Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Experimental single-cell approaches are becoming widely used for many purposes, including investigation of the dynamic behaviour of developing biological systems. Consequently, a large number of computational methods for extracting dynamic information from such data have been developed. One example is RNA velocity analysis, in which spliced and unspliced RNA abundances are jointly modeled in order to infer a ‘direction of change’ and thereby a future state for each cell in the gene expression space. Naturally, the accuracy and interpretability of the inferred RNA velocities depend crucially on the correctness of the estimated abundances. Here, we systematically compare five widely used quantification tools, in total yielding thirteen different quantification approaches, in terms of their estimates of spliced and unspliced RNA abundances in five experimental droplet scRNA-seq data sets. We show that there are substantial differences between the quantifications obtained from different tools, and identify typical genes for which such discrepancies are observed. We further show that these abundance differences propagate to the downstream analysis, and can have a large effect on estimated velocities as well as the biological interpretation. Our results highlight that abundance quantification is a crucial aspect of the RNA velocity analysis workflow, and that both the definition of the genomic features of interest and the quantification algorithm itself require careful consideration.     

Body size and host range in European Heteroptera

We used data on body size and host range of phytophagous Heteroptera in central Europe, an inverse measure of specialisation, to analyse the relationship of body size vs specialisation: 1) we found a clear positive relationship between body size and host range using species as independent data points. 2) However, a nested analysis of variance shows that most of the variance in body size occurred at higher taxonomic levels whereas most of the variance in host specialisation occurred between species. This suggests different phylogenetic inertia of body size and specialisation. Nevertheless, using means of different higher taxonomic levels there is still a significant positive correlation between body size and host range. 3) With more sophisticated methods of correcting for the phylogenetic relatedness between species, the positive correlation between body size and host range still holds, despite the different assumptions of each method. Thus, the relationship between body size and host range is a very robust pattern in true bugs.     

Cover-Encodings of Fitness Landscapes

The traditional way of tackling discrete optimization problems is by using local search on suitably defined cost or fitness landscapes. Such approaches are however limited by the slowing down that occurs when the local minima that are a feature of the typically rugged landscapes encountered arrest the progress of the search process. Another way of tackling optimization problems is by the use of heuristic approximations to estimate a global cost minimum. Here, we present a combination of these two approaches by using cover-encoding maps which map processes from a larger search space to subsets of the original search space. The key idea is to construct cover-encoding maps with the help of suitable heuristics that single out near-optimal solutions and result in landscapes on the larger search space that no longer exhibit trapping local minima. We present cover-encoding maps for the problems of the traveling salesman, number partitioning, maximum matching and maximum clique; the practical feasibility of our method is demonstrated by simulations of adaptive walks on the corresponding encoded landscapes which find the global minima for these problems.     

Loss of Eph-receptor expression correlates with loss of cell adhesion and chondrogenic capacity in Hoxa13 mutant limbs.

Mesenchymal patterning is an active process whereby genetic commands coordinate cell adhesion, sorting and condensation, and thereby direct the formation of morphological structures. In mice that lack the Hoxa13 gene, the mesenchymal condensations that form the autopod skeletal elements are poorly resolved, resulting in missing digit, carpal and tarsal elements. In addition, mesenchymal and endothelial cell layers of the umbilical arteries (UAs) are disorganized, resulting in their stenosis and in embryonic death. To further investigate the role of Hoxa13 in these phenotypes, we generated a loss-of-function allele in which the GFP gene was targeted into the Hoxa13 locus. This allele allowed FACS isolation of mesenchymal cells from Hoxa13 heterozygous and mutant homozygous limb buds. Hoxa13(GFP) expressing mesenchymal cells from Hoxa13 mutant homozygous embryos are defective in forming chondrogenic condensations in vitro. Analysis of pro-adhesion molecules in the autopod of Hoxa13 mutants revealed a marked reduction in EphA7 expression in affected digits, as well as in micromass cell cultures prepared from mutant mesenchymal cells. Finally, antibody blocking of the EphA7 extracellular domain severely inhibits the capacity of Hoxa13(GFP) heterozygous cells to condense and form chondrogenic nodules in vitro, which is consistent with the hypothesis that reduction in EphA7 expression affects the capacity of Hoxa13(-/-) mesenchymal cells to form chondrogenic condensations in vivo and in vitro. EphA7 and EphA4 expression were also decreased in the mesenchymal and endothelial cells that form the umbilical arteries in Hoxa13 mutant homozygous embryos. These results suggest that an important role for Hoxa13 during limb and UA development is to regulate genes whose products are required for mesenchymal cell adhesion, sorting and boundary formation.     

Potential toxicity of chrysophytes affiliated with Poterioochromonas and related 'Spumella-like' flagellates

The chrysophyte genera Poterioochromonas and Ochromonas andtheir heterotrophic analogons, i.e. the ‘Spumella-like’flagellates, account for a significant and often dominatingfraction of the pelagic nanoplankton. Even though several osmotrophicallyand autotrophically grown strains of Ochromonas and Poterioochromonasare assumed to produce toxins, the potential toxicity has beeninvestigated neither for its association with bacterivorousnutrition nor within the related exclusively heterotrophic ‘Spumella-like’flagellates. We investigated the toxic potential of severalflagellate strains using cultures of flagellates, cell extractsand filtrate of flagellate cultures. The effect on potentialpredators was exemplarily tested for the cladoceran Daphniamagna and the rotifer Platyias sp. All tested heterotrophicand mixotrophic flagellate strains were toxic to zooplanktonat abundances exceeding 10⁴ flagellates mL^–1. For therotifers, survival on any of the flagellate strains was significantlylower than that in the control treatment (P < 0.001) alreadyafter 24 h. We conclude that (i) ‘Spumella-like’flagellates can be toxic to zooplankton, (ii) all tested flagellates,i.e. heterotrophic and mixotrophic flagellates, feeding phagotrophicallycan be toxic to zooplankton and (iii) sublethal effects maybe observed at typical field abundances, even though acute toxicityseems to be restricted to flagellate abundances observed onlyat peak events.     

Structural analysis of a plant sucrose carrier using monoclonal antibodies and bacteriophage lambda surface display.

Monoclonal antibodies were raised and selected against recombinant Plantago major PmSUC2 sucrose carrier protein. Epitopes of two monoclonal antibodies (PS2-1A2 and PS2-4D4) were mapped using N-terminally truncated PmSUC2 proteins and a lambda library displaying random PmSUC2 peptides. PS2-1A2 recognizes an octapeptide close to the N-terminus of PmSUC2, PS2-4D4 binds to a decapeptide at the very C-terminus. Analyses of antibody binding to yeast protoplasts with functionally active, tagged PmSUC2 protein revealed that both epitopes are located in cytoplasmic domains of PmSUC2. These results support a model for plant sucrose transporters containing 12 transmembrane helices with the N-terminus and the C-terminus on the cytoplasmic side of the plasma membrane.     

Action of repeat-induced point mutation on both strands of a duplex and on tandem duplications of various sizes in Neurospora.

In Neurospora crassa, DNA sequence duplications are detected and altered efficiently during the sexual cycle by a process known as RIP (repeat-induced point mutation). Affected sequences are subjected to multiple GC-to-AT mutations. To explore the pattern in which base changes are laid down by RIP we examined two sets of strains. First, we examined the products of a presumptive spontaneous RIP event at the mtr locus. Results of sequencing suggested that a single RIP event produces two distinct patterns of change, descended from the two strands of an affected DNA duplex. Equivalent results were obtained using an exceptional tetrad from a cross with a known duplication flanking the zeta-eta (zeta-eta) locus. The mtr sequence data were also used to further examine the basis for the differential severity of C-to-T mutations on the coding and noncoding strands in genes. The known bias of RIP toward CpA/TpG sites in conjunction with the sequence bias of Neurospora accounts for the differential effect. Finally, we used a collection of tandem repeats (from 16 to 935 bp in length) within the mtr gene to examine the length requirement for RIP. No evidence of RIP was found with duplications shorter than 400 bp while all longer tandem duplications were frequently affected. A comparison of these results with vegetative reversion data for the same duplications is consistent with the idea that reversion of long tandem duplications and RIP share a common step.