University of California, Berkeley
  • Berkeley, CA, United States
Recent publications
Lipids are structurally diverse biomolecules that serve multiple roles in cells. As such, they are used as biomarkers in the modern ocean and as paleoproxies to explore the geological past. Here, I review lipid geochemistry, biosynthesis, and compartmentalization; the varied uses of lipids as biomarkers; and the evolution of analytical techniques used to measure and characterize lipids. Advancements in high-resolution accurate-mass mass spectrometry have revolutionized the lipidomic and metabolomic fields, both of which are quickly being integrated into marine meta-omic studies. Lipidomics allows us to analyze tens of thousands of features, providing an open analytical window and the ability to quantify unknown compounds that can be structurally elucidated later. However, lipidome annotation is not a trivial matter and represents one of the biggest challenges for oceanographers, owing in part to the lack of marine lipids in current in silico databases and data repositories. A case study reveals the gaps in our knowledge and open opportunities to answer fundamental questions about molecular-level control of chemical reactions and global-scale patterns in the lipidscape. Expected final online publication date for the Annual Review of Marine Science, Volume 15 is January 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Elastomeric bridge bearings are widely used in bridges to accommodate the deformations produced by mechanical and environmental loads. As their acceptable performance is critical for the bridge performance, finite element analysis (FEA) can be applied to supplement test results on the performance of elastomeric bearings. However, uncertainties are present in both the material properties of their components and the boundary conditions. Therefore, this study provides an initial exploration on how these uncertainties will affect the performance of the bearings under compression. The elastomeric bridge bearing is first modeled using the finite element (FE) method, and then probabilistic analysis is applied using the Monte Carlo simulation (MCS). Material properties of the elastomer and steel components of the bearing and the friction coefficient at the bearing–support interfaces are treated as random variables, and a probabilistic analysis is performed that shows how specific parameters will influence the output response, including the vertical stiffness, and induced stresses and strains. In addition, the study also provides an initial exploration into the sensitivity of the bearing’s response to epistemic uncertainties in these input parameters. The probabilistic FEA results can ease the development of numerical models of elastomeric bridge bearings, and they can be used to improve the code provisions associated with the design of these bearings.
Masonry arch bridges are numerous across European transportation networks. Many are ageing structures, with service lives of 100–150 years to date, and exhibit historic damage and repairs, leading to uncertainty regarding structural behaviour. For skewed bridges particularly, this can be complicated and three-dimensional, and detailed experimental data describing behaviour are rare. In 2018–2019, the authors deployed Fibre Bragg Grating (FBG) strain monitoring at a recently repaired, skewed masonry rail bridge in the UK. Following an on-site trial, the FBG monitoring system was substantially upgraded in 2020 to enable long-term, autonomous, remote sensing. This new system is introduced, including processes to automate data classification based on the date and time of measurements, and train class/operator, direction, and speed. This system has recorded the bridge responses to thousands of trains. Data analysis is presented, focusing particularly on seasonal and long-term variation of behaviour. Findings include the impact of ambient temperature; an inverse relationship is observed. Decreasing temperature causes thermal contraction of the masonry, allowing cracks to open and increasing the potential for bridge movements. After decoupling such effects, residual long-term changes may correspond to damage. Therefore, this system can provide valuable asset management information on the early onset of bridge deterioration.
Historically, Southern California suffers from the worst traffic congestion and air quality levels in the country. During the COVID-19 pandemic in 2020, we observed a major reduction in economic and social activities within the region, leading to changes in roadway traffic and air pollution levels in a variety of ways. Within six weeks of the pandemic-induced lockdowns, freeway traffic volume dropped as low as 50%; however, it has since gradually increased back to pre-pandemic levels. The changes in freeway traffic volume have not been uniform across the Southern California region, and neighborhoods with different socio-economic profiles were affected differently. These disparities have brought up environmental justice concerns, particularly for disadvantaged communities that live adjacent to major roadways and warehouse centers. We monitored the changes in vehicle and human activities across communities in Southern California and explored correlations that are useful for developing various mitigation measures at both the local and regional levels. In this study, we go beyond regional analysis and examine the effects of the pandemic on traffic at a transportation corridor and local levels to examine possible equity issues. Results show that, in general, the level of traffic dropped less in disadvantaged neighborhoods during the pandemic. Further, traffic flow rebounded in these neighborhoods faster than in other communities.
During the COVID-19 outbreak, the risk of infection is not neglectable in a public transportation system. To satisfy the demands while controlling the spread of COVID-19, public transportation agencies have proposed various rules, such as increasing train frequency and requiring face coverings. In this chapter, we summarize newly developed evaluation methodologies, and evaluate the impacts of COVID-19 policies. We also present key findings regarding the impacts of different policies using these new methods. We find that the goal of stopping the pandemic coincided with minimizing the total delay when the service area was homogenous in infection rate. For heterogenous cities, minimizing the risk is equivalent to minimizing weighted travel time, where the weight is the infection rate. We also find that the results obtained from different models could be different due to their assumptions on the lost demand. If the demand is elastic, closing part of the system can prevent the spread of the pandemic, otherwise, closing will lead to longer waiting time, higher passenger density, and infection risk.
The COVID-19 pandemic dramatically affected the ability of localities to pay for their transportation systems. We explore the effects of the pandemic on local option sales taxes (LOSTs), an increasingly common revenue source for transportation in California and across the U.S. LOSTs have many advantages over alternative finance instruments, including that they can raise prodigious amounts of revenue. However, LOSTs rely on consumer spending, which lags during times of economic weakness. This is precisely what we observed in California counties during the initial months of the pandemic. LOST revenues did recover after the initial economic shock of COVID-19, albeit to a lower level than they would likely have otherwise. LOST revenue trends during the pandemic were affected by national and regional economic conditions and government policy as well. This public health crisis illustrates both the pitfalls and resilience of LOSTs during economic downturns and recoveries. The lessons from the pandemic’s effects on LOSTs will be useful for policymakers and analysts in preparing for inevitable future crises and associated economic turbulence.
The global tragedy of the COVID-19 pandemic devastated communities and societies. The pandemic also upended public transit and shared mobility, causing declines in ridership, losses in revenue sources, and challenges in ensuring social equity. Despite ongoing uncertainty, guidance can instruct recovery and build a more resilient, socially equitable, and environmentally friendly transportation future. This chapter summarizes a recent scenario planning exercise conducted by the University of California Institute of Transportation Studies in collaboration with the Transportation Research Board (TRB) Executive Committee in Spring to Fall 2020. The exercise convened 36 transportation experts in the United States who developed policy actions and research options crafted to guide near- and long-term public transit and shared mobility. Clear themes emerged from the study regarding key actions for public transit operators in the areas of: (1) innovation and technology, (2) planning and operations, (3) customer focus, and (4) workforce development. A second grouping of broader policy strategies for both public transit and shared mobility included: (1) immediate policy and actions across actors, (2) alignment of societal objectives, (3) federal transportation spending authorization, and (4) finance and subsidies. While the exercise reiterated the need for rapid actions, thoughtful planning and decision-making can prepare both sectors for a more cooperative, multimodal ecosystem.
During the pandemic, from March 2020 through March 2021, we monitored three San Francisco Bay Area transit agencies: two large—AC Transit and VTA; and one small—Tri Delta Transit. As the lockdown was imposed, white-collar commuters, students and older adults stopped using public transit. Initially, the ridership fell by 90%, and then for a year slowly climbed up to less than 50% for AC Transit and VTA, and to around 60% of the pre-pandemic numbers for Tri Delta Transit. This ridership recovery was not consistent. Local drops occurred during protests in June 2020, during fare reinstatements, and during the second COVID wave in Winter 2021. We found that the agencies’ response to the pandemic consisted of three parts: (1) maintaining health and safety of their employees; (2) minimizing transmission risk for riders by keeping buses clean and enabling social distancing through capping the number of bus passengers; and (3) changing their service. During the pandemic, we also observed a direct relationship between the socioeconomic level of population and transit ridership. More specifically, we observed higher ridership in low-income areas with a high percentage of Latino, Black and Asian population. These communities are populated by people, who generally rent their homes, do not have a car, but need to go to work, either because they belong to an essential workforce and/ or are undocumented immigrants who cannot afford staying jobless. On the other hand, in the wealthy neighborhoods of the Bay Area, transit activity all but disappeared.
Sandy beaches in estuaries and bays (BEBs) are ubiquitous around the world. While some are referred to as “low energy” beaches, there are large differences in wave climate due to fetch, swell exposure and shoreface morphology. In this study, wave-climate controls on BEB morphology are identified relative to bay geometry and focusing on the relative contributions of wind, ocean swell and infragravity waves to the wave signature of a BEB. We focus on two swash-aligned and two drift-aligned BEBs in an urbanized, semi-enclosed bay in SE Australia (Kamay/Botany Bay), with differences in proximity to the bay mouth, beach aspects and fetch, as well as different histories of storm erosion and recovery. Spectral analysis of local wave measurements (June 2018–January 2019) shows that wave signatures at all 4 BEBs are dominated by swell waves (>51%), followed by locally generated wind waves at 3 out of 4 BEBs (<43%), then infragravity waves (<35%). We identified five weather scenarios based on local wind speed/direction and resultant wind waves, combined with infragravity waves, and offshore swell wave conditions. BEBs close to the bay entrance are primarily controlled by swell waves, but at times even BEBs close to the entrance can be sheltered from swell waves depending on their incident angle. Conversely, BEBs farthest from the bay entrance (~8 km) alternated between periods where spectra were dominated by either wind waves or offshore swells. Infragravity waves were only important relative to wind waves and swell at the most sheltered BEBs, where there is limited fetch and swell dissipated over shallow areas. We also show that anthropogenic factors such as constructed revetments or groynes significantly alter wave signatures at BEBs in this bay. Thus, wave spectral signatures are highly variable across BEBs in the same bay and can represent a simple tool to study BEB morphodynamics including storm response and subsequent recovery.
Background Cellular senescence is a complex stress response that impacts cellular function and organismal health. Multiple developmental and environmental factors, such as intrinsic cellular cues, radiation, oxidative stress, oncogenes, and protein accumulation, activate genes and pathways that can lead to senescence. Enormous efforts have been made to identify and characterize senescence genes (SnGs) in stress and disease systems. However, the prevalence of senescent cells in healthy human tissues and the global SnG expression signature in different cell types are poorly understood. Methods This study performed an integrative gene network analysis of bulk and single-cell RNA-seq data in non-diseased human tissues to investigate SnG co-expression signatures and their cell-type specificity. Results Through a comprehensive transcriptomic network analysis of 50 human tissues in the Genotype-Tissue Expression Project (GTEx) cohort, we identified SnG-enriched gene modules, characterized SnG co-expression patterns, and constructed aggregated SnG networks across primary tissues of the human body. Our network approaches identified 51 SnGs highly conserved across the human tissues, including CDKN1A ( p21 )-centered regulators that control cell cycle progression and the senescence-associated secretory phenotype (SASP). The SnG-enriched modules showed remarkable cell-type specificity, especially in fibroblasts, endothelial cells, and immune cells. Further analyses of single-cell RNA-seq and spatial transcriptomic data independently validated the cell-type specific SnG signatures predicted by the network analysis. Conclusions This study systematically revealed the co-regulated organizations and cell type specificity of SnGs in major human tissues, which can serve as a blueprint for future studies to map senescent cells and their cellular interactions in human tissues.
Due to its nature as a strongly correlated quantum liquid, ultracold helium is characterized by the nontrivial interplay of different physical effects. Bosonic $$^4{\text {He}}$$ 4 He exhibits superfluidity and Bose-Einstein condensation. Its physical properties have been accurately determined on the basis of ab initio path integral Monte Carlo (PIMC) simulations. In contrast, the corresponding theoretical description of fermionic $$^3{\text {He}}$$ 3 He is severely hampered by the notorious fermion sign problem, and previous PIMC results have been derived by introducing the uncontrolled fixed-node approximation. In this work, we present extensive new PIMC simulations of normal liquid $$^3{\text {He}}$$ 3 He without any nodal constraints. This allows us to to unambiguously quantify the impact of Fermi statistics and to study the effects of temperature on different physical properties like the static structure factor $$S({\mathbf {q}})$$ S ( q ) , the momentum distribution $$n({\mathbf {q}})$$ n ( q ) , and the static density response function $$\chi ({\mathbf {q}})$$ χ ( q ) . In addition, the dynamic structure factor $$S({\mathbf {q}},\omega )$$ S ( q , ω ) is rigorously reconstructed from imaginary-time PIMC data. From simulations of $$^3{\text {He}}$$ 3 He , we derived the familiar phonon–maxon–roton dispersion function that is well-known for $$^4{\text {He}}$$ 4 He and has been reported previously for two-dimensional $$^3{\text {He}}$$ 3 He films (Nature 483:576–579 (2012)). The comparison of our new results for both $$S({\mathbf {q}})$$ S ( q ) and $$S({\mathbf {q}},\omega )$$ S ( q , ω ) with neutron scattering measurements reveals an excellent agreement between theory and experiment.
Introduction DNA methylation studies have associated methylation levels at different CpG sites or genomic regions with lung function. Moreover, genetic ancestry has been associated with lung function in Latinos. However, no epigenome-wide association study (EWAS) of lung function has been performed in this population. Here, we aimed to identify DNA methylation patterns associated with lung function in pediatric asthma among Latinos. Results We conducted an EWAS in whole blood from 250 Puerto Rican and 148 Mexican American children and young adults with asthma. A total of five CpGs exceeded the genome-wide significance threshold of p = 1.17 × 10 ⁻⁷ in the combined analyses from Puerto Ricans and Mexican Americans: cg06035600 ( MAP3K6 , p = 6.13 × 10 ⁻⁸ ) showed significant association with pre-bronchodilator Tiffeneau–Pinelli index, the probes cg00914963 ( TBC1D16 , p = 1.04 × 10 ⁻⁷ ), cg16405908 ( MRGPRE , p = 2.05 × 10 ⁻⁸ ) , and cg07428101 ( MUC2 , p = 5.02 × 10 ⁻⁹ ) were associated with post-bronchodilator forced vital capacity (FVC), and cg20515679 ( KCNJ6 ) with post-bronchodilator Tiffeneau–Pinelli index ( p = 1.13 × 10 ⁻⁸ ). However, these markers did not show significant associations in publicly available data from Europeans ( p > 0.05). A methylation quantitative trait loci analysis revealed that methylation levels at these CpG sites were regulated by genetic variation in Latinos and the Biobank-based Integrative Omics Studies (BIOS) consortium. Additionally, two differentially methylated regions in REXOC and AURKC were associated with pre-bronchodilator Tiffeneau–Pinelli index (adjusted p < 0.05) in Puerto Ricans and Mexican Americans. Moreover, we replicated some of the previous differentially methylated signals associated with lung function in non-Latino populations. Conclusions We replicated previous associations of epigenetic markers with lung function in whole blood and identified novel population-specific associations shared among Latino subgroups.
Electron-hole asymmetry is a fundamental property in solids that can determine the nature of quantum phase transitions and the regime of operation for devices. The observation of electron-hole asymmetry in graphene and recently in twisted graphene and moiré heterostructures has spurred interest into whether it stems from single-particle effects or from correlations, which are core to the emergence of intriguing phases in moiré systems. Here, we report an effective way to access electron-hole asymmetry in 2D materials by directly measuring the quasiparticle self-energy in graphene/Boron Nitride field-effect devices. As the chemical potential moves from the hole to the electron-doped side, we see an increased strength of electronic correlations manifested by an increase in the band velocity and inverse quasiparticle lifetime. These results suggest that electronic correlations intrinsically drive the electron-hole asymmetry in graphene and by leveraging this asymmetry can provide alternative avenues to generate exotic phases in twisted moiré heterostructures.
Zika virus (ZIKV) is a mosquito-borne arbovirus that can cause severe congenital birth defects. The utmost goal of ZIKV vaccines is to prevent both maternal-fetal infection and congenital Zika syndrome. A Zika purified inactivated virus (ZPIV) was previously shown to be protective in non-pregnant mice and rhesus macaques. In this study, we further examined the efficacy of ZPIV against ZIKV infection during pregnancy in immunocompetent C57BL6 mice and common marmoset monkeys ( Callithrix jacchus ). We showed that, in C57BL/6 mice, ZPIV significantly reduced ZIKV-induced fetal malformations. Protection of fetuses was positively correlated with virus-neutralizing antibody levels. In marmosets, the vaccine prevented vertical transmission of ZIKV and elicited neutralizing antibodies that remained above a previously determined threshold of protection for up to 18 months. These proof-of-concept studies demonstrate ZPIV’s protective efficacy is both potent and durable and has the potential to prevent the harmful consequence of ZIKV infection during pregnancy.
Background For community health workers (CHWs) and promotores de salud (CHWs who primarily serve Latinx communities and are grounded in a social, rather than a clinical model of care) , the process of certification highlights the tension between developing a certified workforce with formal requirements (i.e., certified CHWs) and valuing CHWs, without formal requirements, based on their roles, knowledge, and being part of the communities where they live and work (i.e., non-certified CHWs). California serves as an ideal case study to examine how these two paths can coexist. California’s CHW workforce represents distinct ideologies of care (e.g., clinical CHWs, community-based CHWs, and promotores de salud ) and California stakeholders have debated certification for nearly twenty years but have not implemented such processes. Methods We employed purposive sampling to interview 108 stakeholders (i.e., 66 CHWs, 11 program managers, and 31 system-level participants) to understand their perspectives on the opportunities and risks that certification may raise for CHWs and the communities they serve. We conducted focus groups with CHWs, interviews with program managers and system-level participants, and observations of public forums that discussed CHW workforce issues. We used a thematic analysis approach to identify, analyze, and report themes. Results Some CHW participants supported inclusive certification training opportunities while others feared that certification might erode their identity and undermine their work in communities. Some program managers and system-level participants acknowledged the opportunities of certification but also expressed concerns that certification may distance CHWs from their communities. Program managers and system-level participants also highlighted that certification may not address all challenges related to integrating CHWs into health care systems. CHWs, program managers, and system-level participants agreed that CHWs should be involved in certification discussions and decision making. Conclusions To address participant concerns, our findings recommend California stakeholders build a voluntary certification process structured with multiple pathways to overcome entry barriers of traditional certification processes, maintain CHW identity, and protect diversity within the workforce. Positioning CHWs as decision makers will be critical when designing state certification processes.
Considerable evidence suggests that psychosocial variables can shape the course of bipolar disorder. Here, though, we focus on the more specific idea that the social environment can predict the course of mania. We systematically review evidence from longitudinal studies concerning how social support, family interactions, traumatic life events, and recent life events relate to the age of onset, the frequency of episode recurrence, and the severity of manic symptoms. Although we find some evidence that the course of mania can be worsened by social environmental factors, the links are specific. Among social variables, some studies indicate that conflict and hostility are predictive, but more general social relationship qualities have not been found to predict mania. Some research indicates that childhood trauma, and recent life events involving goal attainment or sleep disruption can predict mania. Taken together, the profile of variables involving recent exposure that are most predictive include those that are activating, reward-related, or sleep-disrupting, which fits with general psychological hypotheses of behavioral activation and sleep disruption as important for mania. We discuss gaps in the literature, and we note future directions for research, including the need for more integrative, longitudinal research on a fuller range of social and biological risk variables.
Background Ambient air pollutant (AAP) exposure is associated with adverse pregnancy outcomes, such as preeclampsia, preterm labor, and low birth weight. Previous studies have shown methylation of immune genes associate with exposure to air pollutants in pregnant women, but the cell-mediated response in the context of typical pregnancy cell alterations has not been investigated. Pregnancy causes attenuation in cell-mediated immunity with alterations in the Th1/Th2/Th17/Treg environment, contributing to maternal susceptibility. We recruited women ( n = 186) who were 20 weeks pregnant from Fresno, CA, an area with chronically elevated AAP levels. Associations of average pollution concentration estimates for 1 week, 1 month, 3 months, and 6 months prior to blood draw were associated with Th cell subset (Th1, Th2, Th17, and Treg) percentages and methylation of CpG sites ( IL4 , IL10, IFNγ, and FoxP3 ). Linear regression models were adjusted for weight, age, season, race, and asthma, using a Q value as the false-discovery-rate-adjusted p -value across all genes. Results Short-term and mid-term AAP exposures to fine particulate matter (PM 2.5 ), nitrogen dioxide (NO 2 ) carbon monoxide (CO), and polycyclic aromatic hydrocarbons (PAH 456 ) were associated with percentages of immune cells. A decrease in Th1 cell percentage was negatively associated with PM 2.5 (1 mo/3 mo: Q < 0.05), NO 2 (1 mo/3 mo/6 mo: Q < 0.05), and PAH 456 (1 week/1 mo/3 mo: Q < 0.05). Th2 cell percentages were negatively associated with PM 2.5 (1 week/1 mo/3 mo/6 mo: Q < 0.06), and NO 2 (1 week/1 mo/3 mo/6 mo: Q < 0.06). Th17 cell percentage was negatively associated with NO 2 (3 mo/6 mo: Q < 0.01), CO (1 week/1 mo: Q < 0.1), PM 2.5 (3 mo/6 mo: Q < 0.05), and PAH 456 (1 mo/3 mo/6 mo: Q < 0.08). Methylation of the IL10 gene was positively associated with CO (1 week/1 mo/3 mo: Q < 0.01), NO 2 (1 mo/3 mo/6 mo: Q < 0.08), PAH 456 (1 week/1 mo/3 mo: Q < 0.01), and PM 2.5 (3 mo: Q = 0.06) while IL4 gene methylation was positively associated with concentrations of CO (1 week/1 mo/3 mo/6 mo: Q < 0.09). Also, IFNγ gene methylation was positively associated with CO (1 week/1 mo/3 mo: Q < 0.05) and PAH 456 (1 week/1 mo/3 mo: Q < 0.06). Conclusion Exposure to several AAPs was negatively associated with T-helper subsets involved in pro-inflammatory and anti-inflammatory responses during pregnancy. Methylation of IL4, IL10 , and IFNγ genes with pollution exposure confirms previous research. These results offer insights into the detrimental effects of air pollution during pregnancy, the demand for more epigenetic studies, and mitigation strategies to decrease pollution exposure during pregnancy.
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins, and some hypothetical proteins. Based on CRISPR spacer targeting, the predominance of bacterial taxonomic affiliations of phage genes with those from Bacteroidetes, and the high sequence similarity of the phage bS21 genes and those from Bacteroidetes classes of Flavobacteriia, Cytophagia and Saprospiria, these phages are predicted to infect diverse Bacteroidetes species that inhabit a range of depths in freshwater lakes. Thus, bS21 phages have the potential to impact microbial community composition and carbon turnover in lake ecosystems. The transcriptionally active bS21-encoding phages were likely in the late stage of replication when collected, as core structural genes and bS21 were highly expressed. Thus, our analyses suggest that the phage bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects preferentially for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.
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Fernando de Juan
  • Department of Physics
Despina Lymperopoulou
  • Department of Plant and Microbial Biology
Peter Hosemann
  • Department of Nuclear Engineering
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