532 research outputs found
Members of the miR-290 cluster modulate in vitro differentiation of mouse embryonic stem cells
No full textWe report the biological effects of miR-290 cluster via gain-of-function or loss-of-function experiments in mouse embryonic stem cells (ESCs) cultured under differentiation conditions. Under these conditions we found that overexpression of miR-290 cluster in ESCs cannot prevent downregulation of Oct-4, but inhibition results in earlier down regulation of Oct-4 compared with the negative control. In consistence with previous findings that report ectopic expression of Brachyury during gastrulation in Argonaute-2 KO mice due to impaired miRNA function, we show that miR-290 cluster regulates negatively differentiation of ESCs towards mesodermal and germ cell lineage. These results suggest that although incapable to maintain pluripotent state alone, miR-290 cluster inhibits ESC differentiation and it is involved in the pathways controlling mesoderm and primordial germ cell differentiation. Finally, we provide proofs that members of this cluster target Dkk-1 gene, a Wnt pathway inhibitor, and affect this pathway, which can partially explain why miR-290 cluster favours pluripotency against differentiation. (C) 2009 International Society of Differentiation. Published by Elsevier Ltd. All rights reserved
Multipotent adult germline stem cells and embryonic stem cells have similar microRNA profiles
No full textSpermatogonial stem cells (SSCs) isolated from the adult mouse testis and cultured have been shown to respond to culture conditions and become pluripotent, so called multipotent adult germline stem cells (maGSCs). microRNAs (miRNAs) belonging to the 290 and 302 miRNA clusters have been previously classified as embryonic stem cell (ESC) specific. Here, we show that these miRNAs generally characterize pluripotent cells. They are expressed not only in ESCs but also in maGSCs as well as in the F9 embryonic carcinoma cell (ECC) line. In addition, we tested the time-dependent influence of different factors that promote loss of pluripotency on levels of these miRNAs in all three pluripotent cell types. Despite the differences regarding time and extent of differentiation observed between ESCs and maGSCs, expression profiles of both miRNA families showed similarities between these two cell types, suggesting similar underlying mechanisms in maintenance of pluripotency and differentiation. Our results indicate that the 290-miRNA family is connected with Oct-4 and maintenance of the pluripotent state. In contrast, members of the 302-miRNA family are induced during first stages of in vitro differentiation in all cell types tested. Therefore, detection of miRNAs of miR-302 family in pluripotent cells can be attributed to the proportion of spontaneously differentiating cells in cultures of pluripotent cells. These results are consistent with ESC-like nature of maGSCs and their potential as an alternative source of pluripotent cells from non-embryonic tissues
Identification of the role of A-to-I editing in SINE RNA stability
No full textSINE RNAs are non-coding RNAs produced by Short Interspersed Nuclear Elements
(SINEs), with SINEs of the B2 and Alu family being among the most frequent in mice and humans,
respectively. Previous studies have shown that the processing of B2 SINE RNAs results in changes
to the cellular stress response in mice through changes in the activation of stress response genes
that are targeted by B2 RNAs. Thus, SINE RNA stability plays an important role in the regulation
of gene expression. However, the factors that affect this processing are unclear. In this thesis, I
investigated whether adenosine to inosine RNA modifications affects the stability of the B2 SINE
RNA. To this end, optimization of solid phase RNA synthesis protocols for long RNAs that can
incorporate the addition of inosines into the RNA sequence to generate in vitro synthesized B2
SINE RNA fragments with specific adenosine to inosine edits. In combination with ligation,
complete in vitro synthesized B2 SINE RNAs were edited at specific positions and their processing
rates could be compared to control synthesized B2 SINE RNA. Subsequently, expanded research
into a cell culture model of neural cells and investigated how inhibition of A to I editing affects
B2 RNA stability. The above study shows that A to I editing indeed affects the stability of the B2
SINE RNAs, and provides new insight into the mechanisms that affect overall SINE RNA stabilit
Role of non-coding RNAs in amyloid beta neuropathology and Alzheimer's disease
No full textAlzheimer’s disease has a complex etiology and pathology. At the forefront of the disease is the amyloid beta neuropathology where amyloid plaques accumulate as the disease progresses, amidst a state of molecular dysfunction. A relatively understudied component of the molecular pathogenesis underlying Alzheimer’s disease is the potential role of non-coding RNAs as well as their RNA modifications. Here, an integrative molecular and computational approach is used to study the role of non-coding RNAs in the APP NL-G-F Alzheimer’s disease mouse model and human Alzheimer’s disease patients, unveiling that non-coding RNAs transcribed from Short Interspersed Nuclear Elements (SINEs) in mice and humans are aberrantly processed in connection with alterations in gene expression. As well, adenosine to inosine RNA editing is shown to be dysregulated in SINE RNAs and non-coding RNAs involved in protein expression are differentially modified in the hippocampus of APP NL-G-F mice
The Δρομοδείχτης της Ελλάδος of 1824 and Athanasios Stageirites (Τίτλος περίληψης)
No full textσ. [281]-290Κείμενο στα ελληνικά με περίληψη στα αγγλικά με τον τίτλο: The Δρομοδείχτης της Ελλάδος of 1824 and Athanasios StageiritesThe article first examines the close relationship between the publication “Δρομοδείχτης της Ελλάδος” [1824] and the publication “Ηπειρωτικά” (1819) by Athanasios Stageirites and then suggests that Athanasios Stageirites is the likeliest author of the “Δρομοδείχτης της Ελλάδος”.Δωδώνη: Τεύχος Πρώτο: επιστημονική επετηρίδα του Τμήματος Ιστορίας και Αρχαιολογίας της Φιλοσοφικής Σχολής του Πανεπιστημίου Ιωαννίνων; Τόμ. 43-44 (2014-2015
Identification of the mode of regulation of SINE sense and antisense RNAs during cellular response to the stress
No full textA large portion of the mammalian genome comprises non-coding sequences, such as B2 SINEs, which play a role in gene regulation during stress. Despite their significance, the regulatory mechanisms governing SINEs remain unclear. This study explores the relationship between sense and antisense B2 SINE transcripts in a mouse cell line model exposed to heat shock and other stress conditions, including transfection with locked nucleic acids and in vitro transcribed B2. The results of qPCR and sequencing data analysis demonstrate an inverse relationship between the expression levels of sense and antisense B2 SINEs, with these effects being transient and diminishing over time. This indicates a complex, dynamic regulatory network that likely involves additional factors or feedback loops
Dissecting the role of B2 SINE RNA processing in activation of stress response genes in mouse brain amyloid and aging pathology
No full textAlzheimer's disease (AD) is a neurodegenerative disorder that results in impairment of learning and memory. Previous work in mice has shown that learning correlates with hippocampus–specific changes in expression of stress response genes (SRGs) and that excess expression of SRGs results in apoptosis. Many mouse SRGs are regulated by a non-coding SINE RNA called B2, but it is unclear how SINE RNAs contribute to AD overall. In this work we show via RNAseq that there is abnormal hyperactivation of SRGs caused by dysregulation of the B2-mediated stress response mouse amyloid-aging pathology. We also show that B2 RNA degradation is abnormally high during active neurodegeneration and that the increase in B2 degradation is due to Hsf1-mediated cleavage of B2 RNA during amyloid beta-induced stress. Our research reveals a novel connection between abnormal SINE RNA processing, SRG hyper-activation, and amyloid-aging pathology. Further study of SINE RNAs may elucidate new AD therapies
Comparative metagenomics in livestock production antimicrobial resistance
No full textAntimicrobial resistance is a global health problem. It affects people suffering from infections and is also able to jeopardize livestock food security. With the rise of this problem, steps have been taken to reduce the use of antimicrobials in livestock production. “Raised Without” antimicrobial livestock production has been described to reduce antimicrobial resistance by removing the selective pressure which would reinforce resistance gene conservation in bacterial genomes. This thesis’ goal was to investigate the extent to which this statement is true. First, optimization of several different methods was used to detect resistance genes and associate them with mobile genetic elements to determine their transferability potential. Taking those methods and applying them to a beef cattle dataset revealed that an absence of antimicrobial use is likely not the cause of differences observed in antimicrobial resistance gene and microbiota abundance. Macrolide resistance genes are more likely to be stably conserved than tetracycline resistance genes. Expanding that analysis to include broiler chickens and swine both raised with and without antimicrobials, revealed there to be no difference between antimicrobial management practices unless at specific antimicrobial resistance gene group-levels
Machine learning methods for the prediction of antimicrobial resistance and identification of novel markers of resistance in Escherichia coli
No full textAntimicrobial resistant strains of pathogenic Escherichia coli are a burden on the healthcare system, causing longer hospital stays and increased treatment costs compared to nonresistant strains. The proportion of E. coli infections in Canada caused by resistant strains producing extended-spectrum beta-lactamase rose from 3.4% in 2007 to 11.1% in 2017. Use of most antimicrobials in the treatment of Shiga-toxin producing E. coli infection is not recommended due to their propensity to increase toxin production. Rapid detection of resistant strains would improve both treatment and prevention of this pathogen. With whole genome sequencing (WGS) now ubiquitous in the analyses of outbreak and surveillance samples, in silico methods can be both faster and cheaper than traditional wet-lab methods. In this work, machine learning (ML) classification methods were used for the prediction of antimicrobial resistance and the identification of potentially novel genomic markers of resistance in E. coli.
There are four supplementary files to accompany Chapter 3. Supplementary Figure 1
is the Phylogenetic tree of the 4300 E. coli isolates with Salmonella as an outgroup; it is
coloured by country of origin and serotype and paired with legends for each. Supplementary
Table 1 contains the list of publicly available genomes collected and their corresponding
metadata. Supplementary Table 2 contains the top features extracted from trained machine
learning models and their annotations. Supplementary Table 3 contains the accuracy data
for training machine learning models across a range of 100 to 5000 features. Supplementary
Table 4 contains the complete performance data for the 11-mer and 25-mer machine
learning models
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