Machine learning prediction of coordination energies for alkali group elements in battery electrolyte solvents.

We combined a data science-driven method with quantum chemistry calculations, and applied it to the battery electrolyte problem. We performed quantum chemistry calculations on the coordination energy (Ecoord) of five alkali metal ions (Li, Na, K, Rb, and Cs) to electrolyte solvent, which is intimately related to ion transfer at the electrolyte/electrode interface. Three regression methods, namely, multiple linear regression (MLR), least absolute shrinkage and selection operator (LASSO), and exhaustive search with linear regression (ES-LiR), were employed to find the relationship between Ecoord and descriptors. Descriptors include both ion and solvent properties, such as the radius of metal ions or the atomic charge of solvent molecules. Our results clearly indicate that the ionic radius and atomic charge of the oxygen atom that is connected to the metal ion are the most important descriptors. Good prediction accuracy for Ecoord of 0.127 eV was obtained using ES-LiR, meaning that we can predict Ecoord for any alkali ion without performing quantum chemistry calculations for ion-solvent pairs. Further improvement in the prediction accuracy was made by applying the exhaustive search with Gaussian process, which yields 0.016 eV for the prediction accuracy of Ecoord.

Liquid electrolyte informatics using an exhaustive search with linear regression.

Exploring new liquid electrolyte materials is a fundamental target for developing new high-performance lithium-ion batteries. In contrast to solid materials, disordered liquid solution properties have been less studied by data-driven information techniques. Here, we examined the estimation accuracy and efficiency of three information techniques, multiple linear regression (MLR), least absolute shrinkage and selection operator (LASSO), and exhaustive search with linear regression (ES-LiR), by using coordination energy and melting point as test liquid properties. We then confirmed that ES-LiR gives the most accurate estimation among the techniques. We also found that ES-LiR can provide the relationship between the "prediction accuracy" and "calculation cost" of the properties via a weight diagram of descriptors. This technique makes it possible to choose the balance of the "accuracy" and "cost" when the search of a huge amount of new materials was carried out.

Nuclear extrusion precedes discharge of genomic DNA fibers during tunicamycin-induced neutrophil extracellular trap-osis (NETosis)-like cell death in cultured human leukemia cells.

We previously reported that the nucleoside antibiotic tunicamycin (TN), a protein glycosylation inhibitor triggering unfolded protein response (UPR), induced neutrophil extracellular trap-osis (NETosis)-like cellular suicide and, thus, discharged genomic DNA fibers to extracellular spaces in a range of human myeloid cell lines under serum-free conditions. In this study, we further evaluated the effect of TN on human promyelocytic leukemia HL-60 cells using time-lapse microscopy. Our assay revealed a previously unappreciated early event induced by TN-exposure, in which, at 30-60 min after TN addition, the cells extruded their nuclei into the extracellular space, followed by discharge of DNA fibers to form NET-like structures. Intriguingly, neither nuclear extrusion nor DNA discharge was observed when cells were exposed to inducers of UPR, such as brefeldin A, thapsigargin, or dithiothreitol. Our findings revealed novel nuclear dynamics during TN-induced NETosis-like cellular suicide in HL-60 cells and suggested that the toxicological effect of TN on nuclear extrusion and DNA discharge was not a simple UPR.

A Convenient Technique to Fix Suspension Cells on a Coverslip for Microscopy.

Human myeloid HL-60 cells are usually cultured in suspension in medium containing 5% to 10% fetal bovine serum (FBS) and thus are often difficult to adhere to a coverslip. In this unit, we describe how removal of FBS from the culture medium facilitates adhesion of HL-60 cells to coverslips. Importantly, HL-60 cells that adhere to the coverslips immersed in FBS-free medium can be immobilized in situ by conventional chemical fixatives and thus permeabilized for probing cellular structures using specific dyes and/or reagents, followed by microscopic observation. All-trans-retinoic-acid-exposed differentiated HL-60 cells, which have properties similar to neutrophils, can also adhere efficiently to coverslips in FBS-free medium. Because the procedure is not complex and special equipment is not required, the simplicity and cost effectiveness of this FBS-free cell adhesion protocol may be beneficial to researchers who are interested in assessing the structure and function of suspension cells using microscopy.

Tunicamycin-induced neutrophil extracellular trap (NET)-like structures in cultured human myeloid cell lines.

The mechanism of neutrophil extracellular trap cell death (NETosis), a regulated cell death pathway relevant to infection, autoimmunity and sepsis, is not completely known. The reason for this, at least in part, is the lack of an in vitro system that recapitulates the NETosis pathway using established human cell lines. We show that exposure of a human promyelocytic leukemia cell line HL-60 to the glycosyltransferase inhibitor tunicamycin (TM) resulted in extrusion of decompacted genomic DNAs to extracellular space, morphologically similar to NETs. Immunostaining using antibodies against NET marker proteins and bacterial trapping assay showed biochemical similarities between the TM-induced extracellular DNA structures and NETs. The NET-like structures were also generated on exposure of TM to other myeloid cell lines, such as U937 and THP-1. Thus, our findings provide an experimental setting to induce NET-like structures using cultured human myeloid cell lines, which may help our understanding of the regulation and function of NETosis.

Adhesion of suspension cells on a coverslip in serum-free conditions.

Here, we present a rapid and damage-free fixation protocol for human cells cultured in suspension. Our results demonstrated that serum-free incubation of myeloid suspension cell lines HL-60, U937, and THP-1 for 10 min resulted in cell adhesion to coverslips, allowing simple and efficient fixation for microscopy. The fixed cells exhibited an intact morphology and were suitable for immunostaining. Such simplicity and cost effectiveness have not been achieved by any previously established fixation technique, and our newly developed method provides an additional fixation technique for researchers working with suspension cells.

Construction of a mouse Aos1-Uba2 chimeric SUMO-E1 enzyme, mAU, and its expression in baculovirus-insect cells.

Small ubiquitin-related modifier (SUMO) is a highly conserved protein that is covalently attached to target proteins. This posttranslational modification, designated SUMOylation, is a major protein-conjugation-driven strategy designed to regulate structure and function of cellular proteins. SUMOylation consists of an enzymatic cascade involving the E1-activating enzyme and the E2-conjugating enzyme. The SUMO-E1 enzyme consists of two subunits, a heterodimer of activation of Smt3p 1 (Aos1) and ubiquitin activating enzyme 2 (Uba2), which resembles the N- and C-terminal halves of ubiquitin E1 (Uba1). Herein, we describe the rational design of a single polypeptide version of SUMO-E1, a chimera of mouse Aos1 and Uba2 subunits, termed mAU, in which the functional domains appear to be arranged in a fashion similar to Uba1. We also describe the construction of a mAU plasmid for expression in a baculovirus-insect cell system and present an in situ SUMOylation assay using the recombinant mAU. Our results showed that mAU has SUMO-E1 activity, thereby indicating that mAU can be expressed in baculovirus-insect cells and represents a suitable source of SUMO-E1.