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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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The School promotes an interdisciplinary approach to both applied and fundamental research problems and to postgraduate training. Research in the School is organised into three major interdisciplinary centres: the Scottish Oceans Institute (SOI), Biomedical Sciences Research Complex (BSRC) and Centre for Biological Diversity (CBD). Together these centres encompass the full spectrum of research in biological sciences, spanning investigations on the properties and behaviour of individual molecules to planetary environmental dynamics.

For more information please visit the School of Biology home page.

This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.

Recent Submissions

Social plasticity within and across generations : testing the role of plasticity in rapid evolution in field cricket teleogryllus oceanicus , rhythmically repeated patterns of pulsed vocalizations in wild narwhals (monodon monoceros) , factors influencing growth and spore germination of species of boletus , density estimation and time trend analysis of large herbivores in nagarhole, india , designing a shipboard line transect survey to estimate cetacean abundance off the azores archipelago, portugal .

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

Molecular Biosciences Theses and Dissertations

Theses/dissertations from 2023 2023.

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

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

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

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

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

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

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

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

Theses/Dissertations from 2022 2022

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

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

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

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

A Holistic Investigation of Acidosis in Breast Cancer , Bryce Ordway

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

Theses/Dissertations from 2021 2021

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

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

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

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

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

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

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

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

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

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

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

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

Theses/Dissertations from 2020 2020

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

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

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

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

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

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

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

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

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

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

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

A Novel Intramolecular Interaction in P53 , Fan He

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

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

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

Mechanistic and Translational Studies on Skeletal Malignancies , Jeremy McGuire

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

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

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

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

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

Theses/Dissertations from 2019 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Theses/Dissertations from 2018 2018

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

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

Molecular Phylogenetics of Floridian Boletes , Arian Farid

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

Quantitative Proteomics to Support Translational Cancer Research , Melissa Hoffman

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

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

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

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

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

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

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

Theses/Dissertations from 2017 2017

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

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

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

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

Mechanisms of IKBKE Activation in Cancer , Sridevi Challa

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

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

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

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

Cell Division Regulation in Staphylococcus aureus , Catherine M. Spanoudis

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

Non-classical regulators in Staphylococcus aureus , Andy Weiss

Theses/Dissertations from 2016 2016

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

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

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

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

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

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

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

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

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

Nonreplicative DNA Helicases Involved in Maintaining Genome Stability , Salahuddin Syed

Theses/Dissertations from 2015 2015

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

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

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

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

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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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This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.

Recent Submissions

Improving monoclonal antibody production from chinese hamster ovary cells , enhancing glycosylated triterpenoid production in saccharomyces cerevisiae , biosynthesis of metallic nanoparticles for use in anti-corrosion and anti-fouling agents , exploring s-nitrosoglutathione reductase function in the non-vascular plant, marchantia polymorpha , bioengineering inducible gene expression in leafy brassicas to address post-harvest-specific requirements , sex determination, sex chromosomes, and supergenes: evolution of an unusual reproductive system , super-resolution imaging of proteins in live cells using reversibly interacting peptide pairs , understanding the role and function of spocd1 in pirna-directed de novo dna methylation , sequencing b cell receptor repertoires in human disease: applications in myalgic encephalomyelitis/chronic fatigue syndrome and in experimental malaria infection , role of tyrosine phosphatase ptpn22 in ctl responses to tumours and t cell exhaustion , rna editing ligases as novel drug targets in trypanosomatid parasites , pifs as a novel target in soybean to modulate the shade avoidance syndrome , structure and function of microtubule nucleation proteins , evaluation of the structural, functional, cellular and molecular basis of heart pathophysiology in mouse models of spinal muscular atrophy , understanding and utilising bacterial growth rate changes at high external osmolarities , origin and maintenance of diversity in british euphrasia (orobanchaceae) , single-cell time-series analysis of metabolic rhythms in yeast , ectopic heterochromatin provides an alternative route to fungal resistance , understanding adaptive immunity using immune receptor repertoire sequencing , mapping inbreeding depression in wild red deer (cervus elaphus) .

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

Microbiology and Molecular Biology Theses and Dissertations

Theses/dissertations from 2024 2024.

Characterization of Cellular Metabolism Regulation by the Transcription Factor Centromere Binding Factor 1 (Cbf1) , Spencer Ellsworth

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

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Master’s Thesis Research

Below is a list of Biology Department Master’s Projects and Theses which are available for download in the Boise State ScholarWorks Database .

Department of Biological Sciences

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M.S. Qualifying Research Paper Writing Guidelines

An important part of your master’s education is the writing of your final master’s qualifying research paper (also called a master’s thesis). To aid you in this process we have assembled the following guidelines.

Qualifying research papers fall into two categories, those based on laboratory research and those based on literature research. Both types are mentored by a faculty member or principal investigator of a research laboratory sought by the student. For laboratory research, the student will write the paper based on original experimental results obtained in the laboratory of the mentor. For a literature-based thesis, after selection of a suitable topic by the student and mentor, the student will research the topic by reading and analyzing original literature on the subject, and then prepare a substantive analysis that will constitute the paper. All qualifying papers are graded "Pass", "Pass with Distinction" or "Fail". Further information can be found at the  M.S. in Biology website .

STYLE INFORMATION

Qualifying papers in the Department of Biology should follow the structure of the types of papers that appear in the journal Cell. Laboratory research based papers should be modeled after a Cell research style articles and library research based papers should be modeled after Cell review style articles. Example articles with links are listed in the notes below.  

IMPORTANT NOTES

• Plagiarism is an act or instance of using or closely imitating the language and thoughts of another author without authorization and the representation of that author's work as one's own, as by not crediting the original author: This means that you cannot copy lines of text from another source without noting that it is a quote (“put quotes around the text”) and citing the reference. In general avoid direct quotes from other sources unless the quote makes a strong point. General facts do not need to be referenced, but more specific facts and ideas must be referenced, even if they have been rewritten in your own words
• Litertaure Review:  Lopez-Otin et al., 2023. Hallmarks of Aging: An Expanding Universe. Cell 186(2), 243-278 .
• Research Research:  Lyons et al., 2023. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 186(2), 327-345 . 
• Seek a thesis mentor and decide on a topic to study.
• After beginning your literature research, provide a list of references you are reading to your mentor.
• Proceed to write a brief outline of the paper with subsection ideas, then a more detailed outline with subsection descriptions, and share with mentor for comment.
• Proceed to write a first draft of paper, which the mentor will read and provide suggestions/questions for comment.
• Revise accordingly and submit the final version of your paper (~ 25 pages double spaced and reference list). Use citation format (Jones et al., 2023) and reference list as done in Cell papers (see above links). All figures taken from articles must be cited in the legend.

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Master's Thesis

Writing, defending and filing your master's thesis.

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

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

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

Master's Applied Research Project

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

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

Thesis/Project Committee

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

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

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

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

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

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

Oral Defense of the Thesis/Project

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

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

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

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

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

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

Filing the Thesis

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

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Current Masters Students

• Masters Thesis Standards

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

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

Thesis Assessment Criteria

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

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

Introduction

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

Materials & Methods

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

Updated Thesis and Graduation Requirements

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

Changes to the original requirements are italicized.

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

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

Thesis preparation and defense

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

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

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Home > USC Columbia > Medicine, School of > Biomedical Science > Biomedical Science Theses and Dissertations

Biomedical Science Theses and Dissertations

Theses/dissertations from 2023 2023.

Gluten Free Diet Ameliorates SI Enteropathy in IGA Deficient Mice , Ryan Albert William Ball

Progressive Neurochemical, Neuroinflammatory and Cognitive Deficits in an Experimental Model of Gulf War Illness , Hannah Elizabeth Burzynski

Effects Of Chronic Stress On Working Memory Are Sex-specific And Age-dependent , Tyler Jamison Cox

Aortopathies: Mechanism of Pathogenesis and Therapy , Mengistu G. Gebere

Leptin, Serotonin, and the Control of Food Intake , Nicholas David Maxwell

Targeting Macrophages in Cancer Models Using Natural Compounds , Sierra Jordan McDonald

Neurodevelopmental and Transient Impacts of Brain Kynurenic Acid Elevation and Sleep-Wake Behavior , Katherine Rentschler

Exploration Into the Relationship Between Colitis and Depression: A Potential Role for the Aryl Hydrocarbon Receptor , Kasie Lynn Roark

B-Cell-Specific MHCII Promotes Host-Microbiome Symbiosis , Mary Melissa Roland

Cardiac Imaging in Mice With Micro-Computed Tomography: An Assessment , Kyle Porter Stegmann

Impact Of Steroid Receptor And Hormone Manipulation In Skeletal Muscle: Implications For Glucose Metabolism And Insulin Sensitivity In Male Mice , Christian Aaron Unger

Theses/Dissertations from 2022 2022

Role of Epigenome in Regulation of Inflammation By AHR Ligands 2,3,7,8-Tetrachlorodibenzo-P-Dioxin and 6-Formylindolo[3,2-B] Carbazole , Alkeiver Cannon

Neurochemical, Molecular, and Behavioral Effects of Intranasal Insulin , Jennifer Marie Erichsen

Sex Differences and Potential Non-invasive Treatments for Calcific Aortic Valve Disease , Henry Pascal Helms

Decellularization Strategies of Naturally Derived Biomaterials for Tissue Engineering Applications , Julia Elizabeth Hohn

Role of AhR in the Epigenetic Regulation of Immune Cells in Lungs During Acute Respiratory Distress Syndrome , Bryan Latrell Holloman

The Submission of a Section 513(g) Request For Information , Morgan Ashley Lano

Engineering and Optimization of an AAV Based Viral Vector to Limit the In-Vitro Expression of SARS-CoV-2 Spike-Protein , Ronald Anderson Smithwick

In Vitro and in Vivo Studies of Mediator Kinase , Lili Wang

Theses/Dissertations from 2021 2021

Role of AhR Ligands in Immune Modulation to Suppress Inflammation Through the Regulation of Microrna and Gut Microbiome , Osama Azeldeen Abdulla

Role of Estrogen in Regulating Diet-Induced Obesity in Females , Ahmed Aladhami

Impact of Acetylcholine on Internal Pathways To Basal Amygdala Pyramidal Neurons , Tyler Daniel Anderson-Sieg

Pseudomyxoma Peritonei Derived Cancers: A Novel Study on Growth and Growth Suppression Utilizing Common Colorectal Cancer Agents , Raymond Kennith Bogdon

Impact of Acetylcholine on Amygdala Network Oscillations , Joshua Xavier Bratsch-Prince

Real Time Neurochemical Analysis of the Brain For Pharmacological Treatments in Mood Disorders And Neurodegeneration , Anna Marie Buchanan

Regulation of Inflammatory Processes by Tryptamine, Cannabidiol and 2,3,7,8-Tetrachlorodibenzo-P-Dioxin , Nicholas Dopkins

Study of the Effect of B-Cell-Intrinsic Mhcii Antigen Presentation on Germinal Center B Cell Evolution Using The Brainbow Mouse Model , Nia Hall

Mechanism of Therapeutic Efficacy of New Drugs in Glioblastoma , Firas Hameed Khathayer

The Effect of Low Dose Penicillin on Tumor Development in Apc Min/+ Mice , Kinsey Ann Sierra Meggett

Defining the Pathophysiology of Gut Humoral Immunodeficiency , Ahmed Dawood Mohammed

The Role PDE11A4 Signaling and Compartmentalization in Social Behavior , Kaitlyn Pilarzyk

Anatomical Correlates of Age-Related Basal Forebrain Dysfunction , Brandy Lynn Somera

A Novel Model to Study Adipose-Derived Stem Cell Differentiation , Austin N. Worden

Theses/Dissertations from 2020 2020

Molecular Mechanisms of Loss of E7 Expression in HPV16 – Transformed Human Keratinocytes , Fadi Farooq Abboodi

17 β-Estradiol and Phytoestrogens Attenuate Apoptotic Cell Death in HIV-1 Tat Exposed Primary Cortical Cultures , Sheila Marie Adams

Helicobacter’s Effects on Colitis/Colon Cancer and the Response to Indole 3-Carbinol , Rasha Raheem Abdulhamza Alkarkoushi

A Comparative Study of Cannabinoids & CB1 Receptor GI Signaling , Haley Kristen Andersen

Expansion Microscopy: A New Approach to Microscopic Evaluation , Ashley Ferri

The Role of Acute and Chronic Neuroinflammation in Depression: Uncovering the Relationship Between Histamine and Serotonin Transmission , Melinda Hersey

The Use of Natural Anthraquinone Emodin as a Primary and Complementary Therapeutic in the Treatment of Colorectal Cancer , Alexander-Jacques Theodore Sougiannis

The Effects of Super-Resolution Microscopy on Colocalization Conclusions Previously Made With Diffraction-Limited Systems in the Biomedical Sciences , Madison Emily Yemc

Theses/Dissertations from 2019 2019

Role of Epigenome and Microbiome in Cannabinoid and Aryl Hydrocarbon Receptor-Mediated Regulation of Inflammatory and Autoimmune Diseases , Zinah Zamil Al-Ghezi

Tissue-Specific Roles of Transforming Growth Factor Beta Ligands in Cardiac Outflow Tract Malformations and Calcific Aortic Valve Disease , Nadia Al-Sammarraie

Role of Epigenetic, Molecular and Cellular Pathways in the Regulation of Inflammation , William James Becker

Neurochemical and Behavioral Outcomes of Intranasal Orexin Administration in Young and Aged Animals , Coleman Blaine Calva

Interdependent Mechanisms of Stress Susceptibility , Julie Elaine Finnell

Astrocyte Sensitivity to Dopamine in Culture and Ex Vivo , Ashley L. Galloway

Three-Dimensional Plasma Cell Survival Microniche in Multiple Myeloma , Katrina A. Harmon

Role of Epigenome and Microbiome in Endocannabinoid-Mediated Regulation of Inflammation During Diet-Induced Obesity , Kathryn Miranda

Epigenetic and Purinergic Regulation of Mast Cells Mediator Release , Zahraa Abdulmohsin Mohammed

Effect of TCDD, an Environmental Contaminant, on Activation of AHR Leading to Induction of Myeloid Derived Suppressor Cells (MDSCS) and the Ability of Resveratrol, a Botanical, to Neutralize this Effect , Wurood Hantoosh Neamah

An Anatomical Basis of the Differential Cholinergic Modulation of Valence-Specific Pyramidal Neurons in the Basolateral Amygdala , Nguyen Vu

Analysis of Cellular Interactions Within a Collagen Hydrogel , Austin N. Worden

Theses/Dissertations from 2018 2018

Role of Mammary Microenvironment in Promoting Left-Right Differences in Tumor Progression, Metastasis, and Therapeutic Response , Huda Issa Atiya

Enhancements in Alginate Microencapsulation Technology & Impacts on Cell Therapy Development , Marwa Belhaj

Effect Of Resveratrol On The Development Of Eczema , Christopher Carlucci

The Nervous System And Cancers Of The Head And Neck , Christian A. Graves

Turning Up Antitumor Immunity Against Breast Cancer , Johnie Hodge

Exploring Alternative Therapeutic Interventions For The Treatment Of Leigh Syndrome , Stephanie Martin

Regulation Of Prostaglandin D2 And Angiogenesis-Related Factors From Human Skin Mast Cells By Interleukin-6 And Resveratrol , Cody Cody McHale

Advanced Clearing Methods and Imaging Techniques for Optimized Three- Dimensional Reconstruction of Dense Tissues , Caleb A. Padgett

Role Of MIR-489 In HER2 Positive Breast Cancer , Yogin Patel

Operation Of The Leica SP8 Multiphoton Confocal System Using Single Or Multiple Fluorochromes , Amy E. Rowley

Theses/Dissertations from 2017 2017

Garlic Inhibits Inflammation during Dengue Infection , Alex R. Hall

Functional Role of the Homeobox Transcription Factor Six1 in Neoplastic Transformation of Human Keratinocytes , Maria Hosseinipour

Individual Differences in Markers of Cholinergic Signaling Correlating to Fear and Extinction Learning , Grace C. Jones

The Role Of Cyclin-Dependent Kinase 8 In Vascular Disease , Desiree Leach

Succination Impairs Protein Folding and Promotes Chop Stability in the Adipocyte during Diabetes , Allison Manuel

Muscarinic Acetylcholine Receptor M1’s Impact on Fear Extinction Learning , Joshua R. McElroy

Hemodynamic Regulation Of Cardiac Valve Development , Vinal Menon

The Role Of Inflammation In Atherosclerosis , Fatma Saaoud

Synergism of Quercetin and Sodium Butyrate for Controlling Growth of Glioblastoma , Matthew Alan Taylor

Mast Cells and Lipid Cross-Talk in Skin Inflammation , Piper Alexandra Wedman

Theses/Dissertations from 2016 2016

Tumor Suppressor p53 Response To UV Light In Normal Human Keratinocyte Strains From Different Individuals , Fadi Farooq Abboodi

Vitamin D and Stress Fractures in Collegiate and Professional Athletes , Christian Michael Askew

Linking Obesity & Breast Cancer: Role Of Monocyte Chemoattractant Protein-1 And High Fat Diet-Induced Inflammation On Mammary Tumorigenesis , Taryn L. Cranford

The Identification Of The Direct And Indirect Pathways Through Which Leptin Facilitates Synaptic Plasticity In The Hippocampus , Catherine Van Doorn

Morphogenic Effects Of Dopamine In Cultured Rat Hippocampal Astrocytes , Ashley L. Galloway

Emodin Regulates Macrophage Polarization: Application In Breast Cancer Treatment , Stephen Iwanowycz

Differences In Resting-State Functional Connectivity Of Chronic Migraine, With And Without Medication Overuse Headache, And The Effectiveness Of Sphenopalatine Ganglion Block As A Treatment For Repairing Dysfunctional Connectivity. , Kaitlin Krebs

Prospective Assessment Of Health Disparities And Injury Risk Factors At Basic Combat Training At Ft. Jackson , Kristin Lescalleet

Transcriptional And Post-Transcriptional Regulation Of NRF2 In The Heart By The Deubiquitinase CYLD , Bryan J. Mathis

Regulation of Chronic and Acute Inflammatory Disease by microRNA and Microbiota , Pegah Mehrpouya-Bahrami

The Effect of Arsenic on Type 2 Diabetes and Inflammation , Kayla Penta

Factors Influencing The Collagen Fiber Angle Distribution in The Mouse Aorta , Shana Roach Watson

The Role of Epidermal Stem/Progenitor-Like Cells In HPV-Mediated Pre-Neoplastic Transformation , Yvon L. Woappi

Theses/Dissertations from 2015 2015

Extensive Genome Rearrangements of Caulobacter K31 and Genomic Diversity of type B3 Bacteriophages of Caulobacter Crescentus , Kurt Taylor Ash

Evaluating Muscle Fiber Architecture , Morgan Ashley Flahive

Characterization of STARD4 and STARD6 Proteins in Human Ovarian Tissue and Human Granulosa Cells and Cloning of Human STARD4 Transcripts , Aisha Shaaban

Cannabinoid-mediated Epigenetic Regulation of Immune Functions , Jessica Margaret Sido

The Effect of 3D Collagen Scaffolds on Regulating Cellular Responses , Chad Simmons

Theses/Dissertations from 2014 2014

Metformin Arrests Growth and Induces Apoptosis of Neuroblastoma Cells , Nadia Al-Sammarraie

Cellular and Biochemical Effects of Sparstolonin B on Endothelial Cells to Inhibit Angiogenesis , Marwa Belhaj

An Evolutionary Perspective on Infectious and Chronic Disease , John Eberth

Status Epilepticus Induced Alterations in Hippocampal Anatomy and Neurotransmission , Denise K. Grosenbaugh

The Cardio-Protective Effects of Substance P in Both Ischemia/Reperfusion and and Short-Term Hypoxia Rat Models , Shaiban Jubair

MUSCARINIC MODULATION OF BASOLATERAL AMYGDALA , Lei Liu

MCP-1 In Colorectal Cancer: Benefits of Exercise , Jamie Lee McClellan

Diethylstilbestrol (DES) mediates immune suppression via modulation of microRNA expression in mice , Martine Menard

Effects of cPLA-2 on the Migration and Proliferation of Human Vascular Smooth Muscle Cells and the 2-D Migratory Patterns of Tropomyosin in Femoral and Abdominal Aorta Tissue , Jaimeson Thomas Powell

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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.
• Biology Writes  offers writing resources, feedback, one-on-one consultations, and more.  
• Duke Biology’s Mission Statement
• AJED Annual and Semester Reports
• AJED Meeting Notes
• Biology Cultural Association (BCA)
• Inclusion, Diversity, Equity, and Antiracism Committee (IDEA)
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Christian-Albrechts-Universität zu Kiel

Mathematisch-naturwissenschaftliche fakultät, sektion biologie.

• Studienangebot
• Master of Science in Molecular Biology and Evolution (MAMBE) (1-Fach)

Advice for writing your Master thesis

General notes.

Your thesis shall give a precise summary of your experiments/studies. Thus, it shall be easy to read, while containing sufficient detail that permit a complete reconstruction of the experiments/studies performed. Note that the thesis must be your own work - both regarding the data and the concepts. Any copy-pasting of entire sentences or even paragraphs from the literature or webpages is plagiarism - equivalent to theft - and absolutely not acceptable!

Scientific reports should have a consistent structure that allow the reader to understand the purpose of the study, the results obtained, and how these results advance our current knowledge. The following structure should be used:

Title page , including title, names of author, and affiliations. The title should be concise, easily understandable, and still precise. It should raise the reader's interest into the topic.

The Abstract provides a short summary of your study, including background and goal ( 1 - 3 sentences ), main findings ( 1 - 5 sentences ), and main conclusions ( 1 - 3 sentences ).

Introduction : Conceptual background ("Why is this interesting?"). 3 - 10 pages for a Master thesis.

Objectives : What is your main research objective? What is your hypothesis? The formulated hypothesis must be precise! The objectives may be an integral part of the introducion (presented at the end of the introduction) or be a separate section of your thesis. 0.5 page.

Materials and Methods : The description of the methods should be sufficiently precise to allow complete reconstruction of the experiments/studies performed. At the same time, it is important that they are not "flooded" with unimportant details, which then may make it impossible to read and understand the approaches used. In case of complicated experiments, use graphical illustrations. The experimental design of the study must be suited to address the main research question or hypothesis! Up to 20 pages.

Results : The results should be sufficiently long and present all results obtained in an objective format. Results are ideally shown in graphs and tables. The accompanying text should be short and focused on the main patterns found, and then refer to the tables and figures  (and not repeat all the tiny little details shown in the tables and graphs). The results should be evaluated with the help of statistical methods. Avoid any interpretation and discussion of the results. Up to 20 pages.

Discussion : The discussion should critically evaluate the results obtained in consideration of the main research question/hypothesis (e.g., "Were the expecations met?"). It should critically and objectively discuss alternative explanations for the results. Do not be misled by your expectations! Moreover, it should take into account the current literature on the topic and explain in how far the results advanced our understanding of the topic. Up to 20 pages for your Master thesis .

Acknowledgments : Point out who provided support for your study. 0.5 page.

References : List all references which were quoted in the report. Usually 1 - 3 pages.

Appendix : Include extra information on methods and results that are not essential for the main report but that may still be useful for understanding of results or future studies (may be long).

The main parts (Introduction, Objectives, Materials and Methods, Results, Discussion) should not exceed 40 - 60 pages for a Master thesis! The quality of your thesis is not equivalent with its length. An excellent paper should be concise!

Use a standard font and a font size of 11 (e.g. Arial) or 12 (e.g. Times New Roman). Headers may be larger or in bold. Additionally, use a line spacer of 1.5 or more (at least 1.15) and leave sufficient space at the page margins (at least 2 cm; ideally 2.5 cm).

In order to reach your audience, clarity of arguments and findings is essential. Many important findings were overseen because the articles were written in an incomprehensible format. Here are some tips on how a clear thesis can be managed:

Use short sentences. Build up arguments step-by-step. Use graphics to illustrate complex relationships.

Use graphics and tables to present your findings. Think about how the reader may best understand your results. Use symbols and colours to emphasize different treatment groups. It is helpful if you use the same X-axis, Y-axis, symbols, colours for related graphs. Graphs should be large enough. Include a legend to explain the details (axes, symbols, etc.) of the graphs.

Avoid unimportant details that do not directly relate to your main study question/hypothesis.

Avoid unjustified speculations in your discussion of the results.

You may use headers for subsections in methods, results, and perhaps discussion.

To ensure clarity of arguments, especially in the introduction and discussion, it is usually a good idea to start formulating internal headers for each single paragraph (i.e. headers that you do not use in the final version of the manuscript), and then add more and more details. It may then be useful to start each paragraph with a clearly formulated statement that is subsequently evaluated/discussed in more detail in the following part of the paragraph. If you have several related points that you would like to introduce or discuss, then it is useful to present them as a numbered list of points. (An example for the discussion: "I can draw three main conclusions from my results: 1) xxx, 2) xxx, 3) xxx"; each listed point should start on a new line.)

Use a format that is appealing to the eye. For example, larger font size or bold font for headers, etc.

Always use a concise and clear title for a table. The title should be given above the table itself. Include a legend (usually below the table) to explain further details or abbreviations. Use an open and simple format, too. Only show horizontal lines of your table, no vertical lines. Headers may be given in bold.

Use a concise and clear title for figures. The figure title and subsequentlegend are presented below the figure.  Include a legend to explain further details, abbreviations, symbols or colours. This should be understandable as stand alone - without any further information from the text. You may also include a symbol legend within the figure. Always use the same standard pattern and colour for the same subgroups throughout the text.

Organize the axes in a meaningful way: The explanatory variable should be given on the X-axis, whereas the response variable should appear on the Y-axis. The chosen axis titles should be brief but sufficiently precise. Include information on the error margin, either standard error, standard deviation, or confidence intervals. Select axis-ranges in such a way that not too much empty space is left. Log transform where useful.

Provide statistics either as part of a figure, table or in text. For statistical tests, always include the following information: Name of the test (e.g. ANOVA), value of the test statistic, sample size or degrees of freedom, probability (p value). The abbreviations of the calculated variables (test statistic and probability) are always given in italics. The methods must include sufficient detail on how the statistical analysis was done.

Use a consistent format for the references in the reference list. The references can be most easily added and formatted with the help of the programmes such as Zotero, Endnote or Reference Manager. Please only cite papers that you actually read!