WriteSim TCExam - An open source text simulation environment for training novice researchers in scientific writing

BACKGROUND: The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) RESULTS: The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. CONCLUSION: WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods

Variation at DENND1B and Asthma on the Island of Tristan da Cunha

A high prevalence of asthma has been documented among the inhabitants of Tristan da Cunha, an isolated island in the South Atlantic. The population derives from just 28 founders. We performed lung function testing, including methacholine inhalation challenge, allergen skin prick testing, and collected DNA from essentially all of the current island population (269 individuals), and genotyped a panel of 43 single-nucleotide polymorphisms (SNPs) reported as associated with asthma and atopy. We carried out a mixed-model association analysis using the known pedigree. There were 96 individuals diagnosed as asthmatic (36%), and heritability estimates were similar to those from nonisolated population samples (multifactorial threshold model, h2 = 48%). The first component from a genetic principal components analysis using the entire SNP panel was nonlinearly associated with asthma, with the maximum risk to those intermediate to reference (Human Genome Diversity Project) European and African samples means. The single most strongly associated SNP was rs2786098 (p = 5.5 × 10-5), known to regulate the gene DENND1B. This explained approximately one-third of the trait heritability, with an allelic odds ratio for the A allele of 2.6. Among A/A carriers, 10 out of 12 individuals were asthmatic. The rs2786098*A variant was initially reported to decrease the risk of childhood (atopic) asthma in European but slightly increase the risk in African-descended populations, and does significantly alter Th2 cell function. Despite an absence of overall association with this variant in recent asthma genome wide association studies meta-analyses, an effect may exist on the particular genetic background of the Tristan da Cunha population

PKC activation induces inflammatory response and cell death in human bronchial epithelial cells.

A variety of airborne pathogens can induce inflammatory responses in airway epithelial cells, which is a crucial component of host defence. However, excessive inflammatory responses and chronic inflammation also contribute to different diseases of the respiratory system. We hypothesized that the activation of protein kinase C (PKC) is one of the essential mechanisms of inflammatory response in airway epithelial cells. In the present study, we stimulated human bronchial lung epithelial (BEAS-2B) cells with the phorbol ester Phorbol 12, 13-dibutyrate (PDBu), and examined gene expression profile using microarrays. Microarray analysis suggests that PKC activation induced dramatic changes in gene expression related to multiple cellular functions. The top two interaction networks generated from these changes were centered on NFκB and TNF-α, which are two commonly known pathways for cell death and inflammation. Subsequent tests confirmed the decrease in cell viability and an increase in the production of various cytokines. Interestingly, each of the increased cytokines was differentially regulated at mRNA and/or protein levels by different sub-classes of PKC isozymes. We conclude that pathological cell death and cytokine production in airway epithelial cells in various situations may be mediated through PKC related signaling pathways. These findings suggest that PKCs can be new targets for treatment of lung diseases

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10.1097/ACM.0b013e3181c48533Academic Medicine8514-5ACME

Ischemia-Reperfusion Injury in a Simulated Lung Transplant Setting Differentially Regulates Transcriptomic Profiles between Human Lung Endothelial and Epithelial Cells

Current understanding of mechanisms of ischemia-reperfusion-induced lung injury during lung preservation and transplantation is mainly based on clinical observations and animal studies. Herein, we used cell and systems biology approaches to explore these mechanisms at transcriptomics levels, especially by focusing on the differences between human lung endothelial and epithelial cells, which are crucial for maintaining essential lung structure and function. Human pulmonary microvascular endothelial cells and human lung epithelial cells were cultured to confluent, subjected to different cold ischemic times (CIT) to mimic static cold storage with preservation solution, and then subjected to warm reperfusion with a serum containing culture medium to simulate lung transplantation. Cell morphology, viability, and transcriptomic profiles were studied. Ischemia-reperfusion injury induced a CIT time-dependent cell death, which was associated with dramatic changes in gene expression. Under normal control conditions, endothelial cells showed gene clusters enriched in the vascular process and inflammation, while epithelial cells showed gene clusters enriched in protein biosynthesis and metabolism. CIT 6 h alone or after reperfusion had little effect on these phenotypic characteristics. After CIT 18 h, protein-biosynthesis-related gene clusters disappeared in epithelial cells; after reperfusion, metabolism-related gene clusters in epithelial cells and multiple gene clusters in the endothelial cells also disappeared. Human pulmonary endothelial and epithelial cells have distinct phenotypic transcriptomic signatures. Severe cellular injury reduces these gene expression signatures in a cell-type-dependent manner. Therapeutics that preserve these transcriptomic signatures may represent new treatment to prevent acute lung injury during lung transplantation

Fractal circuit sensors enable rapid quantification of biomarkers for donor lung assessment for transplantation

Biomarker profiling is being rapidly incorporated in many areas of modern medical practice to improve the precision of clinical decision-making. This potential improvement, however, has not been transferred to the practice of organ assessment and transplantation because previously developed gene-profiling techniques require an extended period of time to perform, making them unsuitable in the time-sensitive organ assessment process. We sought to develop a novel class of chip-based sensors that would enable rapid analysis of tissue levels of preimplantation mRNA markers that correlate with the development of primary graft dysfunction (PGD) in recipients after transplant. Using fractal circuit sensors (FraCS), three-dimensional metal structures with large surface areas, we were able to rapidly (<20 min) and reproducibly quantify small differences in the expression of interleukin-6 (IL-6), IL-10, and ATP11B mRNA in donor lung biopsies. A proof-of-concept study using 52 human donor lungs was performed to develop a model that was used to predict, with excellent sensitivity (74%) and specificity (91%), the incidence of PGD for a donor lung. Thus, the FraCS-based approach delivers a key predictive value test that could be applied to enhance transplant patient outcomes. This work provides an important step toward bringing rapid diagnostic mRNA profiling to clinical application in lung transplantation

Metabolomic heterogeneity of pulmonary arterial hypertension.

Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH), the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the human PAH lung. The results suggest that PAH has specific metabolic pathways contributing to increased ATP synthesis for the vascular remodeling process in severe pulmonary hypertension. These identified metabolites may serve as potential biomarkers for the diagnosis of PAH. By profiling metabolomic alterations of the PAH lung, we reveal new pathogenic mechanisms of PAH, opening an avenue of exploration for therapeutics that target metabolic pathway alterations in the progression of PAH

Metabolomic profiling of pulmonary hypertension.

<p>a), Principal component analysis (PCA) for metabolom PAH tissue exhibited a distinct metabolic signature in comparison to NL. b), Statistical comparisons using Welch's Two-Sample t-Test show significantly altered biochemicals in PAH samples (N = 8) compared with biochemical profiling in normal samples (N = 8). Interestingly, the biochemical profiles of PAH tissue exhibited higher levels of 93 altered metabolites compared with the normal lung (p≤0.05). c), Heat map that represents the non-supervised hierarchical clustering of 93 differential metabolites in PCA relative to normal sample data over eight PAH lungs (n = 8). Shades of light yellow/blue represent the increase and decrease of a metabolite, respectively, relative to the median metabolite levels. d) z-score plots show the 376 metabolites data that were normalized to the mean of the normal samples (truncated at 25).</p

Glycolysis is significantly upregulated in the PAH lung.

<p>a) In all graphs, data for normal lung are shown in green boxes and data for the PAH lung are represented in pink boxes. Quantities are in arbitrary units specific to the internal standards for each quantified metabolite and normalized to protein concentration (N = 8 for each box). PAH patient samples exhibited higher levels of glucose, sorbitol, fructose, and fructose 6-phosphate. This metabolic disruption can contribute to the formation of advanced glycolytic end products that have been shown to directly contribute to the severity of PAH. b) The classical glycolysis/pentose/energy pathways are shown. c)Three genes encoding G6PC3, PFKFB2, and LDHB were significantly changed in PAH lung compared with NL, as shown in all graph) (G6PC3 (p = 8.54e−05), PFKFB2 (p = 2.6e-04) and LDHB (p = 2.19e−09). d) Western Blot analysis of G6PC3 (n = 4/each group) and e) LDHB expression in normal and PAH lungs (n = 4/each group). Lung lysate (20 ug per lane) was loaded and immunoblotted with antibody against G6PC3 or LDHB and GAPDH (loading control). Consistent with a significant decrease of G6PC3 and an increase of LDHB gene expression in PAH, protein expression for G6PC3 (39KD) was significantly decreased while LDH (37KD) was significantly increased in PAH lungs compared with NL lungs. Densitometric analysis of G6PC3 and LDHB were normalized to the intensity of the respective GAPDH band. Data are expressed as mean ±SD (n = 4). *P<0.05 versus NL. f), Representative images of G6PC3 positive immunostaining in the collagen fibers of pulmonary vascular tissue, which was decreased in PAH. Increased LDHB positive staining was found in pulmonary vascular smooth muscle tissue in the PAH lung (bar  =  1∶400).</p