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1.  CD14, a Key Candidate Gene Associated with Specific Immune Response to Cockroach 
Summary
Background
Sensitization to cockroach allergen is one of the strongest predictors of asthma morbidity, especially among African Americans.
Objective
Our aims were to determine the genomic basis of cockroach sensitization and the specific response to cockroach antigen.
Methods
We investigated the Th1/Th2 cytokine profile of co-cultured plasmacytoid DCs (pDCs) and CD4+ T cells and the “transcript signature” of the immune response to cockroach antigen using high-throughput expression profiling of co-cultured cells.
Results
We observed significantly elevated levels of IL-13, IL-10 and TNF-α, but undetectable levels of IL-12p70 and IFN-α, when cultures were exposed to crude cockroach antigen. A significant difference was observed for IL-13 between cockroach allergic and non-allergic individuals (p = 0.039). Microarray analyses demonstrated a greater response at 48 hours compared to 4 hours, with 50 genes being uniquely expressed in cockroach antigen-treated cells, including CD14, S100A8, CCL8, and IFI44L. The increased CD14 expression was further observed in purified pDCs, human monocytic THP-1 cells, and supernatant of co-cultured pDCs and CD4+ T cells in exposure to cockroach extract. Furthermore, the most differential expression of CD14 between cockroach allergy and non-cockroach allergy was only observed among individuals with the CC “high-risk” genotype of the CD14 -260C/T. Ingenuity Pathways Analysis (IPA) analyses suggested the interferon-signaling as the most significant canonical pathway.
Conclusion
Our results suggest these differentially expressed genes, particularly CD14, and genes in the interferon-signaling pathway may be important candidates for further investigation of their role in the immune response to cockroach allergen.
doi:10.1111/j.1365-2222.2010.03561.x
PMCID: PMC2920999  PMID: 20618347
asthma; CD4+ T cells; CD14; cockroach sensitization; Dendritic cells (DCs); high-throughput expression profiling
2.  Mortality in Late Post-Traumatic Seizures 
Journal of Neurotrauma  2009;26(9):1471-1477.
Abstract
The objective of this study was to examine the mortality rates in individuals with traumatic brain injury (TBI) who were classified as having experienced late post-traumatic seizures (LPTS) in the first 2 years post-TBI compared to those who were seizure-free (non-LPTS). Participants were a pooled sample (n = 508) from two studies which enrolled individuals with TBI who were injured between March 31, 1992 and December 20, 1999. The first sample was made up of individuals enrolled in a study of risk factors for LPTS development; the second sample was composed of individuals enrolled in the TBI National Database from a single rehabilitation center. Seventy-one (14%) participants had LPTS, of which 27% had died at 8–15 years post-injury, as compared to 10% of non-LPTS participants. Individuals with LPTS died at a younger age (54.1 versus 67.7 years; p = 0.01), but there were no statistically significant differences in either time from date of injury to death or highest GCS score in the first 24 h. Causes of death were variable and not specifically related to epilepsy. Of those with LPTS, risk factors for death include advanced age at time of injury and presence of subdural hematoma. The higher mortality rate and death at younger age with variable causes in TBI individuals with LPTS warrant close medical evaluation and monitoring of these individuals, particularly accessibility and compliance with ongoing general medical care, and education of primary care colleagues of the unique needs of this at-risk population.
doi:10.1089/neu.2008.0729
PMCID: PMC2864464  PMID: 19508123
epilepsy; rehabilitation; traumatic brain injury
3.  Make it better but don't change anything 
With massive amounts of data being generated in electronic format, there is a need in basic science laboratories to adopt new methods for tracking and analyzing data. An electronic laboratory notebook (ELN) is not just a replacement for a paper lab notebook, it is a new method of storing and organizing data while maintaining the data entry flexibility and legal recording functions of paper notebooks. Paper notebooks are regarded as highly flexible since the user can configure it to store almost anything that can be written or physically pasted onto the pages. However, data retrieval and data sharing from paper notebooks are labor intensive processes and notebooks can be misplaced, a single point of failure that loses all entries in the volume. Additional features provided by electronic notebooks include searchable indices, data sharing, automatic archiving for security against loss and ease of data duplication. Furthermore, ELNs can be tasked with additional functions not commonly found in paper notebooks such as inventory control. While ELNs have been on the market for some time now, adoption of an ELN in academic basic science laboratories has been lagging. Issues that have restrained development and adoption of ELN in research laboratories are the sheer variety and frequency of changes in protocols with a need for the user to control notebook configuration outside the framework of professional IT staff support. In this commentary, we will look at some of the issues and experiences in academic laboratories that have proved challenging in implementing an electronic lab notebook.
doi:10.1186/1759-4499-1-5
PMCID: PMC2810290  PMID: 20098591
4.  Respiratory Epithelial Gene Expression in Patients with Mild and Severe Cystic Fibrosis Lung Disease 
Despite having identical cystic fibrosis transmembrane conductance regulator genotypes, individuals with ΔF508 homozygous cystic fibrosis (CF) demonstrate significant variability in severity of pulmonary disease. This investigation used high-density oligonucleotide microarray analysis of nasal respiratory epithelium to investigate the molecular basis of phenotypic differences in CF by (1) identifying differences in gene expression between ΔF508 homozygotes in the most severe 20th percentile of lung disease by forced expiratory volume in 1 s and those in the most mild 20th percentile of lung disease and (2) identifying differences in gene expression between ΔF508 homozygotes and age-matched non-CF control subjects. Microarray results from 23 participants (12 CF, 11 non-CF) met the strict quality control guidelines and were used for final data analysis. A total of 652 of the 11,867 genes identified as present in 75% of the samples were significantly differentially expressed in one of the three disease phenotypes: 30 in non-CF, 53 in mild CF, and 569 in severe CF. An analysis of genes differentially expressed by severity of CF lung disease demonstrated significant upregulation in severe CF of genes involved in protein ubiquination (P < 0.04), mitochondrial oxidoreductase activity (P < 0.01), and lipid metabolism (P < 0.03). Analysis of genes with decreased expression in patients with CF compared with control subjects demonstrated significant downregulation of genes involved in airway defense (P < 0.047) and protein metabolism (P < 0.048). This study suggests that differences in CF lung phenotype are associated with differences in expression of genes involving airway defense, protein ubiquination, and mitochondrial oxidoreductase activity and identifies specific new candidate modifiers of the CF phenotype.
doi:10.1165/rcmb.2005-0359OC
PMCID: PMC2643286  PMID: 16614352
cystic fibrosis; gene expression; phenotype; respiratory epithelium

Results 1-4 (4)