Transition from geostrophic turbulence to inertia–gravity waves in the atmospheric energy spectrum

Midlatitude fluctuations of the atmospheric winds on scales of thousands of kilometers, the most energetic of such fluctuations, are strongly constrained by the Earth’s rotation and the atmosphere’s stratification. As a result of these constraints, the flow is quasi-2D and energy is trapped at large scales—nonlinear turbulent interactions transfer energy to larger scales, but not to smaller scales. Aircraft observations of wind and temperature near the tropopause indicate that fluctuations at horizontal scales smaller than about 500 km are more energetic than expected from these quasi-2D dynamics. We present an analysis of the observations that indicates that these smaller-scale motions are due to approximately linear inertia–gravity waves, contrary to recent claims that these scales are strongly turbulent. Specifically, the aircraft velocity and temperature measurements are separated into two components: one due to the quasi-2D dynamics and one due to linear inertia–gravity waves. Quasi-2D dynamics dominate at scales larger than 500 km; inertia–gravity waves dominate at scales smaller than 500 km.The midlatitude high- and low-pressure systems visible in weather maps are associated with winds and temperature fluctuations that we experience as weather. These fluctuations arise from a baroclinic instability of the mean zonal winds at horizontal scales of a few thousand kilometers, commonly referred to as the synoptic scales (1–3). The combined effects of rotation and stratification constrain the synoptic-scale winds to be nearly horizontal and to satisfy geostrophic balance, a balance between the force exerted by the changes in pressure and the Coriolis force resulting from Earth’s rotation. It is an open question whether the same constraints dominate in the mesoscale range (i.e., at scales of 10–500 km), or whether qualitatively different dynamics govern flows at these scales.The synoptic-scale flows are turbulent in the sense that nonlinear scale interactions, which lie at the core of the difficulty to predict the weather, exchange energy between different scales of motion (4–7). Under the constraints of rotation and stratification, the synoptic-scale winds are approximately 2D and nondivergent (8, 9). In 2D flows, nonlinear scale interactions tend to transfer energy to larger scales, that is, the synoptic-scale pressure anomalies often merge and form larger ones, contrary to nonlinear scale interactions in 3D flows, which tend to transfer energy to smaller scales (10). Little energy is thus transferred to scales smaller than those at which the synoptic-scale fluctuations are generated through instabilities. Theory and numerical simulations predict that the energy per unit horizontal wavenumber k decays as rapidly as k^?3 at wavenumbers larger than the wavenumber corresponding to the instability scale (9, 11). This predicted kinetic energy spectrum is roughly consistent with synoptic-scale observations (9, 12).Long-range passenger aircraft have been instrumented to collect velocity and temperature measurements as part of the Global Atmospheric Sampling Program in the 1970s and the Measurement of Ozone and Water Vapor by Airbus In-Service Aircraft (MOZAIC) project in the 1990s and 2000s. The resulting dataset, described in Materials and Methods, consists of tens of thousands of flights. Because aircraft travel at altitudes between 9 and 14 km, the data largely reflect the upper troposphere and lower stratosphere, near the tropopause. These measurements confirm that the kinetic energy spectrum drops as k^?3 in the synoptic wavenumber range, but there is a transition in behavior at a scale of about 500 km (13) (Fig. 1A). In the mesoscale range, at scales smaller than 500 km, the kinetic energy spectrum decays more slowly, roughly like k^?5/3 (13–15).Open in a separate windowFig. 1.Observed wavenumber spectra of near-tropopause midlatitude winds and decomposition into geostrophic component and inertia–gravity wave component. (A) Observed spectra of longitudinal kinetic energy S^u(k), transverse kinetic energy S^v(k), and potential energy S^b(k). (B) Helmholtz decomposition of the observed kinetic energy spectrum K(k) into its rotational and divergent components K^ψ(k) and K^?(k). (C) Partitioning of the total energy spectrum E(k) into the diagnosed inertia–gravity wave component E_w(k) and the residual geostrophic component E_g(k).The measured kinetic energy spectrum is intriguing, because it agrees so well with Charney’s theory of geostrophic turbulence at the synoptic scales (9) but deviates from that prediction at the mesoscale. The transition to the flatter k^?5/3 mesoscale spectrum has been interpreted as the signature of small-scale geostrophic flows generated by convective events (14, 16, 17), as the development of fronts at the edge of synoptic-scale cyclones and anticyclones at the top of the troposphere (equivalent to the warm and cold mesoscale fronts we experience at the Earth’s surface) (18), or as the signature of stratified turbulence at scales where the rotational constraints become less important (19). These explanations of the synoptic-to-mesoscale transition invoke turbulent dynamics and strong interactions between the synoptic and mesoscale flows.A rotating and stratified atmosphere, however, supports an additional, much faster set of motions: inertia–gravity waves. These are internal gravity waves, modified by the effect of rotation, that have periods of several minutes to a few hours. In contrast to the strongly nonlinear, turbulent synoptic-scale flow, these motions are wave-like and at small amplitude they are approximately governed by linear dynamics (20). It has been proposed that the mesoscale energy is dominated by inertia–gravity waves (21, 22), which are easily excited by any fast fluctuation of the atmospheric flows (23). In this explanation of the mesoscale part of the spectrum, linear inertia–gravity waves and nonlinear synoptic-scale turbulence coexist with little interaction.In this paper, we present an analysis of the MOZAIC data that uses a decomposition method recently developed by Bühler et al. (24). This analysis provides compelling evidence that linear inertia–gravity waves indeed dominate the observations in the mesoscale.     

Rapid helix--coil transitions in the S-2 region of myosin.

Temperature-jump studies on the long S-2 fragment (100,000 daltons) isolated from myosin show that this structure can undergo alpha-helix--random coil transitions in a time range approximating the cycle time of a crossbridge. Two relaxation times are observed after temperature jumps of 5 degrees C over the range 35--55 degrees C, one in the submillisecond (tau f) and the other in the millisecond (tau s) time ranges. Both processes exhibit maxima near the midpoint of the helix--coil transition (tm = 45 +/- 2 degrees C) as determined by optical rotation melt experiments. Similar results were observed for the low temperature transition (tm = 45 degrees C) of the myosin rod. Viscosity studies reveal that the S-2 particles has significant flexibility at physiological temperature. Results are considered in terms of the Huxley--Simmons and helix--coil transition models for force generation in muscle.     

Reverse nitrogen gradients in the study of phase III and cardiogenic oscillations of the single-breath nitrogen test.

The slope of phase III, phase IV, the slope of phase IV, and cardiac oscillations were measured on tracings obtained by both the regular single-breath N2 test (Tech I) and by a reverse technique (Tech II) in 9 healthy volunteers. Tech II consisted of 3 consecutive vital capacities (VC) of 100% O2 followed by one VC of room air. Theoretically, this should create a reversed apicobasal N2 gradient quantitatively similar to that of Tech I. From the total lung capacity following the VC2 of air, we monitored N2 concentration continuously at the mouth during a slow expiration in a manner similar to that of the single-breath N2 test. With Tech II, it is possible to preserve phase IV and its reversed slope in the presence of an almost flat slope of phase III and markedly blunted cardiac oscillations. When compared to Tech I, the slope of phase III with Tech II decreased from 0.66+/-0.20% N2/L (mean +/-SD) to 0.19+/-0.12 (p is less than 0.001), and cardiac oscillations decreased from a mean % N2 change with each heart beat of 0.87+/-0.37 to 0.24+/-0.21 (p is less than 0.005), whereas phase IV, although reversed in direction, remained quantitatively unchanged (0.35+/-0.15 L with Tech I and 0.37+/-0.14 L with Tech II), and the slope of phase IV tended to increase (2.7+/-1.9% N2 with Tech I and 3.4+/-2.1% N2 with Tech II, p=NS). We conclude that the N2 gradients within the lungs responsible for the slope of phase III and cardiac oscillations are largely independent of the gradients that give rise to phase IV and the slope of phase IV.     

Acute respiratory distress syndrome induced by avian influenza A (H5N1) virus in mice

RATIONALE AND OBJECTIVE: The acute respiratory distress syndrome (ARDS) caused by avian influenza H5N1 viral infection has been reported in many humans since this virus was found to infect humans in Hong Kong in 1997, but no studies regarding an animal model of ARDS with H5N1 viral infection have been found in the literature. Here we present a mouse model of ARDS induced by H5N1 virus. METHODS: Six- to 8-wk-old BALB/c mice were inoculated intranasally (50 micro l) with 1 x 10(2) 50% mouse infectious doses of A/Chicken/Hebei/108/2002 (H5N1) virus. Lung injury was assessed by observation of lung water content and histopathology. Arterial blood gas, white blood cell count in bronchial alveolar lavage fluid, and tumor necrosis factor-alpha and interleukin-6 in bronchoalveolar lavage fluid and serum were measured at the indicated time points. RESULTS: Our data showed that H5N1 viral infection in mice resulted in typical ARDS, which was characterized by the following features: (1) about 80% of mice (13 of 16) dead on Days 6 to 8 postinoculation; (2) highly edematous lungs and dramatically increased lung wet:dry weight ratios and lung wet weight:body weight ratios; (3) inflammatory cellular infiltration, alveolar and interstitial edema, and hemorrhage in lungs; (4) progressive and severe hypoxemia; and (5) significant increase in neutrophils, tumor necrosis factor-alpha, and interleukin-6 in BALF. CONCLUSION: These results suggested that we successfully established a mouse model of ARDS with H5N1 viral infection, which may benefit further investigation into the pathogenesis of human ARDS induced by H5N1 virus.     

Initiation sites for discontinuous DNA synthesis of bacteriophage T7

We have previously shown that the discontinuous replication of bacteriophage T7 DNA is primed by tetraribonucleotides (major component) or pentaribonucleotides. Both tetramers and pentamers start with pppA-C and are rich in A and C at the third and fourth nucleotides. In this study, the sites of transition from primer RNA to DNA in vivo have been located on a 340-nucleotide segment of the H strand of the T7 genome by 32P-labeling in vitro of the 5'-hydroxyl ends of DNA resulting from alkaline hydrolysis of RNA-linked T7 DNA fragments. Five strong transition sites were detected with a common sequence 5'-G-A-C-N1-N2-N3-N4-3', in which N1 was either C or A, N2 ws A, C, or G, and either N3 or N4 was the nucleotide for the switchover to DNA synthesis. We conclude that the complementary sequence 3'-C-T-G-G/T-N'2-(N'3)-5' in the template strand is the most frequently used signal for synthesis of primer RNA. Whereas primer-RNA synthesis starts at a precisely defined nucleotide, the transition to DNA synthesis varies within two nucleotides. Because the observed signal sequence would be present on a statistical basis once per 128 nucleotides, only about 10% of the existing signals are used for primer synthesis in each round of replication so that nascent fragments 1000-2000 long result. This provides an unexpected flexibility for RNA priming of DNA synthesis.     

White lines in L-edge x-ray absorption spectra and their implications for anomalous diffraction studies of biological materials.

We have measured high-resolution x-ray absorption spectra of lanthanide (Ln) and heavy transition metal complexes that display prominent narrow absorption peaks near the L2 and L3 absorption edges. The anomalous scattering factors (f' and f"), which are mathematically related to the absorption cross section, have correspondingly sharp changes in their magnitude within 5-10 eV of the absorption edge. Calculations of the magnitude of the change in f' and f" demonstrate that significant changes (on the order of 20 electrons in f') can be expected for these materials. These substantial changes in the anomalous scattering factors have applications to deriving structural information for macromolecules from x-ray diffraction studies. The magnitude of the changes indicate that the anomalous scattering technique is a powerful means of obtaining structural characteristics for macromolecules in single crystals, in solution, and in biological membranes.     

Effects of pressure and temperature on the binding of RecA protein to single-stranded DNA

The binding and polymerization of RecA protein to DNA is required for recombination, which is an essential function of life. We study the pressure and temperature dependence of RecA binding to single-stranded DNA in the presence of adenosine 5'-[γ-thio]triphosphate (ATP[γ-S]), in a temperature regulated high pressure cell using fluorescence anisotropy. Measurements were possible at temperatures between 5-60 °C and pressures up to 300 MPa. Experiments were performed on Escherichia coli RecA and RecA from a thermophilic bacteria, Thermus thermophilus. For E. coli RecA at a given temperature, binding is a monotonically decreasing and reversible function of pressure. At atmospheric pressure, E. coli RecA binding decreases monotonically up to 42 °C, where a sharp transition to the unbound state indicates irreversible heat inactivation. T. thermophilus showed no such transition within the temperature range of our apparatus. Furthermore, we find that binding occurs for a wider range of pressure and temperature for T. thermophilus compared to E. coli RecA, suggesting a correlation between thermophilicity and barophilicity. We use a two-state model of RecA binding/unbinding to extract the associated thermodynamic parameters. For E. coli, we find that the binding/unbinding phase boundary is hyperbolic. Our results of the binding of RecA from E. coli and T. thermophilus show adaptation to pressure and temperature at the single protein level.     

Hierarchical model of natural images and the origin of scale invariance

The study of natural images and how our brain processes them has been an area of intense research in neuroscience, psychology, and computer science. We introduced a unique approach to studying natural images by decomposing images into a hierarchy of layers at different logarithmic intensity scales and mapping them to a quasi-2D magnet. The layers were in different phases: “cold” and ordered at large-intensity scales, “hot” and disordered at small-intensity scales, and going through a second-order phase transition at intermediate scales. There was a single “critical” layer in the hierarchy that exhibited long-range correlation similar to that found in the 2D Ising model of ferromagnetism at the critical temperature. We also determined the interactions between layers mapped from natural images and found mutual inhibition that generated locally “frustrated” antiferromagnetic states. Almost all information in natural images was concentrated in a few layers near the phase transition, which has biological implications and also points to the hierarchical origin of scale invariance in natural images.     

Force generation by muscle fibers in rigor: a laser temperature-jump study.

A clear prediction of the helix-coil model for force generation in muscle is that force should be produced when the equilibrium (helix-coil) of a rigor (or activated) fiber is perturbed by a temperature jump near the melting temperature of the light meromyosin/heavy meromyosin hinge. An infrared, iodine-photodissociation laser was used to heat the fibers by approximately equal to 5 degrees C in under 1 mus. Under ionic conditions where rigor bridges are predominantly associated with the thick filament backbone, an abrupt drop in tension typical of normal thermoelastic expansion was seen. A similar response was observed below 41 degrees C for thick filament-released rigor bridges. Above this temperature, a rubber-like thermoelastic response was obtained typical of a helix-coil transition. At temperatures near 50 degrees C, the amount of force generated by a rigor fiber was large and comparable to that seen for an activated fiber at 5 degrees C. The relaxation spectra of force generation obtained for both systems (rigor and activated) show a step change followed by a biexponential kinetic process. The reciprocal relaxation times and amplitudes for these individual processes in activated and rigor fibers differ only by factors of 2-4. Force generation in the rigor muscle appears to arise from melting in the subfragment 2 hinge region of the myosin molecule since binding of subfragment 2 to the thick filament backbone inhibits force production. No significant force generation was observed following temperature jumps of relaxed fibers.     

Characterization of H9N2 Avian Influenza Viruses Isolated from Poultry Products in a Mouse Model

Low pathogenic H9N2 avian influenza viruses have spread in wild birds and poultry worldwide. Recently, the number of human cases of H9N2 virus infection has increased in China and other countries, heightening pandemic concerns. In Japan, H9N2 viruses are not yet enzootic; however, avian influenza viruses, including H5N1, H7N9, H5N6, and H9N2, have been repeatedly detected in raw poultry meat carried by international flight passengers from Asian countries to Japan. Although H9N2 virus-contaminated poultry products intercepted by the animal quarantine service at the Japan border have been characterized in chickens and ducks, the biological properties of those H9N2 viruses in mammals remain unclear. Here, we characterized the biological features of two H9N2 virus isolates [A/chicken/Japan/AQ-HE28-50/2016 (Ck/HE28-50) and A/chicken/Japan/AQ-HE28-57/2016 (Ck/HE28-57)] in a mouse model. We found that these H9N2 viruses replicate well in the respiratory tract of infected mice without adaptation, and that Ck/HE28-57 caused body weight loss in the infected mice. Our results indicate that H9N2 avian influenza viruses isolated from raw chicken meat products illegally brought to Japan can potentially infect and cause disease in mammals.     

Hypothermia during reperfusion limits 'no-reflow' injury in a rabbit model of acute myocardial infarction

OBJECTIVE: Reflow following coronary artery occlusion is an important predictor of clinical outcome. This study tests the effects of regional hypothermia, initiated late during ischemia and maintained for 2 h of reperfusion, on the no-reflow phenomenon. METHODS: Anesthetized, open-chest New Zealand White rabbits received 30 min of coronary artery occlusion and 3 h reperfusion. Regional myocardial hypothermia (H, n=14), starting 10 min before reperfusion and continuing for 2 h of reperfusion, was compared with normothermia (N, n=14). Regional myocardial blood flow (microspheres) was measured during occlusion and at the end of reperfusion. The anatomic zone of no-reflow (thioflavin S in vivo injection) and infarct size were measured in the ischemic risk region at the end of the study. RESULTS: Myocardial temperature in H rabbits was decreased by 5.0+/-0.4 degrees C from baseline (37.1+/-0.2 degrees C) and remained about 32 degrees C during the cooling phase, returning to 36.0+/-0.3 degrees C at 3 h. N hearts remained within 0.2 degrees C of baseline (37.3+/-0.1 degrees C) throughout. Both groups were equally ischemic during occlusion, but at the end of reperfusion reflow to the previously ischemic zone was significantly higher in H, 77+/-5% of normal blood flow versus 36+/-4% in N (P=0.0001). The zone of anatomic no-reflow was significantly smaller in H, 11+/-3% of the ischemic risk zone versus 37+/-3% in N (P=0.0001), and was proportionally smaller when represented as a percent of the necrotic zone 36+/-6% compared with 75+/-5% in N. Infarct size, expressed as a percent of the ischemic risk zone was significantly smaller in H vs. N hearts (27+/-4 and 51+/-5%, P=0.0000). CONCLUSION: This study shows that hypothermic therapy initiated late during ischemia and continuing for several hours of reperfusion significantly improves reflow and reduces macroscopic zones of no-reflow and necrosis in this model. The improvement in reflow was greater than would be expected in the H group compared with N, based on the extent of necrosis. As reflow is a predictor of outcome, this intervention may have clinical implications.     

Genetic Characterization and Pathogenesis of Three Novel Reassortant H5N2 Viruses in South Korea, 2018

The outbreaks of H5N2 avian influenza viruses have occasionally caused the death of thousands of birds in poultry farms. Surveillance during the 2018 winter season in South Korea revealed three H5N2 isolates in feces samples collected from wild birds (KNU18-28: A/Wild duck/South Korea/KNU18-28/2018, KNU18-86: A/Bean Goose/South Korea/KNU18-86/2018, and KNU18-93: A/Wild duck/South Korea/KNU18-93/2018). Phylogenetic tree analysis revealed that these viruses arose from reassortment events among various virus subtypes circulating in South Korea and other countries in the East Asia–Australasian Flyway. The NS gene of the KNU18-28 and KNU18-86 isolates was closely related to that of China’s H10N3 strain, whereas the KNU18-93 strain originated from the H12N2 strain in Japan, showing two different reassortment events and different from a low pathogenic H5N3 (KNU18-91) virus which was isolated at the same day and same place with KNU18-86 and KNU18-93. These H5N2 isolates were characterized as low pathogenic avian influenza viruses. However, many amino acid changes in eight gene segments were identified to enhance polymerase activity and increase adaptation and virulence in mice and mammals. Experiments reveal that viral replication in MDCK cells was quite high after 12 hpi, showing the ability to replicate in mouse lungs. The hematoxylin and eosin-stained (H&E) lung sections indicated different degrees of pathogenicity of the three H5N2 isolates in mice compared with that of the control H1N1 strain. The continuing circulation of these H5N2 viruses may represent a potential threat to mammals and humans. Our findings highlight the need for intensive surveillance of avian influenza virus circulation in South Korea to prevent the risks posed by these reassortment viruses to animal and public health.     

On case-fatality rate: review and hypothesis

The relationship between log cumulative number of patients (X) and that of deaths (Y) in an epidemic follows the equation logY = klogX - klogN(0), where k is a constant determining the slope and N(0) is the value of X when Y = 1. Diseases with k = 1 are Ebola hemorrhagic fever, avian influenza H5N1, cholera, and hand, foot, and mouth disease; those with k > 1 are the influenza H1N1 2009 pandemic in countries other than Mexico and the SARS epidemic in some countries; and those with k < 1 include the influenza H1N1 2009 pandemic in Mexico. Epidemics with k > 1 can be simulated by postulating two subpopulations (normal population [NP] and vulnerable population [VP]), where the epidemic proceeds at higher speed and at higher mortality in VP than in NP. Epidemics with k < 1 can be simulated by postulating coexisting high virulence virus (HVV) and low virulence virus (LVV), with the former being propagated at slower speed and with a higher mortality rate than the latter. An epidemic with k > 1 was simulated using parameters that are fractions of subpopulations NP or VP from the total population (f) and NP- or VP-specific patient multiplication (M) and mortality (D) rates. An epidemic with k < 1 was simulated using parameters that are fractions of HVV- or LVV-infected human populations (f), and HVV- or LVV-specific M and D.     

Fluorine-19 chemical shifts as structural probes of metal-sulfur clusters and the cofactor of nitrogenase.

Several properties of the FeMo-cofactor (co) of nitrogenase in N-methylformamide solution at ambient temperature have been investigated by means of 19F NMR spectroscopy. With C6H5CF3 reference signals the magnetic moment per Mo atom was found to be approximately equal to 3.9 BM, consistent with S = 3/2 ground state identified by other spectroscopic methods at low temperature. Reaction of FeMo-co with 1.0 eq of RFS- (RF = p-C6H4CF3, p-C6H4F) afforded isotropically shifted signals indicative of binding to a paramagnetic cluster. By comparison with the spectra of Fe-S and Fe-Mo-S species derivatized with RFS-, including the cubane-type MoFe3S4 clusters with S = 3/2 ground states, it was concluded that the essential FeMo-co cluster structure remains intact and a Fe atom is the probable thiolate binding site. An interaction of FeMo-co with C6H5S- had been detected earlier by low temperature EPR spectroscopy. The binding site assignment is based on large observed isotropic shifts (ca. -12ppm) compared to the much smaller values found for Mo-SRF ligands in MoFe3S4 clusters and anticipated in FeMo-co on the basis of recent spectroscopic results. Isotropic 19F shifts have proven extremely sensitive to electronic and structural features of Fe-S and Fe-Mo-S clusters. The inclusion of a 19F NMR label in FeMo-co should prove of utility in further investigation of cofactor properties and reactions.     

Increasing binding affinity of agonists to glutamate receptors increases synaptic responses at glutamatergic synapses.

This study examined the relationship between the affinity of glutamate agonists for the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and the characteristics of the physiological responses elicited by endogenous activation of the AMPA receptors. We tested the effects of chaotropic ions on [3H]AMPA binding in synaptic membranes as well as on synaptic responses elicited in CA1 by electrical stimulation of the Schaffer/commissural pathway in the in vitro hippocampal slice preparation. Of the chaotropic ions tested, only perchlorate and thiocyanate produced large increases in [3H]AMPA binding to synaptic membranes. The effect was due to an increase in affinity for agonists, as shown by a shift of the displacement curves of 6-cyano-7-nitro[3H]-quinoxaline-2,3-dione binding by AMPA or glutamate. The effect of thiocyanate on [3H]AMPA binding was extremely sensitive to temperature, as the binding was increased almost 10-fold at 0 degree C but only 2- to 3-fold at 35 degrees C. The effect of perchlorate was only weakly temperature dependent. Similarly, thiocyanate and perchlorate were the only chaotropic ions tested that increased the initial slope and amplitude of the extracellularly recorded potentials evoked in CA1 dendritic field. Both ions did not change paired-pulse facilitation, an index of transmitter release, or fiber volley amplitude, an index of afferent recruitment. The chaotropic ions had no significant effects on either [3H]glutamate binding to the N-methyl-D-aspartate receptor or N-methyl-D-aspartate receptor-mediated synaptic responses. Finally, the effect of perchlorate on synaptic responses was significantly reduced after induction of long-term potentiation. These results indicate that an increase in affinity of the AMPA receptors for their agonists results in increased synaptic responses and strongly suggest that characteristics of the AMPA receptor are modified following long-term potentiation.     

Evidence against stabilization of the transition state oxyanion by a pKa-perturbed RNA base in the peptidyl transferase center

The crystal structure of the ribosomal 50S subunit from Haloarcula marismortui in complex with the transition state analog CCdA-phosphate-puromycin (CCdApPmn) led to a mechanistic proposal wherein the universally conversed A2451 in the ribosomal active site acts as an "oxyanion hole" to promote the peptidyl transferase reaction [Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. (2000) Science 289, 920-929]. In the model, close proximity (3 A) between the A2451 N3 and the nonbridging phosphoramidate oxygen of CCdApPmn suggested that the carbonyl oxyanion formed during the tetrahedral transition state is stabilized by hydrogen bonding to the protonated A2451 N3, the pKa of which must be perturbed substantially. We characterize the contribution of the putative hydrogen bond between the N3 of A2451 and the nonbridging phosphoramidate oxygen by using chemical protection and peptidyl transfer inhibition assays. If this putative hydrogen bond makes a significant thermodynamic contribution, then CCdApPmn-binding affinity to the 50S ribosomal subunit should be strongly pH-dependent, with affinity increasing as the pH is lowered. We report that CCdApPmn binds 50S ribosomes with essentially equal affinity at all pH values between 5.0 and 8.5. These data argue against a mechanism for peptidyl transfer in which a residue with near neutral pKa stabilizes the transition-state oxyanion, at least to the extent that CCdApPmn accurately mimics the transition state.     

High frequency of amantadine-resistant influenza A (H3N2) viruses in the 2005-2006 season and rapid detection of amantadine-resistant influenza A (H3N2) viruses by MAMA-PCR

Using the newly designed mismatch amplification mutation assay (MAMA) PCR, we demonstrated the high frequency of amantadine-resistant influenza A (H3N2) viruses isolated during the 2005-2006 season by detecting the mutation at amino acid position 31 of the M2 protein (S31N). Further, phylogenetic analyses of the HA1 sequences of the S31N viruses revealed that they comprised a clonal lineage that would result in the common characteristic amino acid changes at positions 193 (Ser to Phe) and 225 (Asp to Asn) of the HA protein. We also demonstrated that the S31N/S193F/D225N viruses had already emerged in Aichi Prefecture by the end of the previous 2004-2005 season.     

Prevention of influenza pneumonitis by sialic Acid-conjugated dendritic polymers

Influenza A viral infection begins by hemagglutinin glycoproteins on the viral envelope binding to cell membrane sialic acid (SA). Free SA monomers cannot block hemagglutinin adhesion in vivo because of toxicity. Polyvalent, generation 4 (G4) SA-conjugated polyamidoamine (PAMAM) dendrimer (G4-SA) was evaluated as a means of preventing adhesion of 3 influenza A subtypes (H1N1, H2N2, and H3N2). In hemagglutination-inhibition assays, G4-SA was found to inhibit all H3N2 and 3 of 5 H1N1 influenza subtype strains at concentrations 32-170 times lower than those of SA monomers. In contrast, G4-SA had no ability to inhibit hemagglutination with H2N2 subtypes or 2 of 5 H1N1 subtype strains. In vivo experiments showed that G4-SA completely prevented infection by a H3N2 subtype in a murine influenza pneumonitis model but was not effective in preventing pneumonitis caused by an H2N2 subtype. Polyvalent binding inhibitors have potential as antiviral therapeutics, but issues related to strain specificity must be resolved.     

Gas mixing in dog lungs during high frequency ventilation studied by partial washout-single exhalation technique

Gas mixing was studied in 10 anesthetized paralyzed dogs during high-frequency low tidal ventilation (HFV). After simultaneous washin of ethane (1%) and washout of resident argon (0.9%) the gas inflow was switched to atmospheric air for varied time intervals leading to varied levels of C2H6 washout and Ar washin. After the stop of HFV at predetermined test gas washout/washin levels, a constant-flow exhalation by a servo ventilator was performed and expirograms of C2H6 and Ar were recorded. Measurements were performed at varied ventilation frequencies (10-40 Hz), stroke volumes (20-40 ml), lung volumes (730-830 ml), expiratory flow rates (0.1-0.01 L/sec), breath-holding prior to exhalation (0-12 sec) and test gas washout levels achieved by varying the washout time (1 to 65 sec) before onset of exhalation. The expirograms showed a close to linearly rising alveolar plateau. They were analyzed for series dead space and alveolar slope which was normalized to the initial-to-final partial pressure difference. The normalized slopes of C2H6 washout and Ar washin were averaged, whereby the effect of shrinking lung volume due to continuing CO2/O2 exchange at low R was assumed to be suppressed. The slope was little affected by changes of stroke volume, decreased slightly with increasing frequency, and decreased considerably with breath-holding or increasing lung volume. As washout progressed, the alveolar slope first increased, attained a maximum at about half-washout and thereafter decreased. The finite values of the alveolar slope indicated that intrapulmonary gas mixing during HFV was incomplete. The slopes were larger than expected from diffusion calculations on symmetrically branching lung models. The behavior of the slope at varied washout levels suggested involvement of parallel ventilation/volume inhomogeneity coupled with sequential emptying.     

Switchable hardening of a ferromagnet at fixed temperature

The intended use of a magnetic material, from information storage to power conversion, depends crucially on its domain structure, traditionally crafted during materials synthesis. By contrast, we show that an external magnetic field, applied transverse to the preferred magnetization of a model disordered uniaxial ferromagnet, is an isothermal regulator of domain pinning. At elevated temperatures, near the transition into the paramagnet, modest transverse fields increase the pinning, stabilize the domain structure, and harden the magnet, until a point where the field induces quantum tunneling of the domain walls and softens the magnet. At low temperatures, tunneling completely dominates the domain dynamics and provides an interpretation of the quantum phase transition in highly disordered magnets as a localization/delocalization transition for domain walls. While the energy scales of the rare earth ferromagnet studied here restrict the effects to cryogenic temperatures, the principles discovered are general and should be applicable to existing classes of highly anisotropic ferromagnets with ordering at room temperature or above.