Bibliography on inactivation of viruses and rickettsiae by heat

Inactivation of viruses and rickettsiae by heat - bibliograph

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

Earth's first snowball event: Evidence from the early Paleoproterozoic Huronian Supergroup

Ever since it was first proposed that the Earth completely froze during glaciations ∼ 640 million years ago evidence supporting this hypothesis has been increasing, primarily from samples of carbonates directly overlying glacial diamictites, termed cap carbonates. However, this was not the first extensive glacial period that affected planet Earth: ∼1750 million years prior to Neoproterozoic glaciations the Earth went through its first major glacial episode, the early Paleoproterozoic Huronian glaciations. The second Huronian ice advance deposited the Bruce Formation, with its overlying cap carbonate, the Espanola Formation. This up to ∼ 300 m thick succession of limestone, siltstone, dolostone and sandstone overlies diamictite containing a dropstone-bearing layer with δ13Ccarb of −10‰. The 12C-enriched interval also has rare earth element (REE) patterns with negative Eu anomalies, radiogenic Sr isotopes, and negative εNd(0) in the carbonate. The first of these observations is probably due to highly reducing conditions in the sediment, and the possible thawing of methane-rich areas, releasing fluids that mixed with the overlying bottom waters; the last two reflect the diagenetic incorporation into the carbonate of radiogenic Sr, and derivation of REEs, including Nd, from abundant silty loess. This infers a stratified water mass with a relatively stagnant bottom layer during disintegration of an ice shelf. Above this REE patterns through the basal Espanola become increasingly more light depleted upwards, C becomes heavier, Sr is less radiogenic, εNd(0) is near 0 and one area has up to ∼ 1300 ppm Ba incorporated into the carbonate, indicating breakdown of water-mass stratification. Vertically over ∼ 200 m δ13Ccarb increases from −4.5 to −2.5‰ as the environment shallowed incorporating gradually increasing amounts of seawater into the freshwater plume, which initially extended to depths below wave base. Strata deposited in the upper Espanola near the strandline contain layers of Fe-Mn-rich dolomite with positive Eu anomalies reflecting Paleoproterozioc seawater composition dominating even the nearshore by this time. These observations are similar to those from Neoproterozoic cap carbonates, and provide new evidence for the possibly snowball Earth-like nature of the ∼ 2.4 Ga Bruce glaciation

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

Dispersion Relations for Thermally Excited Waves in Plasma Crystals

Thermally excited waves in a Plasma crystal were numerically simulated using a Box_Tree code. The code is a Barnes_Hut tree code proven effective in modeling systems composed of large numbers of particles. Interaction between individual particles was assumed to conform to a Yukawa potential. Particle charge, mass, density, Debye length and output data intervals are all adjustable parameters in the code. Employing a Fourier transform on the output data, dispersion relations for both longitudinal and transverse wave modes were determined. These were compared with the dispersion relations obtained from experiment as well as a theory based on a harmonic approximation to the potential. They were found to agree over a range of 0.9<k<5, where k is the shielding parameter, defined by the ratio between interparticle distance a and dust Debye length lD. This is an improvement over experimental data as current experiments can only verify the theory up to k = 1.5.Comment: 8 pages, Presented at COSPAR '0

Soil Nitrogen Dynamics Following Harvesting and Conversion of Red Alder and Douglas-Fir Stands

Drastic reductions in NO3- leaching have been observed after harvesting of mature red alder (Alnus rubra Bong.) stands. Our objective was to examine whether these reduction were linked to changes in soil N dynamics. Adjacent alder and Douglas fir [Pseudotsuga menziessii (Mirbel.) Franco] stands on young glacial soils (Alderwood; a loamy-skeletal, mixed, mesic, ortstein Aquic Haplorthod) in western Washington were harvested and replanted with either alder or Douglas fir seedlings; reference plots were established in nearby undisturbed stands. Three years after site conversion, when NO3- leaching declined most drastically in the harvested alder plots, net N mineralization and net nitrification in the upper soil were determined seasonally by in situ incubation using the buried-bag technique. There were no significant increases in soil NH4-N during incubation, indicating that nitrification rates closely followed net N mineralization in all plots. In the N-poor soils of the harvested and uncut Douglas fir plots, nitrification was consistently \u3c2 \u3eµg N g–1 per 30 d. In the N-rich alder reference plot, nitrification was highest in summer (52 µg N g–1 per 30 d), lowest in winter (4 µg N g–1), and intermediate in spring (20 µg N g–1). Seasonal fluctuations in nitrification diminished in the harvested alder plots. Nitrification rates were significantly lower than in the uncut alder plot in summer only (5–9 µg N g–1 per 30 d), but this difference was insufficient to account for the lower NO3- leaching rates in the conversion plots. Soils in the harvested plots were drier and experienced greater temperature extremes, but these changes did not correlate well with the variability in N-mineralization rates between uncut and harvested alder plots. Nitrification was positively correlated to soil temperature in the uncut alder plot only. The establishment of red alder seedlings did not appear to have influenced the N dynamics in either N-poor or N-rich soils

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