26 research outputs found
Fluid-crystal coexistence for proteins and inorganic nanocolloids: dependence on ionic strength
We investigate theoretically the fluid-crystal coexistence of solutions of
globular charged nanoparticles like proteins and inorganic colloids. The
thermodynamic properties of the fluid phase are computed via the optimized
Baxter model. This is done specifically for lysozyme and silicotungstates for
which the bare adhesion parameters are evaluated via the experimental second
virial coefficients. The electrostatic free energy of the crystal is
approximated by supposing the cavities in the interstitial phase between the
particles are spherical in form. In the salt-free case a Poisson-Boltzmann
equation is solved to calculate the effective charge on a particle and a Donnan
approximation is used to derive the chemical potential and osmotic pressure in
the presence of salt. The coexistence data of lysozyme and silicotungstates are
analyzed within this scheme, especially with regard to the ionic-strength
dependence of the chemical potentials. The latter agree within the two phases
provided some upward adjustment of the effective charge is allowed for.Comment: 15 pages, 9 figure
Identification of Stably Expressed lncRNAs as Valid Endogenous Controls for Profiling of Human Glioma
Background: Recent research indicates that long non-coding RNAs (lncRNA) represent a new family of RNAs that is of fundamental importance for controlling transcription and translation. Thereby, there is increasing evidence that lncRNAs are also important in tumourigenesis. Thereby valid expression profiling using quantitative PCR requires suitable, stably expressed normalisers to achieve reliable and reproducible data. However, no systematic analysis of suitable references in lncRNA studies in human glioma has been performed yet. Methods: In this study, we investigated 90 lncRNAs in 30 tissue specimen for the expression stability in human diffuse astrocytoma (WHO-Grade II),anaplastic astrocytoma (WHO-Grade III) and glioblastoma (WHO-Grade IV) both alone as well as in comparison with normal white matter. Our identification procedure included a rigorous bioinformatical selection process that resulted in the inclusion of only highly abundant, equally expressed lncRNAs for further analysis. Additionally, lncRNAs were classified according to their stability value using the NormFinder algorithm. Results: We identified 24 appropriate normalisers suitable for studies in diffuse astrocytoma, 22 for studies in anaplastic astrocytoma and 12 for studies in glioblastoma. Comparing all three glioma entities 7 lncRNAs showed stable expression levels. Addition of normal brain tissue resulted in only 4 suitable lncRNAs. Conclusions: Our findings indicate that 4 lncRNAs (HOXA6as, H19 upstream conserved 1 and 2, Zfhx2as and BC200) are suitable as normalisers in glioma and normal brain. These lncRNAs may thus be regarded as universal references being applicable for the accurate normalisation of lncRNA expression profiling in various glioma (WHO-Grades II-IV) alone and in combination with brain tissue. This enables to perform valid longitudinal studies, e.g. of glioma before and after malignisation to identify changes of lncRNA expressions probably driving malignant transformation
Surgeon experience in glioblastoma surgery of the elderly : a multicenter, retrospective cohort study
Purpose To assess the impact of individual surgeon experience on overall survival (OS), extent of resection (EOR) and surgery-related morbidity in elderly patients with glioblastoma (GBM), we performed a retrospective case-by-case analysis. Methods GBM patients aged≥65 years who underwent tumor resection at two academic centers were analyzed. The experience of each neurosurgeon was quantifed in three ways: (1) total number of previously performed glioma surgeries (lifetime experience); (2) number of surgeries performed in the previous fve years (medium-term experience) and (3) in the last two years (short-term experience). Surgeon experience data was correlated with survival (OS) and surrogate parameters for surgical quality (EOR, morbidity). Results 198 GBM patients (median age 73.0 years, median preoperative KPS 80, IDH-wildtype status 96.5%) were included. Median OS was 10.0 months (95% CI 8.0–12.0); median EOR was 89.4%. Surgery-related morbidity afected 19.7% patients. No correlations of lifetime surgeon experience with OS (P=.693), EOR (P=.693), and surgery-related morbidity (P=.435) were identifed. Adjuvant therapy was associated with improved OS (PConclusion Less experienced neurosurgeons achieve similar surgical results and outcome in elderly GBM patients within the setting of academic teaching hospitals. Adjuvant treatment and avoidance of surgery-related morbidity are crucial forgenerating a treatment beneft for this cohort.Peer reviewe
The orbit and stellar masses of the archetype colliding-wind binary WR 140
We present updated orbital elements for the Wolf-Rayet (WR) binary WR 140 (HD
193793; WC7pd + O5.5fc). The new orbital elements were derived using previously
published measurements along with 160 new radial velocity measurements across
the 2016 periastron passage of WR 140. Additionally, four new measurements of
the orbital astrometry were collected with the CHARA Array. With these
measurements, we derive stellar masses of
and . We also include a discussion of the
evolutionary history of this system from the Binary Population and Spectral
Synthesis (BPASS) model grid to show that this WR star likely formed primarily
through mass loss in the stellar winds, with only a moderate amount of mass
lost or transferred through binary interactions.Comment: 10 pages, 5 figure
DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex
Background: Epigenome-wide association studies (EWAS) based on human brain samples allow a deep and direct understanding of epigenetic dysregulation in Alzheimer's disease (AD).However, strong variation of cell-type proportions across brain tissue samples represents a significant source of data noise.Here, we report the first EWAS based on sorted neuronal and non-neuronal (mostly glia) nuclei from postmortem human brain tissues. Results: We show that cell sorting strongly enhances the robust detection of disease-related DNA methylation changes even in a relatively small cohort.We identify numerous genes with eell-type-specific methylation signatures and document differential methylation dynamics associated with aging specifically in neurons such as CLU, SYNJ2 and NCOR2 or in glia RAI1,CXXC5 and INPP5A.Further, we found neuron or glia-specific associations with AD Braak stage progression at genes such as MCF2L,ANK1, MAP2, LRRC8B, STK32C and S100B.A comparison of our study with previous tissue-based EWAS validates multiple AD-associated DNA methylation signals and additionally specifies their origin to neuron, e.g., HOXA3 or glia (ANK1). In a meta-analysis, we reveal two novel previously unrecognized methylation changes at the key AD risk genes APP and ADAM17. Conclusions: Our data highlight the complex interplay between disease, age and cell-type-specific methylation changes in AD risk genes thus offering new perspectives for the validation and interpretation of large EWAS results
Genetic Characterization of Ten-Eleven-Translocation Methylcytosine Dioxygenase Alterations in Human Glioma
Abstract The molecular mechanisms leading to brain tumors still remain unclear. Nevertheless, there is increasing evidence that epigenetic effects play crucial roles in tumor development and progression. Thereby, 5-hydroxymethylcytosine (5hmC) represents a further base modification of cytosine besides 5-methylcytosine (5mC). In addition to the role of 5hmC as an intermediate in demethylation, 5hmC is of reasonable importance for cellular control. Previous studies showed that loss of 5hmC is a hallmark of human malignancies, e.g. in glioma, melanoma, and myeloid tumors. In myeloid malignancies studies showed that loss of 5hmC was due to mutations within ten-eleven-translocation (TET) genes, enzymes being responsible for conversion of 5mC to 5hmC. Nevertheless, till date there are no genetic characterizatio
Methylome Profiling of PD-L1-Expressing Glioblastomas Shows Enrichment of Post-Transcriptional and RNA-Associated Gene Regulation
Glioblastomas are the most frequent primary brain tumors in adults. They show highly malignant behavior and devastating outcomes. Since there are still no targeted therapies available, median survival remains in the range of 12 to 15 months for glioblastoma patients. Programmed Cell Death Ligand 1 (PD-L1) is a promising novel candidate in precision medicine. Here, we performed integrated epigenome-wide methylation profiling of 866,895 methylation-specific sites in 20 glioblastoma samples comparing PD-L1 high- (i.e., TPS (tumor proportion score) > 30%) and PD-L1 low-expressing glioblastomas (i.e., TPS < 10%). We found 12,597 significantly differentially methylated CpGs (DMCG) (Δβ ≥ 0.1 and p-value < 0.05) in PD-L1 high- compared with PD-L1 low-expressing glioblastomas. These DMCGs were annotated to 2546 tiling regions, 139 promoters, 107 genes, and 107 CpG islands. PD-L1 high-expressing glioblastomas showed hypomethylation in 68% of all DMCGs. Interestingly, the list of the top 100 significantly differentially methylated genes showed the enrichment of regulatory RNAs with 19 DMCGs in miRNA, snoRNAs, lincRNAs, and asRNAs. Gene Ontology analysis showed the enrichment of post-transcriptional and RNA-associated pathways in the hypermethylated gene regions. In summary, dissecting the methylomes depending on PD-L1 status revealed significant alterations in RNA regulation and novel molecular targets in glioblastomas
Epigenetic dysregulation in the developing Down syndrome cortex
<p>Using Illumina 450K arrays, 1.85% of all analyzed CpG sites were significantly hypermethylated and 0.31% hypomethylated in fetal Down syndrome (DS) cortex throughout the genome. The methylation changes on chromosome 21 appeared to be balanced between hypo- and hyper-methylation, whereas, consistent with prior reports, all other chromosomes showed 3–11 times more hyper- than hypo-methylated sites. Reduced <i>NRSF/REST</i> expression due to upregulation of <i>DYRK1A</i> (on chromosome 21q22.13) and methylation of REST binding sites during early developmental stages may contribute to this genome-wide excess of hypermethylated sites. Upregulation of <i>DNMT3L</i> (on chromosome 21q22.4) could lead to <i>de novo</i> methylation in neuroprogenitors, which then persists in the fetal DS brain where <i>DNMT3A</i> and <i>DNMT3B</i> become downregulated. The vast majority of differentially methylated promoters and genes was hypermethylated in DS and located outside chromosome 21, including the protocadherin gamma (<i>PCDHG</i>) cluster on chromosome 5q31, which is crucial for neural circuit formation in the developing brain. Bisulfite pyrosequencing and targeted RNA sequencing showed that several genes of <i>PCDHG</i> subfamilies A and B are hypermethylated and transcriptionally downregulated in fetal DS cortex. Decreased <i>PCDHG</i> expression is expected to reduce dendrite arborization and growth in cortical neurons. Since constitutive hypermethylation of <i>PCDHG</i> and other genes affects multiple tissues, including blood, it may provide useful biomarkers for DS brain development and pharmacologic targets for therapeutic interventions.</p