Chloroplasts navigate towards the pathogen interface to counteract infection by the Irish potato famine pathogen, bioRxiv, 2019-01-10
Chloroplasts are light harvesting organelles that arose from ancient endosymbiotic cyanobacteria. Upon immune activation, chloroplasts switch off photosynthesis, produce anti-microbial compounds, and develop tubular extensions called stromules. We report that chloroplasts navigate to the pathogen interface to counteract infection by the Irish potato famine pathogen Phytophthora infestans, physically associating with the specialised membrane that engulfs pathogen haustoria. Outer envelope protein, chloroplast unusual positioning1 (CHUP1), anchors chloroplasts to the host-pathogen interface. Stromules are induced during infection in a CHUP1-dependent manner, embracing haustoria and interconnecting chloroplasts, to form dynamic organelle clusters. Infection-triggered reprogramming of chloroplasts relies on surface immune signalling, whereas pathogen effectors subvert these immune pulses. Chloroplast are deployed focally, and coordinate to restrict pathogen entry into plant cells, a process actively countered by parasite effectors.
biorxiv plant-biology 100-200-users 2019Evolutionary Dynamics Do Not Motivate a Single-Mutant Theory of Human Language Supplementary Sections, bioRxiv, 2019-01-10
One of the most controversial hypotheses in cognitive science is the Chomskyan evolutionary conjecture that language arose instantaneously in our species as the result of a single staggeringly fortuitous mutation. Here we analyze the evolutionary dynamics implied by this hypothesis, which has never been formalized. The theory supposes the emergence and fixation of a single mutant (capable of the syntactic operation Merge) during a narrow historical window as a result of frequency-independent selection under a huge fitness advantage in a population of an effective size that is standardly assumed to have been no larger than ~15 000 early humans. We examine this proposal by combining diffusion analysis and extreme value theory to derive a probabilistic formulation of its dynamics. Perhaps counter-intuitively, a macro-mutation is much more unlikely a priori than multiple mutations with smaller fitness effects, yet both hypotheses predict fixation with high conditional probability. The consequences of this asymmetry have not been accounted for previously. Our results diffuse any suggestion that evolutionary reasoning provides an independent rationale for the controversial single-mutant theory of language.
biorxiv evolutionary-biology 0-100-users 2019Individual-Specific fMRI-Subspaces Improve Functional Connectivity Prediction of Behavior Supplemental, bioRxiv, 2019-01-10
There is significant interest in using resting-state functional connectivity (RSFC) to predict human behavior. Good behavioral prediction should in theory require RSFC to be sufficiently distinct across participants; if RSFC were the same across participants, then behavioral prediction would obviously be poor. Therefore, we hypothesize that removing common resting-state functional magnetic resonance imaging (rs-fMRI) signals that are shared across participants would improve behavioral prediction. Here, we considered 803 participants from the human connectome project (HCP) with four rs-fMRI runs. We applied the common and orthogonal basis extraction (COBE) technique to decompose each HCP run into two subspaces a common (group-level) subspace shared across all participants and a subject-specific subspace. We found that the first common COBE component of the first HCP run was localized to the visual cortex and was unique to the run. On the other hand, the second common COBE component of the first HCP run and the first common COBE component of the remaining HCP runs were highly similar and localized to regions within the default network, including the posterior cingulate cortex and precuneus. Overall, this suggests the presence of run-specific (state-specific) effects that were shared across participants. By removing the first and second common COBE components from the first HCP run, and the first common COBE component from the remaining HCP runs, the resulting RSFC improves behavioral prediction by an average of 11.7% across 58 behavioral measures spanning cognition, emotion and personality.
biorxiv neuroscience 0-100-users 2019The population dynamics of a canonical cognitive circuit Supplementary Information, bioRxiv, 2019-01-10
The brain constructs distributed representations of key low-dimensional variables. These variables may be external stimuli or internal constructs of quantities relevant for survival, such as a sense of one's location in the world. We consider that the high-dimensional population-level activity vectors are the fundamental representational currency of a neural circuit, and these vectors trace out a low-dimensional manifold whose dimension and topology matches those of the represented variable. This manifold perspective -- applied to the mammalian head direction circuit across rich waking behaviors and sleep -- enables powerful inferences about circuit representation and mechanism, including Direct visualization and blind discovery that the network represents a one-dimensional circular variable across waking and REM sleep; fully unsupervised decoding of the coded variable; stability and attractor dynamics in the representation; the discovery of new dynamical trajectories during sleep; the limiting role of external rather than internal noise in the fidelity of memory states; and the conclusion that the circuit is set up to integrate velocity inputs according to classical continuous attractor models.
biorxiv neuroscience 0-100-users 2019False-positive neuroimaging Undisclosed flexibility in testing spatial hypotheses allows presenting anything as a replicated finding, bioRxiv, 2019-01-09
AbstractHypothesis testing in neuroimaging studies relies heavily on treating named anatomical regions (e.g., “the amygdala”) as unitary entities. Though data collection and analyses are conducted at the voxel level, inferences are often based on anatomical regions. The discrepancy between the unit of analysis and the unit of inference leads to ambiguity and flexibility in analyses that can create a false sense of reproducibility. For example, hypothesizing effects on “amygdala activity” does not provide a falsifiable and reproducible definition of precisely which voxels or which patterns of activation should be observed. Rather, it comprises a large number of unspecified sub-hypotheses, leaving room for flexible interpretation of findings, which we refer to as “model degrees of freedom.” From a survey of 135 functional Magnetic Resonance Imaging studies in which researchers claimed replications of previous findings, we found that 42.2% of the studies did not report any quantitative evidence for replication such as activation peaks. Only 14.1% of the papers used exact coordinate-based or a priori pattern-based models. Of the studies that reported peak information, 42.9% of the ‘replicated’ findings had peak coordinates more than 15 mm away from the ‘original’ findings, suggesting that different brain locations were activated, even when studies claimed to replicate prior results. To reduce the flexible and qualitative region-level tests in neuroimaging studies, we recommend adopting quantitative spatial models and tests to assess the spatial reproducibility of findings. Techniques reviewed here include permutation tests on peak distance, Bayesian MANOVA, and a priori multivariate pattern-based models. These practices will help researchers to establish precise and falsifiable spatial hypotheses, promoting a cumulative science of neuroimaging.
biorxiv neuroscience 200-500-users 2019From Habitat Use to Social Behavior Natural History of a Voiceless Poison Frog, Dendrobates tinctorius, bioRxiv, 2019-01-09
Descriptive studies of natural history have always been a source of knowledge on which experimental work and scientific progress rely. Poison frogs are a well-studied group of small Neotropical frogs with diverse parental behaviors, distinct calls, and bright colors that warn predators about their toxicity; and a showcase of advances in fundamental biology through natural history observations. The dyeing poison frog, Dendrobates tinctorius, is emblematic of the Guianas region, widespread in the pet-trade, and increasingly popular in research. This species shows several unusual behaviors, such as the lack of advertisement calls and the aggregation around tree-fall gaps, which remain poorly described and understood. Here, we summarize our observations from a natural population of D. tinctorius in French Guiana collected over various field trips between 2009 and 2017; our aim is to provide groundwork for future fundamental and applied research spanning parental care, animal dispersal, disease spread, habitat use in relation to color patterns, and intra specific communication, to name a few. We report sex differences in habitat use and the striking invasion of tree-fall gaps; describe their courtship and aggressive behaviors; document egg development and tadpole transport; and discuss how the knowledge generated by this study could set the grounds for further research on the behavior, ecology, and conservation of this species.
biorxiv animal-behavior-and-cognition 0-100-users 2019