The Transit Light Source Effect: False Spectral Features and Incorrect Densities for M-dwarf Transiting Planets

Transmission spectra are differential measurements that utilize stellar illumination to probe transiting exoplanet atmospheres. Any spectral difference between the illuminating light source and the disk-integrated stellar spectrum due to starspots and faculae will be imprinted in the observed transmission spectrum. However, few constraints exist for the extent of photospheric heterogeneities in M dwarfs. Here, we model spot and faculae covering fractions consistent with observed photometric variabilities for M dwarfs and the associated 0.3-5.5 $\mu$m stellar contamination spectra. We find that large ranges of spot and faculae covering fractions are consistent with observations and corrections assuming a linear relation between variability amplitude and covering fractions generally underestimate the stellar contamination. Using realistic estimates for spot and faculae covering fractions, we find stellar contamination can be more than $10 \times$ larger than transit depth changes expected for atmospheric features in rocky exoplanets. We also find that stellar spectral contamination can lead to systematic errors in radius and therefore the derived density of small planets. In the case of the TRAPPIST-1 system, we show that TRAPPIST-1's rotational variability is consistent with spot covering fractions $f_{spot} = 8^{+18}_{-7}\%$ and faculae covering fractions $f_{fac} = 54^{+16}_{-46}\%$. The associated stellar contamination signals alter transit depths of the TRAPPIST-1 planets at wavelengths of interest for planetary atmospheric species by roughly 1-15 $\times$ the strength of planetary features, significantly complicating $JWST$ follow-up observations of this system. Similarly, we find stellar contamination can lead to underestimates of bulk densities of the TRAPPIST-1 planets of $\Delta(\rho) = -3^{+3}_{-8} \%$, thus leading to overestimates of their volatile contents.Comment: accepted for publication in Ap

Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data

UNLABELLED: As the volume of patient-specific genome sequences increases the focus of biomedical research is switching from the detection of disease-mutations to their interpretation. To this end a number of techniques have been developed that use mutation data collected within a population to predict whether individual genes are likely to be disease-causing or not. As both sequence data and associated analysis tools proliferate, it becomes increasingly difficult for the community to make sense of these data and their implications. Moreover, no single analysis tool is likely to capture all relevant genomic features that contribute to the gene's pathogenicity. Here, we introduce Web-based Gene Pathogenicity Analysis (WGPA), a web-based tool to analyze genes impacted by mutations and rank them through the integration of existing prioritization tools, which assess different aspects of gene pathogenicity using population-level sequence data. Additionally, to explore the polygenic contribution of mutations to disease, WGPA implements gene set enrichment analysis to prioritize disease-causing genes and gene interaction networks, therefore providing a comprehensive annotation of personal genomes data in disease. AVAILABILITY AND IMPLEMENTATION: wgpa.systems-genetics.net

Single molecule studies of ligand-DNA interactions using atomic force microscopy

This thesis describes the results of experiments into the intra and inter-molecular binding of various ligands with dsDNA via the mechanism of intercalation, principally using the technique of atomic force microscopy (AFM). Since the description of the first AFM in the mid 1980’s, AFM has emerged as a sensitive and versatile analytical tool, capable both of detecting and manipulating artefacts at picometer resolutions. In these studies, AFM imaging, supported by circular dichroism, reveals unusual conformational changes in DNA that occur as a result of the binding of ligands that incorporate the acridine chromophore. These changes are distinct from those observed following the binding of other intercalators such as doxorubicin and echinomycin. Direct measurement of the length of linear DNA strands bound to acridine based ligands reveals a shortening of the DNA at very low ligand concentrations. This observation suggests that the structural changes that occur in DNA following the intercalation of the acridine chromophore are more wide ranging than previously thought and support molecular modeling studies that have proposed that the intercalated DNA duplex exhibits characteristics of both B and A form DNA. Variations in the conformational changes that occur in DNA as a result of intercalation may have implications for the application of new intercalating ligands as chemotherapeutic agents. In addition, single molecule force spectroscopy has been used to examine the capacity of bisintercalators to bind to DNA in an inter-molecular fashion. By stretching individual strands of dsDNA, acridine dimers are shown to bind to separate strands of DNA. Intermolecular binding of this kind remains an unexplored cytotoxic mechanism that may yet find an application in vivo. This observation is supported by a novel assay that utilises the controlled aggregation of gold nanoparticles. These nanoparticles, functionalised with DNA, are shown to aggregate on addition of a bisintercalator. The aggregation is fully reversible with the addition of sodium dodecylsulphate. These force spectroscopy experiments have also uncovered a previously unobserved, intermolecular binding mode of the peptide antibiotics echinomycin and TANDEM. In certain circumstances, these ligands are revealed to bind exclusively to the termini of separate DNA strands in a sequence dependent fashion. This finding may have implications for the employment of these ligands in the nanosciences, as a tool for joining short pieces of DNA or improving the efficiency of the enzymatic, blunt-end ligation of DNA

...Bless her little heart! : The Culture of Honor and Emotion Recognition

Author\u27s abstract: Some researchers assert that cultural display rules may explain differences in perceiving emotions (Matsumoto, Yoo, & Chung, 2010). The current study examined the display rule of masking within the Southern culture of honor. It was hypothesized that masking within the culture of honor negatively affects emotion perception sensitivity, particularly in the speed and accuracy of recognizing anger. Southern undergraduate students were primed with the culture of honor and then presented with the Emotional Expression Multimorph Task. Participants chose one of the six emotions (i.e., sad, happy, surprise, fear, disgust, or anger). It was hypothesized participants in the masking and masking/culture of honor prime groups would take significantly longer recognizing emotions than the mimicking/culture of honor prime and mimicking (control) groups. Results indicated an effect of masking on emotion perception, F(1, 77) = 4.16, p = .04, partial η2 = .05, supporting the hypothesis that participants who mask would take significantly longer than the participants who do not mask to correctly identify emotions. The main effect of the culture of honor prime was not significant. Participants were significantly slower at perceiving anger when compared to happiness and surprise. This study further substantiates masking as a display rule and its effects on facial feedback. It was not determined that the culture of honor affects emotion recognition through the mechanism of masking. Future research studies could use more ecologically generalizable variables to determine if masking occurs within the culture of honor

The Tempest (Selections)

Selection of illustrations from Arthur Rackham\u27s edition of Shakespeare\u27s The Tempesthttps://egrove.olemiss.edu/shakespeare/1008/thumbnail.jp