Spatial and temporal evolution of distal 10q deletion,a prognostically unfavorable event in diffuse low-grade gliomas

Background

The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behavior and can thereby complement the prognostically favorable 1p/19q co-deletion.

Results

Genome-wide, 50 base pair single-end sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analyzed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors.

Conclusions

CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0471-6) contains supplementary material, which is available to authorized users.     

Quantitative Analyse von Korallengemeinschaften des Sanganeb-Atolls (mittleres Rotes Meer). II. Vergleich mit einem Riffareal bei Aqaba (nördliches Rotes Meer) am Nordrande des indopazifischen Riffgürtels

Quantitative studies of coral communities in the central and northern Red Sea were designed for comparison of the community structure in both areas. The central Red Sea provides reef-building Scleractinia and reef-inhabiting Alcyonaria with optimal temperature conditions, whereas the north tip of the Gulf of Aqaba (29°30 N) represents the northernmost outpost of coral reefs in the Indian Ocean. It is generally assumed that coral diversity decreases towards the margins of the global reef-belt. In the Red Sea, generic diversity of hermatypic Scleractinia slightly decreases from the central to the northern part (51 : 48 genera); but cnidarian species abundance (species number per 25 m² area) was found to increase from 62 to 98 species and the Shannon-Wiener diversity index increased from 2.58 to 3.67 with regard to colony number. The mean colony size was 189 cm² at Sanganeb-Atoll, but only 52 cm² at Aqaba. The mean numbers of colonies were inversely related: 662 per 25 m² at Sanganeb-Atoll and 2028 at Aqaba. Uninhabited parts of the studied areas amounted to 47 % at Sanganeb-Atoll and to 56 % at Aqaba. The community structure of the studied areas indicates that occasional perturbations prevent the progress of the community towards a low-diversity equilibrium state. Since severe hydrodynamic damage is extremely rare in 10 m depth, major disturbances may occur by sedimentation, by the interference of grazers (e. g.Diadema setosum) and due to overgrowth by space-competitors (mainly soft corals). These events are to be regarded as throwbacks in the process of monopolization of the area by well adapted species. Recovery from such perturbations (i.e. recolonization of dead areas) obviously takes place at different velocities in the northern and central Red Sea, for the mean water temperature at Aqaba is 5 °C lower than in the central Red Sea. Hence the process of taking over a given space by a few species proceeds further in the central Red Sea than at its northern end. The increase in diversity per area towards high latitudes is comparable to that with depth. It is concluded from the great number of species at Aqaba that these reefs mark the northernmost outpost of the Indian Ocean only geographically but not ecophysiologically; they would occur at even higher latitudes, if the Gulf of Aqaba extended farther north.     

Recycling cell surface glycoproteins undergo limited oligosaccharide reprocessing in LEC1 mutant Chinese hamster ovary cells

The ability of particular cell surface glycoproteins to recycle and become exposed to individual Golgi enzymes has been demonstrated. This study was designed to determine whether endocytic trafficking includes significant reentry into the overall oligosaccharide processing pathway. The Lec1 mutant of Chinese hamster ovary (CHO) cells lack N - acetylglucosaminyltransferase I (GlcNAc-TI) activity resulting in surface expression of incompletely processed Man5GlcNAc2 N -linked oligosaccharides. An oligosaccharide tracer was created by exoglycosylation of cell surface glycoproteins with purified porcine GlcNAc-TI and UDP-[3H]GlcNAc. Upon reculturing, all cell surface glycoproteins that acquired [3H]GlcNAc were acted upon by intracellular mannosidase II, the next enzyme in the Golgi processing pathway of complex N -linked oligosaccharides (t1/2= 3-4 h). That all radiolabeled cell surface glycoproteins were included in this endocytic pathway indicates a common intracellular compartment into which endocytosed cell surface glycoproteins return. Significantly, no evidence was found for continued oligosaccharide processing consistent with transit through the latter cisternae of the Golgi apparatus. These data indicate that, although recycling plasma membrane glycoproteins can be reexposed to individual Golgi-derived enzymes, significant reentry into the overall contiguous processing pathway is not evident.      

Visual contributions to human self-motion perception during horizontal body rotation

It is still an enigma how human subjects combine visual and vestibular inputs for their self-motion perception. Visual cues have the benefit of high spatial resolution but entail the danger of self motion illusions. We performed psychophysical experiments (verbal estimates as well as pointer indications of perceived self-motion in space) in normal subjects (Ns) and patients with loss of vestibular function (Ps). Subjects were presented with horizontal sinusoidal rotations of an optokinetic pattern (OKP) alone (visual stimulus; 0.025-3.2 Hz; displacement amplitude, 8 degrees) or in combinations with rotations of a Bárány chair (vestibular stimulus; 0.025-0.4 Hz; +/- 8 degrees). We found that specific instructions to the subjects created different perceptual states in which their self-motion perception essentially reflected three processing steps during pure visual stimulation: i) When Ns were primed by a procedure based on induced motion and then they estimated perceived self-rotation upon pure optokinetic stimulation (circular vection, CV), the CV has a gain close to unity up to frequencies of almost 0.8 Hz, followed by a sharp decrease at higher frequencies (i.e., characteristics resembling those of the optokinetic reflex, OKR, and of smooth pursuit, SP). ii) When Ns were instructed to "stare through" the optokinetic pattern, CV was absent at high frequency, but increasingly developed as frequency was decreased below 0.1 Hz. iii) When Ns "looked at" the optokinetic pattern (accurately tracked it with their eyes) CV was usually absent, even at low frequency. CV in Ps showed similar dynamics as in Ns in condition i), independently of the instruction. During vestibular stimulation, self-motion perception in Ns fell from a maximum at 0.4 Hz to zero at 0.025 Hz. When vestibular stimulation was combined with visual stimulation while Ns "stared through" OKP, perception at low frequencies became modulated in magnitude. When Ns "looked" at OKP, this modulation was reduced, apart from the synergistic stimulus combination (OKP stationary) where magnitude was similar as during "staring". The obtained gain and phase curves of the perception were incompatible with linear systems prediction. We therefore describe the present findings by a non-linear dynamic model in which the visual input is processed in three steps: i) It shows dynamics similar to those of OKR and SP; ii) it is shaped to complement the vestibular dynamics and is fused with a vestibular signal by linear summation; and iii) it can be suppressed by a visual-vestibular conflict mechanism when the visual scene is moving in space. Finally, an important element of the model is a velocity threshold of about 1.2 degrees/s which is instrumental in maintaining perceptual stability and in explaining the observed dynamics of perception. We conclude from the experimental and theoretical evidence that self-motion perception normally is related to the visual scene as a reference, while the vestibular input is used to check the kinematic state of the scene; if the scene appears to move, the visual signal becomes suppressed and perception is based on the vestibular cue.     

How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

Comparative docking is based on experimentally determined structures of protein-protein complexes (templates), following the paradigm that proteins with similar sequences and/or structures form similar complexes. Modeling utilizing structure similarity of target monomers to template complexes significantly expands structural coverage of the interactome. Template-based docking by structure alignment can be performed for the entire structures or by aligning targets to the bound interfaces of the experimentally determined complexes. Systematic benchmarking of docking protocols based on full and interface structure alignment showed that both protocols perform similarly, with top 1 docking success rate 26%. However, in terms of the models' quality, the interface-based docking performed marginally better. The interface-based docking is preferable when one would suspect a significant conformational change in the full protein structure upon binding, for example, a rearrangement of the domains in multidomain proteins. Importantly, if the same structure is selected as the top template by both full and interface alignment, the docking success rate increases 2-fold for both top 1 and top 10 predictions. Matching structural annotations of the target and template proteins for template detection, as a computationally less expensive alternative to structural alignment, did not improve the docking performance. Sophisticated remote sequence homology detection added templates to the pool of those identified by structure-based alignment, suggesting that for practical docking, the combination of the structure alignment protocols and the remote sequence homology detection may be useful in order to avoid potential flaws in generation of the structural templates library.     

Spin trapping of oxygen and carbon-centered free radicals in ischemic canine myocardium

Oxygen free radical injury has been postulated to occur during myocardial ischemia. We have used Electron Spin Resonance and Spin Trapping techniques to directly demonstrate the production of carbon-centered (R.) and oxygen-centered lipid radical (RO.) in ischemic canine heart. In addition, venous effluent from the ischemic region showed that conjugated dienes (lipid peroxidation products) increased with ischemic duration. Our results suggest that the formation of the oxygen-centered and carbon-centered lipid radical species during ischemia are a consequence of oxy-radical peroxidation of myocardial membrane lipids.