Susceptibility of Juvenile Steelhead to Avian Predation: the Influence of Individual Fish Characteristics and River Conditions

Identification of the factors that influence susceptibility to predation can aid in developing management strategies to recover fish populations of conservation concern. Predator-prey relationships can be influenced by numerous factors, including prey condition, prey size, and environmental conditions. We investigated these factors by using juvenile steelhead Oncorhynchus mykiss from the Snake River (Pacific Northwest, USA), a distinct population segment that is listed as threatened under the U. S. Endangered Species Act. During 2007-2009, steelhead smolts (n = 25,909) were captured, examined for external condition characteristics (e. g., body injuries, descaling, external signs of disease, fin damage, and ectoparasite infestations), marked with passive integrated transponder (PIT) tags, and released to continue their out-migration. Recoveries of PIT tags on a downstream colony of Caspian terns Hydroprogne caspia (n = 913 tags) indicated that steelhead susceptibility to Caspian tern predation increased significantly with decreases in steelhead external condition, decreased water discharge, and decreased water clarity. Susceptibility to Caspian tern predation also increased with increasing steelhead fork length up to 202 mm but then decreased for longer steelhead. Recoveries of PIT tags on a downstream colony of double-crested cormorants Phalacrocorax auritus (n = 493 tags) indicated that steelhead susceptibility to double-crested cormorant predation increased significantly with declining external condition of steelhead, and that steelhead of hatchery origin were more susceptible than their wild counterparts. Results indicate that steelhead susceptibility to avian predation is dependent on fish condition and length and is influenced by river conditions and rearing environment.Keywords: Snake River, Avoidance behavior, Relative vulnerability, Double crested cormorants, Foraging patterns, Chinook salmon, Passive integrated transponders, Caspian terns, Lower Columbia River, Salmon Oncorhynchus tshawytsch

Potential Effects of Management on Caspian Tern Hydroprogne caspia Predation on Juvenile Salmonids at a Colony in San Francisco Bay, California

San Francisco Bay is a proposed relocation site for some of the Caspian terns Hydroprogne caspia currently nesting at the world's largest colony for the species in the Columbia River estuary and consuming salmonids listed under the U. S. Endangered Species Act (ESA). However, several runs of salmonids listed under the ESA occur in San Francisco Bay and managers are concerned that increased Caspian tern predation may pose a threat to the recovery of these fish. We used a bioenergetics modeling approach, employing estimates of tern energy requirements and proportions of energy supplied by various prey types, to estimate the consumption of juvenile salmonids by Caspian terns nesting on Brooks Island in central San Francisco Bay during 2008 and 2009. Estimated salmonid consumption was similar to 205,000 smolts (95% confidence interval, 175,000-245,000 smolts) in 2008 and similar to 167,000 smolts (144,000-191,000 smolts) in 2009. The interannual difference in smolt consumption was due to the smaller size of the tern colony and lower nesting success in 2009. Estimated predation rates on ESA-listed Central Valley spring-run Chinook salmon Oncorhynchus tshawytscha (0.1%) were lower than those on unlisted fall-run Chinook salmon (1.0%). Continuation of the current downward trend in the number of Caspian terns nesting on Brooks Island and the resulting reductions in salmonid predation would not be sufficient to reverse salmonid declines in San Francisco Bay. The proposed enhancement of the Brooks Island Caspian tern colony to 3,000 individuals would at most cause declines in annual population growth rates of 0.28% for fall-run Chinook salmon and 0.02% for threatened spring-run Chinook salmon, assuming that the mortality from tern predation is 100% additive.Keywords: Patterns, Avian predation, Columbia River Estuary, Foraging ecology, Double crested cormorants, Bioenergetics model, Energy, Seabird populations, Waterbird predation, Passive integrated transponder

Quantifying Avian Predation on Fish Populations: Integrating Predator-Specific Deposition Probabilities in Tag Recovery Studies

Accurate assessment of specific mortality factors is vital to prioritize recovery actions for threatened and endangered species. For decades, tag recovery methods have been used to estimate fish mortality due to avian predation. Predation probabilities derived from fish tag recoveries on piscivorous waterbird colonies typically reflect minimum estimates of predation due to an unknown and unaccounted-for fraction of tags that are consumed but not deposited on-colony (i.e., deposition probability). We applied an integrated tag recovery modeling approach in a Bayesian context to estimate predation probabilities that accounted for predator-specific tag detection and deposition probabilities in a multiple-predator system. Studies of PIT tag deposition were conducted across three bird species nesting at seven different colonies in the Columbia River basin, USA. Tag deposition probabilities differed significantly among predator species (Caspian terns Hydroprogne caspia: deposition probability = 0.71, 95% credible interval [CRI] = 0.51–0.89; double-crested cormorants Phalacrocorax auritus: 0.51, 95% CRI = 0.34–0.70; California gulls Larus californicus: 0.15, 95% CRI = 0.11–0.21) but showed little variation across trials within a species or across years. Data from a 6-year study (2008–2013) of PIT-tagged juvenile Snake River steelhead Oncorhynchus mykiss (listed as threatened under the Endangered Species Act) indicated that colony-specific predation probabilities ranged from less than 0.01 to 0.17 and varied by predator species, colony location, and year. Integrating the predator-specific deposition probabilities increased the predation probabilities by a factor of approximately 1.4 for Caspian terns, 2.0 for double-crested cormorants, and 6.7 for California gulls compared with traditional minimum predation rate methods, which do not account for deposition probabilities. Results supported previous findings on the high predation impacts from strictly piscivorous waterbirds nesting in the Columbia River estuary (i.e., terns and cormorants), but our findings also revealed greater impacts of a generalist predator species (i.e., California gulls) than were previously documented. Approaches used in this study allow for direct comparisons among multiple fish mortality factors and considerably improve the reliability of tag recovery models for estimating predation probabilities in multiple-predator systems

Systemwide Evaluation of Avian Predation on Juvenile Salmonids from the Columbia River Based on Recoveries of Passive Integrated Transponder Tags

We recovered passive integrated transponder (PIT) tags from nine piscivorous waterbird colonies in the Columbia River basin to evaluate avian predation on Endangered Species Act (ESA)-listed salmonid Oncorhynchus spp. populations during 2007–2010. Avian predation rates were calculated based on the percentage of PIT-tagged juvenile salmonids that were detected as passing hydroelectric dams and subsequently were consumed and deposited by birds on their nesting colonies. Caspian terns Hydroprogne caspia (hereafter, “terns”) and double-crested cormorants Phalacrocorax auritus (hereafter, “cormorants”) nesting on East Sand Island in the Columbia River estuary consumed the highest proportions of available PIT-tagged salmonids, with minimum predation rates ranging from 2.5% for Willamette River spring Chinook salmon O. tshawytscha to 16.0% for Snake River steelhead O. mykiss. Estimated predation rates by terns, cormorants, gulls of two species (California gull Larus californicus and ring-billed gull L. delawarensis), and American white pelicans Pelecanus erythrorhynchos nesting near the confluence of the Snake and Columbia rivers were also substantial; minimum predation rates ranged from 1.4% for Snake River fall Chinook salmon to 13.2% for upper Columbia River steelhead. Predation on ESA-listed salmonids by gulls and American white pelicans were minor (<2.0% per ESA-listed salmonid population) relative to predation by terns and cormorants. Cumulative impacts were greater for Snake River and upper Columbia River salmonids than for salmonids originating closer to the estuary because upriver salmonids must migrate past more bird colonies to reach the ocean. Predation rates adjusted for colony size (per capita rates) were significantly higher for terns and cormorants nesting at inland colonies (upstream of Bonneville Dam) than for those nesting in the estuary, suggesting that inland colonies have a greater reliance on salmonids as a food source. Management actions to increase salmonid survival by reducing avian predation in the estuary could be offset if birds that disperse from the estuary relocate to inland nesting sites on or near the Columbia River.This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/curren

Recent Population Size, Trends, and Limiting Factors for the Double-Crested Cormorant in Western North America

The status of the double-crested cormorant (Phalacrocorax auritus) in western North America was last evaluated during 1987–2003. In the interim, concern has grown over the potential impact of predation by double-crested cormorants on juvenile salmonids (Oncorhynchus spp.), particularly in the Columbia Basin and along the Pacific coast where some salmonids are listed for protection under the United States Endangered Species Act. Recent re-evaluations of double-crested cormorant management at the local, flyway, and federal level warrant further examination of the current population size and trends in western North America. We collected colony size data for the western population (British Columbia, Washington, Oregon, Idaho, California, Nevada, Utah, Arizona, and the portions of Montana, Wyoming, Colorado and New Mexico west of the Continental Divide) by conducting aircraft-, boat-, or ground-based surveys and by cooperating with government agencies, universities, and non-profit organizations. In 2009, we estimated approximately 31,200 breeding pairs in the western population. We estimated that cormorant numbers in the Pacific Region (British Columbia, Washington, Oregon, and California) increased 72% from 1987–1992 to circa 2009. Based on the best available data for this period, the average annual growth rate (λ) of the number of breeding birds in the Pacific Region was 1.03, versus 1.07 for the population east of the Continental Divide during recent decades. Most of the increase in the Pacific Region can be attributed to an increase in the size of the nesting colony on East Sand Island in the Columbia River estuary, which accounts for about 39% of all breeding pairs in the western population and is the largest known breeding colony for the species (12,087 breeding pairs estimated in 2009). In contrast, numbers of breeding pairs estimated in coastal British Columbia and Washington have declined by approximately 66% during this same period. Disturbance at breeding colonies by bald eagles (Haliaeetus leucocephalus) and humans are likely limiting factors on the growth of the western population at present. Because of differences in biology and management, the western population of double-crested cormorants warrants consideration as a separate management unit from the population east of the Continental Divide.Keywords: Population, Phalacrocorax auritus, Pacific coast, Cormorant, Limiting factors, Status assessmen

Avian Predation on Juvenile Salmonids: Spatial and Temporal Analysis Based on Acoustic and Passive Integrated Transponder Tags

We evaluated the impact of predation on juvenile steelhead Oncorhynchus mykiss and yearling and subyearling Chinook Salmon O. tshawytscha by piscivorous waterbirds from 11 different breeding colonies in the Columbia River basin during 2012 and 2014. Fish were tagged with both acoustic tags and PIT tags and were tracked via a network of hydrophone arrays to estimate total smolt mortality (1 – survival) at various spatial and temporal scales during out-migration. Recoveries of PIT tags on bird colonies, coupled with the last known detections of live fish passing hydrophone arrays, were used to estimate the impact of avian predation relative to total smolt mortality. Results indicated that avian predation was a substantial source of steelhead mortality, with predation probability (proportion of available fish consumed by birds) ranging from 0.06 to 0.28 for fish traveling through the lower Snake River and the lower and middle Columbia River. Predation probability estimates ranged from 0.03 to 0.09 for available tagged yearling Chinook Salmon and from 0.01 to 0.05 for subyearlings. Smolt predation by gulls Larus spp. was concentrated near hydroelectric dams, while predation by Caspian terns Hydroprogne caspia was concentrated within reservoirs. No concentrated areas of predation were identified for double-crested cormorants Phalacrocorax auritus or American white pelicans Pelecanus erythrorhynchos. Comparisons of total smolt mortality relative to mortality from colonial waterbirds indicated that avian predation was one of the greatest sources of mortality for steelhead and yearling Chinook Salmon during out-migration. In contrast, avian predation on subyearling Chinook Salmon was generally low and constituted a minor component of total mortality. Our results demonstrate that acoustic and PIT tag technologies can be combined to quantify where and when smolt mortality occurs and the fraction of mortality that is due to colonial waterbird predation relative to non-avian mortality sources

Downregulation of Homologous Recombination DNA Repair Genes by HDAC Inhibition in Prostate Cancer Is Mediated through the E2F1 Transcription Factor

Histone deacetylase inhibitors (HDACis) re-express silenced tumor suppressor genes and are currently undergoing clinical trials. Although HDACis have been known to induce gene expression, an equal number of genes are downregulated upon HDAC inhibition. The mechanism behind this downregulation remains unclear. Here we provide evidence that several DNA repair genes are downregulated by HDAC inhibition and provide a mechanism involving the E2F1 transcription factor in the process.Applying Analysis of Functional Annotation (AFA) on microarray data of prostate cancer cells treated with HDACis, we found a number of genes of the DNA damage response and repair pathways are downregulated by HDACis. AFA revealed enrichment of homologous recombination (HR) DNA repair genes of the BRCA1 pathway, as well as genes regulated by the E2F1 transcription factor. Prostate cancer cells demonstrated a decreased DNA repair capacity and an increased sensitization to chemical- and radio-DNA damaging agents upon HDAC inhibition. Recruitment of key HR repair proteins to the site of DNA damage, as well as HR repair capacity was compromised upon HDACi treatment. Based on our AFA data, we hypothesized that the E2F transcription factors may play a role in the downregulation of key repair genes upon HDAC inhibition in prostate cancer cells. ChIP analysis and luciferase assays reveal that the downregulation of key repair genes is mediated through decreased recruitment of the E2F1 transcription factor and not through active repression by repressive E2Fs.Our study indicates that several genes in the DNA repair pathway are affected upon HDAC inhibition. Downregulation of the repair genes is on account of a decrease in amount and promoter recruitment of the E2F1 transcription factor. Since HDAC inhibition affects several pathways that could potentially have an impact on DNA repair, compromised DNA repair upon HDAC inhibition could also be attributed to several other pathways besides the ones investigated in this study. However, our study does provide insights into the mechanism that governs downregulation of HR DNA repair genes upon HDAC inhibition, which can lead to rationale usage of HDACis in the clinics

HIV-1 Tat and AIDS-associated cancer: targeting the cellular anti-cancer barrier?

The acquired immunodeficiency syndrome (AIDS) is accompanied by a significant increase in the incidence of neoplasms. Several causative agents have been proposed for this phenomenon. These include immunodeficiency and oncogenic DNA viruses and the HIV-1 protein Tat. Cancer in general is closely linked to genomic instability and DNA repair mechanisms. The latter maintains genomic stability and serves as a cellular anti-cancer barrier. Defects in DNA repair pathway are associated with carcinogenesis

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease