Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea

Climate, which sets broad limits for migrating species, is considered a key filter to species migration between contrasting marine environments. The Southeast Mediterranean Sea (SEMS) is one of the regions where ocean temperatures are rising the fastest under recent climate change. Also, it is the most vulnerable marine region to species introductions. Here, we explore the factors which enabled the colonization of the endemic Red Sea octocoral Melithaea erythraea (Ehrenberg, 1834) along the SEMS coast, using sclerite oxygen and carbon stable isotope composition (delta O-18(SC) and delta C-13(SC)), morphology, and crystallography. The unique conditions presented by the SEMS include a greater temperature range (similar to 15 degrees C) and ultra-oligotrophy, and these are reflected by the lower delta C-13(SC) values. This is indicative of a larger metabolic carbon intake during calcification, as well as an increase in crystal size, a decrease of octocoral wart density and thickness of the migrating octocoral sclerites compared to the Red Sea samples. This suggests increased stress conditions, affecting sclerite deposition of the SEMS migrating octocoral. The delta(OSC)-O-18 range of the migrating M. erythraea indicates a preference for warm water sclerite deposition, similar to the native depositional temperature range of 21-28 degrees C. These findings are associated with the observed increase of minimum temperatures in winter for this region, at a rate of 0.35 +/- 0.27 degrees C decade(-1) over the last 30 years, and thus the region is becoming more hospitable to the IndoPacific M. erythraea. This study shows a clear case study of "tropicalization" of the Mediterranean Sea due to recent warming

Modulation of nitrogen vacancy charge state and fluorescence in nanodiamonds using electrochemical potential

The negatively charged nitrogen vacancy (NV⁻) center in diamond has attracted strong interest for a wide range of sensing and quantum information processing applications. To this end, recent work has focused on controlling the NV charge state, whose stability strongly depends on its electrostatic environment. Here, we demonstrate that the charge state and fluorescence dynamics of single NV centers in nanodiamonds with different surface terminations can be controlled by an externally applied potential difference in an electrochemical cell. The voltage dependence of the NV charge state can be used to stabilize the NV⁻ state for spin-based sensing protocols and provides a method of charge state-dependent fluorescence sensing of electrochemical potentials. We detect clear NV fluorescence modulation for voltage changes down to 100 mV, with a single NV and down to 20 mV with multiple NV centers in a wide-field imaging mode. These results suggest that NV centers in nanodiamonds could enable parallel optical detection of biologically relevant electrochemical potentials.United States. Army Research Office (W911NF-12-1-0594)United States. National Institutes of Health (1R01NS087950)United States. Defense Advanced Research Projects Agency (D14PC00121)United States. Defense Advanced Research Projects Agency (HR0011-14-C-0018)United States. National Institutes of Health (1R43MH102942-01)National Science Foundation (U.S.) (1122374

Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls

Celiac disease (CeD) is a common autoimmune disorder caused by an abnormal immune response to dietary gluten proteins. The disease has high heritability. HLA is the major susceptibility factor, and the HLA effect is mediated via presentation of deamidated gluten peptides by disease-associated HLA-DQ variants to CD4+ T cells. In addition to gluten-specific CD4+ T cells the patients have antibodies to transglutaminase 2 (autoantigen) and deamidated gluten peptides. These disease-specific antibodies recognize defined epitopes and they display common usage of specific heavy and light chains across patients. Interactions between T cells and B cells are likely central in the pathogenesis, but how the repertoires of naïve T and B cells relate to the pathogenic effector cells is unexplored. To this end, we applied machine learning classification models to naïve B cell receptor (BCR) repertoires from CeD patients and healthy controls. Strikingly, we obtained a promising classification performance with an F1 score of 85%. Clusters of heavy and light chain sequences were inferred and used as features for the model, and signatures associated with the disease were then characterized. These signatures included amino acid (AA) 3-mers with distinct bio-physiochemical characteristics and enriched V and J genes. We found that CeD-associated clusters can be identified and that common motifs can be characterized from naïve BCR repertoires. The results may indicate a genetic influence by BCR encoding genes in CeD. Analysis of naïve BCRs as presented here may become an important part of assessing the risk of individuals to develop CeD. Our model demonstrates the potential of using BCR repertoires and in particular, naïve BCR repertoires, as disease susceptibility markers

The effect of patient body mass index and sex on the magnification factor during pre-operative templating for total hip arthroplasty

Introduction: Pre-operative templating prior to hip arthroplasty has traditionally used implant-company-provided acetates, which assumed a magnification factor between 115% and 120%. In recent years, pre-operative planning has been performed with digital calibration devices, in order to calculate the magnification factor. However, these devices are not without their limitations and are not readily available at many institutions. As previous reports suggest a wide range of magnification factors, the determination of an optimal magnification factor is currently unclear. We investigated the relationship between obesity and gender on the magnification factor in order to improve the accuracy of pre-operative templating. Patients and methods: Ninety-seven consecutive pre-operative calibrated pelvic radiographs using the KingMark calibration were analyzed using the TraumaCad templating software. The magnification factor calculated by the software was considered the true magnification factor and analysis was made in order to assess the effect of sex and body mass index (BMI) on the magnification factor. A linear regression analysis was utilized to create a predictive model for optimal magnification factor value. Results: Magnification factor was significantly affected by sex (male, 120.0% vs. female 121.2%, p < 0.01) and by categorized BMI (obese 121.8% vs. non-obese 119.9%, p < 0.001). A positive linear association was found between BMI and the magnification factor (r = 0.544). The magnification factor was significantly different between the following sub-groups: obese female, non-obese female, obese male, and non-obese male (p < 0.001). When applying the model formulated by the linear regression analysis, the calculated magnification factor was within 2% of the true magnification factor for the majority of patients (n = 83, 85.6%). Conclusions: BMI and gender have a significant effect on the magnification factor. Future determination of the magnification factor should consider the influence of these variables in order to improve the accuracy of pre-operative templating in THA

Temporally precise single-cell-resolution optogenetics

© 2017 The Author(s). Optogenetic control of individual neurons with high temporal precision within intact mammalian brain circuitry would enable powerful explorations of how neural circuits operate. Two-photon computer-generated holography enables precise sculpting of light and could in principle enable simultaneous illumination of many neurons in a network, with the requisite temporal precision to simulate accurate neural codes. We designed a high-efficacy soma-targeted opsin, finding that fusing the N-terminal 150 residues of kainate receptor subunit 2 (KA2) to the recently discovered high-photocurrent channelrhodopsin CoChR restricted expression of this opsin primarily to the cell body of mammalian cortical neurons. In combination with two-photon holographic stimulation, we found that this somatic CoChR (soCoChR) enabled photostimulation of individual cells in mouse cortical brain slices with single-cell resolution and <1-ms temporal precision. We used soCoChR to perform connectivity mapping on intact cortical circuits

Population imaging of neural activity in awake behaving mice

© 2019, The Author(s), under exclusive licence to Springer Nature Limited. A longstanding goal in neuroscience has been to image membrane voltage across a population of individual neurons in an awake, behaving mammal. Here we describe a genetically encoded fluorescent voltage indicator, SomArchon, which exhibits millisecond response times and is compatible with optogenetic control, and which increases the sensitivity, signal-to-noise ratio, and number of neurons observable several-fold over previously published fully genetically encoded reagents1–8. Under conventional one-photon microscopy, SomArchon enables the routine population analysis of around 13 neurons at once, in multiple brain regions (cortex, hippocampus, and striatum) of head-fixed, awake, behaving mice. Using SomArchon, we detected both positive and negative responses of striatal neurons during movement, as previously reported by electrophysiology but not easily detected using modern calcium imaging techniques9–11, highlighting the power of voltage imaging to reveal bidirectional modulation. We also examined how spikes relate to the subthreshold theta oscillations of individual hippocampal neurons, with SomArchon showing that the spikes of individual neurons are more phase-locked to their own subthreshold theta oscillations than to local field potential theta oscillations. Thus, SomArchon reports both spikes and subthreshold voltage dynamics in awake, behaving mice

Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics

© 2020 The Author(s) In order to analyze how a signal transduction network converts cellular inputs into cellular outputs, ideally one would measure the dynamics of many signals within the network simultaneously. We found that, by fusing a fluorescent reporter to a pair of self-assembling peptides, it could be stably clustered within cells at random points, distant enough to be resolved by a microscope but close enough to spatially sample the relevant biology. Because such clusters, which we call signaling reporter islands (SiRIs), can be modularly designed, they permit a set of fluorescent reporters to be efficiently adapted for simultaneous measurement of multiple nodes of a signal transduction network within single cells. We created SiRIs for indicators of second messengers and kinases and used them, in hippocampal neurons in culture and intact brain slices, to discover relationships between the speed of calcium signaling, and the amplitude of PKA signaling, upon receiving a cAMP-driving stimulus

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

© 2018 The Author(s). We developed a new way to engineer complex proteins toward multidimensional specifications using a simple, yet scalable, directed evolution strategy. By robotically picking mammalian cells that were identified, under a microscope, as expressing proteins that simultaneously exhibit several specific properties, we can screen hundreds of thousands of proteins in a library in just a few hours, evaluating each along multiple performance axes. To demonstrate the power of this approach, we created a genetically encoded fluorescent voltage indicator, simultaneously optimizing its brightness and membrane localization using our microscopy-guided cell-picking strategy. We produced the high-performance opsin-based fluorescent voltage reporter Archon1 and demonstrated its utility by imaging spiking and millivolt-scale subthreshold and synaptic activity in acute mouse brain slices and in larval zebrafish in vivo. We also measured postsynaptic responses downstream of optogenetically controlled neurons in C. elegans