Charting the native architecture of thylakoid membranes with single-molecule precision, bioRxiv, 2019-09-05
Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light to produce oxygen, NADPH, and ATP. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Using cryo-electron tomography to analyze membrane surface topology, we have mapped the native molecular landscape of thylakoid membranes within green algae cells. Our tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains. This new approach to charting thylakoid topology lays the foundation for dissecting photosynthetic regulation at the level of single protein complexes within the cell.
biorxiv plant-biology 0-100-users 2019GeneWalk identifies relevant gene functions for a biological context using network representation learning, bioRxiv, 2019-09-05
AbstractThe primary bottleneck in high-throughput genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Existing methods such as Gene Ontology (GO) enrichment analysis provide insight at the gene set level. For individual genes, GO annotations are static and biological context can only be added by manual literature searches. Here, we introduce GeneWalk (<jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpgithub.comchurchmanlabgenewalk>github.comchurchmanlabgenewalk<jatsext-link>), a method that identifies individual genes and their relevant functions under a particular experimental condition. After automatic assembly of an experiment-specific gene regulatory network, GeneWalk quantifies the similarity between vector representations of each gene and its GO annotations through representation learning, yielding annotation significance scores that reflect their functional relevance for the experimental context. We demonstrate the use of GeneWalk analysis of RNA-seq and nascent transcriptome (NET-seq) data from human cells and mouse brains, validating the methodology. By performing gene- and condition-specific functional analysis that converts a list of genes into data-driven hypotheses, GeneWalk accelerates the interpretation of high-throughput genetics experiments.
biorxiv bioinformatics 200-500-users 2019Profiling cellular diversity in sponges informs animal cell type and nervous system evolution, bioRxiv, 2019-09-05
AbstractThe evolutionary origin of metazoan cell types such as neurons, muscles, digestive, and immune cells, remains unsolved. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identify 18 distinct cell types comprising four major families. This includes nitric-oxide sensitive contractile cells, digestive cells active in macropinocytosis, and a family of amoeboid-neuroid cells involved in innate immunity. We uncover ‘presynaptic’ genes in an amoeboid-neuroid cell type, and ‘postsynaptic’ genes in digestive choanocytes, suggesting asymmetric and targeted communication. Corroborating this, long neurite-like extensions from neuroid cells directly contact and enwrap choanocyte microvillar collars. Our data indicate a link between neuroid and immune functions in sponges, and suggest that a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.
biorxiv developmental-biology 100-200-users 2019Stimjim open source hardware for precise electrical stimulation, bioRxiv, 2019-09-05
AbstractElectrical stimulation is a simple and powerful tool to perturb and evoke neuronal activity in order to understand the function of neurons and neural circuits. Despite this, devices that can provide precise current or voltage stimulation are expensive and closed-source. Here, we introduce Stimjim, a capable and inexpensive ($200 USD) open-source instrument for electrical stimulation that combines both function generation and electrical isolation. Stimjim provides microsecond temporal resolution with microampere or millivolt scale precision on two electrically isolated output channels. We demonstrate Stimjim’s utility both in vitro by precisely stimulating brain slices, and in vivo by training mice to perform intracranial self-stimulation (ICSS) for brain stimulation reward. During ICSS, Stimjim enables the experimenter to smoothly tune the strength of reward-seeking behavior by varying either the output frequency or amplitude. We envision Stimjim will enable new kinds of experiments due to its open-source and scalable nature.
biorxiv neuroscience 100-200-users 2019A novel weight lifting task for investigating effort and persistence in rats, bioRxiv, 2019-09-04
AbstractHere we present a novel effort-based task for laboratory rats the weight lifting task (WLT). Studies of effort expenditure in rodents have typically involved climbing barriers within T-mazes or operant lever pressing paradigms. These task designs have been successful for neuropharmacological and neurophysiological investigations, but both tasks involve simple action patterns prone to automatization. Furthermore, high climbing barriers present risk of injury to animals andor tethered recording equipment. In the WLT, a rat is placed in a large rectangular arena and tasked with pulling a rope 30 cm to trigger food delivery at a nearby spout; weights can be added to the rope in 45 g increments to increase the intensity of effort. As compared to lever pressing and barrier jumping, 30 cm of rope pulling is a multi-step action sequence requiring sustained effort. The actions are carried out on the single plane of the arena floor, making it safer for the animal and more suitable for tethered equipment and video tracking. A microcontroller and associated sensors enable precise timestamping of specific behaviors to synchronize with electrophysiological recordings. The rope and reward spout are spatially segregated to allow for spatial discrimination of the effort zone and the reward zone. We validated the task across five cohorts of rats (total n=35) and report consistent behavioral metrics. The WLT is well-suited for neuropharmacological andor in vivo neurophysiological investigations surrounding effortful behaviors, particularly when wanting to probe different aspects of effort expenditure (intensity vs. duration).
biorxiv animal-behavior-and-cognition 200-500-users 2019Genomics reveals the origins of ancient specimens, bioRxiv, 2019-09-04
Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We deduced geographical origins of several ancient specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology countless old, poorly documented specimens that serve as irreplaceable embodiments of species concepts. The ability to figure out where they were collected will resolve many on-going disputes. More broadly, we show the utility of genomics applied to ancient museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.
biorxiv zoology 200-500-users 2019