Browsing by Subject "RNAseq"

Now showing 1 - 5 of 5
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    A Cell Proliferation and Inflammatory Signature is Induced by Lawsonia intracellularis Infection in Swine
    (2018-07-24) Leite, Fernando, L; Abrahante, Juan, E; Vasquez, Erika; Vannucci, Fabio; Gebhart, Connie, J; Nathan, Winkelman; Mueller, Adam; Jerry, Torrinson; Rambo, Zachary; Isaacson, Richard, E; isaac015@umn.edu; Isaacson, Richard, E
    Lawsonia intracellularis causes porcine proliferative enteropathy. This is an enteric disease characterized by thickening of the wall of the ileum that leads to decreased growth and diarrhea of animals. In this study, we investigated the host response to L. intracellularis infection by performing transcriptomic and pathway analysis of intestinal tissue in groups of infected and non-infected animals at 14, 21 and 28 days post challenge. The data deposited here are BAM files.
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    Genetics of Resistance to Fusarium Head Blight and Spot Blotch in Hordeum
    (2016-05) Haas, Matthew
    Fusarium head blight (FHB) and spot blotch are two important diseases of barley (Hordeum vulgare) in the Upper Midwest. FHB is caused by Fusarium graminearum which produces deoxynivalenol (DON), a toxin harmful to humans and animals. To characterize the genetic architecture of resistance to FHB and DON accumulation, two wild barley (PI 466423 and W-365) accessions with partial resistance were used as donor parents in advanced backcross populations with six-rowed Minnesota malting barley cultivars. The largest effect quantitative trait locus (QTL) identified in the populations was mapped at or near the photoperiod response gene Ppd-H1, which affects heading date and plant height. This result suggests that the QTL for reduced FHB and DON are a pleiotropic effect of that locus. For over 50 years, spot blotch, caused by Cochliobolus sativus, has been controlled in the Upper Midwest through the deployment of durable resistance derived from the breeding line NDB112. Recently, C. sativus isolates (e.g. ND4008) with virulence for the NDB112 resistance have been reported in the region. PI 466423 is resistant to isolate ND4008; therefore, the Rasmusson/PI 466423 population was used to map QTL for resistance to virulent isolate. Four resistance QTL were identified in chromosomes 1H, 2H, 4H, and 5H. The QTL on chromosomes 1H, 4H, and 5H were contributed by PI 466423, while the one on chromosome 2H was contributed by Rasmusson. A gamma radiation-induced susceptibility mutant from cultivar Morex was used in an RNAseq experiment to study the early infection response of barley to C. sativus. Differential expression analysis between the two genotypes revealed a role for lipid signaling in the resistance response, which may activate the jasmonic acid pathway.
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    Geobacter sulfurreducens inner membrane cytochrome transcriptional and phenotypic data
    (2021-06-15) Joshi, Komal; Chan, Chi Ho; Bond, Daniel R; dbond@umn.edu; Bond, Daniel R; Bond Lab
    Geobacter sulfurreducens utilizes extracellular electron acceptors such as Mn(IV), Fe(III), syntrophic partners, and electrodes that vary from +0.4 to −0.3 V vs. Standard Hydrogen Electrode (SHE), representing a potential energy span that should require a highly branched electron transfer chain. Here we describe CbcBA, a bc-type cytochrome essential near the thermodynamic limit of respiration when acetate is the electron donor. Mutants lacking cbcBA ceased Fe(III) reduction at −0.21 V vs. SHE, could not transfer electrons to electrodes between −0.21 and −0.28 V, and could not reduce the final 10% – 35% of Fe(III) minerals. As redox potential decreased during Fe(III) reduction, cbcBA was induced with the aid of the regulator BccR to become one of the most highly expressed genes in G. sulfurreducens. Growth yield (CFU/mM Fe(II)) was 112% of WT in ∆cbcBA, and deletion of cbcL (an unrelated bc-cytochrome essential near −0.15 V) in ΔcbcBA increased yield to 220%. Together with ImcH, which is required at high redox potentials, CbcBA represents a third cytoplasmic membrane oxidoreductase in G. sulfurreducens. This expanding list shows how metal-reducing bacteria may constantly sense redox potential to adjust growth efficiency in changing environments.
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    Implications of clustering in cell type annotation with single cell RNAseq data
    (2022-07) Cepela, Jason
    Single cell RNA-sequencing (scRNAseq) provides high-resolution data necessary to investigate rare cell populations contributing to treatment resistance commonly observed in many forms of cancer. Generally, the first step in this investigation is understanding the cellular makeup of a tissue sample by annotating cells based on their RNA expression profile. In this study, we compare cluster-based cell type annotation methods with approaches that annotate cells individually without employing clustering. Cell type frequencies are identified across 22 ovarian cancer tumor samples sequenced using 10x Genomics single cell RNA sequencing. These approaches are compared to identify biases, enable the identification of rare cell populations, and ultimately allow the correlation of cellular profiles to clinical response with the long-term goal of using these data to tailor treatment options and improve patient outcomes.
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    Transcriptomics analysis (RNA-sequencing) of Methanococcus maripaludis wild-type strain and moeA deletion mutant.
    (2023-10-02) Abdul Halim, Mohd Farid; Costa, Kyle C.; Fonseca, Dallas; Niehaus, Thomas; kcosta@umn.edu; Costa, Kyle C.; University of Minnesota Costa Lab
    Transcriptomic analysis of total RNA for Methanococcus maripaludis grown in McCas-formate medium. The data compared the RNA abundance between the wild-type strain and the mutant strain with the gene encoding molybdopterin molybdotransferase (moeA, MMP1619) deletion. Released for the submission of manuscript for publication.