Hourly variations in planktonic larval concentrations on the inner shelf: Emerging patterns and processes

Planktonic larvae are unlikely to be randomly distributed over time or in space. Fluctuations in larval density may result from a variety of physical and biological processes. To identify relatively high-frequency patterns of larval variation for an inner-shelf environment, zooplankton were sampled hourly for 3 d using an automated plankton pump. Moored ~80 cm above bottom, the pump was located in 8 m of water on the Outer Banks of North Carolina. Densities of all larval groups were highly variable: 5-746 m-3 for barnacle cyprids, 0-668 m-3 for polychaetes, 0-516 m-3 for bivalves, 6-414 m-3 for gastropods, and 0-86 m-3 for bryozoan cyphonautes. Moreover, maximal and submaximal peaks were nearly coincident for all taxa. One hypothesis to explain these results involves passive larval transport by wind-driven cross-shelf flows (upwelling and downwelling). Larval concentrations were persistently low in warm, downwelled water and highest during a period of cool, upwelled water. During upwelling, however, maximal and submaximal peaks for each taxon corresponded with brief relaxation events, dominated by downwelling-favorable winds. Thus, larvae tracking with cool water would have been moved upslope then offshore at the surface by upwelling currents or to the bottom by downwelling flows. A second hypothesis involves active diel vertical migration (DVM). During the cool-water period, peaks in near-bottom larval density occurred near noon, consistent with daytime descent. Daily peaks were not always separated by 24 h, however, probably due to modulation of DVM by physical processes (e.g., cross- or alongshelf advection or mixing). These relatively simple patterns of variation in larval abundance are surprising, given the complex hydrodynamic processes that typically operate on the inner shelf

Life in the lee: Local distributions and orientations of honeycomb worms along the California coast

In the rocky intertidal, invertebrates living in dense, intraspecific groups may be particularly important community members because they provide structural habitat for other species. Despite the prevalence of conspecific aggregates, there is scant knowledge of the proximate and ultimate causes of their distributions. Phragmatopoma californica is a gregarious, suspension-feeding tubeworm that forms extensive reefs ( honeycombs ) along the California coast. Local distributions and sizes of worm aggregations, tube orientations and worm mass were quantified to identify patterns and generate hypotheses regarding potential structuring processes. Field surveys were conducted at five intertidal boulder fields in northern and southern California, spanning much of this species\u27 range. Observational data were obtained at four ecologically meaningful spatial scales. The most striking patterns occurred at the smallest (\u3c1 m, individual rock), pervading throughout the largest (50–500 km, among beaches), scales. Aggregations were significantly more abundant and larger on back (shoreward) than front (seaward) faces of boulders. Worm tube orientations also showed a significant directional bias that differed between opposing rock surfaces. In contrast, worm mass was not significantly different between the two faces, perhaps due to relatively uniform growth conditions on the scale of a rock or because worms had reached a terminal size. We hypothesize that within-rock aggregation distributions are associated with the local boulder-induced flow regime. The recirculation zone that forms in the lee of a flow obstacle (rock) would preferentially retain larvae, and thus, enhance the flux of settlers to the back surface. Potentially a region of relatively low wave disturbance and high fertilization rate, life in the lee may be yet another adaptation for survival in the hostile rocky intertidal

Flocs, flows, and mechanisms decoupling larval supply from settlement

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 57 (2012): 936-944, doi:10.4319/lo.2012.57.4.0936.Larval supply, settlement (24 h), and recruitment were measured simultaneously with flow and flocculated particulates (flocs) in a muddy, coastal embayment. Fortuitous observations indicated that flocs drifting above the bed touched down at slack tide. Unexpectedly, results showed that larval supply did not portend settlement for the two most abundant polychaetes, Mediomastus ambiseta (resident mud dweller) and Sabellaria vulgaris (nonresident sand dweller). Both variables fluctuated widely and were decoupled. Colonization of mud vs. sand trays was not significantly different, also due to high variances. A statistical power analysis indicated that resolving selectivity would require 45 (median) paired, replicate treatments. Time series of near-bed planktonic larvae showed sizeable and sporadic spikes. Even 24-h means failed to predict settlement. Sabellaria was numerous in zooplankton pump collections, rare in trays, and nonexistent in ambient sediments. In contrast, Mediomastus was absent from pump samples, but dominated mud trays and bottom cores. Floc contents, however, lend insight into these distributions. Densities (of order 105 m-3) of Sabellaria and Mediomastus in flocs greatly exceeded those in tray and pump samples (of order 103 m-3). Located between the water column and seafloor, organic-rich flocs may offer transient larvae food, shelter, transport, and perusal of settlement sites. When aggregates touch down, entrained Mediomastus might exit upon contact with suitable ambient sediments, whereas nonresident Sabellaria remain suspended. Flocs may thus play a critical role in shaping connectivity and structuring species distributions.This study was supported by the National Science Foundation (Division of Ocean Sciences, OCE 08-52361) and the University of California at Los Angeles Council on Research

Larval settlement in flocculated particulates

Author Posting. © The Authors, 2008. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 66 (2008): 275-297, doi:10.1357/002224008785837167.Planktonic larval settlement can be a major determinant of population and community dynamics. Settlement templates of benthic invertebrates have been attributed to biological, chemical, and hydrodynamic mechanisms. Completely unexplored, however, is the role of patchy, but widespread, flocculated particulates (“floc”) that intermittently rest on substrate surfaces. Motivated by observations of very high (of order 106 m-3) larval/postlarval densities in floc from a coastal embayment, this study experimentally identified physical and behavioral mechanisms responsible for these associations. In annular-flume studies, sediment cores were mounted flush with the channel bottom, serving as the floc source. Larval (Capitella sp. I, a polychaete worm) distributions in the flume were consistent with predictions for transported particulates. Floc and larvae accumulated at the channel inner corner in high flows (shear velocities, u*, of 0.8 and 1.6 cm s-1), but not in low flows (u* of 0, 0.2 and 0.4 cm s-1). Inner-corner concentrations of larvae/floc resulted from a predictable, cross-channel, bottom flow in that direction. In still-water behavioral assays, there were no significant differences in percent metamorphosis among flocs fabricated from particulate-laden seawater, conspecific fecal pellets (compact floc) and organic-rich sediment. Surficial aggregates clearly were acceptable settlement substratum. This study is the first to show that settling larvae associate with surficial aggregates via both physical and behavioral mechanisms. Floc may be a transient larval venue facilitating habitat search, providing nutrition, or offering protection from predators. Alternatively, it could confer high mortality, reducing larval flux to the bed. Associations between larvae and floc do not supersede established mechanisms of habitat selection. They just thicken the plot.This study was supported by the National Science Foundation (OCE 97-29972 and OCE 02-42321), NOAA California Sea Grant College Program (R/F-197) and the UCLA Council on Research

Adult macrofauna effects on Capitella sp. I larval settlement: A laboratory flume study

The opportunistic, deposit-feeding polychaete Capitella sp. I is the overwhelming numerical dominant in disturbed and enriched sediments and rarely co-occurs in appreciable numbers with other abundant mud-dwelling macrofauna. Rapid colonization and population increase in organicrich sediments is typically followed by subsequent sharp decline. The mechanistic basis for these characteristics was explored in flume-flow experiments that tested whether settling Capitella sp. I larvae avoid sediments inhabited by macrofaunal adults or sediments reworked by them. The first set of experiments consisted of four treatments: conspecific adults or no adults in reworked or non-reworked sediment. Capitella sp. I settlement was significantly altered (depressed) only by pelletized sediment of conspecific adults. The second set of experiments involved similar treatments, but with adults of the deposit-feeding bivalve Tellina agilis. Neither adult presence nor sediment reworking significantly affected settlement of Capitella sp. I larvae. A third set of experiments that compared settlement in sediments with and without the suspension-feeding bivalve Mulinia lateralis demonstrated no significant treatment effect. These results suggest that larval settlement behavior could contribute to population growth in a boom and bust species when a critical limiting resource is overexploited. That is, sediments completely pelletized by Capitella sp. I adults may signal settling larvae that organic matter is depleted. Larvae may therefore settle in smaller numbers and are more likely to be dispersed away from abundant populations of adults. Active avoidance of conspecific adults or adults of other taxa is unimportant for the taxa at the densities tested here

A multifunctional chemical cue drives opposing demographic processes and structures ecological communities

Foundation species provide critical resources to ecological community members and are key determinants of biodiversity. The barnacle Balanus glandula is one such species and dominates space among the higher reaches of wave-swept shores (Northeastern Pacific Ocean). This animal produces a cuticular glycoprotein (named "MULTIFUNCin") of 199.6\ua0kDa, and following secretion, a 390\ua0kDa homodimer in native form. From field and lab experiments, we found that MULTIFUNCin significantly induces habitat selection by conspecific larvae, while simultaneously acting as a potent feeding stimulant to a major barnacle predator (whelk, Acanthinucella spirata). Promoting immigration via settlement on the one hand, and death via predation on the other, MULTIFUNCin drives opposing demographic processes toward structuring predator and prey populations. As shown here, a single compound is not restricted to a lone species interaction or sole ecological function. Complex biotic interactions therefore can be shaped by simple chemosensory systems and depend on the multifunctional properties of select bioactive proteins

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

Background: A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. Methods: This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. Findings: Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0–75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4–97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8–80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3–4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. Interpretation: ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials. Funding: UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, Bill & Melinda Gates Foundation, Lemann Foundation, Rede D’Or, Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and AstraZeneca

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK.

BACKGROUND: A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. METHODS: This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. FINDINGS: Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0-75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4-97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8-80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3-4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. INTERPRETATION: ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials. FUNDING: UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, Bill & Melinda Gates Foundation, Lemann Foundation, Rede D'Or, Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and AstraZeneca

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

Background A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. Methods This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. Findings Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0–75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4–97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8–80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3–4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. Interpretation ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials