Browsing by Subject "Pyrosequencing"

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  • Sundar, Isaac K.; Yin, Qiangzong; Baier, Brian S.; Yan, Li; Mazur, Witold; Li, Dongmei; Susiarjo, Martha; Rahman, Irfan (2017)
    Background: Epigenetics changes have been shown to be affected by cigarette smoking. Cigarette smoke (CS)-mediated DNA methylation can potentially affect several cellular and pathophysiological processes, acute exacerbations, and comorbidity in the lungs of patients with chronic obstructive pulmonary disease (COPD). We sought to determine whether genome-wide lung DNA methylation profiles of smokers and patients with COPD were significantly different from non-smokers. We isolated DNA from parenchymal lung tissues of patients including eight lifelong non-smokers, eight current smokers, and eight patients with COPD and analyzed the samples using Illumina's Infinium HumanMethylation450 BeadChip. Results: Our data revealed that the differentially methylated genes were related to top canonical pathways (e.g., G beta gamma signaling, mechanisms of cancer, and nNOS signaling in neurons), disease and disorders (organismal injury and abnormalities, cancer, and respiratory disease), and molecular and cellular functions (cell death and survival, cellular assembly and organization, cellular function and maintenance) in patients with COPD. The genome-wide DNA methylation analysis identified suggestive genes, such as NOS1AP, TNFAIP2, BID, GABRB1, ATXN7, and THOC7 with DNA methylation changes in COPD lung tissues that were further validated by pyrosequencing. Pyrosequencing validation confirmed hyper-methylation in smokers and patients with COPD as compared to non-smokers. However, we did not detect significant differences in DNA methylation for TNFAIP2, ATXN7, and THOC7 genes in smokers and COPD groups despite the changes observed in the genome-wide analysis. Conclusions: Our study suggests that DNA methylation in suggestive genes, such as NOS1AP, BID, and GABRB1 may be used as epigenetic signatures in smokers and patients with COPD if the same is validated in a larger cohort. Future studies are required to correlate DNA methylation status with transcriptomics of selective genes identified in this study and elucidate their role and involvement in the progression of COPD and its exacerbations.
  • Santalahti, Minna; Sun, Hui; Sietiö, Outi-Maaria; Köster, Kajar; Berninger, Frank; Laurila, Tuomas; Pumpanen, Jukka; Heinonsalo, Jussi (2018)
    Reindeer grazing in northern boreal zone affects forest floor vegetation heavily and alters the vegetation structure. However, the effect of grazing on soil fungal communities, which are intimately linked to plants, is not currently known. Therefore, our objectives were to investigate changes caused by reindeer grazing on soil fungal communities, litter decomposition rate and litter degrading extracellular enzyme activities. The study was conducted in four areas divided into grazed and non-grazed sites (all together 38 sample plots) in northern boreal forests in Finnish Lapland. Fungal communities were analyzed from humus with high-throughput sequencing technology (454-pyrosequencing), and litter mass loss and extracellular enzyme activities were analyzed after a one-year litterbag experiment. The results showed that grazing significantly affected the fungal community structure and the abundance of certain fungal genera and species. Grazing also decreased laccase and enhanced cellobiohydrolase I activities from the litterbags. Our study is one of the first to describe detailed fungal community composition in sites with long-term history of reindeer grazing and exclusion. Our results indicate that reindeer grazing alter fungal community structure and litter degradation related enzyme activities in the northern boreal forest soils.