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

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

Spatio-temporal canards in neural field equations

Canards are special solutions to ordinary differential equations that follow invariant repelling slow manifolds for long time intervals. In realistic biophysical single-cell models, canards are responsible for several complex neural rhythms observed experimentally, but their existence and role in spatially extended systems is largely unexplored. We identify and describe a type of coherent structure in which a spatial pattern displays temporal canard behavior. Using interfacial dynamics and geometric singular perturbation theory, we classify spatiotemporal canards and give conditions for the existence of folded-saddle and folded-node canards. We find that spatiotemporal canards are robust to changes in the synaptic connectivity and firing rate. The theory correctly predicts the existence of spatiotemporal canards with octahedral symmetry in a neural field model posed on the unit sphere

Urgent vitrectomy with vancomycin infusion, silicone oil endotamponade, and general antibiotic treatment in multiple cases of endophthalmitis from a single day of intravitreal injections—case series

The aim of this study was to report on the anatomical and functional results of surgical management of seven cases of endophthalmitis related to a single day of intravitreal aflibercept injections. Patients with signs of endophthalmitis who underwent aflibercept injections (seven eyes) performed on the same day were retrospectively evaluated. The data of visual acuity and optical coherence tomography (OCT) within nine months of the follow-up and the treatment and results of microbiological cultures are reported. Four of the total seven cases had a positive bacterial culture outcome (Streptococcus mitis). All patients underwent vitrectomy combined with phacoemulsification when the eyes were not pseudophakic, vancomycin infusion, and silicone oil tamponade within 24 h; additionally, systemic antibiotics were administered intravenously. The final best-corrected visual acuity (BCVA) after the treatment was finger counting or light perception in all cases, and all eyes were saved with disruption of the inner retinal layers and stabilization of the retina in regard to changes related to the wet age-related macular degeneration (AMD). Although the retinal anatomy was mostly preserved, most of the patients affected by Streptococcus mitis-induced endophthalmitis did not regain baseline vision after the therapy

Kinetic and static perimetry after 16 years and additional OCT-A analysis in eyes with longlasting optic disc drusen

The aim of the study is to evaluate the progression of visual field (VF) defects over 16 years of observation and to assess abnormalities in vessels and retinal nerve fibre layer (RNFL) thickness in patients with optic disc drusen (ODD). Both static automated perimetry (SAP) and semi-automated kinetic perimetry (SKP) were performed in 16 eyes of 8 patients (mean age 54 years) with ODD among 26 eyes of 13 patients examined 16 years before. The area of I2e, I4e, III4e, and V4e isopters was measured in deg2. The MD and PSD parameters were estimated using SAP. Optical coherence tomography angiography (OCT-A) was additionally performed in 16 ODD eyes and 16 eyes of 8 healthy subjects to estimate the RNFL thickness and vessel density of the optic nerve disc and the macula. The differences in all isopter areas of SKP and SAP parameters after 16 years were not significant. The analysis of OCT-A showed a significant reduction of the vessel density and RNFL of the peripapillary area in each segment in patients with ODD, compared with the control group. The highest reduction of RNFL was observed in the superior segment of the optic disc area (92.56μm vs 126.63μm) also the macular thickness was decreased in ODD patients, compared with the control group. In the macula, there was a significant vascular defect in the whole superficial layer and in the parafoveal deep layer. A strong significant correlation of the parafoveal deep plexus with MD and PSD parameters was detected. In conclusion, VF loss due to ODD after 16 years of the follow-up was not significant both in SKP and SAP. ODD caused a reduced vessel density and RNFL, as well as macular thickness in OCT-A. SAP parameters were influenced by parafoveal deep plexus

Characterization of the pathophysiological role of CD47 in uveal melanoma

Uveal melanoma (UM) represents the most frequent primary intraocular tumor, however, limited therapeutic options are still available. We have previously shown that cluster of differentiation 47 (CD47) is significantly upregulated in UM cells following inflammatory stimuli and that it represents a predictor of disease progression. Here, we aimed to better characterize the pathophysiological role of CD47 in UM. We show that CD47 is not modulated at different cancer stages, although patients with the lowest expression of CD47 show significant better progression-free survival, after correcting for the presence of BAP1, GNAQ, and GNA11 mutations. By stratifying patients based on the expression of CD47 in the tumor, we observed that patients with high levels of CD47 have a significant increase in immune score as compared to patients with low levels of CD47. In particular, deconvolution analysis of infiltrating immune cell populations revealed that a significantly higher number of CD4+ and CD8+ T cells can be found in patients with high CD47 levels, with the most enriched populations being the Th2, Treg, and CD8+ Tcm cells. We also show that a large number of transcripts are significantly modulated between the groups of patients with high and low levels of CD47, with a significant enrichment of interferon IFN-alpha regulated genes. The results from this study may propel the development of anti-CD47 therapies for UM patients

Synchrony-induced modes of oscillation of a neural field model

We investigate the modes of oscillation of heterogeneous ring-networks of quadratic integrate-and-fire (QIF) neurons with non-local, space-dependent coupling. Perturbations of the equilibrium state with a particular wave number produce transient standing waves with a specific temporal frequency, analogous to those in a tense string. In the neuronal network, the equilibrium corresponds to a spatially homogeneous, asynchronous state. Perturbations of this state excite the network’s oscillatory modes, which reflect the interplay of episodes of synchronous spiking with the excitatory-inhibitory spatial interactions. In the thermodynamic limit, an exact low-dimensional neural field model (QIF-NFM) describing the macroscopic dynamics of the network is derived. This allows us to obtain formulas for the Turing eigenvalues of the spatially-homogeneous state, and hence to obtain its stability boundary. We find that the frequency of each Turing mode depends on the corresponding Fourier coefficient of the synaptic pattern of connectivity. The decay rate instead, is identical for all oscillation modes as a consequence of the heterogeneity-induced desynchronization of the neurons. Finally, we numerically compute the spectrum of spatially-inhomogeneous solutions branching from the Turing bifurcation, showing that similar oscillatory modes operate in neural bump states, and are maintained away from onset

Independent data for transparent monitoring of greenhouse gas emissions from the land use sector – What do stakeholders think and need?

The agriculture, forestry and other land use (AFOLU) sectors contribute substantially to the net global anthropogenic greenhouse gas (GHG) emissions. To reduce these emissions under the Paris Agreement, effective mitigation actions are needed that require engagement of multiple stakeholders. Emission reduction also requires that accurate, consistent and comparable datasets are available for transparent reference and progress monitoring. Availability of free and open datasets and portals (referred to as independent data) increases, offering opportunities for improving and reconciling estimates of GHG emissions and mitigation options. Through an online survey, we investigated stakeholders’ data needs for estimating forest area and change, forest biomass and emission factors, and AFOLU GHG emissions. The survey was completed by 359 respondents from governmental, intergovernmental and non-governmental organizations, research institutes and universities, and public and private companies. These can be grouped into data users and data providers. Our results show that current open and freely available datasets and portals are only able to fulfil stakeholder needs to a certain degree. Users require a) detailed documentation regarding the scope and usability of the data, b) comparability between alternative data sources, c) uncertainty estimates for evaluating mitigation options, d) more region-specific and detailed data with higher accuracy for sub-national application, e) regular updates and continuity for establishing consistent time series. These requirements are found to be key elements for increasing overall transparency of data sources, definitions, methodologies and assumptions, which is required under the Paris Agreement. Raising awareness and improving data availability through centralized platforms are important for increasing engagement of data users. In countries with low capacities, independent data can support countries’ mitigation planning and implementation, and related GHG reporting. However, there is a strong need for further guidance and capacity development (i.e. ‘readiness support’) on how to make proper use of independent datasets. Continued investments will be needed to sustain programmes and keep improving datasets to serve the objectives of the many stakeholders involved in climate change mitigation and should focus on increased accessibility and transparency of data to encourage stakeholder involvement