1
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Yan B, Liu Y, Chen YC, Liu F. External Guide Sequence Effectively Suppresses the Gene Expression and Replication of Herpes Simplex Virus 2. Molecules 2024; 29:2052. [PMID: 38731543 PMCID: PMC11085068 DOI: 10.3390/molecules29092052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Ribonuclease P (RNase P) complexed with an external guide sequence (EGS) represents a promising nucleic acid-based gene targeting approach for gene expression knock-down and modulation. The RNase P-EGS strategy is unique as an EGS can be designed to basepair any mRNA sequence and recruit intracellular RNase P for hydrolysis of the target mRNA. In this study, we provide the first direct evidence that the RNase P-based approach effectively blocks the gene expression and replication of herpes simplex virus 2 (HSV-2), the causative agent of genital herpes. We constructed EGSs to target the mRNA encoding HSV-2 single-stranded DNA binding protein ICP8, which is essential for viral DNA genome replication and growth. In HSV-2 infected cells expressing a functional EGS, ICP8 levels were reduced by 85%, and viral growth decreased by 3000 folds. On the contrary, ICP8 expression and viral growth exhibited no substantial differences between cells expressing no EGS and those expressing a disabled EGS with mutations precluding RNase P recognition. The anti-ICP8 EGS is specific in targeting ICP8 because it only affects ICP8 expression but does not affect the expression of the other viral immediate-early and early genes examined. This study shows the effective and specific anti-HSV-2 activity of the RNase P-EGS approach and demonstrates the potential of EGS RNAs for anti-HSV-2 applications.
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Affiliation(s)
- Bin Yan
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Yujun Liu
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Yuan-Chuan Chen
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, CA 94720, USA
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
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2
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Terasaki Hart DE, Wang IJ. Genomic architecture controls multivariate adaptation to climate change. Glob Chang Biol 2024; 30:e17179. [PMID: 38403891 DOI: 10.1111/gcb.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/11/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024]
Abstract
As climate change advances, environmental gradients may decouple, generating novel multivariate environments that stress wild populations. A commonly invoked mechanism of evolutionary rescue is adaptive gene flow tracking climate shifts, but gene flow from populations inhabiting similar conditions on one environmental axis could cause maladaptive introgression when populations are adapted to different environmental variables that do not shift together. Genomic architecture can play an important role in determining the effectiveness and relative magnitudes of adaptive gene flow and in situ adaptation. This may have direct consequences for how species respond to climate change but is often overlooked. Here, we simulated microevolutionary responses to environmental change under scenarios defined by variation in the polygenicity, linkage, and genetic redundancy of two independent traits, one of which is adapted to a gradient that shifts under climate change. We used these simulations to examine how genomic architecture influences evolutionary outcomes under climate change. We found that climate-tracking (up-gradient) gene flow, though present in all scenarios, was strongly constrained under scenarios of lower linkage and higher polygenicity and redundancy, suggesting in situ adaptation as the predominant mechanism of evolutionary rescue under these conditions. We also found that high polygenicity caused increased maladaptation and demographic decline, a concerning result given that many climate-adapted traits may be polygenic. Finally, in scenarios with high redundancy, we observed increased adaptive capacity. This finding adds to the growing recognition of the importance of redundancy in mediating in situ adaptive capacity and suggests opportunities for better understanding the climatic vulnerability of real populations.
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Affiliation(s)
- Drew E Terasaki Hart
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- The Nature Conservancy, Arlington, Virginia, USA
- CSIRO Environment, Brisbane, Queensland, Australia
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
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3
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Moreno F. Moral reasoning about gang violence in context: A comparative study with children and adolescents exposed to maras in Honduras and not exposed in Nicaragua. Child Dev 2024; 95:e1-e20. [PMID: 37589079 DOI: 10.1111/cdev.13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 08/18/2023]
Abstract
This study examined how youth morally deliberate about conditions of gang violence shaping their communities. Participants (N = 80; 10-11 and 14-15 years; 50% female) exposed to gangs (maras) in Honduras and not exposed to maras in Nicaragua evaluated hypothetical situations of physical harm in contexts of chronic gang violence. Results indicated that mara-exposed youth were more likely to endorse harming a rival gang member in some contexts, but not others. Moreover, in some contexts, males were more likely to endorse harming others as necessary. Few age differences emerged, suggesting comparability among children and adolescents. Discussion focuses on how children and adolescents coordinate different moral and social concepts and concerns pertaining to acts of physical harm in situations involving gangs.
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Affiliation(s)
- Franklin Moreno
- Institute for the Study of Global Racial Justice, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
- Department of Psychology, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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4
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Palominos MF, Muhl V, Richards EJ, Miller CT, Martin CH. Jaw size variation is associated with a novel craniofacial function for galanin receptor 2 in an adaptive radiation of pupfishes. Proc Biol Sci 2023; 290:20231686. [PMID: 37876194 PMCID: PMC10598438 DOI: 10.1098/rspb.2023.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/02/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of novel adaptations in new species is a fundamental question in biology. Here we demonstrate a new role for galr2 in vertebrate craniofacial development using an adaptive radiation of trophic specialist pupfishes endemic to San Salvador Island, Bahamas. We confirmed the loss of a putative Sry transcription factor binding site upstream of galr2 in scale-eating pupfish and found significant spatial differences in galr2 expression among pupfish species in Meckel's cartilage using in situ hybridization chain reaction (HCR). We then experimentally demonstrated a novel role for Galr2 in craniofacial development by exposing embryos to Garl2-inhibiting drugs. Galr2-inhibition reduced Meckel's cartilage length and increased chondrocyte density in both trophic specialists but not in the generalist genetic background. We propose a mechanism for jaw elongation in scale-eaters based on the reduced expression of galr2 due to the loss of a putative Sry binding site. Fewer Galr2 receptors in the scale-eater Meckel's cartilage may result in their enlarged jaw lengths as adults by limiting opportunities for a circulating Galr2 agonist to bind to these receptors during development. Our findings illustrate the growing utility of linking candidate adaptive SNPs in non-model systems with highly divergent phenotypes to novel vertebrate gene functions.
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Affiliation(s)
- M. Fernanda Palominos
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Vanessa Muhl
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Emilie J. Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Craig T. Miller
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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5
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Harris A, Ünal E. The transcriptional regulator Ume6 is a major driver of early gene expression during gametogenesis. Genetics 2023; 225:iyad123. [PMID: 37431893 PMCID: PMC10550318 DOI: 10.1093/genetics/iyad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
The process of gametogenesis is orchestrated by a dynamic gene expression program, where a vital subset constitutes the early meiotic genes. In budding yeast, the transcription factor Ume6 represses early meiotic gene expression during mitotic growth. However, during the transition from mitotic to meiotic cell fate, early meiotic genes are activated in response to the transcriptional regulator Ime1 through its interaction with Ume6. While it is known that binding of Ime1 to Ume6 promotes early meiotic gene expression, the mechanism of early meiotic gene activation remains elusive. Two competing models have been proposed whereby Ime1 either forms an activator complex with Ume6 or promotes Ume6 degradation. Here, we resolve this controversy. First, we identify the set of genes that are directly regulated by Ume6, including UME6 itself. While Ume6 protein levels increase in response to Ime1, Ume6 degradation occurs much later in meiosis. Importantly, we found that depletion of Ume6 shortly before meiotic entry is detrimental to early meiotic gene activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger early meiotic gene expression and produce viable gametes in the absence of Ime1. We conclude that Ime1 and Ume6 form an activator complex. While Ume6 is indispensable for early meiotic gene expression, Ime1 primarily serves as a transactivator for Ume6.
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Affiliation(s)
- Anthony Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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6
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Skinner WM, Petersen NT, Unger B, Tang S, Tabarsi E, Lamm J, Jalalian L, Smith J, Bertholet AM, Xu K, Kirichok Y, Lishko PV. Mitochondrial uncouplers impair human sperm motility without altering ATP content†. Biol Reprod 2023; 109:192-203. [PMID: 37294625 PMCID: PMC10427809 DOI: 10.1093/biolre/ioad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/22/2023] [Accepted: 06/01/2023] [Indexed: 06/11/2023] Open
Abstract
In human spermatozoa, the electrochemical potentials across the mitochondrial and plasma membranes are related to sperm functionality and fertility, but the exact role of each potential has yet to be clarified. Impairing sperm mitochondrial function has been considered as an approach to creating male or unisex contraceptives, but it has yet to be shown whether this approach would ultimately block the ability of sperm to reach or fertilize an egg. To investigate whether the mitochondrial and plasma membrane potentials are necessary for sperm fertility, human sperm were treated with two small-molecule mitochondrial uncouplers (niclosamide ethanolamine and BAM15) that depolarize membranes by inducing passive proton flow, and evaluated the effects on a variety of sperm physiological processes. BAM15 specifically uncoupled human sperm mitochondria while niclosamide ethanolamine induced proton current in the plasma membrane in addition to depolarizing the mitochondria. In addition, both compounds significantly decreased sperm progressive motility with niclosamide ethanolamine having a more robust effect. However, these uncouplers did not reduce sperm adenosine triphosphate (ATP) content or impair other physiological processes, suggesting that human sperm can rely on glycolysis for ATP production if mitochondria are impaired. Thus, systemically delivered contraceptives that target sperm mitochondria to reduce their ATP production would likely need to be paired with sperm-specific glycolysis inhibitors. However, since niclosamide ethanolamine impairs sperm motility through an ATP-independent mechanism, and niclosamide is FDA approved and not absorbed through mucosal membranes, it could be a useful ingredient in on-demand, vaginally applied contraceptives.
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Affiliation(s)
- Will M Skinner
- Endocrinology Graduate Group, University of California, Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Natalie T Petersen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Bret Unger
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Emiliano Tabarsi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Julianna Lamm
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Dewpoint Therapeutics, Boston, Massachusetts, USA
| | - Liza Jalalian
- Department of Obstetrics and Gynecology, University of California, San Francisco Center for Reproductive Health, San Francisco, California, USA
| | - James Smith
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
| | - Ambre M Bertholet
- Department of Physiology, University of California, San Francisco, San Francisco, California, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Yuriy Kirichok
- Department of Physiology, University of California, San Francisco, San Francisco, California, USA
| | - Polina V Lishko
- Endocrinology Graduate Group, University of California, Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Cell Biology & Physiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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7
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Robert Y, Siaraferas T, Fratoni M. Hyper-fidelity depletion with discrete motion for pebble bed reactors. Sci Rep 2023; 13:12711. [PMID: 37543615 PMCID: PMC10404221 DOI: 10.1038/s41598-023-39186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/20/2023] [Indexed: 08/07/2023] Open
Abstract
Hyper-fidelity (HxF) depletion of pebble bed reactors (PBRs) is the capability to model depletion for every pebble while accounting for motion through the core. Previous HxF work demonstrated feasibility to deplete hundreds of thousands of stationary pebbles concurrently within reasonable timeframes. This work illustrates the second step towards HxF, coupling depletion with a discrete motion scheme. The model assumes an ordered bed with pebbles occupying fixed positions. Motion is simplified as discrete since pebbles move in straight lines from one set position to another. The methodology was implemented in Serpent 2, combined with its transport and depletion capabilities. Ad-hoc routines were developed ensuring compatibility with domain decomposition and pebble recirculation after each pass based on discharge criteria and fresh pebble insertion. Capabilities of HxF with discrete motion are demonstrated using a full-scale high-temperature gas-cooled reactor model. Specifically, an approach to equilibrium is performed, and example results are shown for in-core and discarded pebbles. The data illustrates how HxF provides unique insights into PBR fuel, producing information on statistical distributions rather than average values only, as obtained by traditional methods that rely on spectral zoning for depletion. Knowledge of these distributions can greatly improve analysis and assessment of PBRs.
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Affiliation(s)
- Yves Robert
- University of California, Berkeley, Berkeley, CA, 94709, USA.
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8
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Thijssen Q, Quaak A, Toombs J, De Vlieghere E, Parmentier L, Taylor H, Van Vlierberghe S. Volumetric Printing of Thiol-Ene Photo-Cross-Linkable Poly(ε-caprolactone): A Tunable Material Platform Serving Biomedical Applications. Adv Mater 2023; 35:e2210136. [PMID: 36827642 DOI: 10.1002/adma.202210136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/10/2023] [Indexed: 05/12/2023]
Abstract
Current thoroughly described biodegradable and cross-linkable polymers mainly rely on acrylate cross-linking. However, despite the swift cross-linking kinetics of acrylates, the concomitant brittleness of the resulting materials limits their applicability. Here, photo-cross-linkable poly(ε-caprolactone) networks through orthogonal thiol-ene chemistry are introduced. The step-growth polymerized networks are tunable, predictable by means of the rubber elasticity theory and it is shown that their mechanical properties are significantly improved over their acrylate cross-linked counterparts. Tunability is introduced to the materials, by altering Mc (or the molar mass between cross-links), and its effect on the thermal properties, mechanical strength and degradability of the materials is evaluated. Moreover, excellent volumetric printability is illustrated and the smallest features obtained via volumetric 3D-printing to date are reported, for thiol-ene systems. Finally, by means of in vitro and in vivo characterization of 3D-printed constructs, it is illustrated that the volumetrically 3D-printed materials are biocompatible. This combination of mechanical stability, tunability, biocompatibility, and rapid fabrication by volumetric 3D-printing charts a new path toward bedside manufacturing of biodegradable patient-specific implants.
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Affiliation(s)
- Quinten Thijssen
- Polymer Chemistry and Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, Ghent, 9000, Belgium
| | - Astrid Quaak
- Polymer Chemistry and Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, Ghent, 9000, Belgium
| | - Joseph Toombs
- Department of Mechanical Engineering, University of California, Berkeley, 6159 Etcheverry Hall, Berkeley, CA, 94720-1740, USA
| | - Elly De Vlieghere
- Polymer Chemistry and Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, Ghent, 9000, Belgium
| | - Laurens Parmentier
- Polymer Chemistry and Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, Ghent, 9000, Belgium
| | - Hayden Taylor
- Department of Mechanical Engineering, University of California, Berkeley, 6159 Etcheverry Hall, Berkeley, CA, 94720-1740, USA
| | - Sandra Van Vlierberghe
- Polymer Chemistry and Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, Ghent, 9000, Belgium
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9
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Liu Y, Chen YC, Yan B, Liu F. Suppressing Kaposi's Sarcoma-Associated Herpesvirus Lytic Gene Expression and Replication by RNase P Ribozyme. Molecules 2023; 28:molecules28083619. [PMID: 37110852 PMCID: PMC10142857 DOI: 10.3390/molecules28083619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Kaposi's sarcoma, an AIDS-defining illness, is caused by Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic virus. In this study, we engineered ribozymes derived from ribonuclease P (RNase P) catalytic RNA with targeting against the mRNA encoding KSHV immediate early replication and transcription activator (RTA), which is vital for KSHV gene expression. The functional ribozyme F-RTA efficiently sliced the RTA mRNA sequence in vitro. In cells, KSHV production was suppressed with ribozyme F-RTA expression by 250-fold, and RTA expression was suppressed by 92-94%. In contrast, expression of control ribozymes hardly affected RTA expression or viral production. Further studies revealed both overall KSHV early and late gene expression and viral growth decreased because of F-RTA-facilitated suppression of RTA expression. Our results indicate the first instance of RNase P ribozymes having potential for use in anti-KSHV therapy.
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Affiliation(s)
- Yujun Liu
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Yuan-Chuan Chen
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
| | - Bin Yan
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Fenyong Liu
- School of Public Health, University of California, Berkeley, CA 94720, USA
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
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10
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Agwamba KD, Nachman MW. The demographic history of house mice (Mus musculus domesticus) in eastern North America. G3 (Bethesda) 2023; 13:jkac332. [PMID: 36546306 PMCID: PMC9911051 DOI: 10.1093/g3journal/jkac332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/17/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022]
Abstract
The Western European house mouse (Mus musculus domesticus) is a widespread human commensal that has recently been introduced to North America. Its introduction to the Americas is thought to have resulted from the transatlantic movements of Europeans that began in the early 16th century. To study the details of this colonization history, we examine population structure, explore relevant demographic models, and infer the timing of divergence among house mouse populations in the eastern United States using published exome sequences from five North American populations and two European populations. For North American populations of house mice, levels of nucleotide variation were lower, and low-frequency alleles were less common than for European populations. These patterns provide evidence of a mild bottleneck associated with the movement of house mice into North America. Several analyses revealed that one North American population is genetically admixed, which indicates at least two source populations from Europe were independently introduced to eastern North America. Estimated divergence times between North American and German populations ranged between ∼1,000 and 7,000 years ago and overlapped with the estimated divergence time between populations from Germany and France. Demographic models comparing different North American populations revealed that these populations diverged from each other mostly within the last 500 years, consistent with the timing of the arrival of Western European settlers to North America. Together, these results support a recent introduction of Western European house mice to eastern North America, highlighting the effects of human migration and colonization on the spread of an invasive human commensal.
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Affiliation(s)
- Kennedy D Agwamba
- Center for Computational Biology, Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Center for Computational Biology, Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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11
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Reisenman CE, Wong J, Vedagarbha N, Livelo C, Scott K. Taste adaptations associated with host specialization in the specialist Drosophila sechellia. J Exp Biol 2023; 226:jeb244641. [PMID: 36637369 PMCID: PMC10088416 DOI: 10.1242/jeb.244641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023]
Abstract
Chemosensory-driven host plant specialization is a major force mediating insect ecological adaptation and speciation. Drosophila sechellia, a species endemic to the Seychelles islands, feeds and oviposits on Morinda citrifolia almost exclusively. This fruit is harmless to D. sechellia but toxic to other Drosophilidae, including the closely related generalists D. simulans and D. melanogaster, because of its high content of fatty acids. While several olfactory adaptations mediating D. sechellia's preference for its host have been uncovered, the role of taste has been much less examined. We found that D. sechellia has reduced taste and feeding aversion to bitter compounds and host fatty acids that are aversive to D. melanogaster and D. simulans. The loss of aversion to canavanine, coumarin and fatty acids arose in the D. sechellia lineage, as its sister species D. simulans showed responses akin to those of D. melanogaster. Drosophila sechellia has increased taste and feeding responses towards M. citrifolia. These results are in line with D. sechellia's loss of genes that encode bitter gustatory receptors (GRs) in D. melanogaster. We found that two GR genes which are lost in D. sechellia, GR39a.a and GR28b.a, influence the reduction of aversive responses to some bitter compounds. Also, D. sechellia has increased appetite for a prominent host fatty acid compound that is toxic to its relatives. Our results support the hypothesis that changes in the taste system, specifically a reduction of sensitivity to bitter compounds that deter generalist ancestors, contribute to the specialization of D. sechellia for its host.
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Affiliation(s)
- Carolina E. Reisenman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Essig Museum of Entomology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joshua Wong
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Namrata Vedagarbha
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | | | - Kristin Scott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
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12
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Heras J, Martin CH. Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating. PLoS One 2022; 17:e0273177. [PMID: 36112615 PMCID: PMC9481044 DOI: 10.1371/journal.pone.0273177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiations offer an excellent opportunity to understand the eco-evolutionary dynamics of gut microbiota and host niche specialization. In a laboratory common garden, we compared the gut microbiota of two novel derived trophic specialist pupfishes, a scale-eater and a molluscivore, to closely related and distant outgroup generalist populations, spanning both rapid trophic evolution within 10 kya and stable generalist diets persisting over 11 Mya. We predicted an adaptive and highly divergent microbiome composition in the trophic specialists reflecting their rapid rates of craniofacial and behavioral diversification. We sequenced 16S rRNA amplicons of gut microbiomes from lab-reared adult pupfishes raised under identical conditions and fed the same high protein diet. In contrast to our predictions, gut microbiota largely reflected phylogenetic distance among species, rather than generalist or specialist life history, in support of phylosymbiosis. However, we did find significant enrichment of Burkholderiaceae bacteria in replicated lab-reared scale-eater populations. These bacteria sometimes digest collagen, the major component of fish scales, supporting an adaptive shift. We also found some enrichment of Rhodobacteraceae and Planctomycetia in lab-reared molluscivore populations, but these bacteria target cellulose. Overall phylogenetic conservation of microbiome composition contrasts with predictions of adaptive radiation theory and observations of rapid diversification in all other trophic traits in these hosts, including craniofacial morphology, foraging behavior, aggression, and gene expression, suggesting that the functional role of these minor shifts in microbiota will be important for understanding the role of the microbiome in trophic diversification.
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Affiliation(s)
- Joseph Heras
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
- * E-mail:
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
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13
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Patton AH, Richards EJ, Gould KJ, Buie LK, Martin CH. Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation. eLife 2022; 11:e72905. [PMID: 35616528 PMCID: PMC9135402 DOI: 10.7554/elife.72905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/14/2022] [Indexed: 12/30/2022] Open
Abstract
Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. However, adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood and processes for surmounting fitness valleys remain controversial. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically novel pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, estimate genotypic fitness networks, and measure the accessibility of adaptive walks on the fitness landscape. We identified 132 single nucleotide polymorphisms (SNPs) that were significantly associated with fitness in field enclosures. Six out of the 13 regions most strongly associated with fitness contained differentially expressed genes and fixed SNPs between trophic specialists; one gene (mettl21e) was also misexpressed in lab-reared hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that scale-eating specialists are the most isolated of the three species on these networks. Intriguingly, introgressed and de novo variants reduced fitness landscape ruggedness as compared to standing variation, increasing the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and de novo mutations alter the shape of the fitness landscape, providing key connections in adaptive walks circumventing fitness valleys and triggering the evolution of novelty during adaptive radiation.
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Affiliation(s)
- Austin H Patton
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Museum of Vertebrate Zoology, University of California, BerkeleyBerkeleyUnited States
| | - Emilie J Richards
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Museum of Vertebrate Zoology, University of California, BerkeleyBerkeleyUnited States
| | - Katelyn J Gould
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Logan K Buie
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Christopher H Martin
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Museum of Vertebrate Zoology, University of California, BerkeleyBerkeleyUnited States
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14
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Kozminsky M, Carey TR, Sohn LL. DNA-Directed Patterning for Versatile Validation and Characterization of a Lipid-Based Nanoparticle Model of SARS-CoV-2. Adv Sci (Weinh) 2021; 8:e2101166. [PMID: 34672117 PMCID: PMC8646752 DOI: 10.1002/advs.202101166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/16/2021] [Indexed: 05/06/2023]
Abstract
Lipid-based nanoparticles have been applied extensively in drug delivery and vaccine strategies and are finding diverse applications in the coronavirus disease 2019 (COVID-19) pandemic-from vaccine-component encapsulation to modeling the virus, itself. High-throughput, highly flexible methods for characterization are of great benefit to the development of liposomes featuring surface proteins. DNA-directed patterning is one such method that offers versatility in immobilizing and segregating lipid-based nanoparticles for subsequent analysis. Here, oligonucleotides are selectively conjugated onto a glass substrate and then hybridized to complementary oligonucleotides tagged to liposomes, patterning them with great control and precision. The power of DNA-directed patterning is demonstrated by characterizing a novel recapitulative lipid-based nanoparticle model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-S-liposomes-that presents the SARS-CoV-2 spike (S) protein on its surface. Patterning a mixture of S-liposomes and liposomes that display the tetraspanin CD63 to discrete regions of a substrate shows that angiotensin-converting enzyme 2 (ACE2) specifically binds to S-liposomes. Subsequent introduction of S-liposomes to ACE2-expressing cells tests the biological function of S-liposomes and shows agreement with DNA-directed patterning-based assays. Finally, multiplexed patterning of S-liposomes verifies the performance of commercially available neutralizing antibodies against the two S variants. Overall, DNA-directed patterning enables a wide variety of custom assays for the characterization of any lipid-based nanoparticle.
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Affiliation(s)
- Molly Kozminsky
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeley174 Stanley HallBerkeleyCA94720USA
| | - Thomas R. Carey
- UC Berkeley–UC San Francisco Graduate Program in BioengineeringUniversity of California, Berkeley306 Stanley HallBerkeleyCA94720USA
| | - Lydia L. Sohn
- UC Berkeley–UC San Francisco Graduate Program in BioengineeringUniversity of California, Berkeley306 Stanley HallBerkeleyCA94720USA
- Department of Mechanical EngineeringUniversity of CaliforniaBerkeley5118 Etcheverry HallBerkeleyCA94720USA
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15
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Ferrick A, Wright V, Manga M, Sitar N. Microstructural differences between naturally-deposited and laboratory beach sands. Granul Matter 2021; 24:9. [PMID: 34785989 PMCID: PMC8581122 DOI: 10.1007/s10035-021-01169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
The orientation of, and contacts between, grains of sand reflect the processes that deposit the sands. Grain orientation and contact geometry also influence mechanical properties. Quantifying and understanding sand microstructure thus provide an opportunity to understand depositional processes better and connect microstructure and macroscopic properties. Using x-ray computed microtomography, we compare the microstructure of naturally-deposited beach sands and laboratory sands created by air pluviation in which samples are formed by raining sand grains into a container. We find that naturally-deposited sands have a narrower distribution of coordination number (i.e., the number of grains in contact) and a broader distribution of grain orientations than pluviated sands. The naturally-deposited sand grains orient inclined to the horizontal, and the pluviated sand grains orient horizontally. We explain the microstructural differences between the two different depositional methods by flowing water at beaches that re-positions and reorients grains initially deposited in unstable grain configurations.
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Affiliation(s)
- Amy Ferrick
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, California 94720 USA
| | - Vanshan Wright
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543 USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037 USA
| | - Michael Manga
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, California 94720 USA
| | - Nicholas Sitar
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California 94720 USA
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16
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Lien KA, Dinshaw K, Nichols RJ, Cassidy-Amstutz C, Knight M, Singh R, Eltis LD, Savage DF, Stanley SA. A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife 2021; 10:e74358. [PMID: 34751132 PMCID: PMC8635971 DOI: 10.7554/elife.74358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/06/2021] [Indexed: 01/18/2023] Open
Abstract
Encapsulin nanocompartments are an emerging class of prokaryotic protein-based organelle consisting of an encapsulin protein shell that encloses a protein cargo. Genes encoding nanocompartments are widespread in bacteria and archaea, and recent works have characterized the biochemical function of several cargo enzymes. However, the importance of these organelles to host physiology is poorly understood. Here, we report that the human pathogen Mycobacterium tuberculosis (Mtb) produces a nanocompartment that contains the dye-decolorizing peroxidase DyP. We show that this nanocompartment is important for the ability of Mtb to resist oxidative stress in low pH environments, including during infection of host cells and upon treatment with a clinically relevant antibiotic. Our findings are the first to implicate a nanocompartment in bacterial pathogenesis and reveal a new mechanism that Mtb uses to combat oxidative stress.
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Affiliation(s)
- Katie A Lien
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Kayla Dinshaw
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Robert J Nichols
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Matthew Knight
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Rahul Singh
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - David F Savage
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, BerkeleyBerkeleyUnited States
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17
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Abstract
Cation-chloride-cotransporters (CCCs) catalyze transport of Cl- with K+ and/or Na+across cellular membranes. CCCs play roles in cellular volume regulation, neural development and function, audition, regulation of blood pressure, and renal function. CCCs are targets of clinically important drugs including loop diuretics and their disruption has been implicated in pathophysiology including epilepsy, hearing loss, and the genetic disorders Andermann, Gitelman, and Bartter syndromes. Here we present the structure of a CCC, the Mus musculus K+-Cl- cotransporter (KCC) KCC4, in lipid nanodiscs determined by cryo-EM. The structure, captured in an inside-open conformation, reveals the architecture of KCCs including an extracellular domain poised to regulate transport activity through an outer gate. We identify binding sites for substrate K+ and Cl- ions, demonstrate the importance of key coordinating residues for transporter activity, and provide a structural explanation for varied substrate specificity and ion transport ratio among CCCs. These results provide mechanistic insight into the function and regulation of a physiologically important transporter family.
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Affiliation(s)
- Michelle S Reid
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
| | - David M Kern
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
| | - Stephen Graf Brohawn
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
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18
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Schultink A, Qi T, Bally J, Staskawicz B. Using forward genetics in Nicotiana benthamiana to uncover the immune signaling pathway mediating recognition of the Xanthomonas perforans effector XopJ4. New Phytol 2019; 221:1001-1009. [PMID: 30156705 DOI: 10.1111/nph.15411] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/23/2018] [Indexed: 05/22/2023]
Abstract
The immune pathway responsible for perception of the Xanthomonas perforans effector XopJ4 was identified in the plant Nicotiana benthamiana. This pathogen causes significant yield loss in commercial tomato cultivation. Genetic mapping and viral-induced gene silencing were used to identify immune signaling components of the XopJ4 perception pathway in N. benthamiana. Transient complementation assays were performed to determine the functionality of gene variants and co-immunoprecipitation assays were used to gain insight into the molecular mechanism of the pathway. Two N. benthamiana ethyl methanesulfonate (EMS) mutants deficient for XopJ4 perception were identified as having loss-of-function mutations in the gene encoding the nucleotide binding, leucine-rich repeat (NLR) protein NbZAR1. Silencing of a receptor-like cytoplasmic kinase family XII gene, subsequently named XOPJ4 IMMUNITY 2 (JIM2), blocks perception of XopJ4. This study demonstrates the feasibility of conducting mutant screens in N. benthamiana to investigate the genetic basis of the plant immune system and other processes. The identification of NbZAR1 and JIM2 as mediating XopJ4 perception in N. benthamiana supports the model of ZAR1 being involved in the perception of many different pathogen effector proteins with specificity dictated by associated receptor-like cytoplasmic kinases.
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Affiliation(s)
- Alex Schultink
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Tiancong Qi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Qld, 4001, Australia
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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19
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Shive KL, Preisler HK, Welch KR, Safford HD, Butz RJ, O'Hara KL, Stephens SL. From the stand scale to the landscape scale: predicting the spatial patterns of forest regeneration after disturbance. Ecol Appl 2018; 28:1626-1639. [PMID: 29809291 DOI: 10.1002/eap.1756] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/18/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Shifting disturbance regimes can have cascading effects on many ecosystems processes. This is particularly true when the scale of the disturbance no longer matches the regeneration strategy of the dominant vegetation. In the yellow pine and mixed conifer forests of California, over a century of fire exclusion and the warming climate are increasing the incidence and extent of stand-replacing wildfire; such changes in severity patterns are altering regeneration dynamics by dramatically increasing the distance from live tree seed sources. This has raised concerns about limitations to natural reforestation and the potential for conversion to non-forested vegetation types, which in turn has implications for shifts in many ecological processes and ecosystem services. We used a California region-wide data set with 1,848 plots across 24 wildfires in yellow pine and mixed conifer forests to build a spatially explicit habitat suitability model for forecasting postfire forest regeneration. To model the effect of seed availability, the critical initial biological filter for regeneration, we used a novel approach to predicting spatial patterns of seed availability by estimating annual seed production from existing basal area and burn severity maps. The probability of observing any conifer seedling in a 60-m2 area (the field plot scale) was highly dependent on 30-yr average annual precipitation, burn severity, and seed availability. We then used this model to predict regeneration probabilities across the entire extent of a "new" fire (the 2014 King Fire), which highlights the spatial variability inherent in postfire regeneration patterns. Such forecasts of postfire regeneration patterns are of importance to land managers and conservationists interested in maintaining forest cover on the landscape. Our tool can also help anticipate shifts in ecosystem properties, supporting researchers interested in investigating questions surrounding alternative stable states, and the interaction of altered disturbance regimes and the changing climate.
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Affiliation(s)
- Kristen L Shive
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94703, USA
| | - Haiganoush K Preisler
- USDA Forest Service, Pacific Southwest Research Station, Albany, California, 94710, USA
| | - Kevin R Welch
- Department of Environmental Science and Policy, University of California, Davis, California, 95616, USA
| | - Hugh D Safford
- USDA Forest Service, Pacific Southwest Region, Vallejo, California, 94592, USA
- Department of Environmental Science and Policy, University of California, Davis, California, 95616, USA
| | - Ramona J Butz
- USDA Forest Service, Pacific Southwest Region, Vallejo, California, 94592, USA
- Department of Forestry and Wildland Resources, Humboldt State University, Arcata, California, 95521, USA
| | - Kevin L O'Hara
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94703, USA
| | - Scott L Stephens
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94703, USA
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