The Structure of theCyprinid herpesvirus 3ORF112-Zα·Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response

In vertebrate species, the innate immune system down-regulates protein translation in response to viral infection through the action of the double-stranded RNA (dsRNA)-activated protein kinase (PKR). In some teleost species another protein kinase, Z-DNA-dependent protein kinase (PKZ), plays a similar role but instead of dsRNA binding domains, PKZ has Zα domains. These domains recognize the left-handed conformer of dsDNA and dsRNA known as Z-DNA/Z-RNA. Cyprinid herpesvirus 3 infects common and koi carp, which have PKZ, and encodes the ORF112 protein that itself bears a Zα domain, a putative competitive inhibitor of PKZ. Here we present the crystal structure of ORF112-Zα in complex with an 18-bp CpG DNA repeat, at 1.5 Å. We demonstrate that the bound DNA is in the left-handed conformation and identify key interactions for the specificity of ORF112. Localization of ORF112 protein in stress granules induced in Cyprinid herpesvirus 3-infected fish cells suggests a functional behavior similar to that of Zα domains of the interferon-regulated, nucleic acid surveillance proteins ADAR1 and DAI.

Surface velocity fields, digital elevation models and ice front positions derived from multi-mission SAR remote sensing data at Sjögren Inlet glaciers, Antarctic Peninsula

Substantial retreat or disintegration of numerous ice shelves have been observed on the Antarctic Peninsula. The ice shelf in the Prince Gustav Channel retreated gradually since the late 1980's and broke-up in 1995. Tributary glaciers reacted with speed-up, surface lowering and increased ice discharge, consequently contributing to sea level rise. We present a detailed long-term study (1993-2014) on the dynamic response of Sjögren Inlet glaciers to the disintegration of Prince Gustav Ice Shelf. We analyzed various remote sensing datasets to observe the reactions of the glaciers to the loss of the buttressing ice shelf. A strong increase in ice surface velocities was observed with maximum flow speeds reaching 2.82±0.48 m/d in 2007 and 1.50±0.32 m/d in 2004 at Sjögren and Boydell glaciers respectively. Subsequently, the flow velocities decelerated, however in late 2014, we still measured about two times the values of our first measurements in 1996. The tributary glaciers retreated 61.7±3.1 km² behind the former grounding line of the ice shelf. In regions below 1000 m a.s.l., a mean surface lowering of -68±10 m (-3.1 m/a) was observed in the period 1993-2014. The lowering rate decreased to -2.2 m/a in recent years. Based on the surface lowering rates, geodetic mass balances of the glaciers were derived for different time steps. High mass loss rate of -1.21±0.36 Gt/a was found in the earliest period (1993-2001). Due to the dynamic adjustments of the glaciers to the new boundary conditions the ice mass loss reduced to -0.59±0.11 Gt/a in the period 2012-2014, resulting in an average mass loss rate of -0.89±0.16 Gt/a (1993-2014). Including the retreat of the ice front and grounding line, a total mass change of -38.5±7.7 Gt and a contribution to sea level rise of 0.061±0.013 mm were computed. Analysis of the ice flux revealed that available bedrock elevation estimates at Sjögren Inlet are too shallow and are the major uncertainty in ice flux computations. This temporally dense time series analysis of Sjögren Inlet glaciers shows that the adjustments of tributary glaciers to ice shelf disintegration are still going on and provides detailed information of the changes in glacier dynamics.

Age models for sediment cores off Peru

Planktonic foraminiferal faunas of the southeast Pacific indicate that sea surface temperatures (SST) have varied by as much as 8-10°C in the Peru Current, and by ?5-7°C along the equator, over the past 150,000 years. Changes in SST at times such as the Last Glacial Maximum reflect incursion of high-latitude species Globorotalia inflata and Neogloboquadrina pachyderma into the eastern boundary current and as far north as the equator. A simple heat budget model of the equatorial Pacific shows that observed changes in Peru Current advection can account for about half of the total variability in equatorial SSTs. The remaining changes in equatorial SST, which are likely related to local changes in upwelling or pycnocline depth, precede changes in polar climates as recorded by d18O. This partitioning of processes in eastern equatorial Pacific SST reveals that net ice-age cooling here reflects first a rapid response of equatorial upwelling to insolation, followed by a later response to changes in the eastern boundary current associated with high-latitude climate (which closely resembles variations in atmospheric CO2 as recorded in the Vostok ice core). Although precise mechanisms responsible for the equatorial upwelling component of climate change remain uncertain, one likely candidate that may operate independently of the ice sheets is insolation-driven changes in El Niño/Southern Oscillation (ENSO) frequency. Early responses of equatorial SST detected both here and elsewhere highlight the sensitivity of tropical systems to small changes in seasonal insolation. The scale of tropical changes we have observed are substantially greater than model predictions, suggesting a need for further quantitative assessment of processes associated with long-term climate change.

Los Angeles and Long Beach Harbors model study : resonant response of the harbors for Phase 1 of the Los Angeles deep-draft dry bulk export terminal /

"January 1984."

Los Angeles and Long Beach harbors model study : Deep-Draft Dry Bulk Export Terminal, alternative no. 6: resonant response and tidal circulation studies /

"July 1985."

Tsunami response of Barbers Point Harbor, Hawaii /

"Prepared for U.S. Army Engineer Division, Pacific Ocean."

River and Hillslope Response to Localized Uplift Along a Left Bend of the San Andreas Fault, Santa Cruz Mountains, CA

Studying landscape evolution of the Earthís surface is difficult because both tectonic forces and surface processes control its response to perturbation, and ultimately, its shape and form. Researchers often use numerical models to study erosional response to deformation because there are rarely natural settings in which we can evaluate both tectonic activity and topographic response over appropriate time scales (103-105 years). In certain locations, however, geologic conditions afford the unique opportunity to study the relationship between tectonics and topography. One such location is along the Dragonís Back Pressure Ridge in California, where the landscape moves over a structural discontinuity along the San Andreas Fault and landscape response to both the initiation and cessation of uplift can be observed. In their landmark study, Hilley and Arrowsmith (2008) found that geomorphic metrics such as channel steepness tracked uplift and that hillslope response lagged behind that of rivers. Ideal conditions such as uniform vegetation density and similar lithology allowed them to view each basin as a developmental stage of response to uplift only. Although this work represents a significant step forward in understanding landscape response to deformation, it remains unclear how these results translate to more geologically complex settings. In this study, I apply similar methodology to a left bend along the San Andreas Fault in the Santa Cruz Mountains, California. At this location, the landscape is translated through a zone of localized uplift caused by the bend, but vegetation, lithology, and structure vary. I examine the geomorphic response to uplift along the San Andreas Fault bend in order to determine whether predicted landscape patterns can be observed in a larger, more geologically complex setting than the Dragonís Back Pressure Ridge. I find that even with a larger-scale and a more complex setting, geomorphic metrics such as channel steepness index remain useful tools for evaluating landscape evolution through time. Steepness indices in selected streams of study record localized uplift caused by the restraining bend, while hillslope adjustment in the form of landsliding occurs over longer time scales. This project illustrates that it is possible to apply concepts of landscape evolution models to complex settings and is an important contribution to the body of geomorphological study.

An analysis of changing management roles in small Australian services exporters in response to the stages in industry development

Life cycle models have become important in explaining the changing size structure of firms based on the carrying capacity of regions or industries. In particular, the population ecology model predicts stages of growth, maturity and eventually decline in the number of firms in an industry. There has been criticism of such models because of their focus on external variables as pre-determinants of the potential for enterprise development. This paper attempts to reconcile the external focus of the population ecology model with relevant internal management factors in enterprise development. A survey was conducted of Australian services exporters, and the results not only confirm the existence of four separate life cycle stages in the population ecology model, but also identify the external and internal variables that are strategically relevant at each of the stages. The findings provide potentially useful information in a range of contexts including the design of small business assistance as well a providing “guide posts” to entrepreneurs engaged in enterprise development.

Analysis of Melanoma Onset: Assessing Familial Aggregation by Using Estimating Equations and Fitting Variance Components via Bayesian Random Effects Models

We investigate whether relative contributions of genetic and shared environmental factors are associated with an increased risk in melanoma. Data from the Queensland Familial Melanoma Project comprising 15,907 subjects arising from 1912 families were analyzed to estimate the additive genetic, common and unique environmental contributions to variation in the age at onset of melanoma. Two complementary approaches for analyzing correlated time-to-onset family data were considered: the generalized estimating equations (GEE) method in which one can estimate relationship-specific dependence simultaneously with regression coefficients that describe the average population response to changing covariates; and a subject-specific Bayesian mixed model in which heterogeneity in regression parameters is explicitly modeled and the different components of variation may be estimated directly. The proportional hazards and Weibull models were utilized, as both produce natural frameworks for estimating relative risks while adjusting for simultaneous effects of other covariates. A simple Markov Chain Monte Carlo method for covariate imputation of missing data was used and the actual implementation of the Bayesian model was based on Gibbs sampling using the free ware package BUGS. In addition, we also used a Bayesian model to investigate the relative contribution of genetic and environmental effects on the expression of naevi and freckles, which are known risk factors for melanoma.

Expanding the scope of the social response context model

Descriptive models of social response are concerned with identifying and discriminating between different types of response to social influence. In a previous article (Nail, MacDonald, & Levy, 2000), the authors demonstrated that 4 conceptual dimensions are necessary to adequately distinguish between such phenomena as conformity, compliance, contagion, independence, and anticonformity in a single model. This article expands the scope of the authors' 4-dimensional approach by reviewing selected experimental and cultural evidence, further demonstrating the integrative power of the model. This review incorporates political psychology, culture and aggression, self-persuasion, group norms, prejudice, impression management, psychotherapy, pluralistic ignorance, bystander intervention/nonintervention, public policy, close relationships, and implicit attitudes.

Using the canonical modelling approach to simplify the simulation of function in functional-structural plant models

Functional-structural plant models that include detailed mechanistic representation of underlying physiological processes can be expensive to construct and the resulting models can also be extremely complicated. On the other hand, purely empirical models are not able to simulate plant adaptability and response to different conditions. In this paper, we present an intermediate approach to modelling plant function that can simulate plant response without requiring detailed knowledge of underlying physiology. Plant function is modelled using a 'canonical' modelling approach, which uses compartment models with flux functions of a standard mathematical form, while plant structure is modelled using L-systems. Two modelling examples are used to demonstrate that canonical modelling can be used in conjunction with L-systems to create functional-structural plant models where function is represented either in an accurate and descriptive way, or in a more mechanistic and explanatory way. We conclude that canonical modelling provides a useful, flexible and relatively simple approach to modelling plant function at an intermediate level of abstraction.

Roles of social pain and defense mechanisms in response to social exclusion: Reply to Panksepp (2005) and Coff (2005)

In comments on G. MacDonald and M. R. Leary (2005), J. Panksepp (2005) argued for more emphasis on social pain mechanisms, whereas P. J. Corr (2005) argued for more emphasis on physical defense mechanisms. In response to the former, the authors clarify their positions on the topics of anger, the usefulness of rat models, the role of analgesic mechanisms, and basic motivational processes. In response to the latter, the authors clarify their positions on the topics of the relation of social exclusion to fear, the value of the pain affect construct, and the nature of the social pain experience. The authors conclude that consideration of the roles of both social pain and defense mechanisms is essential to best understand human response to social exclusion.

Designs for generalized linear models with several variables and model uncertainty

Standard factorial designs sometimes may be inadequate for experiments that aim to estimate a generalized linear model, for example, for describing a binary response in terms of several variables. A method is proposed for finding exact designs for such experiments that uses a criterion allowing for uncertainty in the link function, the linear predictor, or the model parameters, together with a design search. Designs are assessed and compared by simulation of the distribution of efficiencies relative to locally optimal designs over a space of possible models. Exact designs are investigated for two applications, and their advantages over factorial and central composite designs are demonstrated.

Onset of sheath extension and duration of lamina extension are major determinants of the response of maize lamina length to plant density

Background and Aims Plants regulate their architecture strongly in response to density, and there is evidence that this involves changes in the duration of leaf extension. This questions the approximation, central in crop models, that development follows a fixed thermal time schedule. The aim of this research is to investigate, using maize as a model, how the kinetics of extension of grass leaves change with density, and to propose directions for inclusion of this regulation in plant models. • Methods Periodic dissection of plants allowed the establishment of the kinetics of lamina and sheath extension for two contrasting sowing densities. The temperature of the growing zone was measured with thermocouples. Two-phase (exponential plus linear) models were fitted to the data, allowing analysis of the timing of the phase changes of extension, and the extension rate of sheaths and blades during both phases. • Key Results The duration of lamina extension dictated the variation in lamina length between treatments. The lower phytomers were longer at high density, with delayed onset of sheath extension allowing more time for the lamina to extend. In the upper phytomers—which were shorter at high density—the laminae had a lower relative extension rate (RER) in the exponential phase and delayed onset of linear extension, and less time available for extension since early sheath extension was not delayed. • Conclusions The relative timing of the onset of fast extension of the lamina with that of sheath development is the main determinant of the response of lamina length to density. Evidence is presented that the contrasting behaviour of lower and upper phytomers is related to differing regulation of sheath ontogeny before and after panicle initiation. A conceptual model is proposed to explain how the observed asynchrony between lamina and sheath development is regulated.

Intake rates and the functional response in shorebirds (Charadriiformes) eating macro-invertebrates

As field determinations take much effort, it would be useful to be able to predict easily the coefficients describing the functional response of free-living predators, the function relating food intake rate to the abundance of food organisms in the environment. As a means easily to parameterise an individual-based model of shorebird Charadriiformes populations, we attempted this for shorebirds eating macro-invertebrates. Intake rate is measured as the ash-free dry mass (AFDM) per second of active foraging; i.e. excluding time spent on digestive pauses and other activities, such as preening. The present and previous studies show that the general shape of the functional response in shorebirds eating approximately the same size of prey across the full range of prey density is a decelerating rise to a plateau, thus approximating the Holling type 11 ('disc equation') formulation. But field studies confirmed that the asymptote was not set by handling time, as assumed by the disc equation, because only about half the foraging time was spent in successfully or unsuccessfully attacking and handling prey, the rest being devoted to searching. A review of 30 functional responses showed that intake rate in free-living shorebirds varied independently of prey density over a wide range, with the asymptote being reached at very low prey densities (< 150/m(-2)). Accordingly, most of the many studies of shorebird intake rate have probably been conducted at or near the asymptote of the functional response, suggesting that equations that predict intake rate should also predict the asymptote. A multivariate analysis of 468 'spot' estimates of intake rates from 26 shorebirds identified ten variables, representing prey and shorebird characteristics, that accounted for 81 % of the variance in logarithm-transformed intake rate. But four-variables accounted for almost as much (77.3 %), these being bird size, prey size, whether the bird was an oystercatcher Haematopus ostralegus eating mussels Mytilus edulis, or breeding. The four variable equation under-predicted, on average, the observed 30 estimates of the asymptote by 11.6%, but this discrepancy was reduced to 0.2% when two suspect estimates from one early study in the 1960s were removed. The equation therefore predicted the observed asymptote very successfully in 93 % of cases. We conclude that the asymptote can be reliably predicted from just four easily measured variables. Indeed, if the birds are not breeding and are not oystercatchers eating mussels, reliable predictions can be obtained using just two variables, bird and prey sizes. A multivariate analysis of 23 estimates of the half-asymptote constant suggested they were smaller when prey were small but greater when the birds were large, especially in oystercatchers. The resulting equation could be used to predict the half-asymptote constant, but its predictive power has yet to be tested. As well as predicting the asymptote of the functional response, the equations will enable research workers engaged in many areas of shorebird ecology and behaviour to estimate intake rate without the need for conventional time-consuming field studies, including species for which it has not yet proved possible to measure intake rate in the field.