MINFLUX nanoscopy delivers multicolor nanometer 3D-resolution in (living) cells, bioRxiv, 2019-08-14
The ultimate goal of biological superresolution fluorescence microscopy is to provide three-dimensional resolution at the size scale of a fluorescent marker. Here, we show that, by localizing individual switchable fluorophores with a probing doughnut-shaped excitation beam, MINFLUX nanoscopy provides 1–3 nanometer resolution in fixed and living cells. This progress has been facilitated by approaching each fluorophore iteratively with the probing doughnut minimum, making the resolution essentially uniform and isotropic over scalable fields of view. MINFLUX imaging of nuclear pore complexes of a mammalian cell shows that this true nanometer scale resolution is obtained in three dimensions and in two color channels. Relying on fewer detected photons than popular camera-based localization, MINFLUX nanoscopy is poised to open a new chapter in the imaging of protein complexes and distributions in fixed and living cells.
biorxiv biophysics 100-200-users 2019Predicting antigen-specificity of single T-cells based on TCR CDR3 regions, bioRxiv, 2019-08-14
It has recently become possible to assay T-cell specificity with respect to large sets of antigens as well as T-cell receptor sequence in high-throughput single-cell experiments. We propose multiple sequence-data specific deep learning approaches to impute TCR to epitope specificity to reduce the complexity of new experiments. We found that models that treat antigens as categorical variables outperform those which model the TCR and epitope sequence jointly. Moreover, we show that variability in single-cell immune repertoire screens can be mitigated by modeling cell-specific covariates.
biorxiv bioinformatics 0-100-users 2019Dopamine waves as a mechanism for spatiotemporal credit assignment, bioRxiv, 2019-08-13
AbstractSignificant evidence supports the view that dopamine shapes reward-learning by encoding prediction errors. However, it is unknown whether dopamine decision-signals are tailored to the functional specialization of target regions. Here, we report a novel set of wave-like spatiotemporal activity-patterns in dopamine axons across the dorsal striatum. These waves switch between different activational motifs and organize dopamine transients into localized clusters within functionally related striatal subregions. These specific motifs are associated with distinct task contexts At reward delivery, dopamine signals rapidly resynchronize into propagating waves with opponent directions depending on instrumental task contingencies. Moreover, dopamine dynamics during reward pursuit signal the extent to which mice have instrumental control and interact with reward waves to predict future behavioral adjustments. Our results are consistent with a computational architecture in which striatal dopamine signals are sculpted by inference about instrumental controllability and provide evidence for a spatiotemporally “vectorized” role of dopamine in credit assignment.
biorxiv neuroscience 100-200-users 2019Myristate as a carbon and energy source for the asymbiotic growth of the arbuscular mycorrhizal fungus Rhizophagus irregularis, bioRxiv, 2019-08-11
AbstractArbuscular mycorrhiza (AM) is one of the most widespread mutualistic symbioses, which is formed between the majority of land plants and soil-borne fungi belonging to Glomeromycotina. AM fungi are obligate symbionts that cannot complete their natural life cycle without a host. Recent evidence suggests that lipids synthesized by a host are transferred to AM fungi that possess no fatty acid synthase genes in their genome and that mutations in lipid biosynthesis-related genes of the host lead the symbiotic interaction to fail (1–3). We hypothesized that lipids derived from plants are crucial for AM fungal growth and reproduction. In this study, we evaluated whether AM fungi can grow on medium supplied with fatty acids under asymbiotic conditions without the host. Myristate led to an extensive hyphal growth of Rhizophagus irregularis and an increase in biomass production. Other examined fatty acids showed no effect on biomass production. Myristate also induced secondary spore formation. The myristate-induced spores can germinate, colonize carrot hairy roots, and form the next generation of mature daughter spores. A fluorescently labeled fatty acid probe was taken up by branched hyphae of AM fungi. Tracer experiments using 13C-labeled myristic acid showed that myristate and its metabolites were utilized for the synthesis of triacylglycerol and cell wall components of AM fungi. Furthermore, myristate activated ATP generation in the fungal hyphae. Here we demonstrate that myristate is utilized as a carbon and energy source for biomass production and sporulation under asymbiotic conditions.
biorxiv microbiology 0-100-users 2019Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes, bioRxiv, 2019-08-10
SummaryMetagenomic studies have claimed the existence of novel lineages with unprecedented properties never before observed in prokaryotes. Such lineages include Asgard archaea1–3, which are purported to represent archaea with eukaryotic cell complexity, and the Candidate Phyla Radiation (CPR), a novel domain level taxon erected solely on the basis of metagenomic data4. However, it has escaped the attention of most biologists that these metagenomic sequences are not assembled into genomes by sequence overlap, as for cultured archaea and bacteria. Instead, short contigs are sorted into computer files by a process called binning in which they receive taxonomic assignment on the basis of sequence properties like GC content, dinucleotide frequencies, and stoichiometric co-occurrence across samples. Consequently, they are not genome sequences as we know them, reflecting the gene content of real organisms. Rather they are metagenome assembled genomes (MAGs). Debates that Asgard data are contaminated with individual eukaryotic sequences5–7 are overshadowed by the more pressing issue that no evidence exists to indicate that any sequences in binned Asgard MAGs actually stem from the same chromosome, as opposed to simply stemming from the same environment. Here we show that Asgard and CPR MAGs fail spectacularly to meet the most basic phylogenetic criterion8 fulfilled by genome sequences of all cultured prokaryotes investigated to date the ribosomal proteins of Asgard and CPR MAGs do not share common evolutionary histories. Their phylogenetic behavior is anomalous to a degree never observed with genomes of real organisms. CPR and Asgard MAGs are binning artefacts, assembled from environments where up to 90% of the DNA is from dead cells9–12. Asgard and CPR MAGs are unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning.
biorxiv evolutionary-biology 100-200-users 2019Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers, bioRxiv, 2019-08-10
AbstractWe analyzed summary-level data from genome-wide association studies (GWAS) of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) contributing to risk, as well as the distribution of their associated effect sizes. All cancers evaluated showed polygenicity, involving at a minimum thousands of independent susceptibility variants. For some malignancies, particularly chronic lymphoid leukemia (CLL) and testicular cancer, there are a larger proportion of variants with larger effect sizes than those for other cancers. In contrast, most variants for lung and breast cancers have very small associated effect sizes. For different cancer sites, we estimate a wide range of GWAS sample sizes, required to explain 80% of GWAS heritability, varying from 60,000 cases for CLL to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores, compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that polygenic risk scores have substantial potential for risk stratification for relatively common cancers such as breast, prostate and colon, but limited potential for other cancer sites because of modest heritability and lower disease incidence.
biorxiv genetics 0-100-users 2019