1
|
Miller ADC, Chowdhury SP, Hanson HW, Linderman SK, Ghasemi HI, Miller WD, Morrissey MA, Richardson CD, Gardner BM, Mukherjee A. Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types. J Biol Eng 2024; 18:30. [PMID: 38649904 PMCID: PMC11035135 DOI: 10.1186/s13036-024-00424-5] [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: 09/26/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
Collapse
Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hadley W Hanson
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Sarah K Linderman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Wyatt D Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Meghan A Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Arnab Mukherjee
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Bioengineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemistry, University of California, Santa Barbara, CA, 93106, USA.
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.
| |
Collapse
|
2
|
Liu B, Westman Z, Richardson K, Lim D, Stottlemyer AL, Farmer T, Gillis P, Hooshyar N, Vlcek V, Christopher P, Abu-Omar MM. Polyurethane Foam Chemical Recycling: Fast Acidolysis with Maleic Acid and Full Recovery of Polyol. ACS Sustain Chem Eng 2024; 12:4435-4443. [PMID: 38516400 PMCID: PMC10952008 DOI: 10.1021/acssuschemeng.3c07040] [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: 10/27/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/23/2024]
Abstract
Chemical recycling of polyurethane (PU) waste is essential to displace the need for virgin polyol production and enable sustainable PU production. Currently, less than 20% of PU waste is downcycled through rebinding to lower value products than the original PU. Chemical recycling of PU waste often requires significant input of materials like solvents and slow reaction rates. Here, we report the fast (<10 min) and solvent-free acidolysis of a model toluene diisocyanate (TDI)-based flexible polyurethane foam (PUF) at <200 °C using maleic acid (MA) with a recovery of recycled polyol (repolyol) in 95% isolated yield. After workup (hydrolysis of repolyl ester and separations), the repolyol exhibits favorable physical properties that are comparable to the virgin polyol; these include 54.1 mg KOH/g OH number and 624 cSt viscosity. Overall, 80% by weight of the input PUF is isolated into two clean-cut fractions containing the repolyol and toluene diamine (TDA). Finally, end-of-life (EOL) mattress PUF waste is recycled successfully with high recovery of repolyol using MA acidolysis. The solvent-free and fast acidolysis with MA demonstrated in this work with both model and EOL PUF provides a potential pathway for sustainable and closed-loop PU production.
Collapse
Affiliation(s)
- Baoyuan Liu
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
| | - Zach Westman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kelsey Richardson
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Dingyuan Lim
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
| | | | - Thomas Farmer
- The
Dow Chemical Company, Midland, Michigan 48640, United States
| | - Paul Gillis
- The
Dow Chemical Company, Midland, Michigan 48640, United States
| | - Nasim Hooshyar
- The
Dow Chemical Company, Herbert H Dowweg 5, Hoek 4542 NH,The Netherlands
| | - Vojtech Vlcek
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
| | - Phillip Christopher
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Mahdi M. Abu-Omar
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| |
Collapse
|
3
|
Kam JA, Cornejo M, Arch DN, Salehuddin AS. Using resilience theory to examine undocumented students' "know your rights" family communication. Cultur Divers Ethnic Minor Psychol 2024:2024-52697-001. [PMID: 38330369 DOI: 10.1037/cdp0000642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
OBJECTIVES Prior research has found that to keep their family safe, some undocumented immigrants in the United States engage in "Know Your Rights" family communication-talking to family about their rights, should they be approached by the police or U.S. Immigration and Customs Enforcement (ICE). Although "Know Your Rights" family communication plays a functional role, this study used resilience theory to examine when such communication can be a promotive factor and a risk factor. METHOD To test the hypotheses, we utilized three waves of survey data, with 1-month intervals, from 366 U.S. undocumented college students primarily from Latin America (76% cisgender women; Mage = 22 years, SD = 4.26). Path analysis was employed. RESULTS We found that "Know Your Rights" family communication at Wave 1 was positively associated with: (a) greater knowledge of how to respond if approached by police or ICE and (b) greater knowledge of how to help their family if detained 1 month later (Wave 2). Through both types of knowledge taken together, "Know Your Rights" family communication was indirectly associated with higher levels of felt safety 2 months later (Wave 3). Nevertheless, through knowledge of how to help family, "Know Your Rights" family communication was also indirectly associated with higher levels of anxiety 2 months later (Wave 3). CONCLUSION Given the distribution of "Know Your Rights" information on college campuses, our findings can provide evidence for the utility of such messages, while also potentially identifying when it is associated with higher levels of anxiety. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
Collapse
Affiliation(s)
- Jennifer A Kam
- Department of Communication, University of California, Santa Barbara
| | | | - Dina Naji Arch
- Department of Education, University of California, Santa Barbara
| | | |
Collapse
|
4
|
Caves EM, Fernández-Juricic E, Kelley LA. Ecological and morphological correlates of visual acuity in birds. J Exp Biol 2024; 227:jeb246063. [PMID: 38126722 PMCID: PMC10906485 DOI: 10.1242/jeb.246063] [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: 05/05/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Birds use their visual systems for important tasks, such as foraging and predator detection, that require them to resolve an image. However, visual acuity (the ability to perceive spatial detail) varies by two orders of magnitude across birds. Prior studies indicate that eye size and aspects of a species' ecology may drive variation in acuity, but these studies have been restricted to small numbers of species. We used a literature review to gather data on acuity measured either behaviorally or anatomically for 94 species from 38 families. We then examined how acuity varies in relation to (1) eye size, (2) habitat spatial complexity, (3) habitat light level, (4) diet composition, (5) prey mobility and (6) foraging mode. A phylogenetically controlled model including all of the above factors as predictors indicated that eye size and foraging mode are significant predictors of acuity. Examining each ecological variable in turn revealed that acuity is higher in species whose diet comprises vertebrates or scavenged food and whose foraging modes require resolving prey from farther away. Additionally, species that live in spatially complex, vegetative habitats have lower acuity than expected for their eye sizes. Together, our results suggest that the need to detect important objects from far away - such as predators for species that live in open habitats, and food items for species that forage on vertebrate and scavenged prey - has likely been a key driver of higher acuity in some species, helping us to elucidate how visual capabilities may be adapted to an animal's visual needs.
Collapse
Affiliation(s)
- Eleanor M. Caves
- University of California Santa Barbara, Department of Ecology, Evolution, and Marine Biology, Santa Barbara, CA 93106, USA
- University of Exeter, Centre for Ecology and Conservation, Penryn, Cornwall TR10 9FE, UK
| | | | - Laura A. Kelley
- University of Exeter, Centre for Ecology and Conservation, Penryn, Cornwall TR10 9FE, UK
| |
Collapse
|
5
|
Peterson JA, Neris NM, Read de Alaniz J. Tethered together: DASA design towards aqueous compatibility. Chem Sci 2023; 14:13025-13030. [PMID: 38023491 PMCID: PMC10664598 DOI: 10.1039/d3sc02835f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Donor-acceptor Stenhouse adducts (DASAs) are an exciting class of photoswitches due to their facile tunability, visible light absorbance, and negative photochromism. While they have shown use in a variety of applications, to date all reported DASA derivatives have low equilibrium and/or poor photoswitching in polar protic solvents, which is vital for moving towards applications in biological systems. We demonstrate a strategy to introduce a substitution on the DASA triene that results in derivatives that are stable and have high dark equilibrium of the open form in polar protic solvents. Decreasing the charge separation of these new derivatives also allows for reversible switching in polar and protic solvents including THF : water mixtures.
Collapse
Affiliation(s)
- Julie A Peterson
- Department of Chemistry and Biochemistry, University of California, Santa Barbara Santa Barbara 93106 CA USA
| | - Natalia M Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara Santa Barbara 93106 CA USA
| | - Javier Read de Alaniz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara Santa Barbara 93106 CA USA
| |
Collapse
|
6
|
Kraskura K, Hardison EA, Eliason EJ. Body size and temperature affect metabolic and cardiac thermal tolerance in fish. Sci Rep 2023; 13:17900. [PMID: 37857749 PMCID: PMC10587238 DOI: 10.1038/s41598-023-44574-w] [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: 01/20/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Environmental warming is associated with reductions in ectotherm body sizes, suggesting that larger individuals may be more vulnerable to climate change. The mechanisms driving size-specific vulnerability to temperature are unknown but are required to finetune predictions of fisheries productivity and size-structure community responses to climate change. We explored the potential metabolic and cardiac mechanisms underlying these body size vulnerability trends in a eurythermal fish, barred surfperch. We acutely exposed surfperch across a large size range (5-700 g) to four ecologically relevant temperatures (16 °C, 12 °C, 20 °C, and 22 °C) and subsequently, measured their metabolic capacity (absolute and factorial aerobic scopes, maximum and resting metabolic rates; AAS, FAS, MMR, RMR). Additionally, we estimated the fish's cardiac thermal tolerance by measuring their maximum heart rates (fHmax) across acutely increasing temperatures. Barred surfperch had parallel hypoallometric scaling of MMR and RMR (exponent 0.81) and a weaker hypoallometric scaling of fHmax (exponent - 0.05) across all test temperatures. In contrast to our predictions, the fish's aerobic capacity was maintained across sizes and acute temperatures, and larger fish had greater cardiac thermal tolerance than smaller fish. These results demonstrate that thermal performance may be limited by different physiological constraints depending on the size of the animal and species of interest.
Collapse
Affiliation(s)
- Krista Kraskura
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA.
| | - Emily A Hardison
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Erika J Eliason
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| |
Collapse
|
7
|
Cáceres JC, Dolmatch A, Greene BL. The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate. J Am Chem Soc 2023; 145:22504-22515. [PMID: 37797332 PMCID: PMC10591478 DOI: 10.1021/jacs.3c07256] [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: 07/08/2023] [Indexed: 10/07/2023]
Abstract
Pyruvate Formate Lyase (PFL) catalyzes acetyl transfer from pyruvate to coenzyme a by a mechanism involving multiple amino acid radicals. A post-translationally installed glycyl radical (G734· in Escherichia coli) is essential for enzyme activity and two cysteines (C418 and C419) are proposed to form thiyl radicals during turnover, yet their unique roles in catalysis have not been directly demonstrated with both structural and electronic resolution. Methacrylate is an isostructural analog of pyruvate and an informative irreversible inhibitor of pfl. Here we demonstrate the mechanism of inhibition of pfl by methacrylate. Treatment of activated pfl with methacrylate results in the conversion of the G734· to a new radical species, concomitant with enzyme inhibition, centered at g = 2.0033. Spectral simulations, reactions with methacrylate isotopologues, and Density Functional Theory (DFT) calculations support our assignment of the radical to a C2 tertiary methacryl radical. The reaction is specific for C418, as evidenced by mass spectrometry. The methacryl radical decays over time, reforming G734·, and the decay exhibits a H/D solvent isotope effect of 3.4, consistent with H-atom transfer from an ionizable donor, presumably the C419 sulfhydryl group. Acrylate also inhibits PFL irreversibly, and alkylates C418, but we did not observe an acryl secondary radical in H2O or in D2O within 10 s, consistent with our DFT calculations and the expected reactivity of a secondary versus tertiary carbon-centered radical. Together, the results support unique roles of the two active site cysteines of PFL and a C419 S-H bond dissociation energy between that of a secondary and tertiary C-H bond.
Collapse
Affiliation(s)
- Juan Carlos Cáceres
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
| | - August Dolmatch
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Brandon L. Greene
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| |
Collapse
|
8
|
Cho H, Lee J, Nho H, Lee K, Gim B, Lee J, Lee J, Ewert KK, Li Y, Feinstein SC, Safinya CR, Jin KS, Choi MC. Synchrotron X-ray study of intrinsically disordered and polyampholytic Tau 4RS and 4RL under controlled ionic strength. Eur Phys J E Soft Matter 2023; 46:73. [PMID: 37653246 DOI: 10.1140/epje/s10189-023-00328-0] [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] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Aggregated and hyperphosphorylated Tau is one of the pathological hallmarks of Alzheimer's disease. Tau is a polyampholytic and intrinsically disordered protein (IDP). In this paper, we present for the first time experimental results on the ionic strength dependence of the radius of gyration (Rg) of human Tau 4RS and 4RL isoforms. Synchrotron X-ray scattering revealed that 4RS Rg is regulated from 65.4 to 58.5 Å and 4RL Rg is regulated from 70.9 to 57.9 Å by varying ionic strength from 0.01 to 0.592 M. The Rg of 4RL Tau is larger than 4RS at lower ionic strength. This result provides an insight into the ion-responsive nature of intrinsically disordered and polyampholytic Tau, and can be implicated to the further study of Tau-Tau and Tau-tubulin intermolecular structure in ionic environments.
Collapse
Affiliation(s)
- Hasaeam Cho
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Jimin Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Hanjoon Nho
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Keunmin Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Bopil Gim
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Juncheol Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Jaehee Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea
| | - Kai K Ewert
- Materials Department, Molecular, Cellular, and Developmental Biology Department, Physics Department, and Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA, 93106, USA
| | - Stuart C Feinstein
- Molecular, Cellular, and Developmental Biology Department, College of Creative Studies Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Cyrus R Safinya
- Materials Department, Molecular, Cellular, and Developmental Biology Department, Physics Department, and Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106, USA
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
- Division of Advanced Nuclear Engineering, POSTECH, Pohang, 37673, Korea
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 305-701, Korea.
| |
Collapse
|
9
|
Hardison EA, Schwieterman GD, Eliason EJ. Diet changes thermal acclimation capacity, but not acclimation rate, in a marine ectotherm ( Girella nigricans) during warming. Proc Biol Sci 2023; 290:20222505. [PMID: 36987639 PMCID: PMC10050929 DOI: 10.1098/rspb.2022.2505] [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: 12/14/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Global climate change is increasing thermal variability in coastal marine environments and the frequency, intensity and duration of marine heatwaves. At the same time, food availability and quality are being altered by anthropogenic environmental changes. Marine ectotherms often cope with changes in temperature through physiological acclimation, which can take several weeks and is a nutritionally demanding process. Here, we tested the hypothesis that different ecologically relevant diets (omnivorous, herbivorous, carnivorous) impact thermal acclimation rate and capacity, using a temperate omnivorous fish as a model (opaleye, Girella nigricans). We measured acute thermal performance curves for maximum heart rate because cardiac function has been observed to set upper thermal limits in ectotherms. Opaleye acclimated rapidly after raising water temperatures, but their thermal limits and acclimation rate were not affected by their diet. However, the fish's acclimation capacity for maximum heart rate was sensitive to diet, with fish in the herbivorous treatment displaying the smallest change in heart rate throughout acclimation. Mechanistically, ventricle fatty acid composition differed with diet treatment and was related to cardiac performance in ways consistent with homoviscous adaptation. Our results suggest that diet is an important, but often overlooked, determinant of thermal performance in ectotherms on environmentally relevant time scales.
Collapse
Affiliation(s)
| | - Gail D. Schwieterman
- University of California, Santa Barbara, CA 93106, USA
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | | |
Collapse
|
10
|
Tadres D, Wong PH, To T, Moehlis J, Louis M. Depolarization block in olfactory sensory neurons expands the dimensionality of odor encoding. Sci Adv 2022; 8:eade7209. [PMID: 36525486 PMCID: PMC9757753 DOI: 10.1126/sciadv.ade7209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 05/20/2023]
Abstract
Upon strong and prolonged excitation, neurons can undergo a silent state called depolarization block that is often associated with disorders such as epileptic seizures. Here, we show that neurons in the peripheral olfactory system undergo depolarization block as part of their normal physiological function. Typically, olfactory sensory neurons enter depolarization block at odor concentrations three orders of magnitude above their detection threshold, thereby defining receptive fields over concentration bands. The silencing of high-affinity olfactory sensory neurons produces sparser peripheral odor representations at high-odor concentrations, which might facilitate perceptual discrimination. Using a conductance-based model of the olfactory transduction cascade paired with spike generation, we provide numerical and experimental evidence that depolarization block arises from the slow inactivation of sodium channels-a process that could affect a variety of sensory neurons. The existence of ethologically relevant depolarization block in olfactory sensory neurons creates an additional dimension that expands the peripheral encoding of odors.
Collapse
Affiliation(s)
- David Tadres
- Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philip H. Wong
- Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Thuc To
- Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jeff Moehlis
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Matthieu Louis
- Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA
- Corresponding author.
| |
Collapse
|
11
|
Aralis Z, Comer S, Ansorg H, Palmer C, Smith J, Feinstein SC, Fitzgibbons LN, Arias C. Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay. Diagnostics (Basel) 2022; 12:2805. [PMID: 36428863 PMCID: PMC9689663 DOI: 10.3390/diagnostics12112805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022] Open
Abstract
The emergence of the SARS-CoV-2 Omicron variant in 2021 is associated with a global surge of cases in late 2021 and early 2022. Identifying the introduction of novel SARS-CoV-2 variants to a population is imperative to inform decisions by clinicians and public health officials. Here, we describe a quantitative reverse transcription PCR-based assay (RT-qPCR) targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 viral genomes. This assay accurately and precisely detect the presence of these Omicron variants in patient samples in less than four hours. Using this assay, we tested 270 clinical samples and detected the introduction of Omicron BA.1/BA1.1 and BA.2 in the Santa Barbara County (SBC) population in December 2021 and February 2022, respectively. Identifying Omicron variants using this RT-qPCR assay showed complete concordance with whole viral genome sequencing; both assays indicated that Omicron was the dominant variant in SB County. Our data substantiate that RT-qPCR-based virus detection assays offer a fast and inexpensive alternative to NGS for virus variant-specific detection approach, which allows streamlining the detection of Omicron variants in patient samples.
Collapse
Affiliation(s)
- Zach Aralis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Stewart Comer
- Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA
- Department of Pathology, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA
- Pacific Diagnostic Laboratories, Santa Barbara, CA 93106, USA
| | - Henning Ansorg
- Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA
| | - Carl Palmer
- LegacyWorks Group, Santa Barbara, CA 93106, USA
| | - Jennifer Smith
- California NanoSystems Institute, University of California, Santa Barbara, CA 93106, USA
| | - Stuart C. Feinstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Lynn N. Fitzgibbons
- Department of Medical Education, Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
- Infectious Disease Initiative, Chan Zuckerberg BioHub, San Francisco, CA 93106, USA
| |
Collapse
|
12
|
Ewe CK, Sommermann EM, Kenchel J, Flowers SE, Maduro MF, Joshi PM, Rothman JH. Feedforward regulatory logic controls the specification-to-differentiation transition and terminal cell fate during Caenorhabditis elegans endoderm development. Development 2022; 149:dev200337. [PMID: 35758255 PMCID: PMC10656426 DOI: 10.1242/dev.200337] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/13/2022] [Indexed: 11/20/2023]
Abstract
The architecture of gene regulatory networks determines the specificity and fidelity of developmental outcomes. We report that the core regulatory circuitry for endoderm development in Caenorhabditis elegans operates through a transcriptional cascade consisting of six sequentially expressed GATA-type factors that act in a recursive series of interlocked feedforward modules. This structure results in sequential redundancy, in which removal of a single factor or multiple alternate factors in the cascade leads to a mild or no effect on gut development, whereas elimination of any two sequential factors invariably causes a strong phenotype. The phenotypic strength is successfully predicted with a computational model based on the timing and levels of transcriptional states. We found that one factor in the middle of the cascade, END-1, which straddles the distinct events of specification and differentiation, functions in both processes. Finally, we reveal roles for key GATA factors in establishing spatial regulatory state domains by repressing other fates, thereby defining boundaries in the digestive tract. Our findings provide a paradigm that could account for the genetic redundancy observed in many developmental regulatory systems.
Collapse
Affiliation(s)
- Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Erica M. Sommermann
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Josh Kenchel
- Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Chemical and Biomolecular Engineering Department, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sagen E. Flowers
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Morris F. Maduro
- Molecular, Cell and Systems Biology Department, University of California Riverside, Riverside, CA 92521, USA
| | - Pradeep M. Joshi
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Joel H. Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| |
Collapse
|
13
|
Zhao L, Seshadri S, Liang X, Bailey SJ, Haggmark M, Gordon M, Helgeson ME, Read de Alaniz J, Luzzatto-Fegiz P, Zhu Y. Depinning of Multiphase Fluid Using Light and Photo-Responsive Surfactants. ACS Cent Sci 2022; 8:235-245. [PMID: 35233455 PMCID: PMC8875439 DOI: 10.1021/acscentsci.1c01127] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 05/03/2023]
Abstract
The development of noninvasive and robust strategies for manipulation of droplets and bubbles is crucial in applications such as boiling and condensation, electrocatalysis, and microfluidics. In this work, we realize the swift departure of droplets and bubbles from solid substrates by introducing photoresponsive surfactants and applying asymmetric illumination, thereby inducing a "photo-Marangoni" lift force. Experiments show that a pinned toluene droplet can depart the substrate in only 0.38 s upon illumination, and the volume of an air bubble at departure is reduced by 20%, indicating significantly faster departure. These benefits can be achieved with moderate light intensities and dilute surfactant concentrations, without specially fabricated substrates, which greatly facilitates practical applications. Simulations suggest that the net departure force includes contributions from viscous stresses directly caused by the Marangoni flow, as well as from pressure buildup due to flow stagnation at the contact line. The manipulation scheme proposed here shows potential for applications requiring droplet and bubble removal from working surfaces.
Collapse
Affiliation(s)
- Lei Zhao
- Department
of Mechanical Engineering, University of
California, Santa Barbara, Santa
Barbara, California 93106-5070, United States
| | - Serena Seshadri
- Department
of Chemistry, University of California at
Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Xichen Liang
- Department
of Chemical Engineering, University of California
at Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Sophia J. Bailey
- Department
of Chemistry, University of California at
Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Michael Haggmark
- Department
of Chemical Engineering, University of California
at Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Michael Gordon
- Department
of Chemical Engineering, University of California
at Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Matthew E. Helgeson
- Department
of Chemical Engineering, University of California
at Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Javier Read de Alaniz
- Department
of Chemistry, University of California at
Santa Barbara, Santa Barbara, California 93106-5070, United States
| | - Paolo Luzzatto-Fegiz
- Department
of Mechanical Engineering, University of
California, Santa Barbara, Santa
Barbara, California 93106-5070, United States
| | - Yangying Zhu
- Department
of Mechanical Engineering, University of
California, Santa Barbara, Santa
Barbara, California 93106-5070, United States
| |
Collapse
|
14
|
Touchton AJ, Wu G, Hayton TW. [Ni 30S 16(PEt 3) 11]: An Open-shell Nickel Sulfide Nanocluster with a “Metal-like” Core. Chem Sci 2022; 13:5171-5175. [PMID: 35655571 PMCID: PMC9093199 DOI: 10.1039/d2sc00960a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
Reaction of [Ni(1,5-cod)2] (30 equiv.) with PEt3 (46 equiv.) and S8 (1.9 equiv.) in toluene, followed by heating at 115 °C for 16 h, results in the formation of the atomically precise nanocluster (APNC), [Ni30S16(PEt3)11] (1), in 14% isolated yield. Complex 1 represents the largest open-shell Ni APNC yet isolated. In the solid state, 1 features a compact “metal-like” core indicative of a high degree of Ni–Ni bonding. Additionally, SQUID magnetometry suggests that 1 possesses a manifold of closely-spaced electronic states near the HOMO–LUMO gap. In situ monitoring by ESI-MS and 31P{1H} NMR spectroscopy reveal that 1 forms via the intermediacy of smaller APNCs, including [Ni8S5(PEt3)7] and [Ni26S14(PEt3)10] (2). The latter APNC was also characterized by X-ray crystallography and features a nearly identical core structure to that found in 1. This work demonstrates that large APNCs with a high degree of metal–metal bonding are isolable for nickel, and not just the noble metals. The atomically-precise nanocluster, [Ni30S16(PEt3)11], features a compact “metal-like” core indicative of a high degree of Ni–Ni bonding, along with an open-shell ground state.![]()
Collapse
Affiliation(s)
- Alexander J Touchton
- Department of Chemistry and Biochemistry, University of California Santa Barbara California 93106 USA
| | - Guang Wu
- Department of Chemistry and Biochemistry, University of California Santa Barbara California 93106 USA
| | - Trevor W Hayton
- Department of Chemistry and Biochemistry, University of California Santa Barbara California 93106 USA
| |
Collapse
|
15
|
Tuholske C, Halpern BS, Blasco G, Villasenor JC, Frazier M, Caylor K. Mapping global inputs and impacts from of human sewage in coastal ecosystems. PLoS One 2021; 16:e0258898. [PMID: 34758036 PMCID: PMC8580218 DOI: 10.1371/journal.pone.0258898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/06/2021] [Accepted: 10/07/2021] [Indexed: 11/19/2022] Open
Abstract
Coastal marine ecosystems face a host of pressures from both offshore and land-based human activity. Research on terrestrial threats to coastal ecosystems has primarily focused on agricultural runoff, specifically showcasing how fertilizers and livestock waste create coastal eutrophication, harmful algae blooms, or hypoxic or anoxic zones. These impacts not only harm coastal species and ecosystems but also impact human health and economic activities. Few studies have assessed impacts of human wastewater on coastal ecosystems and community health. As such, we lack a comprehensive, fine-resolution, global assessment of human sewage inputs that captures both pathogens and nutrient flows to coastal waters and the potential impacts on coastal ecosystems. To address this gap, we use a new high-resolution geospatial model to measure and map nitrogen (N) and pathogen-fecal indicator organisms (FIO)-inputs from human sewage for ~135,000 watersheds globally. Because solutions depend on the source, we separate nitrogen and pathogen inputs from sewer, septic, and direct inputs. Our model indicates that wastewater adds 6.2Tg nitrogen into coastal waters, which is approximately 40% of total nitrogen from agriculture. Of total wastewater N, 63% (3.9Tg N) comes from sewered systems, 5% (0.3Tg N) from septic, and 32% (2.0Tg N) from direct input. We find that just 25 watersheds contribute nearly half of all wastewater N, but wastewater impacts most coastlines globally, with sewered, septic, and untreated wastewater inputs varying greatly across watersheds and by country. Importantly, model results find that 58% of coral and 88% of seagrass beds are exposed to wastewater N input. Across watersheds, N and FIO inputs are generally correlated. However, our model identifies important fine-grained spatial heterogeneity that highlight potential tradeoffs and synergies essential for management actions. Reducing impacts of nitrogen and pathogens on coastal ecosystems requires a greater focus on where wastewater inputs vary across the planet. Researchers and practitioners can also overlay these global, high resolution, wastewater input maps with maps describing the distribution of habitats and species, including humans, to determine the where the impacts of wastewater pressures are highest. This will help prioritize conservation efforts.Without such information, coastal ecosystems and the human communities that depend on them will remain imperiled.
Collapse
Affiliation(s)
- Cascade Tuholske
- Department of Geography, University of California, Santa Barbara, CA, United States of America
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA, United States of America
- Center for International for International Earth Science Information Network, the Columbia Climate School and its Earth Institute, Columbia University, Palisades, NY, United States of America
- * E-mail:
| | - Benjamin S. Halpern
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA, United States of America
- Bren School of Environmental Science & Management, University of California, Santa Barbara, CA, United States of America
| | - Gordon Blasco
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA, United States of America
| | - Juan Carlos Villasenor
- Bren School of Environmental Science & Management, University of California, Santa Barbara, CA, United States of America
| | - Melanie Frazier
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, CA, United States of America
| | - Kelly Caylor
- Department of Geography, University of California, Santa Barbara, CA, United States of America
- Bren School of Environmental Science & Management, University of California, Santa Barbara, CA, United States of America
| |
Collapse
|
16
|
Tan H, Banerjee A, Shi N, Tang X, Abdel-Fattah A, Squires TM. A two-step strategy for delivering particles to targets hidden within microfabricated porous media. Sci Adv 2021; 7:7/33/eabh0638. [PMID: 34389540 PMCID: PMC8363150 DOI: 10.1126/sciadv.abh0638] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/25/2021] [Indexed: 06/01/2023]
Abstract
The delivery of small particles into porous environments remains highly challenging because of the low permeability to the fluids that carry these colloids. Even more challenging is that the specific location of targets in the porous environment usually is not known and cannot be determined from the outside. Here, we demonstrate a two-step strategy to deliver suspended colloids to targets that are "hidden" within closed porous media. The first step serves to automatically convert any hidden targets into soluto-inertial "beacons," capable of sustaining long-lived solute outfluxes. The second step introduces the deliverable objects, which are designed to autonomously migrate against the solute fluxes emitted by the targets, thereby following chemical trails that lead to the target. Experimental and theoretical demonstrations of the strategy lay out the design elements required for the solute and the deliverable objects, suggesting routes to delivering colloidal objects to hidden targets in various environments and technologies.
Collapse
Affiliation(s)
- Huanshu Tan
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-5080, USA.
| | - Anirudha Banerjee
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-5080, USA
| | - Nan Shi
- Saudi Aramco, EXPEC Advanced Research Center, Dhahran 31311, Saudi Arabia
| | - Xiaoyu Tang
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-5080, USA
| | - Amr Abdel-Fattah
- Saudi Aramco, EXPEC Advanced Research Center, Dhahran 31311, Saudi Arabia
| | - Todd M Squires
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-5080, USA.
| |
Collapse
|
17
|
Steell SC, Cooke SJ, Eliason EJ. Artificial light at night does not alter heart rate or locomotor behaviour in Caribbean spiny lobster ( Panulirus argus): insights into light pollution and physiological disturbance using biologgers. Conserv Physiol 2020; 8:coaa097. [PMID: 33304586 PMCID: PMC7720088 DOI: 10.1093/conphys/coaa097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/08/2020] [Revised: 08/12/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Light pollution is a rapidly growing threat to biodiversity, with many unknown or poorly understood effects on species and ecosystems spanning terrestrial and aquatic environments. Relative to other taxa, the effects of artificial light at night on aquatic invertebrates are poorly understood, despite the abundance and integral significance of invertebrates to marine and freshwater ecosystems. We affixed heart rate and acceleration biologgers to adult Caribbean spiny lobster (Panulirus argus), an ecologically, culturally and economically significant species in the western Atlantic ocean, to test the effect of artificial light at night on this species' physiology and behaviour relative to appropriate controls. The experiment was conducted in a simulated reef mesocosm in The Bahamas with incandescent lighting used to illuminate it at 1 lux, approximating light levels offshore of urban areas. In the conditions tested here, artificial light at night was found to have no effect on heart rate or locomotor activity in P. argus. We observed a dissociation between activity and heart rate at both short-term and long-term temporal scales. Lobsters were more active at night and nocturnal activity was higher in trials closer to new moon; however, heart rate did not vary with diel or lunar cycle. There was less than 8% difference between daytime and night time average heart rate despite the average percentage of time spent active almost tripling in nights versus days, to 19.5% from 7.2%, respectively. Our findings suggest P. argus may have some resilience to low levels of light pollution, which warrants further research on aspects of this species' life history, performance and fitness in the face of this potential anthropogenic disturbance.
Collapse
Affiliation(s)
- S Clay Steell
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Erika J Eliason
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| |
Collapse
|
18
|
Stieglitz J, Hooper PL, Trumble BC, Kaplan H, Gurven MD. Productivity loss associated with functional disability in a contemporary small-scale subsistence population. eLife 2020; 9:e62883. [PMID: 33259289 PMCID: PMC7744098 DOI: 10.7554/elife.62883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/10/2020] [Accepted: 11/30/2020] [Indexed: 12/27/2022] Open
Abstract
In comparative cross-species perspective, humans experience unique physical impairments with potentially large consequences. Quantifying the burden of impairment in subsistence populations is critical for understanding selection pressures underlying strategies that minimize risk of production deficits. We examine among forager-horticulturalists whether compromised bone strength (indicated by fracture and lower bone mineral density, BMD) is associated with subsistence task cessation. We also estimate the magnitude of productivity losses associated with compromised bone strength. Fracture is associated with cessation of hunting, tree chopping, and walking long distances, but not tool manufacture. Age-specific productivity losses from hunting cessation associated with fracture and lower BMD are substantial: ~397 lost kcals/day, with expected future losses of up to 1.9 million kcals (22% of expected production). Productivity loss is thus substantial for high strength and endurance tasks. Determining the extent to which impairment obstructs productivity in contemporary subsistence populations improves our ability to infer past consequences of impairment.
Collapse
Affiliation(s)
- Jonathan Stieglitz
- Université Toulouse 1 CapitoleToulouseFrance
- Institute for Advanced Study in ToulouseToulouseFrance
| | - Paul L Hooper
- Economic Science Institute, Chapman University, 1 University DriveOrangeUnited States
| | - Benjamin C Trumble
- Center for Evolution and Medicine, Life Sciences C, Arizona State UniversityTempeUnited States
- School of Human Evolution and Social Change, Arizona State UniversityTempeUnited States
| | - Hillard Kaplan
- Economic Science Institute, Chapman University, 1 University DriveOrangeUnited States
| | - Michael D Gurven
- Department of Anthropology, University of California, Santa BarbaraSanta BarbaraUnited States
| |
Collapse
|
19
|
Pisor AC, Gervais MM, Purzycki BG, Ross CT. Preferences and constraints: the value of economic games for studying human behaviour. R Soc Open Sci 2020; 7:192090. [PMID: 32742683 PMCID: PMC7353969 DOI: 10.1098/rsos.192090] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 12/01/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
As economic games have spread from experimental economics to other social sciences, so too have critiques of their usefulness for drawing inferences about the 'real world'. What these criticisms often miss is that games can be used to reveal individuals' private preferences in ways that observational and interview data cannot; furthermore, economic games can be designed such that they do provide insights into real-world behaviour. Here, we draw on our collective experience using economic games in field contexts to illustrate how researchers can strategically alter the framing or design of economic games to draw inferences about private-world or real-world preferences. A detailed case study from coastal Colombia provides an example of the subtleties of game design and how games can be combined fruitfully with self-report data. We close with a list of concrete recommendations for how to modify economic games to better match particular research questions and research contexts.
Collapse
Affiliation(s)
- Anne C. Pisor
- Department of Anthropology, Washington State University, Pullman, WA 99164-4910, USA
- Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 LeipzigGermany
| | | | - Benjamin G. Purzycki
- Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 LeipzigGermany
- Department of the Study of Religion, Aarhus University, Aarhus, Denmark
| | - Cody T. Ross
- Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 LeipzigGermany
| |
Collapse
|
20
|
Albertson LK, Sklar LS, Cooper SD, Cardinale BJ. Aquatic macroinvertebrates stabilize gravel bed sediment: A test using silk net-spinning caddisflies in semi-natural river channels. PLoS One 2019; 14:e0209087. [PMID: 30601831 PMCID: PMC6314585 DOI: 10.1371/journal.pone.0209087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 07/11/2018] [Accepted: 11/29/2018] [Indexed: 11/18/2022] Open
Abstract
Organisms can have large effects on the physical properties of the habitats where they live. For example, measurements in laboratory stream microcosms have shown that the presence of silk net-spinning insect larvae (Trichoptera: Hydropsychidae) can increase the shear force required to initiate movement of riverbed sediments. Few studies, however, have moved beyond laboratory settings to quantify the engineering impacts of aquatic insects under more complex field conditions. To bridge the gap between small-scale laboratory experiments and natural stream ecosystems, we conducted experiments in large (50 m2) outdoor river channels where net-spinning aquatic insects were manipulated in sediment patches that were 5 to 25 times larger than in previous studies. We tested whether larvae of two caddisfly species (Arctopsyche californica and Ceratopsyche oslari) influenced the stability of gravel during simulated floods when alone in monoculture and together in polyculture. On average, populations of caddisflies increased the critical shear stress required to initiate sediment movement by 20% compared to treatments without caddisflies. Per capita effects of caddisflies on sediment stability were similar between previous laboratory studies and this field experiment, and Arctopsyche had a larger per capita effect than Ceratopsyche, perhaps because of its larger size and stronger silk. Contrary to prior laboratory flume results, the effects of the two species on critical shear stress when together were similar to the additive expectation of both species when alone, but effects of the two species together were higher than the additive expectation when we accounted for density. Comparisons of total population and per capita effects suggest that caddisfly density, identity, and coexisting species likely have effects on the magnitude of caddisfly impacts on critical shear stress. Our findings imply that consideration of both the abundances and traits of ecosystem engineers is needed to describe and model their effects on sediment mobility.
Collapse
Affiliation(s)
- Lindsey K. Albertson
- Department of Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA, United States of America
- Department of Ecology, Montana State University, Bozeman, MT, United States of America
- * E-mail:
| | - Leonard S. Sklar
- Department of Earth and Climate Sciences, San Francisco State University, San Francisco, CA, United States of America
- Department of Geography, Planning and Environment, Concordia University, De Maisonneuve Blvd. W. Montreal, Quebec, Canada
| | - Scott D. Cooper
- Department of Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA, United States of America
| | - Bradley J. Cardinale
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, United States of America
- Cooperative Institute of Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States of America
| |
Collapse
|
21
|
Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiátová M, Nizhynska V, Kramer EM, Lysak MA, Hodges SA, Nordborg M. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. eLife 2018; 7:e36426. [PMID: 30325307 PMCID: PMC6255393 DOI: 10.7554/elife.36426] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [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: 03/06/2018] [Accepted: 09/17/2018] [Indexed: 12/21/2022] Open
Abstract
The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
Collapse
Affiliation(s)
- Danièle L Filiault
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Evangeline S Ballerini
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Terezie Mandáková
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Gökçe Aköz
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Nathan J Derieg
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Jeremy Schmutz
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jerry Jenkins
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jane Grimwood
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Shengqiang Shu
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Richard D Hayes
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Uffe Hellsten
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Kerrie Barry
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Juying Yan
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | | | - Miroslava Karafiátová
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Elena M Kramer
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
| | - Martin A Lysak
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| |
Collapse
|
22
|
Davison EN, Turner BO, Schlesinger KJ, Miller MB, Grafton ST, Bassett DS, Carlson JM. Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan. PLoS Comput Biol 2016; 12:e1005178. [PMID: 27880785 PMCID: PMC5120784 DOI: 10.1371/journal.pcbi.1005178] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 06/17/2016] [Accepted: 10/03/2016] [Indexed: 11/18/2022] Open
Abstract
Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task") consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory"), in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.
Collapse
Affiliation(s)
- Elizabeth N. Davison
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Benjamin O. Turner
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Kimberly J. Schlesinger
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Michael B. Miller
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Scott T. Grafton
- Department of Psychological & Brain Sciences, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Danielle S. Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jean M. Carlson
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| |
Collapse
|