Automated methods for cell type annotation on scRNA-seq data.

The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type annotation is a crucial step in analyzing single-cell RNA sequencing data, yet manual annotation is time-consuming and partially subjective. As an alternative, tools have been developed for automatic cell type identification. Different strategies have emerged to ultimately associate gene expression profiles of single cells with a cell type either by using curated marker gene databases, correlating reference expression data, or transferring labels by supervised classification. In this review, we present an overview of the available tools and the underlying approaches to perform automated cell type annotations on scRNA-seq data

Interoperability Between GRDC\u27s Data Holding And The GEOSS Infrastructure

The Global Runoff Data Centre (GRDC) operates under the auspices of the World Meteorological Organization as an international data centre for hydrological data and information on a global scale. Its primary objective is to support the water and climate related programmes and projects of the United Nations, its specialised agencies, and the scientific research community on global and climate change and integrated water resources management. The Global Runoff Database maintained by the GRDC is a valuable data resource and a subset of its data is contributed to the Global Earth Observation System of Systems’ (GEOSS) freely accessible Data Core. As a partner in the project GEOSS Interoperability for Weather, Ocean and Water (GEOWOW) the GRDC supports the evolving GEOSS in terms of interoperability, standardization and functionality. In the framework of GEOWOW a profile of the OGC Sensor Observation Service Interface Standard 2.0 (SOS) is being developed. This SOS Profile for the Hydrology Domain specifies extensions to the service interface and uses the OGC WaterML 2.0 standard for encoding hydrological time series data. Moreover, technical partners of the GEOWOW project facilitate software implementations of the standardization advancements. Deploying and incorporating these into GRDC’s data holding infrastructure allows for a seamless integration of GRDC’s data provision capabilities into GEOSS. Furthermore, client web applications to visualize time series data provided via an OGC Web Service infrastructure makes it possible to offer additional benefit and allows for accessing and assessing data more easily

Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA)

Biological and medical sciences are increasingly acknowledging the significance of gene co-expression-networks for investigating complex-systems, phenotypes or diseases. Typically, complex phenotypes are investigated under varying conditions. While approaches for comparing nodes and links in two networks exist, almost no methods for the comparison of multiple networks are available and-to best of our knowledge-no comparative method allows for whole transcriptomic network analysis. However, it is the aim of many studies to compare networks of different conditions, for example, tissues, diseases, treatments, time points, or species. Here we present a method for the systematic comparison of an unlimited number of networks, with unlimited number of transcripts:Co-expression Differential Network Analysis (CoDiNA). In particular, CoDiNA detects linksandnodes that are common, specific or different among the networks. We developed a statistical framework to normalize between these different categories of common or changed network links and nodes, resulting in a comprehensive network analysis method, more sophisticated than simply comparing the presence or absence of network nodes. Applying CoDiNA to a neurogenesis study we identified candidate genes involved in neuronal differentiation. We experimentally validated one candidate, demonstrating that its overexpression resulted in a significant disturbance in the underlying gene regulatory network of neurogenesis. Using clinical studies, we compared whole transcriptome co-expression networks from individuals with or without HIV and active tuberculosis (TB) and detected signature genes specific to HIV. Furthermore, analyzing multiple cancer transcription factor (TF) networks, we identified common and distinct features for particular cancer types. These CoDiNA applications demonstrate the successful detection of genes associated with specific phenotypes. Moreover, CoDiNA can also be used for comparing other types of undirected networks, for example, metabolic, protein-protein interaction, ecological and psychometric networks. CoDiNA is publicly available as anRpackage in CRAN (https://CRAN. R-project.org/package=CoDiNA)

Highly Conductive, Stretchable, and Cell-Adhesive Hydrogel by Nanoclay Doping

Electrically conductive materials that mimic physical and biological properties of tissues are urgently required for seamless brain-machine interfaces. Here, a multinetwork hydrogel combining electrical conductivity of 26 S m-1 , stretchability of 800%, and tissue-like elastic modulus of 15 kPa with mimicry of the extracellular matrix is reported. Engineering this unique set of properties is enabled by a novel in-scaffold polymerization approach. Colloidal hydrogels of the nanoclay Laponite are employed as supports for the assembly of secondary polymer networks. Laponite dramatically increases the conductivity of in-scaffold polymerized poly(ethylene-3,4-diethoxy thiophene) in the absence of other dopants, while preserving excellent stretchability. The scaffold is coated with a layer containing adhesive peptide and polysaccharide dextran sulfate supporting the attachment, proliferation, and neuronal differentiation of human induced pluripotent stem cells directly on the surface of conductive hydrogels. Due to its compatibility with simple extrusion printing, this material promises to enable tissue-mimetic neurostimulating electrodes

A customizable microfluidic platform for medium-throughput modeling of neuromuscular circuits

Neuromuscular circuits (NMCs) are vital for voluntary movement, and effective models of NMCs are needed to understand the pathogenesis of, as well as to identify effective treatments for, multiple diseases, including Duchenne's muscular dystrophy and amyotrophic lateral sclerosis. Microfluidics are ideal for recapitulating the central and peripheral compartments of NMCs, but myotubes often detach before functional NMCs are formed. In addition, microfluidic systems are often limited to a single experimental unit, which significantly limits their application in disease modeling and drug discovery. Here, we developed a microfluidic platform (MFP) containing over 100 experimental units, making it suitable for medium-throughput applications. To overcome detachment, we incorporated a reactive polymer surface allowing customization of the environment to culture different cell types. Using this approach, we identified conditions that enable long-term co-culture of human motor neurons and myotubes differentiated from human induced pluripotent stem cells inside our MFP. Optogenetics demonstrated the formation of functional NMCs. Furthermore, we developed a novel application of the rabies tracing assay to efficiently identify NMCs in our MFP. Therefore, our MFP enables large-scale generation and quantification of functional NMCs for disease modeling and pharmacological drug targeting. © 2019 The Author

Retinal Organoids from Pluripotent Stem Cells Efficiently Recapitulate Retinogenesis.

The plasticity of pluripotent stem cells provides new possibilities for studying development, degeneration, and regeneration. Protocols for the differentiation of retinal organoids from embryonic stem cells have been developed, which either recapitulate complete eyecup morphogenesis or maximize photoreceptor genesis. Here, we have developed a protocol for the efficient generation of large, 3D-stratified retinal organoids that does not require evagination of optic-vesicle-like structures, which so far limited the organoid yield. Analysis of gene expression in individual organoids, cell birthdating, and interorganoid variation indicate efficient, reproducible, and temporally regulated retinogenesis. Comparative analysis of a transgenic reporter for PAX6, a master regulator of retinogenesis, shows expression in similar cell types in mouse in vivo, and in mouse and human retinal organoids. Early or late Notch signaling inhibition forces cell differentiation, generating organoids enriched with cone or rod photoreceptors, respectively, demonstrating the power of our improved organoid system for future research in stem cell biology and regenerative medicine

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis

Non-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 has been assigned as a key player of neuronal differentiation via its complex but little understood regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human induced pluripotent stem cells. Upon neuronal induction, miR-124-deleted cells underwent neurogenesis and became functional neurons, albeit with altered morphology and neurotransmitter specification. Using RNA-induced-silencing-complex precipitation, we identified 98 high-confidence miR-124 targets, of which some directly led to decreased viability. By performing advanced transcription-factor-network analysis, we identified indirect miR-124 effects on apoptosis, neuronal subtype differentiation, and the regulation of previously uncharacterized zinc finger transcription factors. Our data emphasize the need for combined experimental- and system-level analyses to comprehensively disentangle and reveal miRNA functions, including their involvement in the neurogenesis of diverse neuronal cell types found in the human brain

Rapid neurogenesis through transcriptional activation in human stem cells

Advances in cellular reprogramming and stem cell differentiation now enable ex vivo studies of human neuronal differentiation. However, it remains challenging to elucidate the underlying regulatory programs because differentiation protocols are laborious and often result in low neuron yields. Here, we overexpressed two Neurogenin transcription factors in human-induced pluripotent stem cells and obtained neurons with bipolar morphology in 4 days, at greater than 90% purity. The high purity enabled mRNA and microRNA expression profiling during neurogenesis, thus revealing the genetic programs involved in the rapid transition from stem cell to neuron. The resulting cells exhibited transcriptional, morphological and functional signatures of differentiated neurons, with greatest transcriptional similarity to prenatal human brain samples. Our analysis revealed a network of key transcription factors and microRNAs that promoted loss of pluripotency and rapid neurogenesis via progenitor states. Perturbations of key transcription factors affected homogeneity and phenotypic properties of the resulting neurons, suggesting that a systems-level view of the molecular biology of differentiation may guide subsequent manipulation of human stem cells to rapidly obtain diverse neuronal types

Microelectrode Array Electrophysiological Recording of Neuronal Network Activity during a Short-Term Microgravity Phase

During spaceflight, humans are subjected to a variety of environmental factors which deviate from Earth conditions. Especially the lack of gravity poses a big challenge to the human body and has been identified as a major trigger of many detrimental effects observed in returning astronauts but also in participants of spaceflight-analog studies. Structural alterations within the brain as well as declines in cognitive performance have been reported, which has brought the topic of brain health under microgravity into the focus of space research. However, the physiological mechanisms underlying these observations remain elusive. Every aspect of human cognition, behavior and psychomotor function is processed by the brain based on electro-chemical signals of billions of neurons, which relay information via neuronal networks throughout the body. Alterations in neuronal activity are the main cause of a variety of mental disorders and changed neuronal transmission may also lead to diminished human performance in space. Thus, understanding the functioning of these fundamental processes under the influence of altered gravity conditions on a cellular level is of high importance for any manned space mission. Previous electrophysiological experiments using patch clamp have shown that propagation velocity of action potentials (APs) is dependent on gravity. With this project, we aim to advance the electrophysiological approach from a single-cell level to a complex network level by employing Microelectrode array (MEA) technology. MEAs feature the advantage of real-time electrophysiological recording of a complex and mature neuronal network in vitro, without the need for invasive patch clamp insertion into cells. Using a custom-built pressure chamber, we were able to integrate and conduct our experiment on the ZARM Drop Tower platform, exposing the entire system to 4.7 s of high-quality microgravity (10-6 to 10-5 x g0). With this setup we were able to evaluate the functional activity patterns of iPSC-derived neuronal networks subjected to microgravity, while keeping them under controlled and stable temperature and pressure conditions. Activity data was acquired constantly - immediately before the drop, during the free-fall (microgravity) phase and during a subsequent post-drop recording phase. For neuronal activity analysis the action potential frequency in each experiment phase was calculated for the single electrodes. We found that during the 4.7 s lasting microgravity phase the mean action potential frequency across the neuronal networks was significantly elevated. Additionally, electrical activity readapted back to baseline level within 10 minutes of post-drop recordings. Our preliminary data shows that real-time, electrophysiological recording of neuronal network activity based on MEA technology is possible under altered gravity conditions and that differences in activity can be detected already in very short time frames in the second range. Furthermore, the observation that microgravity has an effect on the electrophysiological activity of neuronal networks is in line with previously published findings in single neurons and poses further questions with regards to astronaut brain health on manned space missions. The MEA payload system was approved for autonomous recording of redundant cellular electrophysiological data in the Drop Tower. It will be applied on other microgravity platforms such as sounding rockets and parabolic flights and thus increased experimental time. Apart from neurons, various other electrically active cellular systems such as myocytes or myotubes could be examined using this hardware

Efficient transduction and optogenetic stimulation of retinal bipolar cells by a synthetic adeno-associated virus capsid and promoter

In this report, we describe the development of a modified adeno-associated virus (AAV) capsid and promoter for transduction of retinal ON-bipolar cells. The bipolar cells, which are post-synaptic to the photoreceptors, are important retinal targets for both basic and preclinical research. In particular, a therapeutic strategy under investigation for advanced forms of blindness involves using optogenetic molecules to render ON-bipolar cells light-sensitive. Currently, delivery of adequate levels of gene expression is a limiting step for this approach. The synthetic AAV capsid and promoter described here achieves high level of optogenetic transgene expression in ON-bipolar cells. This evokes high-frequency (∼100 Hz) spiking responses in ganglion cells of previously blind, rd1, mice. Our vector is a promising vehicle for further development toward potential clinical use