We have found the inflammation-associated lung tumorigenesis is differentially regulated by genders and happens with higher frequency and incidence in females than the males. My laboratory developed and published an innovative exposure paradigm that demonstrated the synergistic effect of lung tumorigenesis (> 6 fold, p<0.0001) and higher frequency of lung tumors that harbor K-ras mutation by co-exposure of a cigarette smoke carcinogen NNK and an inflammation eliciting agent from bacteria endotoxin LPS. Inflammation-associated tissue remodeling and lung tumorigenesis:.We are interested in elucidating mechanisms associated with epithelial cell-mediated tissue remodeling and regeneration after recurrent bacterial and viral infection-induced injury. The expression of SPLUNC1 in the lung is dynamic and reflects maturational, functional, and pathological changes of the lung epithelium. We and others have demonstrated multiple functions of SPLUNC1, including host defense, anti-inflammatory effects, a surfactant-like property, and modulation of epithelial lining fluid volume.
Two consecutive R01 grants have supported the SPLUNC1-associated research since 2008, including the ongoing clinical, ancillary study to investigate its association with exacerbation in severe asthma. My laboratory provided influential identification and characterization of a novel lung epithelial cell specific, secretory protein SPLUNC1 and its roles in pulmonary diseases. Lung epithelial cell phenotype, differentiation, and function upon exposure:.The primary focus of my current research is the cellular and molecular actions of exposures to toxic chemicals and microorganisms that underlie the pathogenesis of chronic human diseases. We are particularly interested in infection and immunity on the lung and its associated pathophysiological response during injury, repair, and regeneration. Message me if you'd like to see some codes I've used or have any other questions.The purpose of my laboratory’s research is to investigate the effects of environmental exposure on the host. I would encourage you to seek further support in your research community and start fiddling around with RStudio and these various packages. I feel publishing with these types of R packages are more credible in the literature as well. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. Many others have stood where you're standing, resulting in a lot of blog posts etc. Although, command line analysis is quite difficult at times to learn and incredibly frustrating, it's not impossible. Therefore, I would advise to use CLC as more of a preliminary analysis tool. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method). Hi Cristina, I previously used CLC for RNA-Seq analysis and fiddled with lots of parameters, my final output delivered a low number of differentially expressed genes (DEG) that were uninformative. Message me if you'd like to see some codes I've used or have any other questions.
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