Ecological baselines for Oregon's coast: a report for agencies that manage Oregon's coastal habitats for ecological and economic sustainability, and for all who are interested in the welfare of wildlife that inhabit our coast and its estuaries

Against the backdrop of growing concern about dead zones, rare and endangered sea mammals, depletion of Oregon’s once‐abundant fish stocks, acidification threatening coastal molluscs, and proposals for marine reserves along Oregon’s coastline, a multidisciplinary group of scientists was called together in 2008 to discuss what is known about Oregon’s coastal resources at specific points in the past. They agreed that knowing more about the condition of resources in the past could help state resource agencies understand its ecological potential and such information would be useful in planning restoration projects as well as determining gaps in knowledge that need to be filled. Called together by John Meyer, representing Communication Partnership for Science and the Sea (COMPASS), the group decided to develop an “Ecological Baselines” report on past coastal resources at whatever times empirical data exist. We begin this report with a chapter reviewing archaeological, ethnographic, and historic materials to provide a picture of Oregon’s coastal resources before 1750. Subsequent chapters consider salmon, sea otters, and sub‐tidal sea urchins. The salmon chapter provides details on twentieth century abundance and decline of one of Oregon’s most charismatic and economically important ocean resources. This chapter’s authors also evaluate remedies that have attempted to restore salmon species. Next, the sea otter chapter describes a mammal once abundant but no longer present on the Oregon coast, and discusses what the coast has lost by its demise. A decade ago, the author, a descendant of Aleut and Coos/Siuslaw natives, organized a multi‐disciplinary project, named The Elakha Alliance, to study and consider restoration of this keystone species. The sub‐tidal purple sea urchin, described in our fourth chapter, in contrast to salmon and otter, is so small that the intense labor required to harvest it has protected it from commercial harvesting. However, the urchin is affected by all the forces that impinge on the coast’s ecological web, and warming seas could affect its ability to survive along Oregon’s coast. Not all developments in the past decades have been negative. We discuss major estuary restoration projects on the Salmon River and the Coquille River that show how restoration is working in these areas and that suggest how other estuary restorations could proceed. On Tuesday Feb. 22, 2012, the Oregon legislature passed a bill that will add 38 square miles of marine reserves in Oregon’s territorial waters at five locations. And in our final section, the epilogue discusses a significant new paradigm for understanding the process of ecological collapse, beginning with the removal of top consumers – keystone predators. This multi‐authored review, published in Science in 2011, thereby suggests ecosystem wide strategies for restoration and stability (Estes et al., 2011). Our report on historical, ecological baselines is only a first step in a compilation of information on significant coastal resources that we believe could encourage additional research and longterm strategies for restoration

Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion

ABSTRACT The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture. Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture

Heterologous Epitope-Scaffold Prime∶Boosting Immuno-Focuses B Cell Responses to the HIV-1 gp41 2F5 Neutralization Determinant

The HIV-1 envelope glycoproteins (Env) gp120 and gp41 mediate entry and are the targets for neutralizing antibodies. Within gp41, a continuous epitope defined by the broadly neutralizing antibody 2F5, is one of the few conserved sites accessible to antibodies on the functional HIV Env spike. Recently, as an initial attempt at structure-guided design, we transplanted the 2F5 epitope onto several non-HIV acceptor scaffold proteins that we termed epitope scaffolds (ES). As immunogens, these ES proteins elicited antibodies with exquisite binding specificity matching that of the 2F5 antibody. These novel 2F5 epitope scaffolds presented us with the opportunity to test heterologous prime∶boost immunization strategies to selectively boost antibody responses against the engrafted gp41 2F5 epitope. Such strategies might be employed to target conserved but poorly immunogenic sites on the HIV-1 Env, and, more generally, other structurally defined pathogen targets. Here, we assessed ES prime∶boosting by measuring epitope specific serum antibody titers by ELISA and B cell responses by ELISpot analysis using both free 2F5 peptide and an unrelated ES protein as probes. We found that the heterologous ES prime∶boosting immunization regimen elicits cross-reactive humoral responses to the structurally constrained 2F5 epitope target, and that incorporating a promiscuous T cell helper epitope in the immunogens resulted in higher antibody titers against the 2F5 graft, but did not result in virus neutralization. Interestingly, two epitope scaffolds (ES1 and ES2), which did not elicit a detectable 2F5 epitope-specific response on their own, boosted such responses when primed with the ES5. Together, these results indicate that heterologous ES prime∶boost immunization regimens effectively focus the humoral immune response on the structurally defined and immunogen-conserved HIV-1 2F5 epitope

Parallel and serial processes in visual search

A long-standing issue in the study of how people acquire visual information centers around the scheduling and deployment of attentional resources: Is the process serial, or is it parallel? A substantial empirical effort has been dedicated to resolving this issue (e.g., J. M. Wolfe, 1998a, 1998b). However, the results remain largely inconclusive because the methodologies that have historically been used cannot make the necessary distinctions (J. Palmer, 1995; J. T. Townsend, 1972, 1974, 1990). In this article, the authors develop a rigorous procedure for deciding the scheduling problem in visual search by making improvements in both search methodology and data interpretation. The search method, originally used by A. H. C. van der Heijden (1975), generalizes the traditional single-target methodology by permitting multiple targets. Reaction times and error rates from 29 representative search studies were analyzed using Monte Carlo simulation. Parallel and serial models of attention were defined by coupling the appropriate sequential sampling algorithms to realistic constraints on decision making. The authors found that although most searches are conducted by a parallel limited-capacity process, there is a distinguishable search class that is serial