Research

Eligibility Requirements:

A BMB GPA of 3.0 or higher is required to apply for Undergraduate Research in BMB. If you do not have a BMB GPA of 3.0 or higher, contact Anne Hildebrand to discuss an alternative arrangement.

Courses & Credits:

Freshman BB 140/141  (2 credits)

Sophomore BB 240/241  (2 credits)

Junior BB 340/341  (2 credits), BB 350/351/352 (4 credits)

Senior BB 450/451/452/453  (4 credits)

Note: Senior-level research (including Honors) can be used to satisfy the advanced lab elective if both semesters of research are taken. Alternatively, students can use one semester of four-credit research to fulfill a BMB elective if not using Undergraduate Research or Honors Research for their advanced lab elective.

Hours:

During the fall and spring semesters, students are expected to conduct research for 3-4 hours/week per credit. During the summer 1 and summer 2 sessions, students are expected to work 6-8 hours/week per credit. This time can include other research-related work like attending lab meetings.

Steps:

1. Determine which BMB faculty members (or outside researchers) are conducting research in the field of study you are interested in. Then contact the individual(s) directly to determine if they have openings in their lab.

2. Alternatively, you can ask the Teaching Fellows in your courses if there are openings in the labs they work in or if they know of anyone looking for undergrad help.

3. Once you have a research mentor, you may then apply for Undergraduate Research.

Please note: If you are conducting research outside the BMB Program, you will also need to ask a BMB faculty member to sponsor you (i.e., they will act as a liaison between the BMB Program and the outside researcher). Your BMB sponsor is usually your faculty advisor but could also be another faculty member with whom you have a good relationship and who is familiar with the field of research in which you will be engaged. Both your PI and the BMB faculty sponsor must approve your application.

Deadline:

Applications are due by the date listed at the top of the Undergraduate Research application. Students must be participating in research during the semester(s) of application and thus cannot apply for Undergraduate Research for previously conducted research.

Application:

Undergraduate Research application

Eligibility Requirements:

An overall and BMB GPA of 3.5 or higher is required to apply for Honors Research in BMB. Your BMB GPA is the sum total of all BB/BI/CH/PY/MA courses. Applicants must also have senior standing (at least 96 credits earned).

Program Requirements:

• Research BB 401 & 402 (total of 8 credits)**
• Seminar BB 497 & 498 (total of 2 credits)
• Completion and defense of written senior thesis
• Oral presentation of research at BMB Symposium

** Note: Senior-level research (including Honors) can be used to satisfy the advanced lab elective if both semesters of research are taken. Alternatively, students can use one semester of four-credit research to fulfill a BMB elective if not using Undergraduate Research or Honors Research for their advanced lab elective.

Hours:

Students are expected to conduct research for a minimum of 16 hours per week. The 16 hours can include preparation, evaluation, or group meetings.

Deadline:

Applications are due by the date listed at the top of the Undergraduate Research application.

Application Instructions:

Submit the online application form, noting that you have senior standing and that you’re applying for Honors Research (BB 401 and 402). The form will prompt you to include your unofficial transcript, and your Honors research proposal.

Guidelines and expectations for students and mentors are included in syllabi for each research course below. Please note that beyond the time commitment, there are no additional requirements for 100 and 200-level (first year and sophomore) research courses.

• Guidelines/Expectations for BB 340: Junior Research in BMB 1 (2 credits)
• Guidelines/Expectations for BB 341: Junior Research in BMB 2 (2 credits)
• Guidelines/Expectations for BB 350/450: Junior/Senior Research in BMB 1 (4 credits)
• Guidelines/Expectations for BB 351/451: Junior/Senior Research in BMB 2 (4 credits)
• Guidelines/Expectations for BB 352/452: Junior/Senior Research in BMB 3
• Guidelines/Expectations for BB 453: Senior Research in BMB 4
• Guidelines/Expectations for BB 401/402: Honors Research in BMB

The Undergraduate Research Opportunities Program (UROP) is a University-wide program that helps connect students with research opportunities and provides funding for both research expenses and student stipends. In addition to funding during the academic year, UROP provides funding for full-time, paid research opportunities during the summer.

For program details and application, visit the UROP website.

 (undergraduates or recent alums listed in bold)

Acharya Y, Bhattacharyya S, Dhanda G, Haldar J. 2022 Emerging Roles of Glycopeptide Antibiotics: Moving beyond Gram-Positive Bacteria. ACS Infect. Dis. 2022, 8 (1), 1–28. https://doi.org/10.1021/acsinfecdis.1c00367.

Blackburn PR, Xu Z, Tumelty KE, Zhao RW, Monis WJ, Harris KG, Gass JM, Cousin MA, Boczek NJ, Mitkov MV, Cappel MA, Francomano CA, Parisi JE, Klee EW, Faqeih E, Alkuraya FS, Layne MD, McDonnell NB, Atwal PS (2018). Bi-allelic Alterations in AEBP1 Lead to Defective Collagen Assembly and Connective Tissue Structure Resulting in a Variant of Ehlers-Danlos Syndrome. American Journal of Human Genetics 102(4):696-705.

Bogursky A. (2021) It’s time to combat stubborn insurance companies. Bariatric patients deserve to live. HPHR. 2021; 28.

Bray D, Hook H, Zhao RW, Keenan JL, Penvose A, Osayame Y, Mohaghegh N, Chen X, Parameswaran S, Kottyan LC, Weirauch MT, Siggers T. (2022) CASCADE: High-throughput characterization of regulatory complex binding altered by non-coding variants. Cell Genomics 2:100098

Chandler, K. B, Alamoud, K. A, Stahl, V. L, Nguyen, B, Kartha, V. K, Bais, M. V, Costello, C. E. (2020). β-Catenin/CBP inhibition alters epidermal growth factor receptor fucosylation status in oral squamous cell carcinoma. Molecular Omics, 16(3), 195-209.

Chi B, O’Connell JD, Iocolano AD, Coady JA, Yu Y, Gangopadhyay J, Gygi SP and Reed R (2018) The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex. Nucleic Acids Res.46(22):11939-11951. 

Emont MP, Jacobs C, Essene AL, et al. A single-cell atlas of human and mouse white adipose tissue. Nature. 2020;603:926–933. doi:10.1038/s41586-022-04518-2

Feng, F, Ataca, S. T, Ran, M, Wang, Y, Breen, M, & Kepler, T. B. (2020). Gain-Scanning for Protein Microarray Assays. Journal of Proteome Research, 19(7), 2664-2675.

Fleischman NM, Vo AT, Camire EJ, Cosman JA, Gay KA, Esonwune SU, Grossman JD., Marquez, MD, Perlstein DL (2017) Defining the domains of Cia2 required for its essential function in vivo and in vitro. Metallomics 9, 1645–1654.

Frame, N, Kumanan, M, Wales, T, Bandara, A, Fändrich, M, Straub, J,  Gursky, O. (2020, February 06). Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A.

Garcia-Beltran WF, Miller TE, Kirkpatrick G, Nixon A, Astudillo MG, Yang D, Mahanta LM, Murali M, Dighe AS, Lennerz J, Thierauf J, Naranbhai V, Iafrate AJ. (2021) Remote Fingerstick Blood Collection for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Testing. Arch Pathol Lab Med. 2021 Apr 1;145(4):415-418.

George I. Getz, Kshitij Parag-Sharma, Jonathan Reside, Ricardo J. Padilla, Antonio L. Amelio, (2019) Identification of NSDHL mutations associated with CHILD syndrome in oral verruciform xanthoma, Oral Surgery Oral Medicine Oral Pathology Oral Radiology.

Gupta A, Condakes ML. (2021). Thermodynamic Understanding of an Aza-Michael Reaction Enables Five-Step Synthesis of the Potent Integrin Inhibitor MK-0429. The Journal of Organic Chemistry.

Hamadani CM, Goetz MJ, Mitragotri S, Tanner EEL. (2020, November 25). Protein-avoidant ionic liquid (PAIL)–coated nanoparticles to increase bloodstream circulation and drive biodistribution. ScienceAdvances, 6(48).

Hawkins DY, Zuch DT, Huth J, Rodriguez-Sastre N, McCutcheon KR, Glick A, Lion AT, Johnson WE, Bradham CA. (2022) ICAT: A Novel Algorithm to Robustly Identify Cell States Following Perturbations in Single Cell Transcriptomes. bioRxiv. January 2022:2022.05.26.493603. doi:10.1101/2022.05.26.493603

Heyward FD, Liu N, Jacobs C, et al. Integrated genomic analysis of AgRP neurons reveals that IRF3 regulates leptin’s hunger-suppressing effects. Nature Neuroscience. doi:10.1101/2022.01.03.474708

Hook H, Zhao RW, Bray D, Keenan JL, Siggers T (2021) High-Throughput Analysis of the Cell and DNA Site-Specific Binding of Native NF-kB Dimers using Nuclear Extract Protein-Binding Microarrays (NextPBMs). Methods Mol. Biol. 2366:43-66 

Johnson C, Kretsge LN, Yen WW, Sriram B, O’Connor A, Liu RS, Jimenez JC, Phadke RA, Wingfield KK, Yeung C, Jinadasa TJ, Nguyen TPH, Cho ES, Fuchs E, Spevack ED, Velasco BE, Hausmann FS, Fournier LA, Brack A, Melzer S, Cruz-Martín A. (2022) Highly unstable heterogeneous representations in VIP interneurons of the anterior cingulate cortex. Molecular Psychiatry. 27: 2602-2618. 4 Mar. 2022.

Jumelle C, Sani ES, Taketani Y, Yung A, Gantin F, Chauhan SK, Annabi N, and Dana R. 2021. “Growth Factor-Eluting Hydrogels for Management of Corneal Defects.” Materials Science & Engineering. C, Materials for Biological Applications 120. doi: 10.1016/J.MSEC.2020.111790

Jumelle C, Yung A, Sani ES, Taketani Y, Gantin F, Bourel L, Wang S, Yüksel E, Seneca S, Annabi N, and Dana R. 2021. Development and characterization of a hydrogel-based adhesive patch for sealing open-globe injuries. Acta Biomaterialia. https://doi.org/10.1016/J.ACTBIO.2021.10.021

Katsuyama E, Suarez-Fueyo A, Bradley S, Mizui M, Marin A, Mulki L, Krishfield S, . . . Tsokos, G. (2020, January 7). The CD38/NAD/SIRTUIN1/EZH2 Axis Mitigates Cytotoxic CD8 T Cell Function and Identifies Patients with SLE Prone to Infections.

Katsuyama T, Martin-Delgado I, Krishfield S, Kyttaris V, & Moulton V. (2020, August 1). Splicing factor SRSF1 controls T cell homeostasis and its decreased levels are linked to lymphopenia in systemic lupus erythematosus.

Kshitij Parag-Sharma, Colin P. O’Banion, Erin C. Henry, Adele M. Musicant, John L. Cleveland, David S. Lawrence, Antonio L. Amelio.(2020) Engineered BRET-Based Biologic Light Sources Enable Spatiotemporal Control over Diverse Optogenetic Systems, ACS Synthetic Biology.

Maziarz, M., Federico, A., Zhao, J., Dujmusic, L., Zhao, Z., Monti, S., Varelas, X., & Garcia-Marcos, M. (2020). Naturally-occurring hotspot cancer mutations in Gα13 promote oncogenic signaling. The Journal of biological chemistry, jbc.AC120.014698.

Messerschmidt J. L, Dempsey K. E, Dillon K. S, & Demehri S. (2020). Divergent Roles of Epithelium-Derived Alarmins in Notch Signaling-Deficient Skin. Journal of Investigative Dermatology.

Muratore I, Goolsby B, Fandozzi E, Arganda-Carreras S, Mullen S, and Traniello JF, (2018) “Division of Labor, Neuroanatomy, and Brain Gene Expression in Fungus-Growing Ants” Biology and Genomics of Social Insects, Cold Spring Harbor Labs, N.Y.

Musicant A, Kshitij Parag-Sharma, Weida Gong, Monideepa Sengupta, Arindam Chatterjee, Erin C Henry, Yi-Hsuan Tsai, Michele Hayward, Siddharth Sheth, Renee Betancourt, Trevor Hackman, Ricardo J Padilla, Joel S Parker, Jimena Giudice, Colin A Flaveny, David N Hayes, Antonio L. Amelio (2020) CRTC1-MAML2 Establishes a PGC1α-IGF1 Circuit that Confers Vulnerability to PPARγ Inhibition, BioRxiv

Naranbhai V, Garcia-Beltran WF, Chang CC, Mairena CB, Thierauf JC, Kirkpatrick G, Onozato ML, Cheng J, St Denis KJ, Lam EC, Kaseke C, Tano-Menka R, Yang D, Pavlovic M, Yang W, Kui A, Miller TE, Astudillo MG, Cahill JE, Dighe AS, Gregory DJ, Poznansky MC, Gaiha GD, Balazs AB, Iafrate AJ. (2021) Comparative immunogenicity and effectiveness of mRNA-1273, BNT162b2 and Ad26.COV2.S COVID- 19 vaccines. medRxiv [Preprint]. 2021 Oct 13. Update in: J Infect Dis. 2021 Dec 09

Naranbhai V, Pernat CA, Gavralidis A, St Denis KJ, Lam EC, Spring LM, Isakoff SJ, Farmer JR, Zubiri L, Hobbs GS, How J, Brunner AM, Fathi AT, Peterson JL, Sakhi M, Hambelton G, Denault EN, Mortensen LJ, Perriello LA, Bruno MN, Bertaux BY, Lawless AR, Jackson MA, Niehoff E, Barabell C, Nambu CN, Nakajima E, Reinicke T, Bowes C, Berrios-Mairena CJ, Ofoman O, Kirkpatrick GE, Thierauf JC, Reynolds K, Willers H, Beltran WG, Dighe AS, Saff R, Blumenthal K, Sullivan RJ, Chen YB, Kim A, Bardia A, Balazs AB, Iafrate AJ, Gainor JF. (2021) Immunogenicity and Reactogenicity of SARS-CoV-2 Vaccines in Patients With Cancer: The CANVAX Cohort Study. J Clin Oncol. 2022 Jan 1;40(1):12-23. Epub 2021 Nov 9.

Ouahed JD, Broggi A, Glick A, et al. Variants in Interferon Lambda are Associated with Very Early Onset Inflammatory Bowel Disease. medRxiv. January 2022:2022.03.17.22271929. doi:10.1101/2022.03.17.22271929

Patel SJ, Liu N, Piaker S, Gulko A, et al. (2022) Hepatic IRF3 Fuels Dysglycemia in Obesity Through Direct Regulation of Ppp2r1b. Science Translational Medicine. 2022;14(637):eabh3831. doi:10.1126/scitranslmed.abh3831

Peng Y, Arauz P, Desai P, Byers A, Klemt C, & Kwon, Y. M. (2019). In vivo kinematic analysis of patients with robotic‐assisted total hip arthroplasty during gait at 1‐year follow‐up. The International Journal of Medical Robotics and Computer Assisted Surgery, 15(5), e2021.

Pulukuri S, Abrams B (2020). Step back, translate, extend: Addressing misconceptions relating to energy and free energy in cellular reactions via active‐learning videos. Biochemistry and Molecular Biology Education 48:652– 4.

Pulukuri S, Abrams B (2020). Incorporating an Online Interactive Video Platform to Optimize Active Learning and Improve Student Accountability through Educational Videos. Journal of Chemistry Education 97(12):4505–14.

Pulukuri S, Abrams B. 2021. Improving learning outcomes and metacognitive monitoring: replacing traditional textbook readings with question-embedded videos. J. Chem. Ed. DOI: 10.1021/acs.jchemed.1c00237

Pulukuri S, Torres D, Abrams B. 2021. OrgoPrep: a remote peer-led summer program preparing students for organic chemistry. J. Chem. Ed. DOI: 10.1021/acs.jchemed.1c00846

Registre L, Moreau Y, Ataca ST, Pulukuri S, Henrich TJ, Lin N, Sagar M (2020). HIV-1 Coreceptor Usage and Variable Loop Contact Impact V3 Broadly Neutralizing Antibody Susceptibility. Journal of Virology 94(2):1604-19.

Seidel K, Wan X, Zhang M, Zhou Y, Zang M, Han J. (2021) Alcohol Binge Drinking Selectively Stimulates Protein S-Glutathionylation in Aorta and Liver of ApoE-/- Mice. Front Cardiovasc Med. 2021; 8:649813. PMID: 33796575.

Siegler JE, Klein P, Yaghi S, Vigilante N, Abdalkader M, Coutinho JM, Abdul Khalek F, Nguyen TN. Cerebral Vein Thrombosis With Vaccine-Induced Immune Thrombotic Thrombocytopenia. Stroke. 2021. doi: 10.1161/STROKEAHA.121.035613.

Singh N, Chin I, Gabriel P, Blaum E, Masli S (2018) Dysregulated Marginal Zone B Cell Compartment in a Mouse Model of Sjögren’s Syndrome with Ocular Inflammation.International Journal of Molecular Sciences, 19(10), 3117.

Singh RB, Liu L, Yung A, Anchouche S, Mittal SK, Blanco T, Dohlman TH, Yin J, and Dana R. 2021. “Ocular Redness – II: Progress in Development of Therapeutics for the Management of Conjunctival Hyperemia.” The Ocular Surface 21:66–77. doi: 10.1016/J.JTOS.2021.05.004.

Singh RB, Liu L, Anchouche S, Yung A, Mittal SK, Blanco T, Dohlman TH, Yin J, and Dana R. 2021. “Ocular Redness – I: Etiology, Pathogenesis, and Assessment of Conjunctival Hyperemia.” The Ocular Surface21:134–44. doi: 10.1016/J.JTOS.2021.05.003.

Strickley J, Messerschmidt J, Awad M, Li T, Hasegawa T, Ha D, . . . Demehri, S. (2019, October 30). Immunity to commensal papillomaviruses protects against skin cancer.

Subramanian ML, Vig V, Chung J, Fiorello MG, Xia W, Zetterberg H, Blennow K, Zetterberg M, Shareef F, Siegel NH, Ness S, Jun GR, Stein TD. Neurofilament light chain in the vitreous humor of the eye. (2020). Alzheimer’s Research & Therapy. 12(111)

Thedinger W, Raman E, and Dhingra JK (2021). Comparative Study of ACR TI-RADS and ATA 2015 for Ultrasound Risk Stratification of Thyroid Nodules. Otolaryngology–Head and Neck Surgery

Thomas AS, Coote C, Moreau Y, Isaac JE, Ewing AC, Kourtis AP, Sagar M. 2022. Antibody-dependent cellular cytotoxicity responses and susceptibility influence HIV-1 mother-to-child transmission. JCI Insight. 7(9). 24 Mar. 2022.

Thomas AS, Moreau Y, Jiang W, Isaac JE, Ewing A, White LF, Kourtis AP, Sagar M. 2021. Pre-existing infant antibody-dependent cellular cytotoxicity associates with reduced HIV-1 acquisition and lower morbidity. Cell Reports Medicine. 2(10) 19 Oct. 2021.

Torres D, Pulukuri S, Abrams B. 2022. Embedded questions and targeted feedback transform passive educational videos into effective active learning tools. J. Chem. Ed. DOI: 10.1021/acs.jchemed.2c00342

Tzepos, RG, Raman, E, Toote, LE, Wright, DW and Gerdon, AE (2021), Signal Amplification with Co(III) Protoporphyrin IX Nanoparticles and Anodic Stripping Voltammetry. Electroanalysis. https://doi.org/10.1002/elan.202100108

Williams LM, Sridhar S, Samaroo J, Peart J, BB522 Molecular Biology Laboratory et al. (2021) Comparison of NF-κB from the protists Capsaspora owczarzaki and Acanthoeca spectabilis reveals extensive evolutionary diversification of this transcription factor. Commun Biol 4, 1404 (2021). https://doi.org/10.1038/s42003-021-02924-2

Xu P, Londregan A, Rich C, & Trinkaus-Randall V. (2020, February 07). Changes in Epithelial and Stromal Corneal Stiffness Occur with Age and Obesity.

Yi E, Gujar A, Guthrie M, Kim H, Zhao D, Johnson K, Amin S, Costa M, Yu Q, Das S, Jilette N, Clow P, Cheng A, Verhaak R. (2021). Live-cell imaging shows uneven segregation of extrachromosomal DNA elements and transcriptionally active extrachromosomal DNA hubs in cancer. Cancer Discovery, 12(2): 468-483. https://doi.org/10.1158/2159-8290.CD-21-1376.

Yin S, Iocolano A, Yu Y, Gangopadhyay J, Reed R (2018) In Vitro System for Coupling RNAP II Transcription to Primary microRNA Processing and a Three-Way System for RNAP II Transcription/Splicing/microRNA Processing. Methods Mol Biol, 1823. Springer, New York, NY. 43-50. 

Yu Tang, Kshitij Parag-Sharma, Antonio L. Amelio, Yanguang Cao. (2019) A Bioluminescence Resonance Energy Transfer-Based Approach for Determining Antibody-Receptor Occupancy In Vivo. iScience.

Zhang X, Guarin D, Mohammadzadehhonarvar N, Chen X, Gao X. (2021) Parkinson’s disease and cancer: a systematic review and meta-analysis of over 17 million participants. BMJ Open. 2021 Jul 2;11(7):e046329. doi: 10.1136/bmjopen-2020-046329. Erratum in: BMJ Open. 2021 Sep 22;11(9):e046329corr1. PMID: 34215604; PMCID: PMC8256737.

Zhou Y, Wan X, Seidel K, Zhang M, Goodman JB, Seta F, Hamburg N, Han J. (2021) Aging and Hypercholesterolemia Differentially Affect the Unfolded Protein Response in the Vasculature of ApoE-/- Mice. J Am Heart Assoc. 2021 09 21; 10(18):e020441. PMID: 34533042.