biology master's thesis proposal example

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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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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.

Thesis Proposal Guidelines

I. Thesis Proposal Requirement

As a graduate student in the Department of Biology, you are required to write and defend a thesis proposal. This requirement has been formalized as a milestone credit. The thesis proposal is most helpful when it is completed in the first term, especially for M.Sc. students, but it must be completed by the end of the second term of your graduate program at the latest.

If you would like to try to transfer form the M.Sc. program to the Ph.D. program without first completing the M.Sc. degree, and you have the approval of your Graduate Supervisory Committee to attempt the transfer, then you must also defend a Ph.D. thesis proposal by the end of the third term of your program. Your performance in the thesis proposal along with your performance in the first year of the M.Sc. program form the basis for determining whether a transfer is warranted. Your Graduate Supervisory Committee, along with the Graduate Officers and an additional arms-length committee member, will base the decision on three criteria: excellent academic performance, a M.Sc. research project of sufficient breadth and depth that it can be expanded into a Ph.D. project and evidence that your analytical and writing skills are very strong.

II. Evaluation of the Thesis Proposal

The purpose of the thesis proposal is the clearly identify the scientific question(s) that will be the focus of your graduate research, explain why the question(s) are important, and describe how you will go about answering them. Your Graduate Supervisory Committee will evaluate the written proposal, which they should receive at least two weeks before your scheduled defense of it. The defense normally consists of a short (20 minute) oral presentation followed by questions from the committee. Spectators are not only permitted but invited to the defense and are entitled to ask reasonable questions after the committee has finished its questioning. The committee will take both your written and oral presentation as well as your responses to all questions into account in reaching its decision. The decision may be pass, fail, or deferred. A failure requires withdrawal from the program. A deferred decision requires a written explanation by the committee and a fixed date for a revised proposal and subsequent defense. Decisions cannot be deferred a second time.

At the defense you should show the committee that you have suitable knowledge of your field, grasp of the necessary methods, understanding of the scientific context of the work, and a credible plan for bringing the project to completion within the normal time limits for your program. The depth and sophistication of both knowledge and study design is naturally expected to differ between M.Sc. and Ph.D. proposals. Both should include clearly identified questions, or hypotheses, and an explanation of how the questions will be addressed. The committee will also probably expect to see a defined time line, showing the major milestones and planned completion dates for your project. Progress in your research to date is an additional consideration.

III. Thesis Proposal Format

A good model for the thesis proposal might include the following sections.

1. Introduction and review of prior knowledge. This would typically take the form of a concise literature review to show that you know the background for your work and to show the reader the context and importance of your questions. With limited space (see below) you have to be very judicious in selecting the references. You want the review to be up-to-date and representative of the field; it should not be limited to the writings of those associated with just one or two research groups.

2. Research progress to date. A separate section to describe your own contributions to date may be appropriate, particularly in the case of those attempting to transfer from M.Sc. to Ph.D. In other cases, it may be necessary only to indicate how you have managed to progress relative to the time line for your project.

3. Objectives of proposed research. Include long- and short-term objectives and testable hypotheses.

4. Proposed experiments (from “How to get and keep an NSERC research grant” by I.H. Witten and J.I. Glasgow of Queens University)

“A majority of your proposal should be devoted to a careful description of your research objectives and the methodology by which these objectives will be achieved. For the research plan, you should at least know how you are going to start out and have some ideas for future options. Be prepared to describe alternative scenarios for the later stages, which hinge on how the early research turns out. Be mindful of the need to evaluate your ideas, not just develop and implement them. If successful, what will be the effect of the research? Remember that your methodology must include a clear description of your overall experimental design and some indication of the statistical methods you will undertake to analyze your data.”

5. Milestones/Time line. Provide a term by term list of objectives for your planned graduate program, including coursework, important goals for your experiments, data analysis and writing and defense of the thesis.

The completed thesis proposal should be no longer than 12 pages of text, not including figures and references, double-spaced with 1 inch margins and size 12 font. Figures may be presented on additional pages only if they are informative and are mentioned in the text. References should be presented in full (no abbreviations other than initials and journal titles) in a format similar to a journal in your field of study. Deliver a copy to each committee member and one copy to the Biology Graduate Coordinator, who will handle the details of your defense, at least two weeks in advance of your scheduled defense.

IV. Research Ideas

The supervisor and supervisory committee should be important resources as you develop your research questions and the rest of the proposal. Your questions, and even the major methods, may already be largely formulated for you by your supervisor, or you may be expected to develop them mainly on your own. Generally, more responsibility for formulation of the main questions and the approach to their solution is expected from Ph.D. candidates. In any case, you have the right to expect helpful discussion and guidance from your supervisor and the committee as you develop your proposal.

The following material is modified from “How to get and keep an NSERC research grant” by Witten and Glasgow, which was aimed at professional researchers who deal with the Natural Science and Engineering Research Council (NSERC) of Canada funding. There are important similarities between a good thesis proposal and a good NSERC proposal, and so the comments below may help you in designing your study and carrying out your research.

To do research well, you must formulate a question or hypothesis that forms the basis for your work. This should not be an isolated question, but one related to a particular field of inquiry and one designed to increase our understanding within that field. How do you generate specific, interesting and relevant research questions? Read current research papers and reviews in areas that are relevant to your field. Read more widely in general journals or in areas that overlap your field of research. Good ideas often come from reading, discussing and explaining what someone else is doing. Group discussions can be fertile breeding grounds for new ideas. Force yourself to understand new ideas, perhaps by presenting and explaining them to others, and ideas will strike you. When you think about these papers, it is worthwhile to capitalize on your own detached position to escape from the authors’ mindset and think more laterally.

By its very nature, research is unpredictable, and any avenue of inquiry – no matter how good the idea was originally – may turn out to be sterile, infeasible, or simply incorrect. Propose a mix of questions to work on – some short-term and obviously answerable, others long-term, more risky, but potentially more valuable. On the other hand, beware of promising to work on too many things, for your proposal will be criticized as being “unfocused”. Reviews of proposals sometimes state explicitly that the evaluation would have been higher if fewer ideas had been included. You can spoil a good proposal by adding more to it.

You have to evaluate your own ideas, assess their strengths and weaknesses, sharpen them, and present them clearly. When you specify a goal, how will you know if you reach it? Many research proposals state goals that are so vague they could never be reached. Thus, it is essential to formulate goals precisely and to be able to explain why they are worthwhile. If you do succeed, it is reasonable to ask what contributions will have been made to scientific knowledge or to practice. It is also essential to have some idea of what methods you will attempt to solve your proposed problem. You must plan something concrete. However, because research in unpredictable, it is also useful to think about alternative approaches to solving the problem of proving the hypothesis.

Your proposal will be evaluated by experienced researchers. They understand the difficulty of proposal writing and conducting research. They do not expect to glean every last detail of what you want to do by reading the proposal. However, they can tell a lot about you, and the way you think, from your writing. They expect you to have thought pretty hard about your ideas, and to have worked conscientiously to explain and present them as clearly and straightforwardly as possible. It is up to you to provide evidence for a positive decision.

Revised February 2003

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• 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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Thesis Proposal - BIO 6930

The thesis proposal is a public oral presentation and discussion of a proposed research plan for the master’s thesis. BIO 6930 is required for advancement to candidacy and is a prerequisite for BIO 6940 (Thesis Research in the Biological Sciences). Enroll in BIO 6930 during the semester the proposal presentation will be given. BIO 6930 and 6940 may be taken concurrently.

Purpose of the thesis proposal

To help you plan and avoid problems in your research. It is an opportunity for you discuss what you want to do and get feedback from your thesis committee as well as others on your plan. The purpose is to help you do a better job on your research and thesis. The thesis proposal should be completed in the second semester and no later than the third semester. Students who remain on schedule will receive priority for graduate funds and TA positions.

Timing of the thesis proposal

As soon as you have an idea for your thesis topic. In some cases, you and your major professor may have a project in mind as you’re admitted to the program, in which case you should do the proposal immediately. In other cases, you and your major professor may need to discuss potential projects, so the 6930 would not be done until a topic has been decided upon.

The thesis proposal should be completed in the second semester and no later than the third semester. Students who remain on schedule will receive priority for graduate funds and TA positions.

It is very important not to wait too long to have the thesis proposal. If there are problems or concerns with your research, you need to find out about those as soon as possible. It is much better to have problems identified early, while there is a chance to correct them. You don’t want the problems to be identified at your thesis defense! If you put off your proposal until you are well into your thesis project and your committee requests changes to your research plan, this will lead to substantial delays in completing your research and likely delay your graduation.

What to expect during the proposal

• First, you will start with a public presentation. The presentation should include:
• the relevant scientific background
• the hypotheses to be tested (objectives of your project)
• the procedures to be used for testing your hypotheses (including a timetable for completion and an estimation of required resources)
• the possible outcomes/preliminary data
• Check with your major professor on the expectations for the presentation.
• Make sure to practice your presentation, preferably for people who can give you feedback.
• Following the presentation, there is an opportunity for questions/comments from the general audience. That is followed by a meeting with just you and your committee to discuss the project.
• The committee will ask you more questions about your proposed research. They may also ask you general biology content questions related to your research area. It is best to meet with each committee member before the proposal to know what to expect.
• Your committee might ask you a question you do not know how to answer. This may very well happen – but that’s okay. The proposal is NOT a test – it’s a proposal! If you don’t know some answers it will guide you to what you need to study and learn before your thesis defense. It is okay to not know some answers at your proposal – it’s NOT okay to not know answers at your defense.
• After the proposal the student and all committee members should fill out the appropriate electronic assessment form:

Student form proposal

Faculty form proposal

The online forms are preferred, but a pdf form can be requested from the Graduate Coordinator if needed.

• Your major professor will give you a grade in BIO 6930. The grading is credit/no credit, so it won’t affect your GPA. Your major professor will assign a letter grade, but it will be converted to credit/no credit. The grade of “C” or better is passing.
• Students are responsible for scheduling the proposal. Work with your major professor and thesis committee to find a time when all of you can attend.
• Students should reserve a room for the proposal. Some rooms can be scheduled in the Bio Department office. Conference rooms in Building 4 as well as classrooms are scheduled by the Dean’s office. Make sure the room you schedule has the equipment you need to give your proposal.

Publicizing the proposal

Students are responsible for publicizing their proposal. At least one week prior to the thesis proposal presentation, you must (a) post notices in public places (including the Graduate Program Bulletin Board located outside of the Department mail room) and (b) have your announcement distributed to all Department personnel via email as listed below: Send an email to the Graduate Coordinator including all of the following:

• The subject of the email should be stated as: Thesis Proposal Announcement - Student Name
• The body of the email should include the following: 

Thesis Proposal Announcement

Thesis Title by Student Name

Date, Time, Location Thesis Committee Members: Professor 1 (Committee Chair) Professor 2 Professor 3 Your Thesis Proposal Abstract must be attached to the email as a pdf.

Additional information

• Make sure that you and all committee members fill in the electronic assessment forms after the proposal:
• The thesis proposal should be completed in the second semester and no later than the third semester. Students who remain on schedule will receive priority for graduate funds (when available) and TA positions.

School of Continuing & Professional Studies

MA in Biology Final Project

A master’s thesis in biology is a form of independent study. The purpose of a master’s thesis is to provide a capstone or final project in which the student can use the knowledge and methodology obtained in previous courses for the investigation of some problem in depth. Master’s theses involve six units of independent study, generally taken in two consecutive semesters (i.e. fall/spring), during the first of which the student carries out their research, and during the second of which he or she will write up the project. A thesis can become a meaningful way to bring to a conclusion a student’s work for the Master’s degree.

In general, all the procedures outlined for Independent Study apply to setting up and carrying out a thesis investigation. Like Independent Study, most master’s theses are based on a literature survey, rather than a laboratory investigation. For many students, the problems of setting up and carrying out a successful laboratory project often make this approach impractical. Laboratory-based thesis projects are possible, however, under certain circumstances, as outlined below.

Organization and Scope of a Thesis Project

To carry out a thesis project the student must secure an advisor with whom to work, define the project and fill out the necessary forms to be signed by the advisor, student and  School of Continuing & Professional Studies (CAPS) Program Coordinator. Advisors (mentors) can come from any part of the university or, with approval, from an outside institution or organization. The Biology program coordinator will assist the student in selecting an advisor. The advisor works closely with the student at all stages of the project. A thesis project is expected to encompass a larger range of issues or a more in-depth investigation than an individual independent study. Theses can be anywhere from 40-50 pages minimum, depending on the topic and type of thesis.

Laboratory-Based Thesis Projects

The problem with laboratory-based thesis projects lies in the practicality of getting set up in a new laboratory and learning techniques and methods used in studying that lab’s particular area of research. In most cases, laboratory projects work best when carried out in a laboratory where the student is already working. In most cases, this has involved students who work in a laboratory at one of the local medical schools, or biotechnology laboratories. The student’s PI, supervisor, or a Post-Doc in the lab with appropriate credentials, can serve as the mentor. If a student carries out a M.A. project in their workplace laboratory, the topic must be something they are independently investigating, and cannot be part of their regular paid job assignment.

Thesis Evaluations

When completed, an M.A. thesis will be evaluated by a committee consisting of the mentor, the Biology Department program coordinator, and one other faculty member from the Biology Department or Division of Biology and Biomedical Sciences who is a specialist in the area on which the thesis focuses. The program coordinator will assist the student in selecting the additional faculty member.

Procedures and Timeline

It is important to adhere closely to requirements and deadlines associated with the final project in order to ensure timely completion of the project and fulfillment of program requirements. Please read carefully below for detailed information about procedures, requirements, forms, and deadlines. All students authorized to pursue the Master’s Thesis must complete the  Title, Scope, and Procedure form . See below for detailed information about procedures and deadlines.

If you have authorization to pursue a Thesis, begin planning two semesters prior to your final semester of study. The  Title, Scope and Procedure form  must be completed and returned to CAPS at least six months before the month in which the degree is expected to be conferred (August, December, or May). CAPS will forward approved Title, Scope & Procedure forms to the Graduate School of Arts & Sciences.

Registration

The  Final Project form  must be completed with all required signatures for registration. Registration follows the normal academic schedule. Refer to the current course schedule for registration deadlines. Submit your Final Project Proposal Form  here . This will serve as your registration form.

Schedule Your Oral Defense

The Oral Defense should be scheduled as soon as possible after you have registered. The Oral Defense should take place no later than two weeks prior to the end of the semester you plan to graduate. Consult with your committee to find a time that is agreeable. Your Oral Defense will probably only last 1 hour, but schedule 1.5 hours for the defense to provide a small cushion of extra time if needed. To schedule and reserve space, contact your  academic advisor .

Usually, the defense must be completed by the beginning of September for summer graduates, the beginning of January for fall graduates, and late April or early May for spring graduates. Please note that these dates conform to deadlines for all graduate programs and are not flexible.

Submission of the Master’s Thesis

Submit a copy of your thesis to each member of your committee two weeks in advance of your oral defense to allow time for review. Upon successful defense of the project, the final version must be submitted to CAPS. In addition, thesis candidates must submit an electronic copy and one hard copy for the Master’s Thesis to the Graduate School of Arts & Sciences according to the deadlines listing in the online calendar.

Please refer to the  Graduate School Arts & Sciences Master’s Thesis guidelines  for formatting and presentation requirements.

Independent Study Guidelines

Students enrolled in the MA Program in Biology may receive up to six (6) credits of advanced work toward their degree. Independent study involves work carried with a mentor on a designated project which is approved in advance of the semester in which the work is done. Independent study may be arranged for 1, 2 or 3 credits per semester, up to the total of six. Most independent study projects involve writing a paper describing the student’s work/project at the end of the semester.

Topics may focus on any aspect of biology deemed appropriate by the mentor and the Program Coordinator from the Biology Department. Most independent study projects involve literature search and review, though some hands-on laboratory projects are possible (see above for discussion of the M.A. Thesis). The student would work with his or her mentor to find appropriate journal or other literature on the subject, and then pursue a question or controversy within that literature. Students are expected to come up with their own ideas as a result of reading through the literature, and not merely to present a summary of material they have read.

Choosing A Mentor

Mentors are usually instructors from whom the student has already taken a course, though other non-university or non-CAPS personnel may serve as mentors under special circumstances. Mentors should be individuals with a PhD in their field; if they are not already Washington University faculty or CAPS instructors, they would have to present a C.V. to the Program Coordinator for consideration. Mentors are compensated for their time in guiding independent study projects. It is the student’s responsibility to seek out a mentor and discuss with him/her the possibility of carrying out an independent study project. The mentor has the responsibility not only of helping the student set up the project but also to meet with the student periodically during the semester, and to read and evaluate the student’s paper at the completion of the work.

Credit assignment is based on the extent of the project, which usually translates into a final paper of a certain length. Although there are no hard-and-fast rules on paper length, the following guidelines are helpful in establishing the credit for independent study: 1 credit (5-7 pages); 2 credits (8-12 pages), and 3 credits (15+) pages.

Application

Students wishing to carry out an independent study project should obtain the appropriate form from the CAPS office. It must be signed by the student, the mentor, and the Program Coordinator.

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• How to Write a Research Proposal | Examples & Templates

How to Write a Research Proposal | Examples & Templates

Published on October 12, 2022 by Shona McCombes and Tegan George. Revised on November 21, 2023.

A research proposal describes what you will investigate, why it’s important, and how you will conduct your research.

The format of a research proposal varies between fields, but most proposals will contain at least these elements:

Introduction

Literature review.

• Research design

Reference list

While the sections may vary, the overall objective is always the same. A research proposal serves as a blueprint and guide for your research plan, helping you get organized and feel confident in the path forward you choose to take.

Table of contents

Research proposal purpose, research proposal examples, research design and methods, contribution to knowledge, research schedule, other interesting articles, frequently asked questions about research proposals.

Academics often have to write research proposals to get funding for their projects. As a student, you might have to write a research proposal as part of a grad school application , or prior to starting your thesis or dissertation .

In addition to helping you figure out what your research can look like, a proposal can also serve to demonstrate why your project is worth pursuing to a funder, educational institution, or supervisor.

Research proposal length

The length of a research proposal can vary quite a bit. A bachelor’s or master’s thesis proposal can be just a few pages, while proposals for PhD dissertations or research funding are usually much longer and more detailed. Your supervisor can help you determine the best length for your work.

One trick to get started is to think of your proposal’s structure as a shorter version of your thesis or dissertation , only without the results , conclusion and discussion sections.

Download our research proposal template

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See an example

Writing a research proposal can be quite challenging, but a good starting point could be to look at some examples. We’ve included a few for you below.

• Example research proposal #1: “A Conceptual Framework for Scheduling Constraint Management”
• Example research proposal #2: “Medical Students as Mediators of Change in Tobacco Use”

Like your dissertation or thesis, the proposal will usually have a title page that includes:

• The proposed title of your project
• Your supervisor’s name
• Your institution and department

The first part of your proposal is the initial pitch for your project. Make sure it succinctly explains what you want to do and why.

Your introduction should:

• Introduce your topic
• Give necessary background and context
• Outline your  problem statement  and research questions

To guide your introduction , include information about:

• Who could have an interest in the topic (e.g., scientists, policymakers)
• How much is already known about the topic
• What is missing from this current knowledge
• What new insights your research will contribute
• Why you believe this research is worth doing

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As you get started, it’s important to demonstrate that you’re familiar with the most important research on your topic. A strong literature review  shows your reader that your project has a solid foundation in existing knowledge or theory. It also shows that you’re not simply repeating what other people have already done or said, but rather using existing research as a jumping-off point for your own.

In this section, share exactly how your project will contribute to ongoing conversations in the field by:

• Comparing and contrasting the main theories, methods, and debates
• Examining the strengths and weaknesses of different approaches
• Explaining how will you build on, challenge, or synthesize prior scholarship

Following the literature review, restate your main  objectives . This brings the focus back to your own project. Next, your research design or methodology section will describe your overall approach, and the practical steps you will take to answer your research questions.

To finish your proposal on a strong note, explore the potential implications of your research for your field. Emphasize again what you aim to contribute and why it matters.

For example, your results might have implications for:

• Improving best practices
• Informing policymaking decisions
• Strengthening a theory or model
• Challenging popular or scientific beliefs
• Creating a basis for future research

Last but not least, your research proposal must include correct citations for every source you have used, compiled in a reference list . To create citations quickly and easily, you can use our free APA citation generator .

Some institutions or funders require a detailed timeline of the project, asking you to forecast what you will do at each stage and how long it may take. While not always required, be sure to check the requirements of your project.

Here’s an example schedule to help you get started. You can also download a template at the button below.

Download our research schedule template

If you are applying for research funding, chances are you will have to include a detailed budget. This shows your estimates of how much each part of your project will cost.

Make sure to check what type of costs the funding body will agree to cover. For each item, include:

• Cost : exactly how much money do you need?
• Justification : why is this cost necessary to complete the research?
• Source : how did you calculate the amount?

To determine your budget, think about:

• Travel costs : do you need to go somewhere to collect your data? How will you get there, and how much time will you need? What will you do there (e.g., interviews, archival research)?
• Materials : do you need access to any tools or technologies?
• Help : do you need to hire any research assistants for the project? What will they do, and how much will you pay them?

If you want to know more about the research process , methodology , research bias , or statistics , make sure to check out some of our other articles with explanations and examples.

Methodology

• Sampling methods
• Simple random sampling
• Stratified sampling
• Cluster sampling
• Likert scales
• Reproducibility

 Statistics

• Null hypothesis
• Statistical power
• Probability distribution
• Effect size
• Poisson distribution

Research bias

• Optimism bias
• Cognitive bias
• Implicit bias
• Hawthorne effect
• Anchoring bias
• Explicit bias

Once you’ve decided on your research objectives , you need to explain them in your paper, at the end of your problem statement .

Keep your research objectives clear and concise, and use appropriate verbs to accurately convey the work that you will carry out for each one.

I will compare …

A research aim is a broad statement indicating the general purpose of your research project. It should appear in your introduction at the end of your problem statement , before your research objectives.

Research objectives are more specific than your research aim. They indicate the specific ways you’ll address the overarching aim.

A PhD, which is short for philosophiae doctor (doctor of philosophy in Latin), is the highest university degree that can be obtained. In a PhD, students spend 3–5 years writing a dissertation , which aims to make a significant, original contribution to current knowledge.

A PhD is intended to prepare students for a career as a researcher, whether that be in academia, the public sector, or the private sector.

A master’s is a 1- or 2-year graduate degree that can prepare you for a variety of careers.

All master’s involve graduate-level coursework. Some are research-intensive and intend to prepare students for further study in a PhD; these usually require their students to write a master’s thesis . Others focus on professional training for a specific career.

Critical thinking refers to the ability to evaluate information and to be aware of biases or assumptions, including your own.

Like information literacy , it involves evaluating arguments, identifying and solving problems in an objective and systematic way, and clearly communicating your ideas.

The best way to remember the difference between a research plan and a research proposal is that they have fundamentally different audiences. A research plan helps you, the researcher, organize your thoughts. On the other hand, a dissertation proposal or research proposal aims to convince others (e.g., a supervisor, a funding body, or a dissertation committee) that your research topic is relevant and worthy of being conducted.

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Excellent opening paragraph stating why is the research important and leading to the research goals

Clear and concise presentation of research aims \(questions\)

Research plan is well \ detailed starting from third paragraph.

Pronoun problem: who is the "w\ e"? Earlier, "I" is very clear, but this "we" lacks a clear antecedent.

Writing tip: good use of "signa\ l" words \("first," "second"\) to organize information and highlight key points.

Contributors: P. Pazos, Searle Center for Teaching Excellence and P. Hirsch, The Writing Program, [email protected]

Posted: 2008

TITLE: The Mitochondrial Stress Response and the Communication of Stress Responses Between Subcellular Compart\ ments

Compelling presentation of preparation from courses and prior lab experience.

Very detailed presentation of techni\ ques learned that are relevant to the project

Writing tip: "data" is a p\ lural word. Say, "The data suggest. . . " and "they [meaning the data] indicate."

Overall comments:

Good quality proposal overall. The author clearly explains the aims a\ nd methods to carry out those aims.

Research question: Analysis of mitochondria's unfolding protein response and its crosstalk with other folding envir\ onments in the cell.

Compelling presentation of prior experience in courses and labs. Could include specific techniques learned.

Good use of citations and references

Suggestions:

Should add headings to make it more readable and add some structure.

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Biology Major

University of wisconsin madison, the biology major provides broad knowledge of biology and the scientific process. it is a great choice for students interested in careers in any biological science or health profession..

• Thesis Proposal Guidelines

A senior thesis or senior honors thesis proposal should be two to five double-spaced pages with 1 inch margins and 11-12pt font. The abstract and references are included in the 5-page limit and the proposal should follow disciplinary guidelines and use headers appropriate to the field. If you are uncertain about how to format your proposal, talk to your thesis advisor. All proposals should contain the following:

• An abstract of the proposed research (200 words or less, may be single-spaced)
• Introduction and literature review, detailing the originality and significance of the proposed project
• Methods section, describing plans for data collection and analysis
• Timeline for completion of project
• Conclusion/future directions
• References (may be single-spaced)

These guidelines are adapted from the Hilldale/Holstrom Application with permission from the Office of Undergraduate Academic Awards .

Students should register for Biology 681-682: Senior Honors Thesis or Biology 691-692: Senior Thesis when a thesis will be completed in a biological science department that does not have its own thesis courses. Go to Biology Major Resources for the Course Authorization Form.

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Thesis Proposal

Thesis proposals.

Graduate students begin the thesis process by writing a thesis proposal that describes the central elements of the thesis work.  Those elements vary depending on the type of thesis (research, artistic, or project) that the student plans to write. Students begin drafting the thesis proposal in the course Thesis Proposal Seminar . 

Below, please find detailed information about the following:

• research thesis proposal
• artistic thesis proposal
• project thesis proposal
• formatting your proposal  
• getting your proposal approved  
• submit your proposal  

Research Thesis Proposal

The proposal for a research thesis consists of five sections:

• Thesis Statement Following an optional introduction, the basic function of this section is to articulate a phenomenon that the student proposes to investigate (whether a social event, process, a literary work, an intellectual idea or something else), and the question(s), issue(s) or problem(s) related to that phenomenon that the student plans to address in the thesis. The core of the statement may take the form of a hypothesis that the student will test, of a proposition or argument that the student intends to support, or of a general problem or question the student  will explore. The section puts that basic problem statement in a larger context by explaining its historical origins (where did it come from?) and its intellectual, social, and/or artistic context (what conversation, debate, or line of inquiry does it participate in?). It also describes the sub-questions or themes that constitute the general problem. Students will cite appropriate scholarly, professional and other sources for the ideas, questions and background information contained in the section.
• Research Methods In this section, the student will identify (a) the kinds of information that needed to answer the question(s) raised in the Thesis Statement, (b) the methods the student will use to gather that information, and (c) the strategies by which the student will organize and analyze the information in such a way as to reach and support a conclusion, to construct a sound argument. If the central problem has several facets, the student may need an array of different methods for collecting and analyzing information. Students should be as precise as possible in each stage of the methods statement: Is information needed about the stylistic techniques in a novel, about changes in the poverty rates in Kenya since independence, about the ways children think about nature? Will the student pull out the metaphors in a text, find government reports on household income, interview kids about their experiences in the woods? Will the student deploy statistical forms of content analysis, correlate poverty rates with political changes, interpret themes in children’s stories? Students should reflect on the broad methodological approaches that they propose to use, and cite sources from which they derive their methods and tools. A student's central goal is to demonstrate that they know how to go about answering the question(s) that have been raised. Please note that if students intend to conduct research on living people, they will need to get the approval of the University Committee on Activities Involving Human Subjects (UCAIHS). Before they apply for that approval, students will need to take a tutorial and pass a test on the various regulations. Refer to the  UCAIHS website  for more information.
• Justification and Limitations This section of the proposal should explain the rationale for the thesis and the importance of the topic. Indicate the reasons why this study is important to conduct and whom it will benefit. Identify the limits beyond which the inquiry will not go. For instance, if a student is writing about a historical subject, the student must explain the relevance of the time period selected. Finally, describe the contribution the work will make to the field.
• Conclusion This section should summarize the nature and intention of the student's work. Conclude the discussion and mention any pertinent information which may not have been included above.
• Annotated Bibliography This section consists of a list of books and articles and artworks with accompanying annotations that explain why these readings and other sources are likely to be crucial as the work advances.

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Artistic Thesis Proposal

The artistic thesis consists of an artistic work and supporting essays, and it is important to conceive of each element as contributing to a coherent whole.  The proposal itself consists of five sections:

• Concept Statement This section includes a brief introduction that forms the framework for the entire thesis and articulates the questions around which the creative project and supporting essays revolve.
• Description of the Artistic Work and Artistic Aims This section describes the major artistic work that will comprise the submitted artistic thesis.  Students may want to refer to particular artistic influences or genres that will inform the work, or describe the aesthetic from which the creative work derives. In this section, students should also: refer to some of the artistic reasons that led to their decision to embark on this particular project; discuss the goals that will guide the development of the work; and provide concrete details about the final form and media of the work  (will it be, for example, a collection of short stories, a novel; an evening of dance an exhibition of paintings, a film, or what?).  If the artwork involves live performance, this section should state whether it will be a public or private event, where the event will be held, and any other details relevant to bringing the project to completion.

This section should provide the reader with relevant historical or critical information to place the central research question in context, and this section should also discuss the key theories, methods, and sources to be used within the research essay.  It should demonstrate that the student knows how to begin answering the question(s) they are posing.  What sorts of things will the student need to find out? What research methods will be used?  What kinds of sources will be reviewed, and how will information from them be used? Who, if anyone, will be interviewed, and what kinds of questions will the subjects be asked?  Students should also reflect, in this section, on the broad analytical approach that will structure their research and identify the school(s) of thought that will inform their investigations. 

• Justification and Limitations This section should explain the importance of the student's work in the context of their particular artistic discipline and discuss how all components of the thesis project taken together as a single project will contribute to the scholarly and artistic fields with which it engages. This section should also discuss limitations, personal and practical, relating to the project and the student’s readiness.  If the project is a film, for example, how much direct experience has the student already had in that field, and how will the student allocate the time to finish the project by the desired defense date? How much is the project likely to cost, and how does the student expect to obtain funding?  What kind of spaces will be needed for rehearsal as well as presentation of the work? 

Project Thesis Proposal

The project thesis includes two major components: (a) an activity (program, intervention, campaign, etc.) designed to address (solve, remediate, improve) a problem, issue or opportunity in the student's domain as a professional or activist; and (b) a written document that describes, rationalizes, analyzes, and assesses the activity. It is not strictly a research study, but rather an exercise in reflective practice. Therefore, the proposal takes a form different from that of the research or artistic thesis proposal. Please note, as well, that a project thesis  must  be not only designed but implemented and evaluated.

• Problem Statement This section of the proposal identifies, describes, and analyzes the problem (issue, need, opportunity) that the student will address in the project. Clearly articulate the nature of the problem: its historical, social and professional context; its dimensions and extent; its impact, and perhaps some previous efforts to address it. Present information that explains the student's understanding of the origins or causes of the problem, to set up the rationale for the choice of a strategy to solve it. At each stage, refer to appropriate scholarly and professional literatures.
• Project Plan Students should spell out their plans for addressing the problem. Students should describe the institutional setting within which the project will take place, as well as the individuals, groups, or organizations with whom they will work. What will the student (and, perhaps, others) do? What resources and strategies will be used? If the student need funds, how will they be raised and disbursed? What schedule will be followed? Be efficient, but concrete and clear in specifying the activities that will make up the project. Identify the professional and theoretical sources of the strategies for the project: What precedents and ideas are the student drawing on? Also, the student should discuss the means by which they will record and report the project activities for the members of the thesis committee. Will the student write a journal, shoot videos, keep material artifacts and documents? Students must be clear about how they intend to document the project. They may also elect to invite the members of their committee to witness the project first-hand.
• Assessment The proposal speaks to three aspects of the assessment process. In all three, students should be concrete and refer to appropriate literatures as sources of their plans. Criteria : First, students should describe and justify the criteria by which they will determine whether the project has succeeded. What are the goals and objectives? What changes does the student want to see in the participants, the organization, the larger world? Methods:  What information will be needed to determine whether the goals and objectives have been met? How will that information be collected and organized? Analysis : How will that information be utilized to describe the project’s success or failure? What sorts of lessons does the student hope to draw from the assessment?
• Justification and Limitations This section of the proposal should explain the rationale for the thesis and the importance of the topic. Indicate the reasons why this study is important to conduct and whom it will benefit. Identify the limits beyond which the inquiry will not go. Finally, describe the contribution the work will make to the field.
• Conclusion This section should summarize the nature and intention of the work. Conclude the discussion and mention any pertinent information which may not have been included above.

Format of the Proposal

All thesis proposals should conform to the following specifications:

• Title Page The title should be reasonably succinct, but descriptive enough to convey the nature of the thesis; the title page should include your full name, the date of submission, and your adviser’s name.
• Length The thesis proposal should be approximately 8 pages, excluding the annotated bibliography. Remember that this is a proposal, not the thesis itself; tell us what you propose to do and how, don’t do it.
• Annotated Bibliography This bibliography should contain brief commentaries on no fewer than 10–15 relevant source works.

The Approval Process for the Thesis Proposal

The Thesis Proposal Seminar (TPS) Students write their thesis proposals while enrolled in the Thesis Proposal Seminar (CORE-GG 2401, a 2-credit core requirement offered every spring). Throughout that semester, students work closely with their Adviser and Instructor to draft an acceptable proposal. When the proposal has received approval from both the Thesis Proposal Seminar instructor (Gallatin reviewer) and the adviser, the student is allowed to move on to their thesis research. The three steps of the approval process are outlined below.

• TPS Instructor/Reviewer Approval The Thesis Proposal Seminar instructor serves as the Gallatin reviewer of the thesis proposal. A student must receive a grade of ‘Pass’ in the Thesis Proposal Seminar for the proposal to be considered ‘reviewer approved.’ If the student’s proposal is not finished at the end of the semester, the student will receive a grade of 'Incomplete' in the course and will have until June 15th to submit the proposal before moving on to thesis research.
• Adviser Approval Students work closely with their advisers over the course of the semester to produce a proposal that the adviser can approve. Once the adviser agrees that the proposal is ready, students submit their final proposal via the online Thesis Proposal submission form . The Thesis Proposal submission form allows students to provide Gallatin with additional information about the courses, internships, independent studies, jobs, and other experiences that have prepared the student for their thesis work.
• MA Program Approval Once the M.A. Program verifies adviser approval of the proposal and the student has passed the TPS, the MA Program updates the student record to show that the Thesis Proposal requirement has been satisfied.

The deadline for submitting an adviser approved thesis proposal online is June 15.