scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes.

A major challenge in single-cell biology is identifying cell-type-specific gene functions, which may substantially improve precision medicine. Differential expression analysis of genes is a popular, yet insufficient approach, and complementary methods that associate function with cell type are required. Here, we describe scHumanNet (https://github.com/netbiolab/scHumanNet), a single-cell network analysis platform for resolving cellular heterogeneity across gene functions in humans. Based on cell-type-specific gene networks (CGNs) constructed under the guidance of the HumanNet reference interactome, scHumanNet displayed higher functional relevance to the cellular context than CGNs built by other methods on single-cell transcriptome data. Cellular deconvolution of gene signatures based on network compactness across cell types revealed breast cancer prognostic markers associated with T cells. scHumanNet could also prioritize genes associated with particular cell types using CGN centrality and identified the differential hubness of CGNs between disease and healthy conditions. We demonstrated the usefulness of scHumanNet by uncovering T-cell-specific functional effects of GITR, a prognostic gene for breast cancer, and functional defects in autism spectrum disorder genes specific for inhibitory neurons. These results suggest that scHumanNet will advance our understanding of cell-type specificity across human disease genes.

Synthetic Control of Intrinsic Defect Formation in Metal Oxide Nanocrystals Using Dissociated Spectator Metal Salts.

Crystallographic defects are essential to the functional properties of semiconductors, controlling everything from conductivity to optical properties and catalytic activity. In nanocrystals, too, defect engineering with extrinsic dopants has been fruitful. Although intrinsic defects like vacancies can be equally useful, synthetic strategies for controlling their generation are comparatively underdeveloped. Here, we show that intrinsic defect concentration can be tuned during the synthesis of colloidal metal oxide nanocrystals by the addition of metal salts. Although not incorporated in the nanocrystals, the metal salts dissociate at high temperatures, promoting the dissociation of carboxylate ligands from metal precursors, leading to the introduction of oxygen vacancies. For example, the concentration of oxygen vacancies can be controlled up to 9% in indium oxide nanocrystals. This method is broadly applicable as we demonstrate by generating intrinsic defects in metal oxide nanocrystals of various morphologies and compositions.

First-principles prediction on antimony-doping effects on the cyclic stability of tin anodes for lithium-ion batteries.

Tin-based materials are considered as promising anode materials for advanced Li-ion batteries (LIBs) due to their relatively high capacity and suitable working voltage, but they suffer from poor structural stability during electrochemical cycling. Herein, we present the possibility that the cyclic stability of the Sn LIB anode can be enhanced by adding a small amount of antimony (Sb), based on first-principles investigation of lithiation behavior of amorphous Sn doped with 3 at% Sb. At low Li contents (x < 1.5 in a-LixSn0.97Sb0.03), our simulations show that the preferential reaction of Li with Sb over Sn tends to lead to the formation of small lithiated Sb clusters. However, the aggregated Sb, if any, become fully separated upon further lithiation, implying that they may remain well dispersed in the lithiation/delithiation process if the Sb-doping concentration is sufficiently low. The weak aggregation and preferential lithiation tendency of Sb in the Sb-doped Sn anode can be expected to contribute to enhancing its structural stability during cycling, in comparison with pure Sn and SnSb alloy cases. We also compare lithiation-induced changes in the electrochemical, transport and mechanical properties between the Sb-doped and pure Sn systems. Our study highlights the importance of low concentration and uniform distribution of Sb in order to obtain desired properties of Sb-doped Sn as an anode for LIBs. This finding also provides some hints for the further development of Sn-based anodes via fine-tuning of doping.

Three-dimensional atomic mapping of ligands on palladium nanoparticles by atom probe tomography.

Capping ligands are crucial to synthesizing colloidal nanoparticles with functional properties. However, the synergistic effect between different ligands and their distribution on crystallographic surfaces of nanoparticles during colloidal synthesis is still unclear despite powerful spectroscopic techniques, due to a lack of direct imaging techniques. In this study, atom probe tomography is adopted to investigate the three-dimensional atomic-scale distribution of two of the most common types of these ligands, cetrimonium (C19H42N) and halide (Br and Cl) ions, on Pd nanoparticles. The results, validated using density functional theory, demonstrate that the Br anions adsorbed on the nanoparticle surfaces promote the adsorption of the cetrimonium cations through electrostatic interactions, stabilizing the Pd {111} facets. In contrast, the Cl anions are not strongly adsorbed onto the Pd surfaces. The high density of adsorbed cetrimonium cations for Br anion additions results in the formation of multiple-twinned nanoparticles with superior oxidation resistance.

Calibration of In-Plane Center Alignment Errors in the Installation of a Circular Slide with Machine-Vision Sensor and a Reflective Marker.

This paper describes a method for calibrating in-plane center alignment error (IPCA) that occurs when installing the circular motion slide (CMS). In this study, by combini ng the moving carriage of the CMS and the planar PKM (parallel kinematic mechanism) with the machine tool, the small workspace of the PKM is expanded, and the workpiece is placed on the table with the CMS installed is processed through the machine tool. However, to rigidly mount the CMS on the table, the preload between the guide and the support bearings must be adjusted with the eccentric bearing, and in this process, the IPCA occurs. After installing a reflective marker on the PKM, the PKM is slowly rotated along with the ring guide in the way of stop-and-go without the PKM's own motion. Then, using a machine vision camera installed at the top of the CMS, the IPCA, which is the difference between the actual center position and the nominal center position of the CMS with respect to the camera, can be successfully calibrated through the circular fitting process. Consequently, it was confirmed that the IPCA of 0.37 mm can be successfully identified with the proposed method.

Search for bacterial α1,2-fucosyltransferases for whole-cell biosynthesis of 2'-fucosyllactose in recombinant Escherichia coli.

2'-Fucosyllactose (2'-FL) is the most abundant human milk oligosaccharide and is important for infant nutrition and health. Because 2'-FL has potential as a functional ingredient in advanced infant formula and as a prebiotic in various foods, a cost-effective method for 2'-FL production is desirable. α1,2-Fucosyltransferase (α1,2-FT) is one of the key enzymes enabling the microbial biosynthesis of this complex sugar. However, the α1,2-FTs reported so far for the whole-cell biosynthesis of 2'-FL originate from pathogens, posing a potential hurdle for approval as a food production method depending on countries. In this study, 10 α1,2-FT genes from bacteria of biosafety level one were identified, and the main features of the deduced amino acid sequences were characterized. Four codon-optimized α1,2-FT genes were synthesized and introduced into Escherichia coli ΔL M15 strain containing the plasmid pBCGW encoding guanosine 5'-diphosphate-l-fucose biosynthetic enzymes. Among the four genes, 2'-FL was produced only by the α1,2-FT from Thermosynechococcus elongatus (Te2FT). Bifidobacterium thermacidophilum α1,2-FT (Bt2FT) showed high expression but was not active in E. coli ΔL M15. The other two α1,2-FTs were not expressed to a detectable level. During batch flask fermentation of Te2FT-expressing E. coli ΔL M15 cells, 0.49 g/L 2'-FL was obtained after 72 h of induction. This is comparable to the values previously reported for α1,2-FTs from Helicobacter pylori and Bacteroides fragilis.

Endocytosing Escherichia coli as a Whole-Cell Biocatalyst of Fatty Acids.

Whole cell biocatalysts can be used to convert fatty acids into various value-added products. However, fatty acid transport across cellular membranes into the cytosol of microbial cells limits substrate availability and impairs membrane integrity, which in turn decreases cell viability and bioconversion activity. Because these problems are associated with the mechanism of fatty acid transport through membranes, a whole-cell biocatalyst that can form caveolae-like structures was generated to promote substrate endocytosis. Caveolin-1 ( CAV1) expression in Escherichia coli increased both the fatty acid transport rate and intracellular fatty acid concentrations via endocytosis of the supplemented substrate. Furthermore, fatty-acid endocytosis alleviated substrate cytotoxicity in E. coli. These traits attributed to bacterial endocytosis resulted in dramatically elevated biotransformation efficiencies in fed-batch and cell-recycle reaction systems when caveolae-forming E. coli was used for the bioconversion of ricinoleic acid (12-hydroxyoctadec-9-enoic acid) to ( Z)-11-(heptanoyloxy) undec-9-enoic acid. We propose that CAV1-mediated endocytosing E. coli represents a versatile tool for the biotransformation of hydrophobic substrates.

A Simple Enzymatic Method for Quantitation of 2'-Fucosyllactose.

2'-Fucosyllactose (2'-FL) is one of the most important human milk oligosaccharides and has several health benefits for infants. The levels of 2'-FL in breast milk or samples from other sources can bequantified by high-performance liquid chromatography. However, this method cannot be used for simultaneous detection of the target compound in numerous samples. Here, we developed a simple method for quantifying 2'-FL in a microplate format. The method involves two steps: (1) release of L-fucose from 2'-FL by α-(1-2,3,4,6)-L-fucosidase and (2) measurement of NADPH formed during the oxidation of L-fucose by L-fucose dehydrogenase. This method enables measurement of up to 5 g/l 2'-FL in 50 min using a 96-well microplate. The efficiency and simplicity of the proposed method make it suitable for the analyses of a large number of samples simultaneously.

Engineering of α-1,3-fucosyltransferases for production of 3-fucosyllactose in Escherichia coli.

Fucosyllactoses (FLs), present in human breast milk, have been reported to benefit human health immensely. Especially, 3-fucosyllactose (3-FL) has numerous benefits associated with a healthy gut ecosystem. Metabolic engineering of microorganisms is thought to be currently the only option to provide an economically feasible route for large-scale production of 3-FL. However, engineering principles for α-1,3-fucosyltransferases (1,3-FTs) are not well-known, resulting in the lower productivity of 3-FL than that of 2'-fucosyllactose (2'-FL), although both 2'-FL and 3-FL follow a common pathway to produce GDP-L-fucose. The C-terminus of 1,3-FTs is composed of heptad repeats, responsible for dimerization of the enzymes, and a peripheral membrane anchoring region. It has long been thought that truncation of most heptad repeats, retaining just 1 or 2, helps the soluble expression of 1,3-FTs. However, whether the introduction of truncated version of 1,3-FTs enhances the production of 3-FL in a metabolically engineered strain, is yet to be tested. In this study, the effect of these structural components on the production of 3-FL in Escherichia coli was evaluated through systematic truncation and elongation of the C-terminal regions of three 1,3-FTs from Helicobacter pylori. Although these three 1,3-FTs contained heptad repeats and membrane-anchoring regions of varying lengths, they commonly exhibited an optimal performance when the number of heptad repeats was increased, and membrane-binding region was removed. The production of 3-FL could be increased 10-20-fold through this simple strategy.

Diffuse infiltrative hepatocellular carcinomas in a hepatitis B-endemic area: diagnostic and therapeutic impediments.

BACKGROUND/AIMS: Clinical features of diffuse infiltrative hepatocellular carcinoma (D-HCC) are distinct from those of mass-forming HCCs, and also dependent on etiologic viruses. Moreover, despite a regular HCC-surveillance in those with chronic liver diseases, patients sometimes present with advanced D-HCCs. Thus, in the present study, we were to assess the risk factors, mode of diagnosis and prognosis of D-HCCs in a hepatitis B virus-endemic area. METHODOLOGY: From January to June 2003, 35 patients who had been newly diagnosed as having D-HCC were enrolled. Their clinical characteristics were compared with those with other types of HCCs, who had been enrolled during the same period. Survival rates were analyzed using Kaplan-Meier method and Cox proportional hazard model. RESULTS: D-HCC patients were younger and more commonly positive for HBsAg than those with other types of HCCs. During a regular follow-up, these tumors were not readily detectable in ultrasonography. Transarterial chemoembolization was beneficial in patients with good liver function as compared to supportive care, while this was not evident in those with poor hepatic reserve. CONCLUSIONS: D-HCCs are not readily diagnosed using ultrasonography. These tumors are mostly resistant to treatment, while transarterial chemoembolization might be applied in patients with good liver function.