Project description:This experiment tested the affects of different diets on mice prostate metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
Project description:This experiment tested the affects of different diets on mice esophagus metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
Project description:MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.
Project description:Azithromycin (AZM) reduces pulmonary inflammation and exacerbations in chronic obstructive pulmonary disease patients with emphysema. The antimicrobial effects of AZM on the lung microbiome are not known and may contribute to its beneficial effects. Methods. Twenty smokers with emphysema were randomized to receive AZM 250 mg or placebo daily for 8 weeks. Bronchoalveolar lavage (BAL) was performed at baseline and after treatment. Measurements included: rDNA gene quantity and sequence. Results. Compared with placebo, AZM did not alter bacterial burden but reduced α-diversity, decreasing 11 low abundance taxa, none of which are classical pulmonary pathogens. Conclusions. AZM treatment the lung microbiome Randomized trial comparing azithromycin (AZM) treatment with placebo for eight weeks. Bronchoalveolar lavage (BAL) samples were obtained before and after treatment to explore the effects of AZM on microbiome, in the lower airways. 16S rRNA was quantified and sequenced (MiSeq) The amplicons from total 39 samples are barcoded and the barcode is provided in the metadata_complete.txt file.
Project description:Bovine genital campylobacteriosis (BGC) is a globally important venereal disease of cattle caused by Campylobacter fetus subspecies (C. fetus) venerealis. Diagnosis of BGC is highly challenging due to the lack of accurate diagnostic tests. To characterise the immune biomarkers for C. fetus venerealis infection, a total of twelve six cycling heifers were selected and categorised as vaccinated (n=6) with Vibrovax® (Zoetis™) and unvaccinated (n=6). All heifers were oestrous synchronised with a double dose of prostaglandin (PGF2) 11 days apart and when in oestrous intravaginally challenged with 2.7x109 CFU live C. fetus venerealis. Relative abundances of serum proteins were calculated using sequential window acquisition of all theoretical fragment ion spectra coupled to tandem mass spectrometry (SWATH-MS) for all heifers at three timepoints: pre-challenge, post-challenge and post-recovery.
Project description:With annually 2.56 million deaths worldwide, pneumonia is one of the leading causes of death. Most frequent causative pathogens are Streptococcus pneumoniae and influenza A virus. Lately, the interaction between pathogens, the host and its microbiome gained more attention. A healthy microbiome is known to enhance the immune response towards pathogens, however, our knowledge on how infections affect the microbiome is still scarce. In this study, a meta-omics approach was used to investigate the impact of S. pneumoniae and influenza A virus infection on structure and function of the respiratory and gastrointestinal microbiomes of mice. In particular, the taxonomic composition of the respiratory microbiome was less affected by bacterial colonization and viral infection compared to S. pneumoniae infection. Pneumococcal pneumonia led to reduction of bacterial families and lower diversity in the respiratory microbiome, whereas diversity/richness was unaffected following H1N1 infection. Within the gastrointestinal microbiome we found exclusive changes in structure and function depending on the pneumonia inducing pathogen. Exemplarily, increased abundance of Akkermansiaceae and Spirochaetaceae, as well as decreased amounts of Clostridiaceae in response to S. pneumoniae infection, while increased presence of Enterococcaceae and Staphylococcaceae was specific for viral-induced pneumonia. Investigation of the intestinal microbiomes functional composition revealed reduced expression of flagellin and rubrerythrin and increased levels of ATPase during pneumococcal infection, while increased amounts of acetyl-CoA acetyltransferase and, enoyl-CoA transferase were unique after H1N1 infection. The identification of specific taxonomical and functional profiles during infection with a respective pathogen could deliver new insights in the role of the microbiome during disease and be beneficial for discrimination of pneumococcal- or viral-induced pneumonia.
Project description:The aim of our study is to investigate the effects of carbon ion and photon irradiation on A549 tumor cells and analyse how these effects are altered by PML knockdown. Therefore we created PML knockdown A549 cells (shPML) and irradiated them with either 2Gy carbon ion or 6Gy Photon (bioequivalent doses). 4 days after irradiation microarray analysis was performed. All experiments were performed in 3 biological replicates and control groups were transduced with an empty vector.
Project description:To better understand proteostasis in health and disease, determination of protein half-lives is essential. We improved the precision and accuracy of peptide-ion intensity based quantification in order to enable accurate determination of protein turnover in non-dividing cells using dynamic-SILAC. This enabled precise and accurate protein half-life determination ranging from 10 to more than 1000 hours. We achieve good proteomic coverage ranging from four to six thousand proteins in several types of non-dividing cells, corresponding to a total of 9699 unique proteins over the entire dataset. Good agreement was observed in half-lives between B-cells, natural killer cells and monocytes, while hepatocytes and mouse embryonic neurons showed substantial differences. Our comprehensive dataset enabled extension and statistical validation of the previous observation that subunits of protein complexes tend to have coherent turnover. Furthermore, we observed complex architecture dependent turnover within complexes of the proteasome and the nuclear pore complex. Our method is broadly applicable and might be used to investigate protein turnover in various cell types.
Project description:Metabolic and endocrine disturbances are common in donkeys. This species has an inherent ability to thrive with limited and poor-quality roughage. Donkeys are extremely efficient in energy storage and mobilization, which predisposes to hyperlipemia, obesity, and metabolic syndrome. The prevalence of dyslipidemias is higher in donkeys than other equids, which is more evident under stressful conditions. Diagnosis of endocrine and metabolic disorders in donkeys should be based on species-specific information considering that differences in a multitude of variables compared with horses have been demonstrated. Protocols to assess endocrine disorders (e.g., pituitary pars intermedia dysfunction, metabolic syndrome, and thyroid illness) are unavailable, and extrapolation from horse data can be misleading. Treatment guidelines for these conditions in donkeys are currently not reported. On the other hand, the typical stoic and hardy behavior of donkeys can hinder prompt diagnosis of gastrointestinal problems, specifically colic, which is commonly caused by dental issues in this species. Moreover, subclinical gastric ulcer syndrome appears to be a common pathology in this species, especially in working donkeys. Highlights • Donkeys are different to horses.• Numerous physiological and clinic-pathologic idiosyncrasies are reported in horses.• Data published for horses should not be extrapolated for donkeys.• Specific reference ranges, doses, and protocols have to be used for donkeys.