Genetics - Getting closer to the whole picture

A quantitative data set of RNA, proteins, and metabolites provides an unprecedented starting point to understand, at a systems level, the effects of perturbations on a cell

TGFβ signaling is associated with changes in inflammatory gene expression and perineuronal net degradation around inhibitory neurons following various neurological insults.

Brain damage due to stroke or traumatic brain injury (TBI), both leading causes of serious long-term disability, often leads to the development of epilepsy. Patients who develop post-injury epilepsy tend to have poor functional outcomes. Emerging evidence highlights a potential role for blood-brain barrier (BBB) dysfunction in the development of post-injury epilepsy. However, common mechanisms underlying the pathological hyperexcitability are largely unknown. Here, we show that comparative transcriptome analyses predict remodeling of extracellular matrix (ECM) as a common response to different types of injuries. ECM-related transcriptional changes were induced by the serum protein albumin via TGFβ signaling in primary astrocytes. In accordance with transcriptional responses, we found persistent degradation of protective ECM structures called perineuronal nets (PNNs) around fast-spiking inhibitory interneurons, in a rat model of TBI as well as in brains of human epileptic patients. Exposure of a naïve brain to albumin was sufficient to induce the transcriptional and translational upregulation of molecules related to ECM remodeling and the persistent breakdown of PNNs around fast-spiking inhibitory interneurons, which was contingent on TGFβ signaling activation. Our findings provide insights on how albumin extravasation that occurs upon BBB dysfunction in various brain injuries can predispose neural circuitry to the development of chronic inhibition deficits

Activity-Dependent Changes in Extracellular Ca2+ and K+ Reveal Pacemakers in the Spinal Locomotor-Related Network

SummaryChanges in the extracellular ionic concentrations occur as a natural consequence of firing activity in large populations of neurons. The extent to which these changes alter the properties of individual neurons and the operation of neuronal networks remains unknown. Here, we show that the locomotor-like activity in the isolated neonatal rodent spinal cord reduces the extracellular calcium ([Ca2+]o) to 0.9 mM and increases the extracellular potassium ([K+]o) to 6 mM. Such changes in [Ca2+]o and [K+]o trigger pacemaker activities in interneurons considered to be part of the locomotor network. Experimental data and a modeling study show that the emergence of pacemaker properties critically involves a [Ca2+]o-dependent activation of the persistent sodium current (INaP). These results support a concept for locomotor rhythm generation in which INaP-dependent pacemaker properties in spinal interneurons are switched on and tuned by activity-dependent changes in [Ca2+]o and [K+]o

TGFβ signaling is associated with changes in inflammatory gene expression and perineuronal net degradation around inhibitory neurons following various neurological insults

Brain damage due to stroke or traumatic brain injury (TBI), both leading causes of serious long-term disability, often leads to the development of epilepsy. Patients who develop post-injury epilepsy tend to have poor functional outcomes. Emerging evidence highlights a potential role for blood- brain barrier (BBB) dysfunction in the development of post-injury epilepsy. However, common mechanisms underlying the pathological hyperexcitability are largely unknown. Here, we show that comparative transcriptome analyses predict remodeling of extracellular matrix (ECM) as a common response to different types of injuries. ECM-related transcriptional changes were induced by the serum protein albumin via TGFβ signaling in primary astrocytes. In accordance with transcriptional responses, we found persistent degradation of protective ECM structures called perineuronal nets (PNNs) around fast-spiking inhibitory interneurons, in a rat model of TBI as well as in brains of human epileptic patients. Exposure of a naïve brain to albumin was sufficient to induce the transcriptional and translational upregulation of molecules related to ECM remodeling and the persistent breakdown of PNNs around fast-spiking inhibitory interneurons, which was contingent on TGFβ signaling activation. Our findings provide insights on how albumin extravasation that occurs upon BBB dysfunction in various brain injuries can predispose neural circuitry to the development of chronic inhibition deficits

Application and Benchmark of SPH for Modeling the Impact in Thermal Spraying

The properties of a thermally sprayed coating, such as its durability or thermal conductivity depend on its microstructure, which is in turn directly related to the particle impact process. To simulate this process we present a 3D Smoothed Particle Hydrodynamics (SPH) model, which represents the molten droplet as an incompressible fluid, while a semi-implicit Enthalpy-Porosity method is applied for the mushy zone during solidification. In addition, we present an implicit correction for SPH simulations, based on well known approaches, from which we can observe improved performance and simulation stability. We apply our SPH method to the impact and solidification of Al$_2$O$_3$ droplets onto a free slip substrate and perform a rigorous quantitative comparison of our method with the commercial software Ansys Fluent using the Volume of Fluid (VOF) approach, while taking identical physical effects into consideration. The results are evaluated in depth and we discuss the applicability of either method for the simulation of thermal spray deposition. We show that SPH is an excellent method for solving this free surface problem accurately and efficiently

State-dependencies of learning across brain scales

Learning is a complex brain function operating on different time scales, from milliseconds to years, which induces enduring changes in brain dynamics. The brain also undergoes continuous “spontaneous” shifts in states, which, amongst others, are characterized by rhythmic activity of various frequencies. Besides the most obvious distinct modes of waking and sleep, wake-associated brain states comprise modulations of vigilance and attention. Recent findings show that certain brain states, particularly during sleep, are essential for learning and memory consolidation. Oscillatory activity plays a crucial role on several spatial scales, for example in plasticity at a synaptic level or in communication across brain areas. However, the underlying mechanisms and computational rules linking brain states and rhythms to learning, though relevant for our understanding of brain function and therapeutic approaches in brain disease, have not yet been elucidated. Here we review known mechanisms of how brain states mediate and modulate learning by their characteristic rhythmic signatures. To understand the critical interplay between brain states, brain rhythms, and learning processes, a wide range of experimental and theoretical work in animal models and human subjects from the single synapse to the large-scale cortical level needs to be integrated. By discussing results from experiments and theoretical approaches, we illuminate new avenues for utilizing neuronal learning mechanisms in developing tools and therapies, e.g., for stroke patients and to devise memory enhancement strategies for the elderly

The Giant Pacific Oyster (Crassostrea gigas) as a modern analog for fossil ostreoids: Isotopic (Ca, O, C) and elemental (Mg/Ca, Sr/Ca, Mn/Ca) proxies

Modern analogs are an essential part of palaeoclimate studies, because they provide the basis for the understanding of geochemical signatures of fossils. Ostreoids are common in many sedimentary sequences and because of their fast growth, high temporal resolution sampling of past seasonal variability is possible. Here, two shell structures of modern Giant Pacific Oysters (Crassostrea gigas), the chalky substance and foliate layers, have been sampled for trace element distributions (Mg, Sr, Mn) and stable isotope variability (C, O, Ca). Oxygen isotopes exhibit a clear seasonal signature. Mean carbon isotope values of different oysters agree within 0.1‰, but ontogenic variability is complicated by shell growth patterns and potential small vital effects. The calcium isotope ratios are found to be constant throughout ontogeny within analytical precision at a value of δ44/40Ca = 0.68 ± 0.16‰ (2 sd) SRM–915a which is consistent with other bivalve species. Calcium isotope ratios in oyster shell material might thus be a possible proxy for palaeo seawater calcium isotope ratios. Element/Ca ratios are significantly higher in the chalky substance than in the foliate layers and especially high Sr/Ca and Mn/Ca ratios are observed for the first growth season of the oysters. Mg/Ca ratios in the chalky substance show a negative correlation with δ18O values, compatible with a temperature dependence, whereas this correlation is absent in the foliate layers. Seasonal changes of Sr/Ca are controlled by metabolic processes, whereas for Mn/Ca an additional environmental control is evident

Mass spectrometry-based metabolomics:a guide for annotation, quantification and best reporting practices

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics-derived data.</p