Twirling and Whirling: Viscous Dynamics of Rotating Elastica

Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity. Competition between twist injection, twist diffusion, and writhing instabilities is described by a novel pair of coupled PDEs for twist and bend evolution. Analytical and numerical methods elucidate the twist/bend coupling and reveal two dynamical regimes separated by a Hopf bifurcation: (i) diffusion-dominated axial rotation, or twirling, and (ii) steady-state crankshafting motion, or whirling. The consequences of these phenomena for self-propulsion are investigated, and experimental tests proposed.Comment: To be published in Physical Review Letter

Accurate laboratory rest frequencies of vibrationally excited CO up to varv=3varv = 3 and up to 2 THz

Astronomical observations of (sub)millimeter wavelength pure rotational emission lines of the second most abundant molecule in the Universe, CO, hold the promise of probing regions of high temperature and density in the innermost parts of circumstellar envelopes. The rotational spectrum of vibrationally excited CO up to \varv = 3 has been measured in the laboratory between 220 and 1940 GHz with relative accuracies up to $5.2 \times 10^{-9}$, corresponding to $\sim 5$ kHz near 1 THz. The rotational constant $B$ and the quartic distortion parameter $D$ have been determined with high accuracy and even the sextic distortion term $H$ was determined quite well for \varv = 1 while reasonable estimates of $H$ were obtained for \varv = 2 and 3. The present data set allows for the prediction of accurate rest frequencies of vibrationally excited CO well beyond 2 THz.Comment: Astron. Astrophys, accepted; 5 pages, 2 Figures, 2 Table

Purification of a 31,000-dalton insulin-like growth factor binding protein from human amniotic fluid. Isolation of two forms with different biologic actions.

Human amniotic fluid has been shown to contain a protein that binds insulin-like growth factor I and II (IGF-I and IGF-II). Partially purified preparations of this protein have been reported to inhibit the biologic actions of the IGFs. In these studies our laboratory has used a modified purification procedure to obtain a homogeneous preparation of this protein as determined by polyacrylamide gel electrophoresis and amino acid sequence analysis. During purification the ion exchange chromatography step resulted in two peaks of material with IGF binding activity termed peaks B and C. Each peak was purified separately to homogeneity. Both peaks were estimated to be 31,000 daltons by polyacrylamide gel electrophoresis and their amino acid compositions were nearly identical. Amino acid sequence analysis showed that both peaks had identical N-terminal sequences through the first 28 residues. Neither protein had detectable carbohydrate side chains and each had a similar affinity for radiolabeled IGF-I (1.7-2.2 x 10(10) liters/mol). In contrast, these two forms had marked differences in bioactivity. Concentrations of peak C material between 2 and 20 ng/ml inhibited IGF-I stimulation of [3H]thymidine incorporation into smooth muscle cell DNA. In contrast, when peak B (100 ng/ml) was incubated with IGF-I there was a 4.4-fold enhancement of stimulation of DNA synthesis. Additionally, pure peak B was shown to adhere to cell surfaces, whereas peak C was not adherent. The non-adherent peak C inhibited IGF-I binding to its receptor and to adherent peak B. We conclude that human amniotic fluid contains two forms of IGF binding protein that have very similar physiochemical characteristics but markedly different biologic actions. Since both have similar if not identical amino acid compositions, N-terminal sequences, and do not contain carbohydrate, we conclude that they differ in some other as yet undefined post-translational modification

The Viscous Nonlinear Dynamics of Twist and Writhe

Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal evolution of the filament's complex curvature and twist density embodies the dynamic interplay of twist and writhe. These are used to illustrate a novel nonlinear phenomenon: ``geometric untwisting" of open filaments, whereby twisting strains relax through a transient writhing instability without performing axial rotation. This may explain certain experimentally observed motions of fibers of the bacterium B. subtilis [N.H. Mendelson, et al., J. Bacteriol. 177, 7060 (1995)].Comment: 9 pages, 4 figure

Wild-Type and Mutant Hemagglutinin Fusion Peptides Alter Bilayer Structure as Well as Kinetics and Activation Thermodynamics of Stalk and Pore Formation Differently: Mechanistic Implications

Viral fusion peptides are short N-terminal regions of type-1 viral fusion proteins that are critical for virus entry. Although the importance of viral fusion peptides in virus-cell membrane fusion is established, little is known about how they function. We report the effects of wild-type (WT) hemagglutinin (HA) fusion peptide and its G1S, G1V, and W14A mutants on the kinetics of poly(ethylene glycol)(PEG)-mediated fusion of small unilamellar vesicles composed of dioleoylphosphatidylcholine, dioleoylphosphatidylethanolamine, sphingomyelin, and cholesterol (molar ratio of 35:30:15:20). Time courses of lipid mixing, content mixing, and content leakage were obtained using fluorescence assays at multiple temperatures and analyzed globally using either a two-step or three-step sequential ensemble model of the fusion process to obtain the rate constant and activation thermodynamics of each step. We also monitored the influence of peptides on bilayer interfacial order, acyl chain order, bilayer free volume, and water penetration. All these data were considered in terms of a recently published mechanistic model for the thermodynamic transition states for each step of the fusion process. We propose that WT peptide catalyzes Step 1 by occupying bilayer regions vacated by acyl chains that protrude into interbilayer space to form the Step 1 transition state. It also uniquely contributes a positive intrinsic curvature to hemi-fused leaflets to eliminate Step 2 and catalyzes Step 3 by destabilizing the highly stressed edges of the hemi-fused microstructures that dominate the ensemble of the intermediate state directly preceding fusion pore formation. Similar arguments explain the catalytic and inhibitory properties of the mutant peptides and support the hypothesis that the membrane-contacting fusion peptide of HA fusion protein is key to its catalytic activity

ACME encoded speG abrogates the unique hypersensitivity of Staphylococcus aureus to exogenous polyamines

Polyamines, including spermine (Spm) and spermidine (Spd), are aliphatic cations that are reportedly synthesized by all living organisms. They exert pleiotropic effects on cells and are required for efficient nucleic acid and protein synthesis. Here, we report that the human pathogen Staphylococcus aureus lacks identifiable polyamine biosynthetic genes, and consequently produces no Spm/Spd or their precursor compounds putrescine and agmatine. Moreover, while supplementing defined medium with polyamines generally enhances bacterial growth, Spm and Spd exert bactericidal effects on S. aureus at physiologic concentrations. Small colony variants specifically lacking menaquinone biosynthesis arose after prolonged Spm exposure and exhibited reduced polyamine-sensitivity. However, other respiratory-defective mutants were no less susceptible to Spm implying menaquinone itself rather than general respiration is required for full Spm-toxicity. Polyamine hypersensitivity distinguishes S. aureus from other bacteria and is exhibited by all tested strains save those belonging to the USA-300 group of Community-Associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA). We identified one gene within the USA-300-specific Arginine Catabolic Mobile Element (ACME) encoding a Spm/Spd N-acetyltransferase that is necessary and sufficient for polyamine resistance. S. aureus encounters significant polyamine levels during infection, however the acquisition of ACME encoded speG allows USA-300 clones to circumvent polyamine-hypersensitivity, a peculiar trait of S. aureus

Evidence for a singularity in ideal magnetohydrodynamics: implications for fast reconnection

Numerical evidence for a finite-time singularity in ideal 3D magnetohydrodynamics (MHD) is presented. The simulations start from two interlocking magnetic flux rings with no initial velocity. The magnetic curvature force causes the flux rings to shrink until they come into contact. This produces a current sheet between them. In the ideal compressible calculations, the evidence for a singularity in a finite time $t_c$ is that the peak current density behaves like $|J|_\infty \sim 1/(t_c-t)$ for a range of sound speeds (or plasma betas). For the incompressible calculations consistency with the compressible calculations is noted and evidence is presented that there is convergence to a self-similar state. In the resistive reconnection calculations the magnetic helicity is nearly conserved and energy is dissipated.Comment: 4 pages, 4 figure

The fate of the homoctenids (Tentaculitoidea) during the Frasnian-Famennian mass extinction (Late Devonian)

The homoctenids (Tentaculitoidea) are small, conical-shelled marine animals which are amongst the most abundant and widespread of all Late Devonian fossils. They were a principal casualty of the Frasnian-Famennian (F-F, Late Devonian) mass extinction, and thus provide an insight into the extinction dynamics. Despite their abundance during the Late Devonian, they have been largely neglected by extinction studies. A number of Frasnian-Famennian boundary sections have been studied, in Poland, Germany, France, and the United States. These sections have yielded homoctenids, which allow precise recognition of the timing of the mass extinction. It is clear that the homoctenids almost disappear from the fossil record during the latest Frasnian “Upper Kellwasser Event”. The coincident extinction of this pelagic group, and the widespread development of intense marine anoxia within the water column, provides a causal link between anoxia and the F-F extinction. Most notable is the sudden demise of a group, which had been present in rock-forming densities, during this anoxic event. One new species, belonging to Homoctenus is described, but is not formally named here

Niche partitioning of a pathogenic microbiome driven by chemical gradients

© 2018 The Authors, some rights reserved. Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states

An adherens junction protein is a member of the family of lactose-binding lectins.

We previously described a pig junction protein of M(r) 37,000 found in oral epithelium but not in epidermis, limited to suprabasal cells, and colocalizing by immunofluorescence with adherens junction proteins. A 1.1-kilobase pair cDNA of the 37-kDa protein yielded an open reading frame encoding a 323-amino acid protein of 35,852 Da, and Northern analysis demonstrated a band of 1.2 kilobases in tongue RNA. Secondary structure predictions indicate that the 37% identical 16-17-kDa N- and C-terminal domains from beta-sheet-rich barrels linked by a compact proline-rich segment. The protein is 72% identical in amino acid sequence and shares symmetrical two-domain structure with L-36, a lectin of unknown function from rat intestine, indicating that the 37-kDa protein is the porcine form of L-36. Of the homologous lactose binding lectins known, two others, invertebrate lectins, share this symmetrical structure. Expression of the C-terminal domain of the pig lectin in bacteria yields a lectin which binds lactosyl-Sepharose, and binding is inhibited by lactose. The expressed protein binds a glycoprotein of 120 kDa from pig tongue epithelium on Western blots, and this is also inhibited by lactose. The findings suggest that the lectin function may be involved in the assembly of adherens junctions