Modeling of Exoplanet Atmospheres

Spectrally characterizing exoplanet atmospheres will be one of the fastest moving astronomical disciplines in the years to come. Especially the upcoming James Webb Space Telescope (JWST) will provide spectral measurements from the near- to mid-infrared of unprecedented precision. With other next generation instruments on the horizon, it is crucial to possess the tools necessary for interpretating observations. To this end I wrote the petitCODE, which solves for the self-consistent atmospheric structures of exoplanets, assuming chemical and radiative-convective equilibrium. The code includes scattering, and models clouds. The code outputs the planet’s observable emission and transmission spectra. In addition, I constructed a spectral retrieval code, which derives the full posterior probability distribution of atmospheric parameters from observations. I used petitCODE to systematically study the atmospheres of hot jupiters and found, e.g., that their structures depend strongly on the type of their host stars. Moreover, I found that C/O ratios around unity can lead to atmospheric inversions. Next, I produced synthetic observations of prime exoplanet targets for JWST, and studied how well we will be able to distinguish various atmospheric scenarios. Finally, I verified the implementation of my retrieval code using mock JWST observations

Transcriptomic Analysis of <i>Laribacter hongkongensis</i> Reveals Adaptive Response Coupled with Temperature

<div><p>Bacterial adaptation to different hosts requires transcriptomic alteration in response to the environmental conditions. <i>Laribacter hongkongensis</i> is a gram-negative, facultative anaerobic, urease-positive bacillus caused infections in liver cirrhosis patients and community-acquired gastroenteritis. It was also found in intestine from commonly consumed freshwater fishes and drinking water reservoirs. Since <i>L</i>. <i>hongkongensis</i> could survive as either fish or human pathogens, their survival mechanisms in two different habitats should be temperature-regulated and highly complex. Therefore, we performed transcriptomic analysis of <i>L</i>. <i>hongkongensis</i> at body temperatures of fish and human in order to elucidate the versatile adaptation mechanisms coupled with the temperatures. We identified numerous novel temperature-induced pathways involved in host pathogenesis, in addition to the shift of metabolic equilibriums and overexpression of stress-related proteins. Moreover, these pathways form a network that can be activated at a particular temperature, and change the physiology of the bacteria to adapt to the environments. In summary, the dynamic of transcriptomes in <i>L</i>. <i>hongkongensis</i> provides versatile strategies for the bacterial survival at different habitats and this alteration prepares the bacterium for the challenge of host immunity.</p></div

The graphs showed the mRNA expression of a) LHK_02129–02131 b) LHK_02825–02827 at 20°C and 37°C.

<p>Vertical error bars showed the standard deviations of biological triplicates. Expression level at 20°C was taken as reference for comparison. *P-value<0.05; **P-value<0.01.</p

The relative expression of genes known to be related to heat shock, cold shock, stress response protein and two component systems were compared at 20°C and 37°C by RNA-seq.

<p>Each square represents for a single gene, is categorized according to its function. The dashed lines represent a 2-fold over-expression at 37°C (upper line) and 20°C (lower line) conditions.</p

Model of temperature-induced pathways involved in host pathogenesis.

<p>Gene operons induced at 20°C and 37°C were drawn in blue and red region respectively.</p

The growth curve of L. hongkongensis at 20°C and 37°C.

<p>Vertical error bars represented standard deviation of biological triplicate.</p

Gene categories distribution of differentially expressed genes in KEGG pathway at 20°C and 37°C.

<p>Bars represented the abundance of genes up-regulated at 20°C (blue), 37°C (orange) and no expression difference (grey) in each category.</p

The relative expressions of genes known to be related to amino acid transporters and degradation were compared at 20°C and 37°C by RNA-seq.

<p>Each triangle or cross represents for a single gene. The dashed lines represent a 2-fold over-expression at 37°C (upper line) and 20°C (lower line) conditions.</p