A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex, bioRxiv, 2018-06-29

SummaryTo understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.

biorxiv neuroscience 100-200-users 2018

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells, bioRxiv, 2018-06-27

AbstractEnvironmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogenenous cellular responses to environmental signals at the mRNA and phospho-proteome level.

biorxiv genomics 100-200-users 2018

Analysis and Correction of Inappropriate Image Duplication The Molecular and Cellular Biology Experience, bioRxiv, 2018-06-24

AbstractThe present study analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009-2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 42 corrections, 5 retractions and 12 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, ~10% of papers with inappropriate image duplications in MCB were retracted. If this proportion is representative, then as many as 35,000 papers in the literature are candidates for retraction due to image duplication. The resolution of inappropriate image duplication concerns after publication required an average of 6 h of journal staff time per published paper. MCB instituted a pilot program to screen images of accepted papers prior to publication that identified 12 manuscripts (14.5% out of 83) with image concerns in two months. The screening and correction of papers before publication required an average of 30 min of staff time per problematic paper. Image screening can identify papers with problematic images prior to publication, reduces post-publication problems and requires significantly less staff time than the correction of problems after publication.

biorxiv scientific-communication-and-education 100-200-users 2018

Spatial Organization of Rho GTPase signaling by RhoGEFRhoGAP proteins, bioRxiv, 2018-06-24

AbstractRho GTPases control cell morphogenesis and thus fundamental processes in all eukaryotes. They are regulated by 145 RhoGEF and RhoGAP multi-domain proteins in humans. How the Rho signaling system is organized to generate localized responses in cells and prevent their spreading is not understood. Here, we systematically characterized the substrate specificities, localization and interactome of the RhoGEFsRhoGAPs and revealed their critical role in contextualizing and spatially delimiting Rho signaling. They localize to multiple compartments providing positional information, are extensively interconnected to jointly coordinate their signaling networks and are widely autoinhibited to remain sensitive to local activation. RhoGAPs exhibit lower substrate specificity than RhoGEFs and may contribute to preserving Rho activity gradients. Our approach led us to uncover a multi-RhoGEF complex downstream of G-protein-coupled receptors controlling a Cdc42RhoA crosstalk. The spatial organization of Rho signaling thus differs from other small GTPases and expands the repertoire of mechanisms governing localized signaling activity.

biorxiv cell-biology 100-200-users 2018

DoubletFinder Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors, bioRxiv, 2018-06-20

SUMMARYSingle-cell RNA sequencing (scRNA-seq) using droplet microfluidics occasionally produces transcriptome data representing more than one cell. These technical artifacts are caused by cell doublets formed during cell capture and occur at a frequency proportional to the total number of sequenced cells. The presence of doublets can lead to spurious biological conclusions, which justifies the practice of sequencing fewer cells to limit doublet formation rates. Here, we present a computational doublet detection tool – DoubletFinder – that identifies doublets based solely on gene expression features. DoubletFinder infers the putative gene expression profile of real doublets by generating artificial doublets from existing scRNA-seq data. Neighborhood detection in gene expression space then identifies sequenced cells with increased probability of being doublets based on their proximity to artificial doublets. DoubletFinder robustly identifies doublets across scRNA-seq datasets with variable numbers of cells and sequencing depth, and predicts false-negative and false-positive doublets defined using conventional barcoding approaches. We anticipate that DoubletFinder will aid in scRNA-seq data analysis and will increase the throughput and accuracy of scRNA-seq experiments.

biorxiv bioinformatics 100-200-users 2018

Enzymatic DNA synthesis for digital information storage, bioRxiv, 2018-06-16

AbstractDNA is an emerging storage medium for digital data but its adoption is hampered by limitations of phosphoramidite chemistry, which was developed for single-base accuracy required for biological functionality. Here, we establish a de novo enzymatic DNA synthesis strategy designed from the bottom-up for information storage. We harness a template-independent DNA polymerase for controlled synthesis of sequences with user-defined information content. We demonstrate retrieval of 144-bits, including addressing, from perfectly synthesized DNA strands using batch-processed Illumina and real-time Oxford Nanopore sequencing. We then develop a codec for data retrieval from populations of diverse but imperfectly synthesized DNA strands, each with a ~30% error tolerance. With this codec, we experimentally validate a kilobyte-scale design which stores 1 bit per nucleotide. Simulations of the codec support reliable and robust storage of information for large-scale systems. This work paves the way for alternative synthesis and sequencing strategies to advance information storage in DNA.

biorxiv synthetic-biology 100-200-users 2018