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

Strategy for construction of the <i>atfA</i> complemented strain.

<p>(A) The restriction map demonstrates recognition sites of <i>Eco</i>RV (EV) and <i>Bss</i>SI (BsI) used in Southern blot analysis to detect the presence of <i>atfA</i> gene in the <i>atfA</i> complemented strain (AC1) comparing to the wild type strain (WT). The grey bar indicates the position of probe that is specific to the <i>atfA</i> gene. (B) Southern blot hybridization of genomic DNA from the wild type (F4) and the <i>atfA</i>-complemented (AC1) strains using probe in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111200#pone-0111200-g002" target="_blank">Figure 2A</a>. Probe (a 0.9 kb fragment of <i>atfA</i>) hybridized with 5.6 kb fragment and unpredicted fragment (10.0 kb fragment) of <i>Eco</i>RV- and BssSI-digested DNA from the wild type strain, respectively. For the <i>atfA</i> complemented strain, probe hybridized with unpredicted fragment (3.5 kb fragment) and 7.5 kb fragment of <i>Eco</i>RV- and BssSI-digested DNA from the <i>atfA</i> complemented strain, respectively.</p

Gene expressions and survival of <i>P. marneffei</i> under heat stress at 42°C.

<p>(A) Relative RNA expression of <i>sakA</i> and <i>atfA</i> genes of conidia from <i>P. marneffei</i> wild type determined by real-time PCR. Conidia were incubated at 42°C for 10, 20, 30 or 40 minutes. Total RNA was extracted from conidia and subjected to real-time PCR. Expression level of heat stress cells is presented as relative value to the expression level from no stress cells which is given a value of 1. GAPDH gene expression level was used to normalize amounts of input RNA. (B) Survival of conidia from <i>P. marneffei</i> wild type (WT), <i>atfA</i> mutant (Δ<i>atfA</i>) and complemented strains (Δ<i>atfA</i> + <i>atfA</i>) after incubating in BHI at 42°C for one hour. (C) Relative RNA expression level of <i>atfA</i> gene of conidia from <i>P. marneffei</i> wild type (WT), <i>sakA</i> mutant (Δ<i>sakA</i>). Conidia were incubated at 42°C for 20 minutes and total RNA was extracted and subject to real-time PCR. Results were obtained from three independent experiments and standard error bars of the mean bars are shown (p<0.05).</p

Susceptibility of conidia from <i>P. marneffei</i> wild type, <i>sakA</i> mutant (Δ<i>sakA</i>) and <i>atfA</i> mutant (Δ<i>atfA</i>) to UV light.

<p>Conidia of each strain were plated in duplicate on SDA and exposed to different UV light radiation at 0, 2000, 4000, 6000 and 8000 microjoules/cm². Data are from three independent experiments and standard error bars of the mean bars are shown (p<0.05).</p

Strategy for deletion of the <i>atfA</i> gene by replacing the entire <i>atfA</i> ORF with two DNA fragments using modified split marker method.

<p>(A) For the first DNA fragment, PCR amplification of 500 nucleotides of the <i>atfA</i> gene with 5′ flanking region from genomic DNA of wild type is performed. The PCR product is ligated to pAN7-1 containing the <i>hph</i> gene. The DNA fragment containing 500 nucleotides of the <i>atfA</i> gene with 5′ flanking region and the <i>hph</i> gene without terminator (<i>hph</i>) is obtained by digestion of recombinant plasmid with <i>Hin</i>dIII and <i>Bam</i>HI. For the second fragment, 3′ <i>atfA</i> flanking region of <i>atfA</i> is amplified and PCR product is used as a template with pAN7-1 in the second round PCR. Product form this PCR step consists of 3′ <i>atfA</i> flanking region and the truncated sequence of the <i>hph</i> gene (<i>ph</i>) with terminator. Two DNA fragments are then transformed into <i>P. marneffei</i> wild type to generate <i>atfA</i> mutant strain. The primers used for mutant construction and the predicted results of three homologous recombinations of 5′ and 3′ <i>atfA</i> flanking regions and <i>hph</i> gene at the <i>P. marneffei atfA</i> locus in split marker recombination method are shown (B) The restriction map demonstrates recognition sites of <i>Eco</i>RV (EV) used in Southern blot analysis to detect the deletion of <i>atfA</i> gene in the <i>atfA</i> mutant strain (Δ<i>atfA</i>) comparing to the wild type strain (WT). The positions of probe that is specific to both 3′ flanking region of <i>atfA</i> gene (grey bar) and <i>hph</i> gene (empty bar) are identified. EV represents <i>Eco</i>RV. (C) Result of Southern blot hybridization. Probe containing 0.8 kb fragment of 3′ flanking region of <i>atfA</i> gene and 1.5 kb fragment of <i>hph</i> gene hybridized with 5.6 kb fragments of <i>Eco</i>RV-digested DNA from the wild type strain and hybridized with a 11 kb fragment of <i>Eco</i>RV-digested DNA from the <i>atfA</i> mutant strain.</p

PCR primers used in this study.

<p>*<i>Hin</i>dIII restriction site sequence,</p><p>**<i>Kpn</i>I restriction site sequence.</p><p>PCR primers used in this study.</p

<i>atfA</i> expression during phase transition.

<p>RNA was isolated from <i>P. marneffei</i> strain F4 cells including conidia collected from cultures grown for seven days on PDA at 25°C, three days in SDB at 25°C (mycelia), and six days in BHI broth at 37°C (yeast). 18S rRNA was used as loading control of each growth phase.</p

Susceptibility to oxidative stresses of <i>P. marneffei</i>.

<p>Growth of <i>P. marneffei</i> wild type (F4), the <i>atfA</i> mutant (SC) and <i>atfA</i> complemented strain (AC1) at 25°C and 37°C on MM agar supplemented with 2 and 0.5 mM <i>t</i>-BOOH (B and F), 2 and 1 mM H₂O₂ (C and G), and 0.25 mM and 25 µM menadione (D and H). Five microliters of cell dilutions (5×10⁴ to 5 cells) were inoculated on MM agar containing each compound. (A) and (E) represent MM control plates at 25°C and 37°C, respectively.</p

Morphology of <i>P. marneffei atfA</i> mutant compared with wild type strain.

<p>(A) Colonies of wild type (F4) and <i>atfA</i> mutant (SC) on PDA incubated at 25°C for seven days. (B to D) Conidia isolated from wild type (F4) and <i>atfA</i> mutant (SC) were inoculated on SDA and SDB and were incubated at 37°C for ten days and six days, respectively. Scale bar represents five micrometers.</p

Deletion of <i>atfA</i> does not affect chitin deposition and cell wall integrity.

<p>(A) <i>P. marneffei</i> wild type (F4), <i>atfA</i> mutant (SC) and <i>atfA</i> complemented (AC1) strains were grown for seven day at 25°C on PDA and stained with CFW day four and day seven to visualize cell wall and septa. Scale bar represents five micrometers. (B to M) five microliters of cell dilutions (5×10⁴ to 5 cells) of wild type, <i>atfA</i> mutant and <i>atfA</i> complemented strains were inoculated on media supplemented with 5 µg/ml CFW(C and I), 0.004% SDS (D and J), 10 µg/ml and 4 µg/ml amphotericin B (F and L) and 8 µg/ml and 0.8 µg/ml itraconazole (G and M). (B and E) and (H and K) represent MM control plates at 25°C and 37°C, respectively.</p