Precise tuning of cortical contractility regulates cell shape during cytokinesis, bioRxiv, 2019-05-13
ABSTRACTThe mechanical properties of the cellular cortex regulate shape changes during cell division, cell migration and tissue morphogenesis. During cell division, contractile force generated by the molecular motor myosin II (MII) at the equatorial cortex drives cleavage furrow ingression. Cleavage furrow ingression in turn increases stresses at the polar cortex, where contractility must be regulated to maintain cell shape during cytokinesis. How polar cortex contractility controls cell shape is poorly understood. We show a balance between MII paralogs allows a fine-tuning of cortex tension at the polar cortex to maintain cell shape during cytokinesis, with MIIA driving cleavage furrow ingression and bleb formation, and MIIB serving as a stabilizing motor and mediating completion of cytokinesis. As the majority of non-muscle contractile systems are cortical, this tuning mechanism will likely be applicable to numerous processes driven by MII contractility.
biorxiv cell-biology 200-500-users 2019Proximity labeling of protein complexes and cell type-specific organellar proteomes in Arabidopsis enabled by TurboID, bioRxiv, 2019-05-13
AbstractDefining specific protein interactions and spatially or temporally restricted local proteomes improves our understanding of all cellular processes, but obtaining such data is challenging, especially for rare proteins, cell types, or events. Proximity labeling enables discovery of protein neighborhoods defining functional complexes andor organellar protein compositions. Recent technological improvements, namely two highly active biotin ligase variants (TurboID and miniTurboID), allowed us to address two challenging questions in plants (1) what are in vivo partners of a low abundant key developmental transcription factor and (2) what is the nuclear proteome of a rare cell type? Proteins identified with FAMA-TurboID include known interactors of this stomatal transcription factor and novel proteins that could facilitate its activator and repressor functions. Directing TurboID to stomatal nuclei enabled purification of cell type- and subcellular compartment-specific proteins. Broad tests of TurboID and miniTurboID in Arabidopsis and N. benthamiana and versatile vectors enable customization by plant researchers.
biorxiv plant-biology 100-200-users 2019Ultrastructure of the axonal periodic scaffold reveals a braid-like organization of actin rings, bioRxiv, 2019-05-13
AbstractRecent super-resolution microscopy studies have unveiled a periodic scaffold of actin rings regularly spaced by spectrins under the plasma membrane of axons. However, ultrastructural details are unknown, limiting a molecular and mechanistic understanding of these enigmatic structures. Here, we combine platinum-replica electron and optical super-resolution micros-copy to investigate the cortical cytoskeleton of axons at the ultrastructural level. We resolve actin rings as braids made of two long, intertwined actin filaments connected by a dense mesh of aligned spectrins. This molecular arrangement contrasts with the currently assumed model of actin rings made of short, capped actin filaments. We propose that braided rings explain the stability of the actin-spectrin scaffold and ultimately help preserving the axon integrity.
biorxiv cell-biology 200-500-users 2019A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity, bioRxiv, 2019-05-11
AbstractEnvironmental DNA (eDNA) is one of the most promising approaches to meet the demand for the fast and frequent monitoring of ecosystems needed to tackle the current decline in biodiversity. However, before eDNA can establish itself as a robust alternative for mammal monitoring, comparison with existing approaches is necessary, yet has not been done. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases.To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed species observations from a long-term (∼9-yr) camera trapping study. At the same time, we considered multiple experimental parameters, including two sampling designs, two DNA extraction kits and two metabarcodes of different sizes.All mammals consistently recorded with cameras were detected in eDNA. In addition, eDNA reported many small mammals not recorded by camera traps, but whose presence in the study area is otherwise documented. A long metabarcode (≈220bp) offering a high taxonomic resolution, achieved a similar efficiency as a shorter one (≈70bp) and a phosphate buffer-based extraction gave similar results as a total DNA extraction method for a fraction of the price. Our results support that eDNA-based monitoring should become a valuable part of terrestrial mammal surveys. Yet, the lack of coverage of mammal mitochondrial genomes in public databases must be addressed before eDNA can be used to its full potential.
biorxiv ecology 200-500-users 2019Dsuite - fast D-statistics and related admixture evidence from VCF files, bioRxiv, 2019-05-11
AbstractSummaryThe D-statistic, also known as the ABBA-BABA statistic, and related statistics are commonly used to assess evidence of gene flow between populations or closely related species. While the calculations are not computationally intensive, currently available implementations require custom file formats and are impractical to evaluate all gene flow hypotheses across datasets that include many populations or species. Dsuite is a fast C++ implementation, allowing genome scale calculations of the D-statistic across all combinations of tens or even hundreds of populations or species directly from a variant call format (VCF) file. Furthermore, the program can estimate the admixture fraction and provide evidence of whether introgression is confined to specific loci. Thus Dsuite facilitates assessment of gene flow across large genomic datasets.Availability and implementationSource code and documentation are available at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsgithub.commillanekDsuite>httpsgithub.commillanekDsuite<jatsext-link>
biorxiv genomics 0-100-users 2019Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen, bioRxiv, 2019-05-11
ABSTRACTIdentifying the forces that create and shape ecologically meaningful variation in bacteria remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show derived alleles less than 300bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles compared to synonymous alleles. While linkage is shaped by many evolutionary processes, extensive simulations show only two distinct forms of positive selection can drive an excess of coupling linkage between neighboring nonsynonymous alleles directional selection on introgressed alleles or selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.
biorxiv evolutionary-biology 0-100-users 2019