocentrus) nigrofasciatum, a commonly bred fish reared by aquarists known as the Convict Cichlid, a “typical” medium-sized cichlid also of South American origin. The Convicts will be examined at various stages in development, from juvenile to adult, and will be compared to A.cacatuoides.

The first part of this project will involve whole mount preparation of A. cacatuoides, utilizing the staining and clearing procedures described by Taylor and Van Dyke, 1985. This procedure involves the use of Alizarin Red and Alcian Blue to stain bone and cartilage, and takes into account the adaptations and recommendations Proposed in an earlier paper (Hanken and Wassersug 1981). The Taylor and Van Dyke procedure is specifically for the staining and clearing of small fish and other vertebrates. I tested the procedure during last semester¹s Independent Study and made a few minor adjustments to the protocol.

First, the specimens will be placed serially into an absolute ethyl alcohol solution and stained with Alcian Blue. The fish will then be neutralized in a saturated borax solution, transferred to a 20% hydrogen peroxide solution in potassium hydroxide, and then bleached under a fluorescent light. The unwanted soft tissues will then be cleared using trypsin powder, and then stained in KOH again with alizarin red. The final preparation of the fish involves rinsing the fish, and placing them serially into 40%, 70%, and finally 100% glycerin.

Following the above preparation of the specimens, the crania of the A. cacatuoides specimens will be examined for morphological variation and compared to the cranial anatomy of the Convict cichlid as a progenitor reference point examined at various developmental stages to see if paedomorphosis in indeed the mechanism of miniaturization in A. cacatuoides.

Expected Costs:

The project is estimated to cost no more that five hundred dollars for chemicals and supplies for the entire year.

Literature Cited:

Hanken, J., 1983. Miniaturization and its Effects on Cranial Morphology in Plethodontid Salamanders, Genus Thorius (Amphibia: Plethodontidae). I. Osteological Variation”. Biological Journal of the Linnean Society (London) 23: 55-75.

Hanken, James, 1983. Miniaturization and its Effects on Cranial Morhology in Plethodontid Salamanders, Genus Thorius (Amphibia, Plethodintidae): II.The Fate of the Brain and Sense Organs and Their Role in Skull Morphogenesis and Evolution . Journal of Morphology 177: 255-268.

Hanken, James and David Wake, 1993. Miniaturization of Body Size: Origanismal Consequences and Evolutionary Significance. Annual Review of Ecological Systems 24: 501-19.

Harrison, I. J., 1996. Interface Areas in Small Fish. Zoological Symposium No. 69. The Zoological Society of London: London.

Miller, P. J., 1996. Miniature Vertebrates: The Implications of Small Body Size. Symposium of the Zoological Society of London. No. 69: 15-45.

Taylor, William R. and George Van Dyke, 1985. Revised Procedures for Staining and Clearing Small Fishes and Other Vertebrates for Small Bone and Cartilage Study. Cybium. 9(2): 107-119.

Trueb, L. and P. Alberch, 1985. Miniaturization and the Anuran Skull: a Case Study of Heterochrony. Fortschritte der Zoologie. Bund 30.

Williams, T. Walley, 1941 Bone and Cartilage. Stain. Tech. 16:23-25.

Writing Tips and Examples

Writing tips for grants & thesis dissertations, from the duke department of medicine:.

The Department of Medicine's vice chair for faculty development and diversity has collected a number of grant writing resources and successful sample grants that are available for review by Duke faculty and trainees. Follow the link below to view a list of resources - log into Duke Box  using your Duke Net ID and password and click a link below to access the documents.  Note: Do no use anyone else's text without permission.

• https://medicine.duke.edu/research/research-resources/templates-and-examples

Making a Poster: 

making_a_poster.pdf

Powerpoint Presentation Design: 

powerpointpresentation.pdf

Research Paper Writing: 

writing_a_research_paper.pdf

On NSF Grants:

Full NSF Proposal Example 2010

Sample Grant Proposals - Indiana University

• From the National Science Foundation: " A Guide for Proposal Writing "
• From National Science Foundation: " How to Get NSF Funding: A View from the 'Inside' "
• From Carnegie Mellon University: " Advice on Writing Proposals to the National Science Foundation "
• From the Principal Investigator's Association: " Executive Report: How to Write a Winning NSF Proposal "
• From Sunshine Consultants Int'l: " Writing a Compelling Grant Proposal to NSF "
• " Writing an NSF Grant Proposal: A First Timer's Perspective " by Philip J. Guo, Associate Professor @ UC San Diego

On NRSA Grants:

• From Science Direct: A Practical Guide to Writing a Ruth L. Kirschstein NRSA Grant
• From Illinois University: How to Win an NIH/Kirschstein/F30-F31 Predoctoral Fellowship - The Nuts & Bolts
• How to Write an F30 - Sidenote, Tumblr
• Thoughts on Writing an F31 NRSA Award - University of Pittsburgh School of Medicine
• From the University of Colorado: Sample NRSA Proposals

T32 Training Grants - Unlocking the Mystery - UNC Chapel Hill

• From the Burroughs Wellcome Fund & Howard Hughes Medical Institute: " Making the Right Moves: A Practical Guide to Scientific Management for Postdocs & New Faculty "

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Quantifying the impacts of multiple stressors on the production of marine benthic resources , the biology and ecology of regionally endothermic fishes in irish waters , assessing novel cultivation methods, baseline fish assemblages and survey methodologies of cultivated and wild kelp in the southwest of ireland , dietary conservatism: the influences and determinants of alternative foraging strategies , understanding variation in ecology and physiology of marine migratory species. .

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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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Dissertation examples

Listed below are some of the best examples of research projects and dissertations from undergraduate and taught postgraduate students at the University of Leeds We have not been able to gather examples from all schools. The module requirements for research projects may have changed since these examples were written. Refer to your module guidelines to make sure that you address all of the current assessment criteria. Some of the examples below are only available to access on campus.

• Undergraduate examples
• Taught Masters examples

Division of Biology and Medicine

Biology undergraduate education.

More than 30 percent of concentrators in the Biological Sciences earn honors each year.

Honors Application Due Dates for AY 23-24

Students graduating in May: October 2, 2023 Students graduating in December: March 1, 2024

Application for Honors : Students should complete the Honors Proposal Application in collaboration with the Thesis Advisor and Second Reader. Both advisor signatures are due at the application proposal deadline (above).

HONORS PROPOSAL APPLICATION

Honors Eligibility

To be eligible for honors, students must meet  three  requirements: .

• Completion of an original research  thesis  that is recommended for honors by both the Thesis Advisor and Second Reader.
• Formal and public  presentation  of the thesis (oral seminar or by poster presentation).
• Demonstration of quality  grades  in the concentration.  

Students concentrating in Biology AB/ScB, Health & Human Biology, and Biophysics are all eligible to apply for Honors , and the process is the same for each concentration.

Concentrators in Biochemistry apply via Biochemistry advisors; Applied Math-Biology students apply via Applied Mathematics; Computational Biology students apply via CCMB; Biomedical Engineering concentrators proceed via Engineering.

As per University policy, students may not use the same thesis to gain honors in more than one concentration. If pursuing honors in two concentrations, the theses must be fully distinct in content. 

Honors: Policy and Procedure for Biology Concentrations

The senior honors thesis is typically developed through a minimum of two, but more often three, semesters of research. Students intending to pursue a thesis in Biology often have a Brown faculty mentor and project secured in the summer prior to the senior year. Many students use  UTRAs to help support research, though this is not the only mechanism of support. Often faculty members provide student support from their own grants.

Students may also register for BIOL 1950/1960 independent study courses to support honors theses research, though this is not required.  Please note :  The Honors application process is  separate  from the  independent study BIOL 1950/1960 registration project proposal . The application for Honors is below.

Students graduating in May:

Students graduating in december*:.

A senior honors thesis in Biology is a substantial body of original scholarly research. Successful theses can be grounded in a number of methodological approaches including bench or field research, clinical study, mathematical models, computer simulations, meta-analyses that test hypotheses or yield new synthesis in a scholarly context. Regardless of the approach, successful theses will be inquiry-based and demonstrate contextual understanding of the work, formal assessment of scientific information, critical thinking, clear communication and a high level of independence.

The Thesis Advisor and Second Reader will evaluate and recommend the thesis for honors. Their roles are outlined below.

• The  Thesis Advisor  is the primary investigator who will mentor the project, and who will be available to the student in developing the thesis aims, designing methods, analyzing data, interpreting outcomes and casting the work in the context of the scholarly field(s) of relevance. The Thesis Advisor is also expected to guide the student in developing and delivering a polished final presentation of the thesis. The Thesis Advisor should be a Brown faculty member, usually but not always, from the Division of Biology and Medicine.
• The  Second Reader  will be a faculty member or associated scientist who is identified by the student, in consult with the Thesis Advisor, as appropriate to review the work. The Second Reader will evaluate the thesis, and provide an evaluation of the work. Second Readers should be acquainted with the field of research described by the project, and be willing and able to provide input and critique that will challenge and strengthen the thesis. The Second Reader should be at the doctoral level and ideally  not  from the same laboratory or research group where the project originates.

Presentation of the thesis can be fulfilled by participation in the Annual Biology Senior Research, Capstone, and Declaration Day or an arranged oral seminar.   If the oral seminar format is chosen the student will make scheduling arrangements with guidance from the Thesis Advisor. The oral presentation should be scheduled early to mid-April in order to meet the Thesis Advisor and Second Reader Final Evaluation Deadline.

While formal presentation of the thesis is required, there is not a specific set of criteria for evaluation. Advisors have the opportunity to comment on the presentation in the formal evaluation. Advisors should develop a mentoring plan to teach students about the various approaches to presenting scientific research. Opportunities for students to practice the presentation, receive, and incorporate feedback is especially helpful and encouraged.

Biology honors applicants are required to present their thesis research and senior capstone students are encouraged to do the same (though this is not a requirement). The Program in Biology will host the Annual Biology Senior Research, Capstone, and Declaration Day event on Wednesday, April 17th, 2024 in Alumnae Hall Auditorium . 

Students are required to submit a pdf of their final thesis to their Thesis Advisor, Second Reader and the BUE Office via email by the third Friday in April (see timeline above).  

Submission Instructions

1. Email a copy of the final thesis to  [email protected]  as a single pdf document. The format of the thesis is determined by the faculty advisor and student. The pdf file name should be the student’s first name initial(s) in all caps, followed by the last name (no spaces). For example, Dean Smith’s thesis file name would read KFSmith.pdf. The BUE Office will maintain a copy of the thesis for programming purposes. The thesis will not be shared or made public without the student’s permission.

2. The email subject heading should read: Honors thesis for BUE filing only.

Thesis Evaluation for Honors

The Thesis Advisor and Second Reader will evaluate and recommend the thesis for honors based on the criteria outlined below. An electronic honors evaluation form will be provided directly, via email, to the Thesis Advisor and Second Reader by the Office of Biology Undergraduate Education. This form will be sent well in advance of the final evaluation due date (above). It is up to the student and Thesis Advisors to develop internal project deadlines for submitting drafts and final copies of the thesis so there is time for revisions, as well as formal presentation of your honors thesis (poster/oral) so that the final evaluation can be submitted. The entire thesis presentation should be delivered prior to the final evaluation deadline. Please adhere to the BUE internal deadlines above.

Students who have earned a majority of "A" grades in courses required for the concentration and who are in good academic standing are eligible to apply for honors at the start of their penultimate (typically 7th) semester at Brown. Classes taken S/NC will count as qualifying towards that majority if they are marked "S* with distinction" indicating that had the student taken the course for a grade, the grade would have been an "A". Courses with a grade of S may be counted when a Course Performance Report indicates a grade of A. Students just shy of meeting the grade requirement for honors are encouraged to apply. Grades earned in penultimate semester concentration courses will be accounted for in the determination of quality grades made in the final semester. In order to verify quality grades efficiently, please make sure that your concentration course plan in ASK is up to date and that the number of required courses is listed.

Thesis Guidelines & Expectations

Faculty Advisors recommend the thesis for honors based on the following criteria:

• The writing, format, and presentation of the thesis are appropriate for the intended audience.
• The introduction of the thesis offers a formal review of the literature that presents the state of the field to date, and in doing so sets up a clear argument for the value of the work presented.
• The introduction of the thesis offers a clearly articulated goal, aim, question, and /or hypothesis to be tested.
• The methods and analyses selected are clearly justified.
• Results are interpreted appropriately and based on the analyses presented in the methods.
• The discussion section offers a compelling consideration of a) unexpected findings or challenges during the research process that may have influenced the results, b) implications of overall findings and their impact on the relevant field(s), c) future directions / next steps.

A thesis in Biology, Health & Human Biology, and Biophysics make take a variety of forms and formats. It is up to the honors candidate and Thesis Advisors to determine the specific expectations for the final thesis form and format. Elements of a thesis in Biology vary greatly depending on the nature of the project, the specific sub-field, and the student's learning goals. Communication about these expectations should be clearly articulated and agreed upon early in the research process. A common choice is for students to prepare the thesis as if they were to submit the work to a peer-reviewed journal. This approach offers the opportunity for students to experience the first step of the publication process. Another option is to prepare the thesis manuscript following the  dissertation guidelines  set forth by Brown's Graduate School. Previous students have found this useful in preparing for doctoral or master's research programs. Students and Advisors may also look to  Brown University's Digital Repository of Undergraduate Theses  in Biology for examples of formatting previously followed. Regardless of format, a thesis in Biology, Health & Human Biology, and Biophysics will exhibit the highest quality writing, novel content, context of findings, and documentation of sources expected at the undergraduate level. STEM theses generally include an abstract, robust introduction, complete methods, results, full discussion & conclusion, a complete list of references that illustrate the state of the field of relevance, clear figures and tables with appropriate captions, and necessary appendices. Regardless of format, a thesis in Biology, Health & Human Biology, and Biophysics will exhibit the highest quality writing, clear articulation of the state of the field relevant to the work, novel content, context of findings, and documentation of sources expected at the undergraduate level. 

“There is no such thing as a failed experiment, only experiments with unexpected outcomes (Richard Buckminster Fuller).”

Science does not always go as planned. Methodological hurdles and insignificant results are common experiences of researchers at every stage. Regular communication with the Thesis Advisors is essential for navigating hurdles that arise during the research process. Students with an approved application to the honors program are encouraged to submit the thesis even when challenges occur along the way. When outcomes are not as planned the student and Advisors are encouraged to work together to develop a new plan for presenting the work in the form of a formal thesis. Indeed, there is great value in presenting work completed and formally discussing challenges, unexpected outcomes, and insignificant findings. Dean Achilli is available to assist with planning during this process and to discuss alternative means of evaluation as necessary.

Thesis Archival in the Brown Digital Repository

Fill out the archiving form and upload your thesis.    The BDR is Brown University's online archive of student and faculty scholarship maintained by the Brown University Library. By choosing to deposit your honors thesis in the BDR, you are making your scholarly work discoverable and accessible into the future.

Brown Archiving Form 

Students wishing to archive their thesis with the BDR should follow these instructions:

• Fill out the  archiving form online . Information on access and licensing is provided on the form.
• June 10  is the deadline to submit a thesis for BDR archiving.

Students who encounter any issues with the upload process to BDR can email  [email protected] .