Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis

DETERMINISTIC-BASED SHIP ANTI-COLLISION ROUTE OPTIMIZATION WITH WEB-BASED APPLICATION

fiskin, remzi/0000-0002-5949-0193WOS: 000505080600003Most of the accidents are caused by human error at sea so, decision making process made by navigators should be more computerised and automated. the supported decision making can be a step forward to decrease the risk of collision. This paper, in this respect, aims to present a deterministic approach to support optimum collision avoidance trajectory. This approach involves a collision avoidance course alteration. A web-based application coded with "JavaScript" programming language on the "Processing" software platform which allows the own ship to change her course in a deterministic manner to avoid collision optimally has been introduced. Algorithm structure of the method has been formulated and organized according to the International Regulation for Preventing Collision at Sea (COLREGs). the experimental tests results have revealed that the system is practicable and feasible and considerably outperforms heuristic-based method. It is thought that the developed method can be applied in an intelligent avoidance system on board and provides contribution to ship collision avoidance process, automation of ship motion control and ship traffic engineering

A Fuzzy Rule-Based Approach to Determine an Asymmetrical Polygonal Ship Domain

2019 Innovations in Intelligent Systems and Applications Conference, ASYU 2019 -- 31 October 2019 through 2 November 2019 -- -- 156545Navigators expect to feel comfortable while passing a ship and an obstacle at sea. This feeling has led to reveal the concept of ship domain. The ship domain is one of the criteria for navigational risk assessment and one of the parameters used in collision avoidance planning and traffic engineering at sea. Generally, navigators determine the domain size by experience, and they form it as a circle in practice. This is because it is called a fully subjective and imprecise value. Although elliptical and circle ship domains are mostly proposed, there have been some complex ship domains such as hexagonal, polygonal, etc. The methods and models to form a ship domain in the related literature are mainly based on analytical, statistical and artificial intelligence methods. In this study, a novel fuzzy rule-based approach has been proposed to determine an asymmetrical polygonal ship domain. The proposed domain is assumed to be around the own ship and its size and shape depend on the directions according to various parameters such as ship length, ship speed, maneuverability, traffic state, navigator experience, day time (daylight or night), sea state, visibility and relative bearing of the target ship (TS). A C# application based on fuzzy inference system (FIS) with Mamdani model has been implemented to form the size and shape of the domain. The logical implication rules used by navigators define the fuzzy domain. In conclusion, it is thought that the proposed model will undoubtedly contribute to the path planning, collision avoidance optimization, ship traffic engineering, and ship motion control. © 2019 IEEE

A Fuzzy Ship Domain-Based Method for Collision Avoidance at Sea

4th International Conference on Computer Science and Engineering, UBMK 2019 -- 11 September 2019 through 15 September 2019 -- -- 154916The paper presents an asymmetrical polygonal fuzzy ship domain-based ship collision avoidance method considering COLREGs. The user interface is formed for practical collision avoidance decision support function via using form application developed with the C# programming language on the Microsoft Visual Studio software platform. Experimental study shows that the presented method can provide a reasonable solution. The system is expected to provide an effective assistance to system operators and to make a contribution to the ship automation and e-navigation strategy. © 2019 IEEE

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Multimodal measurements of single-cell profiles are proving increasingly useful for characterizing cell states and regulatory mechanisms. In the present study, we developed PHAGE-ATAC (Assay for Transposase-Accessible Chromatin), a massively parallel droplet-based method that uses phage displaying, engineered, camelid single-domain antibodies ('nanobodies') for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, and mitochondrial DNA-based clonal tracing. We use PHAGE-ATAC for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis and the detection of SARS-CoV-2 spike protein in human cell populations. Finally, we construct a synthetic high-complexity phage library for selection of antigen-specific nanobodies that bind cells of particular molecular profiles, opening an avenue for protein detection, cell characterization and screening with single-cell genomics

Fluorescence-Based Sensors to Monitor Localization and Functions of Linear and K63-Linked Ubiquitin Chains in Cells

Ubiquitin chains modify a major subset of the proteome, but detection of ubiquitin signaling dynamics and localization is limited due to a lack of appropriate tools. Here, we employ ubiquitin-binding domain (UBD)-based fluorescent sensors to monitor linear and K63-linked chains in vitro and in vivo. We utilize the UBD in NEMO and ABIN (UBAN) for detection of linear chains, and RAP80 ubiquitin-interacting motif (UIM) and TAB2 Npl4 zinc finger (NZF) domains to detect K63 chains. Linear and K63 sensors decorated the ubiquitin coat surrounding cytosolic Salmonella during bacterial autophagy, whereas K63 sensors selectively monitored Parkin-induced mitophagy and DNA damage responses in fixed and living cells. In addition, linear and K63 sensors could be used to monitor endogenous signaling pathways, as demonstrated by their ability to differentially interfere with TNF- and IL-1-induced NF-κB pathway. We propose that UBD-based biosensors could serve as prototypes to track and trace other chain types and ubiquitin-like signals in vivo