Labs interested in BS/MS students

With BISP 199 availabilities


Primary Investigator Contact & Info

Projects Available Desired Qualitifcations

Tyler Doherty
tdoherty@ucsd.edu

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.

Kellie B. Church

Department of Reproductive Medicine

kbchurch@ucsd.edu

 

Our laboratory studies the mechanisms by which the brain, pituitary and gonad communicate to control reproduction.  We are interested in the pathways whereby stress alters fertility in males and females and utilize a combination of mouse and cell culture models to assess molecular mechanisms underlying reproductive disease.

Required: General Biology and General Chemistry

Preferred: Physiology, Cell Biology and/or Neurobiology

Soumita Das

Department of Pathology

sodas@ucsd.edu

 

 

 

Tightening the Gut Barrier to combat infectious, chronic diseases: The compromised intestinal barrier is associated with chronic diseases such as obesity, diabetes, inflammatory bowel diseases, metabolic endotoxemia and so far there is no clinical treatment is viable for the treatment of barrier loss. After encountering the pathogenic attacks or with the exposure of microbial products or toxic components from the environment, the epithelial tight junctions collapse and promote the diseases. Here we propose to understand the molecular mechanism of host pathway that can protect the integrity of the epithelial barrier that can be targeted to prevent the progression of chronic diseases. The project will use the cutting-edge stem cell based technology to isolate enteroids from murine and human (healthy and inflammatory bowel diseases) intestine, infection with pathogenic and non-pathogenic gut bacteria, testing of several signalling pathways and functional assays to understand the mechanism of gut barrier loss.

PI: Soumita Das, Department of Pathology, Collaborators/Co-PI: Drs. Pradipta Ghosh and Kim E Barrett; Department of Medicine.

Scott Rifkin

Ecology, Behavior, and Evolution

sarifkin@ucsd.edu

 

General theme

The projects in the Rifkin lab generally focus on why individuals vary in some ways but not others.
For example, if you look around you'll see tons of variation between different people, but very few
people have third arms growing out of their chests. Some kinds of variation are allowed by how
an organism develops while other kinds are excluded. We use techniques from developmental,
evolutionary, and systems biology to study the processes that generate variation and their
evolutionary consequences.

Project 1
Organisms respond to environmental conditions using sets of signaling pathways where
receptors sense the environment and transmit this signal through a series of protein
intermediates to the nucleus of a cell where new proteins are made. There can be variation
between individuals at any step in this process from how they actually sense the environment to
the fidelity with which they transmit the signal to how they interpret it to how they act on that
interpretation. We are using nematode worms as a model system to dissect variation in how
organisms make consequential decisions about their environments. During larval life, worms
decide whether the conditions are good enough to continue to reproductive development or to put
their development on pause and proceed to a spore-like state called dauer until things get better.
This decision is influenced by the environment (obviously) but also by genetics and randomness.
The project would involve setting up and using a microfluidic and microscopy system to
manipulate this decision and monitor the developmental processes that underlie it at both the
organismal and molecular levels. An ideal student for this project would be someone who is
interested in evolutionary or developmental biology, who likes to tinker and get devices to work,
and is excited about quantitative approaches to analyzing biology.

Project 2
When two species breed, their progeny often die before completing development. However,
speciation is an ongoing process and so there are cases where two species haven't completely
separated and so their offspring sometimes survive. We are studying the developmental biology
of species incompatibility using the nematode genus Caenorhabditis as a model system. Hybrids
between different species of worms often die during embryogenesis, but some species pairs can
breed and produce viable and even fertile offspring. We are tagging histones with a fluorescent
protein and then using confocal microscopy to visualize the development of these worms from
very early in their life and measuring where things go wrong in inviable hybrids and how their
development differs from hybrids that are successful. This project involves developmental
biology, evolutionary biology, microscopy, and image analysis. This project requires a student
who wants to learn how to work with worms and microscopy and who is excited about learning to
analyze image data.

Project 3
Developmental processes are controlled by networks of interacting genes. Often these genes are
transcription factors that regulate the activity of other genes. In Caenorhabditis elegans (the
model roundworm), a cell becomes a gut cell if a short network of genes culminates in the
expression of a particular transcription factor that then regulates hundreds of other genes to build
the gut. Despite the fact that building a gut is important if an animal is to survive, this network
originated within the evolutionary history of this genus. In other words, some species that are
relatively closely related to C. elegans don't build their guts in this way. We are using this set of
genes as a model system to study how a new developmental network can arise and evolve. This
project would involve working and measuring proteins and also measuring gene expression at
single molecule resolution in some non-model organisms. This project requires a student who has
experience in wet lab molecular genetics and who wants to learn image analysis. Familiarity with
evolutionary biology or developmental biology would also be useful. There will also be the
opportunity to learn some techniques for measuring properties of protein-DNA interactions.

Project 4
Genes interact in complex networks. Various researchers have developed simplified,
computational models of gene networks they can use for in silico (in the computer) experiments.
We are using one such model to study the role of gene duplication in evolution of different cell
types. A student who works on this project should already have programming experience (ideally
in R, Matlab, or Python) and be interested in computational and evolutionary biology.

Project 5
Water bears (a.k.a. tardigrades) are an incredible group of organisms found all over the world
(look them up online!) They are around 1/2 millimeter long, can weather extreme conditions,
have survived trips to outer space, and can be revived after being frozen for 30 years! Very little
is known about their developmental biology. This project would involve setting up a colony of
water bears in the lab and starting to look at some basic developmental biology using
microscopy. This project would require someone who is intrepid and independent, who is creative
in troubleshooting and tinkering with conditions and protocols and who wants to explore a
relatively understudied area of biology.

Stephanie Stanford

Clinical and Translational Research Institute

ststanford@ucsd.edu

We study protein tyrosine phosphatases, enzymes that play an important role in signal transduction and are critical for numerous cellular processes in health and disease. We have a project available to study how dysregulation of a protein tyrosine phosphatase contributes to cancer by causing anomalous signal transduction in tumor cells. The student will have the opportunity to gain exposure to cell biology, signal transduction, mouse models of cancer, and the basic biochemistry of protein tyrosine phosphatases.