Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape.

Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are prevalent at centromeres across taxa and represent a potential mechanism for promoting transcription to aid in CENP-A incorporation or for generating RNA transcripts to maintain centromere integrity. Here, we probe into the transcription and RNA localization of the centromere-enriched retroelement G2/Jockey-3 (hereafter referred to as Jockey-3 ) in Drosophila melanogaster , currently the only in vivo model with assembled centromeres. We find that Jockey-3 is a major component of the centromeric transcriptome and produces RNAs that localize to centromeres in metaphase. Leveraging the polymorphism of Jockey-3 and a de novo centromere system, we show that these RNAs remain associated with their cognate DNA sequences in cis , suggesting they are unlikely to perform a sequence-specific function at all centromeres. We show that Jockey-3 transcription is positively correlated with the presence of CENP-A, and that recent Jockey-3 transposition events have occurred preferentially at CENP-A-containing chromatin. We propose that Jockey-3 contributes to the epigenetic maintenance of centromeres by promoting chromatin transcription, while inserting preferentially within these regions, selfishly ensuring its continued expression and transmission. Given the conservation of retroelements as centromere components through evolution, our findings have broad implications in understanding this association in other species.

Normalization of clonal diversity in gene therapy studies using shape constrained splines.

Viral vectors are used to insert genetic material into semirandom genomic positions of hematopoietic stem cells which, after reinfusion into patients, regenerate the entire hematopoietic system. Hematopoietic cells originating from genetically modified stem cells will harbor insertions in specific genomic positions called integration sites, which represent unique genetic marks of clonal identity. Therefore, the analysis of vector integration sites present in the genomic DNA of circulating cells allows to determine the number of clones in the blood ecosystem. Shannon diversity index is adopted to evaluate the heterogeneity of the transduced population of gene corrected cells. However, this measure can be affected by several technical variables such as the DNA amount used and the sequencing depth of the library analyzed and therefore the comparison across samples may be affected by these confounding factors. We developed an advanced spline-regression approach that leverages on confounding effects to provide a normalized entropy index. Our proposed method was first validated and compared with two state of the art approaches in a specifically designed in vitro assay. Subsequently our approach allowed to observe the expected impact of vector genotoxicity on entropy level decay in an in vivo model of hematopoietic stem cell gene therapy based on tumor prone mice.

The biocompatibility of rapidly degrading polymeric stents in porcine carotid arteries.

The goal of this study was to evaluate the biocompatibility of materials for use in fully bioabsorbable vascular stents. 10:90 poly(L-lactic-co-glycolic acid) (10:90 L-PLGA), 85:15 poly(L-lactic-co-glycolic acid) (85:15 L-PLGA), polydioxanone (PDO), and poly-L-lactic acid (L-PLA) polymers were chosen as materials. Polymeric fibers were woven into a braided structure with a mass equivalent to or greater than that expected for a vascular stent, secured to balloon-expandable bare metal stents and implanted into porcine carotid arteries. The in vivo response was analyzed at 30 and 90 days by angiography, histopathology, and histomorphometry. All vessels were patent at 30 and 90 days. Injury score and neointima formation was mild for all samples. The faster-degrading 10:90 L-PLGA had the highest inflammatory response at 30 days, but was completely absorbed with minimal inflammation and neointimal formation at 90 days. PDO showed signs of partial absorption at 90 days, while 85:15 L-PLGA and L-PLA demonstrated minimal absorption at 30 and 90 days. The inflammatory response to these three groups was similar over the experimental period. Using a robust materials-testing platform, we demonstrated long-term patency and intravascular biocompatibility of bioabsorbable polymers with varying rates of resorption. The data point to biocompatibility of a polymeric stent in the vascular space that is fully absorbable in less than a year.

A free terminal carboxylate group is required for PhrA pentapeptide inhibition of RapA phosphatase.

In the Bacillus subtilis phosphorelay signal transduction system for sporulation initiation, signals competing with the differentiation process are interpreted by aspartyl-phosphate phosphatases that specifically dephosphorylate the Spo0F or Spo0A response regulators. The RapA phosphatase is regulated by the PhrA pentapeptide that directly and specifically inhibits its activity. PhrA specificity for RapA inhibition is dependent upon the amino acid sequence of the peptide. Here we show that the pentapeptide affinity for the phosphatase requires a free carboxylate group at the C-terminal amino acid. A free C-terminal carboxylic acid PhrA pentapeptide inhibits RapA phosphatase activity at a 1:1 ratio and it is approximately 200 fold more active than a C-terminal amide peptide. Therefore, coordination of the terminal carboxylate group appears to be critical for peptide binding to RapA.

Magnetic resonance imaging findings of amygdala-anterior hippocampus shrinkage in male patients with schizophrenia.

Recent magnetic resonance imaging (MRI) studies found abnormalities of medial temporal lobe and basal ganglia structures. We used an inversion recovery (IR) protocol with the assistance of the Talairach atlas to identify neuroanatomical regions of interest in 19 male schizophrenic patients and 14 matched control subjects. The patient group showed smaller amygdala-hippocampus volume as compared with normal control subjects. This finding was more pronounced for the left side, although no diagnosis X side interaction was present. Third ventricle volume was also enlarged in schizophrenic patients. Trends toward an overall reduction of basal ganglia (striatum and lenticular nucleus) and limbic structures and toward an increase in ventricle-brain ratio were also seen. The study confirms previous evidence of mesial temporal lobe shrinkage, more evident on the left side in a group of relapsing noninstitutionalized male schizophrenic patients.