mcbUSA’s Summer Undergraduate Research Program (SURP) at UC Berkeley strives to connect undergraduate UC Berkeley students to biology-related labs for meaningful summer research.
We have extended deadlines for eight projects. The link to the application is here. It will be due on 5PM, April 12th.
Please come out to the SURP Info Sessions on Friday, March 6, 5:00-6:00PM at Barrows 170, and
on Tuesday, March 17, 8:00-9:00PM at Barrows 170 to hear from several labs’ representatives and/or ask logistical application questions!
The mcbUSA club advisor has asked us to cancel the info session on March 17, 8:00-9:00PM. We apologize if you were planning on going to the info session.
Slides from several labs that presented/planned to present in SURP info sessions are posted here:
- Jenny Mortimer – Testing the effect of drought on the emission of poplar volatile organic compounds
- Jannick Van Cauwenberghe – Have invasive rhizobia escaped their bacteriophage enemies?
- Elçin Unal – Investigating Mitochondrial Inheritance during Meiosis
Lab descriptions are out! Please note that some lab descriptions may be posted at a later date. Errors in the descriptions are reflective of the SURP coordinators, not the labs. Please contact us at email@example.com if you notice anything you think might not be quite right.
|Project Name||Extended Deadline||Topic||Professor/PI/Postdoc||Organization||Qualifications||Time Commitment||Lab’s Preferred Research Start Date|
|Building a novel data integration for biogeochemical datasets||Yes||Data infrastructure, Software development||Esther Singer||LBNL||software development, computational biology, bioinformatics, programming in R and/or python and/or C++||flexible, full-time or 3-5 full days per week||June 1|
|Cloning, expression and purification of DNA repair proteins and/or protein complexes from E. coli vs. insect cells for biochemical, biophysical and structrual characterization.||DNA repair, protein complexes, protein-protein interactions, recombinant protein expression technologies from vector constructions to protein purification||Miaw-Sheue Tsai||Biological Systems and Engineering Division at Lawrence Berkeley National Laboratory||Junior or senior standing, taken chemistry and biology lectures and lab courses, familiar with wet lab settings; punctual, organized, reliable, communicative, responsive, inquisitive, attention to detail, independent, team player||15-20 hours per week or 3 days a week (5-6 hours each day), 10-12 weeks||6/1/2020 Monday|
|Construction of a heteromeric clamp loader in T4 bacteriophage to study subunit-specific roles of the DNA clamp loader.||synthetic biology, deep mutational scanning, DNA replication, clamp loader, sliding clamp, T4 bacteriophage||John Kuriyan||MCB||interest in biochemistry, protein design and synthetic biology.||12+ hours per week||Jun-20|
|cryo-EM of PRC2||Investigating the structural underpinnings of epigenetics by cryo-EM||Eva Nogales||MCB||The candidate is expected to have a foundation of biochemical knowledge and the desire to expand on it. Previous experience with experimental molecular biology is preferred. Good documentation habits, reliability, patience, eye for detail and the ability to work in a team are very important.||To start as soon as possible and stay for as long as possible. Absolute minimum of 12 hour/week. 20 prefered.||ASAP|
|Development of computational tools for the analyses of biophysical data||Yes||Computational Biophysics||Petrus Zwart||MCB department at UC Berkeley||Programming in python. Decent math skills||Minimum time commitment depends on project.||Depends on project and student.|
|Engineering Pseudomonas putida for Heterologous Gene Expression||Yes||synthetic biology, genetic engineering, bioreactor and consolidated bioprocessing development||Thomas Eng||LBNL / Biosciences Area / Biological Systems and Engineering / Joint Bioenergy Institute||MCB.140L is suggested, or other biology laboratory experience.||For the summer, ~20-30hrs a week. Time commitment is flexible but should be discussed in advance.||Flexible.|
|From bacteria to cancer: radionuclide applications||radionuclides, drug development, theranostics||Dahlia An||Lawrence Berkeley National Laboratory (LBL); Nuclear Engineering department at UC Berkeley||CHEM 1A, CHEM 1AL, comfortable working with animal models and radionuclides, excellent written and verbal communication skills||Full-time over the summer||ASAP|
|FUNgal BIG Data||Yes||data mining in fungal genomes||Igor Grigoriev||JGI @ LBNL and PMB @ UCBerkeley||programming and data mining skills with biological background||flexible||any time|
|Have invasive rhizobia escaped their bacteriophage enemies?||phages, rhizobia, host range, biogeography, invasion biology||Jannick Van Cauwenberghe||IB department at UC Berkeley||You must have a strong work ethic and an interest in microbiology and ecology. You must be dedicated to learning from and contributing to the project, which involves meticulous laboratory procedures, attention to detail, continuous care of bacteria, and sometimes boring and repetitive protocols, but exciting and rewarding results. Experience with sterile technique and bacterial culturing is a plus, but not required. Applicants with a genuine interest in biology will be favored.||about 9-10 hours per week||26-May|
|How neurons talk to the blood: Neuronal regulation of blood cell transdifferentiation by oxygen sensing||Cell signaling, developmental & stem cell biology, hematopoiesis, nervous system, microenvironment, Drosophila, oxygen sensing, sensory neurons, transdifferentiation, blood cell, tissue macrophage, adaptation, neuronal channels, calcium signaling, activin signaling, transcription factors, scRNAseq||Katja Brueckner||UCSF/ Broad Center; Cell & Tissue Biology; CVRI||We are looking for talented and enthusiastic students with some previous lab experience; experience with Drosophila is preferred.||Full time during the summer; continuation during the school year and future paid position possible.||TBD|
|Identification of novel lipoprotein particles associated with cardiovascular disease and other disorders.||Lipoprotein metabolism||Ronald Krauss||NST Dept at UC Berkeley and Depts of Medicine and Pediatrics, UCSF||At least introductory biochemistry and molecular biology, with previous experience in a research laboratory.||At least 30 hours/wk||1-Jun|
|Improving Biofuel Crop Yield under Drought Stress from Field to Lab||Yes||Microbial ecology, bioinformatics, computational modeling||Esther Singer||Lawrence Berkeley National Laboratory||Background in computational biology (e.g. working with R/python, statistics, DNA sequence analysis), molecular methods (DNA extraction, PCR, pipetting) and/or soil chemistry, microscopy (confocal and electron)||3-5 full days per week||June 1, 2020|
|Investigating Mitochondrial Inheritance During Meiosis||Meiotic rejuvenation, organelle remodeling||Elcin Unal||MCB||curious mind, attention to detail, good organization skills and time management, familiarity with basic molecular biology techniques (PCR, transformation, cloning)- preferred but not necessary||15-20h during the summer, can be adjusted later||May 2020 or later|
|Investigation of intracellular trafficking and secretory pathways involved in regulating inflammatory proteins by Chlamydia trachomatis to detect drug targets and develop a rational vaccine.||C. trachomatis, intracellular trafficking, immune response, primary cells, dual RNA-seq||Deborah Dean||MCB, UC Berkeley; School of Medicine, UCSF||Undergrads interested in multidimentional and fulfilling lab experience – no prior experience required although some courses in molecular biology and genetic/genomics would be helpful||Full time in the summer – opportunity to continue during the school year||Mid to late May or 1st week in June|
|Kinetics of DNA target search in CRISPR-Cas Systems||protein/nucleic acid interactions, biochemistry, enzyme mechanism, conformational dynamics, CRISPR, prokaryotic adaptive immunity||John Kuriyan||MCB||strong quantitative analytical skills, interest in biochemistry/biophysics, intention to take MCB C100A (or similar)||20+ hours per week during the summer (flexible, will be discussed in advance), potentially to continue into the academic year||flexible (early June)|
|Microbial Community Analysis and Functional Evaluation in Soils||Yes||environmental microbiology||Romy Chakraborty||Ecology, LBNL||microbiology courses, laboratory experience- media formulation, genomic DNA extraction||30-40 hours/week.||May 15th|
|Molecular regulation of IgE class switch recombination||Immunology, Allergy, Asthma, B cells, IgE||Christopher Allen||UCSF||Should already have some experience working in lab and knowledge of basic techniques, such as pipetting.||Ideally the student would do full time research in lab for several weeks during the summer. It may be possible to continue this research part-time during the school year.||Ideally in late May / early June|
|New approaches to understanding and treating asthma and cystic fibrosis||asthma, cystic fibrosis, airway epithelial cell biology, gene regulation, gene editing||David Erle||UCSF Department of Medicine||College-level courses in cell biology, biochemistry, and genetics (at least two of these three areas). Basic lab skills (eg pipetting) gained either through lab courses or previous work or volunteer experience. Experience with cell culture and molecular biology are desirable but not necessary; training in techniques will be provided.||Minimum of three full days per week for 2 months (or equivalent)||Flexible|
|Regulation of MSC differentiation by macrophages||Mesenchymal stem cells, osteogenesis, macrophage, inflammation, progranulin||Robert Nissenson||VAMC Endocrine Unit, UCSF. Located at 1700 Owens St., Mission Bay.||Basic laboratory skills with a high level of motivation.||Ideally full time (or close to it).||By June. Earlier if possible.|
|Role of C. trachomatis, microbiota and host immune and signaling pathways in urogenital and rectal infections||C. trachomatis, microbiota, host immune response, host-pathogen interactions, dual RNA-seq||Deborah Dean||MCB, UC Berkeley; School of Medicine, UCSF||Undergrads interested in multidimentional and fulfilling lab experience – no prior experience required although some courses in molecular biology and genetic/genomics would be helpful||Full time during the summer – opportunity to continue during the school year||Mid to late May or 1st week in June|
|Roles of TGF-beta signaling in epithelial-mesenchymal transdifferentiation||cell signaling, TGF-beta, cancer stem cell biology, epithelial-mesenchymal transdifferentiation||Rik Derynck||UCSF: Broad Center of Regeneration Medicine, Cell & Tissue Biology, Cancer Center||We are looking for talented and enthusiastic students with some previous lab experience in molecular biology and cell culture.||Full time during the summer; continuation during the school year and future paid position possible.||TBD|
|Subcellular Dynamics in Multicellular Systems||Yes||imaging, microscopy, zebrafish, cell-cell signaling||Gokul Upadhyayula||MCB at UC Berkeley||Cell culture, transfections, molecular cloning / python, C/C++||8 hrs/ day||ASAP|
|Structural studies of plant immune receptors||Cryo-electron microscopy, Biochemistry, Immunology, Plant biology||Eva Nogales||MCB at UC Berkeley||The candidate is expected to have a foundation of biochemical knowledge and the desire to expand on it. Previous experience with experimental molecular biology is preferred. Good documentation habits, reliability, patience, eye for detail and the ability to work in a team are very important.||15 hours/week||April-May 2020|
|Testing the effect of drought on the emission of poplar volatile organic compounds||biofuels, climate change, renewable energy, plant cell walls, poplar, pectin, volatiles||Jenny Mortimer||LBNL Biosciences, EGSB Department; Joint Bioenergy Institute, Feedstocks Division||Basic analytical chemistry, but all methods will be taught. Experience of working with plants perferred.||We would prefer full time for 8-10 weeks, but we can be flexible. A stipend will be available.||June 8th (but again, this can be negotiated)|
|The Ecological Genetics of Daily Rhythms in Sunflower Reproduction||plant biology, developmental biology, circadian clock, plant-environment interaction, sunflower, fieldwork, natural variation, evolution, genetics, image analysis||Benjamin Blackman||Plant and Microbial Biology||Students with strong interests in plant-environment interaction, genetics, evolution, and ecology will find the experience most rewarding. Attention to detail and good record-keeping skills are essential. The student should be comfortable and enthusiastic about working in field conditions for extended periods, and they will be expected to follow guidelines for safely doing so. Students who are interested in working full time (wage or stipend support may be available) are especially encouraged to apply.||40 hr/week for 10 weeks minimum||26-May-19|
|The impact of phages on their bacterial hosts||bacteria, phage, microbiology, molecular biology, genetics||Yolanda Huang||Biosciences at LBNL; Bioengineering at UC Berkeley||Pipetting, basic microbiology or molecular biology techniques, some Python / R (if want to pursue computational work)||Full time (or close to)||May|
|The interplay of the ocular microbiome, chlamydial species, and host immune responses in the heathy versus diseased eye among trachoma patients||Chlamydia species, host-pathogen interactions, trachoma||Deborah Dean||MCB, UC Berkeley; School of Medicine, UCSF||Undergrads interested in multidimentional and fulfilling lab experience – no prior experience required although some courses in molecular biology and genetic/genomics would be helpful||Full time in the summer – opportunity to continue during the school year||Mid to late May or 1st week in June|
|Using X ray free electron laser to study the mechanism of water oxidation in Photosystem II||Yes||Photosynthesis, X ray crystallography, X ray spectroscopy, catalysis, protein biochemistry||Ruchira Chatterjee||MBIB, Lawrence Berkeley National Laboratory||Pursuing bachelors in Molecular and Cellular Biology or Chemistry||2 or 3 months||‘May 15|
Q: How do I join?
A: Fill out the SURP participation form for each project you want to have undergraduate Berkeley students for through SURP. (Note that the SURP application deadline for undergraduates is March 22, thus a lab who joins SURP on March 21 will likely not attract many applicants.)
Please email the SURP coordinators soon after you submit the participation form so that we can display your project description onto this website as soon as possible. (We will try to do so within one day.)
In order to protect the privacy of undergraduate applicants, we have withheld the participation form link. Please email firstname.lastname@example.org for the participation form link. We apologize for the inconvenience.
Q: Why should I join?
A: Only if you are in need of undergraduate researchers. SURP provides a communication link between you and UC Berkeley undergraduates interested in summer research.
Q: Do I need to pay the undergraduates I accept from SURP?
A: It is your choice whether or not to pay the undergraduates you accept.
Q: How are students matched to projects?
A: Students apply to up to three projects. If applicants apply to your project(s) through SURP, SURP will send you all such applications. You decide which students your lab wishes to accept.
Q: If my lab is full, should I still join SURP?
A: No. SURP’s purpose is to connect undergraduates looking for summer research to labs who want undergraduate researchers. If your lab does not need more undergraduates for summer 2020, you do not have a reason to join.
Q: When will I receive the undergraduates’ applications?
A: You will receive them by April 1. Please select the applicants you wish to accept by April 24th by contacting them directly and notifying the SURP coordinators of your decision by emailing email@example.com.
Q: What information will I get from the applications?
A: The application includes the applicant’s:
- general information (name, year, classes taken, contact info, etc.)
- statement of interest for your project
- unofficial transcript
- any supplemental questions you wish to include*
Q: Will I be able to receive extra information from my applicants?
A: You will have the chance to interview your applicants before and/or after you select them on April 24. *If you wish to ask extra supplemental questions to applicants applying to your project(s), please email the SURP coordinators at firstname.lastname@example.org.
If you have any residual questions, please email the SURP coordinators at email@example.com.