Novel Sequence Features of Leucine-rich Repeats in Proteins from Nucleo-cytoplasmic Large DNA Viruses

: Leucine-rich repeats (LRRs) occurring in tandem are 20-29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs, 549 LRR proteins were identified and analyzed. A comprehensive analysis of TpLRR and FNIP that belong to an LRR class was first performed. The repeating unit lengths (RULs) in five types are 19 residues, which are the shortest among all LRRs. Some RULs are one to five residues shorter than those of the known, corresponding LRR types. The shrinking of RUL is also observed in FNIP. The conserved hydrophobic residues, such as Leu, Val or Ile, in the consensus sequences are frequently substituted by cysteine at one or two positions. Some unique LRR types that are different from those identified previously have been observed. The present study confirms the previous result that the sequence novelty is a general feature of viral LRR proteins.

Downstroke and upstroke conflict during banked turns in butterflies

For all flyers, aeroplanes or animals, making banked turns involve a rolling motion which, due to higher induced drag on the outer than the inner wing, results in a yawing torque opposite to the turn. This adverse yaw torque can be counteracted using a tail, but how animals that lack tail, e.g. all insects, handle this problem is not fully understood. Here, we quantify the performance of turning take-off flights in butterflies and find that they use force vectoring during banked turns without fully compensating for adverse yaw. This lowers their turning performance, increasing turn radius, since thrust becomes misaligned with the flight path. The separation of function between downstroke (lift production) and upstroke (thrust production) in our butterflies, in combination with a more pronounced adverse yaw during the upstroke increases the misalignment of the thrust. This may be a cost the butterflies pay for the efficient thrust-generating upstroke clap, but also other insects fail to rectify adverse yaw during escape manoeuvres, suggesting a general feature in functionally two-winged insect flight. When lacking tail and left with costly approaches to counteract adverse yaw, costs of flying with adverse yaw may be outweighed by the benefits of maintaining thrust and flight speed.

On Johnson’s “Sufficientness” Postulates for Feature-Sampling Models

In the 1920s, the English philosopher W.E. Johnson introduced a characterization of the symmetric Dirichlet prior distribution in terms of its predictive distribution. This is typically referred to as Johnson’s “sufficientness” postulate, and it has been the subject of many contributions in Bayesian statistics, leading to predictive characterization for infinite-dimensional generalizations of the Dirichlet distribution, i.e., species-sampling models. In this paper, we review “sufficientness” postulates for species-sampling models, and then investigate analogous predictive characterizations for the more general feature-sampling models. In particular, we present a “sufficientness” postulate for a class of feature-sampling models referred to as Scaled Processes (SPs), and then discuss analogous characterizations in the general setup of feature-sampling models.

Hyperembodiment

The article introduces hyperembodiment as a general feature of artefacts for perception and representation and as a research agenda for cognitive semiotics and cognitive science at large. At the heart of the article, I offer analyses of two different selected examples: Hyperembodiment in a Facetime conversation and in a Snapchat message. These digital productions of appearances of social interactants are analysed with particular attention to their intercorporeal qualities and it is argued that social perception is facilitated which takes the users of visual, interpersonal communication devices beyond the corporeal limits of ordinary ways of being present for each other. Broadening the scope, I then discuss how a general focus on hyperembodiment opens new, productive avenues of inquiry. First, I relate hyperembodiment to the heterogenous field of social presence research and suggest how it may contribute to it. Thereafter I discuss hyperembodiment as a topic of cognitive semiotics.

Extremal lifetimes of persistent cycles

Persistent homology captures the appearances and disappearances of topological features such as loops and cavities when growing disks centered at a Poisson point process. We study extreme values for the lifetimes of features dying in bounded components and with birth resp. death time bounded away from the threshold for continuum percolation and the coexistence region. First, we describe the scaling of the minimal lifetimes for general feature dimensions, and of the maximal lifetimes for cavities in the Čech filtration. Then, we proceed to a more refined analysis and establish Poisson approximation for large lifetimes of cavities and for small lifetimes of loops. Finally, we also study the scaling of minimal lifetimes in the Vietoris-Rips setting and point to a surprising difference to the Čech filtration.

Apoptosis resistance of senescent cells is an intrinsic barrier for senolysis induced by cardiac glycosides

Targeted elimination of senescent cells, senolysis, is one of the core trends in the anti-aging therapy. Cardiac glycosides were recently proved to be a broad-spectrum senolytics. Here we tested senolytic properties of cardiac glycosides towards human mesenchymal stem cells (hMSCs). Cardiac glycosides had no senolytic ability towards senescent hMSCs of various origins. Using biological and bioinformatic approaches we compared senescence development in ‘cardiac glycosides-sensitive’ A549 and ‘-insensitive’ hMSCs. The absence of senolysis was found to be mediated by the effective potassium import and increased apoptosis resistance in senescent hMSCs. Weakening “antiapoptotic defense” predisposes hMSCs to senolysis. We revealed that apoptosis resistance, previously recognized as a common characteristic of senescence, in fact, is not a general feature of senescent cells. Moreover, only apoptosis-prone senescent cells are sensitive to cardiac glycosides-induced senolysis. Thus, we can speculate that the effectiveness of senolysis might depend on whether senescent cells indeed become apoptosis-resistant as compared to their proliferating counterparts. Graphic abstract

How Running Give Us a High Expectations to Overcome Neurological Disorders

Whether chasing down dinner, pushing a stroller up a hill or running errands for a neighbor, we can take joy in the effort. And the more physically active you are, the more rewarding these experiences become. One of the ways that regular exercise changes your brain is by increasing the density of binding sites for endocannabinoids. Spring-like leg behavior is a general feature of mammalian bouncing gaits, such as running and hopping. Although increases in step frequency at a given running speed are known to increase the stiffness of the leg spring (kleg) in non-amputees, little is known about stiffness regulation in unilateral transfemoral amputees. Thus Consequently, the unilateral transfemoral amputees attained the desired step frequency in the unaffected limb, but were unable to match the three highest step frequencies using their affected limbs

Forgiveness as Renunciation of Moral Protest

Chapter 5 sets out an account of forgiveness consistent with the rejection of the retributive emotions. On the standard view, forgiveness is the renunciation and overcoming of resentment, which is at least typically a retributive emotion. Thus on the standard view forgiveness involves the renunciation of an attitude that for the skeptic about retribution was inappropriate in the first place. If forgiveness is instead understood as renunciation of the stance of moral protest, then for the skeptic forgiveness is in the clear, since that stance need not presuppose desert. Renunciation of moral protest potentially qualifies as a general feature of forgiveness, by contrast with renunciation of resentment. In a range of cases of wrongdoing resentment is initially unfitting for reasons independent of concerns about retribution.

Cellular organization in lab-evolved and extant multicellular species obeys a maximum entropy law

The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains unknown about how cell packing geometries arise, and how they are affected by random noise during growth - especially absent developmental programs. Here, we quantify the statistics of cellular neighborhoods of two different multicellular eukaryotes: lab-evolved "snowflake" yeast and the green alga Volvox carteri. We find that despite large differences in cellular organization, the free space associated with individual cells in both organisms closely fits a modified gamma distribution, consistent with maximum entropy predictions originally developed for granular materials. This 'entropic' cellular packing ensures a degree of predictability despite noise, facilitating parent-offspring fidelity even in the absence of developmental regulation. Together with simulations of diverse growth morphologies, these results suggest that gamma-distributed cell neighborhood sizes are a general feature of multicellularity, arising from conserved statistics of cellular packing.