Barrier mechanisms in neonatal stroke.

Clinical data continue to reveal that the incidence of perinatal stroke is high, similar to that in the elderly. Perinatal stroke leads to significant morbidity and severe long-term neurological and cognitive deficits, including cerebral palsy. Experimental models of cerebral ischemia in neonatal rodents have shown that the pathophysiology of perinatal brain damage is multifactorial. Cerebral vasculature undergoes substantial structural and functional changes during early postnatal brain development. Thus, the state of the vasculature could affect susceptibility of the neonatal brain to cerebral ischemia. In this review, we discuss some of the most recent findings regarding the neurovascular responses of the immature brain to focal arterial stroke in relation to neuroinflammation. We also discuss a possible role of the neonatal blood-CSF barrier in modulating inflammation and the long-term effects of early neurovascular integrity after neonatal stroke on angiogenesis and neurogenesis

Mechanisms of Lead, Copper, and Zinc Retention by Phosphate Rock

The solid–liquid interface reaction between phosphate rock (PR) and metals (Pb, Cu, and Zn) was studied. Phosphate rock has the highest affinity for Pb, followed by Cu and Zn, with sorption capacities of 138, 114, and 83.2 mmol/kg PR, respectively. In the Pb–Cu–Zn ternary system, competitive metal sorption occurred with sorption capacity reduction of 15.2%, 48.3%, and 75.6% for Pb, Cu, and Zn, respectively compared to the mono-metal systems. A fractional factorial design showed the interfering effect in the order of Pb \u3e Cu \u3e Zn. Desorption of Cu and Zn was sensitive to pH change, increasing with pH decline, whereas Pb desorption was decreased with a strongly acidic TCLP extracting solution (pH=2.93). The greatest stability of Pb retention by PR can be attributed to the formation of insoluble fluoropyromorphite [Pb10(PO4)6F2], which was primarily responsible for Pb immobilization (up to 78.3%), with less contribution from the surface adsorption or complexation (21.7%), compared to 74.5% for Cu and 95.7% for Zn. Solution pH reduction during metal retention and flow calorimetry analysis both supported the hypothesis of retention of Pb, Cu, and Zn by surface adsorption or complexation. Flow calorimetry indicated that Pb and Cu adsorption onto PR was exothermic, while Zn sorption was endothermic. Our research demonstrated that PR can effectively remove Pb from solutions, even in the presence of other heavy metals (e.g. Cu, Zn). ‘‘Capsule’’: Phosphate-induced formation of fluoropyromorphite is primarily responsible for Pb immobilization by phosphate rock, whereas Cu and Zn retention is mainly attributable to the surface adsorption or complexation

Experimental Evaluation of Wireless Simulation Assumptions

All analytical and simulation research on ad hoc wireless networks must necessarily model radio propagation using simplifying assumptions. We provide a comprehensive review of six assumptions that are still part of many ad hoc network simulation studies, despite increasing awareness of the need to represent more realistic features, including hills, obstacles, link asymmetries, and unpredictable fading. We use an extensive set of measurements from a large outdoor routing experiment to demonstrate the weakness of these assumptions, and show how these assumptions cause simulation results to differ significantly from experimental results. We close with a series of recommendations for researchers, whether they develop protocols, analytic models, or simulators for ad hoc wireless networks

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied TranspoSeq, a computational framework that identifies retrotransposon insertions from sequencing data, to whole genomes from 200 tumor/normal pairs across 11 tumor types as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Project. In addition to novel germline polymorphisms, we find 810 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal, and endometrial carcinomas. Many somatic retrotransposon insertions occur in known cancer genes. We find that high somatic retrotransposition rates in tumors are associated with high rates of genomic rearrangement and somatic mutation. Finally, we developed TranspoSeq-Exome to interrogate an additional 767 tumor samples with hybrid-capture exome data and discovered 35 novel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of the PTEN tumor suppressor gene. The results of this large-scale, comprehensive analysis of retrotransposon movement across tumor types suggest that somatic retrotransposon insertions may represent an important class of structural variation in cancer.National Cancer Institute (U.S.) (grant U24CA143867)National Cancer Institute (U.S.) (grant U24CA126546

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 95 tumor genome sequences from breast, head and neck, colorectal, and prostate carcinomas, and from melanoma, multiple myeloma, and chronic lymphocytic leukemia. We discover three genomic factors that are significantly correlated with the distribution of rearrangements: replication time, transcription rate, and GC content. The correlation is complex, and different patterns are observed between tumor types, within tumor types, and even between different types of rearrangements. Mutations in the APC gene correlate with and, hence, potentially contribute to DNA breakage in late-replicating, low %GC, untranscribed regions of the genome. We show that somatic rearrangements display less microhomology than germline rearrangements, and that breakpoint loci are correlated with local hypermutability with a particular enrichment for C ↔ G transversions

Mechanisms of lead, copper, and zinc retention by phosphate rock

Mitteilungen des Förderkreises Archive und Bibliotheken zur Geschichte der Arbeiterbewegung, Nr. 37 / März 2010. Ausführliche Rezension hier in der Tageszeitung junge welt vom Montag 29. März 2010

Demarcation of Sepsis-Induced Peripheral and Central Acidosis with pH (Low) Insertion Cycle Peptide

Acidosis is a key driver for many diseases, including cancer, sepsis, and stroke. The spatiotemporal dynamics of dysregulated pH across disease remain elusive, and current diagnostic strategies do not provide localization of pH alterations. We sought to explore if PET imaging using hydrophobic cyclic peptides that partition into the cellular membrane at low extracellular pH (denoted as pH [low] insertion cycles, or pHLIC) can permit accurate in vivo visualization of acidosis. Methods: Acid-sensitive cyclic peptide c[E4W5C] pHLIC was conjugated to bifunctional maleimide-NO2A and radiolabeled with 64Cu (half-life, 12.7 h). C57BL/6J mice were administered lipopolysaccharide (15 mg/kg) or saline (vehicle) and serially imaged with [64Cu]Cu-c[E4W5C] over 24 h. Ex vivo autoradiography was performed on resected brain slices and subsequently stained with cresyl violet to enable high-resolution spatial analysis of tracer accumulation. A non–pH-sensitive cell-penetrating control peptide (c[R4W5C]) was used to confirm specificity of [64Cu]Cu-c[E4W5C]. CD11b (macrophage/microglia) and TMEM119 (microglia) immunostaining was performed to correlate extent of neuroinflammation with [64Cu]Cu-c[E4W5C] PET signal. Results: [64Cu]Cu-c[E4W5C] radiochemical yield and purity were more than 95% and more than 99%, respectively, with molar activity of more than 0.925 MBq/nmol. Significantly increased [64Cu]Cu-c[E4W5C] uptake was observed in lipopolysaccharide-treated mice (vs. vehicle) within peripheral tissues, including blood, lungs, liver, and small intestines (P \u3c 0.001–0.05). Additionally, there was significantly increased [64Cu]Cu-c[E4W5C] uptake in the brains of lipopolysaccharide-treated animals. Autoradiography confirmed increased uptake in the cerebellum, cortex, hippocampus, striatum, and hypothalamus of lipopolysaccharide-treated mice (vs. vehicle). Immunohistochemical analysis revealed microglial or macrophage infiltration, suggesting activation in brain regions containing increased tracer uptake. [64Cu]Cu-c[R4W5C] demonstrated significantly reduced uptake in the brain and periphery of lipopolysaccharide mice compared with the acid-mediated [64Cu]Cu-c[E4W5C] tracer. Conclusion: Here, we demonstrate that a pH-sensitive PET tracer specifically detects acidosis in regions associated with sepsis-driven proinflammatory responses. This study suggests that [64Cu]Cu-pHLIC is a valuable tool to noninvasively assess acidosis associated with both central and peripheral innate immune activation

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.National Human Genome Research Institute (U.S.) (HG03067-05

Le Forum, Vol. 44 #1

https://digitalcommons.library.umaine.edu/francoamericain_forum/1103/thumbnail.jp