Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study.

BACKGROUND: A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this exploratory investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing to identify potential blood-based biomarkers. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina's Infinium MethylationEPIC BeadChip arrays (n = 862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p ≤ × 10-8 and fold change ± 2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM. RESULTS: Top-ranked genes within which several dmCpGs were located and supported by functional data with methylation look-ups in other cohorts include: AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9 and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-ß signalling and Th17 cell differentiation. CONCLUSIONS: Epigenetic alterations provide a dynamic link between an individual's genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.

Combination anti-coronavirus therapies based on nonlinear mathematical models.

Using nonlinear mathematical models and experimental data from laboratory and clinical studies, we have designed new combination therapies against COVID-19.

Utilizing supervised machine learning to identify microglia and astrocytes in situ: implications for large-scale image analysis and quantification.

BACKGROUND: The evaluation of histological tissue samples plays a crucial role in deciphering preclinical disease and injury mechanisms. High-resolution images can be obtained quickly however data acquisition are often bottlenecked by manual analysis methodologies. NEW METHOD: We describe and validate a pipeline for a novel machine learning-based analytical method, using the Opera High-Content Screening system and Harmony software, allowing for detailed image analysis of cellular markers in histological samples. RESULTS: To validate the machine learning pipeline, analyses of single proteins in mouse brain sections were utilized. To demonstrate adaptability of the pipeline for multiple cell types and epitopes, the percent brain coverage of microglial cells, identified by ionized calcium binding adaptors molecule 1 (Iba1), and of astrocytes, by glial fibrillary acidic protein (GFAP) demonstrated no significant differences between automated and manual analyses protocols. Further to examine the robustness of this protocol for multiple proteins simultaneously labeling of rat brain sections were utilized; co-localization of astrocytic endfeet on blood vessels, using aquaporin-4 and tomato lectin respectively, were efficiently identified and quantified by the novel pipeline and were not significantly different between the two analyses protocols. Comparison with Existing Methods: The automated platform maintained the sensitivity and accuracy of manual analysis, while accomplishing the analyses in 1/200th of the time. CONCLUSIONS: We demonstrate the benefits and potential of adapting an automated high-throughput machine-learning analytical approach for the analysis ofin situ tissue samples, show effectiveness across different animal models, while reducing analysis time and increasing productivity.

The Neuroanatomy of Autism Spectrum Disorder Symptomatology in 22q11.2 Deletion Syndrome.

22q11.2 Deletion Syndrome (22q11.2DS) is a genetic condition associated with a high prevalence of neuropsychiatric conditions that include autism spectrum disorder (ASD). While evidence suggests that clinical phenotypes represent distinct neurodevelopmental outcomes, it remains unknown whether this translates to the level of neurobiology. To fractionate the 22q11.2DS phenotype on the level of neuroanatomy, we examined differences in vertex-wise estimates of cortical volume, surface area, and cortical thickness between 1) individuals with 22q11.2DS (n = 62) and neurotypical controls (n = 57) and 2) 22q11.2DS individuals with ASD symptomatology (n = 30) and those without (n = 25). We firstly observed significant differences in surface anatomy between 22q11.2DS individuals and controls for all 3 neuroanatomical features, predominantly in parietotemporal regions, cingulate and dorsolateral prefrontal cortices. We also established that 22q11.2DS individuals with ASD symptomatology were neuroanatomically distinct from 22q11.2DS individuals without ASD symptoms, particularly in brain regions that have previously been linked to ASD (e.g., dorsolateral prefrontal cortices and the entorhinal cortex). Our findings indicate that different clinical 22q11.2DS phenotypes, including those with ASD symptomatology, may represent different neurobiological subgroups. The spatially distributed patterns of neuroanatomical differences associated with ASD symptomatology in 22q11.2DS may thus provide useful information for patient stratification and the prediction of clinical outcomes.

Molecular Tensor Analysis of Third-Harmonic Scattering in Liquids.

Third-harmonic scattering is a nonlinear optical process that involves the molecular second-hyperpolarizability, γ. This work presents a rigorous quantum electrodynamical analysis of the scattering process, involving a partially index-symmetric construction of the fourth-rank γ tensor-dispensing with the Kleinman symmetry condition. To account for stochastic molecular rotation in fluids, methods of isotropic averaging must be employed to relate the molecular properties to accessible experimental quantities such as depolarization ratio. A complete eighth-rank tensor rotational average yields results for observable third-harmonic scattering rates, cast as a function of the natural-invariant γ components, and the polarization geometry of the experiment. Decomposing the tensor γ into irreducible weights allows specific predictions to be made for each molecular point group, allowing greater discrimination between the results for different molecular symmetries.

In situ measurements of Saturn's ionosphere show that it is dynamic and interacts with the rings.

The ionized upper layer of Saturn's atmosphere, its ionosphere, provides a closure of currents mediated by the magnetic field to other electrically charged regions (for example, rings) and hosts ion-molecule chemistry. In 2017, the Cassini spacecraft passed inside the planet's rings, allowing in situ measurements of the ionosphere. The Radio and Plasma Wave Science instrument detected a cold, dense, and dynamic ionosphere at Saturn that interacts with the rings. Plasma densities reached up to 1000 cubic centimeters, and electron temperatures were below 1160 kelvin near closest approach. The density varied between orbits by up to two orders of magnitude. Saturn's A- and B-rings cast a shadow on the planet that reduced ionization in the upper atmosphere, causing a north-south asymmetry.

Acceleration of collimated 45 MeV protons by collisionless shocks driven in low-density, large-scale gradient plasmas by a 1020 W/cm2, 1 µm laser.

A new type of proton acceleration stemming from large-scale gradients, low-density targets, irradiated by an intense near-infrared laser is observed. The produced protons are characterized by high-energies (with a broad spectrum), are emitted in a very directional manner, and the process is associated to relaxed laser (no need for high-contrast) and target (no need for ultra-thin or expensive targets) constraints. As such, this process appears quite effective compared to the standard and commonly used Target Normal Sheath Acceleration technique (TNSA), or more exploratory mechanisms like Radiation Pressure Acceleration (RPA). The data are underpinned by 3D numerical simulations which suggest that in these conditions a Low Density Collisionless Shock Acceleration (LDCSA) mechanism is at play, which combines an initial Collisionless Shock Acceleration (CSA) to a boost procured by a TNSA-like sheath field in the downward density ramp of the target, leading to an overall broad spectrum. Experiments performed at a laser intensity of 1020 W/cm2 show that LDCSA can accelerate, from ~1% critical density, mm-scale targets, up to 5 × 109 protons/MeV/sr/J with energies up to 45(±5) MeV in a collimated (~6° half-angle) manner.

miR302 regulates SNAI1 expression to control mesangial cell plasticity.

Cell fate decisions are controlled by the interplay of transcription factors and epigenetic modifiers, which together determine cellular identity. Here we elaborate on the role of miR302 in the regulation of cell plasticity. Overexpression of miR302 effected silencing of the TGFß type II receptor and facilitated plasticity in a manner distinct from pluripotency, characterized by increased expression of Snail. miR302 overexpressing mesangial cells also exhibited enhanced expression of EZH2 coincident with Snail upregulation. esiRNA silencing of each component suggest that Smad3 and EZH2 are part of a complex that regulates plasticity and that miR302 regulates EZH2 and Snail independently. Subsequent manipulation of miR302 overexpressing cells demonstrated the potential of using this approach for reprogramming as evidenced by de novo expression of the tight junction components ZO-1 and E-cadherin and the formation of ZO-1 containing tight junctions. Understanding the processes through which dynamic epigenetic silencing is controlled in adults cells will allow us to address the epigenetic state of acquired disease and whether original states, regenerative in nature, can be restored with therapy.

Do twisted laser beams evoke nuclear hyperpolarization?

The hyperpolarization of nuclear spins promises great advances in chemical analysis and medical diagnosis by substantially increasing the sensitivity of nuclear magnetic resonance (NMR). Current methods to produce a hyperpolarized sample, however, are arduous, time-consuming or costly and require elaborate equipment. Recently, a much simpler approach was introduced that holds the potential, if harnessed appropriately, to revolutionize the production of hyperpolarized spins. It was reported that high levels of hyperpolarization in nuclear spins can be created by irradiation with a laser beam carrying orbital angular momentum (twisted light). Aside from these initial reports however, no further experimental verification has been presented. In addition, this effect has so far evaded a critical theoretical examination. In this contribution, we present the first independent attempt to reproduce the effect. We exposed a sample of immersion oil or a fluorocarbon liquid that was placed within a low-field NMR spectrometer to Laguerre-Gaussian and Bessel laser beams at a wavelength of 514.5nm and various topological charges. We acquired (1)H and (19)F NMR free induction decay data, either during or alternating with the irradiation that was parallel to B0. We observed an irregular increase in NMR signal in experiments where the sample was exposed to beams with higher values of the topological charge. However, at no time did the effect reach statistical significance of 95%. Given the measured sensitivity of our setup, we estimate that a possible effect did not exceed a hyperpolarization (at 5mT) of 0.14-6%, depending on the assumed hyperpolarized volume. It should be noted though, that there were some differences between our setup and the previous implementation of the experiment, which may have inhibited the full incidence of this effect. To approach a theoretical description of this effect, we considered the interaction of an electron with a plane wave, which is known to be able to induce electronic (e.g. in rubidium) and subsequent nuclear hyperpolarization. Compared to the plane wave, the additional transitions caused by a twisted wave are of the order of 10(-3) less. This suggests that the twist of the laser is unlikely to be responsible for the hyperpolarization of nuclear spins, unless a new mechanism of momentum transfer is identified.

Relationship Between Cortical Gyrification, White Matter Connectivity, and Autism Spectrum Disorder.

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition, which is accompanied by differences in gray matter neuroanatomy and white matter connectivity. However, it is unknown whether these differences are linked or reflect independent aetiologies. Using a multimodal neuroimaging approach, we therefore examined 51 male adults with ASD and 48 neurotypical controls to investigate the relationship between gray matter local gyrification (lGI) and white matter diffusivity in associated fiber tracts. First, ASD individuals had a significant increase in gyrification around the left pre- and post-central gyrus. Second, white matter fiber tracts originating and/or terminating in the cluster of increased lGI had a significant increase in axial diffusivity. This increase in diffusivity was predominantly observed in tracts in close proximity to the cortical sheet. Last, we demonstrate that the increase in lGI was significantly correlated with increased diffusivity of short tracts. This relationship was not significantly modulated by a main effect of group (i.e., ASD), which was more closely associated with gray matter gyrification than white matter diffusivity. Our findings suggest that differences in gray matter neuroanatomy and white matter connectivity are closely linked, and may reflect common rather than distinct aetiological pathways.

The SMAC mimetic, LCL-161, reduces survival in aggressive MYC-driven lymphoma while promoting susceptibility to endotoxic shock.

Inhibitor of apoptosis proteins (IAPs) antagonize caspase activation and regulate death receptor signaling cascades. LCL-161 is a small molecule second mitochondrial activator of caspase (SMAC) mimetic, which both disengages IAPs from caspases and induces proteasomal degradation of cIAP-1 and -2, resulting in altered signaling through the NFκB pathway, enhanced TNF production and sensitization to apoptosis mediated by the extrinsic pathway. SMAC mimetics are undergoing clinical evaluation in a range of hematological malignancies. Burkitt-like lymphomas are hallmarked by a low apoptotic threshold, conveying sensitivity to a range of apoptosis-inducing stimuli. While evaluating LCL-161 in the Eµ-Myc model of aggressive Burkitt-like lymphoma, we noted unexpected resistance to apoptosis induction despite 'on-target' IAP degradation and NFκB activation. Moreover, LCL-161 treatment of lymphoma-bearing mice resulted in apparent disease acceleration concurrent to augmented inflammatory cytokine-release in the same animals. Indiscriminate exposure of lymphoma patients to SMAC mimetics may therefore be detrimental due to both unanticipated prolymphoma effects and increased susceptibility to endotoxic shock.

Plasma observations during the Mars atmospheric "plume" event of March-April 2012.

We present initial analysis and conclusions from plasma observations made during the reported "Mars plume event" of March - April 2012. During this period, multiple independent amateur observers detected a localized, high-altitude "plume" over the Martian dawn terminator [Sanchez-Lavega et al., Nature, 2015, doi:10.1038/nature14162], the cause of which remains to be explained. The estimated brightness of the plume exceeds that expected for auroral emissions, and its projected altitude greatly exceeds that at which clouds are expected to form. We report on in-situ measurements of ionospheric plasma density and solar wind parameters throughout this interval made by Mars Express, obtained over the same surface region, but at the opposing terminator. Measurements in the ionosphere at the corresponding location frequently show a disturbed structure, though this is not atypical for such regions with intense crustal magnetic fields. We tentatively conclude that the formation and/or transport of this plume to the altitudes where it was observed could be due in part to the result of a large interplanetary coronal mass ejection (ICME) encountering the Martian system. Interestingly, we note that the only similar plume detection in May 1997 may also have been associated with a large ICME impact at Mars.

Ion and aerosol precursor densities in Titan's ionosphere: A multi-instrument case study.

The importance of the heavy ions and dust grains for the chemistry and aerosol formation in Titan's ionosphere has been well established in the recent years of the Cassini mission. In this study we combine independent in situ plasma (Radio Plasma and Wave Science Langmuir Probe (RPWS/LP)) and particle (Cassini Plasma Science Electron Spectrometer, Cassini Plasma Science Ion Beam Spectrometer, and Ion and Neutral Mass Spectrometer) measurements of Titan's ionosphere for selected flybys (T16, T29, T40, and T56) to produce altitude profiles of mean ion masses including heavy ions and develop a Titan-specific method for detailed analysis of the RPWS/LP measurements (applicable to all flybys) to further constrain ion charge densities and produce the first empirical estimate of the average charge of negative ions and/or dust grains. Our results reveal the presence of an ion-ion (dusty) plasma below ~1100 km altitude, with charge densities exceeding the primary ionization peak densities by a factor ≥2 in the terminator and nightside ionosphere (n e /n i ≤ 0.1). We suggest that ion-ion (dusty) plasma may also be present in the dayside ionosphere below 900 km (n e /n i < 0.5 at 1000 km altitude). The average charge of the dust grains (≥1000 amu) is estimated to be between -2.5 and -1.5 elementary charges, increasing toward lower altitudes.

MAVEN observations of the response of Mars to an interplanetary coronal mass ejection.

Coupling between the lower and upper atmosphere, combined with loss of gas from the upper atmosphere to space, likely contributed to the thin, cold, dry atmosphere of modern Mars. To help understand ongoing ion loss to space, the Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft made comprehensive measurements of the Mars upper atmosphere, ionosphere, and interactions with the Sun and solar wind during an interplanetary coronal mass ejection impact in March 2015. Responses include changes in the bow shock and magnetosheath, formation of widespread diffuse aurora, and enhancement of pick-up ions. Observations and models both show an enhancement in escape rate of ions to space during the event. Ion loss during solar events early in Mars history may have been a major contributor to the long-term evolution of the Mars atmosphere.

Dust observations at orbital altitudes surrounding Mars.

Dust is common close to the martian surface, but no known process can lift appreciable concentrations of particles to altitudes above ~150 kilometers. We present observations of dust at altitudes ranging from 150 to above 1000 kilometers by the Langmuir Probe and Wave instrument on the Mars Atmosphere and Volatile Evolution spacecraft. Based on its distribution, we interpret this dust to be interplanetary in origin. A comparison with laboratory measurements indicates that the dust grain size ranges from 1 to 12 micrometers, assuming a typical grain velocity of ~18 kilometers per second. These direct observations of dust entering the martian atmosphere improve our understanding of the sources, sinks, and transport of interplanetary dust throughout the inner solar system and the associated impacts on Mars's atmosphere.

Early MAVEN Deep Dip campaign reveals thermosphere and ionosphere variability.

The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability.

COMETARY SCIENCE. CHO-bearing organic compounds at the surface of 67P/Churyumov-Gerasimenko revealed by Ptolemy.

The surface and subsurface of comets preserve material from the formation of the solar system. The properties of cometary material thus provide insight into the physical and chemical conditions during their formation. We present mass spectra taken by the Ptolemy instrument 20 minutes after the initial touchdown of the Philae lander on the surface of comet 67P/Churyumov-Gerasimenko. Regular mass distributions indicate the presence of a sequence of compounds with additional -CH2- and -O- groups (mass/charge ratios 14 and 16, respectively). Similarities with the detected coma species of comet Halley suggest the presence of a radiation-induced polymer at the surface. Ptolemy measurements also indicate an apparent absence of aromatic compounds such as benzene, a lack of sulfur-bearing species, and very low concentrations of nitrogenous material.

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015.

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.

Prevalence and penetrance of ZFPM2 mutations and deletions causing congenital diaphragmatic hernia.

Zinc finger protein, FOG2 family member 2 (ZFPM2) (previously named FOG2) gene defects result in the highly morbid congenital diaphragmatic hernia (CDH) in humans and animal models. In a cohort of 275 CDH patient exomes, we estimated the prevalence of damaging ZFPM2 mutations to be almost 5%. Genetic analysis of a multigenerational family identified a heritable intragenic ZFPM2 deletion with an estimated penetrance of 37.5%, which has important implications for genetic counseling. Similarly, a low penetrance ZFPM2 frameshift mutation was observed in a second multiplex family. Isolated CDH was the predominant phenotype observed in our ZFPM2 mutation patients. Findings from the patients described herein indicate that ZFPM2 point mutations or deletions are a recurring cause of CDH.

One- and two-photon absorption in solution: the effects of a passive auxiliary beam.

The efficiencies of one- and two-photon absorption by chromophores in solution may be significantly modified by a sufficiently intense beam of off-resonant light. A molecular analysis based on quantum electrodynamics (QED) fully accounts for this phenomenon of laser-modified absorption. A time-dependent perturbation-theory treatment describes the process in terms of stimulated forward Rayleigh-scattering of the auxiliary beam occurring simultaneously with the absorption interaction(s). Our formulation accommodates media modifications to the basic character of light-matter interactions, taking into account the refractive and dispersive properties of a solution-phase environment. This introduces the bulk refractive index of the solvent directly into the QED framework. The measurable electronic response of molecules freely rotating in solution is defined by an average of all orientations. We explicitly derive fixed-orientation and rotationally averaged calculations for the Fermi-rule rate of laser-modified one- and two-photon absorption. For a given beam polarization geometry, the solution-phase molecular response is expressible as a set of natural invariant scalars. These results reveal details of the dependence on the beam polarisations and on the rotationally averaged molecular response: we illustrate the breadth of variation available via geometric manipulation of beam polarization, and raise new possibilities for quantum weak measurements of laser states.