Revealing uncertainty in the status of biodiversity change.

Biodiversity faces unprecedented threats from rapid global change1. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses have not fully accounted for spatial, temporal and phylogenetic structures in the data. Here, using a new statistical framework, we show across ten high-profile biodiversity datasets2-11 that increases and decreases under existing approaches vanish once spatial, temporal and phylogenetic structures are accounted for. This is a consequence of existing approaches severely underestimating trend uncertainty and sometimes misestimating the trend direction. Under our revised average abundance trends that appropriately recognize uncertainty, we failed to observe a single increasing or decreasing trend at 95% credible intervals in our ten datasets. This emphasizes how little is known about biodiversity change across vast spatial and taxonomic scales. Despite this uncertainty at vast scales, we reveal improved local-scale prediction accuracy by accounting for spatial, temporal and phylogenetic structures. Improved prediction offers hope of estimating biodiversity change at policy-relevant scales, guiding adaptive conservation responses.

A generalized approach to x-ray data modeling for high-energy-density plasma experiments.

Accurate understanding of x-ray diagnostics is crucial for both interpreting high-energy-density experiments and testing simulations through quantitative comparisons. X-ray diagnostic models are complex. Past treatments of individual x-ray diagnostics on a case-by-case basis have hindered universal diagnostic understanding. Here, we derive a general formula for modeling the absolute response of non-focusing x-ray diagnostics, such as x-ray imagers, one-dimensional space-resolved spectrometers, and x-ray power diagnostics. The present model is useful for both data modeling and data processing. It naturally accounts for the x-ray crystal broadening. The new model verifies that standard approaches for a crystal response can be good approximations, but they can underestimate the total reflectivity and overestimate spectral resolving power by more than a factor of 2 in some cases near reflectivity edge features. We also find that a frequently used, simplified-crystal-response approximation for processing spectral data can introduce an absolute error of more than an order of magnitude and the relative spectral radiance error of a factor of 3. The present model is derived with straightforward geometric arguments. It is more general and is recommended for developing a unified picture and providing consistent treatment over multiple x-ray diagnostics. Such consistency is crucial for reliable multi-objective data analyses.

Radiation, optical, power flow, and electrical diagnostics at the Z facility: Layout and techniques utilized to operate in the harsh environment.

The Z machine is a current driver producing up to 30 MA in 100 ns that utilizes a wide range of diagnostics to assess accelerator performance and target behavior conduct experiments that use the Z target as a source of radiation or high pressures. We review the existing suite of diagnostic systems, including their locations and primary configurations. The diagnostics are grouped in the following categories: pulsed power diagnostics, x-ray power and energy, x-ray spectroscopy, x-ray imaging (including backlighting, power flow, and velocimetry), and nuclear detectors (including neutron activation). We will also briefly summarize the primary imaging detectors we use at Z: image plates, x-ray and visible film, microchannel plates, and the ultrafast x-ray imager. The Z shot produces a harsh environment that interferes with diagnostic operation and data retrieval. We term these detrimental processes "threats" of which only partial quantifications and precise sources are known. We summarize the threats and describe techniques utilized in many of the systems to reduce noise and backgrounds.

Technique for inferring angle change as a function of time for high-current electron beams using a dose-rate monitor array.

Intense electron beams striking a high-atomic number target produce high-output pulsed photon fluxes for flash x-ray experiments. Without an external guide field, such beams are subject to the dynamics of high-current electron beam propagation, including changes to electron trajectories either from self-fields or from development of beam instabilities. The bremsstrahlung output (dose-rate) scales approximately as IVx, where I is the beam current, V the electron energy, and x is in the range 2.0-2.65 and depends upon the electron angle on the converter. Using experimental beam data (dose-rate, I and V), this equation can be solved for x, a process known as "inverting the radiographer's equation." Inversion methods that rely on thermoluminescent dosimeters, which are time-integrated, yield no information about evolution of the electron beam angle in time. We propose here an inversion method that uses several dose-rate monitors at different angles with respect to the beam axis. By measuring dose-rates at different angles, one can infer the time-dependent beam voltage and angle. This method compares well with estimates of corrected voltage and results in a self-consistent picture of beam dynamics. Techniques are demonstrated using data from self-magnetic pinch experiments at the RITS-6 facility at Sandia National Laboratories.

Zeeman spectroscopy as a method for determining the magnetic field distribution in self-magnetic-pinch diodes (invited).

In the self-magnetic-pinch diode, the electron beam, produced through explosive field emission, focuses on the anode surface due to its own magnetic field. This process results in dense plasma formation on the anode surface, consisting primarily of hydrocarbons. Direct measurements of the beam's current profile are necessary in order to understand the pinch dynamics and to determine x-ray source sizes, which should be minimized in radiographic applications. In this paper, the analysis of the C IV doublet (580.1 and 581.2 nm) line shapes will be discussed. The technique yields estimates of the electron density and electron temperature profiles, and the method can be highly beneficial in providing the current density distribution in such diodes.

Fewer invited talks by women in evolutionary biology symposia.

Lower visibility of female scientists, compared to male scientists, is a potential reason for the under-representation of women among senior academic ranks. Visibility in the scientific community stems partly from presenting research as an invited speaker at organized meetings. We analysed the sex ratio of presenters at the European Society for Evolutionary Biology (ESEB) Congress 2011, where all abstract submissions were accepted for presentation. Women were under-represented among invited speakers at symposia (15% women) compared to all presenters (46%), regular oral presenters (41%) and plenary speakers (25%). At the ESEB congresses in 2001-2011, 9-23% of invited speakers were women. This under-representation of women is partly attributable to a larger proportion of women, than men, declining invitations: in 2011, 50% of women declined an invitation to speak compared to 26% of men. We expect invited speakers to be scientists from top ranked institutions or authors of recent papers in high-impact journals. Considering all invited speakers (including declined invitations), 23% were women. This was lower than the baseline sex ratios of early-mid career stage scientists, but was similar to senior scientists and authors that have published in high-impact journals. High-quality science by women therefore has low exposure at international meetings, which will constrain Evolutionary Biology from reaching its full potential. We wish to highlight the wider implications of turning down invitations to speak, and encourage conference organizers to implement steps to increase acceptance rates of invited talks.

Are parental care trade-offs in shorebirds driven by parental investment or sexual selection?

Sexual selection, mating systems and parental behaviour are closely linked, although the exact nature of their relationship is controversial. The parental investment hypothesis (PIH) states that parental care disparity drives sexual selection intensity, because the sex providing less care competes for the sex that provides more. In contrast, the sexual selection hypothesis (SSH) asserts that more intense sexual selection on males leads to reduced male parental investment. We tested these hypotheses using directional phylogenetic comparative methods in shorebirds, which have an unusually diverse array of breeding systems. Changes in parental care and sexual selection intensity were tightly correlated, and we carried out three sets of analyses focusing on changes in male behaviour, female behaviour and in either sex. The results from the analyses were consistent with both PIH and SSH, although the patterns in male transition were sensitive to model values. We propose two explanations for these results. First, phylogenetic transitions may be idiosyncratic so that they depend on the ecological circumstances of individual species. Second, transitions in social traits, such as breeding systems, may be rapid and take place in ecological time, so directional phylogenetic methods that work through longer time scales may not infer accurately the timing and direction of all changes.

Silencing S1P1 receptors regulates collagen-V reactive lymphocyte-mediated immunobiology in the transplanted lung.

Type V collagen (col[V])-reactive lymphocytes contribute to lung transplant rejection, but the mechanisms for emigration into the graft are unknown. Sphingosine-1-phosphate-1 receptors (S1P(1R)) are believed to be required for lymphocyte emigration in other studies, but their role in col(V)-reactive lymphocyte rejection responses is not known. Utilizing small interfering RNA (siRNA) to reduce S1P(1R) expression on col(V)-reactive lymphocytes, we examined the role of S1P(1R) in the rejection response. Quantitative polymerase chain reaction (PCR) revealed strong expression of S1P(1R) messenger RNA (mRNA)on col(V)-reactive lymphocytes isolated from immunized rats. S1P(1R)-specific siRNA (S1P(1R) siRNA) reduced expression of S1P(1R) mRNA and protein, whereas scramble siRNA (SC siRNA) had no effect. Adoptive transfer of lymphocytes treated with S1P(1R) siRNA to rat Wistar Kyoto (WKY) lung isograft recipients resulted in retention of cells within the liver with fewer cells in mediastinal lymph nodes when compared to cells exposed to SC siRNA. S1P(1R)-deficient cells proliferated in response to alloantigens, but not in response to col(V), and produced less interferon (IFN)-gamma in response to col(V) compared to controls. Downregulating S1P(1R) did not affect production of interleukin (IL)-10and tumor necrosis factor (TNF)-alpha, or expression of adhesion molecules critical for migration, but prevented rejection pathology and lowered local levels of IFN-gamma post adoptive transfer. These data demonstrate novel roles of S1P(1R,) which include regulating emigration and modulating lymphocyte activation.

Anti-type V collagen lymphocytes that express IL-17 and IL-23 induce rejection pathology in fresh and well-healed lung transplants.

Immunity to collagen V [col(V)] contributes to lung 'rejection.' We hypothesized that ischemia reperfusion injury (IRI) associated with lung transplantation unmasks antigenic col(V) such that fresh and well-healed lung grafts have differential susceptibility to anti-col(V)-mediated injury; and expression of the autoimmune cytokines, IL-17 and IL-23, are associated with this process. Adoptive transfer of col(V)-reactive lymphocytes to WKY rats induced grade 2 rejection in fresh isografts, but induced worse pathology (grade 3) when transferred to isograft recipients 30 days post-transplantation. Immunhistochemistry detected col(V) in fresh and well-healed isografts but not native lungs. Hen egg lysozyme-reactive lymphocytes (HEL, control) did not induce lung disease in any group. Col(V), but not HEL, immunization induced transcripts for IL-17 and IL-23 (p19) in the cells utilized for adoptive transfer. Transcripts for IL-17 were upregulated in fresh, but not well-healed isografts after transfer of col(V)-reactive cells. These data show that IRI predisposes to anti-col(V)-mediated pathology; col(V)-reactive lymphocytes express IL-17 and IL-23; and anti-col(V)-mediated lung disease is associated with local expression of IL-17. Finally, because of similar histologic patterns, the pathology of clinical rejection may reflect the activity of autoimmunity to col(V) and/or alloimmunity.

Comparison of parasitism by Cotesia glomerata with bacterial infection and wounding in Pieris brassicae: induction of new haemolymph polypeptides and changes in humoral immune response.

In Pieris brassicae, parasitism by Cotesia glomerata and bacterial infection are differentiated with respect to haemolymph protein arrays, and production or suppression of antibacterial agents. Bacteriolytic activity in haemolymph from parasitized larvae was slightly, but significantly, higher 24h post-treatment than that of untreated and wounded controls. Micrococcus lysodeikticus- or lipopolysaccharide-(LPS) injected insects exhibited an 11-fold greater response than those parasitized. At 24h post-treatment, antibacterial activity against Escherichia coli was observed in haemolymph from all but untreated larvae. Injection of Grace's medium, M. lysodeikticus or LPS, caused a greater than threefold response than parasitization or wounding. The protein banding patterns of parasitized hosts did not correspond to those of the other treatments. Two parasitoid-induced proteins (38 and 128 kDa) were examined. Both were found in parasitized insects, not in those wounded, injected with Grace's medium, M. lysodeikticus or LPS. Neither protein was bacteriolytic or bacteriostatic in inhibition zone assays.

Geographic range size and evolutionary age in birds.

Together with patterns of speciation and extinction, post-speciation transformations in the range sizes of individual species determine the form of contemporary species range-size distributions. However, the methodological problems associated with tracking the dynamics of a species' range size over evolutionary time have precluded direct study of such range-size transformations, although indirect evidence has led to several models being proposed describing the form that they might take. Here, we use independently derived molecular data to estimate ages of species in six monophyletic groups of birds, and examine the relationship between species age and global geographic range size. We present strong evidence that avian range sizes are not static over evolutionary time. In addition, it seems that, with the regular exception of certain taxa (for example island endemics and some threatened species), range-size transformations are non-random in birds. In general, range sizes appear to expand relatively rapidly post speciation; subsequently; and perhaps more gradually, they then decline as species age. We discuss these results with reference to the various models of range-size dynamics that have been proposed.

The Interplay between Patency, Microsomal Na(+)/K(+) ATPase Activity and Juvenile Hormone, in Tenebrio molitor Parasitized by Hymenolepsis diminuta.

Beetles infected with metacestodes of the rat tapeworm, Hymenolepis diminuta, exhibit reduced fecundity, due to alterations in vitellogenesis. Follicle cell patency is retarded and inefficient vitellogenin uptake ensues. Here, we have reassessed patency and its stimulation by JH III at day 3 post-infection, when the most detrimental changes are observed in other ovarian processes. In Rhodnius prolixus, patency is believed to be brought about by the action of a JH-dependent membrane-bound Na(+)/K(+) ATPase (EC 3.6.1.3); however, this had not been established in Tenebrio molitor. Therefore, the properties of the enzyme, with respect to optimal assay conditions and juvenile hormone dependency, are reported. Maximal stimulation occurred between 50 and 500 nM JH III, a range over which greatest increases in patency were also observed. In infected insects, a 35% reduction in Na(+)/K(+) ATPase activity was noted, but exposure to 50 nM JH III is sufficient for stimulation to a specific activity 89% that of JH-treated controls. In a similar fashion, patency in infected insects is reduced, but can be 'rescued' by 50 nM JH III. Moreover, in the absence of exogenous hormone, patency in infected beetles can be elevated to control levels after in vitro culture (6 h), with exchange of medium every 2 h. The possibility that such reversible decreases in enzyme activity and patency are caused by a JH binding inhibitor molecule is discussed. Copyright 1997 Elsevier Science Ltd. All rights reserved

Haemolymph from female beetles infected with Hymenolepis diminuta metacestodes retards the development of ovarian follicles in recipient Tenebrio molitor (Coleoptera).

Infection with developing metacestodes of the rat tapeworm, Hymenolepis diminuta, is known to retard the accumulation of the yolk protein, vitellin, in the terminal ovarian follicles of the intermediate host, Tenebrio molitor. It is probable that this is the result of competitive inhibition of juvenile hormone binding at a microsomal binding site in the beetle follicular epithelium. Experiments were designed to test the hypothesis that inhibitor molecules were circulating in the haemolymph of infected beetles. Whole haemolymph, collected from male or female beetles at various stages post-infection, was injected into non-infected female recipients 2 days post-emergence. Ovaries were removed 3 days later and the vitellin content of the same sized follicles measured using an ELISA. The vitellin content of follicles from recipients of haemolymph from females infected with metacestodes at stage 1 and stage 3-4 was significantly reduced (24 and 27.9%) compared to sham-infected females. However, haemolymph from females infected with mature metacestodes did not affect the vitellin content. Results were thus comparable to those obtained by monitoring ovarian vitellin levels in female T. molitor with bona fide infections. Haemolymph from infected males did not affect ovarian vitellin content. These results indicate that molecules that can modulate vitellogenesis may be present in the haemolymph of females infected with developing metacestodes but that these factors disappear later in infection.

Purification and characterisation of haemolymph 3-dehydroecdysone 3 beta-reductase in relation to ecdysteroid biosynthesis in the cotton leafworm Spodoptera littoralis.

The in vitro secretion of ecdysteroids from the prothoracic glands of last instar larvae of Spodoptera littoralis was detected and analysed by HPLC-RIA. The primary product was identified as 3-dehydroecdysone (approximately 82%), with lesser amounts of ecdysone (approximately 18%). Interconversion of ecdysone and 3-dehydroecdysone by prothoracic glands was not detectable. 3-Dehydroecdysone 3 beta-reductase activity was demonstrated in the haemolymph. Ecdysone, the endproduct, was characterised by reverse-phase and adsorption HPLC, chemical transformation into ecdysone 2, 3-acetonide, and mass spectrometry. The conditions for optimal activity were determined. The enzyme requires NADPH or NADH as cofactor and Km values for NADPH and NADH were determined to be 0.94 microM, and 22.8 microM, respectively. Investigation of the kinetic properties of the enzyme, using either NADPH or NADH as cofactor, revealed that it exhibits maximal activity at low 3-dehydroecdysone substrate concentrations, with a drastic inhibition of activity at higher concentrations (> 5 microM). The results suggest that the 3-dehydroecdysone 3 beta-reductase has a high-affinity (low Km) binding site for 3-dehydroecdysone substrate, together with a lower-affinity inhibition site. The 3 beta-reductase enzyme was purified to homogeneity using a combination of poly(ethylene glycol) 6000 precipitation and successive FPLC fractionation on Mono-Q, phenyl Superose (twice), and hydroxyapatite columns. The native enzyme was shown to be a monomer with molecular mass of 36 kDa by SDS/PAGE and gel-filtration chromatography. Furthermore, the activity of the enzyme during the last larval instar was found to reach a peak prior to that of the haemolymph ecdysteroid titre, supporting a role for the enzyme in development.

Hymenolepis diminuta: metacestode-induced reduction in the synthesis of the yolk protein, vitellogenin, in the fat body of Tenebrio molitor.

Vitellogenin synthesis by the fat body has been monitored using in vitro culture and immunoprecipitation. This system was found to be efficient for measuring vitellogenin production in both non-infected Tenebrio molitor and those infected with Hymenolepis diminuta. In fat bodies from infected beetles, vitellogenin production was decreased by up to 75% (day 24 post-infection) and, at all times investigated, vitellogenin synthesis was significantly below control levels (days 3-30 post-infection). Incubating fat bodies from control insects with isolated metacestodes indicated that this may be a direct effect by the parasite which is developmental stage-specific. Stage II, but not Stage III-IV, not heat-killed parasites could bring about this decrease in vitellogenin. In addition, these effects may be density dependent within the range of 2-20 parasites per fat body; only 2 metacestodes were necessary to cause a significant decrease. Since metacestodes do not take up vitellogenin, nor limit the amount of [14C]leucine available to the fat body for vitellogenin production, it is conceivable that the parasite produces a potent inhibitor of vitellogenin synthesis, or a molecule which induces cells within the fat body.

Enzymes of ecdysteroid transformation and inactivation in the midgut of the cotton leafworm, Spodoptera littoralis: properties and developmental profiles.

In the midgut cytosol of Lepidoptera, ecdysteroids undergo inactivation by transformation via the 3-dehydro derivative to the corresponding 3-epiecdysteroid (3 alpha-hydroxy) and by phosphate conjugation. The oxygen-dependent oxidase catalyses formation of 3-dehydroecdysteroid, which can be reduced either irreversibly by 3-dehydroecdysone 3 alpha-reductase to 3-epiecdysteroid, or by 3-dehydroecdysone 3 beta-reductase back to the initial ecdysteroid. Furthermore, these ecdysteroids undergo further inactivation by phosphorylation. These ecdysteroid transformations have been investigated in last instar larvae of the cotton leafworm, Spodoptera littoralis. The products of the phosphorylation have been characterized as predominantly ecdysteroid 2-phosphate accompanied by smaller amounts of the corresponding 22-phosphate. The phosphotransferases require Mg2+ and ATP. Whereas the 3-dehydroecdysone 3 alpha-reductase has a clear preference for NADPH rather than NADH, the corresponding 3 beta-reductase markedly favours NADH. The physiological significance of the latter enzyme is unclear. The profiles of the various enzymic activities in dialysed midgut cytosol supplemented with appropriate cofactors were determined throughout the last larval instar. All activities were detectable throughout the instar, but the respective enzymes exhibited maxima at different times. Ecdysone oxidase showed a peak early in the instar, with 3-dehydroecdysone 3 alpha-reductase increasing to a peak as the former activity declined. The 3-dehydroecdysone 3 beta-reductase exhibited peak activity late in the instar, a profile similar to that observed for the corresponding haemolymph enzyme involved in reduction of the 3-dehydroecdysone product of the prothoracic glands to ecdysone. Thus, the significance of the midgut 3 beta-reductase may be related to production of active hormone. Both ecydsteroid 22- and 2-phosphotransferases showed high activities early in the instar and then declined. The physiological significance of the profiles for the ecdysone oxidase, the 3-dehydroecdysone 3 alpha-reductase and phosphotransferases is unclear.

Hymenolepis diminuta-induced fecundity reduction may be caused by changes in hormone binding to Tenebrio molitor ovaries.

Aspects of vitellogenesis, known to be controlled by juvenile hormone, are adversely affected by Hymenolepis diminuta infection of Tenebrio molitor, in spite of circulating titres of the hormone remaining unchanged. It has therefore been proposed that juvenile hormone binding is disrupted at the tissue site level. Juvenile hormone III binding sites were located in the nuclear, microsomal and post-microsomal supernatant fractions of the follicle cells of Tenebrio molitor. When JH-III binding was quantified for both control and Hymenolepis diminuta-infected beetles, binding in the nucleus and cytosol were found to be largely unaffected. However, microsomal binding was severely disrupted; on days 3 and 6 post-infection, binding was greatly diminished, on day 9 post-infection, binding was slightly reduced and, by day 15, binding was 'restored' to that of control insects. Using follicle cell microsomes at day 3 post-infection, previous Scatchard analysis revealed the presence of at least two JH-III binding sites. The first is of higher affinity, Kd = 5.3 x 10(-8) M, Bmax = 1.5 x 10(-11) mol/mg protein and the second of lower affinity Kd = 7.7 x 10(-7) M, Bmax = 9.75 x 10(-11) mol/mg protein. A comparison with microsomal binding parameters of follicle cells from non-infected Tenebrio indicated that although the Bmax values were unchanged, the Kd value of the higher affinity site was increased by approximately 5-fold. These data are indicative of a parasite-induced competitive binding inhibitor.

Microsomal juvenile hormone binding proteins in the follicle cells of Tenebrio molitor.

The microsomal fraction of Tenebrio molitor follicle cells has been found to contain both high and low affinity binding sites for juvenile hormone (JH) III. Using Scatchard analysis, the equilibrium dissociation constants, Kd, were calculated as 1.0 x 10(-8) and 4.3 x 10(-7) M respectively. Kinetic data support a rapid binding of the hormone to the site(s), with rate constants of ka = 3.77 x 10(8) M-1 min-1 and kd = 0.0075 min-1. Affinity of the binding site(s) for JH III was higher than for either JH I or methoprene. The significance and possible function of such microsomal binding proteins are discussed, with reference to the perturbance of vitellogenesis found in beetles parasitized by Hymenolepis diminuta.