Orbital Stability of Multi-Planet Systems: Behavior at High Masses

In the coming years, high contrast imaging surveys are expected to reveal the characteristics of the population of wide-orbit, massive, exoplanets. To date, a handful of wide planetary mass companions are known, but only one such multi-planet system has been discovered: HR8799. For low mass planetary systems, multi-planet interactions play an important role in setting system architecture. In this paper, we explore the stability of these high mass, multi-planet systems. While empirical relationships exist that predict how system stability scales with planet spacing at low masses, we show that extrapolating to super-Jupiter masses can lead to up to an order of magnitude overestimate of stability for massive, tightly packed systems. We show that at both low and high planet masses, overlapping mean motion resonances trigger chaotic orbital evolution, which leads to system instability. We attribute some of the difference in behavior as a function of mass to the increasing importance of second order resonances at high planet-star mass ratios. We use our tailored high mass planet results to estimate the maximum number of planets that might reside in double component debris disk systems, whose gaps may indicate the presence of massive bodies.Comment: Accepted to Ap

The involvement of cap-independent mRNA translation in cell fate decisions

During cell stress many biochemical processes are shut down. For example, global mRNA translation initiation is inhibited due to the disruption of the cap-dependent mRNA recruitment mechanism. One specific example of stress, apoptosis, results in activated caspases that cleave the translation initiation factor eIF4G. This cleavage disrupts cap-dependent mRNA translation initiation by removing the cap-binding domain. However, a specific subset of mRNAs can still be recruited for protein synthesis in a cap-independent manner by the residual initiation machinery. This selective recruitment of stress and apoptosis-related mRNAs promotes stress response and further induction of apoptosis. Many of these mRNAs contain internal ribosome entry sites (IRESes) that promote their enhanced translation during these conditions. Still other mRNAs have little dependence on the cap recognition mechanism. The expression of the encoded proteins, both anti- and pro-apoptotic, promote an initial period of attempted cell survival, then commitment to cell death when damage is extensive. This switch in mode of translation initiation and how it allows for selective mRNA translation is not well understood. This study focuses on the utilization of cap-independent protein synthesis in the nematode worm, C. elegans. Due to their relative genetic simplicity, while maintaining molecular pathways found in higher organisms, and semi transparency that permits direct observation of cell fate decisions, C. elegans are the fitting in vivo model in which to study changes in translational regulation and how they affect cell fate. In this study we address the translational regulation of the stress and apoptosis-related mRNAs in C. elegans: BiP (hsp-3) (hsp-4), Hif-1 (hif-1), p53 (cep-1), Bcl-2 (ced-9) and Apaf-1 (ced-4). Altered translational efficiency of these messages was observed upon depletion of cap-dependent translation and induction of apoptosis within the C. elegans gonad. Our findings suggest a physiological link between the cap-independent mechanism and the enhanced translation of hsp-3 and ced-9. This increase in the efficiency of translation may be integral to the stress response during the induction of physiological apoptosis. Further organism wide RNA-seq studies have begun to identify the entire population of mRNAs that rely highly on cap-dependent and independent translation. Development of this methodology, for detecting changes in translational efficiency on a global level, enables future follow-up studies to confirm additional mRNAs whose translation results in changes in cell fate decisions. Additionally, we carefully and specifically characterized C. elegans ced-4 mRNA, the Apaf-1 homologue, and observed that its structure and mode of translation initiation differed from its mammalian homologue. ced-4 mRNA translation illustrates one example of how selective translation in germ cells may differ from that observed in cultured mammalian cells responding to toxic treatments such as chemotherapy agents and hypoxia. Networks of translational regulation are particularly important during germ cell development. The silencing of transcription, associated with chromosome condensation during meiosis, results in protein expression patterns that are dependent translational regulation. Genetic analysis shows that loss of key translational regulators leads to the onset of germ cell tumors within the C. elegans gonad. Cell growth and mitotic mRNAs typically rely highly on cap-dependent translation initiation in mammalian cell culture. Thus, we predicted that knockdown of cap-dependent translation would decrease expression of growth and mitotic proteins and result in a reversion of tumor phenotype. However, germ cell tumor progression was not grossly affected by knockdown of cap-associated eIF4G. The inability to revert this cell fate is most likely due to other regulators of translation at work in the germ line. Reversion of tumor phenotype require knockdown of multiple regulators of translation. Overall, these results indicate an important balance between cap-dependent and -independent translation initiation during stress and the affect of this balance on germ cell fate decisions.Ph.D

Cap-Independent Translation Promotes C. elegans Germ Cell Apoptosis through Apaf-1/CED-4 in a Caspase-Dependent Mechanism

Apoptosis is a natural process during animal development for the programmed removal of superfluous cells. During apoptosis general protein synthesis is reduced, but the synthesis of cell death proteins is enhanced. Selective translation has been attributed to modification of the protein synthesis machinery to disrupt cap-dependent mRNA translation and induce a cap-independent mechanism. We have previously shown that disruption of the balance between cap-dependent and cap-independent C. elegans eIF4G isoforms (IFG-1 p170 and p130) by RNA interference promotes apoptosis in developing oocytes. Germ cell apoptosis was accompanied by the appearance of the Apaf-1 homolog, CED-4. Here we show that IFG-1 p170 is a native substrate of the worm executioner caspase, CED-3, just as mammalian eIF4GI is cleaved by caspase-3. Loss of Bcl-2 function (ced-9ts) in worms induced p170 cleavage in vivo, coincident with extensive germ cell apoptosis. Truncation of IFG-1 occurred at a single site that separates the cap-binding and ribosome-associated domains. Site-directed mutagenesis indicated that CED-3 processes IFG-1 at a non-canonical motif, TTTD456. Coincidentally, the recognition site was located 65 amino acids downstream of the newly mapped IFG-1 p130 start site suggesting that both forms support cap-independent initiation. Genetic evidence confirmed that apoptosis induced by loss of ifg-1 p170 mRNA was caspase (ced-3) and apoptosome (ced-4/Apaf-1) dependent. These findings support a new paradigm in which modal changes in protein synthesis act as a physiological signal to initiate cell death, rather than occur merely as downstream consequences of the apoptotic event

An AMPKa2-specific phospho-switch controls lysosomal targeting for activation

AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1) are metabolic kinases that co-ordinate nutrient supply with cell growth. AMPK negatively regulates mTORC1, and mTORC1 reciprocally phosphorylates S345/7 in both AMPK α-isoforms. We report that genetic or torin1-induced loss of α2-S345 phosphorylation relieves suppression of AMPK signaling; however, the regulatory effect does not translate to α1-S347 in HEK293T or MEF cells. Dephosphorylation of α2-S345, but not α1-S347, transiently targets AMPK to lysosomes, a cellular site for activation by LKB1. By mass spectrometry, we find that α2-S345 is basally phosphorylated at 2.5-fold higher stoichiometry than α1-S347 in HEK293T cells and, unlike α1, phosphorylation is partially retained after prolonged mTORC1 inhibition. Loss of α2-S345 phosphorylation in endogenous AMPK fails to sustain growth of MEFs under amino acid starvation conditions. These findings uncover an α2-specific mechanism by which AMPK can be activated at lysosomes in the absence of changes in cellular energy

Variability in dengue titer estimates from plaque reduction neutralization tests poses a challenge to epidemiological studies and vaccine development.

BACKGROUND: Accurate determination of neutralization antibody titers supports epidemiological studies of dengue virus transmission and vaccine trials. Neutralization titers measured using the plaque reduction neutralization test (PRNT) are believed to provide a key measure of immunity to dengue viruses, however, the assay's variability is poorly understood, making it difficult to interpret the significance of any assay reading. In addition there is limited standardization of the neutralization evaluation point or statistical model used to estimate titers across laboratories, with little understanding of the optimum approach. METHODOLOGY/PRINCIPAL FINDINGS: We used repeated assays on the same two pools of serum using five different viruses (2,319 assays) to characterize the variability in the technique under identical experimental conditions. We also assessed the performance of multiple statistical models to interpolate continuous values of neutralization titer from discrete measurements from serial dilutions. We found that the variance in plaque reductions for individual dilutions was 0.016, equivalent to a 95% confidence interval of 0.45-0.95 for an observed plaque reduction of 0.7. We identified PRNT75 as the optimum evaluation point with a variance of 0.025 (log10 scale), indicating a titer reading of 1∶500 had 95% confidence intervals of 1∶240-1∶1000 (2.70±0.31 on a log10 scale). The choice of statistical model was not important for the calculation of relative titers, however, cloglog regression out-performed alternatives where absolute titers are of interest. Finally, we estimated that only 0.7% of assays would falsely detect a four-fold difference in titers between acute and convalescent sera where no true difference exists. CONCLUSIONS: Estimating and reporting assay uncertainty will aid the interpretation of individual titers. Laboratories should perform a small number of repeat assays to generate their own variability estimates. These could be used to calculate confidence intervals for all reported titers and allow benchmarking of assay performance

Advances in understanding and treating ADHD

Attention deficit hyperactivity disorder (ADHD) is a neurocognitive behavioral developmental disorder most commonly seen in childhood and adolescence, which often extends to the adult years. Relative to a decade ago, there has been extensive research into understanding the factors underlying ADHD, leading to far more treatment options available for both adolescents and adults with this disorder. Novel stimulant formulations have made it possible to tailor treatment to the duration of efficacy required by patients, and to help mitigate the potential for abuse, misuse and diversion. Several new non-stimulant options have also emerged in the past few years. Among these, cognitive behavioral interventions have proven popular in the treatment of adult ADHD, especially within the adult population who cannot or will not use medications, along with the many medication-treated patients who continue to show residual disability

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The contribution of X-linked coding variation to severe developmental disorders

Abstract: Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders

The involvement of cap-independent mRNA translation in cell fate\r\ndecisions

During cell stress many biochemical processes are shut down. For\r\nexample, global mRNA translation initiation is inhibited due to the\r\ndisruption of the cap-dependent mRNA recruitment mechanism. One\r\nspecific example of stress, apoptosis, results in activated caspases\r\nthat cleave the translation initiation factor eIF4G. This cleavage\r\ndisrupts cap-dependent mRNA translation initiation by removing the\r\ncap-binding domain. However, a specific subset of mRNAs can still be recruited for protein synthesis in a cap-independent manner by the\r\nresidual initiation machinery. This selective recruitment of stress\r\nand apoptosis-related mRNAs promotes stress response and further\r\ninduction of apoptosis. Many of these mRNAs contain internal ribosome entry sites (IRESes) that promote their enhanced translation during these conditions. Still other mRNAs have little dependence on the cap recognition mechanism. The expression of the encoded proteins, both anti- and pro-apoptotic, promote an initial period of attempted cell survival, then commitment to cell death when damage is extensive. This switch in mode of translation initiation and how it allows for selective mRNA translation is not well understood. This study focuses on the utilization of cap-independent protein synthesis in the nematode worm, C. elegans. Due to their relative genetic\r\nsimplicity, while maintaining molecular pathways found in higher\r\norganisms, and semi transparency that permits direct observation of\r\ncell fate decisions, C. elegans are the fitting in vivo model in\r\nwhich to study changes in translational regulation and how they\r\naffect cell fate. In this study we address the translational\r\nregulation of the stress and apoptosis-related mRNAs in C. elegans:\r\nBiP (hsp-3) (hsp-4), Hif-1 (hif-1), p53 (cep-1), Bcl-2 (ced-9) and\r\nApaf-1 (ced-4). Altered translational efficiency of these messages\r\nwas observed upon depletion of cap-dependent translation and\r\ninduction of apoptosis within the C. elegans gonad. Our findings\r\nsuggest a physiological link between the cap-independent mechanism and the enhanced translation of hsp-3 and ced-9. This increase in the efficiency of translation may be integral to the stress response during the induction of physiological apoptosis. Further organism wide RNA-seq studies have begun to identify the entire population of mRNAs that rely highly on cap-dependent and independent translation. Development of this methodology, for detecting changes in translational efficiency on a global level, enables future follow-up studies to confirm additional mRNAs whose translation results in changes in cell fate decisions. Additionally, we carefully and specifically characterized C. elegans ced-4 mRNA, the Apaf-1 homologue, and observed that its structure and mode of translation initiation differed from its mammalian homologue. ced-4 mRNA translation illustrates one example of how selective translation in germ cells may differ from that observed in cultured mammalian cells responding to toxic treatments such as chemotherapy agents and hypoxia. Networks of translational regulation are particularly\r\nimportant during germ cell development. The silencing of\r\ntranscription, associated with chromosome condensation during\r\nmeiosis, results in protein expression patterns that are dependent\r\ntranslational regulation. Genetic analysis shows that loss of key\r\ntranslational regulators leads to the onset of germ cell tumors\r\nwithin the C. elegans gonad. Cell growth and mitotic mRNAs typically\r\nrely highly on cap-dependent translation initiation in mammalian cell\r\nculture. Thus, we predicted that knockdown of cap-dependent\r\ntranslation would decrease expression of growth and mitotic proteins\r\nand result in a reversion of tumor phenotype. However, germ cell\r\ntumor progression was not grossly affected by knockdown of\r\ncap-associated eIF4G. The inability to revert this cell fate is most\r\nlikely due to other regulators of translation at work in the germ\r\nline. Reversion of tumor phenotype require knockdown of multiple\r\nregulators of translation. Overall, these results indicate an\r\nimportant balance between cap-dependent and -independent translation initiation during stress and the affect of this balance on germ cell fate decisions