Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility

The outermost cell layer of plant roots (epidermis) constantly encounters environmental challenges. The epidermal outer plasma membrane domain harbours the PENETRATION3 (PEN3)/ABCG36/PDR8 ATP-binding cassette transporter that confers non-host resistance to several pathogens. Here, we show that the Arabidopsis ENDOPLASMIC RETICULUM-ARRESTED PEN3 (EAP3) BTB/POZ-domain protein specifically mediates PEN3 exit from the endoplasmic reticulum and confers resistance to a root-penetrating fungus, providing prime evidence for BTB/POZ- domain protein-dependent membrane trafficking underlying disease resistance.The PENETRATION3 (PEN3/ABCG36/PDR8) ATP-binding cassette transporter of Arabidopsis thaliana is a crucial component of preinvasive defence against some fungal and bacterial non-host pathogens entering by direct penetration1,2,3,4. In above-ground organs, PEN3 is recruited to sites of pathogen attack at the cell surface3,4. In seedling roots, PEN3 polarly localizes to the epidermal outer membrane domain in the absence of pathogens5,6. Root epidermal cells display four major polar plasma membrane domains: the outer domain facing the environment, the inner domain oriented towards the cortical cell layer, the shootward-oriented, apical, and the root tip-oriented, basal, domain6. Proteins in the outer domain that function in regulating the transport of inorganic compounds include, for example, the NIP5;1 boric acid uptake channel7. Factors required for PEN3 and NIP5;1 trafficking from the trans-Golgi network to the outer domain have been identified8,9,10, and exocyst complex components promote polar tethering of several outer domain proteins9,11. However, factors that specifically mediate trafficking of polar outer membrane cargos involved in responses to root-penetrating pathogens remain to be discovered.In a genetic screen for mislocalization of PEN3 fused to green-fluorescent protein (PEN3- GFP) in the root epidermis of seedlings9, we recovered one recessive mutant in which PEN3-GFP localized to a cytoplasmic structure resembling the endoplasmic reticulum (ER) (Fig. 1a–d). This er-arrested pen3-1 (eap3-1) mutation indistinguishably affected localization of PEN3-GFP from that of PEN3-mCherry (Supplementary Fig. 1a,b), which colocalized with the ER-intrinsic chaperone BIP in the eap3-1 mutant (Supplementary Fig. 1c,d), corroborating an ER arrest of PEN3

Engineering for a Science-Centric Experimentation Platform

Netflix is an internet entertainment service that routinely employs experimentation to guide strategy around product innovations. As Netflix grew, it had the opportunity to explore increasingly specialized improvements to its service, which generated demand for deeper analyses supported by richer metrics and powered by more diverse statistical methodologies. To facilitate this, and more fully harness the skill sets of both engineering and data science, Netflix engineers created a science-centric experimentation platform that leverages the expertise of data scientists from a wide range of backgrounds by allowing them to make direct code contributions in the languages used by scientists (Python and R). Moreover, the same code that runs in production is able to be run locally, making it straightforward to explore and graduate both metrics and causal inference methodologies directly into production services. In this paper, we utilize a case-study research method to provide two main contributions. Firstly, we report on the architecture of this platform, with a special emphasis on its novel aspects: how it supports science-centric end-to-end workflows without compromising engineering requirements. Secondly, we describe its approach to causal inference, which leverages the potential outcomes conceptual framework to provide a unified abstraction layer for arbitrary statistical models and methodologies.Comment: 10 page

Engineering for a science-centric experimentation platform

Netflix is an internet entertainment service that routinely employs experimentation to guide strategy around product innovations. As Netflix grew, it had the opportunity to explore increasingly specialized improvements to its service, which generated demand for deeper analyses supported by richer metrics and powered by more diverse statistical methodologies. To facilitate this, and more fully harness the skill sets of both engineering and data science, Netflix engineers created a science-centric experimentation platform that leverages the expertise of scientists from a wide range of backgrounds working on data science tasks by allowing them to make direct code contributions in the languages used by them (Python and R). Moreover, the same code that runs in production is able to be run locally, making it straightforward to explore and graduate both metrics and causal inference methodologies directly into production services. In this paper, we provide two main contributions. Firstly, we report on the architecture of this platform, with a special emphasis on its novel aspects: how it supports science-centric end-to-end workflows without compromising engineering requirements. Secondly, we describe its approach to causal inference, which leverages the potential outcomes conceptual framework to provide a unified abstarction layer for arbitrary statistical models and methodologies

Real-time and label free determination of ligand binding-kinetics to primary cancer tissue specimens; a novel tool for the assessment of biomarker targeting

In clinical oncology, diagnosis and evaluation of optimal treatment strategies are mostly based on histopathological examination combined with immunohistochemical (IHC) expression analysis of cancer-associated antigens in formalin fixed paraffin-embedded (FFPE) tissue biopsies. However, informative IHC analysis depends on both the specificity and affinity of the binding reagent, which are inherently difficult to quantify in situ. Here we describe a label-free method that allows for the direct and real-time assessment of molecular binding kinetics in situ on FFPE tissue specimens using quartz crystal microbalance (QCM) enabled biosensor technology. We analysed the interaction between the rVAR2 protein and its placental-like chondroitin sulfate (pl-CS) receptor in primary human placenta tissue and in breast and prostate tumour specimens in situ. rVAR2 interacted with FFPE human placenta and cancer tissue with an affinity in the nanomolar range, and showed no detectable interaction with pl-CS negative normal tissue. We further validated the method by including analysis with the androgen receptor N-20 antibody (anti-AR). As the KD value produced by this method is independent of the number of epitopes available, this readout offers a quantitative and unbiased readout for in situ binding-avidity and amount of binding epitopes. In summary, this method adds a new and important dimension to classical IHC-based molecular pathology by adding information about the binding characteristics in biologically relevant conditions. This can potentially be used to select optimal biologics for diagnostic and for therapeutic applications as well as guide the development of novel high affinity binding drugs. Keywords: Quartz crystal microscale, Biomarker, Biosensor, VAR2CSA, Cancer, Malari

Glucosylsphingosine Is a Highly Sensitive and Specific Biomarker for Primary Diagnostic and Follow-Up Monitoring in Gaucher Disease in a Non-Jewish, Caucasian Cohort of Gaucher Disease Patients

Gaucher disease (GD) is the most common lysosomal storage disorder (LSD). Based on a deficient β-glucocerebrosidase it leads to an accumulation of glucosylceramide. Standard diagnostic procedures include measurement of enzyme activity, genetic testing as well as analysis of chitotriosidase and CCL18/PARC as biomarkers. Even though chitotriosidase is the most well-established biomarker in GD, it is not specific for GD. Furthermore, it may be false negative in a significant percentage of GD patients due to mutation. Additionally, chitotriosidase reflects the changes in the course of the disease belatedly. This further enhances the need for a reliable biomarker, especially for the monitoring of the disease and the impact of potential treatments.Here, we evaluated the sensitivity and specificity of the previously reported biomarker Glucosylsphingosine with regard to different control groups (healthy control vs. GD carriers vs. other LSDs).Only GD patients displayed elevated levels of Glucosylsphingosine higher than 12 ng/ml whereas the comparison controls groups revealed concentrations below the pathological cut-off, verifying the specificity of Glucosylsphingosine as a biomarker for GD. In addition, we evaluated the biomarker before and during enzyme replacement therapy (ERT) in 19 patients, demonstrating a decrease in Glucosylsphingosine over time with the most pronounced reduction within the first 6 months of ERT. Furthermore, our data reveals a correlation between the medical consequence of specific mutations and Glucosylsphingosine.In summary, Glucosylsphingosine is a very promising, reliable and specific biomarker for GD

Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks

Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene dose alterations on the cellular proteome, we carried out a proteomic investigation on murine embryonic stem cells that either overexpressed individual genes or displayed aneuploidy over a genomic region encompassing 14 genes. The number of variant proteins detected per cell line ranged between 70 and 110, and did not correlate with the number of modified genes. In cell lines with single gene mutations, up and down-regulated proteins were always in balance in comparison to parental cell lines regarding number as well as concentration of differentially expressed proteins. In contrast, dose alteration of 14 genes resulted in an unequal number of up and down-regulated proteins, though the balance was kept at the level of protein concentration. We propose that the observed protein changes might partially be explained by a proteomic network response. Hence, we hypothesize the existence of a class of “balancer” proteins within the proteomic network, defined as proteins that buffer or cushion a system, and thus oppose multiple system disturbances. Through database queries and resilience analysis of the protein interaction network, we found that potential balancer proteins are of high cellular abundance, possess a low number of direct interaction partners, and show great allelic variation. Moreover, balancer proteins contribute more heavily to the network entropy, and thus are of high importance in terms of system resilience. We propose that the “elasticity” of the proteomic regulatory network mediated by balancer proteins may compensate for changes that occur under diseased conditions

1.5 years of TROPOMI CO measurements: comparisons to MOPITT and ATom

We have analyzed TROPOspheric Monitoring Instrument (TROPOMI) carbon monoxide (CO) data acquired between November 2017 and March 2019 with respect to other satellite (MOPITT, Measurement Of Pollution In The Troposphere) and airborne (ATom, Atmospheric Tomography mission) datasets to better understand TROPOMI's contribution to the global tropospheric CO record (2000 to present). MOPITT and TROPOMI are two of only a few satellite instruments to ever derive CO from solar-reflected radiances. Therefore, it is particularly important to understand how these two datasets compare. Our results indicate that TROPOMI CO retrievals over land show excellent agreement with respect to MOPITT: relative biases and their SD (i.e., accuracy and precision) are on average , , and compared to the MOPITT TIR (thermal infrared), NIR (near infrared), and TIR&thinsp;+&thinsp;NIR (multispectral) products, respectively. TROPOMI and MOPITT data also show good agreement in terms of temporal and spatial patterns.</p

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

HFR1 Is Crucial for Transcriptome Regulation in the Cryptochrome 1-Mediated Early Response to Blue Light in Arabidopsis thaliana

Cryptochromes are blue light photoreceptors involved in development and circadian clock regulation. They are found in both eukaryotes and prokaryotes as light sensors. Long Hypocotyl in Far-Red 1 (HFR1) has been identified as a positive regulator and a possible transcription factor in both blue and far-red light signaling in plants. However, the gene targets that are regulated by HFR1 in cryptochrome 1 (cry1)-mediated blue light signaling have not been globally addressed. We examined the transcriptome profiles in a cry1- and HFR1-dependent manner in response to 1 hour of blue light. Strikingly, more than 70% of the genes induced by blue light in an HFR1-dependent manner were dependent on cry1, and vice versa. High overrepresentation of W-boxes and OCS elements were found in these genes, indicating that this strong cry1 and HFR1 co-regulation on gene expression is possibly through these two cis-elements. We also found that cry1 was required for maintaining the HFR1 protein level in blue light, and that the HFR1 protein level is strongly correlated with the global gene expression pattern. In summary, HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling, especially for the function of genes containing W-boxes and OCS elements