52 research outputs found
Progressive GAA·TTC Repeat Expansion in Human Cell Lines
Trinucleotide repeat expansion is the genetic basis for a sizeable group of inherited neurological and neuromuscular disorders. Friedreich ataxia (FRDA) is a relentlessly progressive neurodegenerative disorder caused by GAA·TTC repeat expansion in the first intron of the FXN gene. The expanded repeat reduces FXN mRNA expression and the length of the repeat tract is proportional to disease severity. Somatic expansion of the GAA·TTC repeat sequence in disease-relevant tissues is thought to contribute to the progression of disease severity during patient aging. Previous models of GAA·TTC instability have not been able to produce substantial levels of expansion within an experimentally useful time frame, which has limited our understanding of the molecular basis for this expansion. Here, we present a novel model for studying GAA·TTC expansion in human cells. In our model system, uninterrupted GAA·TTC repeat sequences display high levels of genomic instability, with an overall tendency towards progressive expansion. Using this model, we characterize the relationship between repeat length and expansion. We identify the interval between 88 and 176 repeats as being an important length threshold where expansion rates dramatically increase. We show that expansion levels are affected by both the purity and orientation of the repeat tract within the genomic context. We further demonstrate that GAA·TTC expansion in our model is independent of cell division. Using unique reporter constructs, we identify transcription through the repeat tract as a major contributor to GAA·TTC expansion. Our findings provide novel insight into the mechanisms responsible for GAA·TTC expansion in human cells
An Active Site Aromatic Triad in Escherichia coli DNA Pol IV Coordinates Cell Survival and Mutagenesis in Different DNA Damaging Agents
DinB (DNA Pol IV) is a translesion (TLS) DNA polymerase, which inserts a
nucleotide opposite an otherwise replication-stalling
N2-dG lesion in vitro, and
confers resistance to nitrofurazone (NFZ), a compound that forms these lesions
in vivo. DinB is also known to be part of the cellular
response to alkylation DNA damage. Yet it is not known if DinB active site
residues, in addition to aminoacids involved in DNA synthesis, are critical in
alkylation lesion bypass. It is also unclear which active site aminoacids, if
any, might modulate DinB's bypass fidelity of distinct lesions. Here we
report that along with the classical catalytic residues, an active site
“aromatic triad”, namely residues F12, F13, and Y79, is critical for
cell survival in the presence of the alkylating agent methyl methanesulfonate
(MMS). Strains expressing dinB alleles with single point
mutations in the aromatic triad survive poorly in MMS. Remarkably, these strains
show fewer MMS- than NFZ-induced mutants, suggesting that the aromatic triad, in
addition to its role in TLS, modulates DinB's accuracy in bypassing
distinct lesions. The high bypass fidelity of prevalent alkylation lesions is
evident even when the DinB active site performs error-prone NFZ-induced lesion
bypass. The analyses carried out with the active site aromatic triad suggest
that the DinB active site residues are poised to proficiently bypass distinctive
DNA lesions, yet they are also malleable so that the accuracy of the bypass is
lesion-dependent
Cancer Biomarker Discovery: The Entropic Hallmark
Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases
Studies on epidemiology, clinical markers and pathological alterations in equines trypanosomosis in semi-arid zone of northern plains of India
Intra-articular dexmedetomidine in knee arthroscopy: A systematic review and meta-analysis
Variations in morpho-physiological and yield attributes of kabuli chickpea genotypes in relation to seed size
- …