URAP

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: Full- no new appr needed     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: Current Term Now Closed     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...

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...

Kristina Hill - Professor, Landscape Architecture and Environmental Planning

Status: Current Term Now Closed     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...

Laurence Huang - Professor, UC San Francisco

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

Chronic obstructive pulmonary disease (COPD) is the most frequent HIV-associated chronic lung disease and its clinical significance is increasing as the HIV+ population ages worldwide. Although both HIV-related and COPD-specific causes are postulated, our understanding of the mechanisms underlying HIV+ COPD is limited. An improved understanding is...

Susan Ivey - Professor, Public Health

Status: Current Term Now Closed     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 Fall. 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...

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

Research in our laboratory addresses various aspects of human performance and cognition, and how these abilities are impacted by degenerative neurological disorders such as Parkinson's disease or cerebellar degeneration. We are looking for an apprentice who could help with running and programming online experiments...

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: Current Term Now Closed     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: Current Term Now Closed     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: 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 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...

Mimi Koehl - Professor, Integrative Biology

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

We are studying the biomechanics and biofluiddynamics of how organisms interact with their physical environments. Our interdisciplinary work is at the interface between biology and engineering, so students majoring in biology, engineering, physics, or math have all participated in research in our lab. There are a variety of projects that...

Michelle Koo - Staff Curator, Museum of Vertebrate Zoology

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

The world's natural history museums are responsible for documenting over 1.8 billion species known as a result of 300 years of biological exploration of the planet. The information contained in museums include observational and specimen-based data, text, images, sound and video and form the foundation of what we know...

Michelle Koo - Staff Curator, Museum of Vertebrate Zoology

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

The Museum of Vertebrate Zoology (MVZ) is a vibrant research and informatics center for the campus and the natural history communities around the world. The world's natural history museums are responsible for documenting over 1.8 billion species known as a result of 300 years of biological exploration of the planet...

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: Current Term Now Closed     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: Current Term Now Closed     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: Full- no new appr needed     Weekly Hours: 12 or more hours     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: Current Term Now Closed     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: Current Term Now Closed     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...

Layla Kwong - Professor, Public Health

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

As temperatures continue to rise, workplace heat exposure presents an increasing challenge to occupational health and safety. This reality positions climate change as an important labor rights issue. Workers in developing countries will be among those most affected. Still, there exists limited research on the impacts of climate change on...

Peggy G. Lemaux - Professor of Cooperative Extension, Plant and Microbial Biology

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

General Description and Research Approach. Every country is facing effects of climate change – not just heatwaves but also more severe and frequent rainstorms, increased threat of wildfires and more intense drought. All these factors have negative effects on crop yields, causing food insecurity worldwide. Greenhouse gases, e.g., CO2, and methane...

Peggy G. Lemaux - Professor of Cooperative Extension, Plant and Microbial Biology

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

Sorghum (Sorghum bicolor L. Moench), is the fifth most important cereal crop worldwide and is a critical food, forage, and emerging biofuel crop. Understanding the photosynthetic mechanisms by which sorghum can capture sunlight more efficiently under adverse climate conditions is critical to using this crop to remove carbon dioxide that...

Dennis Levi - Professor, Optometry

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

Research in my lab focuses on how we perceive visual forms and patterns, and how form and depth perception are degraded by abnormal visual experience early in life (amblyopia). Specifically, we use psychophysics, eye-movements, computational modelling and brain imaging (fMRI) to study the neural mechanisms of normal pattern vision...

Dennis Levi - Professor, Optometry

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

Most observers experience the world in three dimensions (3D) made possible by a combination of monocular and binocular cues to depth. In Amblyopia, a developmental disorder of spatial vision, a significant portion of observers have very coarse or no stereopsis (a cue for 3D perception). Previous research has shown that...

Dennis Levi - Professor, Optometry

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

Amblyopia is a neurodevelopmental disorder of spatial vision characterized by a reduction in visual acuity. Previous research has shown that several neuro, oculomotor and perceptual deficits are also present in persons with amblyopia. Particularly, research has shown that amblyopes have longer saccadic and manual latencies to stimuli (i.e., the time...

Dennis Levi - Professor, Optometry

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

Most people with degraded vision (amblyopia) lack 3D-depth vision (stereoblindness). Using a simple training, the depth perceptual sense can be recovered and some people can experience depth in 3D movie theatres for the first time. The goal of the project is to test this phenomenon extensively and investigate what...

Jennifer Lewis - Professor, Plant and Microbial Biology

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

The plant pathogen Pseudomonas syringae causes disease in a large number of different plant species, using the type III secretion system to secrete and translocate effector proteins into the plant. Many of these effector proteins are believed to function primarily in the suppression of host defense signaling. However recognition of...

Jennifer Lewis - Professor, Plant and Microbial Biology

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

The plant pathogen Pseudomonas syringae causes disease in a large number of different plant species. Virulence is primarily achieved by the type III secretion system, which secretes and translocates effector proteins into the plant. Many of these effector proteins are believed to suppress host defense signaling. However recognition of these...

Samantha Lewis - Professor, Molecular and Cell Biology

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

Fatty acid entry into peripheral tissues is known to contribute to the onset of metabolic disorders, such as non-alcoholic fatty liver disease (NAFLD) and Type 2 diabetes mellitus (T2DM). Mitochondria play a crucial role in the oxidation, synthesis, and storage of fatty acids, and there is evidence to suggest...