Sanna Abrahamsson
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View article: Whole genome transcriptional analysis of intestinal biopsies and blood cells indicate genes involved in antioxidant defense systems and antigen presentation in the pathogenesis of celiac disease
Whole genome transcriptional analysis of intestinal biopsies and blood cells indicate genes involved in antioxidant defense systems and antigen presentation in the pathogenesis of celiac disease Open
Background: Celiac disease is closely linked to HLA-risk haplotypes, but non-HLA genes also play a significant role in disease susceptibility. In this study, we explore the molecular pathways involved in celiac disease by analyzing the dif…
View article: Landscape of Epstein-Barr virus gene expression and perturbations in cancer
Landscape of Epstein-Barr virus gene expression and perturbations in cancer Open
Epstein-Barr virus (EBV) is the causative agent for multiple neoplastic diseases of epithelial and lymphocytic origin1-3. The heterogeneity of the viral elements expressed and the mechanisms by which these coding and non-coding genes maint…
View article: Enrichment Reveals Extensive Integration of Hepatitis B Virus DNA in Hepatitis Delta Virus-Infected Patients
Enrichment Reveals Extensive Integration of Hepatitis B Virus DNA in Hepatitis Delta Virus-Infected Patients Open
Background Hepatitis B virus (HBV) DNA may become integrated into the human genome of infected human hepatocytes. Expression of integrations can produce the surface antigen (HBsAg) that is required for synthesis of hepatitis D virus (HDV) …
View article: Transplantation of gut microbiota from old mice into young healthy mice reduces lean mass but not bone mass
Transplantation of gut microbiota from old mice into young healthy mice reduces lean mass but not bone mass Open
Aging is associated with low bone and lean mass as well as alterations in the gut microbiota (GM). In this study, we determined whether the reduced bone mass and relative lean mass observed in old mice could be transferred to healthy young…
View article: Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells
Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells Open
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lea…
View article: Dietary restriction and medical therapy drives PPARα-regulated improvements in early diabetic kidney disease in male rats
Dietary restriction and medical therapy drives PPARα-regulated improvements in early diabetic kidney disease in male rats Open
The attenuation of diabetic kidney disease (DKD) by metabolic surgery is enhanced by pharmacotherapy promoting renal fatty acid oxidation (FAO). Using the Zucker Diabetic Fatty and Zucker Diabetic Sprague Dawley rat models of DKD, we condu…
View article: Transcriptomics unravels molecular changes associated with cilia and COVID-19 in chronic rhinosinusitis with nasal polyps.
Transcriptomics unravels molecular changes associated with cilia and COVID-19 in chronic rhinosinusitis with nasal polyps. Open
Chronic rhinosinusitis with nasal polyps is a common condition where the pathogenesis is largely unknown. We measured total gene expression in nasal mucosa using RNA sequencing technology. Pathways involving “Ciliated epithelial cells” wer…
View article: Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery
Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery Open
Background Intrauterine infection and inflammation caused by microbial transfer from the vagina are believed to be important factors causing spontaneous preterm delivery (PTD). Multiple studies have examined the relationship between the ce…
View article: Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells
Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells Open
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lea…
View article: Detection of latent Epstein-Barr virus gene expression in single-cell sequencing of peripheral blood mononuclear cells
Detection of latent Epstein-Barr virus gene expression in single-cell sequencing of peripheral blood mononuclear cells Open
Epstein-Barr virus (EBV) DNA is regularly found in the blood of patients with EBV associated diseases and occasionally in healthy individuals. However, EBV infected primary B-lymphocytes have not yet been detected using scRNA seq. Here, we…
View article: Medications Activating Tubular Fatty Acid Oxidation Enhance the Protective Effects of Roux-en-Y Gastric Bypass Surgery in a Rat Model of Early Diabetic Kidney Disease
Medications Activating Tubular Fatty Acid Oxidation Enhance the Protective Effects of Roux-en-Y Gastric Bypass Surgery in a Rat Model of Early Diabetic Kidney Disease Open
Background Roux-en-Y gastric bypass surgery (RYGB) improves biochemical and histological parameters of diabetic kidney disease (DKD). Targeted adjunct medical therapy may enhance renoprotection following RYGB. Methods The effects of RYGB a…
View article: Additional file 3 of PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data
Additional file 3 of PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data Open
Additional file 3: Tables S1–S5. Sequencing data summary statistics and output from PΨFinder of case samples, downsampled data and simulated data. Benchmarking results.
View article: A primary nasopharyngeal three-dimensional air-liquid interface cell culture model of the pseudostratified epithelium reveals differential donor- and cell type-specific susceptibility to Epstein-Barr virus infection
A primary nasopharyngeal three-dimensional air-liquid interface cell culture model of the pseudostratified epithelium reveals differential donor- and cell type-specific susceptibility to Epstein-Barr virus infection Open
Epstein-Barr virus (EBV) is a ubiquitous γ-herpesvirus with latent and lytic cycles. EBV replicates in the stratified epithelium but the nasopharynx is also composed of pseudostratified epithelium with distinct cell types. Latent infection…
View article: Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education
Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education Open
Motivation Due to the worldwide COVID-19 pandemic, new strategies had to be adopted to move from classroom-based education to online education, in a very short time. The lack of time to set up these strategies, hindered a proper design of …
View article: RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling
RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling Open
Cancer cell lines allow the identification of clinically relevant alterations and the prediction of drug response. However, sequencing data for hepatobiliary cancer cell lines in general, and particularly gallbladder cancer (GBC), are spar…
View article: A three-dimensional Air-Liquid Interface Culture Model for the Study of Epstein-Barr virus Infection in the Nasopharynx
A three-dimensional Air-Liquid Interface Culture Model for the Study of Epstein-Barr virus Infection in the Nasopharynx Open
Epstein-Barr virus (EBV) infection is ubiquitous in humans and is associated with the cancer, nasopharyngeal carcinoma. EBV replicates in the differentiated layers of stratified keratinocytes but whether the other cell types of the airway …
View article: Deep sequencing of liver explant transcriptomes reveals extensive expression from integrated hepatitis B virus DNA
Deep sequencing of liver explant transcriptomes reveals extensive expression from integrated hepatitis B virus DNA Open
Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). Integration of HBV DNA into the human genome may contribute to oncogenesis and to the production of the hepatitis B surface antigen (HBsAg). Whether integrations c…
View article: Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics
Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics Open
Background Infection in the central nervous system is a severe condition associated with high morbidity and mortality. Despite ample testing, the majority of encephalitis and meningitis cases remain undiagnosed. Metagenomic sequencing of c…