Spontaneous phenotypic suppression of GacA-defective Vibrio fischeri is achieved via mutation of csrA and ihfA

Background: Symbiosis defective GacA-mutant derivatives of Vibrio fischeri are growth impaired thereby creating a selective advantage for growth-enhanced spontaneous suppressors. Suppressors were isolated and characterized for effects of the mutations on gacA-mutant defects of growth, siderophore activity and luminescence. The mutations were identified by targeted and whole genome sequencing. Results: Most mutations that restored multiple phenotypes were non-null mutations that mapped to conserved domains in or altered expression of CsrA, a post-transcriptional regulator that mediates GacA effects in a number of bacterial species. These represent an array of unique mutations compared to those that have been described previously. Different substitutions at the same amino acid residue were identified allowing comparisons of effects such as at the R6 residue, which conferred relative differences in luminescence and siderophore levels. The screen revealed residues not previously identified as critical for function including a single native alanine. Most csrA mutations enhanced luminescence more than siderophore activity, which was especially evident for mutations predicted to reduce the amount of CsrA. Although CsrA mutations compensate for many known GacA mutant defects, not all CsrA suppressors restore symbiotic colonization. Phenotypes of a suppressor allele of ihfA that encodes one subunit of the integration host factor (IHF) heteroduplex indicated the protein represses siderophore and activates luminescence in a GacA-independent manner. Conclusions: In addition to its established role in regulation of central metabolism, the CsrA regulator represses luminescence and siderophore as an intermediate of the GacA regulatory hierachy. Siderophore regulation was less sensitive to stoichiometry of CsrA consistent with higher affinity for the targets of this trait. The lack of CsrA null-mutant recovery implied these mutations do not enhance fitness of gacA mutants and alluded to this gene being conditionally essential. This study also suggests a role for IHF in the GacA-CsrB-CsrA regulatory cascade by potentially assisting with the binding of repressors of siderohphore and activators of luminescence. As many phosphorelay proteins reduce fitness when mutated, the documented instability used in this screen also highlights a potentially universal and underappreciated problem that, if not identified and strategically avoided, could introduce confounding variability during experimental study of these regulatory pathways

Stripe to spot transition in a plant root hair initiation model

A generalised Schnakenberg reaction-diffusion system with source and loss terms and a spatially dependent coefficient of the nonlinear term is studied both numerically and analytically in two spatial dimensions. The system has been proposed as a model of hair initiation in the epidermal cells of plant roots. Specifically the model captures the kinetics of a small G-protein ROP, which can occur in active and inactive forms, and whose activation is believed to be mediated by a gradient of the plant hormone auxin. Here the model is made more realistic with the inclusion of a transverse co-ordinate. Localised stripe-like solutions of active ROP occur for high enough total auxin concentration and lie on a complex bifurcation diagram of single and multi-pulse solutions. Transverse stability computations, confirmed by numerical simulation show that, apart from a boundary stripe, these 1D solutions typically undergo a transverse instability into spots. The spots so formed typically drift and undergo secondary instabilities such as spot replication. A novel 2D numerical continuation analysis is performed that shows the various stable hybrid spot-like states can coexist. The parameter values studied lead to a natural singularly perturbed, so-called semi-strong interaction regime. This scaling enables an analytical explanation of the initial instability, by describing the dispersion relation of a certain non-local eigenvalue problem. The analytical results are found to agree favourably with the numerics. Possible biological implications of the results are discussed.Comment: 28 pages, 44 figure

Laguerre polynomials of derivations

We introduce a grading switching for arbitrary non-associative algebras of prime characteristic p, aimed at producing a new grading of an algebra from a given one. We take inspiration from a fundamental tool in the classification theory of modular Lie algebras known as toral switching, which relies on a delicate adaptation of the exponential of a derivation. Our grading switching is achieved by evaluating certain generalized Laguerre polynomials of degree p − 1, which play the role of generalized exponentials, on a derivation of the algebra. A crucial part of our argument is establishing a congruence for them which is an appropriate analogue of the functional equation exp(x) · exp(y) = exp(x+y) for the classical exponential. Besides having a wider scope, our treatment provides a more transparent explanation of some aspects of the original toral switching, which can be recovered as a special case

Widening use of dexamethasone implant for the treatment of macular edema

Sustained-release intravitreal 0.7 mg dexamethasone (DEX) implant is approved in Europe for the treatment of macular edema related to diabetic retinopathy, branch retinal vein occlusion, central retinal vein occlusion, and non-infectious uveitis. The implant is formulated in a biodegradable copolymer to release the active ingredient within the vitreous chamber for up to 6 months after an intravitreal injection, allowing a prolonged interval of efficacy between injections with a good safety profile. Various other ocular pathologies with inflammatory etio­pathogeneses associated with macular edema have been treated by DEX implant, including neovascular age-related macular degeneration, Irvine–Gass syndrome, vasoproliferative retinal tumors, retinal telangiectasia, Coats’ disease, radiation maculopathy, retinitis pigmentosa, and macular edema secondary to scleral buckling and pars plana vitrectomy. We undertook a review to provide a comprehensive collection of all of the diseases that benefit from the use of the sustained-release DEX implant, alone or in combination with concomitant therapies. A MEDLINE search revealed lack of randomized controlled trials related to these indications. Therefore we included and analyzed all available studies (retrospective and prospective, com­parative and non-comparative, randomized and nonrandomized, single center and multicenter, and case report). There are reports in the literature of the use of DEX implant across a range of macular edema-related pathologies, with their clinical experience supporting the use of DEX implant on a case-by-case basis with the aim of improving patient outcomes in many macular pathologies. As many of the reported macular pathologies are difficult to treat, a new treat­ment option that has a beneficial influence on the clinical course of the disease may be useful in clinical practice

Gradings of non-graded Hamiltonian Lie algebras

A thin Lie algebra is a Lie algebra graded over the positive integers satisfying a certain narrowness condition. We describe several cyclic grading of the modular Hamiltonian Lie algebras H(2\colon\n;\omega_2) (of dimension one less than a power of $p$) from which we construct infinite-dimensional thin Lie algebras. In the process we provide an explicit identification of H(2\colon\n;\omega_2) with a Block algebra. We also compute its second cohomology group and its derivation algebra (in arbitrary prime characteristic).Comment: 36 pages, to be published in J. Austral. Math. Soc. Ser.

Numerical bifurcation study of superconducting patterns on a square

This paper considers the extreme type-II Ginzburg-Landau equations that model vortex patterns in superconductors. The nonlinear PDEs are solved using Newton's method, and properties of the Jacobian operator are highlighted. Specifically, it is illustrated how the operator can be regularized using an appropriate phase condition. For a two-dimensional square sample, the numerical results are based on a finite-difference discretization with link variables that preserves the gauge invariance. For two exemplary sample sizes, a thorough bifurcation analysis is performed using the strength of the applied magnetic field as a bifurcation parameter and focusing on the symmetries of this system. The analysis gives new insight in the transitions between stable and unstable states, as well as the connections between stable solution branches.Comment: 31 page

Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs) : Emerging therapeutics applications

ncRNAs are emerging as key regulators of physiological and pathological processes and therefore have been identified as pharmacological targets and as markers for some diseases. Oligonucleotide analogues represent so far the most widely employed tool for the modulation of the expression of ncRNAs. In this perspective we briefly describe most of the known classes of ncRNAs and then we discuss the design and the applications of oligonucleotide analogues for their targeting. The effects of modifications of the chemical structure of the oligonucleotides on properties such as the binding affinity toward targets and off targets, and the stability to degradation and their biological effects (when known) are discussed. Examples of molecules currently used in clinical trials are also reported

The antimicrobial peptide Temporin L impairs E. coli cell division by interacting with FtsZ and the divisome complex

Background: The comprehension of the mechanism of action of antimicrobial peptides is fundamental for the design of new antibiotics. Studies performed looking at the interaction of peptides with bacterial cells offer a faithful picture of what really happens in nature. Methods: In this work we focused on the interaction of the peptide Temporin L with E. coli cells, using a variety of biochemical and biophysical techniques that include: functional proteomics, docking, optical microscopy, TEM, DLS, SANS, fluorescence. Results: We identified bacterial proteins specifically interacting with the peptides that belong to the divisome machinery; our data suggest that the GTPase FtsZ is the specific peptide target. Docking experiments supported the FtsZ-TL interaction; binding and enzymatic assays using recombinant FtsZ confirmed this hypothesis and revealed a competitive inhibition mechanism. Optical microscopy and TEM measurements demonstrated that, upon incubation with the peptide, bacterial cells are unable to divide forming long necklace-like cell filaments. Dynamic light scattering studies and Small Angle Neutron Scattering experiments performed on treated and untreated bacterial cells, indicated a change at the nanoscale level of the bacterial membrane. Conclusions: The peptide temporin L acts by a non-membrane-lytic mechanism of action, inhibiting the divisome machinery. General significance: Identification of targets of antimicrobial peptides is pivotal to the tailored design of new antimicrobials

Incidence and prevalence analysis of non-small-cell and small-cell lung cancer using administrative data

Treatment of lung cancer depends on the stage of the tumor and the histological type. In recent years, the histological confirmation of lung non-small-cell lung cancer has become crucial since the availability of selective target therapeutic approaches. The aim of the study was to develop a validated procedure to estimate the incidence and prevalence of non-small-cell and small-cell lung cancer from healthcare administrative data. A latent class model for categorical variables was applied. The following observed variables were included in the analysis: ICD-9-CM codes in the Hospital Discharge Registry, ATC codes of medications dispensed present in the Drugs Prescriptions Registry, and the procedure codes in the Outpatient Registry. The proportion of non-small-cell lung cancer diagnoses was estimated to be 85% of the total number of lung cancer on the cohort of incident cases and 89% on the cohort of prevalent cases. External validation on a cohort of 107 patients with a lung cancer diagnosis and histological confirmation showed a sensitivity of 95.6% (95%CI: 89–98.8%) and specificity of 94.1% (95%CI: 71.3–99.9%). The procedure is an easy-to-use tool to design subpopulation-based studies on lung cancer and to better plan resource allocation, which is important since the introduction of new targeted therapies in non-small-cell lung carcinoma