Changes in Alternative Splicing as Pharmacodynamic Markers for Sudemycin D6

Objective: The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. Methods: Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. Results: Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment. However, lymphocytes in blood respond slower than immortalized cultured cells. Conclusions: Exon skipping in the DUSP11 and SRRM1 pre-mRNAs are pharmacodynamic markers for sudemycin D6 treatment and show effects beginning at 9 hours after treatment

Lines pinning lines

A line g is a transversal to a family F of convex polytopes in 3-dimensional space if it intersects every member of F. If, in addition, g is an isolated point of the space of line transversals to F, we say that F is a pinning of g. We show that any minimal pinning of a line by convex polytopes such that no face of a polytope is coplanar with the line has size at most eight. If, in addition, the polytopes are disjoint, then it has size at most six. We completely characterize configurations of disjoint polytopes that form minimal pinnings of a line.Comment: 27 pages, 10 figure

Coloring translates and homothets of a convex body

We obtain improved upper bounds and new lower bounds on the chromatic number as a linear function of the clique number, for the intersection graphs (and their complements) of finite families of translates and homothets of a convex body in \RR^n.Comment: 11 pages, 2 figure

The Fermat-Torricelli problem in normed planes and spaces

We investigate the Fermat-Torricelli problem in d-dimensional real normed spaces or Minkowski spaces, mainly for d=2. Our approach is to study the Fermat-Torricelli locus in a geometric way. We present many new results, as well as give an exposition of known results that are scattered in various sources, with proofs for some of them. Together, these results can be considered to be a minitheory of the Fermat-Torricelli problem in Minkowski spaces and especially in Minkowski planes. This demonstrates that substantial results about locational problems valid for all norms can be found using a geometric approach

Exosomal cell-to-cell transmission of alpha synuclein oligomers

Background: Aggregation of alpha-synuclein (αsyn) and resulting cytotoxicity is a hallmark of sporadic and familial Parkinson’s disease (PD) as well as dementia with Lewy bodies, with recent evidence implicating oligomeric and pre-fibrillar forms of αsyn as the pathogenic species. Recent in vitro studies support the idea of transcellular spread of extracellular, secreted αsyn across membranes. The aim of this study is to characterize the transcellular spread of αsyn oligomers and determine their extracellular location. Results: Using a novel protein fragment complementation assay where αsyn is fused to non-bioluminescent amino-or carboxy-terminus fragments of humanized Gaussia Luciferase we demonstrate here that αsyn oligomers can be found in at least two extracellular fractions: either associated with exosomes or free. Exosome-associated αsyn oligomers are more likely to be taken up by recipient cells and can induce more toxicity compared to free αsyn oligomers. Specifically, we determine that αsyn oligomers are present on both the outside as well as inside of exosomes. Notably, the pathway of secretion of αsyn oligomers is strongly influenced by autophagic activity. Conclusions: Our data suggest that αsyn may be secreted via different secretory pathways. We hypothesize that exosome-mediated release of αsyn oligomers is a mechanism whereby cells clear toxic αsyn oligomers when autophagic mechanisms fail to be sufficient. Preventing the early events in αsyn exosomal release and uptake by inducing autophagy may be a novel approach to halt disease spreading in PD and other synucleinopathies

Insight into Sulfur Confined in Ultramicroporous Carbon

Here, we provide a deeper insight into the state of sulfur confined in ultramicroporous carbon (UMC) and clarify its electrochemical reaction mechanism with lithium by corroborating the results obtained using various experimental techniques, such as X-ray photoelectron spectroscopy, electron energy loss spectroscopy, in situ Raman spectroscopy, and in situ electrochemical impedance spectroscopy. In combination, these results indicate that sulfur in UMC exists as linear polymeric sulfur rather than smaller allotropes. The electrochemical reactivity of lithium with sulfur confined in UMC (pore size ≤0.7 nm) is different from that of sulfur confined in microporous carbon (≤2 nm, or ultramicroporous carbon containing significant amount of micropores) and mesoporous carbon (>2 nm). The observed quasi-solid-state reaction of lithium with sulfur in UMC with a single voltage plateau during the discharge/charge process is due to the effective separation of solvent molecules from the active material. The size of carbon pores plays a vital role in determining the reaction path of lithium with sulfur confined in UMC

Hadron Spectroscopy with Dynamical Chirally Improved Fermions

We simulate two dynamical, mass degenerate light quarks on 16^3x32 lattices with a spatial extent of 2.4 fm using the Chirally Improved Dirac operator. The simulation method, the implementation of the action and signals of equilibration are discussed in detail. Based on the eigenvalues of the Dirac operator we discuss some qualitative features of our approach. Results for ground state masses of pseudoscalar and vector mesons as well as for the nucleon and delta baryons are presented.Comment: 26 pages, 17 figures, 10 table

The strong thirteen spheres problem

The thirteen spheres problem is asking if 13 equal size nonoverlapping spheres in three dimensions can touch another sphere of the same size. This problem was the subject of the famous discussion between Isaac Newton and David Gregory in 1694. The problem was solved by Schutte and van der Waerden only in 1953. A natural extension of this problem is the strong thirteen spheres problem (or the Tammes problem for 13 points) which asks to find an arrangement and the maximum radius of 13 equal size nonoverlapping spheres touching the unit sphere. In the paper we give a solution of this long-standing open problem in geometry. Our computer-assisted proof is based on a enumeration of the so-called irreducible graphs.Comment: Modified lemma 2, 16 pages, 12 figures. Uploaded program packag

Prenatal Cocaine Exposure and Its Influence on Pediatric Epigenetic Clocks and Epigenetic Scores in Humans

The investigation of the effects of prenatal cocaine exposure (PCE) on offspring has been inconsistent, with few studies investigating biological outcomes in humans. We profiled genome-wide DNA methylation (DNAm) of umbilical cord blood (UCB) from newborns with (n = 35) and without (n = 47) PCE. We used DNAm data to (1) assess pediatric epigenetic clocks at birth and (2) to estimate epigenetic scores (ES) for lifetime disorders. We generated gestational epigenetic age estimates (DNAmGA) based on Knight and Bohlin epigenetic clocks. We also investigated the association between DNAmGA and UCB serum brain-derived neurotrophic factor (BDNF) levels. Considering the large-scale DNAm data availability and existing evidence regarding PCE as a risk for health problems later in life, we generated ES for tobacco smoking, psychosis, autism, diabetes, and obesity. A gene ontology (GO) analysis on the CpGs included in the ES with group differences was performed. PCE was associated with lower DNAmGA in newborns, and this effect remained significant when controlling for potential confounders, such as blood cell type composition predicted by DNAm and obstetric data. DNAmGA was negatively correlated with BDNF levels in the serum of UCB. Higher tobacco smoking, psychosis, and diabetes ES were found in the PCE group. The GO analysis revealed GABAergic synapses as a potential pathway altered by PCE. Our findings of decelerated DNAmGA and ES for adverse phenotypes associated with PCE, suggest that the effects of gestational cocaine exposure on the epigenetic landscape of human newborns are detectable at birth

Multimodal imaging of pancreatic beta cells in vivo by targeting transmembrane protein 27 (TMEM27)

Aims/hypothesis: Non-invasive diagnostic tools specific for pancreatic beta cells will have a profound impact on our understanding of the pathophysiology of metabolic diseases such as diabetes. The objective of this study was to use molecular imaging probes specifically targeting beta cells on human samples and animal models using state-of-the-art imaging modalities (fluorescence and PET) with preclinical and clinical perspective. Methods: We generated a monoclonal antibody, 8/9-mAb, targeting transmembrane protein 27 (TMEM27; a surface N-glycoprotein that is highly expressed on beta cells), compared its expression in human and mouse pancreas, and demonstrated beta cell-specific binding in both. In vivo imaging was performed in mice with subcutaneous insulinomas overexpressing the human TMEM27 gene, or transgenic mice with beta cell-specific hTMEM27 expression under the control of rat insulin promoter (RIP-hTMEM27-tg), using fluorescence and radioactively labelled antibody, followed by tissue ex vivo analysis and fluorescence microscopy. Results: Fluorescently labelled 8/9-mAb showed beta cell-specific staining on human and mouse pancreatic sections. Real-time PCR on islet cDNA indicated about tenfold higher expression of hTMEM27 in RIP-hTMEM27-tg mice than in humans. In vivo fluorescence and PET imaging in nude mice with insulinoma xenografts expressing hTMEM27 showed high 8/9-mAb uptake in tumours after 72h. Antibody homing was also observed in beta cells of RIP-hTMEM27-tg mice by in vivo fluorescence imaging. Ex vivo analysis of intact pancreas and fluorescence microscopy in beta cells confirmed these findings. Conclusions/interpretation: hTMEM27 constitutes an attractive target for in vivo visualisation of pancreatic beta cells. Studies in mouse insulinoma models and mice expressing hTMEM27 demonstrate the feasibility of beta cell-targeted in vivo imaging, which is attractive for preclinical investigations and holds potential in clinical diagnostic