A novel machine learning-based approach for the detection and analysis of spontaneous synaptic currents

Spontaneous synaptic activity is a hallmark of biological neural networks. A thorough description of these synaptic signals is essential for understanding neurotransmitter release and the generation of a postsynaptic response. However, the complexity of synaptic current trajectories has either precluded an in-depth analysis or it has forced human observers to resort to manual or semi-automated approaches based on subjective amplitude and area threshold settings. Both procedures are time-consuming, error-prone and likely affected by human bias. Here, we present three complimentary methods for a fully automated analysis of spontaneous excitatory postsynaptic currents measured in major cell types of the mouse retina and in a primary culture of mouse auditory cortex. Two approaches rely on classical threshold methods, while the third represents a novel machine learning-based algorithm. Comparison with frequently used existing methods demonstrates the suitability of our algorithms for an unbiased and efficient analysis of synaptic signals in the central nervous system

The structure dilemma in biological and artificial neural networks

Brain research up to date has revealed that structure and function are highly related. Thus, for example, studies have repeatedly shown that the brains of patients suffering from schizophrenia or other diseases have a different connectome compared to healthy people. Apart from stochastic processes, however, an inherent logic describing how neurons connect to each other has not yet been identified. We revisited this structural dilemma by comparing and analyzing artificial and biological-based neural networks. Namely, we used feed-forward and recurrent artificial neural networks as well as networks based on the structure of the micro-connectome of C. elegans and of the human macro-connectome. We trained these diverse networks, which markedly differ in their architecture, initialization and pruning technique, and we found remarkable parallels between biological-based and artificial neural networks, as we were additionally able to show that the dilemma is also present in artificial neural networks. Our findings show that structure contains all the information, but that this structure is not exclusive. Indeed, the same structure was able to solve completely different problems with only minimal adjustments. We particularly put interest on the influence of weights and the neuron offset value, as they show a different adaption behaviour. Our findings open up new questions in the fields of artificial and biological information processing research

Development of an N-1 perfusion medium to intensify seed train operation

Seed train expansion of cells before the final production step is often time-consuming and a major source of process variability. For the intensification of seed train operations there are several opportunities discussed across the biopharma industry today. One of the possibilities is to operate N-1 bioreactors in perfusion mode to shorten timelines and improve bioreactor utilization. In this work, we investigated the influence of using an expansion medium especially designed for N-1 perfusion to gain optimal results in the whole manufacturing campaign. For screening and designing an N-1 perfusion expansion medium, a scale down model which represents a typical production campaign, including the seed train, was established. Expansion medium prototypes were combined with different production media in the final production step, e.g. EX-CELL® Advanced HD Perfusion as medium designed for high-density perfusion, and Cellvento® 4CHO Medium and 4FEED as exemplary fed-batch process. After determining a suitable expansion medium formulation, the prototype was evaluated for solubility and streamlined to ensure a simple hydration and robust supply chain. Afterwards, results were confirmed using a simulated manufacturing process using benchtop bioreactor systems, showing that the positive impact of the expansion medium on the final yield is present both when using perfusion or fed-batch as final production stage. Our results indicate that using the right companion medium in seed train expansion - specifically designed for the purpose - can prepare the cells optimally for the final N-stage and increase productivity while using low CSPRs. Combining these findings with the application of a perfused N-1 step in the manufacturing campaign leads to a great opportunity for the intensification of the whole upstream process

Upstream process intensification using frozen high cell density intermediates

Typical seed train operations start by thawing of a single vial followed by several expansion steps. Reaching sufficient absolute cell numbers for production bioreactor inoculation is time-consuming and reduces plant flexibility. Besides long ramp up times, open cell culture operations are a major source of process variability. High cell density cryopreservation (HCDC) is a method of freezing cells in bags instead of vials and at higher cell densities. This offers the advantage of decoupling expansion and production: both steps can be separated in space and time. Room classification could be decreased due to fully closed processing and reproducibility increased due to a reduction of manual handling steps. Furthermore, these frozen seed train intermediates allow global distribution from a central expansion facility to decentralized global production facilities. Besides from advantages in production, these HCDC bags can be used in process development to ensure equal starting points in experimental setups. In this study, we developed a single-use bag assembly that supports closed filling, freezing, thawing, and inoculation. Before using the bag application, relevant parameters for this process from filling to inoculation were evaluated in vials with different cell lines. We found that the DMSO concentration for optimal freezing must not be higher than 7,5%. Furthermore, direct freezing at -80 °C instead of using a controlled rate freezing method is possible. Maximum concentration of DMSO in cell cultures should not be higher than 0,5 % when cryopreserved cells in bags are used for inoculation. For the idea of seed train intensification, we tested increasing freezing cell densities from 10 to 100 million cells/mL showing comparable growth. Functionality test of this HCDC method in comparison to vials was demonstrated in 4,2 L bioreactors simulating a manufacturing process. Applicability of this cryopreservation technology has been demonstrated using different bioreactors, perfusion systems, and various CHO cell lines

Simplifying the analysis of software design variants with a colorful alloy

Formal modeling and automatic analysis are essential to achieve a trustworthy software design prior to its implementation. Alloy and its Analyzer are a popular language and tool for this task. Frequently, rather than a single software artifact, the goal is to develop a full software product line (SPL) with many variants supporting different features. Ideally, software design languages and tools should provide support for analyzing all such variants (e.g., by helping pinpoint combinations of features that could break a property), but that is not currently the case. Even when developing a single artifact, support for multi-variant analysis is desirable to explore design alternatives. Several techniques have been proposed to simplify the implementation of SPLs. One such technique is to use background colors to identify the fragments of code associated with each feature. In this paper we propose to use that same technique for formal design, showing how to add support for features and background colors to Alloy and its Analyzer, thus easing the analysis of software design variants. Some illustrative examples and evaluation results are presented, showing the benefits and efficiency of the implemented technique.This work is financed by the ERDF - European Regional Development Fund - through the Operational Programme for Competitiveness and Internationalisation - COMPETE 2020 - and by National Funds through the Portuguese funding agency, FCT - Fundação para a Ciência e a Tecnologia, within project POCI-01- 0145-FEDER-016826. The third author was also supported by the FCT sabbatical grant with reference SFRH/BSAB/143106/2018

Nimodipine Exerts Beneficial Effects on the Rat Oligodendrocyte Cell Line OLN-93

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS). Therapy is currently limited to drugs that interfere with the immune system; treatment options that primarily mediate neuroprotection and prevent neurodegeneration are not available. Here, we studied the effects of nimodipine on the rat cell line OLN-93, which resembles young mature oligodendrocytes. Nimodipine is a dihydropyridine that blocks the voltage-gated L-type calcium channel family members Cav1.2 and Cav1.3. Our data show that the treatment of OLN-93 cells with nimodipine induced the upregulation of myelin genes, in particular of proteolipid protein 1 (Plp1), which was confirmed by a significantly greater expression of PLP1 in immunofluorescence analysis and the presence of myelin structures in the cytoplasm at the ultrastructural level. Whole-genome RNA sequencing additionally revealed the upregulation of genes that are involved in neuroprotection, remyelination, and antioxidation pathways. Interestingly, the observed effects were independent of Cav1.2 and Cav1.3 because OLN-93 cells do not express these channels, and there was no measurable response pattern in patch-clamp analysis. Taking into consideration previous studies that demonstrated a beneficial effect of nimodipine on microglia, our data support the notion that nimodipine is an interesting drug candidate for the treatment of MS and other demyelinating diseases

Connexin30.2:<i>In vitro</i> interaction with connexin36 in hela cells and expression in AII amacrine cells and intrinsically photosensitive ganglion cells in the mouse retina

Electrical coupling via gap junctions is an abundant phenomenon in the mammalian retina and occurs in all major cell types. Gap junction channels are assembled from different connexin subunits, and the connexin composition of the channel confers specific properties to the electrical synapse. In the mouse retina, gap junctions were demonstrated between intrinsically photosensitive ganglion cells and displaced amacrine cells but the underlying connexin remained undetermined. In the primary rod pathway, gap junctions play a crucial role, coupling AII amacrine cells among each other and to ON cone bipolar cells. Although it has long been known that connexin36 and connexin45 are necessary for the proper functioning of this most sensitive rod pathway, differences between homocellular AII/AII gap junctions and AII/ON bipolar cell gap junctions suggested the presence of an additional connexin in AII amacrine cells. Here, we used a connexin30.2-lacZ mouse line to study the expression of connexin30.2 in the retina. We show that connexin30.2 is expressed in intrinsically photosensitive ganglion cells and AII amacrine cells. Moreover, we tested whether connexin30.2 and connexin36 – both expressed in AII amacrine cells – are able to interact with each other and are deposited in the same gap junctional plaques. Using newly generated anti-connexin30.2 antibodies, we show in HeLa cells that both connexins are indeed able to interact and may form heteromeric channels: both connexins were co-immunoprecipitated from transiently transfected HeLa cells and connexin30.2 gap junction plaques became significantly larger when co-expressed with connexin36. These data suggest that connexin36 is able to form heteromeric gap junctions with another connexin. We hypothesize that co-expression of connexin30.2 and connexin36 may endow AII amacrine cells with the means to differentially regulate its electrical coupling to different synaptic partners

Systemisches Denken im Fachunterricht

The ability to think in terms of time, in models, and to act in a systematic way is regarded as an important learning goal in most natural and sociological subjects. Particularly suitable for the promotion of systemic thinking are causal loop diagrams and system dynamics, which this book focuses on. The first contributions address the theoretical foundations of systems thinking, the design of causal loop diagrams, learning with system dynamics, the modeling tool Insight Maker, and generic structures or system archetypes, which are found in many different situations. The other articles show the importance of systems thinking and the design of learning environments in several several subjects: - Biology - German - Physics - Geography - History - Politics - EconomyDie Fähigkeit, sowohl vernetzt, in Zeitabläufen und in Modellen zu denken als auch systemgerecht zu handeln – kurz: systemisch zu denken – wird in den meisten natur- und gesellschaftswissenschaftlichen Fächern als wichtiges Lernziel angesehen. Besonders geeignet zur Förderung des systemischen Denkens sind Wirkungsdiagramme und System Dynamics, die im Zentrum des vorliegenden Buchs stehen. Die ersten Beiträge widmen sich den theoretischen Grundlagen des systemischen Denkens, der Gestaltung von Wirkungsdiagrammen, dem Lernen mit System Dynamics, dem Modelliertool Insight Maker und generischen Strukturen bzw. Systemarchetypen, die sich sich in vielen unterschiedlichen Situationen finden und somit ein hohes Transferpotenzial aufweisen. Die weiteren Artikel zeigen die Bedeutung des systemischen Denkens und die Unterrichtsgestaltung anhand exemplarischer Beispiele in mehreren Fächern auf: - Deutsch - Biologie - Physik - Geographie - Geschichte - Politik - Wirtschaft Auf der Website des Buchs (www.wirtschaft-lernen.de/systemisches_denken) finden sich Materialien wie Aufgabenblätter, Screencasts und die verwendeten Modelle

AII amacrine cells discriminate between heterocellular and homocellular locations when assembling connexin36-containing gap junctions

Electrical synapses (gap junctions) rapidly transmit signals between neurons and are composed of connexins. In neurons, connexin36 (C×36) is the most abundant isoform; however, the mechanisms underlying formation of C×36-containing electrical synapses are unknown. We focus on homocellular and heterocellular gap junctions formed by an AII amacrine cell, a key interneuron found in all mammalian retinas. In mice lacking native C×36 but expressing a variant tagged with enhanced green fluorescent protein at the C-terminus (KO-C×36-EGFP), heterocellular gap junctions formed between AII cells and ON cone bipolar cells are fully functional, whereas homocellular gap junctions between two AII cells are not formed. A tracer injected into an AII amacrine cell spreads into ON cone bipolar cells but is excluded from other AII cells. Reconstruction of C×36-EGFP clusters on an AII cell in the KO-C×36-EGFP genotype confirmed that the number, but not average size, of the clusters is reduced - as expected for AII cells lacking a subset of electrical synapses. Our studies indicate that some neurons exhibit at least two discriminatory mechanisms for assembling C×36. We suggest that employing different gapjunction- forming mechanisms could provide the means for a cell to regulate its gap junctions in a target-cell-specific manner, even if these junctions contain the same connexin