Data Mining Practical Machine Learning Tools and Techniques

https://www.cell.com/cell/pdf/S0092-8674(15)00549-8.pdf

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

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Table Of Integrals Series And Products

Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.

Pyramidal neurons are the most common cell type in the cerebral cortex. Understanding how they differ between species is a key challenge in neuroscience. A recent study provided a unique set of human and mouse pyramidal neurons of the CA1 region of the hippocampus, and used it to compare the morphology of apical and basal dendritic branches of the two species. The study found inter-species differences in the magnitude of the morphometrics and similarities regarding their variation with respect to morphological determinants such as branch type and branch order. We use the same data set to perform additional comparisons of basal dendrites. In order to isolate the heterogeneity due to intrinsic differences between species from the heterogeneity due to differences in morphological determinants, we fit multivariate models over the morphometrics and the determinants. In particular, we use conditional linear Gaussian Bayesian networks, which provide a concise graphical representation of the independencies and correlations among the variables. We also extend the previous study by considering additional morphometrics and by formally testing test whether a morphometric increases or decreases with the distance from the soma. This study introduces a multivariate methodology for inter-species comparison of morphology.

/pdf/comparing-basal-dendrite-branches-in-human-and-mouse-4h9hiocfsj.pdf

Comparing basal dendrite branches in human and mouse hippocampal CA1 pyramidal neurons with Bayesian networks

Investigating and modelling the functionality of human neurons remains challenging due to the technical limitations, resulting in scarce and incomplete 3D anatomical reconstructions. Here we used a morphological modelling approach based on optimal wiring to repair the parts of a dendritic morphology that were lost due to incomplete tissue samples. In Drosophila, where dendritic regrowth has been studied experimentally using laser ablation, we found that modelling the regrowth reproduced a bimodal distribution between regeneration of cut branches and invasion by neighbouring branches. Interestingly, our repair model followed growth rules similar to those for the generation of a new dendritic tree. To generalise the repair algorithm from Drosophila to mammalian neurons, we artificially sectioned reconstructed dendrites from mouse and human hippocampal pyramidal cell morphologies, and showed that the regrown dendrites were morphologically similar to the original ones. Furthermore, we were able to restore their electrophysiological functionality, as evidenced by the recovery of their firing behaviour. Importantly, we show that such repairs also apply to other neuron types including hippocampal granule cells and cerebellar Purkinje cells. We then extrapolated the repair to incomplete human CA1 pyramidal neurons, where the anatomical boundaries of the particular brain areas innervated by the neurons in question were known. Interestingly, the repair of incomplete human dendrites helped to simulate the recently observed increased synaptic thresholds for dendritic NMDA spikes in human versus mouse dendrites. To make the repair tool available to the neuroscience community, we have developed an intuitive and simple graphical user interface (GUI), which is available in the TREES Toolbox (www.treestoolbox.org). In brief We use morphological modelling inspired by the regeneration of various artificially cut neuron types and repair incomplete human and nonhuman neuronal dendritic reconstructions. Author summary Reconstructing neuronal dendrites by drawing their 3D branching structures in the computer has proven to be crucial for interpreting the flow of electrical signals and therefore the computations that dendrites implement on their inputs. These reconstructions are tedious and prone to disruptive limitations imposed by experimental procedures. In recent years, complementary computational procedures have emerged that reproduce the fine details of morphology in theoretical models. These models allow, for example, to populate large-scale neural networks and to study structure-function relationships. In this work we use a morphological model based on optimised wiring for signal conduction and material cost to repair faulty reconstructions, in particular those of human hippocampal dendrites, which are rare and precious but often cut due to technical limitations. Interestingly, we find that our synthetic repair mechanism reproduces the two distinct modes of repair observed in real dendrites: regeneration from the severed branch and invasion from neighbouring branches. Our model therefore provides both a useful tool for single-cell electrophysiological simulations and a useful theoretical concept for studying the biology of dendrite repair. Highlights Optimal wiring-based growth algorithm replicates regrowth of artificially cut dendrites The growth algorithm repairs cut dendrites in incomplete reconstructions The algorithm works for diverse neuron types in multiple species The repair of morphology restores original electrophysiology The repair of morphology supports simulations of high synaptic thresholds for NMDA spikes in human dendrites The repair tool with user interface is available in the TREES Toolbox

/pdf/a-biologically-inspired-repair-mechanism-for-neuronal-3gxihbhx.pdf

A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites

Axonal outgrowth and the formation of the axon initial segment (AIS) are early events in the acquisition of neuronal concentration of voltage-dependent sodium and potassium channels. However, the specific ion channel subunits pr subdomain vary both during development and among the types of neurons, probably determining their firing charac characterize the developmental expression of different subfamilies of voltage-gated potassium channels in the AIS including subunits Kv1.2, Kv2.2 and Kv7.2. In contrast to the early appearance of voltage-gated sodium channels a subunits were tethered at the AIS only after 10 days in vitro. Interestingly, we observed different patterns of Kv1.2 to distinct neuronal populations. The accumulation of Kv1.2 and Kv2.2 subunits at the AIS was dependent on ankyr the actin cytoskeleton and it was resistant to detergent extraction, as described previously for other AIS proteins. further emphasizes the heterogeneity of this structure in different neuronal populations, as proposed previously, an potential regulation.

/pdf/developmental-expression-of-kv-potassium-channels-segment-of-17ul2l0isd.pdf

Developmental Expression of Kv Potassium Channels Segment of Cultured Hippocampal Neurons

P-111 The human cortex in vitro: Characterization and neuromodulation of spontaneous and evoked network dynamics

The structural complexity of nervous tissue makes it very difficult to unravel the connectivity between neural elements at different scales. Numerous methods are available to trace long-range projections at the light microscopic level, and to identify the actual synaptic connections at the electron microscopic level. However, correlating mesoscopic and nanoscopic scales in the same cell, cell population or brain region is a problematic, laborious and technically demanding task. Here we present an effective method for the 3D reconstruction of labeled subcellular structures at the ultrastructural level, after single-neuron labeling in fixed tissue. The brain is fixed by intracardial perfusion of aldehydes and thick vibratome sections (250 μm) are obtained. Single cells in these vibratome sections are intracellularly injected with horseradish peroxidase (HRP), so that the cell body and its processes can be identified. The thick sections are later flat-embedded in epoxy resin and re-sectioned into a series of thinner (7 μm) sections. The sections containing the regions of interest of the labeled cells are then imaged with automated focused ion beam milling and scanning electron microscopy (FIB-SEM), acquiring long series of high-resolution images that can be reconstructed, visualized, and analyzed in 3D. With this methodology, we can accurately select any cellular segment at the light microscopic level (e.g., proximal, intermediate or distal dendrites, collateral branches, axonal segments, etc.) and analyze its synaptic connections at the electron microscopic level, along with other ultrastructural features. Thus, this method not only facilitates the mapping of the synaptic connectivity of single-labeled neurons, but also the analysis of the surrounding neuropil. Since the labeled processes can be located at different layers or subregions, this method can also be used to obtain data on the differences in local synaptic organization that may exist at different portions of the labeled neurons.

Javier DeFelipe

Papers

Comparing basal dendrite branches in human and mouse hippocampal CA1 pyramidal neurons with Bayesian networks

A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites

Developmental Expression of Kv Potassium Channels Segment of Cultured Hippocampal Neurons

P-111 The human cortex in vitro: Characterization and neuromodulation of spontaneous and evoked network dynamics

Single-Neuron Labeling in Fixed Tissue and Targeted Volume Electron Microscopy