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Labs interested in BS/MS students

With BISP 199 availabilities


Primary Investigator Contact & Info

Projects Available Desired Qualitifcations

Tyler Doherty
tdoherty@ucsd.ed

Department of Medicine

Lab website

Our laboratory uses both mouse models of asthma as well as human cells to identify the role of group 2 innate lymphocytes in promoting allergic diseases including asthma. The students will be using gene deficient mice to test the role of these lymphocytes in disease models Some lab exposure previously as undergraduate as well as sufficient GPA to meet the MS/BS requirements.

Mike Sander, MD
masander@ucsd.edu

Sanford Consortium for Regenerative Medicine

Lab website

The Sander laboratory addresses these and other important questions in the context of beta cell function by employing human genetics, genomics, and stem cell engineering. Potential CIRM interns will have the opportunity to play an important role in this exciting project. The intern will work closely with stem cell scientists in the laboratory to introduce diabetes-associated SNPs into hESC lines using CRISPR-Cas9. Interns will then work to differentiate these hESC lines into pancreatic beta cells to test if these engineered mutations have any effect on beta cell function. Through this experience, the intern will learn all aspects of CRISPR-Cas9 gene editing such as guide design and Cas9 delivery. Previous laboratory and cell culture experience is highly advantageous.

John T. Chang. MD
changj@ucsd.edu

Department of Medicine

Lab website

The Chang lab is broadly interested in investigating basic immune mechanisms underlying lymphocyte fate determination in the context of infectious diseases and inflammatory bowel diseases. The laboratory has developed single-cell gene expression profiling approaches to understand the molecular mechanisms underlying lymphocyte differentiation in vivo. A second area of interest focuses on improving the molecular understanding of inflammatory bowel disease (IBD) and identifying new diagnostic and therapeutic targets for these diseases. Available Projects: 1) Uncovering mechanisms of action for vedlizumab in IBD. 2) Using algae expressing immunomodulatory cytokines as a novel therapy for IBD

Renate Pilz
rpilz@ucsd.edu

Department of Medicine

Faculty Profile

We study cGMP signaling, and it's role in bone homeostasis and in vascular tissue.

Gerad Boss
gboss@ucsd.edu

Department of Medicine

Faculty Profile

We study amino acid regulation of purine synthesis and I am developing drugs against cyanide and hydrogen sulfide poisoning.

Eric A. Schmelz
eschmelz@ucsd.edu

Biological Sciences

Faculty Profile

We study a hormone signaling pathway that can drive cell death processes in plants. The molecules are closely related positional isomers of a highly studied pathway, known as jasmonates, that are cell protective. The 2 parallel pathways produce very similar molecules with very different activities. The key focus is proving the new biosynthetic pathway branch in maize and knocking it out to demonstrate the endogenous function and altered plant phenotypes (likely many). For more info, see this paper. Mtivated students with genuine interest in plant research.

Stanley Lo
smlo@ucsd.edu

Biological Sciences

Faculty Profile

Education research MS track: Analyzing how students understand important biology concepts, such as chromosome segregation in genetics, and how students view biology and research. For this Education research track, students will take BISP 193 (and not BISP 199) research for credit course.

Lisa McDonnell
lmcdonnell@ucsd.edu

Biological Sciences

Faculty Profile

Investigating what knowledge structures students have related to research as they progress through their degree. Questions being asked include 1) How do class-based research experiences influence their knowledge structures? 2) How do student’s knowledge structures compare to those of practicing researchers? 3) How can we modify the class-based research experiences to facilitate students developing a more expert-like understanding of research? How does writing and peer review affect the development of reasoning and argumentation in undergraduate biology students? Here we are looking at the influence of adding structured writing and peer review in large biology classes, and how this impacts: 1) reasoning ability, 2) reviewing ability, 3) argumentation. An interest in biology education and learning more about how people learn, and how teaching impacts learning. Comfortable learning new methods of data analysis and statistical analysis. For this Education research track, students will take BISP 193 (and not BISP 199) research for credit course.

David K. Welsh
welshdk@ucsd.edu

Department of Psychiatry

Faculty Profile

Project related to circadian rhythms in brain cells, and relation to depression-like behavior in mice. Preferred: students who have taken Circadian Biology course and have some lab experience

Nicole Purcell
npurcell@ucsd.edu

Department of Pharmacology

Faculty Profile

Her research focuses on the role of PHLPP in pathophysiological disease processes, in particular, cardiac hypertrophy and stroke. For more information, please see her lab website.

Milton Saier
msaier@ucsd.edu

Biological Sciences

Lab website

We have two labs, a bioinformatics lab (the dry lab) and a molecular genetics/biochemistry lab (the wet lab). In the dry lab, we use computers to (1) characterize transport protein families, (2) identify distant relationships between transport protein families with the creation of superfamilies, (3) use bioinformatics to make functional predictions from genome data, (4) do whole genome analyses of transport protein contents, (5) develop novel software to support our research and database, and (6) conduct database management work. We maintain the Transporter Classification DataBase (TCDB), and our bioinformatics NIH grant supports this IUBMB-approved database.

Sergey Kryazhimskiy
skryazhi@ucsd.edu

Biological Sciences

Lab website

1. How do mutation rates change along the genome? ? Genetic mutations cause cancer and many other diseases, allow viruses like influenza to evade our immune system, and drive adaptation – for example, many bacteria evolve resistance to antibiotics by acquiring certain mutations in their genomes. Why, how often, and where in the genome do mutations happen? A student would work on this project together with a postdoc in the lab. They will learn how to work with yeast, how to sequence the genome, and how to analyze sequencing data.2. Can we predict evolution? The goal of this project is to use available knowledge of how the bacterium E.coli works, to predict how it will evolve. A student would work on this project with a postdoc in the lab. They will learn how to work with E.coli, how to do basic genetic engineering, how to measure growth curves, how to do high-throughput sequencing, and how to analyze growth-curve and sequencing data. Required. (1) Strong commitment to research work; (2) Responsibility and punctuality; (3) Good oral and written communications skills; (4) Ability and desire to work in a team; (5) Basic knowledge of molecular, cell, evolutionary biology, and biochemistry.

Lin Chao
LChao@ucsd.edu

Biological Sciences

Lab website

We study the evolution of biological aging in bacterial cells such as E. coli. Biological organisms, as non-biological entities, can age or deteriorate with time. Environmental agents such as oxidation are common causes of the deterioration. However, biological organisms are different because they can evolve, and we believe that evolution may have accelerated the aging process of E. coli cells. If a mother bacterium has oxidative damage, when she divides into a two daughter cells, she has to make a decision. Does she give equal amounts of damage to each daughter, or should she partition the damage asymmetrically and give more to one daughter? Making such a decison is similar to asking someone to choose between a bank account with $1,000 at 8% per year versus split accounts of $500 at 6% and $500 at 10%. Because the split accounts will give you more money over many years (check it out), the mother bacterium will have more daughters over time is she partitions the damage asymmetrically. The daughter receiving more damage is like the 6% account and the daughter receiving less is the 10% account. Thus, asymmetry provides an evolutionary advantage. Note then that the daughter receiving more damage experiences an accelerate amount of aging compared to a symmetrical process. We study this accelerated aging by taking through a high magnification microscope time-lapse videos of dividing mother and daughter E. coli cells. Because we work with both living cells and video analysis, we are particularly interested in students who have a background in either computational biology, microbiology, and cell biology. Computer science students with little or no biology background, as well as biology students with little or no background in computer science, are encouraged to apply.

William Joiner
wjoiner@ucsd.edu

Department of Pharmacology

Lab website

Potential projects: 1) Screen for genes that regulate sleep need. This work will involve fruit fly husbandry, genetics, quantitative sleep and memory assays, and potentially molecular cloning and confocal microscopy. 2) Determine how Ly6 genes affect the properties of neurotransmitter receptors in cell lines commonly used for drug screens. This work will involve molecular cloning, CRISPR, cell culture, biochemistry, and FRET-based fluorescent pharmacological assays of brain receptor activity. 3) Determine the mechanisms of action of newly discovered regulators of brain neurotransmitter receptors. This work will involve molecular cloning, cell culture, biochemistry, and FRET-based fluorescent pharmacological assays of brain receptor activity.

Christina Sigurdson
csigurdson@ucsd.edu

Department of Pathology

Lab website

Our laboratory investigates the molecular mechanisms that underlie prion disease, a fatal neurodegenerative disorder with no available treatment. We are particularly interested in how the structure of the misfolded prion aggregate impacts the disease pathogenesis. Projects available would involve investigating the pathology in the brain of mice that develop neurologic disease from prions having different conformations, as well as investigating the toxicity of different prion mutations using cell-based models.

Chitra Mandyam
cmandyam@ucsd.edu

Department of Anesthesiology

Lab website

Project 1) Determine gender differences in propensity for relapse in methamphetamine addicted rats and the role of neurogenesis in the hippocampus in these behaviors. (techniques include animal behavior, histology and Western blotting) Project 2) Determine the synaptic properties of granule cell neurons in the hippocampus in drug naïve and methamphetamine addicted rats. (techniques include animal behavior and electrophysiology) Project 3) Determine the effects of chronic ethanol experience on oligodendrogenesis and neurovasculature in the prefrontal cortex of adult rats. (techniques include animal behavior, histology and Western blotting). I would also like to let the students know that I have successfully graduated 2 BS/MS students and their work is either published or in submission. I have 3 students currently in the lab who will complete their BS/MS in Spring/fall quarters. You are more than welcome to contact me and visit my lab if they are interested in my research activities.

Julian Schroeder

Division of Biological Sciences

jischroeder@ucsd.edu

Our research is focused on how plants respond to and mount resistance to drought stress, and how they respond to the continuing increase in atmospheric CO2 concentration.

Sanjay Nigam

Medicine, and Cellular and Molecular Medicine

snigam@ucsd.edu

http://labs.biology.ucsd.edu/schroeder/

 A major focus of our lab is the biology and clinical importance of multi-specific "drug" transporters. We are particularly interested in the SLC22 family of transporters. Among these are the organic anion transporters (OATs) and organic cation transporters (OCTs) as well as other interesting SLC22 transporters--including a number discovered in the lab. These transporters are involved in the handling of many small molecule drugs, toxins and metabolites in the kidney and other organs.

Alan R. Hargens.

Professor of Orthopaedic Surgery

http://bones.ucsd.edu

 

Some of the projects in the lab:

  • Altered Microvascular Flow and Leg Circumference as a Function of Lower-Extremity Pressure Exposure

 

  • Increasing Microvascular Blood Flow with Mild External Compression to Induce Foot Sensation

 

  • Hand Volume during Immersion as a Marker of Cardiovascular Health with Age

 

  • Simulated Microgravity-Induced Elevation of Intracranial Pressure and Changes in Ocular Structures and Functions of People and Bats

 

  • Risk of Intervertebral Disc Damage After Prolonged Space Flight

David K. Welsh

Department of Psychiatry

welshdk@ucsd.edu

 Project related to circadian rhythms in brain cells, and relation to depression-like behavior in mice. Preference will be given to students with some lab experience who has taken the basic undergrad Circadian Biology course.

Contiguous BS/MS Program