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Background In order to develop treatments or preventive measures for auditory hair cell loss, an understanding of both the process of auditory hair cell regeneration and factors that influence this process, is needed. Our previous microarray analysis showed that growth hormone (GH) was significantly upregulated during zebrafish auditory hair cell regeneration, coupled with cell proliferation [1,2]. We further tested the effects of GH on zebrafish auditory hair cell regeneration by injecting GH after sound exposure and found that GH can efficiently promote post-trauma auditory hair cell regeneration, which may be achieved through stimulating proliferation and suppressing apoptosis [3]. In the current study, we used Next Generation Sequencing (NGS) to examine the possible GH pathways involved in zebrafish auditory hair cell regeneration.

Background Toxoplasmosis, caused by the protozoan parasite Toxoplasma gondii is a major cause of morbidity and mortality in patients with AIDS and an important cause of miscarriage, stillbirth and congenital disease in newborns. Previous studies have provided evidence that dietary supplementation with vitamin E and selenium is harmful during experimental toxoplasmosis in mice, whereas a diet deficient in vitamin E and selenium results in decreased numbers of tissue cysts in the brain and dramatically reduced brain pathology. The overall goal of the present study was to determine the impact of dietary supplementation with antioxidants on gene expression in the brains of non-infected mice and in mice infected with T. gondii using microarray analysis. RNA was isolated from the brains of C57BL/6 mice, and an Agilent Oligo Whole Mouse Genome Microarray (Agilent Technologies, Inc.) was performed. A total of 48 chips were normalized by Z ratios and the Data Driven Harr Fisch Normalization methods. Differentially expressed genes were identified by applying thresholds to identify significant values and the results were compared between the normalization methods. These differentially expressed genes and their respective fold change ratios were used in Ingenuity Pathway Analysis (IPA) software to analyze the pathways involved with these genes.

Material and methods The Wizard007 bacteriophage was isolated from a soil sample taken at N36° 49’36.8” W87° 29’42.5” in Hopkinsville, KY. It was plaque purified on Mycobacterium smegmatis and DNA was isolated using the Promega Wizard DNA purification kit. The DNA was sequenced at the Virginia Commonwealth University by Roche 454 DNA sequencing. The genome quality was confirmed in Consed [1] and found to be 51,034 bp in length. Genes were called from the assembled sequence with a workflow consisting of Glimmer [2], GeneMark [3], tRNAscan [4], and SDFinder to identify potential gene features. Gbrowse [5], Apollo [6], and BLAST [7] were used to call and annotate genes. A 10 base 3’ overhang was found at the ends by ligating the genomic DNA and sequencing a PCR product produced across the ligated ends.