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We report a colloid–polymer model system with tunable bridging interactions for microscopic studies of structure and dynamics using confocal imaging. The interactions between trifluoroethyl methacrylate-co- tert-butyl methacrylate copolymer particles and poly(acrylic acid) (PAA) polymers were controllable via polymer concentration and pH. The strength of adsorption of PAA on the particles, driven by pH-dependent interactions with polymer brush stabilizers on the particle surfaces, was tuned via solution pH. Particle–polymer suspensions formulated at low pH, where polymers strongly adsorbed to the particles, contained clusters or weak gels at particle volume fractions of ϕ = 0.15 and ϕ = 0.40. At high pH, where the PAA only weakly adsorbed to the particle surface, particles largely remained dispersed, and the suspensions behaved as a dense fluid. The ability to visualize the suspension structure is likely to provide insight into the role of polymer-driven bridging interactions in the behavior of colloidal suspensions.

Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in microbial genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present a new read-clustering algorithm, called RBRC, for improving

Background Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads. Results In this study, we present a new method called PLR-GEN. It creates pseudo–long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo–long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo–long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes. Conclusions PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.

Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop “Nanchukmacdon” a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.

Baculovirus expression systems have been widely used to produce recombinant mammalian proteins owing to the lack of viral replication in vertebrates. Although several lines of evidence have demonstrated impacts of baculovirus infection in mammalian hosts, genome-wide effects have not been fully elucidated. Here, we provide comparative transcriptome profiles of baculovirus and host-immune response genes in recombinant baculovirus-infected mammalian and insect cells. Specifically, to decipher the impacts of baculovirus infection in mammalian cells, we conducted total RNA-seq on human 293TT cells and insect Sf9 cells infected with recombinant baculovirus. We found that baculovirus genes were rarely expressed under the control of baculoviral promoters in 293TT cells. Although some baculovirus early genes, such as PE38 and IE-01, showed limited expression in 293TT cells, baculoviral late genes were mostly silent. We also found modest induction of a small number of mammalian immune response genes associated with Toll-like receptors, cytokine signaling, and complement in baculovirus-infected 293TT cells. These comprehensive transcriptome data will contribute to improving recombinant baculovirus as tools for gene delivery, gene therapy, and vaccine development.

Simple Summary The present study shows the role of Drosophila USP14 under ER stress and ER stress related disease, autosomal dominant retinitis pigmentosa. Drosophila USP14 protects cell from ER stress triggered by ER stress-causing chemicals Drosophila S2 cells and suppresses the retinal degeneration in disease model for retinitis pigmentosa by regulating the stability of Rhodopsin-1. This study also indicates the dynamic reorganization of proteasome complex under ER stress. The modulation of USP14 could be a potential therapeutic strategy for treating the diseases associated with protein folding. Abstract Endoplasmic reticulum (ER) stress and its adaptive cellular response, the unfolded protein response (UPR), are involved in various diseases including neurodegenerative diseases, metabolic diseases, and even cancers. Here, we analyzed the novel function of ubiquitin-specific peptidase 14 (USP14) in ER stress. The overexpression of Drosophila USP14 protected the cells from ER stress without affecting the proteasomal activity. Null Hong Kong (NHK) and alpha-1-antitrypsin Z (ATZ) are ER-associated degradation substrates. The degradation of NHK, but not of ATZ, was delayed by USP14. USP14 restored the levels of rhodopsin-1 protein in a Drosophila model for autosomal dominant retinitis pigmentosa and suppressed the retinal degeneration in this model. In addition, we observed that proteasome complex is dynamically reorganized in response to ER stress in human 293T cells. These findings suggest that USP14 may be a therapeutic strategy in diseases associated with ER stress.

The organisms have the capacity to sense and adapt to their surroundings for their life in a dynamic environment. In response to amino acid starvation, cells activate a rectifying physiological program, termed the integrated stress response (ISR), to restore cellular homeostasis. General controlled non-repressed (GCN2) kinase is a master regulator of the ISR and modulates protein synthesis in response to amino acid starvation. We previously established the GCN2/ATF4/4E-BP pathway in development and aging. Here, we investigated the tissue-specific roles of GCN2 upon dietary restriction of amino acid in a Drosophila model. The knockdown of GCN2 in the gut and fat body, an energy sensing organ in Drosophila, abolished the beneficial effect of GCN2 in lifespan extension upon dietary restriction of amino acids. Proteome analysis in an autosomal dominant retinitis pigmentosa (ADRP) model showed that dietary restriction of amino acids regulates the synthesis of proteins in several pathways, including mitochondrial translation, mitochondrial gene expression, and regulation of biological quality, and that gcn2-mutant flies have reduced levels of these mitochondria-associated proteins, which may contribute to retinal degeneration in ADRP. These results indicate that the tissue-specific regulation of GCN2 contributes to normal physiology and ADRP progression.

Asthma is one of the most common chronic inflammatory diseases of the airways. Essential oil from Abies holophylla leaf (EOA) has been reported to have anti-inflammatory property. This study aimed to predict the inhibitory effect of EOA against asthma by network analysis and to confirm the underlying mechanism of EOA on airway inflammation.The effects and underlying mechanisms of EOA on asthma were investigated by in silico network pharmacology and an experimental in vivo study.To define the effectiveness of EOA on asthma, the network pharmacology was constructed using major components of EOA. EOA (0.0003 and, 0.03 v/v%) was aerosolized by nebulizer 3 times a week for 5 min for 7 weeks. After 3 weeks of treating the mice with EOA, asthma was induced by sensitizing them with ovalbumin (OVA) and PM10. The effects of EOA on the IL-17 related signaling pathway was confirmed using an asthmatic model.The network analysis showed that EOA is highly associated with the IL-17-related signaling pathway. EOA inhibited respiratory epithelium hyperplasia, collagen deposition and goblet cell activation in the lung and trachea tissues. In addition, EOA reduced the number of eosinophils, lymphocytes and macrophages in BALF. Furthermore, in the asthmatic model of mice, we showed that EOA inhibited IL-17-related cytokines, increased Treg-related cytokines and decreased the TRAF6 and MAPK and, suppressed the nuclear transcriptional activities of NF-kB.The network pharmacology and in vivo study indicated that EOA may have an inhibitory effect on airway inflammation in asthma exposure through the IL-17-related signaling pathway.

We investigated the effect of two brush parameters, thickness and dispersity in the molecular weight distribution, on the adhesion of bacteria to pH-responsive poly(acrylic acid) (PAA) brushes synthesized using surface-initiated atom transfer radical polymerization. The attachment and detachment of Staphylococcus epidermidis to PAA brushes at pH 4 and pH 9, respectively, were examined with confocal microscopy. An optimal range of brush thickness, 13-18 nm, was identified for minimizing bacterial adhesion on PAA brushes at pH 4, and bacterial attachment did not depend on the brush dispersity. Increasing either the brush thickness or dispersity detached bacteria from the brushes when the pH was increased from 4 to 9. Bacterial detachment likely arose from an enhanced actuation effect in thick or high-dispersity brushes, as PAA brushes change conformation from collapsed to extended states when the pH is increased from 4 to 9. These results suggest that manipulating the molecular weight distribution provides a route to separately tune the attachment and detachment of bacteria.

Increased shear thinning arising due to strong attractive interactions between colloidal particles is thought to obscure shear thickening. Here, we demonstrate how moderate attractions, induced by adding a nonadsorbing polymer, can instead enhance shear thickening. We measure the rheology of colloidal suspensions at a constant particle volume fraction of ϕ=0.40 with dilute to weakly semidilute concentrations of three polyacrylamide depletants of different molecular weights. Suspensions containing large polymer exhibit increased shear thickening and positive first normal stress differences at high shear stress, and increased heterogeneous fluctuations in the boundary stress. These results are consistent with a friction-based model for shear thickening, suggesting that the presence of large, extended polymers induces the formation of near-spanning networks of interparticle contacts.

In this study, a pellet-type adsorbent was prepared by using the water-treatment sludge as a raw material, and its physical and chemical properties were analyzed through -adsorption, XRD, XRF, and -TPD measurements. Adsorption performance for gaseous ammonia and formaldehyde was compared between the pellet-type adsorbents prepared from water-treatment sludge and the impregnated activated carbon. Although the surface area and pore volume of the pellet-type adsorbent produced from water-treatment sludge were much smaller than those of the impregnated activated carbon, the pellet-type adsorbent produced from water-treatment sludge could adsorb ammonia gas even more than that of using the impregnated activated carbon. The pellet-type adsorbent prepared from water-treatment sludge showed a superior adsorption capacity for ammonia which can be explained by chemical adsorption ascribed to the higher amount of acid sites on the pellet-type adsorbent prepared from water-treatment sludge. In the case of formaldehyde adsorption, the impregnated activated carbon was far superior to the adsorbent made from the water-treatment sludge, which can be attributed to the increased surface area of the impregnated activated carbon.

We developed a model depletion system with colloidal particles that were refractive index- and density-matched to 80 (w/w)% glycerol in water, and characterized the effect of interparticle interactions on the structure and dynamics of non-equilibrium phases. 2,2,2-trifluoroethyl methacrylate-co-tert-butyl methacrylate copolymer particles were synthesized following Kodger et al. (Sci. Rep. 5, 14635 (2015)). Particles were dispersed in glycerol/water solutions to generate colloidal suspensions with good control over electrostatic interactions and a moderately high background viscosity of 55 mPa-s. To probe the effects of charge screening and depletion attractions on the suspension phase behavior, we added NaCl and polyacrylamide (M_w = 186 kDa) at various concentrations to particle suspensions formulated at volume fractions of phi = 0.05 and 0.3 and imaged the suspensions using confocal microscopy. The particles were nearly hard spheres at a NaCl concentration of 20 mM, but aggregated when the concentration of NaCl was further increased. Changes in the particle structure and dynamics with increasing concentration of the depletant polyacrylamide followed the trends expected from earlier experiments on depletion-driven gelation. Additionally, we measured the viscosity and corrected first normal stress difference of suspensions formulated at phi = 0.4 with and without added polymer. The solvent viscosity was suitable for rheology measurements without the onset of instabilities such as secondary flows or edge fracture. These results validate this system as an alternative to one common model system, suspensions of poly(methyl methacrylate) particles and polystyrene depletants in organic solvents, for investigating phase behavior and flow properties in attractive colloidal suspensions.

This study optimizes the synthesis process of pellet-type adsorbents using alum sludge. The effect of the binder and heat treatment temperature on the nanopore formation in the adsorbent is investigated. The pellet-type adsorbent prepared using the powder-type sludge from water treatment is determined to be a material that contains nanopores. The specific surface area is increased significantly after the calcination process in the range of 132-172 m2/g. With the calcination treatment, the breakthrough time in the formaldehyde adsorption increases remarkably with an optimum calcination temperature of 400 °C. The breakthrough capacity of the formaldehyde increases to a maximum 2.96 mg/g at this temperature.

A novel water-soluble fluorescent naphthalimide derivative as a sensor for Cu(II) has been synthesized. The sensor, conjugated with DPA (as the Cu(II)-binding moiety) and TPP (as the mitochondrial-targeting moiety) was further decorated with a galactose unit at the fluorophore’s terminal using the click reaction. Although confocal fluorescence imaging revealed that probe 1 was not localized in mitochondria, and was neither quenched under Cu-overloading conditions, probe 1 did exhibit a high selectivity for Cu(II) ions over various metal ions in HEPES-buffered solutions. Furthermore the fluorescence was dramatically quenched upon the addition 1 equivalent of Cu(II), and the response was stable in the range of pH 6–10. A fluorophore conjugated with DPA (as the Cu(II)-binding moiety) and TPP (as the mitochondrial-targeting moiety) was further decorated with a galactose unit at the fluorophore’s terminal. The sensor exhibited selectivity over other biologically relevant ions.

Correction for ‘Phase behavior of colloid–polymer depletion mixtures with unary or binary depletants’ by Nayoung Park et al., Soft Matter, 2017, 13, 2781–2792.

In the eukaryotic circadian clock machinery, negative feedback repression of CLOCK (CLK) and BMAL1 transcriptional activity by PERIOD (PER) and CRYPTOCHROME (CRY) underlies the basis for 24 h rhythmic gene expression. Thus, precise regulation of the time-dependent nuclear entry of circadian repressors is crucial to generating normal circadian rhythms. Here, we sought to identify novel kinase(s) that regulate nuclear entry of mammalian CRY1 (mCRY1) with an unbiased screening using red fluorescent protein (RFP)-tagged human kinome expression plasmids in mammalian cells. Transient expression of human vaccinia-related kinase 3 (hVRK3) reduced the nuclear presence of mCRY1. hVRK3 expression also induced alterations in the subcellular localization of other core clock proteins, including mCRY2, mPER2, and BMAL1. In contrast, the subcellular localization of mCLK was not changed. Given that singly expressed mCLK mostly resides in the cytoplasm and that nuclear localization sequence (NLS) mutation of hVRK3 attenuated the effect of hVRK3 co-expression on subcellular localization, ectopically expressed hVRK3 presumably reduces the retention of proteins in the nucleus. Finally, downregulation of hvrk3 using siRNA reduced the amplitude and lengthened the period of the cellular bioluminescence rhythm. Taken together, these data suggest that VRK3 plays a role in setting the amplitude and period length of circadian rhythms in mammalian cells.

Adding depletants to a colloidal suspension induces an attractive interparticle interaction that can be tuned to obtain desired structures or to probe phase behavior. When the depletant is not uniform in size, however, both the range and strength of the attraction become difficult to predict and hence control. We investigated the effects of depletant bidispersity on the non-equilibrium phase behavior of colloid–polymer mixtures. We added unary or binary mixtures of polystyrene as the depletant to suspensions of charged poly(methyl methacrylate) particles. The structure and dynamics of the particles were compared over three sets of samples with various mixtures of two different polystyrenes whose size varied by an order of magnitude. The structure and dynamics were nearly independent of depletant dispersity if the polymer concentration was represented as a sum of normalized concentrations of each species. Near the transition region between a fluid of clusters and an interconnected gel at intermediate volume fractions, partitioning of polymers in a binary mixture into colloid-rich and polymer-rich phase leads to a slightly different gelation pathway.

The purpose of this study was to identify the characteristic magnetic resonance imaging (MRI) findings in neuropsychiatric systemic lupus erythematosus (NPSLE) and to investigate the association between MRI findings and neuropsychiatric manifestations in SLE. Brain MRIs with a diagnosis of SLE from 2002 to 2013 from three tertiary university hospitals were screened. All clinical manifestations evaluated by brain MRI were retrospectively reviewed. If the clinical manifestations were compatible with the 1999 NPSLE American College of Rheumatology (ACR) nomenclature and case definitions, the brain MRIs were assessed for the presence of white matter hyperintensities, gray matter hyperintensities, parenchymal defects, atrophy, enhancement, and abnormalities in diffusion-weighted images (DWI). The number, size, and location of each lesion were evaluated. The neuropsychiatric manifestation of each brain MRI was classified according to the 1999 ACR NPSLE case definitions. The associations between MRI findings and NPSLE manifestations were examined. In total, 219 brain MRIs with a diagnosis of SLE were screened, and 133 brain MRIs met the inclusion criteria for NPSLE. The most common MRI abnormality was white matter hyperintensities, which were observed in 76 MRIs (57.1 %). Gray matter hyperintensities were observed in 41 MRIs (30.8 %). Parenchymal defects were found in 31 MRIs (23.3 %), and atrophy was detected in 20 MRIs (15.0 %). Patients who had seizures were more associated with gray matter hyperintensities than patients with other neuropsychiatric manifestations. Patients with cerebrovascular disease were more associated with gray matter hyperintensity, parenchymal defects, and abnormal DWI than patients with other neuropsychiatric manifestations. In addition to white matter hyperintensities, which were previously known as SLE findings, we also noted the presence of gray matter hyperintensities, parenchymal defects, and abnormal DWI in a substantial portion of SLE patients, particularly in those with cerebrovascular disease or seizures.

We report here a mitochondria-targetable pH-sensitive probe that allows for a quantitative measurement of mitochondrial pH changes, as well as the real-time monitoring of pH-related physiological effects in live cells. This system consists of a piperazine-linked naphthalimide as a fluorescence off–on signaling unit, a cationic triphenylphosphonium group for mitochondrial targeting, and a reactive benzyl chloride subunit for mitochondrial fixation. It operates well in a mitochondrial environment within whole cells and displays a desirable off–on fluorescence response to mitochondrial acidification. Moreover, this probe allows for the monitoring of impaired mitochondria undergoing mitophagic elimination as the result of nutrient starvation. It thus allows for the monitoring of the organelle-specific dynamics associated with the conversion between physiological and pathological states.

Thioredoxin (Trx) is a redox-active protein that plays a key role in mitigating the effects of oxidative stress. The secretion of Trx on the plasma membrane has been suggested as a distinctive feature of inflammation. However, selective monitoring of membrane-associated Trx activity has proved challenging because of the ubiquity of Trx action in cells. Here, we report a Trx-specific probe that allows visualization of Trx activity associated with the membranes via fluorescence microscopy. The ability of this probe to act as a possible screening tool for agents that modulate Trx secretion was demonstrated in HeLa cells under oxidative stress conditions and in a cellular hepatosteatosis model. Control experiments serve to confirm that the response seen for the present probe is due to Trx and that it is selective over various potentially competing metabolites, including thiol-containing small molecules and test proteins.

The adsorption characteristics of the pellet-type adsorbent prepared from water treatment sludge for trimethylamine and ammo- nia were studied. The surface area and pore volume of the pellet-type adsorbent increased during calcination at 500 ℃. It was confirmed that the adsorbent prepared from water treatment sludge contained Bronsted and Lewis acid sites. The break- through time of the adsorbent for both trimethylamine and ammonia was measured at different adsorbent weights and linear velocities while maintaining constant amounts of trimethylamine and ammonia. The kinetic saturation capacity and the adsorp- tion rate constant for trimethylamine and ammonia were determined at different linear velocities by using the Wheeler equation. It was found that the kinetic saturation capacity and the adsorption rate constant were dependent on the linear velocity. An experimental equation could be derived to predict the breakthrough time of the adsorbent prepared from water treatment sludge for trimethylamine and ammonia at different adsorption conditions.

We optimized the preparation method of pellet-type adsorbents based on alum sludge with the aim of de- veloping a high-performance material for the adsorption of gaseous trimethylamine. Effects of calcination tempera- ture on physical and chemical properties of pellet-type adsorbents were investigated. The porous structure and surface characteristics of the adsorbents were studied using N2 adsorption and desorption isotherms, scanning electron micro- scope, X-ray diffraction, temperature-programmed desorption of ammonia, and infrared spectroscopy of adsorbed pyr- idine. The adsorbents obtained from the water treatment sludge are microporous materials with well-developed mesopo- rosity. The pellet-type adsorbent calcined at 500 o C had the highest percentage of micropore volume and the smallest average pore diameter. The highest adsorption capacity in trimethylamine removal attained over the pellet-type adsorbent calcined at 500 o C can be attributed to the highest number of acid sites as well as the well-developed microporosity.

Two novel Cu(2+) sensors, 1 and 2, bearing naphthalimide and a DPA moiety were synthesized to study copper accumulation in organelles by selective Cu(2+) sensing. The ER-selective Cu(2+) sensor 1 that we developed serves as a valuable tool for understanding the subcellular compartmentalization and roles of copper ions in physiology and pathophysiology.

A series of heptamethine cyanine (1-3) derivatives bearing a carbamate ethyl disulfide group and gemcitabine, an anticancer drug, have been newly synthesized. Their disulfide bonds are readily cleaved by various thiols including glutathione, to result in a subsequent decomposition of the carbamate into amine followed by release of the active gemcitabine, which can be monitored by the fluorescence changes. In the biological experiment, prodrug 1 is preferentially up-taken by folate-positive KB cells over folate-negative A549 cells via receptor-mediated endocytosis to release gemcitabine causing cell death and to emit fluorescence in endoplasmic reticulum. Moreover, it is selectively accumulated in the KB cells which were treated to mice by dorsal subcutaneous injection. This drug delivery system is a new theranostic agent, wherein both therapeutic effect and drug uptake can be easily monitored at the subcellular level, by in vivo and in vitro fluorescence imaging.

The objective of this study is optimization of extrusion process for preparation of pellet-type adsorbents employed with alum sludge. Effects of water content and methyl cellulose as a binder on the possibility of extrusion and physical properties of pellet-type adsorbents were investigated. The physical characteristics of the pellet-type adsorbents were studied using nitrogen adsorption and compression strength. With a ratio of water to sludge, 63/100, the adsorbent was well extruded with a cylindrical form and the compressive strength was the highest. With increasing methyl cellulose content, the compressive strength of pellet-type adsorbent could be improved, but the specific surface area decreased. The breakthrough time of the hydrogen sulfide could be increased significantly through calcination and the breakthrough capacity reached to 1,700 mg/g, which seems to be due to increase of surface area during calcination.

A self-calibrating bipartite viscosity sensor 1 for cellular mitochondria, composed of coumarin and boron-dipyrromethene (BODIPY) with a rigid phenyl spacer and a mitochondria-targeting unit, was synthesized. The sensor showed a direct linear relationship between the fluorescence intensity ratio of BODIPY to coumarin or the fluorescence lifetime ratio and the media viscosity, which allowed us to determine the average mitochondrial viscosity in living HeLa cells as ca. 62 cP (cp). Upon treatment with an ionophore, monensin, or nystatin, the mitochondrial viscosity was observed to increase to ca. 110 cP.

The nucleation and growth of Co clusters on vacuum-annealed (reduced) and oxidized TiO2(110) have been studied by scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and de...

Data exist in various persistent-storage formats, and Hadoop distributed file system (HDFS) has been recognized to be effective for distributed storage and processing. Recently, the research of Hybrid NAND flash-based solid state drives (SSD) is rapidly expanding into the storage areas including Hybrid ReRAM/MLC NAND SSD. Most existing researches of Hybrid SSD are based on a single storage, while the management of multiple nodes like HDFS is still immature. In this paper a new efficient cold data eviction scheme is proposed which is based on the state of node congestion of Hybrid SSD for HDFS. It computer simulation reveals that the proposed scheme significantly reduces average recovery and execution time in comparison to the existing replication schemes.