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

miR-375-3p targeted LRP5 and β-catenin.

<p>(A) The binding sites between miR-375-3p and the 3’UTR of LRP5 and β-catenin. (B) The relative luciferase activity of MC3T3-E1 cells transfected with luciferase-wild type (or mutant) LRP5 plasmids and miR-375-3p mimics. (C) The relative luciferase activity of MC3T3-E1 cells transfected with luciferase-wild type (or mutant) β-catenin plasmids and miR-375-3p mimics. * p < 0.05. ** p < 0.01, NS, not significant. n = 3/group.</p

Sequences of all primers.

<p>Sequences of all primers.</p

The baseline of mice.

<p>The baseline of mice.</p

The flowchart of the main study factors and their relationships.

The flowchart of the main study factors and their relationships.</p

The expression dynamics of effectors of miR-375-3p during osteogenesis.

<p>(A) Relative expression levels of LRP5 during MC3T3-E1 differentiation and osteogenesis. (B) Relative expression levels of β-catenin during MC3T3-E1 differentiation. (C) Relative expression levels of β-catenin in bone tissues from osteoporotic patients and their controls. * p < 0.05. ** p < 0.01.</p

Data_Sheet_2_Malate-Dependent Carbon Utilization Enhances Central Metabolism and Contributes to Biological Fitness of Laribacter hongkongensis via CRP Regulation.xlsx

Metabolic adaptation in various environmental niches is crucial for bacterial extracellular survival and intracellular replication during infection. However, the metabolism of carbon/nitrogen sources and related regulatory mechanisms in Laribacter hongkongensis, an asaccharolytic bacterium associated with invasive infections and gastroenteritis, are still unknown. In the present study, we demonstrated that malate can be exploited as a preferred carbon source of L. hongkongensis. Using RNA-sequencing, we compared the transcription profiles of L. hongkongensis cultivated with or without malate supplementation, and observed that malate utilization significantly inhibits the use of alternative carbon sources while enhancing respiratory chain as well as central carbon, sulfur, and urease-mediated nitrogen metabolisms. The tight connection among these important metabolic pathways indicates that L. hongkongensis is capable of integrating information from different metabolism branches to coordinate the expression of metabolic genes and thereby adapt to environmental changing. Furthermore, we identified that a transcription factor, CRP, is repressed by malate-mediated metabolism while negatively regulating the effect of malate on these central metabolic pathways. Remarkably, CRP also responds to various environmental stresses, influences the expression of other transcription factors, and contributes to the biological fitness of L. hongkongensis. The regulatory network and cross-regulation enables the bacteria to make the appropriate metabolic responses and environmental adaptation.</p

miR-375-3p arrested the expression of LRP5 and β-catenin.

<p>(A) Relative expression levels of LRP5 in MC3T3-E1 cells upon transfection of miR-375-3p mimics or inhibitors. (B) Relative expression levels of β-catenin in MC3T3-E1 cells upon transfection of miR-375-3p mimics or inhibitors. (C) Representative staining images of MC3T3-E1 cells. Less green cells were found after the cells were transfected with miR-375-3p mimics. * p < 0.05. ** p < 0.01. n = 3/group.</p

Data_Sheet_1_Malate-Dependent Carbon Utilization Enhances Central Metabolism and Contributes to Biological Fitness of Laribacter hongkongensis via CRP Regulation.docx

Metabolic adaptation in various environmental niches is crucial for bacterial extracellular survival and intracellular replication during infection. However, the metabolism of carbon/nitrogen sources and related regulatory mechanisms in Laribacter hongkongensis, an asaccharolytic bacterium associated with invasive infections and gastroenteritis, are still unknown. In the present study, we demonstrated that malate can be exploited as a preferred carbon source of L. hongkongensis. Using RNA-sequencing, we compared the transcription profiles of L. hongkongensis cultivated with or without malate supplementation, and observed that malate utilization significantly inhibits the use of alternative carbon sources while enhancing respiratory chain as well as central carbon, sulfur, and urease-mediated nitrogen metabolisms. The tight connection among these important metabolic pathways indicates that L. hongkongensis is capable of integrating information from different metabolism branches to coordinate the expression of metabolic genes and thereby adapt to environmental changing. Furthermore, we identified that a transcription factor, CRP, is repressed by malate-mediated metabolism while negatively regulating the effect of malate on these central metabolic pathways. Remarkably, CRP also responds to various environmental stresses, influences the expression of other transcription factors, and contributes to the biological fitness of L. hongkongensis. The regulatory network and cross-regulation enables the bacteria to make the appropriate metabolic responses and environmental adaptation.</p

The examples of region of interests.

<p>The examples of region of interests.</p