36 results on '"Andrew L. Chang"'
Search Results
2. Outcomes and toxicities after proton partial breast radiotherapy for early stage, hormone receptor positive breast cancer: 3-Year results of a phase II multi-center trial
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J. Isabelle Choi, Kiran Prabhu, William F. Hartsell, Todd DeWees, Christopher Sinesi, Carlos Vargas, Rashmi K. Benda, Oren Cahlon, and Andrew L. Chang
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Breast cancer ,Proton therapy ,Partial breast irradiation ,Breast conservation therapy ,Outcomes ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Purpose: Proton therapy (PT) for partial breast irradiation (PBI) in early-stage breast cancer can decrease morbidity versus photon PBI with superior organs-at-risk sparing. We report 3-year outcomes of the first prospective, multicenter, phase II trial of proton PBI. Methods and Materials: This Proton Collaborative Group phase II trial (PCG BRE007-12) recruited women ≥ 50 years with node-negative, estrogen receptor (ER)-positive, ≤3cm, invasive ductal carcinoma (IDC) or ductal carcinoma in situ undergoing breast conserving surgery followed by proton PBI (40 Gy(RBE), 10 daily fractions). Primary endpoint was freedom from ipsilateral breast cancer recurrence. Adverse events were prospectively graded using CTCAEv4.0. Breast Cancer Treatment Outcome Scale (BCTOS) assessed patient-reported quality of life (PRQOL). Results: Thirty-eight evaluable patients enrolled between 2/2013–11/2016. Median age was 67 years (range 50–79); 55 % had left-sided disease, and median tumor size was 0.9 cm. Treatment was delivered in ≥ 2 fields predominantly with uniform scanning PT (n = 37). At 35-month median follow-up (12–62), all patients were alive, and none had local, regional or distant disease progression. One patient developed an ER-negative contralateral IDC. Seven grade 2 adverse events occurred; no radiotherapy-related grade ≥ 3 toxicities occurred. Changes in BCTOS subdomain mean scores were maximum 0.36, indicating no meaningful change in PRQOL. Median heart volume receiving 5 Gy (V5Gy), lung V20Gy, and lung V10Gy were 0 %, 0 % and 0.19 %, respectively. Conclusion: At 3 years, proton PBI provided 100 % cancer control for early-stage, ER-positive breast cancer. Toxicities are minimal, and PRQOL remains acceptable with continued follow-up. These findings support PT as a safe and effective PBI delivery option.
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- 2022
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3. Differences in fouling community composition and space occupation across broad spatial and temporal scales
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Elizabeth B. Jewett, Katherine N. Lawson, Kristen J. Larson, Brianna M. Tracy, Safra Altman, Andrew L. Chang, Scott Cowan, Jeffrey A. Crooks, Tamar Huber, Elizabeth H. Wells, and Gregory M. Ruiz
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benthic ,community development ,fouling ,hard substrate ,invasive ,marine ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Sessile marine invertebrate (biofouling) communities have served as an important model in ecology for evaluating fundamental patterns and processes, including invasion dynamics, which vary at broad spatial and temporal scales. Here, we tested for differences in biofouling community development among three biogeographically distinct bays in North America (Chesapeake Bay, Tampa Bay, and San Francisco Bay), exploring possible explanations for differential non-native species success. In particular, we aimed to examine if San Francisco Bay (a global hotspot for non-native species richness) differed in composition and space occupation, especially since open space can facilitate colonization. Additionally, we explored how biogeography, assembly and succession dynamics over the short and long term, and space availability affect marine communities across broad spatial scales. Patterns of community assembly differed among bays, with more bare space and less secondary cover (species settling on species) in San Francisco Bay. San Francisco Bay was also distinguished by a higher percent cover of Tunicata (almost all of which are non-native and historically absent) over multiple time scales. Cirripedia recruited on bare panels in all three Bays but cover increased only in Tampa Bay, as soak time increased. Tube-dwelling Polychaeta distinguished Chesapeake Bay from Tampa Bay and San Francisco Bay. Low-salinity events temporarily restructured the communities in all three bays. Whether differences among bays reflect coastal versus bay-specific patterns remains to be tested.
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- 2022
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4. The Transcription Factor Pdr802 Regulates Titan Cell Formation and Pathogenicity of Cryptococcus neoformans
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Julia C. V. Reuwsaat, Daniel P. Agustinho, Heryk Motta, Andrew L. Chang, Holly Brown, Michael R. Brent, Livia Kmetzsch, and Tamara L. Doering
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Microbiology ,QR1-502 - Abstract
The pathogenic yeast Cryptococcus neoformansC. neoformans
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- 2021
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5. Evaluating Performance of Photographs for Marine Citizen Science Applications
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Katherine Newcomer, Brianna M. Tracy, Andrew L. Chang, and Gregory M. Ruiz
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photographic methods ,marine ,invertebrates ,non-native ,citizen science ,taxonomy ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Long-term measurements are imperative to detect, understand, and predict changes in coastal biological communities, but can be both costly and difficult to implement. Here, we compare measurement methods used to document community structure and assess changes in marine systems, and explore potential applications in citizen science. The use of photographs for species identifications and monitoring has become a popular and useful data collection tool, but its use requires evaluation of its effectiveness in comparison to data collected from live examinations. We used settlement panels in San Francisco Bay, a well-studied and vital coastal ecosystem, to compare standardized measures of the invertebrate fouling community through examination of live organisms in the field and via photographs. Overall, our study found that live measurements were more accurate and better represented these marine communities, having higher richness, and diversity measurements than photographic measurements. However, photographic analyses accurately captured the relative abundances of some species and functional groups. We suggest that highly recognizable target taxa or broad scale comparisons of functional group composition are easily tracked through photographs and offer the best potential for research conducted by citizen scientists.
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- 2019
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6. Cdk8 and Ssn801 Regulate Oxidative Stress Resistance and Virulence in Cryptococcus neoformans
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Andrew L. Chang, Yiming Kang, and Tamara L. Doering
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Cdk8 ,Cryptococcus neoformans ,Mediator complex ,Ssn801 ,mitochondria ,Microbiology ,QR1-502 - Abstract
ABSTRACT Cryptococcus neoformans kills 200,000 people worldwide each year. After inhalation, this environmental yeast proliferates either extracellularly or within host macrophages. Under conditions of immunocompromise, cryptococci disseminate from the lungs to the brain, causing a deadly meningoencephalitis that is difficult and expensive to treat. Cryptococcal adaptation to the harsh lung environment is a critical first step in its pathogenesis, and consequently a compelling topic of study. This adaptation is mediated by a complex transcriptional program that integrates cellular responses to environmental stimuli. Although several key regulators in this process have been examined, one that remains understudied in C. neoformans is the Mediator complex. In other organisms, this complex promotes transcription of specific genes by increasing assembly of the RNA polymerase II preinitiation complex. We focused on the Kinase Module of Mediator, which consists of cyclin C (Ssn801), cyclin-dependent kinase 8 (Cdk8), Med12, and Med13. This module provides important inhibitory control of Mediator complex assembly and activity. Using transcriptomics, we discovered that Cdk8 and Ssn801 together regulate cryptococcal functions such as the ability to grow on acetate and the response to oxidative stress, both of which were experimentally validated. Deletion of CDK8 yielded altered mitochondrial morphology and the dysregulation of genes involved in oxidation-reduction processes. This strain exhibited increased susceptibility to oxidative stress, resulting in an inability of mutant cells to proliferate within phagocytes, decreased lung burdens, and attenuated virulence in vivo. These findings increase our understanding of cryptococcal adaptation to the host environment and its regulation of oxidative stress resistance and virulence. IMPORTANCE Cryptococcus neoformans is a fungal pathogen that primarily affects severely immunocompromised patients, resulting in 200,000 deaths every year. This yeast occurs in the environment and can establish disease upon inhalation into the lungs of a mammalian host. In this harsh environment it must survive engulfment by host phagocytes, including the oxidative stresses it experiences inside them. To adapt to these challenging conditions, C. neoformans deploys a variety of regulatory proteins to alter gene expression levels and enhance its ability to survive. We have elucidated the role of a protein complex that regulates the cryptococcal response to oxidative stress, survival within phagocytes, and ability to cause disease. These findings are important because they advance our understanding of cryptococcal disease, which we hope will help in the efforts to control this devastating infection.
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- 2019
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7. Maintenance of Mitochondrial Morphology in Cryptococcus neoformans Is Critical for Stress Resistance and Virulence
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Andrew L. Chang and Tamara L. Doering
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Cryptococcus neoformans ,Mitochondria ,Mitochondrial morphology ,Pathogenic fungi ,Microbiology ,QR1-502 - Abstract
ABSTRACT Mitochondria are essential organelles that act in pathways including ATP production, β-oxidation, and clearance of reactive oxygen species. They occur as a complex reticular network that constantly undergoes fusion and fission, mediated by dynamin-related proteins (DRPs). DRPs include Fzo1, which mediates fusion, and Dnm1, Mdv1, and Fis1, which mediate fission. Mitochondrial morphology has been implicated in virulence in multiple fungi, as with the association between virulence and increased mitochondrial fusion in Cryptococcus gattii. This relationship, however, has not been studied in Cryptococcus neoformans, a related opportunistic pathogen. C. neoformans is an environmental yeast that can adapt to the human host environment, overcome the innate immune system, and eventually disseminate and cause lethal meningoencephalitis. We used gene deletion of key DRPs to study their role in mitochondrial morphology and pathogenesis of this yeast. Interestingly, increasing mitochondrial fusion did not increase resistance to oxidative stress, unlike in model yeast. Blocking mitochondrial fusion, however, yielded increased susceptibility to oxidative and nitrosative stresses as well as complete avirulence. This lack of virulence was not mediated by any effects of altered mitochondrial function on two major virulence factors, capsule and melanin. Instead, it was due to decreased survival within macrophages, which in turn was a consequence of increased susceptibility to oxidative and nitrosative stress. Supporting this conclusion, reactive oxygen species (ROS) scavengers rescued the ability of fusion mutants to survive intracellularly. These findings increase our understanding of cryptococcal biology and virulence and shed light on an important group of proteins and cellular processes in this pathogen. IMPORTANCE C. neoformans is a yeast that causes fatal brain infection in close to 200,000 people worldwide every year, mainly afflicting individuals with AIDS or others who are severely immunocompromised. One feature of this microbe that helps it cause disease is that it is able to withstand toxic molecules it encounters when host cells engulf it in their efforts to control the infection. Mitochondria are important organelles responsible for energy production and other key cellular processes. They typically exist in a complex network that changes morphology by fusing and dividing; these alterations also influence mitochondrial function. Using genetic approaches, we found that changes in mitochondrial morphology dramatically influence cryptococcal virulence. We showed that this occurs because the altered mitochondria are less able to eliminate the harmful molecules that host cells produce to kill invading microbes. These findings are important because they elucidate fundamental biology and virulence and may suggest avenues for therapy.
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- 2018
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8. An Update From the Pediatric Proton Consortium Registry
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Clayton B. Hess, Daniel J. Indelicato, Arnold C. Paulino, William F. Hartsell, Christine E. Hill-Kayser, Stephanie M. Perkins, Anita Mahajan, Nadia N. Laack, Ralph P. Ermoian, Andrew L. Chang, Suzanne L. Wolden, Victor S. Mangona, Young Kwok, John C. Breneman, John P. Perentesis, Sara L. Gallotto, Elizabeth A. Weyman, Benjamin V. M. Bajaj, Miranda P. Lawell, Beow Y. Yeap, and Torunn I. Yock
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proton ,radiation ,pediatrics ,cancer ,registry ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Background/objectivesThe Pediatric Proton Consortium Registry (PPCR) was established to expedite proton outcomes research in the pediatric population requiring radiotherapy. Here, we introduce the PPCR as a resource to the oncology community and provide an overview of the data available for further study and collaboration.Design/methodsA multi-institutional registry of integrated clinical, dosimetric, radiographic, and patient-reported data for patients undergoing proton radiation therapy was conceived in May 2010. Massachusetts General Hospital began enrollment in July of 2012. Subsequently, 12 other institutions joined the PPCR and activated patient accrual, with the latest joining in 2017. An optional patient-reported quality of life (QoL) survey is currently implemented at six institutions. Baseline health status, symptoms, medications, neurocognitive status, audiogram findings, and neuroendocrine testing are collected. Treatment details of surgery, chemotherapy, and radiation therapy are documented and radiation plans are archived. Follow-up is collected annually. Data were analyzed 25 September, 2017.ResultsA total of 1,854 patients have consented and enrolled in the PPCR from October 2012 until September 2017. The cohort is 55% male, 70% Caucasian, and comprised of 79% United States residents. Central nervous system (CNS) tumors comprise 61% of the cohort. The most common CNS histologies are as follows: medulloblastoma (n = 276), ependymoma (n = 214), glioma/astrocytoma (n = 195), craniopharyngioma (n = 153), and germ cell tumors (n = 108). The most common non-CNS tumors diagnoses are as follows: rhabdomyosarcoma (n = 191), Ewing sarcoma (n = 105), Hodgkin lymphoma (n = 66), and neuroblastoma (n = 55). The median follow-up is 1.5 years with a range of 0.14 to 4.6 years.ConclusionA large prospective population of children irradiated with proton therapy has reached a critical milestone to facilitate long-awaited clinical outcomes research in the modern era. This is an important resource for investigators both in the consortium and for those who wish to access the data for academic research pursuits.
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- 2018
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9. Decoupling the response of an estuarine shrimp to architectural components of habitat structure
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Jeffrey A. Crooks, Andrew L. Chang, and Gregory M. Ruiz
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Habitat complexity ,Structure ,Palaemon macrodactylus ,Behavioral attraction ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
In order to explore biotic attraction to structure, we examined how the amount and arrangement of artificial biotic stalks affected responses of a shrimp, Palaemon macrodactylus, absent other proximate factors such as predation or interspecific competition. In aquaria, we tested the effect of differing densities of both un-branched and branched stalks, where the amount of material in the branched stalk equaled four-times that of the un-branched. The results clearly showed that it was the amount of material, not how it was arranged, that elicited responses from shrimp. Also, although stalks were not purposefully designed to mimic structural elements found in nature, they did resemble biogenic structure such as hydroids, algae, or plants. In order to test shrimp attraction to a different, perhaps more unfamiliar habitat type, we examined responses to plastic “army men.” These structural elements elicited similar attraction of shrimp, and, in general, shrimp response correlated well with the fractal dimension of both stalks and army men. Overall, these results indicate that attraction to physical structure, regardless of its nature, may be an important driver of high abundances often associated with complex habitats.
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- 2016
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10. Increasing the resilience of ecological restoration to extreme climatic events
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Chela J Zabin, Laura J Jurgens, Jillian M Bible, Melissa V Patten, Andrew L Chang, Edwin D Grosholz, and Katharyn E Boyer
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Ecology ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
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11. Severe introduced predator impacts despite attempted functional eradication
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Chela J. Zabin, Andrew L. Chang, Matthew C. Ferner, Brian S. Cheng, Gregory M. Ruiz, Jeffrey Blumenthal, Jordanna Barley, and Karina J. Nielsen
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Oyster ,Ecology ,Urosalpinx cinerea ,biology ,fungi ,Biodiversity ,food and beverages ,Introduced species ,equipment and supplies ,biology.organism_classification ,Predation ,Fishery ,biology.animal ,Biological dispersal ,Ostrea lurida ,Predator ,Ecology, Evolution, Behavior and Systematics - Abstract
Established non-native species can have significant impacts on native biodiversity without any possibility of complete eradication. In such cases, one management approach is functional eradication, the reduction of introduced species density below levels that cause unacceptable effects on the native community. Functional eradication may be particularly effective for species with limited dispersal ability, which may limit rates of reinvasion from distant populations. Here, we evaluate the potential for functional eradication of introduced predatory oyster drills (Urosalpinx cinerea) using a community science approach in San Francisco Bay. We combined observational surveys, targeted removals, and a caging experiment to evaluate the effectiveness of this approach in mitigating the mortality of prey Olympia oysters (Ostrea lurida), a conservation and restoration priority species. Despite the efforts of over 300 volunteers that removed over 30,000 oyster drills, we report limited success and discuss several possible mechanisms for this result with broad relevance to management for this and other introduced species. We also found a strong negative relationship between oyster drills and oysters, showing virtually no coexistence across eight sites. At two removal sites, there was no effect of oyster drill removal on oyster survival, which was only observed by caging treatment (0 and 1.6% survival in open and partial cage treatments, as compared to 89.1% in predator exclusion treatments). We conclude that functional eradication of this species requires significantly greater effort and may not be a viable management strategy. Oyster restoration efforts should not be undertaken where Urosalpinx is established or is likely to invade.
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- 2021
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12. Down the up staircase: Equatorward march of a cold‐water ascidian and broader implications for invasion ecology
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James T. Carlton, Gregory M. Ruiz, Christopher W. Brown, and Andrew L. Chang
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Geography ,Fouling community ,biology ,Ecology ,Ecology (disciplines) ,Biological dispersal ,Corella inflata ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics ,Corella willmeriana - Published
- 2020
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13. Stage-specific overcompensation, the hydra effect, and the failure to eradicate an invasive predator
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Gail V. Ashton, Lina Ceballos-Osuna, Andrew L. Chang, Marko Bradley, Julie Anne Gonzalez, Carolyn K. Tepolt, Marcella Heineke, Erica Pollard, Brian Turner, Michelle Marraffini, Ian Pritchard, Christopher W. Brown, Linda McCann, Edwin D. Grosholz, Catherine E. de Rivera, and Gregory M. Ruiz
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Population Density ,Aquatic Organisms ,education.field_of_study ,Multidisciplinary ,Ecology ,Population Dynamics ,Population ,Cannibalism ,Biodiversity ,Models, Theoretical ,Biological Sciences ,Biology ,Invasive species ,Abundance (ecology) ,Predatory Behavior ,Animals ,Juvenile ,Population growth ,Marine ecosystem ,Introduced Species ,education ,Predator ,Ecosystem - Abstract
As biological invasions continue to increase globally, eradication programs have been undertaken at significant cost, often without consideration of relevant ecological theory. Theoretical fisheries models have shown that harvest can actually increase the equilibrium size of a population, and uncontrolled studies and anecdotal reports have documented population increases in response to invasive species removal (akin to fisheries harvest). Both findings may be driven by high levels of juvenile survival associated with low adult abundance, often referred to as overcompensation. Here we show that in a coastal marine ecosystem, an eradication program resulted in stage-specific overcompensation and a 30-fold, single-year increase in the population of an introduced predator. Data collected concurrently from four adjacent regional bays without eradication efforts showed no similar population increase, indicating a local and not a regional increase. Specifically, the eradication program had inadvertently reduced the control of recruitment by adults via cannibalism, thereby facilitating the population explosion. Mesocosm experiments confirmed that adult cannibalism of recruits was size-dependent and could control recruitment. Genomic data show substantial isolation of this population and implicate internal population dynamics for the increase, rather than recruitment from other locations. More broadly, this controlled experimental demonstration of stage-specific overcompensation in an aquatic system provides an important cautionary message for eradication efforts of species with limited connectivity and similar life histories.
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- 2021
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14. Impacts of a temperate to tropical voyage on the microalgal hull fouling community of an atypically-operated vessel
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Christine A. Edmiston, Christopher E. Ikeda, William P. Cochlan, and Andrew L. Chang
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0106 biological sciences ,Biomass (ecology) ,Salinity ,Fouling community ,010604 marine biology & hydrobiology ,010501 environmental sciences ,Aquatic Science ,Oceanography ,01 natural sciences ,Pollution ,Hawaii ,Abundance (ecology) ,Temperate climate ,Microalgae ,Environmental science ,San Francisco ,Negative reaction ,Bay ,Ships ,0105 earth and related environmental sciences - Abstract
Microalgal communities that colonize the hulls of at-risk vessels – those which have the highest port residency times, lowest speeds, and most stationary time in water - are expected to change as a function of environmental factors during ocean voyages, but are rarely studied. The microalgal communities on the hull of an atypically operated ship, the T.S. Golden Bear, were quantified during the course of a voyage from San Francisco Bay to the South Pacific and back. Here we clearly demonstrate that microalgal communities can be highly resilient, and can survive physiologically strenuous journeys through extreme variation in salinity and temperature. A 42% reduction in microalgal biomass and a 62% reduction in algal cellular abundance indicated a community-wide negative reaction to an increase in both salinity and temperature after the ship left San Francisco Bay, CA and cruised southward to Long Beach, although in vivo cellular fluorescence capacity increased. Further reductions in biomass (36%) and cellular abundance (26%) occurred once the ship encountered high-temperature, high-salinity waters in Hawaii. A 17% reduction of cellular fluorescence capacity was also observed in Hawaii. Despite previous environmental stressors, upon return to temperate waters off Vallejo, CA, biomass increased 230%, cellular abundance remained stable, and cellular fluorescence capacity increased from 0.45 ± 0.26 to 0.60 ± 0.07. The methods used in the current research provide efficient, cost-effective procedures for analyzing microalgal (and macrofouling) communities, which can in turn aid regulators in creating such necessary thresholds for enforcement.
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- 2020
15. Distribution patterns of the introduced encrusting bryozoan Conopeum chesapeakensis (Osburn 1944; Banta et al. 1995) in an estuarine environment in upper San Francisco Bay
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Katherine Newcomer, Andrew L. Chang, and Michelle Marraffini
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0106 biological sciences ,geography ,Zooid ,geography.geographical_feature_category ,Ecology ,010604 marine biology & hydrobiology ,Estuary ,Interspecific competition ,Aquatic Science ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Transplantation ,Salinity ,Ficopomatus enigmaticus ,Dominance (ecology) ,Bay ,Ecology, Evolution, Behavior and Systematics - Abstract
The factors shaping the distributions of nonindigenous species (NIS) are of particular interest for understanding their success and potential impacts within their invaded ranges. In the San Francisco Bay estuary, the encrusting bryozoan Conopeum chesapeakensis (Osburn, 1944; Banta et al., 1995) occurs in peak abundances in lower salinity hard substrate habitats, with lower abundances upstream and downstream; however, little is known about the factors that control its distribution. To investigate several hypotheses about what allows this broadly tolerant invader to be numerically dominant in this region, a field transplant experiment was conducted across three sites in upper San Francisco Bay estuary. Colonies settled on PVC plates in the peak abundance zone and transplanted to upstream and downstream treatment sites, or returned to the settlement site, which served as a control. Salinity, temperature, chlorophyll a levels, and the abundance of interspecific competitors varied at each site and were measured throughout the experiment. Mixed effects models incorporating these measurements compared net growth rate and zooid size observed across treatment sites. Colonies transplanted upstream experienced high barnacle settlement, a potential competitive threat, and decreased salinity, and exhibited an average net growth rate of 6.60 zooids/day. Colonies at the control site faced almost no potential interspecific competition, intermediate salinity, and had an average net growth rate of 4.96 zooids/day. At the downstream site, colonies grew an average of 4.62 zooids/day and experienced high potential competition from serpulid polychaete settlement and the highest salinity of all sites. The best-fit models indicated that overall abundance of potential competitors, especially the serpulid Ficopomatus enigmaticus (Fauvel, 1923), was negatively correlated with the net growth rate of C. chesapeakensis colonies. Zooid size was also negatively correlated with F. enigmaticus abundance and temperature, though the relationship weakened over time. Many colonies at both the upstream and downstream transplant sites experienced fast initial growth following transplantation, but then experienced partial colony loss corresponding with an increase in the abundance of potential competitors. In contrast, colonies at the control site showed slow but continuous growth throughout the study in absence of interspecific competitors. These results suggest that the numerical dominance of C. chesapeakensis in upper-estuary habitat may be partly explained by a lack of potential interspecific competitors. As San Francisco Bay and other estuaries face high invasion pressure in brackish upper-estuarine regions, understanding which factors influence the distribution of NIS can help predict impacts to resident communities.
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- 2018
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16. Northward range expansion of three non-native ascidians on the west coast of North America
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Gretchen Gretchen, Andrew L. Chang, Kristen Larson, Gregory M. Ruiz, Brianna M. Tracy, and Gail V. Ashton
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,Ecology ,Range (biology) ,010604 marine biology & hydrobiology ,Introduced species ,Aquatic animal ,01 natural sciences ,Aquatic organisms ,Geography ,Oceanography ,Zoogeography ,West coast ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Published
- 2017
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17. Settlement plates as monitoring devices for non-indigenous species in marine fouling communities
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Gail V. Ashton, Christopher W. Brown, Greg Ruiz, Andrew L. Chang, and Michelle Marraffini
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0106 biological sciences ,Fishery ,Geography ,Ecology ,Fouling ,Settlement (structural) ,010604 marine biology & hydrobiology ,Management, Monitoring, Policy and Law ,010603 evolutionary biology ,01 natural sciences ,Ecology, Evolution, Behavior and Systematics ,Indigenous - Published
- 2017
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18. Syndesmotic Ligaments of the Ankle: Anatomy, Multimodality Imaging, and Patterns of Injury
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Jacob C. Mandell and Andrew L. Chang
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Syndesmosis ,business.industry ,Persistent pain ,Radiography ,fungi ,food and beverages ,Anatomy ,Mr imaging ,Multimodal Imaging ,030218 nuclear medicine & medical imaging ,Diagnosis, Differential ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Chronic ankle instability ,Ligaments, Articular ,medicine ,Sprains and Strains ,Humans ,Radiology, Nuclear Medicine and imaging ,Ankle Injuries ,Ankle ,business ,Early osteoarthritis - Abstract
Injuries to the syndesmotic ligaments of the ankle or "high ankle sprains" are common in acute ankle trauma but can be difficult to diagnose both clinically and on imaging. Missed injuries to the syndesmosis can lead to chronic ankle instability, which can cause persistent pain and lead to early osteoarthritis. This review will illustrate the anatomy of the syndesmotic ligamentous complex, describe radiographic, CT, and MR imaging of the syndesmosis, demonstrate typical mechanisms of injuries and associated fracture patterns, and provide an overview of important management considerations.
- Published
- 2019
19. Coast-wide recruitment dynamics of Olympia oysters reveal limited synchrony and multiple predictors of failure
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Paul A. Dinnel, Andrew L. Chang, Matthew C. Ferner, Jennifer L. Ruesink, Danielle C. Zacherl, Charlie Endris, Alan C. Trimble, Dick Vander Schaaf, Sarah E. Dudas, John S. Berriman, Chela J. Zabin, Kerstin Wasson, Anna Deck, Brent B. Hughes, Michael Espinoza, Edwin D. Grosholz, and David L. Kimbro
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0106 biological sciences ,Canada ,Oyster ,Population Dynamics ,Population ,Biology ,010603 evolutionary biology ,01 natural sciences ,Propagule ,Abundance (ecology) ,biology.animal ,Animals ,Ostrea lurida ,14. Life underwater ,education ,Ecology, Evolution, Behavior and Systematics ,geography ,education.field_of_study ,Pacific Ocean ,geography.geographical_feature_category ,Ecology ,010604 marine biology & hydrobiology ,Estuary ,Population ecology ,biology.organism_classification ,Ostreidae ,United States ,Fishery ,Population cycle ,Animal Distribution - Abstract
Recruitment of new propagules into a population can be a critical determinant of adult density. We examined recruitment dynamics in the Olympia oyster (Ostrea lurida), a species occurring almost entirely in estuaries. We investigated spatial scales of interannual synchrony across 37 sites in eight estuaries along 2500 km of Pacific North American coastline, predicting that high vs. low recruitment years would coincide among neighboring estuaries due to shared exposure to regional oceanographic factors. Such synchrony in recruitment has been found for many marine species and some migratory estuarine species, but has never been examined across estuaries in a species that can complete its entire life cycle within the same estuary. To inform ongoing restoration efforts for Olympia oysters, which have declined in abundance in many estuaries, we also investigated predictors of recruitment failure. We found striking contrasts in absolute recruitment rate and frequency of recruitment failure among sites, estuaries, and years. Although we found a positive relationship between upwelling and recruitment, there was little evidence of synchrony in recruitment among estuaries along the coast, and only limited synchrony of sites within estuaries, suggesting recruitment rates are affected more strongly by local dynamics within estuaries than by regional oceanographic factors operating at scales encompassing multiple estuaries. This highlights the importance of local wetland and watershed management for the demography of oysters, and perhaps other species that can complete their entire life cycle within estuaries. Estuaries with more homogeneous environmental conditions had greater synchrony among sites, and this led to the potential for estuary-wide failure when all sites had no recruitment in the same year. Environmental heterogeneity within estuaries may thus buffer against estuary-wide recruitment failure, analogous to the portfolio effect for diversity. Recruitment failure was correlated with lower summer water temperature, higher winter salinity, and shorter residence time, all indicators of stronger marine influence on estuaries. Recruitment failure was also more common in estuaries with limited networks of nearby adult oysters. Large existing oyster networks are thus of high conservation value, while estuaries that lack them would benefit from restoration efforts to increase the extent and connectivity of sites supporting oysters. This article is protected by copyright. All rights reserved.
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- 2016
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20. Upstream—Downstream Shifts in Peak Recruitment of the Native Olympia Oyster in San Francisco Bay During Wet and Dry Years
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Matthew C. Ferner, Lindsay J. Sullivan, Andrew L. Chang, Anna Deck, and Steven G. Morgan
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0106 biological sciences ,geography ,Oyster ,geography.geographical_feature_category ,010504 meteorology & atmospheric sciences ,Ecology ,Range (biology) ,010604 marine biology & hydrobiology ,Estuary ,Aquatic animal ,Introduced species ,Aquatic Science ,Biology ,biology.organism_classification ,01 natural sciences ,Salinity ,biology.animal ,Ostrea lurida ,Bay ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
Understanding the conditions that drive variation in recruitment of key estuarine species can be important for effective conservation and management of their populations. The Olympia oyster (Ostrea lurida) is native to the Pacific coast of North America and has been a target of conservation efforts, though relatively little information on larval recruitment exists across much of its range. This study examined the recruitment of Olympia oysters at biweekly to monthly intervals at four sites in northern San Francisco Bay from 2010 to 2015 (except 2013). Mean monthly temperatures warmed at all sites during the study, while winter (January–April) mean monthly salinity decreased significantly during a wet year (2011), but otherwise remained high as a result of a drought. A recurring peak in oyster recruitment was identified in mid-estuary, in conditions corresponding to a salinity range of 25–30 and >16 °C at the time of settlement (April–November). Higher average salinities and temperatures were positively correlated with greater peak recruitment. Interannual variation in the timing of favorable conditions for recruitment at each site appears to explain geographic and temporal variation in recruitment onset. Higher winter/spring salinities and warmer temperatures at the time of recruitment corresponded with earlier recruitment onset within individual sites. Across all sites, higher winter/spring salinities were also correlated with earlier onset and earlier peak recruitment. Lower winter salinities during 2011 also resulted in a downstream shift in the location of peak recruitment.
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- 2016
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21. Invasions in Marine Communities: Contrasting Species Richness and Community Composition Across Habitats and Salinity
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Erica Keppel, Andrew L. Chang, Gregory M. Ruiz, and H. Jimenez
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0106 biological sciences ,NIS ,Invasions ,Estuaries ,Soft sediments ,Hard bottoms ,Community structure ,Ecology ,010604 marine biology & hydrobiology ,Introduced species ,Aquatic Science ,Biology ,010603 evolutionary biology ,01 natural sciences ,Salinity ,Habitat ,Benthic zone ,Species richness ,Bay ,Ecology, Evolution, Behavior and Systematics ,health care economics and organizations ,Invertebrate - Abstract
While many studies of non-native species have examined either soft-bottom or hard-bottom marine communities, including artificial structures at docks and marinas, formal comparisons across these habitat types are rare. The number of non-indigenous species (NIS) may differ among habitats, due to differences in species delivery (trade history) and susceptibility to invasions. In this study, we quantitatively compared NIS to native species richness and distribution and examined community similarity across hard-bottom and soft-sediment habitats in San Francisco Bay, California (USA). Benthic invertebrates were sampled using settlement panels (hard-bottom habitats) and sediment grabs (soft-bottom habitats) in 13 paired sites, including eight in higher salinity areas and five in lower salinity areas during 2 years. Mean NIS richness was greatest in hard-bottom habitat at high salinity, being significantly higher than each (a) native species at high salinity and (b) NIS richness at low salinity. In contrast, mean NIS richness in soft-bottom communities was not significantly different from native species richness in either high- or low-salinity waters, nor was there a difference in NIS richness between salinities. For hard-bottom communities, NIS represented an average of 79% of total species richness per sample at high salinity and 78% at low salinity, whereas the comparable values for soft bottom were 46 and 60%, respectively. On average, NIS occurred at a significantly higher frequency (percent of samples) than native species for hard-bottom habitats at both salinities, but this was not the case for soft-bottom habitats. Finally, NIS contributed significantly to the existing community structure (dissimilarity) across habitat types and salinities. Our results show that NIS richness and occurrence frequency is highest in hard-bottom and high-salinity habitat for this Bay but also that NIS contribute strongly to species richness and community structure across each habitat evaluated.
- Published
- 2018
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22. Dry and wet periods drive rapid shifts in community assembly in an estuarine ecosystem
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Andrew L. Chang, Gregory M. Ruiz, Jeffrey A. Crooks, and Christopher W. Brown
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0106 biological sciences ,Salinity ,Climate ,Climate Change ,Climate change ,Fresh Water ,Context (language use) ,010603 evolutionary biology ,01 natural sciences ,Water Cycle ,Animals ,Humans ,Environmental Chemistry ,Ecosystem ,Water cycle ,General Environmental Science ,Global and Planetary Change ,geography ,geography.geographical_feature_category ,Ecology ,010604 marine biology & hydrobiology ,Estuary ,Invertebrates ,Bays ,Habitat ,Disturbance (ecology) ,Environmental science ,San Francisco ,Seasons ,Estuaries ,Bay - Abstract
The impacts of changing climate regimes on emergent processes controlling the assembly of ecological communities remain poorly understood. Human alterations to the water cycle in the western United States have resulted in greater interannual variability and more frequent and severe extremes in freshwater flow. The specific mechanisms through which such extremes and climate regime shifts may alter ecological communities have rarely been demonstrated, and baseline information on current impacts of environmental variation is widely lacking for many habitats and communities. Here, we used observations and experiments to show that interannual variation in winter salinity levels in San Francisco Bay controls the mechanisms determining sessile invertebrate community composition during the following summer. We found consistent community changes in response to decadal-scale dry and wet extremes during a 13-year period, producing strikingly different communities. Our results match theoretical predictions of major shifts in species composition in response to environmental forcing up to a threshold, beyond which we observed mass mortality and wholesale replacement of the former community. These results provide a window into potential future community changes, with environmental forcing altering communities by shifting the relative influences of the mechanisms controlling species distributions and abundances. We place these results in the context of historical and projected future environmental variation in the San Francisco Bay Estuary.
- Published
- 2017
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23. Advanced Imaging Techniques of the Wrist
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Hon J. Yu, Saya Horiuchi, Donald von Borstel, Taiki Nozaki, Hiroshi Yoshioka, Andrew L Chang, and Yasuhiko Terada
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Diagnostic Imaging ,Wrist Joint ,Pathology ,medicine.medical_specialty ,T2 mapping ,Contrast Media ,Wrist ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,Image Interpretation, Computer-Assisted ,Medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Computer vision ,Mri techniques ,business.industry ,General Medicine ,Image Enhancement ,Wrist Injuries ,Compressed sensing ,medicine.anatomical_structure ,Artificial intelligence ,Cube ,Joint Diseases ,business ,030217 neurology & neurosurgery - Abstract
This article covers the technical aspects and clinical applications of recent advancements in wrist MRI techniques, including T2 and T1rho mapping, compressed sensing, and isotropic 3D imaging using driven equilibrium sequences, variable-flip-angle refocusing pulse sequences, and parallel imaging. The clinical applications of these techniques include the quantitative analysis of cartilage and triangular fibrocartilaginous complex (TFCC) degeneration, faster scanning times, and improved resolution of complex wrist anatomy, allowing differentiation of degenerative from traumatic TFCC tears and improved morphologic evaluation of chondromalacia.MRI of the wrist and of the musculoskeletal system has had multiple novel and exciting advancements in recent years. Several of these advancements, such as parallel imaging, are already in clinical use, and others will be entering the clinical realm in the near future. An understanding of these techniques allows one to use their advantages to greatest effect.
- Published
- 2017
24. Pediatric Proton Therapy: Patterns of Care across the United States
- Author
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Kevin P. McMullen, Daniel J. Indelicato, Andrew L. Chang, Sameer R. Keole, Christine Hill-Kaiser, Toruun I. Yock, Anita Mahajan, Oren Cahlon, Lilia N. Loredo, and William F. Hartsell
- Subjects
Response rate (survey) ,Patterns of care ,Pediatrics ,medicine.medical_specialty ,business.industry ,medicine.medical_treatment ,Normal tissue ,Tumor site ,Atomic and Molecular Physics, and Optics ,Radiation therapy ,Pediatric patient ,Patient information ,medicine ,Radiology, Nuclear Medicine and imaging ,business ,Proton therapy - Abstract
Purpose: Children are particularly prone to the late side effects of normal tissue irradiation. For this reason, pediatric solid tumors are a commonly cited indication for proton therapy worldwide. The aim of this survey was to assess pediatric patterns of care across proton centers in the United States. Patients and Methods: A survey was developed and distributed annually to each clinical proton therapy facility in the United States in operation during the years of 2010, 2011, and 2012. Anonymized patient information including age range, tumor site, and diagnosis were collected annually for each patient 18 years old or younger treated between January 1, 2010 and December 31, 2012. Results: There was a 100% response rate from the United States proton therapy centers in operation for each year surveyed. All facilities treated at least 1 pediatric patient each year. A total of 694 pediatric patients were treated in 2012, an increase from 613 patients in 2011 and 465 patients in 2010. Fifty-seven pe...
- Published
- 2014
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25. The Pediatric Proton Consortium Registry: A Multi-institutional Collaboration in U.S. Proton Centers
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Atif J. Khan, Heather Symecko, Christine E. Hill-Kayser, Torunn I. Yock, Beow Y. Yeap, Stephanie M. Perkins, Stephanie Childs, Jeffrey C. Buchsbaum, Andrew L. Chang, Daniel J. Indelicato, Anita Mahajan, William F. Hartsell, C. Giraud, Fran Laurie, Lisa Raeke, and Hallie Bieber Kasper
- Subjects
medicine.medical_specialty ,business.industry ,Pediatric health ,Medicine ,Radiology, Nuclear Medicine and imaging ,Medical physics ,Proton radiation therapy ,business ,Proton therapy ,Atomic and Molecular Physics, and Optics - Abstract
Purpose: Survival rates for children with cancer have increased dramatically over several decades, revealing a host of late effects associated with treatment. Proton therapy promises to reduce late effects because of its ability to better localize dose, but the question is by how much? Pediatric health outcomes must be prospectively studied to determine what the margin of benefit is. To facilitate such research, a consortium consisting of pediatric investigators from the US was formed. The goals of the Pediatric Proton Consortium Registry (PPCR) study are to create a comprehensive database of pediatric patients treated with proton radiation therapy in the United States to be used and accessed by participating institutions, to describe the patterns of follow-up at proton facilities, and to describe the acute and late effects in the children treated with proton therapy. Patients and Methods: REDCap is the platform for the ∼600-field database which was designed to capture baseline, treatment, and fo...
- Published
- 2014
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26. Soft-sediment community stability across years in San Francisco Bay
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H. Jimenez, Andrew L. Chang, and Gregory M. Ruiz
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0106 biological sciences ,geography ,geography.geographical_feature_category ,010504 meteorology & atmospheric sciences ,Ecology ,010604 marine biology & hydrobiology ,Introduced species ,Estuary ,Aquatic Science ,Biology ,Oceanography ,01 natural sciences ,Invasive species ,Benthos ,Benthic zone ,Abundance (ecology) ,Species richness ,Bay ,0105 earth and related environmental sciences - Abstract
Macrobenthos is used commonly in disturbance-related studies of coastal ecosystems, including those that evaluate invasions by non-native species (NIS), but still little is known about temporal variation in community characteristics, especially in bays and estuaries. In this study we investigated inter-annual changes in the soft-sediment benthic communities of San Francisco Bay over a period of five years, evaluating the contribution of NIS vs. native species to community attributes (species richness, abundance) and the efficacy of sampling (percent richness detected for each NIS and native species). Benthic macrofauna were collected, identified, and quantified from 10 stations (48–50 replicate samples) per year across the high salinity region of the Bay. A total of 36,872 individuals belonging to 126 morphospecies were collected; 61 species were native, accounting for 22% of total abundance, and 31 species were NIS, which reached 74% of total abundance. The other 34 species were either cryptogenic or unresolved taxa. Soft-sediment communities were mainly comprised of amphipods (Ampelisca abdita, Sinocorophium heteroceratum, Monocorophium acherusicum), polychaetes (Sabaco elongatus, Euchone limnicola) and bivalves (Venerupis philippinarum). Community structure and composition were stable across years during the period of the study, despite a major marine heat wave and a record-breaking drought that raised average salinity levels for several years. The sampling was effective, especially for NIS, detecting a higher proportion (94–100%) of estimated richness for NIS compared to native species (74–89%) across the five year period, suggesting NIS were more evenly distributed in space and time and many native species occurred more patchily and less frequently.
- Published
- 2019
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27. Recreational boats as potential vectors of marine organisms at an invasion hotspot
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Gregory M. Ruiz, Chela J. Zabin, Mark D. Sytsma, Ian C. Davidson, Christopher W. Brown, and Andrew L. Chang
- Subjects
Membranipora ,Ecology ,biology ,Botrylloides violaceus ,Bugula neritina ,Aquatic Science ,Oceanography ,biology.organism_classification ,Ficopomatus enigmaticus ,Specimen collection ,Benthic zone ,Bay ,Ecology, Evolution, Behavior and Systematics ,Clathria prolifera - Abstract
With more than 200 aquatic nonindigenous species (NIS), San Francisco Bay (California, USA) is among the world's most invaded harbors. Hard-substratum benthic (biofouling) organisms, which dominate NIS richness, have arrived primarily as a result of shipping and aquaculture activity over past centuries. To date there has been no assessment of the leisure craft vector in the Bay. We aimed to characterize (1) biofouling on boats' submerged surfaces and (2) boater behavior likely to affect the risk of NIS transfers. We used an underwater pole-cam, specimen collections, and a boater questionnaire to quantify the extent and composition of biofouling on recreational boats and to eval- uate boater behavior at a subset of the Bay's marinas. Several NIS, already established within the Bay, were recorded from vessel hulls, including the bryozoans Bugula neritina, Membranipora chesa- peakensis and Watersipora sp., the ascidians Botrylloides violaceus, Styela clava and Ciona intesti- nalis, the polychaete Ficopomatus enigmaticus, and the sponge Clathria prolifera. Only 16% of ques- tionnaire respondents had traveled to sites outside the Bay in the previous 12 mo. Frequency of hull painting and cleaning varied substantially, but we did not find strong patterns of biofouling extent associated with hull husbandry or boat usage. The potential for within-Bay and coastwise regional spread of NIS is high, and recreational boats probably interact in close proximity to other vectors (e.g. commercial ships), causing a ratchet effect of vector events; however, there remains a gap in under- standing the levels and condition of biofouling on transient boats. Transient vessels from San Fran- cisco Bay and other West Coast sites should be the focus of future studies to evaluate the extent to which organisms are being transferred among bays and how vector management could be applied to prevent NIS transfers and impacts.
- Published
- 2010
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28. Preventing horticultural introductions of invasive plants: potential efficacy of voluntary initiatives
- Author
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Jennifer W. Burt, Adrianna A. Muir, Kari E. Veblen, Judah D. Grossman, Andrew L. Chang, Jonah Piovia-Scott, and Heidi W. Weiskel
- Subjects
2. Zero hunger ,0106 biological sciences ,Voluntary Program ,Ecology ,business.industry ,010604 marine biology & hydrobiology ,Environmental resource management ,Introduced species ,15. Life on land ,Biology ,010603 evolutionary biology ,01 natural sciences ,Invasive species ,St louis ,Outreach ,Incentive ,Government regulation ,Turnover ,business ,Socioeconomics ,Ecology, Evolution, Behavior and Systematics - Abstract
Although prevention is the most cost- effective way to avoid the enormous expenses associated with plant invasions, invasive plants continue to be imported as trade commodities for horticultural use. With very little government regulation of horticultural imports of invasive plants, efforts have turned toward fostering volun- tary initiatives to encourage self-regulation by the horticulture trade. Our study takes the first step toward evaluating the potential success of these voluntary initiatives. We conducted a survey of nursery professionals to gauge their perceptions of invasive species, the role of the horticulture trade in invasive plant introductions, and their participa- tion—potential and actual—in preventive mea- sures outlined in the St Louis Voluntary Codes of Conduct for nursery professionals. We found nurs- ery professionals to be highly aware of invasive plants and to accept responsibility as a trade for horticultural introductions. Although only 7% of respondents had heard of the St Louis Voluntary Codes of Conduct, the majority (57%) reported having participated in at least two of seven preventive measures, and most (78%) reported willingness to engage in the majority of preventive measures. We found that several factors signifi- cantly predict increased participation in preventive measures, particularly awareness of invasive plants and involvement in trade associations. We also identified incentives and obstacles to participating in preventive behaviors, including ''concern for the environment'' and ''lack of information,'' respec- tively. Our results suggest that participation in voluntary initiatives will improve through increased outreach, and we provide specific recommenda- tions for improving participation in voluntary programs in the horticulture trade.
- Published
- 2007
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29. A NEW RECORD AND ERADICATION OF THE NORTHERN ATLANTIC ALGAASCOPHYLLUM NODOSUM(PHAEOPHYCEAE) FROM SAN FRANCISCO BAY, CALIFORNIA, USA
- Author
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Andrew L. Chang, Gregory M. Ruiz, A. Whitman Miller, and Natalie Cosentino-Manning
- Subjects
Shore ,geography ,geography.geographical_feature_category ,biology ,Ecology ,Intertidal zone ,Asexual reproduction ,macromolecular substances ,Plant Science ,Aquatic Science ,biology.organism_classification ,Wrack ,Fishery ,Habitat ,Algae ,Bay ,Ascophyllum - Abstract
A new record of the Northern Atlantic fucoid Ascophyllum nodosum (L.) Le Jolis (Knotted wrack) was discovered on a shoreline in San Francisco Bay, California during a survey of intertidal habitats in 2001–2002. The alga showed no signs of deterioration 2.5 months after its initial detection. The healthy condition, presence of receptacles with developing oogonia, potential for asexual reproduction, and ability to withstand environmental conditions, both inside the Bay and on the outer Pacific coast, prompted a multiagency eradication effort. Given the relatively small area of shoreline inhabited by the alga, in combination with its absence in 125 other surveyed locations, we decided that manual removal of the seaweed would be the most environmentally sensitive yet effective eradication approach. No A. nodosum has been detected at the site since December 2002, and the species is thought to have been locally eradicated. The site continues to be monitored to assess the success of the eradication efforts.
- Published
- 2004
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30. Testing local and global stressor impacts on a coastal foundation species using an ecologically realistic framework
- Author
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Matthew C. Ferner, Brian S. Cheng, Anna Deck, Kerstin Wasson, Marilyn Latta, Andrew L. Chang, Jillian M. Bible, Anne E. Todgham, Chela J. Zabin, and Edwin D. Grosholz
- Subjects
additive ,Low salinity ,warming ,synergy ,Climate change ,Biology ,Ostrea lurida ,salinity ,Environmental data ,Environmental Chemistry ,latent ,Olympia oyster ,General Environmental Science ,Global and Planetary Change ,diel-cycling hypoxia ,Ecology ,Stressor ,Hypoxia (environmental) ,Biological Sciences ,multiple stressors ,climate change ,Interactive effects ,Latent effects ,Foundation species ,Environmental Sciences - Abstract
© 2015 John Wiley & Sons Ltd. Despite the abundance of literature on organismal responses to multiple environmental stressors, most studies have not matched the timing of experimental manipulations with the temporal pattern of stressors in nature. We test the interactive effects of diel-cycling hypoxia with both warming and decreased salinities using ecologically realistic exposures. Surprisingly, we found no evidence of negative synergistic effects on Olympia oyster growth; rather, we found only additive and opposing effects of hypoxia (detrimental) and warming (beneficial). We suspect that diel-cycling provided a temporal refuge that allowed physiological compensation. We also tested for latent effects of warming and hypoxia to low-salinity tolerance using a seasonal delay between stressor events. However, we did not find a latent effect, rather a threshold survival response to low salinity that was independent of early life-history exposure to warming or hypoxia. The absence of synergism is likely the result of stressor treatments that mirror the natural timing of environmental stressors. We provide environmental context for laboratory experimental data by examining field time series environmental data from four North American west coast estuaries and find heterogeneous environmental signals that characterize each estuary, suggesting that the potential stressor exposure to oysters will drastically differ over moderate spatial scales. This heterogeneity implies that efforts to conserve and restore oysters will require an adaptive approach that incorporates knowledge of local conditions. We conclude that studies of multiple environmental stressors can be greatly improved by integrating ecologically realistic exposure and timing of stressors found in nature with organismal life-history traits.
- Published
- 2014
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31. Atmospheric rivers and the mass mortality of wild oysters: insight into an extreme future?
- Author
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Matthew C. Ferner, Brian S. Cheng, Anna Deck, and Andrew L. Chang
- Subjects
0106 biological sciences ,Salinity ,Oyster ,010504 meteorology & atmospheric sciences ,Environmental change ,Range (biology) ,Climate Change ,Climate change ,01 natural sciences ,California ,General Biochemistry, Genetics and Molecular Biology ,Abundance (ecology) ,biology.animal ,Animals ,Precipitation ,Mortality ,Research Articles ,0105 earth and related environmental sciences ,General Environmental Science ,General Immunology and Microbiology ,biology ,Atmosphere ,Ecology ,010604 marine biology & hydrobiology ,General Medicine ,Atmospheric river ,Ostreidae ,Steam ,Geography ,Bays ,General Agricultural and Biological Sciences ,Bay - Abstract
Climate change is predicted to increase the frequency and severity of extreme events. However, the biological consequences of extremes remain poorly resolved owing to their unpredictable nature and difficulty in quantifying their mechanisms and impacts. One key feature delivering precipitation extremes is an atmospheric river (AR), a long and narrow filament of enhanced water vapour transport. Despite recent attention, the biological impacts of ARs remain undocumented. Here, we use biological data coupled with remotely sensed and in situ environmental data to describe the role of ARs in the near 100% mass mortality of wild oysters in northern San Francisco Bay. In March 2011, a series of ARs made landfall within California, contributing an estimated 69.3% of the precipitation within the watershed and driving an extreme freshwater discharge into San Francisco Bay. This discharge caused sustained low salinities (less than 6.3) that almost perfectly matched the known oyster critical salinity tolerance and was coincident with a mass mortality of one of the most abundant populations throughout this species' range. This is a concern, because wild oysters remain a fraction of their historical abundance and have yet to recover. This study highlights a novel mechanism by which precipitation extremes may affect natural systems and the persistence of sensitive species in the face of environmental change.
- Published
- 2016
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32. A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity
- Author
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Andrew Kennedy, Andrew L. Chang, Christina D. Smolke, and Joe C. Liang
- Subjects
Color ,Computational biology ,Biology ,03 medical and health sciences ,Genes, Reporter ,Genetics ,RNA, Catalytic ,Gene ,030304 developmental biology ,Gene Library ,RNA Cleavage ,0303 health sciences ,030302 biochemistry & molecular biology ,Ribozyme ,Sorting ,RNA ,Cell sorting ,Flow Cytometry ,Kinetics ,Gene Expression Regulation ,biology.protein ,Methods Online ,Biological network ,Cytokinesis - Abstract
Recent advances have demonstrated the use of RNA-based control devices to program sophisticated cellular functions; however, the efficiency with which these devices can be quantitatively tailored has limited their broader implementation in cellular networks. Here, we developed a high-efficiency, high-throughput and quantitative two-color fluorescence-activated cell sorting-based screening strategy to support the rapid generation of ribozyme-based control devices with user-specified regulatory activities. The high-efficiency of this screening strategy enabled the isolation of a single functional sequence from a library of over 10(6) variants within two sorting cycles. We demonstrated the versatility of our approach by screening large libraries generated from randomizing individual components within the ribozyme device platform to efficiently isolate new device sequences that exhibit increased in vitro cleavage rates up to 10.5-fold and increased in vivo activation ratios up to 2-fold. We also identified a titratable window within which in vitro cleavage rates and in vivo gene-regulatory activities are correlated, supporting the importance of optimizing RNA device activity directly in the cellular environment. Our two-color fluorescence-activated cell sorting-based screen provides a generalizable strategy for quantitatively tailoring genetic control elements for broader integration within biological networks.
- Published
- 2012
33. Urgent radiotherapy is effective in the treatment of metastatic medulloblastoma causing symptomatic brainstem edema
- Author
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Ronald H, Shapiro and Andrew L, Chang
- Subjects
Male ,Spinal Neoplasms ,Treatment Outcome ,Child, Preschool ,Antineoplastic Combined Chemotherapy Protocols ,Humans ,Brain Edema ,Cerebellar Neoplasms ,Medulloblastoma - Abstract
A 3-year-old male who presented with hydrocephalus symptoms was found to have metastatic medulloblastoma with diffuse spinal disease. Thirteen days following surgical resection of his primary tumor, he clinically deteriorated due to worsening brainstem edema. Following intubation, stress-dose steroids, and mannitol, urgent radiotherapy was initiated to the whole brain and cervical cord. The patient improved clinically with a repeat MRI showing decreased leptomeningeal enhancement in the radiation fields. In the literature, there are no reports of successful urgent radiotherapy in medulloblastoma, but in this instance, it proved to be a viable option.
- Published
- 2010
34. Establishment Failure in Biological Invasions: A Case History of Littorina littorea in California, USA
- Author
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Andrew L. Chang, A. Whitman Miller, April M. H. Blakeslee, and Gregory M. Ruiz
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Gastropoda ,Population Dynamics ,lcsh:Medicine ,Zoology ,Population genetics ,Introduced species ,DNA, Mitochondrial ,California ,Invasive species ,Genetic variation ,Animals ,lcsh:Science ,Biology ,Ecosystem ,Genetic diversity ,Multidisciplinary ,Ecology ,biology ,lcsh:R ,Marine Ecology ,Genetic Variation ,Littorina ,biology.organism_classification ,Europe ,Biogeography ,North America ,Genetic structure ,lcsh:Q ,Population Ecology ,Introduced Species ,Research Article - Abstract
Background: The early stages of biological invasions are rarely observed, but can provide significant insight into the invasion process as well as the influence vectors have on invasion success or failure. Methodology/Principal Findings: We characterized three newly discovered populations of an introduced gastropod, Littorina littorea (Linne´, 1758), in California, USA, comparing them to potential source populations in native Europe and the North American East Coast, where the snail is also introduced. Demographic surveys were used to assess spatial distribution and sizes of the snail in San Francisco and Anaheim Bays, California. Mitochondrial DNA was sequenced and compared among these nascent populations, and various populations from the North American East Coast and Europe, to characterize the California populations and ascertain their likely source. Demographic and genetic data were considered together to deduce likely vectors for the California populations. We found that the three large California L. littorea populations contained only adult snails and had unexpectedly high genetic diversity rather than showing an extreme bottleneck as typically expected in recent introductions. Haplotype diversity in Californian populations was significantly reduced compared to European populations, but not compared to East Coast populations. Genetic analyses clearly suggested the East Coast as the source region for the California introductions. Conclusions and Significance: The California L. littorea populations were at an early, non-established phase of invasion with no evidence of recruitment. The live seafood trade is the most likely invasion vector for these populations, as it preferentially transports large numbers of adult L. littorea, matching the demographic structure of the introduced California L. littorea populations. Our results highlight continued operation of live seafood trade vectors and the influence of vectors on the demographic and genetic structure of the resulting populations, especially early stages of the invasion process.
- Published
- 2011
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35. Tackling aquatic invasions: risks and opportunities for the aquarium fish industry
- Author
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Judah D. Grossman, Adrianna A. Muir, Kari E. Veblen, Teresa Sabol Spezio, Jonah Piovia-Scott, Andrew L. Chang, Julia C. Blum, Edwin D. Grosholz, Heidi W. Weiskel, and Jennifer W. Burt
- Subjects
Fishery ,Chain store ,Ecology ,Fish species ,%22">Fish ,Introduced species ,Aquarium fish ,Biology ,Invasive species ,Ecology, Evolution, Behavior and Systematics ,Aquatic organisms - Abstract
The aquarium trade is an important and rapidly growing vector for introduced species in the United States. We examined this vector by surveying pet stores in the San Francisco Bay-Delta region to compile a list of aquarium fish species commonly stocked. We identified which of these species might be able to survive in the Bay-Delta, and investigated store representatives' knowledge and attitudes about bio- logical invasions. A restrictive analysis using conservative estimates of fish temperature tolerances and environmental conditions found that the local aquarium trade includes 5 fish species that can survive in a temperate system such as the Bay-Delta. Under more inclusive parameters, up to 27 fish species met the criteria for survival in the Bay-Delta. We further explored these results by comparing potential invader incidence between different types of stores. In the more restrictive analysis, three national retail chains stocked significantly more potentially invasive species than independent aquarium stores, but there was no differ- ence in the more inclusive analysis. A significantly higher percentage of fish taxa were easily identifiable and well-labeled in chain stores than in independent stores. Most aquarium store representatives indicated willingness to take action to reduce the threat of trade- related introductions, although chain store employees were more willing to assign responsibility for reducing this threat to the aquarium industry than were inde- pendent store employees. Management efforts for this vector should focus on (a) improving labeling and identification of fish species in stores, (b) expanding the often spotty data on fish physiological tolerances, especially for saltwater species, (c) educating custom- ers and store employees about the risks posed by pet release, and (d) providing better options for responsible disposal of unwanted fish.
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36. Aquatic pollution increases the relative success of invasive species
- Author
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Gregory M. Ruiz, Jeffrey A. Crooks, and Andrew L. Chang
- Subjects
Abiotic component ,Propagule ,Habitat ,Ecology ,Propagule pressure ,Introduced species ,Ecosystem ,Species richness ,Biology ,Invasive species ,Ecology, Evolution, Behavior and Systematics - Abstract
Although individual ecosystems vary greatly in the degree to which they have been invaded by exotic species, it has remained difficult to isolate mechanisms influencing invader success. One largely anecdotal observation is that polluted or degraded areas will accumulate more invaders than less-impacted sites. However, the role of abiotic factors alone in influencing invisibility has been difficult to isolate, often because the supply of potential invaders is confounded with conditions thought to increase vulnerability to invasion. Here, we conducted a field experiment to test how the assemblages of exotic versus native marine invertebrates changed during community assembly under different exposure levels of a common pollutant, copper. The experiment was conducted by deploying fouling panels in a Randomized Block Design in San Francisco Bay. Panels were periodically removed, placed into buckets with differing copper concentrations, and returned to the field after 3 days. This design allowed propagule availability to the plates to be statistically independent of short-term copper exposure. The results demonstrate that copper caused significant differences in community structure. Average native species richness was significantly affected by copper exposure, but average exotic richness was not. The total native species pool within treatments exhibited a greater than 40% decline within increasing copper, while the exotic species pool did not change significantly. These results confirm that anthropogenic alteration of abiotic factors influences invader success, indicating that management strategies to reduce invader impacts should include both efforts to improve environmental conditions as well as reduce invader supply.
- Full Text
- View/download PDF
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