A perturbation of the geometric spectral sequence in Khovanov homology

We study the relationship between Bar-Natan's perturbation in Khovanov homology and Szabo's geometric spectral sequence, and construct a link invariant that generalizes both into a common theory. We study a few properties of the new invariant, and introduce a family of s-invariants from the new theory in the same spirit as Rasmussen's s-invariant

Anti-phage islands force their target phage to directly mediate island excision and spread.

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is antagonized by the lytic phage ICP1 in the aquatic environment and in human hosts. Mobile genetic elements called PLEs (phage-inducible chromosomal island-like elements) protect V. cholerae from ICP1 infection and initiate their anti-phage response by excising from the chromosome. Here, we show that PLE 1 encodes a large serine recombinase, Int, that exploits an ICP1-specific protein as a recombination directionality factor (RDF) to excise PLE 1 in response to phage infection. We show that this phage-encoded protein is sufficient to direct Int-mediated recombination in vitro and that it is highly conserved in all sequenced ICP1 genomes. Our results uncover an aspect of the molecular specificity underlying the conflict between a single predatory phage and V. cholerae PLE and contribute to our understanding of long-term evolution between phage and their bacterial hosts

Comparative psychometrics: establishing what differs is central to understanding what evolves

Cognitive abilities cannot be measured directly. What we can measure is individual variation in task performance. In this paper, we first make the case for why we should be interested in mapping individual differences in task performance on to particular cognitive abilities: we suggest that it is crucial for examining the causes and consequences of variation both within and between species. As a case study, we examine whether multiple measures of inhibitory control for non-human animals do indeed produce correlated task performance; however, no clear pattern emerges that would support the notion of a common cognitive ability underpinning individual differences in performance. We advocate a psychometric approach involving a three-step programme to make theoretical and empirical progress: first, we need tasks that reveal signature limits in performance. Second, we need to assess the reliability of individual differences in task performance. Third, multi-trait multi-method test batteries will be instrumental in validating cognitive abilities. Together, these steps will help us to establish what varies between individuals that could impact their fitness and ultimately shape the course of the evolution of animal minds. Finally, we propose executive functions, including working memory, inhibitory control and attentional shifting, as a sensible starting point for this endeavour