Transmission Spectra of Transiting Planet Atmospheres: Model Validation and Simulations of the Hot Neptune GJ 436b for JWST

We explore the transmission spectrum of the Neptune-class exoplanet GJ 436b, including the possibility that its atmospheric opacity is dominated by a variety of non- equilibrium chemical products. We also validate our transmission code by demonstrating close agreement with analytic models that use only Rayleigh scattering or water vapor opacity. We find broad disagreement with radius variations predicted by another published model. For GJ 436b, the relative coolness of the planet's atmosphere, along with its implied high metallicity, may make it dissimilar in character compared to "hot Jupiters." Some recent observational and modeling efforts suggest low relative abundances of H2O and CH4 present in GJ 436b's atmosphere, compared to calculations from equilibrium chemistry. We include these characteristics in our models and examine the effects of absorption from methane-derived higher order hydrocarbons. Significant absorption from HCN and C2H2 are found throughout the infrared, while C2H4 and C2H6 are less easily seen. We perform detailed simulations of JWST observations, including all likely noise sources, and find that we will be able to constrain chemical abundance regimes from this planet's transmission spectrum. For instance, the width of the features at 1.5, 3.3, and 7 microns indicates the amount of HCN versus C2H2 present. The NIRSpec prism mode will be useful due to its large spectral range and the relatively large number of photo-electrons recorded per spectral resolution element. However, extremely bright host stars like GJ 436 may be better observed with a higher spectroscopic resolution mode in order to avoid detector saturation. We find that observations with the MIRI low resolution spectrograph should also have high signal-to-noise in the 5 - 10 micron range due to the brightness of the star and the relatively low spectral resolution (R ~ 100) of this mode.Comment: 33 pages, 12 figures, Accepted to Ap

Default mode network connectivity predicts sustained attention deficits following traumatic brain injury

Traumatic brain injury (TBI) frequently produces impairments of attention in humans. These can result in a failure to maintain consistent goal-directed behavior. A predominantly right-lateralized frontoparietal network is often engaged during attentionally demanding tasks. However, lapses of attention have also been associated with increases in activation within the default mode network (DMN). Here, we study TBI patients with sustained attention impairment, defined on the basis of the consistency of their behavioral performance over time. We show that sustained attention impairments in patients are associated with an increase in DMN activation, particularly within the precuneus and posterior cingulate cortex. Furthermore, the interaction of the precuneus with the rest of the DMN at the start of the task, i.e., its functional connectivity, predicts which patients go on to show impairments of attention. Importantly, this predictive information is present before any behavioral evidence of sustained attention impairment, and the relationship is also found in a subgroup of patients without focal brain damage. TBI often results in diffuse axonal injury, which produces cognitive impairment by disconnecting nodes in distributed brain networks. Using diffusion tensor imaging, we demonstrate that structural disconnection within the DMN also correlates with the level of sustained attention. These results show that abnormalities in DMN function are a sensitive marker of impairments of attention and suggest that changes in connectivity within the DMN are central to the development of attentional impairment after TBI

Evolutionary Toggling of Vpx/Vpr Specificity Results in Divergent Recognition of the Restriction Factor SAMHD1

SAMHD1 is a host restriction factor that blocks the ability of lentiviruses such as HIV-1 to undergo reverse transcription in myeloid cells and resting T-cells. This restriction is alleviated by expression of the lentiviral accessory proteins Vpx and Vpr (Vpx/Vpr), which target SAMHD1 for proteasome-mediated degradation. However, the precise determinants within SAMHD1 for recognition by Vpx/Vpr remain unclear. Here we show that evolution of Vpx/Vpr in primate lentiviruses has caused the interface between SAMHD1 and Vpx/Vpr to alter during primate lentiviral evolution. Using multiple HIV-2 and SIV Vpx proteins, we show that Vpx from the HIV-2 and SIVmac lineage, but not Vpx from the SIVmnd2 and SIVrcm lineage, require the C-terminus of SAMHD1 for interaction, ubiquitylation, and degradation. On the other hand, the N-terminus of SAMHD1 governs interactions with Vpx from SIVmnd2 and SIVrcm, but has little effect on Vpx from HIV-2 and SIVmac. Furthermore, we show here that this difference in SAMHD1 recognition is evolutionarily dynamic, with the importance of the N- and C-terminus for interaction of SAMHD1 with Vpx and Vpr toggling during lentiviral evolution. We present a model to explain how the head-to-tail conformation of SAMHD1 proteins favors toggling of the interaction sites by Vpx/Vpr during this virus-host arms race. Such drastic functional divergence within a lentiviral protein highlights a novel plasticity in the evolutionary dynamics of viral antagonists for restriction factors during lentiviral adaptation to its hosts. © 2013 Fregoso et al

Vibrational Excitations in Weakly Coupled Single-Molecule Junctions: A Computational Analysis

In bulk systems, molecules are routinely identified by their vibrational spectrum using Raman or infrared spectroscopy. In recent years, vibrational excitation lines have been observed in low-temperature conductance measurements on single molecule junctions and they can provide a similar means of identification. We present a method to efficiently calculate these excitation lines in weakly coupled, gateable single-molecule junctions, using a combination of ab initio density functional theory and rate equations. Our method takes transitions from excited to excited vibrational state into account by evaluating the Franck-Condon factors for an arbitrary number of vibrational quanta, and is therefore able to predict qualitatively different behaviour from calculations limited to transitions from ground state to excited vibrational state. We find that the vibrational spectrum is sensitive to the molecular contact geometry and the charge state, and that it is generally necessary to take more than one vibrational quantum into account. Quantitative comparison to previously reported measurements on pi-conjugated molecules reveals that our method is able to characterize the vibrational excitations and can be used to identify single molecules in a junction. The method is computationally feasible on commodity hardware.Comment: 9 pages, 7 figure

Anthropogenic edge effects in habitat selection by sun bears in a protected area

Wildlife populations in southeast Asia are increasingly experiencing a broad array of anthropogenic threats, and mammalian carnivores are particularly vulnerable. Populations of the Malayan sun bear Helarctos malayanus are estimated to have declined by 30% over the last 30 years from forest conversion to industrial plantations and mortality associated with human–bear conflicts and illegal wildlife trade. However, the effects of industrial plantations on habitat selection and activity patterns of mammals that live at the protected area-plantation interface, including sun bears, are not well known. We investigated habitat selection and activity patterns of sun bears in Tabin Wildlife Reserve in Sabah, Malaysia. We deployed 83 remote camera sites to record sun bear detections during two sampling periods (2012–2013 and 2017). We used generalized linear models to examine relationships between sun bear presence and site covariates representing physical, environmental and anthropogenic elements of the landscape. Relative probability of sun bear presence was positively associated with distance to roads and elevation. Because most roads were on the reserve boundary and often associated with oil palm plantations, proximity to roads likely served as a surrogate measure of human accessibility and activity in peripheral areas of the reserve. Supporting that interpretation, sun bears close to the reserve boundary were primarily active at night, whereas daytime activity was more common for bears in the interior. Our findings indicate that sun bears alter behaviour and habitat selection likely in response to anthropogenic activities at the edges of Tabin Wildlife Reserve (112 200 ha). Because the ratio of edge to interior increases steeply with declining habitat area, smaller protected areas bordered by plantations are predicted to have greater impacts on sun bear behaviour and, potentially, population persistence. Effective conservation actions may benefit from management to improve the security of edge habitats for sun bears and other vulnerable species

Callous-unemotional traits, low cortisol reactivity and physical aggression in children: findings from the Wirral Child Health and Development Study

Callous-unemotional (CU) traits are thought to confer risk for aggression via reduced amygdala responsivity to distress cues in others. Low cortisol reactivity is thought to confer risk for aggression via reduced arousal and this effect may be confined to boys. We tested the hypothesis that the association between childhood CU traits and aggression would be greatest in the absence of the inhibitory effects of cortisol reactivity, and that this effect would be sex dependent. Participants were 283 members of a stratified subsample within an epidemiological longitudinal cohort (WCHADS). Cortisol reactivity to a social stressor was assessed at 5 years. CU traits were reported by mothers at 5 years, and physical aggression by mothers and teachers at age 7. Results showed that CU traits were associated with elevated aggression at 7 years controlling for earlier aggression. There was no main effect of cortisol reactivity on regression. The association between CU traits and aggression was moderated by cortisol reactivity (p = .011) with a strong association between CU traits and aggression in the presence of low reactivity, and a small and non-significant association in the presence of high reactivity. This association was further moderated by child sex (p = .041) with the joint effect of high CU traits and low cortisol reactivity seen only in boys (p = .016). We report first evidence that a combined deficit in inhibitory processes associated with CU traits and low cortisol reactivity increases risk for childhood aggression, in a sex-dependent manner

Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: Varying the number of double-stranded RNA binding domains and lineage-specific duplications

BackgroundDouble-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2alpha leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far.ResultsHere we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of PKR and PKZ in this latter species. Analyses of their genomic organization revealed up to three tandemly arrayed PKR genes, which are arranged in head-to-tail orientation. At least five duplications occurred independently in fish and amphibian lineages. Phylogenetic analyses reveal that the kinase domains of fish PKR genes are more closely related to those of fish PKZ than to the PKR kinase domains of other vertebrate species. The duplication leading to fish PKR and PKZ genes occurred early during teleost fish evolution after the divergence of the tetrapod lineage. While two dsRBDs are found in mammalian and amphibian PKR, one, two or three dsRBDs are present in fish PKR. In zebrafish, both PKR and PKZ were strongly upregulated after immunostimulation with some tissue-specific expression differences. Using genetic and biochemical assays we demonstrate that both zebrafish PKR and PKZ can phosphorylate eIF2alpha in yeast.ConclusionConsidering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both dsRNA and Z-DNA/RNA, and perhaps by altering sensitivity to viral PKR inhibitors. Further implications of our findings for the evolution of the PKR family and for studying PKR/PKZ interactions with viral gene products and their roles in viral infections are discussed

Cytomolecular identification of individual wheat-wheat chromosome arm associations in wheat-rye hybrids

Chromosome pairing in the meiotic metaphase I of wheatrye hybrids has been characterized by sequential genomic and fluorescent in situ hybridization allowing not only the discrimination of wheat and rye chromosomes, but also the identification of the individual wheat and rye chromosome arms involved in the chromosome associations. The majority of associations (93.8%) were observed between the wheat chromosomes. The largest number of wheat-wheat chromosome associations (53%) was detected between the A and D genomes, while the frequency of B-D and A-B associations was significantly lower (32 and 8%, respectively). Among the A-D chromosome associations, pairing between the 3AL and 3DL arms was observed with the highest frequency, while the most frequent of all the chromosome associations (0.113/ cell) was found to be the 3DS-3BS. Differences in the pairing frequency of the individual chromosome arms of wheat-rye hybrids have been discussed in relation to the homoeologous relationships between the constituent genomes of hexaploid wheat

Lung adenocarcinoma originates from retrovirus infection of proliferating type 2 pneumocytes during pulmonary post-natal development or tissue repair

Jaagsiekte sheep retrovirus (JSRV) is a unique oncogenic virus with distinctive biological properties. JSRV is the only virus causing a naturally occurring lung cancer (ovine pulmonary adenocarcinoma, OPA) and possessing a major structural protein that functions as a dominant oncoprotein. Lung cancer is the major cause of death among cancer patients. OPA can be an extremely useful animal model in order to identify the cells originating lung adenocarcinoma and to study the early events of pulmonary carcinogenesis. In this study, we demonstrated that lung adenocarcinoma in sheep originates from infection and transformation of proliferating type 2 pneumocytes (termed here lung alveolar proliferating cells, LAPCs). We excluded that OPA originates from a bronchioalveolar stem cell, or from mature post-mitotic type 2 pneumocytes or from either proliferating or non-proliferating Clara cells. We show that young animals possess abundant LAPCs and are highly susceptible to JSRV infection and transformation. On the contrary, healthy adult sheep, which are normally resistant to experimental OPA induction, exhibit a relatively low number of LAPCs and are resistant to JSRV infection of the respiratory epithelium. Importantly, induction of lung injury increased dramatically the number of LAPCs in adult sheep and rendered these animals fully susceptible to JSRV infection and transformation. Furthermore, we show that JSRV preferentially infects actively dividing cell in vitro. Overall, our study provides unique insights into pulmonary biology and carcinogenesis and suggests that JSRV and its host have reached an evolutionary equilibrium in which productive infection (and transformation) can occur only in cells that are scarce for most of the lifespan of the sheep. Our data also indicate that, at least in this model, inflammation can predispose to retroviral infection and cancer