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Colombano DD, Carlson SM, Hobbs JA, Ruhi A. Four decades of climatic fluctuations and fish recruitment stability across a marine-freshwater gradient. Glob Chang Biol 2022; 28:5104-5120. [PMID: 35583053 PMCID: PMC9545339 DOI: 10.1111/gcb.16266] [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: 10/28/2021] [Revised: 04/13/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
Investigating the effects of climatic variability on biological diversity, productivity, and stability is key to understanding possible futures for ecosystems under accelerating climate change. A critical question for estuarine ecosystems is, how does climatic variability influence juvenile recruitment of different fish species and life histories that use estuaries as nurseries? Here we examined spatiotemporal abundance trends and environmental responses of 18 fish species that frequently spend the juvenile stage rearing in the San Francisco Estuary, CA, USA. First, we constructed multivariate autoregressive state-space models using age-0 fish abundance, freshwater flow (flow), and sea surface temperature data (SST) collected over four decades. Next, we calculated coefficients of variation (CV) to assess portfolio effects (1) within and among species, life histories (anadromous, marine opportunist, or estuarine dependent), and the whole community; and (2) within and among regions of the estuary. We found that species abundances varied over space and time (increasing, decreasing, or dynamically stable); and in 83% of cases, in response to environmental conditions (wet/dry, cool/warm periods). Anadromous species responded strongly to flow in the upper estuary, marine opportunist species responded to flow and/or SST in the lower estuary, and estuarine dependent species had diverse responses across the estuary. Overall, the whole community when considered across the entire estuary had the lowest CV, and life histories and species provided strong biological insurance to the portfolio (2.4- to 3.5-fold increases in stability, respectively). Spatial insurance also increased stability, although to a lesser extent (up to 1.6-fold increases). Our study advances the notion that fish recruitment stability in estuaries is controlled by biocomplexity-life history diversity and spatiotemporal variation in the environment. However, intensified drought and marine heatwaves may increase the risk of multiple consecutive recruitment failures by synchronizing species dynamics and trajectories via Moran effects, potentially diminishing estuarine nursery function.
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Affiliation(s)
- Denise D. Colombano
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Stephanie M. Carlson
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - James A. Hobbs
- Region 3 Bay‐Delta Stockton IEP OfficeCalifornia Department of Fish and WildlifeStocktonCaliforniaUSA
| | - Albert Ruhi
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
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2
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Campbell MA, Joslin SEK, Goodbla AM, Willmes M, Hobbs JA, Lewis LS, Finger AJ. Polygenic discrimination of migratory phenotypes in an estuarine forage fish. G3 Genes|Genomes|Genetics 2022; 12:6595021. [PMID: 35640553 PMCID: PMC9339312 DOI: 10.1093/g3journal/jkac133] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/14/2022] [Indexed: 11/24/2022]
Abstract
Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined Restriction site Associated DNA sequencing data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, discriminant analysis of principal components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.
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Affiliation(s)
- Matthew A Campbell
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis , Davis, CA 95616, USA
| | - Shannon E K Joslin
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis , Davis, CA 95616, USA
| | - Alisha M Goodbla
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis , Davis, CA 95616, USA
| | - Malte Willmes
- Institute of Marine Sciences, UC Santa Cruz , Santa Cruz, CA 95064, USA
- National Marine Fisheries Service, Southwest Fisheries Science Center , Santa Cruz, CA 95064, USA
| | - James A Hobbs
- Otolith Geochemistry and Fish Ecology Lab, Department of Wildlife, Fish and Conservation Biology, University of California, Davis , Davis, CA 95616, USA
| | - Levi S Lewis
- Otolith Geochemistry and Fish Ecology Lab, Department of Wildlife, Fish and Conservation Biology, University of California, Davis , Davis, CA 95616, USA
| | - Amanda J Finger
- Genomic Variation Laboratory, Department of Animal Science, University of California, Davis , Davis, CA 95616, USA
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Yanagitsuru YR, Daza IY, Lewis LS, Hobbs JA, Hung TC, Connon RE, Fangue NA. Growth, osmoregulation and ionoregulation of longfin smelt ( Spirinchus thaleichthys) yolk-sac larvae at different salinities. Conserv Physiol 2022; 10:coac041. [PMID: 35795015 PMCID: PMC9252123 DOI: 10.1093/conphys/coac041] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/22/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Longfin smelt (Spirinchus thaleichthys) is a threatened anadromous fish species that spawns in freshwater to moderately brackish (i.e. 5-10 ppt) reaches of the upper San Francisco Estuary and has declined to ~1% of its pre-1980s abundances. Despite 50+ years of population monitoring, the efficacy of 10+ years of conservation efforts for longfin smelt remain uncertain due to a limited understanding of how the species responds to environmental variation, such as salinity. For example, high mortality during larval stages has prevented culture efforts from closing the life cycle in captivity. Here, we investigated the effects of salinity on longfin smelt yolk-sac larvae. Newly hatched larvae from four single-pair crosses were acutely transferred to and reared at salinities of 0.4, 5, 10, 20 or 32 ppt. We compared whole-body water and sodium ion (Na+) content, notochord length and yolk-sac volume at 12, 24, 48, 72, and 96 hours post-transfer for each salinity treatment. We found that larvae maintained osmotic and ionic balance at 0.4-10 ppt, whereas salinities ˃10 ppt resulted in decreased water and increased whole-body Na+ content. We also found that larvae grew largest and survived the longest when reared at 5 and 10 ppt, respectively, and that yolk resorption stalled at 0.4 ppt. Finally, there were significant but small interclutch variations in responses to different salinities, with clutch accounting for <8% of the variance in our statistical models. Overall, our results indicate that longfin smelt yolk-sac larvae likely perform best at moderately brackish conditions, thus yielding a mechanism that explains their distribution in field surveys and providing key information for future conservation efforts.
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Affiliation(s)
- Yuzo R Yanagitsuru
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, 95616, USA
| | - Itza Y Daza
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, 95616, USA
| | - Levi S Lewis
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, 95616, USA
| | - James A Hobbs
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, 95616, USA
- California Department of Fish and Wildlife, Bay-Delta IEP, Stockton, CA, 95206, USA
| | - Tien-Chieh Hung
- Fish Conservation and Culture Laboratory, Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, USA
| | - Richard E Connon
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, CA, 95616, USA
| | - Nann A Fangue
- Corresponding author: Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA. Tel: 530-752-4997.
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Xieu W, Lewis LS, Zhao F, Fichman RA, Willmes M, Hung TC, Ellison L, Stevenson T, Tigan G, Schultz AA, Hobbs JA. Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish. PeerJ 2021; 9:e12280. [PMID: 34820160 PMCID: PMC8605759 DOI: 10.7717/peerj.12280] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such experimental assessments across multiple developmental stages are key steps toward assessing confidence in otolith-derived metrics that are often used to assess the dynamics of wild fish populations.
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Affiliation(s)
- Wilson Xieu
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, United States of America
| | - Levi S Lewis
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, United States of America
| | - Feng Zhao
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, United States of America
| | - Rachel A Fichman
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, United States of America
| | - Malte Willmes
- Institute of Marine Sciences, University of California, Santa Cruz, CA, United States of America.,Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, United States of America
| | - Tien-Chieh Hung
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Luke Ellison
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Troy Stevenson
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Galen Tigan
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Andrew A Schultz
- Bay-Delta Office, United States Bureau of Reclamation, Sacramento, CA, United States of America
| | - James A Hobbs
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, United States of America.,Bay-Delta Region, California Department of Fish and Wildlife, Stockton, CA, United States of America
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Naslund AW, Davis BE, Hobbs JA, Fangue NA, Todgham AE. Warming, not CO2-acidified seawater, alters otolith development of juvenile Antarctic emerald rockcod (Trematomus bernacchii). Polar Biol 2021. [DOI: 10.1007/s00300-021-02923-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe combustion of fossil fuels is currently causing rapid rates of ocean warming and acidification worldwide. Projected changes in these parameters have been repeatedly observed to stress the physiological limits and plasticity of many marine species from the molecular to organismal levels. High latitude oceans are among the fastest changing ecosystems; therefore, polar species are projected to be some of the most vulnerable to climate change. Antarctic species are particularly sensitive to environmental change, having evolved for millions of years under stable ocean conditions. Otoliths, calcified structures found in a fish’s inner ear used to sense movement and direction, have been shown to be affected by both warming and CO2-acidified seawater in temperate and tropical fishes but there is no work to date on Antarctic fishes. In this study, juvenile emerald rockcod (Trematomus bernacchii) were exposed to projected seawater warming and CO2-acidification for the year 2100 over 28 days. Sagittal otoliths were analyzed for changes in area, perimeter, length, width and shape. We found ocean warming increased the growth rate of otoliths, while CO2-acidified seawater and the interaction of warming and acidification did not have an effect on otolith development. Elevated temperature also altered the shape of otoliths. If otolith development is altered under future warming scenarios, sensory functions such as hearing, orientation, and movement may potentially be impaired. Changes in these basic somatic abilities could have broad implications for the general capabilities and ecology of early life stages of Antarctic fishes.
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Lewis LS, Willmes M, Barros A, Crain PK, Hobbs JA. Newly discovered spawning and recruitment of threatened Longfin Smelt in restored and underexplored tidal wetlands. Ecology 2019; 101:e02868. [PMID: 31461779 PMCID: PMC9285352 DOI: 10.1002/ecy.2868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Levi S Lewis
- Wildlife, Fish and Conservation Biology, University of California Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Malte Willmes
- Wildlife, Fish and Conservation Biology, University of California Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Arthur Barros
- Wildlife, Fish and Conservation Biology, University of California Davis, One Shields Avenue, Davis, California, 95616, USA
| | - Patrick K Crain
- Wildlife, Fish and Conservation Biology, University of California Davis, One Shields Avenue, Davis, California, 95616, USA
| | - James A Hobbs
- Wildlife, Fish and Conservation Biology, University of California Davis, One Shields Avenue, Davis, California, 95616, USA
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Willmes M, Lewis LS, Davis BE, Loiselle L, James HF, Denny C, Baxter R, Conrad JL, Fangue NA, Hung TC, Armstrong RA, Williams IS, Holden P, Hobbs JA. Calibrating temperature reconstructions from fish otolith oxygen isotope analysis for California's critically endangered Delta Smelt. Rapid Commun Mass Spectrom 2019; 33:1207-1220. [PMID: 30993783 DOI: 10.1002/rcm.8464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/22/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Oxygen isotope ratios (δ18 O values) of fish otoliths (ear bones) are valuable geochemical tracers of water conditions and thermal life history. Delta Smelt (Hypomesus transpacificus) are osmerid forage fish endemic to the San Francisco Estuary, California, USA, that are on the verge of extinction. These fish exhibit a complex life history that allows them to survive in a dynamic estuarine environment; however, a rapidly warming climate threatens this thermally sensitive species. Here we quantify the accuracy and precision of using δ18 O values in otoliths to reconstruct the thermal life histories of Delta Smelt. METHODS Delta Smelt were reared for 360 days using three different water sources with different ambient δ18 Owater values (-8.75‰, -5.28‰, and -4.06‰) and different water temperatures (16.4°C, 16.7°C, 18.7°C, and 20.5°C). Samples were collected after 170 days (n = 28) and 360 days (n = 14) post-hatch. In situ δ18 O values were measured from the core of the otolith to the dorsal edge using secondary ion mass spectrometry (SIMS) to reconstruct temporally resolved thermal life histories. RESULTS The δ18 Ootolith values for Delta Smelt varied as a linear inverse function of water temperature: 1000 ln α = 18.39 (±0.43, 1SE)(103 TK-1 ) - 34.56 (±1.49, 1SE) and δ18 Ootolith(VPDB) - δ18 Owater (VPDB) = 31.34(±0.09, 1SE) - 0.19(±0.01, 1SE) × T ° C. When the ambient δ18 Owater value is known, this species-specific temperature-dependent oxygen isotope fractionation model facilitated the accurate (0.25°C) and precise (±0.37°C, 2σ) reconstruction of the water temperature experienced by the fish. In contrast, the use of existing general fractionation equations resulted in inaccurate temperature reconstructions. CONCLUSIONS The species-specific δ18 Ootolith fractionation equation allowed for accurate and precise reconstructions of water temperatures experienced by Delta Smelt. Characterization of ambient δ18 Owater values remains a critical next step for reconstructing thermal life histories of wild Delta Smelt. This tool will provide new insights into habitat utilization, potential thermal refugia, and resilience to future warming for this critically endangered fish.
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Affiliation(s)
- Malte Willmes
- Wildlife, Fish and Conservation Biology, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Levi S Lewis
- Wildlife, Fish and Conservation Biology, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Brittany E Davis
- Wildlife, Fish and Conservation Biology, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
- California Department of Water Resources, 1416 9th Street, Sacramento, CA, 95814, USA
| | - Liane Loiselle
- Research School of Earth Sciences, Australian National University, Building 142 Mills Road, Acton, ACT, 2601, Australia
| | - Hannah F James
- Research School of Earth Sciences, Australian National University, Building 142 Mills Road, Acton, ACT, 2601, Australia
| | - Christian Denny
- Wildlife, Fish and Conservation Biology, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Randall Baxter
- California Department of Fish and Wildlife, 1416 9th Street, Sacramento, CA, 95814, USA
| | - J Louise Conrad
- California Department of Water Resources, 1416 9th Street, Sacramento, CA, 95814, USA
| | - Nann A Fangue
- Wildlife, Fish and Conservation Biology, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Tien-Chieh Hung
- Biological and Agricultural Engineering, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Richard A Armstrong
- Research School of Earth Sciences, Australian National University, Building 142 Mills Road, Acton, ACT, 2601, Australia
| | - Ian S Williams
- Research School of Earth Sciences, Australian National University, Building 142 Mills Road, Acton, ACT, 2601, Australia
| | - Peter Holden
- Research School of Earth Sciences, Australian National University, Building 142 Mills Road, Acton, ACT, 2601, Australia
| | - James A Hobbs
- Wildlife, Fish and Conservation Biology, UC Davis, One Shields Avenue, Davis, CA, 95616, USA
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Mahardja B, Hobbs JA, Ikemiyagi N, Benjamin A, Finger AJ. Role of freshwater floodplain-tidal slough complex in the persistence of the endangered delta smelt. PLoS One 2019; 14:e0208084. [PMID: 30601817 PMCID: PMC6314582 DOI: 10.1371/journal.pone.0208084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022] Open
Abstract
Seasonal floodplain wetland is one of the most variable and diverse habitats found in coastal ecosystems, yet it is also one of the most highly altered by humans. The Yolo Bypass, the primary floodplain of the Sacramento River in California's Central Valley, USA, has been shown to provide various benefits to native fishes when inundated. However, the Yolo Bypass exists as a tidal dead-end slough during dry periods and its value to native fishes has been less studied in this state. During the recent drought (2012-2016), we found higher abundance of the endangered Delta Smelt (Hypomesus transpacificus), than the previous 14 years of fish monitoring within the Yolo Bypass. Meanwhile, Delta Smelt abundance elsewhere in the estuary was at record lows during this time. To determine the value of the Yolo Bypass as a nursery habitat for Delta Smelt, we compared growth, hatch dates, and diets of juvenile Delta Smelt collected within the Yolo Bypass with fish collected among other putative nursery habitats in the San Francisco Estuary between 2010 and 2016. Our results indicated that when compared to other areas of the estuary, fish in the Yolo Bypass spawned earlier, and offspring experienced both higher quality feeding conditions and growth rates. The occurrence of healthy juvenile Delta Smelt in the Yolo Bypass suggested that the region may have acted as a refuge for the species during the drought years of 2012-2016. However, our results also demonstrated that no single region provided the best rearing habitat for juvenile Delta Smelt. It will likely require a mosaic of habitats that incorporates floodplain-tidal sloughs in order to promote the resilience of this declining estuarine fish species.
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Affiliation(s)
- Brian Mahardja
- California Department of Water Resources, Division of Environmental Services, West Sacramento, California, United States of America
- * E-mail:
| | - James A. Hobbs
- University of California–Davis, Department of Wildlife, Fish and Conservation Biology, Davis, California, United States of America
| | - Naoaki Ikemiyagi
- California Department of Water Resources, Division of Environmental Services, West Sacramento, California, United States of America
| | - Alyssa Benjamin
- University of California–Davis, Department of Animal Science, Genomic Variation Laboratory, Davis, California, United States of America
| | - Amanda J. Finger
- University of California–Davis, Department of Animal Science, Genomic Variation Laboratory, Davis, California, United States of America
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Willmes M, Ransom KM, Lewis LS, Denney CT, Glessner JJG, Hobbs JA. IsoFishR: An application for reproducible data reduction and analysis of strontium isotope ratios (87Sr/86Sr) obtained via laser-ablation MC-ICP-MS. PLoS One 2018; 13:e0204519. [PMID: 30261018 PMCID: PMC6160113 DOI: 10.1371/journal.pone.0204519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 06/01/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
The IsoFishR application is a data reduction and analysis tool for laser-ablation strontium isotope data, following common best practices and providing reliable and reproducible results. Strontium isotope ratios (87Sr/86Sr) are a powerful geochemical tracer commonly applied in a wide range of scientific fields and laser-ablation inductively coupled mass spectrometry is considered the method of choice to obtain spatially resolved 87Sr/86Sr isotope ratios from a variety of sample materials. However, data reduction and analyses methods are variable between different research groups and research communities limiting reproducibility between studies. IsoFishR provides a platform to standardize these methods and can be used for both spot and time-resolved line transects. Furthermore, it provides advanced data analysis tools and filters for outlier removal, noise reduction, and visualization of time resolved data. The application can be downloaded from GitHub (https://github.com/MalteWillmes/IsoFishR) and the source code is available, encouraging future development and evolution of this software.
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Affiliation(s)
- Malte Willmes
- Department of Wildlife, Fish and Conservation Biology, UC Davis, Davis, California, United States of America
- * E-mail:
| | - Katherine M. Ransom
- Department of Wildlife, Fish and Conservation Biology, UC Davis, Davis, California, United States of America
- Department of Land, Air, and Water Department, UC Davis, Davis, California, United States of America
| | - Levi S. Lewis
- Department of Wildlife, Fish and Conservation Biology, UC Davis, Davis, California, United States of America
| | - Christian T. Denney
- Department of Wildlife, Fish and Conservation Biology, UC Davis, Davis, California, United States of America
| | - Justin J. G. Glessner
- Interdisciplinary Center for Plasma Mass Spectrometry, UC Davis, Davis, California, United States of America
| | - James A. Hobbs
- Department of Wildlife, Fish and Conservation Biology, UC Davis, Davis, California, United States of America
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Hammock BG, Hobbs JA, Slater SB, Acuña S, Teh SJ. Contaminant and food limitation stress in an endangered estuarine fish. Sci Total Environ 2015; 532:316-26. [PMID: 26081734 PMCID: PMC4843802 DOI: 10.1016/j.scitotenv.2015.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 04/30/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
The abundance of Delta Smelt (Hypomesus transpacificus), a fish species endemic to the upper San Francisco Estuary (SFE), is declining. Several causes for the population decline have been proposed, including food limitation and contaminant effects. Here, using juvenile Delta Smelt collected from throughout their range, we measured a suite of indices across three levels of biological organization (cellular, organ, individual) that reflect fish condition at temporal scales ranging from hours to weeks. Using these indices, the relative conditions of fish collected from five regions in the SFE were compared: Cache Slough, Sacramento River Deep Water Ship Channel, Confluence, Suisun Bay and Suisun Marsh. Fish sampled from Suisun Bay and, to a lesser extent the Confluence, exhibited relatively poor short-term nutritional and growth indices and morphometric condition, while fish from the freshwater regions of the estuary, and Cache Slough in particular, exhibited the most apparent histopathological signs of contaminant exposure. In contrast, fish from the Suisun Marsh region exhibited higher short-term nutrition and growth indices, and better morphometric and histopathological condition. For instance, fish collected from Suisun Marsh had a mean stomach fullness, expressed as a percentage of fish weight, that was 3.4-fold higher than fish collected from Suisun Bay, while also exhibiting an incidence of histopathological lesions that was 11-fold lower than fish collected from Cache Slough. Thus, our findings support the hypothesis that multiple stressors, including food limitation and contaminants, are contributing to the decline of Delta Smelt, and that these stressors influence Delta Smelt heterogeneously across space.
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Affiliation(s)
- Bruce G Hammock
- Aquatic Health Program, School of Veterinary Medicine, Department of Anatomy, Physiology, and Cell Biology, One Shields Avenue, University of California, Davis, CA 95616, USA.
| | - James A Hobbs
- Wildlife, Fish and Conservation Biology, One Shields Avenue, Davis, CA, 95616, USA
| | - Steven B Slater
- California Department of Fish and Wildlife, 2109 Arch Airport Road, Suite 100, Stockton, CA, 95206, USA
| | - Shawn Acuña
- Metropolitan Water District of Southern California, 1121 L Street, Suite 900, Sacramento, CA 95814, USA
| | - Swee J Teh
- Aquatic Health Program, School of Veterinary Medicine, Department of Anatomy, Physiology, and Cell Biology, One Shields Avenue, University of California, Davis, CA 95616, USA
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Hammond CJ, Hobbs JA. Parvovirus B19 infection of brain: possible role of gender in determining mental illness and autoimmune thyroid disorders. Med Hypotheses 2006; 69:113-6. [PMID: 17196758 DOI: 10.1016/j.mehy.2006.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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: 11/09/2006] [Accepted: 11/11/2006] [Indexed: 11/29/2022]
Abstract
Major theories about the etiologies of chronic mental illnesses such as bipolar disorder and schizophrenia include genetic and environmental factors such as famine and infection. It is likely that multiple genes play a role in the pathogenesis of these disorders, but no single gene has been identified as causative. Several viruses have been investigated as potential candidates, but conflicting reports exist. Although a relationship between bipolar disorder and schizophrenia with autoimmune disorders has also been documented for many years, reports are often conflicting. We hypothesize that parvovirus B19 (B19), a common human pathogen, due to its ability to infect the brain and induce autoimmunity, is a strong candidate that may unite prevailing theories. In particular, our preliminary data suggest that B19 may be most likely involved in co-morbid bipolar and autoimmune thyroid disorders in females. In schizophrenics, the gender trend may be reversed. We propose that there is a complex interaction between immuno-genetics, autoimmunity, gender, and B19 infection that leads to at least some forms of bipolar disorder and schizophrenia. Future studies that investigate this hypothesis are warranted and outlined.
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Affiliation(s)
- C J Hammond
- Department of Psychiatry, University of Florida College of Medicine, P.O. Box 100256, Gainesville, FL 32610, USA
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Rose WL, Hobbs JA, Nisbet RM, Green PG, Cherr GN, Anderson SL. Validation of otolith growth rate analysis using cadmium-exposed larval topsmelt (Atherinops affinis). Environ Toxicol Chem 2005; 24:2612-20. [PMID: 16268164 DOI: 10.1897/04-516r.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We applied otolith growth rate analysis to an investigation of cadmium (Cd)-exposed larval topsmelt (Atherinops affinis) to determine if growth rate was a more sensitive measure than somatic growth (body wt or length). Topsmelt otoliths, calcareous concretions in the fish inner ear, formed daily increments, and otolith growth was proportional to somatic growth. Nine-day posthatch larval topsmelt were exposed to Cd (0-100 ppb) in seawater for 14 d and fed low or high ration levels in separate experiments. Whereas Cd impaired topsmelt growth and growth rates, the extent of growth reduction was dependent on the ration level. At high ration levels, otolith and somatic growth rates of fish exposed to Cd (50 and 100 ppb) were significantly reduced; however, no differences in final mean weight and only marginal differences in final mean length of Cd-exposed topsmelt were observed. At low ration levels, we detected reductions in both somatic growth as well as otolith and somatic growth rates of topsmelt exposed to Cd (50 and 100 ppb). Otolith growth rate analysis was more sensitive than growth measurements of Cd-exposed topsmelt, because it allowed the detection of small differences in growth rates even when differences in somatic growth were not observed.
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Affiliation(s)
- Wendy L Rose
- Bodega Marine Laboratory, University of California-Davis, Bodega Bay, California 94923, USA.
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Csipo I, Montel AH, Hobbs JA, Morse PA, Brahmi Z. Effect of Fas+ and Fas- target cells on the ability of NK cells to repeatedly fragment DNA and trigger lysis via the Fas lytic pathway. Apoptosis 2003; 3:105-14. [PMID: 14646508 DOI: 10.1023/a:1009696908600] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We and others have recently shown that human NK cells express the Fas ligand (FasL) constitutively and that they can trigger the lysis of Fas positive (Fas+) target cells (TC) by apoptosis. We have also previously demonstrated that NK cells exposed to sensitive TC temporarily lose their ability to lyse sensitive TC via the granule-mediated pathway and that this loss is recovered when inactivated NK cells (NKi) are incubated in medium supplemented with IL-2, IL-12 or IL-15. In this study, we investigated the fate of the Fas-lytic pathway in NK cells exposed to either Fas+ or Fas- TC. To this end, we exposed NK cells to Jurkat (Fas-) or Jurkat (Fas+) TC for up to 6 h, separated NK cells from the TC and assessed the residual lytic activity against K562, a traditional human NK cell target, Jurkat Fas+ and Jurkat Fas- TC. Fas lytic activity was determined in calcium free medium, in the presence or absence of two distinct Fas-blocking monoclonal antibodies and a Fas.Fc fusion protein. In parallel experiments, the extent of DNA fragmentation in the three TCs was also assayed by the JAM test. Our results indicate that: (i) NK cells exposed to susceptible Fas+ TC temporarily lose most of their lytic potential due to the granule-mediated pathway, while only partially losing the Fas-lytic pathway. They also partially lose their ability to fragment DNA. (ii) NK cells exposed to Fas+ TC completely recover the Fas lytic pathway and the ability to fragment DNA via the Fas/Fas ligand when incubated in medium supplemented with IL-2 for 18 h.
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Affiliation(s)
- I Csipo
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202-5200, USA
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Hobbs JA, Schloemer RH, Hommel-Berrey G, Brahmi Z. Caspase-3-like proteases are activated by infection but are not required for replication of vesicular stomatitis virus. Virus Res 2001; 80:53-65. [PMID: 11597748 DOI: 10.1016/s0168-1702(01)00350-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Infection with vesicular stomatitis virus (VSV), the prototype rhabdovirus, causes apoptotic DNA fragmentation, but the role of apoptosis in the VSV-host interaction remains unclear. Apoptosis is the gene-regulated mechanism triggered by a wide variety of stimuli that lead to cell death in a choreographed manner. In the present study, infection of the Jurkat T cell line with VSV led to activation of caspase-3 and caspase-7, with subsequent apoptotic events involving poly (ADP ribose) polymerase (PARP) cleavage, DNA fragmentation, and membrane damage. Caspase activation was correlated with viral protein expression suggesting a link between viral replication and apoptosis. We hypothesized that VSV replication might depend on apoptosis and that the inhibition of apoptosis would lead to significant decreases in viral titers. When various inhibitors of apoptosis in VSV-infected cells were used, PARP cleavage and DNA fragmentation were inhibited but the production of infectious progeny was not affected. In addition, we demonstrated that the activation of caspase-3-like proteases is required for VSV-induced apoptosis but not in vitro viral replication. Apoptosis following VSV infection is likely to be either a host-cell attempt to control viral replication or may be a ploy used by the virus to facilitate its in vivo replication and spread.
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Affiliation(s)
- J A Hobbs
- Department of Microbiology and Immunology, Indiana University School of Medicine, 702 Barnhill Dr., Riley Hospital Rm. 0615, Indianapolis, IN 46202-5200, USA
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Hobbs JA, Cho S, Roberts TJ, Sriram V, Zhang J, Xu M, Brutkiewicz RR. Selective loss of natural killer T cells by apoptosis following infection with lymphocytic choriomeningitis virus. J Virol 2001; 75:10746-54. [PMID: 11602716 PMCID: PMC114656 DOI: 10.1128/jvi.75.22.10746-10754.2001] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [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] [Indexed: 01/12/2023] Open
Abstract
Natural killer T (NKT) cells, a unique subpopulation of T cells, coexpress markers also present on NK cells and recognize the major histocompatibility complex class I-like CD1d1 molecule. We studied the effect of an acute virus infection on NKT cells. Mice were infected with the nonhepatotropic Armstrong strain of lymphocytic choriomeningitis virus (LCMV), and at various times postinfection, mononuclear cells from the liver, peritoneum, and spleen were isolated. It was found that within 2 to 3 days, there was a selective loss of NKT cells from the liver with an apparent rapid recovery within 8 to 14 days. There was no increase in peritoneal or splenic NKT cells, indicating that NKT cells did not traffic to these tissues. This loss of NKT cells was independent of gamma interferon (IFN-gamma) and interleukin 12 (IL-12) production, but did occur in mice treated with poly(I-C), a classical inducer of IFN-alpha/beta. The reduction in NKT cells was CD28 and fas/fasL independent and occurred via apoptosis. It was not observed in LCMV-infected DNA fragmentation factor 45-deficient mice, and an increase in active caspase 3-specific staining was found in liver NKT cells from LCMV-infected and poly(I-C)-treated mice compared to uninfected wild-type mice. Interestingly, it was also found that liver NKT cells from LCMV-infected mice were themselves infected. These results suggest that the loss of NKT cells following an acute LCMV infection could be due to the induction of IFN-alpha/beta resulting in NKT-cell apoptosis and is important for the host's immune response to LCMV.
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Affiliation(s)
- J A Hobbs
- Department of Microbiology and Immunology and The Walther Oncology Center, The Walther Cancer Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Spence PM, Sriram V, Van Kaer L, Hobbs JA, Brutkiewicz RR. Generation of cellular immunity to lymphocytic choriomeningitis virus is independent of CD1d1 expression. Immunology 2001; 104:168-74. [PMID: 11683957 PMCID: PMC1783302 DOI: 10.1046/j.1365-2567.2001.01302.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [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] [Indexed: 12/22/2022] Open
Abstract
CD1 molecules are cell surface glycoproteins, structurally similar to major histocompatibility complex (MHC) class I molecules. The murine CD1d1 molecule has been shown to be essential for the positive selection of a unique subpopulation of T cells [the natural killer (NK) T cells], as CD1d1-deficient mice lack NK T cells. These cells have recently been suggested to play an important role in the induction of innate immunity (i.e. NK cells) and the regulation of immune homeostasis. As such, it was asked whether NK T cells were necessary for the generation of cellular immunity to an acute virus infection. In these studies, the Armstrong strain of lymphocytic choriomeningitis virus (LCMV), a classic inducer of NK cells, and its pathogenic variant clone 13 were used. When NK-cell activity was assessed on day 3 post-LCMV infection, surprisingly, it was found that CD1d1-deficient mice could generate NK-cell activity at wild-type levels. Likewise, LCMV-specific cytotoxic T-lymphocyte (CTL) activity in CD1d1-deficient mice was indistinguishable from that generated in wild-type mice. Additionally, viral titres in the spleen (LCMV Armstrong) and blood (LCMV clone 13) of infected CD1d1-deficient mice were at comparable levels to those found in wild-type mice, as were virus infection-induced increases in cell surface H-2Kb in the spleen. Therefore, these results suggest that the LCMV-induced generation of NK-cell and virus-specific CTL activity, as well as viral clearance, are independent of CD1d1 expression.
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Affiliation(s)
- P M Spence
- Department of Microbiology and Immunology, Indiana University School of Medicine, The Walther Oncology Centre, Indianapolis, IN 46202-5254, USA
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N'cho M, Hobbs JA, Brahmi Z. Over-expression of multidrug resistance P-glycoprotein inhibits NK granule-mediated lytic ability without affecting the Fas lytic pathway. Hum Immunol 1999; 60:223-30. [PMID: 10321958 DOI: 10.1016/s0198-8859(98)00112-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multidrug resistance (MDR) in tumor cells is commonly associated wich the over-expression of P-glycoprotein (Pgp), the product of the MDR1 gene. In this study, we investigated whether over-expression of Pgp in natural killer (NK) cells would influence their granule- as well as fas-mediated cytolytic activities. YT-INDY, a human NK-like cell line, was transfected with the MDR 1 gene, then tested for Pgp activity the presence of various concentrations of R-verapamil, a potent Pgp inhibitor. We showed that, unlike control YT-INDY, the Pgp activity of the transfectants (YT-mdr(+)) was only partially inhibited by R-verapamil. We also showed that Fas lytic activity was unaltered and that the loss of granule-mediated cytotoxicity was not due to reduced LFA-1 expression or to a decrease in target cell (TC) binding. Our data indicate that Pgp may be involved in the release of cytotoxic molecules.
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Affiliation(s)
- M N'cho
- Department of Microbiology/Immunology, Indiana University School of Medicine, Indianapolis 46202-5200, USA
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Anderson YS, Curtis NJ, Hobbs JA, Thompson CH, Winearls CG, Radda GK, Clarke K, Altmann P. High serum D-lactate in patients on continuous ambulatory peritoneal dialysis. Nephrol Dial Transplant 1997; 12:981-3. [PMID: 9175054 DOI: 10.1093/ndt/12.5.981] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND As abnormally high serum D-lactate levels may cause neurological impairment, we determined whether patients undergoing continuous ambulatory peritoneal dialysis (CAPD) with lactate-containing fluids have increased serum D-lactate concentrations. METHODS D- and L-lactate concentrations were determined in peritoneal dialysis fluids and in serum from control subjects (n = 10), haemodialysis patients (n = 10), and CAPD patients (n = 30) before and after 1 h of dialysis. RESULTS We found the median D-lactate concentration in Dianeal CAPD fluid to be 26 mM (range 19-27), whereas it was less than 0.5 mM in DPCA2 fluid. Control, haemodialysis, and CAPD (DPCA2) patient median serum D-lactate concentrations were below 0.07 mM. However, CAPD (Dianeal) patient serum D-lactate concentrations were 4-fold higher than controls (P < 0.0001), at 0.28 mM, an hour after instillation of D-lactate-containing fluid. Three patients, whose serum D-lactate averaged 0.59 mM, were found to have D-lactate concentrations at 0.22 mM after overnight cessation of dialysis. CONCLUSION We conclude that CAPD with D-lactate-containing fluids raises serum D-lactate to abnormal levels.
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Affiliation(s)
- Y S Anderson
- Department of Biochemistry, University of Oxford, UK
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Abstract
Lysis of target cells (TC) by cytolytic lymphocytes involves the secretion of cytoplasmic granules containing perforin and serine esterases by the effector cell (EC). Recently, a granule-independent cytolytic mechanism involving the interaction of the apoptosis-triggering Fas antigen (CD95) with Fas ligand (FasL) has been revealed in T cells. However, whether the Fas lytic pathway also functions in NK cells has not been established. We purified human peripheral NK cells (> 98% CD56+) and found that PMA and ionomycin treatment upregulated FasL message and stimulated the NK cells to lyse a Fas+ TC. This lysis was partially inhibited by the anti-Fas-blocking antibody M3 or by Fas.Fc fusion protein. We also found that FasL is constitutively expressed on the human NK-like leukemia cell line YT-INDY and that YT-INDY utilizes a Ca(2+)-independent Fas lytic pathway, as well as the granule pathway. We have previously shown that CD28/B7 interactions are involved in TC recognition by YT-INDY. K562 cotransfected with Fas and B7-1 (K562/Fas/B7) was lysed by YT-INDY at a higher level than a vector-transfected K562 line, whereas K562 transfected with Fas alone was not. Lysis of K562/Fas/B7 cotransfectants was partially Fas-mediated, as indicated by the presence of Ca(2+)-independent, M3-inhibitable lysis. Ca(2+)-independent, Fas-mediated lysis of several TC by YT-INDY was inhibited by anti-CD28 antibody. Anti-LFA-1 also inhibited Fas-mediated cytotoxicity in YT-INDY. Thus, fresh human NK cells and the human NK-like cell line YT-INDY are capable of using the Fas lytic pathway. In YT-INDY, CD28/B7 and LFA-1/ICAM interactions appear to influence the Fas lytic pathway.
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Affiliation(s)
- A H Montel
- Department of Microbiology/Immunology, Indiana University School of Medicine, Indianapolis 46202-5200, USA
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Abstract
Four varieties of fracture, of dislocation, or of fracture dislocation of the hip are described that occur in car occupants after road accidents. It is suggested that, whereas most hip injuries to car occupants are produced by application of force to the knee, one important variety (central fracture dislocation) is the result of the direct application of force to the great trochanter. Central fracture dislocations might be prevented, or their severity minimized, by strengthening the sides of cars and of car doors and by improving the energy absorption characteristics of the facia panel.
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