Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo proximity ligation reveals endogenous candidate interactors of Neurexin’s intracellular domain

Neurexins are highly-spliced transmembrane cell adhesion molecules that bind an array of partners via their extracellular domains. However, much less is known about the signaling pathways downstream of neurexin’s largely-invariant intracellular domain. C. elegans contains a single neurexin gene that we have previously shown is required for presynaptic assembly and stabilization. To gain insight into the signaling pathways mediating neurexin’s presynaptic functions, we employed a proximity ligation method, endogenously tagging neurexin’s intracellular domain with the promiscuous biotin ligase TurboID, allowing us to isolate adjacent biotinylated proteins by streptavidin pull-down and mass spectrometry. We compared our experimental strain to a control strain in which neurexin, endogenously tagged with TurboID, was dispersed from presynaptic active zones by the deletion of its C-terminal PDZ-binding motif. Using this approach we identified both known and novel intracellular interactors of neurexin, including active zone scaffolds, actin-binding proteins (including almost every member of the Arp2/3 complex), signaling molecules, and mediators of RNA trafficking, protein synthesis and degradation, among others. Characterization of mutants for candidate neurexin interactors revealed that they recapitulate aspects of the nrx-1 mutant phenotype, suggesting they may be involved in neurexin signaling. Finally, to investigate a possible role for neurexin in local actin assembly, we endogenously tagged its intracellular domain with actin depolymerizing and sequestering peptides (DeActs), and found that this led to defects in active zone assembly.
Cyclitol secondary metabolism is a central feature of Burkholderia leaf symbionts

The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled seventeen new endophyte genomes representing endophytes from thirteen plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.
Single cell transcriptomics delineates the immune-cell landscape in equine lower airways and reveals upregulation of the FKBP5 gene in horses with asthma

Background Equine asthma (EA) is a heterogenous, complex disease with a significant negative impact on horse welfare and performance. EA and human asthma have fundamental similarities, making EA a useful large animal disease model. Bronchoalveolar lavage (BAL) fluid provides a snapshot sample of the immune cells occupying the alveolar space and is one of the most relevant sample types for studies of chronic inflammation in the lung. In this study, we sequenced single equine BAL-cells in order to study the immune cell landscape of the respiratory tract of horses diagnosed with mild-to-moderate EA and healthy controls. Results ScRNA-seq analysis of ~63,000 cells from eleven horses diagnosed with mild-moderate asthma (mEA) and eight healthy controls were performed using the Drop-Seq technology. We identified five major immune cell populations in equine BAL; alveolar macrophages (AM), T cells, neutrophils, mast cells and dendritic cells, as well as subtypes thereof. The cellular subtypes demonstrated herein have previously not been characterized in horses. Differential gene expression analysis revealed upregulation of genes in mEA horses, including FKBP5 and CCL24, which have previously been associated with asthma in other species. The most significantly upregulated gene across the cell types in EA was FKBP5, a chaperone protein involved in regulating the assembly, activity, and sensitivity of the glucocorticoid receptor Conclusion Herein we demonstrate the first comprehensive scRNA-seq map of the immune-cell populations in BAL from horses with asthma and healthy individuals. The glucocorticoid receptor associated protein FKBP5 was identified as a potential biomarker for EA.
Single-cell resolution genetic association analysis of heterogeneous bacterial communities by utilizing droplet digital PCR

Microbial communities often respond to various challenges, such as the presence of antibiotics, as a whole. Dissecting these community-level effects into separate acting entities requires the identification of organisms that carry functional genes for the observed feature. However, unculturable microbes abound in various environments, hence making the identification challenging. Here we present a cultivation-free technique that can be utilized to link functional genes with carrying bacterial species at single-cell resolution. The developed protocol is relatively simple to use, utilizes commercially available droplet microfluidics devices, does not require toxic reagents (as compared to some previous methods), eliminates invalid signals emerging from extracellular DNA, and allows simultaneous analysis of community diversity via 16S rRNA gene sequencing. The method can be customized for any given genetic trait to accurately identify its hosting subpopulation from a heterogeneous and potentially uncultivable bacterial community.
Kazrin is an endosomal adaptor for dynein/dynactin

Kazrin is a protein widely expressed in vertebrates whose depletion causes a myriad of developmental defects, in part derived from altered cell adhesion, impaired cell migration and failure to undergo Epidermal to Mesenchymal Transition (EMT). However, the primary molecular role of kazrin, which might contribute to all these functions, has not been elucidated yet. We previously identified one of its isoforms, kazrin C, as a protein that potently inhibits clathrin-mediated endocytosis when overexpressed. We now generated kazrin knock out Mouse Embryonic Fibroblasts (MEFs) to investigate its endocytic function. We found that kazrin depletion delays perinuclear enrichment of internalized material, indicating a role in endocytic traffic from Early (EE) to Recycling Endosomes (REs). Consistently, we found that the C-terminal domain of kazrin C, predicted to be an Intrinsically Disordered Region (IDR), directly interacts with several components of the EEs, and that kazrin depletion impairs centripetal motility of EEs. Further, we noticed that the N-terminus of kazrin C shares homology with dynein/dynactin adaptors and that it directly interacts with the dynactin complex and the dynein Light Intermediate Chain 1 (LIC1). Altogether, the data indicate that one of the primary kazrin functions is to facilitate endocytic recycling via the perinuclear endocytic compartment, by promoting microtubule and dynein/dynactin-dependent transport of EEs or EE-derived transport intermediates to the RE.
α2-Adrenergic modulation of Ih in adult-born granule cells in the olfactory bulb

In the olfactory bulb (OB), a large population of axon-less inhibitory interneurons, the granule cells (GCs), coordinate network activity and tune the output of principal neurons, the mitral and tufted cells (MCs), through dendrodendritic interactions. Furthermore, GCs undergo neurogenesis throughout life, providing a source of plasticity to the neural network of the OB. The function and integration of GCs in the OB is regulated by several afferent neuromodulatory signals, including noradrenaline (NA), a state-dependent neuromodulator that plays a crucial role in the regulation of cortical function and task-specific decision processes. However, the mechanisms by which NA regulates GC function are not fully understood. Here, we show that NA modulates hyperpolarization-activated currents (Ih) via the activation of α2-adrenergic receptors in adult-born GCs (abGCs), thus directly acting on channels that play essential roles in regulating neuronal excitability and network oscillations in the brain. This modulation affects the dendrodendritic output of GCs leading to an enhancement of lateral inhibition onto the MCs. Furthermore, we show that NA modulates subthreshold resonance in GCs, which could affect the temporal integration of abGCs. Together, these results provide a novel mechanism by which a state-dependent neuromodulator acting on Ih can regulate GC function in the bulb.
Stability boundaries for massive stars in the sHR diagram

Abstract Stability boundaries of radial pulsations in massive stars are compared with positions of variable and non-variable blue-supergiants in the spectroscopic HR (sHR) diagram (Langer & Kudritzki 2014), whose vertical axis is 4 log Teff - log g(= log L/M). Observational data indicate that variables tend to have higher L/M than non-variables in agreement with the theoretical prediction. However, many variable blue-supergiants are found to have values of L/M below the theoretical stability boundary; i.e., surface gravities seem to be too high by around 0.2-0.3 dex.
Cardiac muscle-restricted partial loss of Nos1ap expression has limited impact on electro- and echo-cardiographic features

Genome-wide association studies (GWAS) of QT interval variation have identified common noncoding variants at the NOS1AP gene as the most common genetic regulators of trait variation in the general population. Invoking a cis-regulatory mechanistic hypothesis, we have reported identification of a functional enhancer variant underlying the GWAS signal that influenced human cardiac NOS1AP expression. Functional studies based on in vitro overexpression in murine cardiomyocytes and ex vivo knockdown in zebrafish embryonic hearts, by us and others, have demonstrated that NOS1AP expression levels can alter cellular electrophysiology. Here, to explore the role of NOS1AP in cardiac electrophysiology at an organismal level, we generated and characterized constitutive and heart muscle-restricted Nos1ap knockout mice to assess whether NOS1AP disruption alters the QT interval in vivo. Constitutive loss of Nos1ap led to genetic background-dependent variable lethality at or right before birth. Heart muscle-restricted Nos1ap knockouts generated using cardiac specific alpha-myosin heavy chain promoter-driven tamoxifen-inducible Cre resulted in tissue-level Nos1ap expression reduced by half. This partial loss of expression had no detectable effect on the QT interval, but led to a small yet significant reduction in the QRS interval. Given that challenges associated with defining the end of T wave on murine electrocardiogram can limit identification of subtle effects on QT interval, and that common noncoding NOS1AP variants are also associated with QRS interval, our findings support the role of NOS1AP in regulation of the cardiac electrical cycle.
Historical Demography and Climate Driven Range Shifts in the Blue-spotted Salamander Under the Climate Change Scenarios

This study integrates phylogeography with distributional analysis to understand the demographic history and range dynamics of a limited dispersal capacity amphibian species, Blue-spotted Salamander (Ambystoma laterale), under several climate change scenarios. For this we used an ecological niche modeling approach, together with Bayesian based demographic analysis, to develop inferences regarding this species’ demographic history and range dynamics. The current model output was mostly congruent with the present distribution of the Blue-spotted Salamander. However, under both the Last Interglacial and the Last Glacial Maximum bioclimatic conditions, the model predicted a substantially narrower distribution than the present. These predictions showed almost no suitable area in the current distribution range of the species during almost the last 22.000 y before present (ybp). The predictions indicated that the distribution of this species shifted from eastern coast of northern North America to the southern part of the current distribution range of the species. The Bayesian Skyline Plot analysis, which provided good resolution of the effective population size changes over the Blue-spotted Salamander history, was mostly congruent with ecological niche modeling predictions for this species. This study provides the first investigation of the Blue-spotted Salamander’s late-Quaternary history based on ecological niche modeling and Bayesian-based demographic analysis. In terms of the main result of this study, we found that the species’ present genetic structure has been substantially affected by past climate changes, and this species has reached current distribution range almost from nothing since the Last Glacial Maximum.
Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry

Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a very high sample-throughput. However, FI-MS is prone to in-source modifications of analytes because samples are directly injected into the electrospray ionization source of a mass spectrometer without prior chromatographic separation. Here, we spiked authentic standards of 160 primary metabolites individually into an Escherichia coli metabolite extract and measured the thus derived 160 spike-in samples by FI-MS. Our results demonstrate that FI-MS can capture a wide range of chemically divers analytes within 30 seconds measurement time. However, the data also revealed extensive in-source modifications. Across all 160 spike-in samples, we identified significant increases of 11,013 ion peaks in positive and negative mode combined. To explain these unknown m/z features, we connected them to the m/z feature of the (de-)protonated metabolite using information about mass differences and MS2 spectra. This resulted in networks that explained on average 49 % of all significant features. The networks showed that a single metabolite undergoes compound specific and often sequential in-source modifications like adductions, chemical reactions, and fragmentations. Our results show that FI-MS generates complex MS1 spectra, which leads to an overestimation of significant features, but neutral losses and MS2 spectra explain many of these features. Highlights FI-MS enables measurements of chemically divers metabolites. Extensive in-source modifications during electrospray ionization are detected by FI-MS. A network approach explains 49 % of all recorded in-source modifications.
ROCKETS – a novel one-for-all toolbox for light sheet microscopy in drug discovery

Advancing novel immunotherapy strategies requires refined tools in preclinical research to thoroughly assess drug targets, biodistribution, safety, and efficacy. Light sheet fluorescence microscopy (LSFM) offers unprecedented fast volumetric ex vivo imaging of large tissue samples in high resolution. Yet, to date laborious and unstandardized tissue processing procedures have limited throughput and broader applications in immunological research. Therefore, we have developed a simple and harmonized protocol for processing, clearing and imaging of all mouse organs and even entire mouse bodies. Applying this Rapid Optical Clearing Kit for Enhanced Tissue Scanning (ROCKETS) in combination with LSFM allowed us to comprehensively study the in vivo biodistribution of an antibody targeting Epithelial Cell Adhesion Molecule (EpCAM) in 3D. Quantitative high-resolution scans of whole organs did not only reveal known EpCAM expression patterns but, importantly, uncovered several new EpCAM-binding sites. We identified choroid plexi in the brain and duodenal papillae as unexpected locations of high EpCAM-expression. These tissue locations may be considered as particularly sensitive sites due their importance for liquor production or as critical junctions draining bile and digestive pancreatic enzymes into the small bowel, respectively. These newly gained insights appear highly relevant for clinical translation of EpCAM-addressing immunotherapies. Thus, ROCKETS in combination with LSFM may help to set new standards for preclinical evaluation of immunotherapeutic strategies. Conclusively, we propose ROCKETS as an ideal platform for a broader application of LSFM in immunological research optimally suited for quantitative co-localization studies of immunotherapeutic drugs and defined cell populations in the microanatomical context of organs or even whole mice.
NEW OPTICAL/ULTRAVIOLET COUNTERPARTS AND THE SPECTRAL ENERGY DISTRIBUTIONS OF NEARBY, THERMALLY EMITTING, ISOLATED NEUTRON STARS

We present Hubble Space Telescope optical and ultraviolet photometry for five nearby, thermally emitting neutron stars. With these measurements, all seven such objects have confirmed optical and ultraviolet counterparts. Combining our data with archival space-based photometry, we present spectral energy distributions for all sources and measure the “optical excess”: the factor by which the measured photometry exceeds that extrapolated from X-ray spectra. We find that the majority have optical and ultraviolet fluxes that are inconsistent with that expected from thermal (Rayleigh–Jeans) emission, exhibiting more flux at longer wavelengths. We also find that most objects have optical excesses between 5 and 12, but that one object (RX J2143.0+0654) exceeds the X-ray extrapolation by a factor of more than 50 at 5000 Å, and that this is robust to uncertainties in the X-ray spectra and absorption. We consider explanations for this ranging from atmospheric effects, magnetospheric emission, and resonant scattering, but find that none is satisfactory.
Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter

Fluoride is a natural antibiotic abundantly present in the environment and, in micromolar concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is the case with many antibiotics, bacteria have evolved resistance methods, including through the use of recently discovered membrane proteins. One such protein is the CLCF F-/H+ antiporter protein, a member of the CLC superfamily of anion-transport proteins, most notably known for their ability to transport chloride ions. While it possesses many similarities to the other CLC proteins, it also differs in several key ways, and though previous studies have examined this F- transporter, many questions are still left unanswered. To reveal details of the transport mechanism used by CLCF, we have employed molecular dynamics simulations and umbrella sampling calculations. Our results have led to several discoveries, including the mechanism of proton import and how it is able to aid in the fluoride export. Additionally, we have determined the role of the previously identified residues Glu118, Glu318, Met79, and Tyr396. This work is among the first computational studies of the CLCF F-/H+ antiporter and is the first to propose a mechanism which couples both the proton and anion transport.
Virtual histology of Alzheimer’s Disease: why are amyloid- β plaques visible with X-ray phase-contrast imaging?

Amyloid- β (A β ) plaques from Alzheimer’s Disease (AD) can be visualized ex vivo in label-free brain samples using synchrotron X-ray phase-contrast tomography (XPCT). However, for XPCT to be useful as a screening method for amyloid pathology, it is mandatory to understand which factors drive the detection of A β plaques. The current study was designed to test the hypothesis that the A β probed the fibrillar and elemental compositions of A β plaques in brain samples from different types of AD patients and different AD animal models to establish a relationship between XPCT contrast and A β plaque characteristics. XPCT, micro-Fourier-Transform Infrared (µFTIR) spectroscopy and micro-X-Ray Fluorescence (µXRF) spectroscopy were conducted under synchrotron radiation on human samples (genetic and sporadic cases) and on four transgenic rodent strains (mouse: APPPS1, ArcA β , J20; rat: TgF344). A β plaques from the genetic AD patient were visible using XPCT, and had higher β –sheet content and higher metal levels than those from the sporadic AD patient, which remained undetected by XPCT. A β plaques in J20 mice and TgF344 rats appeared hyperintense on XPCT images, while they were hypointense in the case of APPPS1 and ArcA β mice. In all four transgenic strains, β -sheet content was similar, while metal levels were highly variable: J20 mice (zinc and iron), and TgF344 (copper) showed greater metal accumulation than APPPS1 and ArcA β mice. In humans, the greater and more diffuse metal accumulation led to a positive contrast in the genetic case of AD. Hence, contrast formation of A β plaques in XPCT images depended mostly on biometal entrapment.
Effects of domain walls in quantum anomalous Hall insulator/superconductor heterostructures

In a recent experiment, half-quantized longitudinal conductance plateaus (HQCPs) of height $\frac{e^2}{2h}$ have been observed in quantum anomalous Hall (QAH) insulator/superconductor heterostructure transport measurements. It was predicted that these HQCPs are signatures of chiral Majorana edge states. The HQCPs are supposed to appear in the regimes where the Hall conductance $\sigma_{xy}$ is quantized. However, experimentally, a pair of the HQCPs appear when the Hall conductance $\sigma_{xy}$ is only 80% of the quantized value when dissipative channels appear in the bulk. The dissipative channels in the bulk are expected to induce Andreev reflections and ruin the HQCPs. In this work, we explain how domain walls can cause $\sigma_{xy}$ to deviate from its quantized value and at the same time maintain the quantization of HQCPs. Our work supports the claim that the experimentally observed HQCPs are indeed caused by chiral Majorana modes in the QAH insulator/superconductor heterostructure.
Comments on the boundary scattering phase

We present a simple solution to the crossing equation for an open string worldsheet reflection matrix, with boundaries preserving a SU(1|2)2 residual symmetry, which constrains the boundary dressing factor. In addition, we also propose an analogous crossing equation for the dressing factor where extra boundary degrees of freedom preserve a SU(2|2)2 residual symmetry.
Lifetimes of ultralong-range Rydberg molecules in vibrational ground and excited states

Since their first experimental observation, ultralong-range Rydberg molecules consisting of a highly excited Rydberg atom and a ground state atom [1, 2] have attracted the interest in the field of ultracold chemistry [3, 4]. Especially the intriguing properties such as size, polarizability and type of binding they inherit from the Rydberg atom are of interest. An open question in the field is the reduced lifetime of the molecules compared to the corresponding atomic Rydberg states [2]. In this paper we present an experimental study on the lifetimes of the 3Σ(5s − 35s) molecule in its vibrational ground state and in an excited state. We show that the lifetimes depend on the density of ground state atoms and that this can be described in the frame of a classical scattering between the molecules and ground state atoms. We also find that the excited molecular state has an even more reduced lifetime compared to the ground state which can be attributed to an inward penetration of the bound atomic pair due to imperfect quantum reflection that takes place in the special shape of the molecular potential [5].