The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments

Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.

Mutation of the polyadenylation complex subunit CstF77 reveals that mRNA 3' end formation and HSP101 levels are critical for a robust heat stress response

Heat shock protein 101 (HSP101) in plants, and bacterial and yeast orthologs, is essential for thermotolerance. To investigate thermotolerance mechanisms involving HSP101, we performed a suppressor screen in Arabidopsis thaliana of a missense HSP101 allele (hot1-4). hot1-4 plants are sensitive to acclimation heat treatments that are otherwise permissive for HSP101 null mutants, indicating that the hot1-4 protein is toxic. We report one suppressor (shot2, suppressor of hot1-4 2) has a missense mutation of a conserved residue in CLEAVAGE STIMULATION FACTOR77 (CstF77), a subunit of the polyadenylation complex critical for mRNA 3' end maturation. We performed ribosomal RNA depletion RNA-Seq and captured transcriptional readthrough with a custom bioinformatics pipeline. Acclimation heat treatment caused transcriptional readthrough in hot1-4 shot2, with more readthrough in heat-induced genes, reducing the levels of toxic hot1-4 protein and suppressing hot1-4 heat sensitivity. Although shot2 mutants develop like the wild type in the absence of stress and survive mild heat stress, reduction of heat-induced genes and decreased HSP accumulation makes shot2 in HSP101 null and wild-type backgrounds sensitive to severe heat stress. Our study reveals the critical function of CstF77 for 3' end formation of mRNA and the dominant role of HSP101 in dictating the outcome of severe heat stress.

A method for experimental warming of developing tree seeds with a common garden demonstration of seedling responses

BACKGROUND

Forest dieback driven by rapid climate warming threatens ecosystems worldwide. The health of forested ecosystems depends on how tree species respond to warming during all life history stages. While it is known that seed development is temperature-sensitive, little is known about possible effects of climate warming on seed development and subsequent seedling performance. Exposure of seeds to high air temperatures may influence subsequent seedling performance negatively, though conversely, warming during seed development may aid acclimation of seedlings to subsequent thermal stress. Technical challenges associated with in-situ warming of developing tree seeds limit understanding of how tree species may respond to seed development in a warmer climate.

RESULTS

We developed and validated a simple method for passively warming seeds as they develop in tree canopies to enable controlled study of climate warming on seedling performance. We quantified thermal effects of the cone-warming method across individual pine trees and stands by measuring the air temperature surrounding seed cones using thermal loggers and the temperature of seed cone tissue using thermocouples. We then investigated seedling phenotypes in relation to the warming method through a common garden study. We assessed seedling morphology, physiology, and mycorrhizal nodulation in response to experimental cone-warming in 20 seed-source-tree canopies on the San Francisco Peaks in northern Arizona, USA. The warming method increased air temperature surrounding developing seed cones by 2.1 °C, a plausible increase in mean air temperature by 2050 under current climate projections. Notable effect sizes of cone-warming were detected for seedling root length, shoot length, and diameter at root collar using Cohen's Local f². Root length was affected most by cone-warming, but effect sizes of cone-warming on root length and diameter at root collar became negligible after the first year of growth. Cone-warming had small but significant effects on mycorrhizal fungal richness and seedling multispectral near-infrared indices indicative of plant health.

CONCLUSIONS

The method was shown to reliably elevate the temperature surrounding seed cones and thereby facilitate experimental in-situ climate warming research on forest trees. The method was furthermore shown to influence plant traits that may affect seedling performance under climate warming.

Nix Pro Color Sensor Provides Comparable Color Measurements to Hunterlab Colorimeter

ObjectivesMeat color is the most important quality attribute that influences consumer purchase decisions. Monitoring color to maximize shelf life and consumer acceptability is routinely used in meat science research. The HunterLab MiniScan EZ (HunterLab) colorimeter is the widely used industry standard for objectively measuring meat color. This device can collect tristimulus values of CIE L* (lightness), a* (redness), and b* (yellowness) for color measurements based on the light reflectance from the meat surface. While the HunterLab colorimeter serves as an accurate measure of meat color, it is relatively expensive and bulky. The Nix Pro Color Sensor (Nix) colorimeter is a less expensive and smaller handheld device that can capture the CIE L*, a*, b* values which can be downloaded to a smartphone app. However, limited research has been performed to compare the efficiency of these colorimeters for measuring beef color. Therefore, the objective of this study was to investigate the capabilities of the Nix colorimeter as an additional resource for objective fresh beef color measurements.Materials and MethodsThe longissimus dorsi muscle from one side of A maturity beef carcasses (n = 200) were evaluated using the HunterLab and Nix colorimeters. Carcasses were allowed approximately 1 h to bloom after being ribbed (between the 12th and 13th rib) prior to color measurements. Three (technical replicate) scans were obtained using the HunterLab colorimeter (illuminant A and 10° standard observer) and the mean readings were recorded. A series of independent technical replication (3, 5, 7, and 9) scans were obtained using the Nix colorimeter with illuminant A and 10° standard observer as well. The differences in color measurements between colorimeters were analyzed by using the Bland Altman Limits of Agreement and CORR (correlation) procedure of SAS with α < 0.05.ResultsCorrelation between the HunterLab and Nix was highest for a* value (redness) with 3 scans (r = 0.85, P < 0.01), followed by 7, 5, and 9 scans (r = 0.84, 0.82, and 0.82, respectively; P < 0.01). Additionally, L* values (lightness) were highly correlated for all the scanning series (r = 0.79–0.81; P < 0.01). Similar to a* values, 3 scans with the Nix for b* values (yellowness) demonstrated the best correlation with HunterLab (r = 0.83; P < 0.01), whereas the 5, 7, and 9 scans were still highly correlated (r = 0.79–0.82; P < 0.01). The Bland Altman Limits of Agreement analysis indicated that the mean difference in a* values using 3 scans of both colorimeters was –1.68, whereas it was –0.91 for L* values and 0.25 for b* values. Moreover, the analysis indicated good agreement between the Nix and the Hunterlab colorimeters for all the color parameters.ConclusionThree replicate scans using the Nix was highly correlated with color measurements using the HunterLab colorimeter and can serve as an acceptable additional resource for objectively measuring beef color. The Nix provides an opportunity for a less expensive, more mobile, and multipurpose device. Although these colorimeters are not equivalent, the Nix could be an adequate method for objective beef color measurements and is comparable to the HunterLab.

Interplay between hydration water and headgroup dynamics in lipid bilayers

In this study, the interplay between water and lipid dynamics has been investigated by broadband dielectric spectroscopy and modulated differential scanning calorimetry (MDSC). The multilamellar lipid bilayer system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been studied over a broad temperature range at three different water contents: about 3, 6, and 9 water molecules per lipid molecule. The results from the dielectric relaxation measurements show that at temperatures <250 K the lipid headgroup rotation is described by a super-Arrhenius temperature dependence at the lowest hydration level and by the Arrhenius law at the highest hydration level. This difference in the temperature dependence of the lipid headgroup rotation can be explained by the increasing interaction between the headgroups with decreasing water content, which causes their rotational motion to be more cooperative in character. The main water relaxation shows an anomalous dependence on the water content in the supercooled and glassy regime. In contrast to the general behavior of interfacial water, the water dynamics is fastest in the driest sample and its temperature dependence is best described by a super-Arrhenius temperature dependence. The best explanation for this anomalous behavior is that the water relaxation becomes more determined by fast local lipid motions than by the intrinsic water dynamics at low water contents. In support for this interpretation is the finding that the relaxation time of the main water process is faster than that in most other host systems at temperatures below 180 K. Thus, the dielectric relaxation data show clearly the strong interplay between water and lipid dynamics; the water influences the lipid dynamics and vice versa. In the MDSC data, we observe a weak enthalpy relaxation at 203 K for the driest sample and at 179 K for the most hydrated sample, attributed to the freezing-in of the lipid headgroup rotation observed in the dielectric data, since this motion reaches a time scale of about 100 s at about the same temperatures.

Biomechanical effects of environmental and engineered particles on human airway smooth muscle cells

The past decade has seen significant increases in combustion-generated ambient particles, which contain a nanosized fraction (less than 100 nm), and even greater increases have occurred in engineered nanoparticles (NPs) propelled by the booming nanotechnology industry. Although inhalation of these particulates has become a public health concern, human health effects and mechanisms of action for NPs are not well understood. Focusing on the human airway smooth muscle cell, here we show that the cellular mechanical function is altered by particulate exposure in a manner that is dependent upon particle material, size and dose. We used Alamar Blue assay to measure cell viability and optical magnetic twisting cytometry to measure cell stiffness and agonist-induced contractility. The eight particle species fell into four categories, based on their respective effect on cell viability and on mechanical function. Cell viability was impaired and cell contractility was decreased by (i) zinc oxide (40-100 nm and less than 44 microm) and copper(II) oxide (less than 50 nm); cell contractility was decreased by (ii) fluorescent polystyrene spheres (40 nm), increased by (iii) welding fumes and unchanged by (iv) diesel exhaust particles, titanium dioxide (25 nm) and copper(II) oxide (less than 5 microm), although in none of these cases was cell viability impaired. Treatment with hydrogen peroxide up to 500 microM did not alter viability or cell mechanics, suggesting that the particle effects are unlikely to be mediated by particle-generated reactive oxygen species. Our results highlight the susceptibility of cellular mechanical function to particulate exposures and suggest that direct exposure of the airway smooth muscle cells to particulates may initiate or aggravate respiratory diseases.

The dynamics of water in hydrated white bread investigated using quasielastic neutron scattering

The dynamics of water in fresh and in rehydrated white bread is studied using quasielastic neutron scattering (QENS). A diffusion constant for water in fresh bread, without temperature gradients and with the use of a non-destructive technique, is presented here for the first time. The self-diffusion constant for fresh bread is estimated to be D_s = 3.8 × 10^-10 m² s^-1 and the result agrees well with previous findings for similar systems. It is also suggested that water exhibits a faster dynamics than previously reported in the literature using equilibration of a hydration-level gradient monitored by vibrational spectroscopy. The temperature dependence of the dynamics of low hydration bread is also investigated for T = 280-350 K. The average relaxation time at constant momentum transfer (Q) shows an Arrhenius behavior in the temperature range investigated.

A dual role for the API2 moiety in API2-MALT1-dependent NF-kappaB activation: heterotypic oligomerization and TRAF2 recruitment

Mucosa-associated lymphoid tissue (MALT) lymphoma is the most common extranodal lymphoid neoplasm. Chromosomal translocation t(11;18)(q21,q21) is found in 30% of gastric MALT lymphomas and is associated with a failure to respond to standard treatment and a tendency to disseminate. This translocation generates a chimeric protein composed of N-terminal sequences of Inhibitor of Apoptosis 2 (API2, also known as BIRC3 and cIAP2) fused to C-terminal sequences of MALT1. API2-MALT1 promotes cell survival and proliferation via activation of nuclear factor-kappaB (NF-kappaB). Here, we investigate the mechanism by which the API2 moiety contributes to NF-kappaB stimulation. We find that the API2 moiety mediates oligomerization of API2-MALT1 as well as interaction with tumor necrosis factor receptor-associated factor 2 (TRAF2). Surprisingly, oligomerization does not occur via homotypic interaction; rather, the API2 moiety of one monomer interacts with the MALT1 moiety of another monomer. Further, the specific region of the API2 moiety responsible for mediating oligomerization is distinct from that mediating TRAF2 binding. Although deletion or mutation of the TRAF2 binding site does not inhibit oligomerization, it does lead to dramatically decreased NF-kappaB activation. Deletion of both TRAF2 binding and oligomerization regions results in near-complete loss of NF-kappaB activation. Thus, API2 moiety-mediated heterotypic oligomerization and TRAF2 binding both contribute to maximal API2-MALT1-dependent NF-kappaB stimulation.

Dynamics of Fresh and Freeze-Dried Strawberry and Red Onion by Quasielastic Neutron Scattering

The microscopic behavior of fresh and freeze-dried strawberry and red onion at different water contents (45 and 20 wt % water) has been investigated by quasielastic neutron scattering (QENS). To distinguish between the dynamics of the water and the biological material isotopic (H/D) substitution was used. The results show that all samples exhibit an onset of anharmonic motions on the experimental time scale (3-100 ps) at about 230-240 K. Above 250 K the dynamics is mainly of translational character and strongly dependent on the hydration level. The diffusion constant increases rapidly with increasing water content and at 280 K it is approximately 20% higher for the hydration water in freeze-dried strawberry than in freeze-dried red onion and around 2 orders of magnitude faster for the hydration water than for the biological material. Moreover, the diffusion constant of the biological part is about 50% faster in freeze-dried strawberry than in freeze-dried red onion. It was also found that the average relaxation time is slightly faster in fresh strawberry than in freeze-dried strawberry. From the results we can conclude that the water dynamics is not only promoting motions in the biological material, it is also affected by the structure (and possibly also the dynamics) of the biological material. Thus, the microscopic properties of the biological materials are interrelated with the properties of their hydration water.

Water dynamics in n-propylene glycol aqueous solutions

The relaxation dynamics of dipropylene glycol and tripropylene glycol (nPG-n=2,3) water solutions on the nPG-rich side has been studied by broadband dielectric spectroscopy and differential scanning calorimetry in the temperature range of 130-280 K. Two relaxation processes are observed for all the hydration levels; the slower process (I) is related to the alpha relaxation of the solution whereas the faster one (II) is associated with the reorientation of water molecules in the mixture. Dielectric data for process (II) at temperatures between 150 and 200 K indicate the existence of a critical water concentration (x(c)) below which water mobility is highly restricted. Below x(c), nPG-water domains drive the dielectric signal whereas above x(c), water-water domains dominate the dielectric response at low temperatures. The results also show that process (II) at low temperatures is due to local motions of water molecules in the glassy frozen matrix. Additionally, we will show that the glass transition temperatures (T(g)) for aqueous PG, 2PG, and 3PG solutions do not extrapolate to approximately 136 K, regardless of the extrapolation method. Instead, we find that the extrapolated T(g) value for water from these solutions lies in the neighborhood of 165 K.

Dynamics of propylene glycol and its oligomers confined to a single molecular layer

The dynamics of propylene glycol (PG) and its oligomers 7-PG and poly-propylene glycol (PPG), with M(w) = 4000 (approximately 70 monomers), confined in a Na-vermiculite clay have been investigated by quasielastic neutron scattering. The liquids are confined to single molecular layers between clay platelets, giving a true two-dimensional liquid. Data from three different spectrometers of different resolutions were Fourier transformed to S(Q,t) and combined to give an extended dynamical time range of 0.3-2000 ps. An attempt was made to distinguish the diffusive motion from the methyl group rotation and a fast local motion of hydrogen in the polymer backbone. The results show that the average relaxation time tau(d) of this diffusive process is, as expected, larger than the relaxation time tau averaged over all dynamical processes observed in the experimental time window. More interesting, it is evident that the severe confinement has a relatively small effect on tau(d) at T = 300 K, this holds particularly for the longest oligomer, PPG. The most significant difference is that the chain-length dependence of tau(d) is weaker for the confined liquids, although the slowing down in bulk PG due to the formation of a three-dimensional network of OH-bonded end groups reduces this difference. The estimated average relaxation time tau at Q = 0.92 Angstroms(-1) for all the observed processes is in excellent agreement with the previously reported dielectric alpha relaxation time in the studied temperature range of 260-380 K. The average relaxation time tau (as well as the dielectric alpha relaxation time) is also almost unaffected by the confinement to a single molecular layer, suggesting that the interaction with the clay surfaces is weak and that the reduced dimensionality has only a weak influence on the time scale of all the dynamical processes observed in this study.

Diffusive solvent dynamics in a polymer gel electrolyte studied by quasielastic neutron scattering

A quasielastic neutron scattering study has been performed on a polymer gel electrolyte consisting of lithium perchlorate dissolved in ethylene carbonate/propylene carbonate and stabilized with poly(methyl methacrylate). The dynamics of the solvent, which is crucial for the ion conduction in this system, was probed using the hydrogen/deuterium contrast variation method with nondeuterated solvent and a deuterated polymer matrix. Two relaxation processes of the solvent were studied in the 10-400 microeV range at different temperatures. From analysis of the momentum transfer dependence of the processes we conclude that the faster process ( approximately 100 microeV) is related to rotational diffusion of the solvent and the slower process ( approximately 10 microeV) to translational diffusion of the solvent. The translational diffusion is found to be similar to the diffusion in the corresponding liquid electrolyte at short distances, but geometrically constrained by the polymer matrix at distances beyond approximately 5 A. The study indicates that the hindered diffusion of the solvent on a length scale of the polymer network interchain distance ( approximately 5-20 A) is sufficient to explain the reduced macroscopic diffusivity and ion conductivity of the gel electrolyte compared to the liquid electrolyte.

Dynamics of water in a molecular sieve by quasielastic neutron scattering

We have investigated the dynamics of water confined in a molecular sieve, with a cylindrical pore diameter of 10 A, by means of quasielastic neutron scattering (QENS). Both the incoherent and coherent intermediate scattering functions I(Q,t) were determined by time-of-flight QENS and the neutron spin-echo technique, respectively. The results show that I(Q,t) is considerably more stretched in time with a slightly larger average relaxation time in the case of coherent scattering. From the Q dependence of I(Q,t) it is clear that the observed dynamics is almost of an ordinary translational nature. A comparison with previous dielectric measurements suggests a possible merging of the alpha and beta relaxations of the confined water at T=185 K, although the alpha relaxation cannot be directly observed at lower temperatures due to the severe confinement. The present results are discussed in relation to previous results for water confined in a Na-vermiculite clay, where the average relaxation time from spin-echo measurements was found to be slower than in the present system (particularly at low temperatures).

Dynamics of water in strawberry and red onion as studied by dielectric spectroscopy

We have investigated the microscopic dynamics of strawberry and red onion by means of broadband dielectric spectroscopy. In contrast to most of the previous experiments on carbohydrate-rich biological materials, which have mainly considered the more global dynamics of the "biological matrix," we are here focusing on the microscopic dynamics of mainly the associated water. The results for both strawberry and red onion show that the imaginary part of the permittivity contains one conductivity term and a clear dielectric loss peak, which was found to be similar to the strongest relaxation process of water in carbohydrate solutions. The temperature dependence of the relaxation process was analyzed for different water content. The relaxation process slows down, and its temperature dependence becomes more non-Arrhenius, with decreasing water content. The reason for this is most likely that, on average, the water molecules interact more strongly with carbohydrates and other biological materials at low water content, and the dynamical properties of this biological matrix changes substantially with increasing temperature (from an almost rigid matrix where the water is basically unable to perform long-range diffusion due to confinement effects, to a dynamic matrix with no static confinement effects), which also changes (i.e., reduces) the activation energy of the relaxation process with increasing temperature (i.e., causes a non-Arrhenius temperature dependence). This further changes the conductivity from mainly polarization effects at low temperatures, due to hindered ionic motions, to long-range diffusivity at T>250 K . Thus, around this temperature ions in the carbohydrate solution no longer get stuck in confined cavities, since the motion of the biological matrix "opens up" the cavities and the ions are then able to perform long-range migration.

Structural investigations of polymer electrolyte poly(propylene oxide)-LiClO4 using diffraction experiments and reverse Monte Carlo simulation

The structure of an amorphous polymer electrolyte, poly(propylene oxide) (PPO) complexed with LiClO4, has been studied using reverse Monte Carlo (RMC) simulations. The simulations require no force field but are based on experimental data only, in this case from x-ray and neutron diffraction experiments. Excellent agreement between the experimental data and the structures resulting from the RMC simulation is obtained. Samples with ether-oxygen to lithium concentrations (molar ratios) O:Li=16:1 and 5:1 were studied and compared to results of pure PPO from a previous study. We focus on the effects of the solvated salt on the structure of the polymer matrix, the spatial distribution of ions, and the correlations between the anions and the polymer chains. Analyzing the structures produced in the simulations, we find that for a concentration 16:1, the interchain distance is approximately the same as in pure PPO but more well defined. For a concentration 5:1, we find a larger and less well-defined interchain distance compared to the 16:1 concentration. This signifies that at the 16:1 salt concentration, there is enough free volume in the polymer host to accommodate the ions, and that the solvation of salt induces ordering of the polymer matrix. At the higher salt concentration 5:1, the polymer network must expand and become less ordered to host the ions. We also note, in accordance with previous studies, that the solvation of salt changes the conformation of the polymer chain towards more gauche states. The simulations furthermore reveal marked correlations between the polymer chains and the anions, which we suggest arise predominantly from an interaction mediated via cations, which can simultaneously coordinate both ether oxygens in the polymer chains and anions. Interanionic distances at 5 A, which are consistent with two or more anions being coordinated around the same cation, are also observed. On a larger scale, the RMC structure of PPO-LiClO4 16:1 clearly indicates the presence of salt-rich and salt-depleted domains having a length scale of <20 A. In view of such a heterogeneous structure of PPO-LiClO4 16:1, it is plausible that the increased ordering of the polymer matrix is due to rather well-defined structural arrangements within the salt-rich domains, and that the characteristic interchain distance in the salt-rich domains is similar to that of the pure polymer.

Dielectric relaxation studies of poly(propylene glycol) confined in vermiculite clay

The molecular dynamics of oligomeric poly(propylene glycol) (PPG) liquids (M(w)=1200, 2000 and 4000 g/mol) confined in a two-dimensional layer-structured Na-vermiculite clay has been studied by broadband dielectric spectroscopy. In addition to the alpha-relaxation, the normal mode relaxation process was studied for all samples both in bulk and confinement. For the normal mode process the relaxation rate in the clay is drastically shifted to lower frequencies compared to that of the bulk material in contrast to the alpha-process whose relaxation time is only slightly affected by the confinement. Also the temperature dependence of the relaxation time for the normal mode process is strongly affected by the confinement. Moreover, in the clay the intensity of the normal mode is stronger than that of the alpha-process, in contrast to the bulk samples where the opposite is observed.

Dynamics of water in molecular sieves by dielectric spectroscopy

We present recent dielectric data on the dynamics of water confined in molecular sieves with pore sizes 5 and 10 A. The dielectric measurements in the frequency and temperature ranges 10(-2)-10(6) Hz and 120-300 K show three relaxation processes for both samples. In the case of the 10 A pore the slowest process shows an Arrhenius temperature dependence at low temperatures (<220 K), while at high temperatures the relaxation appears to follow a more Vogel-Fulcher-Tammann (VFT) like behaviour. The relaxation time for this process is 100 s at about 170 K. The second slowest process is at low temperatures very similar to the main process of (bulk-like) water in a fully hydrated clay, but also this process seems to exhibit some kind of dynamical transition, in this case at T approximately 185 K. All the three processes in the 5 A pore exhibit Arrhenius temperature dependence, and two of them are considerably slower than the main relaxation in the hydrated clay. Thus, dynamics of bulk-like water is only observed in the 10 A molecular sieves, and most of the water molecules in both 5 and 10 A pores have considerably slower dielectric relaxation than has been observed for water confined in clay, most likely due to strong interactions with the considerably more hydrophilic inner surfaces of molecular sieves.

Dynamics of propylene glycol and its oligomers confined in clay

The dynamics of propylene glycol (PG) and its oligomers 7-PG and PPG, with Mw = 4000 (about 70 monomers), confined in a Na-vermiculite clay have been investigated by quasi-elastic neutron scattering and dielectric spectroscopy. The liquids are confined to a single molecular layer between the clay platelets, thus giving a true 2D liquid. The results show that the average relaxation time [tau], deduced from neutron scattering at a momentum transfer Q of about 1 A(-1) is in perfect agreement with the dielectric alpha-relaxation time, although neutron scattering does not only probe the main (alpha-) relaxation, but all motions of hydrogens on the experimental time scale. At room temperature 1/[tau] is proportional to Q(2), indicating that the relaxations are mainly due to ordinary translational diffusion. The most unexpected finding is that [tau](or the dielectric alpha-relaxation time) is almost unaffected by the 2D confinement, in contrast to the dielectrically active normal mode of PPG which is substantially slower in the confinement. Only the 7-mer has a significantly slower segmental translational diffusion in the clay. The results suggest that the interactions to the clay surfaces are weak and that the present 2D confinement has a very small influence on the time scale of all our observed relaxation processes, except the normal-mode relaxation.

Historical biogeography and a mitochondrial DNA phylogeny of grouse and ptarmigan

We sequenced 2690 nucleotides of mitochondrial DNA (mtDNA) including the entire control region (CR), partial 12S and 16S ribosomal RNAs, NADH dehydrogenase subunit 2, and cytochrome b genes from representatives of all the 17 living species of grouse and ptarmigan (Aves; Galliformes; subfamily Tetraoninae). Substitution rates and phylogenetic signals were variable among genes, with the CR being more informative than protein-coding and rRNA genes. Phylogenetic trees, computed with the CR or the concatenated sequences, indicate that: (1) genus Bonasa is monophyletic and basal within the subfamily, (2) all the other currently recognized genera of Tetraoninae are monophyletic, except Dendragapus; (3) D. obscurus is related to Centrocercus urophasianus and divergent from former D. canadensis and D. falcipennis, which, accordingly, may be ascribed to the distinct genus Falcipennis; (4) Tympanuchus, Dendragapus, and Centrocercus form a clade comprising taxa distributed exclusively in North America; and (5) the North American species of Bonasa (B. umbellus) and Lagopus (L. leucurus) are basal to their Eurasian and Holarctic congeneric species. These findings, and a dispersal-vicariance analysis, support a North American origin of the subfamily and of all the genera of Tetraoninae, with the possible exception of Tetrao. Present species distributions might have been attained by at least three dispersal events from North America to Eurasia, involving the ancestors to Palearctic Bonasa, the ancestors to circumpolar Lagopus mutus/L. lagopus, and the clade leading to Tetrao/Falcipennis. According to a "standard calibration" of the mtDNA molecular clock (2% sequence divergence per million years), Bonasa split about 5-6 million years ago, the other genera diverged during the upper Pliocene, and most of the congeneric species with North American and Eurasian distributions (Bonasa, Lagopus, and Falcipennis) originated during the lower Pleistocene, well before the last interruption of the Beringian land bridge.

Insecticidal proteins from Bacillus thuringiensis protect corn from corn rootworms

Field tests of corn co-expressing two new delta-endotoxins from Bacillus thuringiensis (Bt) have demonstrated protection from root damage by western corn rootworm (Diabrotica virgifera virgifera LeConte). The level of protection exceeds that provided by chemical insecticides. In the bacterium, these proteins form crystals during the sporulation phase of the growth cycle, are encoded by a single operon, and have molecular masses of 14 kDa and 44 kDa. Corn rootworm larvae fed on corn roots expressing the proteins showed histopathological symptoms in the midgut epithelium.

Determining ionic conductivity from structural models of fast ionic conductors

Reverse Monte Carlo produced structural models of silver ion conducting glasses and crystals have been investigated by the bond-valence technique. Both absolute ionic conductivity and activation energy can be determined directly from the "pathway volume" of the structural models, i.e., from the volume fraction of the percolating pathway cluster. This pathway volume-conductivity relation was found to hold for glassy and crystalline systems with silver ion conductivities differing by more than 11 orders of magnitude. Earlier, less universal rules were rationalized and unified by means of this approach.

Epstein-Barr virus immediate-early proteins BZLF1 and BRLF1 activate the ATF2 transcription factor by increasing the levels of phosphorylated p38 and c-Jun N-terminal kinases

Expression of either Epstein-Barr virus (EBV) immediate-early protein BZLF1 (Z) or BRLF1 (R) is sufficient to convert EBV infection from the latent to lytic form. Disruption of viral latency requires transcriptional activation of the Z and R promoters. The Z and R proteins are transcriptional activators, and each immediate-early protein activates expression of the other immediate-early protein. Z activates the R promoter through a direct binding mechanism. However, R does not bind directly to the Z promoter. In this study, we demonstrate that the ZII element (a cyclic AMP response element site) in the Z promoter is required for efficient activation by R. The ZII element has been shown to be important for induction of lytic EBV infection by tetradecanoyl phorbol acetate and surface immunoglobulin cross-linking and is activated by Z through an indirect mechanism. We demonstrate that both R and Z activate the cellular stress mitogen-activated protein (MAP) kinases, p38 and JNK, resulting in phosphorylation (and activation) of the cellular transcription factor ATF2. Furthermore, we show that the ability of R to induce lytic EBV infection in latently infected cells is significantly reduced by inhibition of either the p38 kinase or JNK pathways. In contrast, inhibition of stress MAP kinase pathways does not impair the ability of Z expression vectors to disrupt viral latency, presumably because expression of Z under the control of a strong heterologous promoter bypasses the need to activate Z transcription. Thus, both R and Z can activate the Z promoter indirectly by inducing ATF2 phosphorylation, and this activity appears to be important for R-induced disruption of viral latency.

Induction of lytic Epstein-Barr virus (EBV) infection in EBV-associated malignancies using adenovirus vectors in vitro and in vivo

The consistent presence of EBV genomes in certain tumor types (in particular, AIDS-related central nervous system lymphomas and nasopharyngeal carcinomas) may allow novel, EBV-based targeting strategies. Tumors contain the latent (transforming) form of EBV infection. However, expression of either of the EBV immediate-early proteins, BZLF1 and BRLF1, is sufficient to induce lytic EBV infection, resulting in death of the host cell. We have constructed replication-deficient adenovirus vectors expressing the BZLF1 or BRLF1 immediate-early genes and examined their utility for killing latently infected lymphoma cells in vitro and in vivo. We show that both the BZLF1 and BRLF1 vectors efficiently induce lytic EBV infection in Jijoye cells (an EBV-positive Burkitt lymphoma cell line). Furthermore, lytic EBV infection converts the antiviral drug, ganciclovir (GCV), into a toxic (phosphorylated) form, which inhibits cellular as well as viral DNA polymerase. When Jijoye cells are infected with the BZLF1 or BRLF1 adenovirus vectors in the presence of GCV, viral reactivation is induced, but virus replication is inhibited (thus preventing the release of infectious EBV particles); yet cells are still efficiently killed. Finally, we demonstrate that the BZLF1 and BRLF1 adenovirus vectors induce lytic EBV infection when they are directly inoculated into Jijoye cell tumors grown in severe combined immunodeficiency mice. These results suggest that induction of lytic EBV infection in tumors, in combination with GCV, may be an effective strategy for treating EBV-associated malignancies.

Engineering secondary metabolism in maize cells by ectopic expression of transcription factors

Manipulation of plant natural product biosynthesis through genetic engineering is an attractive but technically challenging goal. Here, we demonstrate that different secondary metabolites can be produced in cultured maize cells by ectopic expression of the appropriate regulatory genes. Cell lines engineered to express the maize transcriptional activators C1 and R accumulate two cyanidin derivatives, which are similar to the predominant anthocyanin found in differentiated plant tissues. In contrast, cell lines that express P accumulate various 3-deoxy flavonoids. Unexpectedly, P-expressing cells in culture also accumulate phenylpropanoids and green fluorescent compounds that are targeted to different subcellular compartments. Two endogenous biosynthetic genes (c2 and a1, encoding chalcone synthase and flavanone/dihydroflavonol reductase, respectively) are independently activated by ectopic expression of either P or C1/R, and there is a dose-response relationship between the transcript level of P and the degree to which c2 or a1 is expressed. Our results support a simple model showing how the gene encoding P may act as a quantitative trait locus controlling insecticidal C-glycosyl flavone level in maize silks, and they suggest how p1 might confer a selective advantage against insect predation in maize.