URAP

Richard Harland - Professor, Molecular and Cell Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Though sleep is pervasive across animals, the core function of this deeply conserved behavior remains unknown. Sleep has been hypothesized to serve many roles, from the replenishing of molecules consumed during periods of activity, to the facilitation of learning and the formation of long term memories. Recently, colleagues and I...

Eva Harris - Professor, Public Health; Div of Infectious Diseases and Vaccinology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

With 3.6 billion people living at risk of infection, and approximately 400 million infections and 96 million cases per year, dengue is the most prevalent mosquito-borne viral illness. The disease spectrum includes dengue fever, characterized by debilitating symptoms such as high fever and myalgia; and dengue hemorrhagic fever/dengue...

Eva Harris - Professor, Public Health; Div of Infectious Diseases and Vaccinology

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

The four dengue virus serotypes (DENV1-4) cause the most important mosquito-borne viral disease of humans, with 100 million cases annually. The mechanisms by which the human immune response to DENV provides either protection against or enhancement of a subsequent infection with a different DENV serotype are not fully understood...

Eva Harris - Professor, Public Health; Div of Infectious Diseases and Vaccinology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Previous studies in the Harris laboratory have demonstrated the ability of the secreted flaviviral protein, nonstructural protein 1 (NS1), to induce both hyperpermeability in vitro and vascular leak in vivo, both mediated by the disruption of endothelial glycocalyx components and intercellular junction degradation. Further work in the lab aims at...

Eva Harris - Professor, Public Health; Div of Infectious Diseases and Vaccinology

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Dengue (DENV) and Zika (ZIKV) flaviruses are mosquito-borne viruses that are major medical and public health problems worldwide. DENV causes the most prevalent mosquito-borne viral disease of humans, and severe cases manifesting vascular leakage can be fatal. Nonstructural protein 1 (NS1) is a flaviviral protein that participates in...

John Harte - Professor, Energy and Resources

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Students will work with Prof. Harte to formulate and explore mathematical models describing ecosystems that are far from steady state as a consequence of human and/or natural disturbance. Testing of model predictions with available data sets will also be carried...

John Harte - Professor, Energy and Resources

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Vegetation and microclimate data collected from Sierran red fir forest will be used to assess the role of environmental parameters (e.g., temperature, soil moisture) in successful establishment of conifer tree seedlings. The project will advance niche theory by examining spatially-explicit relationships between the environmental parameters and measures of seedling...

Cori Hayden - Professor, Anthropology

Status: Current Term Now Closed     Weekly Hours: 3-5 hrs     Location: On Campus

This project is a study of emergent and contested paradigms for understanding post-viral chronic illness. It has a historical dimension, a social theory dimension, and an anthro/science studies component. It focuses on how the proponents of competing paradigms are participating in a complicated public performance of power, legitimacy...

Lin He - Professor, Molecular and Cell Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Choroid plexus (ChP) epithelia contain multiple cilia per cells. Its major function is to secrete cerebrospinal fluid (CSF) to provide nutrients to the neurons and to cushion the brain from injury and inflammation. Defects in ChP lead to hydrocephalus, an abnormal buildup of fluid in the brain ventricles. Aberrant CSF...

Lin He - Professor, Molecular and Cell Biology

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Transposable elements (TEs) are DNA sequences capable of “moving” (transpose) within a genome. RNA transposons (retrotransposon) use RNA intermediate and a “copy and paste” mechanism to transpose. Retrotransposons, with their “copy and paste” mechanism, have accumulated and become abundant in our genome, comprising ~38% of the human and mouse genome...

Lin He - Professor, Molecular and Cell Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

In mammals, female fertility is determined by the ovarian reserve of primordial follicles and the quality of mature MII oocytes. In humans, female fertility declines significantly after 35, with a rapid reduction in ovarian reserve and a severe deterioration in oocyte competence. On one hand, the pool of primordial follicles...

Lin He - Professor, Molecular and Cell Biology

Status: Check back for status     Weekly Hours: 12 or more hours     Location: On Campus

Throughout evolution, ancient foreign nucleic acid sequences have infected and spread across the genomes of nearly all organisms. Approximately 40% of the mammalian genome originates from mobile elements known as retrotransposons, which hijack the host's cellular machinery to replicate and integrate into the host genome via RNA intermediates. In most...

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

This cutting-edge research project focuses on developing and optimizing machine learning tools to automatically identify cell types and states from single-cell genomics data. Single-cell technologies have revolutionized our understanding of cellular diversity, but the manual annotation of cell types remains a significant bottleneck in data analysis. This...

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

This project investigates the fascinating world of long non-coding RNAs (lncRNAs) and their crucial role in maintaining stem cell pluripotency. While most RNA molecules are known to encode proteins, lncRNAs represent a mysterious class of RNAs that regulate gene expression through various mechanisms. This research focuses on understanding how...

Peng He - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

This innovative research project aims to uncover the complex organization of tissues by analyzing spatial gene expression patterns. Using cutting-edge spatial transcriptomics technology, we can now measure gene expression while preserving information about where cells are located within a tissue. This project will adapt and apply advanced analytical methods...

Roland Henry - Professor, UC San Francisco

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: Off Campus

The ability to quantitatively measure changes to the central nervous system is approaching a crucial milestone for neuro-imaging - the ability to measure change on an individual patient level. The Multiple Sclerosis Center at UCSF, in concert with our partners, has prioritized the development of a panoply of neuro-imaging...

Roland Henry - Professor, UC San Francisco

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: Off Campus

UCSF’s Department of Radiology and Biomedical Imaging and Department of Neurology are excited to offer a combined educational and research opportunity for motivated undergraduate students in the medical imaging research team. 3D segmentation of structures in the brain and spinal cord is a problem that deep learning is uniquely equipped...

Roland Henry - Professor, UC San Francisco

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: Off Campus

UCSF’s Department of Neurology has some of the largest clinical neuroimaging datasets in the world. As the director of imaging for the multiple sclerosis group, Dr. Roland Henry’s laboratory is in charge of making sense of this data and applying next generation analytical techniques to translate this raw data into...

Amy Herr - Professor, Bioengineering

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

We are addressing a major blocker in microfluidic design: the macro-to-micro interface. Here, we consider how to precisely move and situation an array of single nuclei (from single mammalian cells). We have a vacuum-driven manifold that does the job, but we need to understand best operating parameters...

Kristina Hill - Professor, Landscape Architecture and Environmental Planning

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Air pollution can have major effects on people's health, with impacts ranging from asthma to Type II diabetes. We wanted to support SF Bay Area disadvantaged communities by giving them data that tracks their exposure to pollutants like PM2.5. By making an interpolated surface of Purple Air sensor data for...

Julian Hong - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

The Hong lab is part of the UCSF Department of Radiation Oncology and Bakar Computational Health Sciences Institute. We focus on combining clinical domain knowledge with data science to generate insights from real world data, develop actionable computational tools, and evaluate the benefit of these advances for personalized cancer care...

Guo Huang - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

As shown in our recent publication (Hirose*, Payumo*, et al Science 2019), we aim to understand the divergent regenerative potential in ontogeny and phylogeny. For example, heart regeneration is remarkably robust in adult zebrafish and newborn mice while very limited in adult mammals. We use the heart as a model...

Guo Huang - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

We aim to study whether there are extreme physiological phenomena (1) in individuals with healthy low heart rates (less than 45 beats/min) and (2) among identical twins that can not be explained by any known biological mechanism. We will exploit classical and non-classical model systems to explore these...

Guo Huang - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Current studies of mouse heart regeneration are largely limited to postmortem analysis of heart tissue to explore cellular activity and molecular mechanisms. We aim to combine a novel imaging window system designed and surgically implanted on the mouse chest by the Huang Lab at UCSF with the free-space angular...

Guo Huang - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

There are emerging AI-trained models that integrate tremendous genomic, genetic and gene expression datasets to successfully predict complex gene networks and functional outcomes after in silico gene perturbation. Now we are exploring these models to understand organ physiology and pathology from developmental and evolutionary perspectives. ------------------------- Publications from previous URAP...

Sarah Inkelis - Professor, Neurology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

The Dyslexia Phenotyping Project involves a large-scale collaboration of UCSF investigators to understand the phenotype (the neural, genetic, cognitive, and behavioral expression) of dyslexia throughout the lifespan. Our aim is not only to identify language-specific weaknesses associated with dyslexia, but also the associated individual strengths. Participants complete a...

Susan Ivey - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 3-5 hrs     Location: On Campus

We are looking for one junior student who would be interested in working with Dr. Susan Ivey and Dr. Winston Tseng (School of Public Health) to analyze county-level data on overdoses and deaths from overdose, risk factors, and harm reduction policies (fentanyl testing, xylazine testing, Narcan) to evaluate programs...

Susan Ivey - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

We are seeking 1 additional student for Spring. This project is a consortium of UCB, CSUEB/CSULB, and community colleges around the state to shape a training program in PH informatics which is use of data and visualization of data for public health surveillance, disease tracking, program evaluation, and mapping...

Susan Ivey - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Students will be trained to take blood pressure readings and to use motivational interviewing strategies to help individuals in Alameda and Contra Costa Counties to make change in diet, physical activity, smoking, or other lifestyle behaviors. Coaches will work 1:1 with participants to give telephone and person to person support...

Susan Ivey - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

This is a qualitative study of Medicaid-insured pregnant patients and barriers to care in safety net obstetric settings. Patients are in the UCSF system and will be interviewed about barriers to care and videovisit access using open-ended questions, in English and Spanish...

Richard Ivry - Professor, Psychology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Research in our laboratory addresses how people learn new motor skills. We study this topic using behavioral and computational methods with healthy and neurologically impaired humans. The neurological studies examine the contribution of different brain structures, especially the cerebellum and basal ganglia, in motor learning to develop functional hypotheses regarding...

Richard Ivry - Professor, Psychology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Aims: While humans are remarkably adept at adjusting their movements to operate in uncertain environments, motor control remains a major challenge for AI systems. This project aims to study the computational rules underlying human motor control to improve algorithms for human-like robots: 1. We will conduct longitudinal studies to...

Richard Ivry - Professor, Psychology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

The goal of this project is to test the efficacy of a new non-invasive brain stimulation (NIBS) device that has been developed at Berkeley. NIBS methods have been around for about 40 years and involve applying weak electrical or magnetic fields to the scalp (non-invasive) in order to...

Babak Javid - Professor, Medicine/Experimentsl Medicine

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: Off Campus

We have shown (in unpublished data) that antibodies specific for Mycobacterium tuberculosis (Mtb), complexed to live Mtb, can stimulate NLRP3 inflammasomes -- a multi-protein complex that is involved in pro-inflammatory signaling. However, the precise molecular mechanisms are not known. In this URAP project, the student will use latex-beads...

Babak Javid - Professor, Medicine/Experimentsl Medicine

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: Off Campus

Almost everything known about bacterial protein synthesis is from the study of "canonical" mRNAs in E. coli and other model organisms. However, many bacteria translate non-canonical mRNAs. A quarter of mRNAs in mycobacteria lack 5' UTRs -- but the "rules" governing leaderless translation are not fully understood. This project will...

Sona Kang - Professor, Nutritional Sciences and Toxicology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

DNA methylation is a reversible epigenetic mark involving the covalent transfer of a methyl group to the C-5 position of a cytosine residue and is mediated by DNA methyltransferases (DNMTs). DNMT1 maintains DNA methylation patterns during DNA replication, while DNMT3A and DNMT3B are involved in establishing de novo patterns...

Galateia Kazakia - Professor, UC San Francisco, Electrical Engineering and Computer Science

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: Off Campus

Our research group focuses on advanced imaging techniques for the study of musculoskeletal structure and function (for details please see: http://www.radiology.ucsf.edu/research/kazakia). For this project, we plan to use two recently developed imaging tools to investigate the structure and composition of bone. State-of-the-art micro computed...

Galateia Kazakia - Professor, UC San Francisco, Electrical Engineering and Computer Science

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: Off Campus

Our research group focuses on advanced imaging techniques for the study of musculoskeletal structure and function (for details please see: http://www.radiology.ucsf.edu/research/kazakia). For this project, we will be performing advanced image processing and analysis on high resolution computed tomography (CT) images of the skeleton. These images are being...

Andrew Kim - Professor, Anthropology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

This project examines the neuroendocrine, immunological, and psychiatric pathways underlying the consequences of trauma exposure in adults living in South Africa. Data come from two separate studies: the first on intergenerational trauma from apartheid in a longitudinal birth cohort study in Soweto, South Africa and the second on long COVID...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Microbiomes change over time, often with important functional consequences for their hosts. But the ecological drivers of microbiome succession are poorly understood. We are studying the role that microbial interactions play in this process by examining the constituents of the digestive microbiome of the insectivorous California pitcher plant (Darlingtonia californica...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Phage, viruses that infect and kill bacteria, are ubiquitous, yet their impacts on beneficial bacteria that colonize plants are not well understood. Phage are abundant in the soil and therefore soil-dwelling bacteria must hone defenses against phage in order to survive. Likewise, phage must hone their capacity to infect...

Britt Koskella - Professor, Integrative Biology

Status: Check back for status     Weekly Hours: 6-8 hrs     Location: On Campus

We are building a new system (fire blight of pear trees) to better understand how bacteriophage viruses might impact the ability of a bacterial pathogen (Erwinia amylovora) to colonize and infect pear trees. We are tracking bacteria-phage interactions through time by isolating individual phages from each of 25 diseased...

Britt Koskella - Professor, Integrative Biology

Status: Check back for status     Weekly Hours: 6-8 hrs     Location: On Campus

In natural systems, microorganisms interact with myriad other microbial populations which influence their evolution and ecology. When associated with a eukaryotic host, these complex microbial communities (known as microbiomes) also interact with and impact their host’s ecology and evolution, nutrient acquisition, and pathogen susceptibility. Despite the microbiome's vast importance on...

Ksenia Krasileva - Professor, Plant and Microbial Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Filamentous fungi are hosts to pathogens such as viruses, bacteria, parasitic fungi, and grazing nematodes. Besides RNAi to protect fungal genomes from mycoviruses, a fungal inducible defense upon recognition of bacteria has yet to be fully described. Genes encoding nucleotide-binding domain Leucine-rich repeat-like (NLR-like) proteins are...

Ksenia Krasileva - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Plants have powerful defense mechanisms, which rely on an arsenal of plant immune receptors. Major classes of plant immune receptors include Receptor like kinases (RLKs), receptor like proteins (RLPs), and Nucleotide Binding Leucine Rich Repeat (NLR) proteins. On the population level, plant immune receptors provide plants with enough diversity to...

Ksenia Krasileva - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Plant diseases pose a significant threat to global agricultural crop production. Developing genetically modified plants with boosted disease resistance offers an economical and environmental solution. Plant immune receptors are naturally evolved resistance determinants that recognize target pathogen molecules to initiate defense responses. They have been widely used as transgenes. However...

Ksenia Krasileva - Professor, Plant and Microbial Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Stripe rust along with stem and leaf rust are the major threat to wheat production worldwide. It is estimated that wheat rust pathogens cause a global annual loss of approximately 15 million tons, with a value of US$ 2.9 billion. Plant breeders are constantly putting in the effort to develop...

Layla Kwong - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Influenzas infect 3-5 million hosts annually. Originating in avian hosts, novel strains of influenza virus have high mortality when they are transmitted to humans. Live poultry markets, including those in Bangladesh, are known focal points of disease transmission. We have collected data on building dynamics, worker exposures, and airborne avian...

Layla Kwong - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

In large parts of Sub Saharan Africa, health facilities (e.g. hospitals and clinics) lack appropriate energy infrastructure. In the Democratic Republic of the Congo, where much of the continent's unelectrified are exposed to both climate and conflict pressures, the near-total absence of a central grid requires the health sector...

Layla Kwong - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Exposure to animal feces can cause diarrhea, but not all animal feces are the same. While chicken poop can cause many child health issues, cow dung is used for many practical and spiritual purposes. What are people using cow dung for? How does this affect their spiritual lives, health, and...