Project description:Predictive modeling of wild microbial and viral community dynamics in Pseudoalteromonas sp. 13-15, evaluation using two viral systems under phosphate presence and absence conditions.
Project description:Lung tissues from a mouse model sensitized to SARS-CoV-2 infection were serially collected at different time points for evaluation of transcriptome, proteome and phosphoproteome. We showed the ebb and flow of several host responses in the lung across viral infection. The signaling pathways and kinases regulating networks were alternated at different phases of infection. Our study not only revealed the dynamics of lung pathophysiology and their underlying molecular mechanisms during SARS-CoV-2 infection, but also highlighted some molecules and signaling pathways that might guide future investigations on COVID-19 therapies.
Project description:The primary objective of this prospective observational study is to characterize the gut and oral microbiome as well as the whole blood transcriptome in gastrointestinal cancer patients and correlate these findings with cancer type, treatment efficacy and toxicity. Participants will be recruited from existing clinical sites only, no additional clinical sites are needed.
Project description:The aim with this study was to evaluate the miRNA-transcriptome in whole blood in cats with or without pre-clinical HCM. Twelve age, sex and breed matched cats were included. Six cats were Norwegian forest cats and six were domestic mixed breed cats. Each breed represented with three healthy and three preclinical cats. The intention was to evaluate if there were differences in miRNA-profiles between healthy and affected cats, but also to evaluate breed differences and which potential targets the identified miRNAs might have. Bioinformatical pipeline included: bcl2fastq was used to convert sequence files to fastq-format. CutAdapt for adapter and sequence quality trimming, statification and quality evaluation with STAR, FastQC and MultiQC, followed by miRNA-prediction in miRDeep2. Human miRNA-sequences were used as main reference, along with mouse and dog as additional references. Predicted miRNAs were further evaluated for data stratification in DESeq2, followed by differential evaluation analyses based on single or more complex group models (includinig initeraction model). For target prediction IntaRNA was used to identify potential gene transcripts targeted in the feline genome, based on exported feline 3'UTR-sequences from Ensemble. As a comparison human targets were evaluated based on lists in miRDB, since miRNAs are usually conserved between species and the feline genome is less well annotated compared to the human. The results highlighted the importance of considering breed differences when evaluating circulating miRNAs in feline whole blood. This is of high relevance for studies trying to identify miRNAs as potential biomarkers. Also, our results only identified one miRNA differentially expressed between healthy and pre-clinical HCM cats within the Norwegian Forest cats, also highlighting breed differences. One reason for only identifying one miRNA may be that the cats were in pre-clinical state, instead of in congestive heart failure.
Project description:The outbreak of Coronavirus disease 2019 (COVID-19) throughout the world has caused millions of death, while the dynamics of host responses and the underlying regulation mechanisms during SARS-CoV-2 infection are not well depicted. Lung tissues from a mouse model sensitized to SARS-CoV-2 infection were serially collected at different time points for evaluation of transcriptome, proteome and phosphoproteome. We showed the ebb and flow of several host responses in the lung across viral infection. The signaling pathways and kinases regulating networks were alternated at different phases of infection. Our study not only revealed the dynamics of lung pathophysiology and their underlying molecular mechanisms during SARS-CoV-2 infection, but also highlighted some molecules and signaling pathways that might guide future investigations on COVID-19 therapies.