Super-resolution fight club A broad assessment of 2D & 3D single-molecule localization microscopy software, bioRxiv, 2018-07-04
ABSTRACTWith the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. We generated realistic simulated datasets for popular imaging modalities – 2D, astigmatic 3D, biplane 3D, and double helix 3D – and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.
biorxiv biophysics 100-200-users 2018Systematic assessment of GFP tag position on protein localization and growth fitness in yeast, bioRxiv, 2018-07-02
AbstractWhile protein tags are ubiquitously utilized in molecular biology, they harbor the potential to interfere with functional traits of their fusion counterparts. Systematic evaluation of the effect of protein tags on localization and function would promote accurate use of tags in experimental setups. Here we examine the effect of Green Fluorescent Protein (GFP) tagging at either the N or C terminus of budding yeast proteins on localization and functionality. We use a competition-based approach to decipher the relative fitness of two strains tagged on the same protein but on opposite termini and from that infer the correct, physiological localization for each protein and the optimal position for tagging. Our study provides a first of a kind systematic assessment of the effect of tags on the functionality of proteins and provides step towards broad investigation of protein fusion libraries.Highlights<jatslist list-type=bullet><jatslist-item>Protein tags are widely used in molecular biology although they may interfere with protein function.<jatslist-item><jatslist-item>The subcellular localization of hundreds of proteins in yeast is different when tagged at the N or the C terminus.<jatslist-item><jatslist-item>A competition based assay enables systematic deciphering of correct tagging terminus for essential proteins.<jatslist-item><jatslist-item>The presented approach can be used to derive physiologically relevant tagged libraries.<jatslist-item>
biorxiv cell-biology 200-500-users 2018A 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 2018Nested oscillatory dynamics in cortical organoids model early human brain network development, bioRxiv, 2018-06-29
SUMMARYStructural and transcriptional changes during early brain maturation follow fixed developmental programs defined by genetics. However, whether this is true for functional network activity remains unknown, primarily due to experimental inaccessibility of the initial stages of the living human brain. Here, we developed cortical organoids that spontaneously display periodic and regular oscillatory network events that are dependent on glutamatergic and GABAergic signaling. These nested oscillations exhibit cross-frequency coupling, proposed to coordinate neuronal computation and communication. As evidence of potential network maturation, oscillatory activity subsequently transitioned to more spatiotemporally irregular patterns, capturing features observed in preterm human electroencephalography (EEG). These results show that the development of structured network activity in the human neocortex may follow stable genetic programming, even in the absence of external or subcortical inputs. Our approach provides novel opportunities for investigating and manipulating the role of network activity in the developing human cortex.HIGHLIGHTS<jatslist list-type=bullet><jatslist-item>Early development of human functional neural networks and oscillatory activity can be modeled in vitro.<jatslist-item><jatslist-item>Cortical organoids exhibit phase-amplitude coupling between delta oscillation (2 Hz) and high-frequency activity (100-400 Hz) during network-synchronous events.<jatslist-item><jatslist-item>Differential role of glutamate and GABA in initiating and maintaining oscillatory network activity.<jatslist-item><jatslist-item>Developmental impairment of MECP2-KO cortical organoids impacts the emergence of oscillatory activity.<jatslist-item><jatslist-item>Cortical organoid network electrophysiological signatures correlate with human preterm neonatal EEG features.<jatslist-item>eTOCBrain oscillations are a candidate mechanism for how neural populations are temporally organized to instantiate cognition and behavior. Cortical organoids initially exhibit periodic and highly regular nested oscillatory network events that eventually transition to more spatiotemporally complex activity, capturing features of late-stage preterm infant electroencephalography. Functional neural circuitry in cortical organoids exhibits emergence and development of oscillatory network dynamics similar to those found in the developing human brain.
biorxiv neuroscience 0-100-users 2018A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, bioRxiv, 2018-06-27
AbstractGenome-, transcriptome- and proteome-wide measurements provide valuable insights into how biological systems are regulated. However, even fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we have generated a systematic, quantitative and deep proteome and transcriptome abundance atlas from 29 paired healthy human tissues from the Human Protein Atlas Project and representing human genes by 17,615 transcripts and 13,664 proteins. The analysis revealed that few proteins show truly tissue-specific expression, that vast differences between mRNA and protein quantities within and across tissues exist and that the expression levels of proteins are often more stable across tissues than those of transcripts. In addition, only ~2% of all exome and ~7% of all mRNA variants could be confidently detected at the protein level showing that proteogenomics remains challenging, requires rigorous validation using synthetic peptides and needs more sophisticated computational methods. Many uses of this resource can be envisaged ranging from the study of geneprotein expression regulation to protein biomarker specificity evaluation to name a few.
biorxiv systems-biology 200-500-users 2018Combined 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