Nanoscale subcellular architecture revealed by multicolor 3D salvaged fluorescence imaging, bioRxiv, 2019-04-19
AbstractCombining the molecular specificity of fluorescent probes with three-dimensional (3D) imaging at nanoscale resolution is critical for investigating the spatial organization and interactions of cellular organelles and protein complexes. We present a super-resolution light microscope that enables simultaneous multicolor imaging of whole mammalian cells at ~20 nm 3D resolution. We show its power for cell biology research with fluorescence images that resolved the highly convoluted Golgi apparatus and the close contacts between the endoplasmic reticulum and the plasma membrane, structures that have traditionally been the imaging realm of electron microscopy.One Sentence SummaryComplex cellular structures previously only resolved by electron microscopy can now be imaged in multiple colors by 4Pi-SMS.
biorxiv biophysics 0-100-users 2019Shared morphological consequences of global warming in North American migratory birds, bioRxiv, 2019-04-19
ABSTRACTIncreasing temperatures associated with climate change are predicted to cause reductions in body size, a key determinant of animal physiology and ecology. Using a four-decade specimen series of 70,716 individuals of 52 North American migratory bird species, we demonstrate that increasing annual summer temperature over the 40-year period drove consistent reductions in body size across these diverse taxa. Concurrently, wing length – which impacts nearly all aspects of avian ecology and behavior – has consistently increased across taxa. Our findings suggest that warming-induced body size reduction is a general response to climate change, and reveal a similarly consistent shift in an ecologically-important dimension of body shape. We hypothesize that increasing wing length represents a compensatory adaptation to maintain migration as reductions in body size have increased the metabolic cost of flight. An improved understanding of warming-induced morphological changes, and their limits, are important for predicting biotic responses to global change.
biorxiv ecology 200-500-users 2019Single Cortical Neurons as Deep Artificial Neural Networks, bioRxiv, 2019-04-19
AbstractWe propose a novel approach based on modern deep artificial neural networks (DNNs) for understanding how the morpho-electrical complexity of neurons shapes their inputoutput (IO) properties at the millisecond resolution in response to massive synaptic input. The IO of integrate and fire point neuron is accurately captured by a DNN with a single unit and one hidden layer. A fully connected DNN with one hidden layer faithfully replicated the IO relationship of a detailed model of Layer 5 cortical pyramidal cell (L5PC) receiving AMPA and GABAA synapses. However, when adding voltage-gated NMDA-conductances, a temporally-convolutional DNN with seven layers was required. Analysis of the DNN filters provides new insights into dendritic processing shaping the IO properties of neurons. This work proposes a systematic approach for characterizing the functional “depth” of a biological neurons, suggesting that cortical pyramidal neurons and the networks they form are computationally much more powerful than previously assumed.
biorxiv neuroscience 500+-users 2019The user’s guide to comparative genomics with EnteroBase. Three case studies micro-clades within Salmonella enterica serovar Agama, ancient and modern populations of Yersinia pestis, and core genomic diversity of all Escherichia, bioRxiv, 2019-04-19
AbstractEnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera including pathogens. It currently contains more than 300,000 genomes that have been assembled from Illumina short reads from the genera Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio, and Moraxella. With the recent introduction of hierarchical clustering of core genome MLST sequence types, EnteroBase now facilitates the identification of close relatives of bacteria within those genera inside of a few hours of uploading their short reads. It also supports private collaborations between groups of users, and the comparison of genomic data that were assembled from short reads with SNP calls that were extracted from metagenomic sequences. Here we provide an overview for its users on how EnteroBase works, what it can do, and its future prospects. This user’s guide is illustrated by three case studies ranging in scale from the miniscule (local transmission of Salmonella between neighboring social groups of badgers) through pandemic transmission of plague and microevolution of Yersinia pestis over the last 5,000 years to a novel, global overview of the population structure of all of Escherichia.
biorxiv microbiology 100-200-users 2019A revised model for promoter competition based on multi-way chromatin interactions, bioRxiv, 2019-04-18
AbstractSpecific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements and genes contained within a single chromatin domain are coordinated. Recent technological advances allow for the investigation of multi-way chromatin interactions at single alleles in individual nuclei. This can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. We have used these techniques in a mouse model in which the α-globin domain is extended to include several additional genes. This allows us to determine how the interactions of the α-globin super-enhancer are distributed between multiple promoters in a single domain. Our data show that gene promoters do not form mutually exclusive interactions with the super-enhancer, but all interact simultaneously in a single complex. These finding show that promoters within the same domain do not structurally compete for interactions with enhancers, but form a regulatory hub structure, consistent with the recent model of transcriptional activation in phase-separated nuclear condensates.
biorxiv genomics 100-200-users 2019deSALT fast and accurate long transcriptomic read alignment with de Bruijn graph-based index, bioRxiv, 2019-04-18
AbstractLong-read RNA sequencing (RNA-seq) is a promising approach in transcriptomics studies, however, the alignment of the long reads is a fundamental but still non-trivial task due to sequencing errors and complicated gene structures. We propose de Bruijn graph-based Spliced Aligner for Long Transcriptome read (deSALT), a tailored two-pass long RNA-seq read alignment approach, which constructs graph-based alignment skeletons to sensitively infer exons and uses them to generate high-quality spliced reference sequences to produce refined alignments. deSALT addresses several difficult technical issues, such as small exons and serious sequencing errors, which breakthroughs the bottlenecks of long RNA-seq read alignment. Benchmarks demonstrate that this approach has a greater ability to produce accurate and homogeneous full-length alignments and thus has enormous potentials in transcriptomics studies.
biorxiv bioinformatics 100-200-users 2019