Lagrangian Statistics of Navier-Stokes- and MHD-Turbulence

We report on a comparison of high-resolution numerical simulations of Lagrangian particles advected by incompressible turbulent hydro- and magnetohydrodynamic (MHD) flows. Numerical simulations were performed with up to $1024^3$ collocation points and 10 million particles in the Navier-Stokes case and $512^3$ collocation points and 1 million particles in the MHD case. In the hydrodynamics case our findings compare with recent experiments from Mordant et al. [1] and Xu et al. [2]. They differ from the simulations of Biferale et al. [3] due to differences of the ranges choosen for evaluating the structure functions. In Navier-Stokes turbulence intermittency is stronger than predicted by a multifractal approach of [3] whereas in MHD turbulence the predictions from the multifractal approach are more intermittent than observed in our simulations. In addition, our simulations reveal that Lagrangian Navier-Stokes turbulence is more intermittent than MHD turbulence, whereas the situation is reversed in the Eulerian case. Those findings can not consistently be described by the multifractal modeling. The crucial point is that the geometry of the dissipative structures have different implications for Lagrangian and Eulerian intermittency. Application of the multifractal approach for the modeling of the acceleration PDFs works well for the Navier-Stokes case but in the MHD case just the tails are well described.Comment: to appear in J. Plasma Phy

Dominant gain-of-function mutations in Hsp104p reveal crucial roles for the middle region

Heat-shock protein 104 (Hsp104p) is a protein-remodeling factor that promotes survival after extreme stress by disassembling aggregated proteins and can either promote or prevent the propagation of prions (protein-based genetic elements). Hsp104p can be greatly overexpressed without slowing growth, suggesting tight control of its powerful protein-remodeling activities. We isolated point mutations in Hsp104p that interfere with this control and block cell growth. Each mutant contained alterations in the middle region (MR). Each of the three MR point mutations analyzed in detail had distinct phenotypes. In combination with nucleotide binding site mutations, Hsp104p(T499I) altered bud morphology and caused septin mislocalization, colocalizing with the misplaced septins. Point mutations in the septin Cdc12p suppressed this phenotype, suggesting that it is due to direct Hsp104p–septin interactions. Hsp104p(A503V) did not perturb morphology but stopped cell growth. Remarkably, when expressed transiently, the mutant protein promoted survival after extreme stress as effectively as did wild-type Hsp104p. Hsp104p(A509D) had no deleterious effects on growth or morphology but had a greatly reduced ability to promote thermotolerance. That mutations in an 11-amino acid stretch of the MR have such profound and diverse effects suggests the MR plays a central role in regulating Hsp104p function

Effect of turbulence on collisions of dust particles with planetesimals in protoplanetary disks

Planetesimals in gaseous protoplanetary disks may grow by collecting dust particles. Hydrodynamical studies show that small particles generally avoid collisions with the planetesimals because they are entrained by the flow around them. This occurs when $St$, the Stokes number, defined as the ratio of the dust stopping time to the planetesimal crossing time, becomes much smaller than unity. However, these studies have been limited to the laminar case, whereas these disks are believed to be turbulent. We want to estimate the influence of gas turbulence on the dust-planetesimal collision rate and on the impact speeds. We used three-dimensional direct numerical simulations of a fixed sphere (planetesimal) facing a laminar and turbulent flow seeded with small inertial particles (dust) subject to a Stokes drag. A no-slip boundary condition on the planetesimal surface is modeled via a penalty method. We find that turbulence can significantly increase the collision rate of dust particles with planetesimals. For a high turbulence case (when the amplitude of turbulent fluctuations is similar to the headwind velocity), we find that the collision probability remains equal to the geometrical rate or even higher for $St\geq 0.1$, i.e., for dust sizes an order of magnitude smaller than in the laminar case. We derive expressions to calculate impact probabilities as a function of dust and planetesimal size and turbulent intensity

Retinal adaptation to spatial correlations

The classical center-surround retinal ganglion cell receptive field is thought to remove the strong spatial correlations in natural scenes, enabling efficient use of limited bandwidth. While early studies with drifting gratings reported robust surrounds (Enroth-Cugell and Robson, 1966), recent measurements with white noise reveal weak surrounds (Chichilnisky and Kalmar, 2002). This might be evidence for dynamical weakening of the retinal surround in response to decreased spatial correlations, which would be predicted by efficient coding theory. Such adaptation is reported in LGN (Lesica et al., 2007), but whether the retina also adapts to correlations is unknown. 

We tested for adaptation by recording simultaneously from ~40 ganglion cells on a multi-electrode array while presenting white and exponentially correlated checkerboards and strips. Measuring from ~200 cells responding to 90 minutes each of white and correlated stimuli, we were able to extract precise spatiotemporal receptive fields (STRFs). We found that a difference-of-Gaussians was not a good fit and the surround was generally displaced from the center. Thus, to assess surround strength we found the center and surround regions and the total weight on the pixels in each region. The relative surround strength was then defined as the ratio of surround weight to center weight. Surprisingly, we found that the majority of recorded cells have a stronger surround under white noise than under correlated noise (p<.05), contrary to naive expectation from theory. The conclusion was robust to different methods of extracting STRFs and persisted with checkerboard and strip stimuli.

To test, without assuming a model, whether the retina decorrelates stimuli, we also measured the pairwise correlations between spike trains of simultaneously recorded neurons under three conditions: white checkerboard, exponentially correlated noise, and scale-free noise. The typical amount of pairwise correlation increased with extent of input correlation, in line with our STRF measurements

How community initiatives are making a difference in goat farmers’ lives in Central Mozambique

In risk prone farming areas like Marara District, goats are a profitable and resilient source of income. A goat restocking and pass-on approach – providing goats to extremely poor farmers who would then pass on the goats’ first offspring to other farmers – was developed, thus enabling the farmers to participate in local development pathways via goat farming. Benefits were identified at different levels of participation. Selling goats enables smallholder farmers with the means to pay for food, education, human health and farm labor, enabling them to transition to a better livelihood. For communities, an activity such as restocking strengthens their capacity to respond to threats (drought, theft) by building a common knowledge base and developing assets. Stakeholder networks bring goat market partners closer for cost-effective collection and sale/purchase of goat

Morphological adaptations of 3.22 Ga-old tufted microbial mats to Archean coastal habitats (Moodies Group, Barberton Greenstone Belt, South Africa)

Microbial life was well established and widespread by the Paleoarchean; however, the degree of evolutionary advancement such as microbial motility, intra- and inter-species interactions, phototropism, or oxygenic photosynthesis by that time remains highly debated. The 3.22 Ga Moodies Group in the Barberton Greenstone Belt (BGB, South Africa) are Earth's oldest well-preserved siliciclastic tidal deposits. They exhibit a unique assemblage of microbial mats, providing an excellent opportunity to decipher the morphological adaptations of microbial communities to different paleoenvironmental settings. The fossil mats are preserved as kerogenous laminations (0.5–1 mm thick) that can be traced laterally for ∼15 km in a ∼1000 m-thick succession of fine- to coarse-grained tidal sandstones and conglomerates. We here present a detailed stratigraphic and depositional facies analysis, documenting the association of the three principal mat morphotypes with specific environmental settings: (1) planar-type in coastal floodplain, (2) wavy-type in intertidal, and (3) tufted-type in upper inter- to supratidal facies. All mat types indicate a flourishing phototrophic biota; moreover, the tufted morphology suggests an intricate level of coordinated growth commonly known from cyanobacterial mats in modern environments

Transformation of stimulus correlations by the retina

Redundancies and correlations in the responses of sensory neurons seem to waste neural resources but can carry cues about structured stimuli and may help the brain to correct for response errors. To assess how the retina negotiates this tradeoff, we measured simultaneous responses from populations of ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure. We found that pairwise correlations in the retinal output remained similar across stimuli with widely different spatio-temporal correlations including white noise and natural movies. Meanwhile, purely spatial correlations tended to increase correlations in the retinal response. Responding to more correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the similarity of pairwise correlations across stimuli where receptive field measurements were possible.Comment: author list corrected in metadat

Nudging sustainability transitions in Central Mozambique

An Agricultural Innovation Platform (AIP) facilitates and accelerates transition of farmers from subsistence farming to socially inclusive, environmentally sound and market-oriented farming. AIPs adapt interventions around interlinked levers in the food value chains, with entry points based on a good understanding of farming systems and input/output market requirements. Learning activities around these entry points strengthen stakeholder networks. Capacitating farmers through stakeholder networks, using mutual learning and additional technical training sessions, improves their self-organization and helps them become entrepreneurs, with the private sector as business mentors and government and extension as facilitators and support. Prospects for change in complex farming systems often appear few and uncertain, leaving farmers feeling helpless in the face of challenges. AIPs demonstrate that small interventions around significant leverage points will have far-reaching benefits. With time, stakeholders facilitate multiple changes through AIPs, magnifying the impact and paving the way for initiatives beyond a project’s lifespan. The ‘AIP experience’ changes their self-perception, resilience, motivation and empowerment forever

Regulation of peptide import through phosphorylation of Ubr1, the ubiquitin ligase of the N-end rule pathway

Substrates of the N-end rule pathway include proteins with destabilizing N-terminal residues. These residues are recognized by E3 ubiquitin ligases called N-recognins. Ubr1 is the N-recognin of the yeast Saccharomyces cerevisiae. Extracellular amino acids or short peptides up-regulate the peptide transporter gene PTR2, thereby increasing the capacity of a cell to import peptides. Cup9 is a transcriptional repressor that down-regulates PTR2. The induction of PTR2 by peptides or amino acids involves accelerated degradation of Cup9 by the N-end rule pathway. We report here that the Ubr1 N-recognin, which conditionally targets Cup9 for degradation, is phosphorylated in vivo at multiple sites, including Ser300 and Tyr277. We also show that the type-I casein kinases Yck1 and Yck2 phosphorylate Ubr1 on Ser300, and thereby make possible (“prime”) the subsequent (presumably sequential) phosphorylations of Ubr1 on Ser296, Ser292, Thr288, and Tyr277 by Mck1, a kinase of the glycogen synthase kinase 3 (Gsk3) family. Phosphorylation of Ubr1 on Tyr277 by Mck1 is a previously undescribed example of a cascade-based tyrosine phosphorylation by a Gsk3-type kinase outside of autophosphorylation. We show that the Yck1/Yck2-mediated phosphorylation of Ubr1 on Ser300 plays a major role in the control of peptide import by the N-end rule pathway. In contrast to phosphorylation on Ser300, the subsequent (primed) phosphorylations, including the one on Tyr277, have at most minor effects on the known properties of Ubr1, including regulation of peptide import. Thus, a biological role of the rest of Ubr1 phosphorylation cascade remains to be identified