Forced Symmetry Breaking from SO(3) to SO(2) for Rotating Waves on the Sphere

We consider a small SO(2)-equivariant perturbation of a reaction-diffusion system on the sphere, which is equivariant with respect to the group SO(3) of all rigid rotations. We consider a normally hyperbolic SO(3)-group orbit of a rotating wave on the sphere that persists to a normally hyperbolic SO(2)-invariant manifold $M(\epsilon)$. We investigate the effects of this forced symmetry breaking by studying the perturbed dynamics induced on $M(\epsilon)$ by the above reaction-diffusion system. We prove that depending on the frequency vectors of the rotating waves that form the relative equilibrium SO(3)u_{0}, these rotating waves will give SO(2)-orbits of rotating waves or SO(2)-orbits of modulated rotating waves (if some transversality conditions hold). The orbital stability of these solutions is established as well. Our main tools are the orbit space reduction, Poincare map and implicit function theorem

Draft genome sequences of Streptomyces virginiae strain CMAA1738, Paenibacillus ottowiistrain CMAA1739 and Pseudomonas inefficax strain CMAA1741, isolated from rhizosphere of wheat landraces.

Abstract: In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of Triticum aestivum. Streptomyces virginiae CMAA1738 and Paenibacillus ottowii CMAA1739 were obtained from the wheat landrace Iran 1-29-11334, and Pseudomonas inefficax CMAA1741 was isolated from the wheat landrace Karakilcik.On-line first

Quantum Knizhnik-Zamolodchikov equation, generalized Razumov-Stroganov sum rules and extended Joseph polynomials

We prove higher rank analogues of the Razumov--Stroganov sum rule for the groundstate of the O(1) loop model on a semi-infinite cylinder: we show that a weighted sum of components of the groundstate of the A_{k-1} IRF model yields integers that generalize the numbers of alternating sign matrices. This is done by constructing minimal polynomial solutions of the level 1 U_q(\hat{sl(k)}) quantum Knizhnik--Zamolodchikov equations, which may also be interpreted as quantum incompressible q-deformations of fractional quantum Hall effect wave functions at filling fraction nu=1/k. In addition to the generalized Razumov--Stroganov point q=-e^{i pi/k+1}, another combinatorially interesting point is reached in the rational limit q -> -1, where we identify the solution with extended Joseph polynomials associated to the geometry of upper triangular matrices with vanishing k-th power.Comment: v3: misprint fixed in eq (2.1

Hopf algebras in dynamical systems theory

The theory of exact and of approximate solutions for non-autonomous linear differential equations forms a wide field with strong ties to physics and applied problems. This paper is meant as a stepping stone for an exploration of this long-established theme, through the tinted glasses of a (Hopf and Rota-Baxter) algebraic point of view. By reviewing, reformulating and strengthening known results, we give evidence for the claim that the use of Hopf algebra allows for a refined analysis of differential equations. We revisit the renowned Campbell-Baker-Hausdorff-Dynkin formula by the modern approach involving Lie idempotents. Approximate solutions to differential equations involve, on the one hand, series of iterated integrals solving the corresponding integral equations; on the other hand, exponential solutions. Equating those solutions yields identities among products of iterated Riemann integrals. Now, the Riemann integral satisfies the integration-by-parts rule with the Leibniz rule for derivations as its partner; and skewderivations generalize derivations. Thus we seek an algebraic theory of integration, with the Rota-Baxter relation replacing the classical rule. The methods to deal with noncommutativity are especially highlighted. We find new identities, allowing for an extensive embedding of Dyson-Chen series of time- or path-ordered products (of generalized integration operators); of the corresponding Magnus expansion; and of their relations, into the unified algebraic setting of Rota-Baxter maps and their inverse skewderivations. This picture clarifies the approximate solutions to generalized integral equations corresponding to non-autonomous linear (skew)differential equations.Comment: International Journal of Geometric Methods in Modern Physics, in pres

Borrelia recurrentis employs a novel multifunctional surface protein with anti-complement, anti-opsonic and invasive potential to escape innate immunity

Borrelia recurrentis, the etiologic agent of louse-borne relapsing fever in humans, has evolved strategies, including antigenic variation, to evade immune defence, thereby causing severe diseases with high mortality rates. Here we identify for the first time a multifunctional surface lipoprotein of B. recurrentis, termed HcpA, and demonstrate that it binds human complement regulators, Factor H, CFHR-1, and simultaneously, the host protease plasminogen. Cell surface bound factor H was found to retain its activity and to confer resistance to complement attack. Moreover, ectopic expression of HcpA in a B. burgdorferi B313 strain, deficient in Factor H binding proteins, protected the transformed spirochetes from complement-mediated killing. Furthermore, HcpA-bound plasminogen/plasmin endows B. recurrentis with the potential to resist opsonization and to degrade extracellular matrix components. Together, the present study underscores the high virulence potential of B. recurrentis. The elucidation of the molecular basis underlying the versatile strategies of B. recurrentis to escape innate immunity and to persist in human tissues, including the brain, may help to understand the pathological processes underlying louse-borne relapsing fever

Cloning and sequence analysis of cDNAs encoding the cytosolic precursors of subunits GapA and GapB of chloroplast glyceraldehyde-3-phosphate dehydrogenase from pea and spinach

Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is composed of two different subunits, GapA and GapB. cDNA clones containing the entire coding sequences of the cytosolic precursors for GapA from pea and for GapB from pea and spinach have been identified, sequenced and the derived amino acid sequences have been compared to the corresponding sequences from tobacco, maize and mustard. These comparisons show that GapB differs from GapA in about 20% of its amino acid residues and by the presence of a flexible and negatively charged C-terminal extension, possibly responsible for the observed association of the enzyme with chloroplast envelopes in vitro. This C-terminal extension (29 or 30 residues) may be susceptible to proteolytic cleavage thereby leading to a conversion of chloroplast GAPDH isoenzyme I into isoenzyme II. Evolutionary rate comparisons at the amino acid sequence level show that chloroplast GapA and GapB evolve roughly two-fold slower than their cytosolic counterpart GapC. GapA and GapB transit peptides evolve about 10 times faster than the corresponding mature subunits. They are relatively long (68 and 83 residues for pea GapA and spinach GapB respectively) and share a similar amino acid framework with other chloroplast transit peptides

Evaluation of a laboratory-based high-throughput SARS-CoV-2 antigen assay for non-COVID-19 patient screening at hospital admission

Several rapid antigen tests (RATs) for the detection of SARS-CoV-2 were evaluated recently. However, reliable performance data for laboratory-based, high-throughput antigen tests are lacking. Therefore and in response to a short-term shortage of PCR reagents, we evaluated DiaSorin's LIAISON SARS-CoV-2 antigen test in comparison to RT-qPCR, and concerning the application of screening non-COVID-19 patients on hospital admission. Applying the manufacturer-recommended cut-off of 200 arbitrary units (AU/mL) the specificity of the LIAISON Test was 100%, the overall analytical sensitivity 40.2%. Lowering the cut-off to 100 AU/mL increased the sensitivity to 49.7% and decreased the specificity to 98.3%. Confining the analysis to samples with an RT-qPCR result < 25 Ct resulted in a sensitivity of 91.2%. The quality of the LIAISON test is very similar to that of good RATs described in the literature with the advantage of high throughput and the disadvantage of relatively long analysis time. It passes the WHO quality criteria for rapid antigen tests and is characterized by particularly high specificity. The LIAISON test can therefore be used for the same applications as recommended for RATs by the WHO. Due to limited sensitivity, the LIAISON test should only be used for screening, if PCR-based assays are not available

Opportunities and challenges of Web 2.0 for vaccination decisions.

A growing number of people use the Internet to obtain health information, including information about vaccines. Websites that allow and promote interaction among users are an increasingly popular source of health information. Users of such so-called Web 2.0 applications (e.g. social media), while still in the minority, represent a growing proportion of online communicators, including vocal and active anti-vaccination groups as well as public health communicators. In this paper, the authors: define Web 2.0 and examine how it may influence vaccination decisions; discuss how anti-vaccination movements use Web 2.0 as well as the challenges Web 2.0 holds for public health communicators; describe the types of information used in these different settings; introduce the theoretical background that can be used to design effective vaccination communication in a Web 2.0 environment; make recommendations for practice and pose open questions for future research. The authors conclude that, as a result of the Internet and Web 2.0, private and public concerns surrounding vaccinations have the potential to virally spread across the globe in a quick, efficient and vivid manner. Web 2.0 may influence vaccination decisions by delivering information that alters the perceived personal risk of vaccine-preventable diseases or vaccination side-effects. It appears useful for public health officials to put effort into increasing the effectiveness of existing communication by implementing interactive, customized communication. A key step to providing successful public health communication is to identify those who are particularly vulnerable to finding and using unreliable and misleading information. Thus, it appears worthwhile that public health websites strive to be easy to find, easy to use, attractive in its presentation and readily provide the information, support and advice that the searcher is looking for. This holds especially when less knowledgeable individuals are in need of reliable information about vaccination risks and benefits

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page