Egg production rates of the copepod Calanus marshallae in relation to seasonal and interannual variations in microplankton biomass and species composition in the coastal upwelling zone off Oregon, USA

In this study, we assessed trophic interactions between microplankton and copepods by studying the functional response of egg production rates (EPR; eggs female⁻¹day⁻¹) of the copepod Calanus marshallae to variations in microplankton biomass, species composition and community structure. Female C. marshallae and phytoplankton water samples were collected biweekly at an inner-shelf station off Newport, Oregon USA for four years, 2011–2014, during which a total of 1213 female C. marshallae were incubated in 63 experiments. On average, 80% of the females spawned with an overall mean EPR of 30.4. EPRs in spring (Apr–May, average of 40.2) were significantly higher than summer (Jun–Oct; 26.4). EPRs were intermediate in winter (Jan–Feb; 32.5). Interannually, EPRs were significantly higher in 2014 than 2011 and 2012. Total chlorophyll a (Chl a) concentration and diatom abundance both were significantly higher in summer while no seasonal differences were found in abundance of dinoflagellates, ciliates or Cryptophytes. Although total Chl a showed no interannual differences in bulk biomass of phytoplankton, community structure analysis indicated differences among years. More diverse diatom communities were observed in 2013 and 2014 compared to 2011 and 2012. Relationships between EPR and potential food variables (phytoplankton and ciliates) were significant by season: a hyperbolic functional response was found between EPR and total Chl a in winter–spring and summer, separately, and between EPR and ciliate abundance in winter–spring; a linear model fit best the functional response of EPR to diatom abundance in summer. The estimate of potential population recruitment rate (the number of females × EPR; eggs day⁻¹m⁻²) was highest in spring (Apr–May), and annually was highest in 2013 (11,660), followed by 2011 (6209), 2012 (3172) and 2014 (1480). Our observations of in situ EPR were far higher than published laboratory rates of 23.5, calling into question our past laboratory studies that used mono-algae cultures as food for copepods. Moreover, an increasing number of studies (including this study) are showing an apparent greater importance of ciliates as a nutritious food source for Calanus species demonstrating the importance of the microbial loop to secondary production.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/progress-in-oceanography

Seasonal Cycle of Phytoplankton Community Composition in the Coastal Upwelling System Off Central Oregon in 2009

Coastal upwelling in the northern California Current varies seasonally, with downwelling in winter and upwelling in summer, resulting in pronounced variability in hydrography, nutrients, phytoplankton biomass, and species composition. Winter was characterized by moderate concentrations of nitrate and silicate (averages of 10 and 18 μM, respectively) and low concentrations of chlorophyll a (Chl a). During the upwelling season, concentrations of the same nutrients ranged from near 0 μM to approximately 27 and 43 μM and Chl a 0.5<x<15 μg L⁻¹. During autumn, upwelling weakened and nutrient concentrations were reduced, but large phytoplankton blooms continued to occur. Variations in hydrography, nutrients, and phytoplankton also occurred within the upwelling season due to alternation of the winds between northerly (active upwelling) and southerly (relaxation of upwelling), on a 5- to 10-day time scale. Eleven blooms were observed, most of which occurred near the end of active upwelling events and during relaxation of upwelling. Nonmetric multidimensional scaling ordination of species composition of the microplankton revealed four distinct communities: a winter community, early upwelling and late upwelling season communities, and an autumn community. Diatoms (Asterionellopsis glacialis, Eucampia zodiacus, and several Chaetoceros, Thalassiosira, and Pseudo-nitzschia species) dominated early in the upwelling season, averaging 80% of the phytoplankton biomass, and dinoflagellates dominated near the end of the upwelling season, averaging 68% of the phytoplankton biomass. Dinoflagellates formed two monospecific blooms—Prorocentrum gracile in late summer and Akashiwo sanguinea in autumn. Changes in community composition were correlated with bottom temperature and salinity (representing seasonal variability) and sea surface salinity (representing within-season event-scale variability in upwelling).Keywords: Community structure, Seasonality, Oregon Coast, Phytoplankton, Upwellin

HRAS Mutations Define a Distinct Subgroup in Head and Neck Squamous Cell Carcinoma

Purpose: In head and neck squamous cell carcinoma (HNSCC), HRAS mutation is a new actionable oncogene driver. We aimed to evaluate HRAS mutational variants, comutation profile, and survival outcomes of this molecularly defined population. Methods: We leveraged four deidentified patient data sets with HRAS-mutant HNSCC, MD Anderson Cancer Center, Kura Oncology, Inc trial, Foundation Medicine, and American Association for Cancer Research GENIE v.12. Patient demographic information and clinical courses were extracted, when available, in addition to HRAS mutation type and co-occurring mutations. Survival outcomes were analyzed (Kaplan-Meier method). Results: Two hundred forty-nine patients with HRAS-mutant HNSCC were identified from the four data sets. Median age ranged from 55 to 65 years, with a higher frequency in male patients (64%); the majority of HRAS-mutant HNSCC occurred in human papillomavirus-negative HNSCC. HRAS mutation patterns were similar across data sets; G12S was the most common (29%). Treatment responses to tipifarnib were not codon-specific. Compared with wild-type, significantly co-occurring mutations with HRAS were Casp8 (Fisher\u27s exact test, P \u3c .00013), TERT (P \u3c .0085), and NOTCH1 (P \u3c .00013). Analysis of clinical courses from the MD Anderson Cancer Center and Kura Oncology, Inc data sets demonstrated poor clinical outcomes with a high rate of recurrence following primary definitive treatment (50%-67% relapse \u3c 6 months) and short disease-free survival (4.0 months; 95% CI, 1.0 to 36.0) and overall survival (OS; 15.0 months; 95% CI, 6.0 to 52.0). Use of tipifarnib in this data set demonstrated improved OS (25.5 months; 95% CI, 18.0 to 48.0). Conclusion: Oncogenic mutations in HRAS occur in 3%-4% of HNSCC, with G12S being the most frequent. Without targeted therapy, patients with HRAS-mutant HNSCC had poor clinic outcomes; observable trend toward improvement in OS has been noted in cohorts receiving treatments such as tipifarnib. The comutation pattern of HRAS-mutant in HNSCC is distinct, which may provide insight to future therapeutic combination strategies

Large-scale bloom of Akashiwo sanguinea in the Northern California current system in 2009

Significant seabird mortality on the Oregon (OR) and Washington (WA) coast in 2009 has been attributed to a massive bloom of the dinoflagellate Akashiwo sanguinea (K. Hirasaka) G. Hansen & Ø. Moestrup. Initial, albeit limited, observations suggested this bloom began in WA and reached OR waters through southward transport. Here, we explore a combination of remote sensing products and an exceptional latitudinal dataset of plankton counts collected in the surfzone and offshore in OR and WA coastal waters. Records of satellite ocean color for this period support the new finding that blooms were concurrent in OR and WA waters, with no evidence for latitudinal propagation as had been previously suggested. Plankton analyses further indicate that there was a rapid and synchronized increase of A. sanguinea between late August and mid-September of 2009 along wide swaths of the OR and WA coasts. Bloom onset occurred during a prolonged quiescent and warm period in late August–early September, near the end of the March–October upwelling phase. An upwelling event in October likely contributed to foam production through vertical mixing of A. sanguinea rich waters. Bloom intensity peaked earlier and at higher levels in WA waters as compared to OR with cell concentrations exceeding 1.5 x 10⁶ cells L⁻¹ (WA) and ~350,000 cells L⁻¹ (OR). In OR samples, A. sanguinea cells comprised upwards of 90% of dinoflagellate cell counts and ~30% of total phytoplankton cells. At some locations, A. sanguinea persisted well into November–December of 2009, during which time satellite sea surface temperature records indicated anomalously warm surface waters (up to ~5°C greater than climatological means). Taken together, the data reveal a HAB event of a magnitude unprecedented in over a decade of observations. We hypothesize that these blooms originated from either a cryptic cyst bed and/or a pelagic seed bank of viable vegetative cells.Keywords: Upwelling, Seabird mortality, Cysts, Akashiwo sanguinea, HABS, Harmful algal blooms, Surf zone, DinoflagellatesKeywords: Upwelling, Seabird mortality, Cysts, Akashiwo sanguinea, HABS, Harmful algal blooms, Surf zone, Dinoflagellate

Monitoring Oregon Coastal Harmful Algae: Observations and implications of a harmful algal bloom-monitoring project

The accumulation of domoic acid (DA) and saxitoxins (STX), phycotoxins produced by some species of Pseudo-nitzschia and Alexandrium, respectively, in coastal food webs are a focus of research on the West Coast of the United States due to the deleterious effects they have on coastal ecosystems and economies. Results are presented from the 2007–2012 Monitoring Oregon Coastal Harmful Algae (MOCHA) project, the Oregon coast's first HAB monitoring and research program. Both historical toxin databases and more detailed case-study observations of individual HAB events are compiled to provide the first detailed overview of HAB occurrence in this region. These results are also presented in the context of informing future HAB monitoring in this and other upwelling regimes affected by STX and DA. A 2009–2010 warming event was associated with the greatest HAB activity during the MOCHA project, including anomalously high sea surface temperatures and shellfish harvesting closures due to STX and DA in 2009 and 2010, respectively. In regards to HAB monitoring, it is shown that (1) razor clams are a more sensitive indicator of DA than mussels; (2) water column concentrations of particulate domoic acid greater than 10³ng L⁻¹ can be used as a threshold for early-warning of shellfish DA toxicity and (3) approximately bi-weekly, or shorter, monitoring of Alexandrium in the surf zone and/or offshore can provide advance notice of STX contamination of shellfish. Both of the latter two metrics gain added value when coupled with local wind stress, a proxy of downwelling/relaxation events that facilitate greater interaction between offshore blooms and shellfish.Keywords: Oregon coast, Saxitoxin, Domoic acid, Alexandrium, Harmful algal bloom, Pseudo-nitzschi

Brief Report: Clinical Response, Toxicity, and Resistance Mechanisms to Osimertinib Plus MET Inhibitors in Patients With EGFR-Mutant MET-Amplified NSCLC

INTRODUCTION:MET amplification is a known resistance mechanism to EGFR tyrosine kinase inhibitor (TKI) treatment in EGFR-mutant NSCLC. Dual EGFR-MET inhibition has been reported with success in overcoming such resistance and inducing clinical benefit. Resistance mechanisms to dual EGFR-MET inhibition require further investigation and characterization. METHODS: Patients with NSCLC with both MET amplification and EGFR mutation who have received crizotinib, capmatinib, savolitinib, or tepotinib plus osimertinib (OSI) after progression on OSI at MD Anderson Cancer Center were included in this study. Molecular profiling was completed by means of fluorescence in situ hybridization (FISH) and next-generation sequencing (NGS). Radiological response was assessed on the basis of Response Evaluation Criteria in Solid Tumors version 1.1. RESULTS: From March 2016 to March 2022, 23 treatments with dual MET inhibitor and osi were identified with a total of 20 patients included. Three patients received capmatinib plus OSI after progression on crizotinib plus OSI. Median age was 64 (38–89) years old and 75% were female. MET amplification was detected by FISH in 14 patients in the tissue, NGS in 10 patients, and circulating tumor DNA in three patients. Median MET gene copy number was 13.6 (6.4–20). Overall response rate was 34.8% (eight of 23). In assessable patients, tumor shrinkage was observed in 82.4% (14 of 17). Median time on treatment was 27 months. Two of three patients responded to capmatinib plus OSI after progression on crizotinib plus OSI. Dual EGFR-MET inhibition was overall well tolerated. Two patients on crizotinib plus OSI and one pt on capmatinib plus OSI discontinued therapy due to pneumonitis. One pt discontinued crizotinib plus OSI due to gastrointestinal toxicity. Six patients were still on double TKI treatment. At disease progression to dual EGFR-MET inhibition, FISH and NGS on tumor and plasma were completed in six patients. Notable resistance mechanisms observed include acquired MET D1246H (n = 1), acquired EGFR C797S (n = 2), FGFR2 fusion (n = 1, concurrent with C797S), and EGFR G796S (n = 1, concurrent with C797S). Four patients lost MET amplification. CONCLUSIONS: Dual EGFR and MET inhibition yielded high clinical response rate after progression on OSI. Resistance mechanisms to EGFR-MET double TKI inhibition include MET secondary mutation, EGFR secondary mutation, or loss of MET amplification

Feeding rates and selectivity of adult Euphausia pacifica on natural particle assemblages in the coastal upwelling zone off Oregon, USA, 2010

Filtration by adult Euphausia pacifica was measured before and during the upwelling season, using both “disappearance of chlorophyll” and “disappearance of cells” techniques. Results show that feeding rates and selectivity varied with food assemblages. Filtration rate (F) was best modeled by the Ivlev function: the average F on total Chl-a was 92 mL euphausiid⁻¹ h⁻¹, and 119 mL euphausiid⁻¹ h⁻¹ on microscopy cell counts. F averaged 36 for the 20 µm fraction. The average F values were 155 and 163 mL euphausiid⁻¹ h⁻¹ for chain-diatoms and single diatoms, respectively, and 115 and 137 mL euphausiid⁻¹ h⁻¹ for the 40 µm ciliates, respectively. Ingestion rates based on total Chl-a and size fractions, total cell counts and ciliates were significantly correlated using Hollings' models (P < 0.01). Maximum daily ration was 23% body C day⁻¹ when a high food concentration (700 µC L⁻¹) was available, but over the carbon range of 50–200 µg C L⁻¹, daily ration averaged 4% body C day⁻¹. Diatoms were consumed almost exclusively during blooms associated with summer upwelling events; larger types of ciliates and dinoflagellates were fed upon preferentially compared with their smaller counterparts.Keywords: Phytoplankton, Filtration rate, Ciliate, Ingestion rate, Euphausia pacific

Interannual variations in phytoplankton community structure in the northern California Current during the upwelling seasons of 2001−2010

Phytoplankton species were enumerated from 72 samples collected biweekly during the upwelling season (May to August) of 2001−2010 to test for effects of interannual variations in upwelling and decadal basin-scale variability on phytoplankton species composition and community structure. Cluster analysis of phytoplankton community structure identified 7 groups; 1 group was dominated by dinoflagellates while the other groups were dominated by diatoms but with variable ratios of diatom-to-dinoflagellate abundance ranging from 4 to 847. The most abundant diatoms were Thalassiosira spp., Chaetoceros spp., Asterionellopsis glacialis, Cylindrotheca closterium, Leptocylindrus spp., Nitzschia and Pseudo-nitzschia spp., with dominance varying among the 7 groups. Variations in phytoplankton community structure were not related to the strength of upwelling within a given year; rather, differences were related to when a sample was collected within an upwelling/downwelling cycle. Community structure was also analyzed by non-metric multidimensional scaling ordination. The x-axis scores of the ordination, which is an index of community structure, were correlated with the Pacific Decadal Oscillation (PDO) but not with seasonally averaged coastal upwelling strength. Positive values of the index corresponded with positive PDO years (2002−2007), and negative index values with negative PDO years (2001, 2008−2010). Thus changes in the sign of the PDO seem to be more influential in explaining the interannual variations in phytoplankton community structure than seasonally averaged coastal upwelling.Keywords: Pacific Decadal Oscillation, Northern California Current, Dinoflagellate, Diatom, Coastal upwellingKeywords: Pacific Decadal Oscillation, Northern California Current, Dinoflagellate, Diatom, Coastal upwellin

Initiation and Development of a Toxic and Persistent <i>Pseudo-nitzschia</i> Bloom off the Oregon Coast in Spring/Summer 2015

<div><p>In spring/summer 2015, a toxic bloom by the diatom <i>Pseudo-nitzschia</i> (PN) occurred along the west coast of the United States which led to closures of the harvest of razor clams and Dungeness crabs. Twice monthly observations of temperature, salinity, nutrients, chlorophyll and phytoplankton species composition allowed us to track oceanographic conditions preceding and during the development of the bloom. PN cells were first detected during late winter 2015. A PN bloom was initiated following the onset of coastal upwelling in mid-April; subsequent peaks in May and June were sustained by episodic upwelling events and reached magnitudes of 10⁵ cells/L and 10⁶ cells/L, 40% and 90% of the total diatom abundance, respectively. The bloom temporarily crashed in July due to a lack of upwelling, but PN cells increased again in August due to a resumption of upwelling, albeit with lower magnitude. Macronutrient conditions prior to this bloom likely played a critical role in triggering the bloom and its toxicity (particularly silicic acid limitation stress). Nutrient stress preceding the toxic bloom was related to two oceanographic events: an anomalously warm and thick water mass that occupied the northern North Pacific from September 2014 through 2015 leading to a highly-stratified water column, and the drawdown of nitrate and silicic acid during an unusually intense winter phytoplankton bloom in February and early March 2015.</p></div