Artificial induction of chromosome aneuploidy in CHO cells alters their function as host cells.

Chinese hamster ovary (CHO) cells are major host cells for biopharmaceuticals. During culture, the chromosome number of CHO cells alters spontaneously. Here, we investigated the effects of artificial changes in the chromosome number on productivity. When cell fusion between antibody-producing CHO-K1-derived cells was induced, we observed a wide range of aneuploidy that was not detected in controls. In particular, antibody productivities were high in clone-derived cell populations that retained a diverse chromosome number distribution. We also induced aneuploid cells using 3-aminobenzamide that causes chromosome non-disjunction. After induction of aneuploidy by 3-aminobenzamide, cells with an increased chromosome number were isolated, but cells with a decreased chromosome number could not be isolated. When antibody expression vectors were introduced into these isolated clones, productivity tended to increase in cells with an increased chromosome number. Further analysis was carried out by focusing on clone 5E8 with an average chromosome number of 37. When 5E8 cells were used as host, the productivity of multiple antibodies, including difficult-to-express antibodies, was improved compared with CHO-K1 cells. The copies of exogenous genes integrated into the genome were significantly increased in 5E8 cells. These findings expand the possibilities for host cell selection and contribute to the efficient construction of cell lines for recombinant protein production.

Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies.

Self-assembly is promising for construction of a wide variety of supramolecular assemblies, whose 1D/2D/3D structures are typically relevant to their functions. In-depth understanding of their structure-function relationships is essential for rational design and development of functional molecular assemblies. Microscopic imaging has been used as a powerful tool to elucidate structures of individual molecular assemblies with subnanometer to millimeter resolution, which is complementary to conventional spectroscopic techniques that provide the ensemble structural information. In this review, we highlight the representative examples of visualization of molecular assemblies by use of electron microscopy, atomic force microscopy, confocal microscopy, and super-resolution microscopy. This review comprehensively describes imaging of supramolecular nanofibers/gels, micelles/vesicles, coacervate droplets, polymer assemblies, and protein/DNA assemblies. Advanced imaging techniques that can address key challenges, like evaluation of dynamics of molecular assemblies, multicomponent self-assembly, and self-assembly/disassembly in complex cellular milieu, are also discussed. We believe this review would provide guidelines for deeper structural analyses of molecular assemblies to develop the next-generation materials.

Edge-Topological Regulation for in Situ Fabrication of Bridging Nanosensors.

In situ fabrication of well-defined bridging nanostructures is an interesting and unique approach to three-dimensionally design nanosensor structures, which are hardly attainable by other methods. Here, we demonstrate the significant effect of edge-topological regulation on in situ fabrication of ZnO bridging nanosensors. When employing seed layers with a sharp edge, which is a well-defined structure in conventional lithography, the bridging angles and electrical resistances between two opposing electrodes were randomly distributed. The stochastic nature of bridging growth direction at the sharp edges inherently causes such unintentional variation of structural and electrical properties. We propose an edgeless seed layer structure using a two-layers resist method to solve the above uncontrollability of bridging nanosensors. Such bridging nanosensors not only substantially improved the uniformity of structural and electrical properties between two opposing electrodes but also significantly enhanced the sensing responses for NO2 with the smaller variance and the lower limit of detection via in situ controlled electrical contacts.

Selective Consumption of Fish Oil at End of the Day Increases the Physiological Fatty Acid Compositions of Eicosapentaenoic Acid and Docosahexaenoic Acid in Mice.

Diets with high daily fat consumption are associated with excess weight. However, the effects of fat type and consumption timing on excess weight remain unclear. We investigated the selection of a 30% (w/w) fat diet of soybean oil (SOY), lard (LARD), and fish oil (FISH) on the metabolic parameters of mice. Male C57BL/6 mice were divided into the double SOY-box (w-SOY), SOY-box/LARD-box (SOY-vs-LARD), or SOY-box/FISH-box (SOY-vs-FISH) groups and allowed to selectively consume for 8 weeks. The total energy intake was similar for all groups, but the mice selectively chose to consume LARD over SOY and SOY over FISH. Body weight in the SOY-vs-LARD group was significantly higher than that in the w-SOY and SOY-vs-FISH groups. Additionally, minimal but selective consumption of an omega-3 fatty-acid-rich FISH diet at the end of the active period increased the physiological fatty acid compositions of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in the SOY-vs-FISH group; their metabolic parameters were also lower than the SOY-vs-LARD group. In conclusion, selectively consuming small amounts of fish oil at the end of the day may prevent excess weight compared with LARD consumption.

[A Case of Giant Multilocular Prostatic Cystadenoma Resected by Laparoscopic Pelvic Cystectomy : A Case Report].

A 60-year-old man visited our hospital to treat a large cystic mass in the pelvis which had been found by abdominal ultrasonography in December 201X. Computed tomography (CT) and magnetic resonance imaging (MRI) showed a multilocular cyst with a maximum diameter of about 10 cm. CT-guided drainage and sclerotherapy with minocycline reduced the size of tumor by 40%, but symptoms such as difficulty of defecation and urinary frequency appeared a year and a half later due to re-enlargement of the cysts. Laparoscopic resection of the multilocular cysts was performed, and all cysts were removed almost completely using transrectal ultrasonography. The multilocular cyst was positive for NKX3.1 by immunohistochemical staining, and was diagnosed as a giant multilocular prostatic cystadenoma. After surgery, the symptoms such as difficulty of defecation and urinary frequency were relieved promptly. One year after the surgery, the patient was free from recurrence of the disease.

Phototriggered Spatially Controlled Out-of-Equilibrium Patterns of Peptide Nanofibers in a Self-Sorting Double Network Hydrogel.

Out-of-equilibrium patterns arising from diffusion processes are ubiquitous in nature, although they have not been fully exploited for the design of artificial materials. Here, we describe the formation of phototriggered out-of-equilibrium patterns using photoresponsive peptide-based nanofibers in a self-sorting double network hydrogel. Light irradiation using a photomask followed by thermal incubation induced the spatially controlled condensation of peptide nanofibers. According to confocal images and spectroscopic analyses, metastable nanofibers photodecomposed in the irradiated areas, where thermodynamically stable nanofibers reconstituted and condensed with a supply of monomers from the nonirradiated areas. These supramolecular events were regulated by light and diffusion to facilitate the creation of unique out-of-equilibrium patterns, including two lines from a one-line photomask and a line pattern of a protein immobilized in the hydrogel.

Image Processing and Machine Learning for Automated Identification of Chemo-/Biomarkers in Chromatography-Mass Spectrometry.

We present a method named NPFimg, which automatically identifies multivariate chemo-/biomarker features of analytes in chromatography-mass spectrometry (MS) data by combining image processing and machine learning. NPFimg processes a two-dimensional MS map (m/z vs retention time) to discriminate analytes and identify and visualize the marker features. Our approach allows us to comprehensively characterize the signals in MS data without the conventional peak picking process, which suffers from false peak detections. The feasibility of marker identification is successfully demonstrated in case studies of aroma odor and human breath on gas chromatography-mass spectrometry (GC-MS) even at the parts per billion level. Comparison with the widely used XCMS shows the excellent reliability of NPFimg, in that it has lower error rates of signal acquisition and marker identification. In addition, we show the potential applicability of NPFimg to the untargeted metabolomics of human breath. While this study shows the limited applications, NPFimg is potentially applicable to data processing in diverse metabolomics/chemometrics using GC-MS and liquid chromatography-MS. NPFimg is available as open source on GitHub (http://github.com/poomcj/NPFimg) under the MIT license.

Nanowire-based sensor electronics for chemical and biological applications.

Detection and recognition of chemical and biological species via sensor electronics are important not only for various sensing applications but also for fundamental scientific understanding. In the past two decades, sensor devices using one-dimensional (1D) nanowires have emerged as promising and powerful platforms for electrical detection of chemical species and biologically relevant molecules due to their superior sensing performance, long-term stability, and ultra-low power consumption. This paper presents a comprehensive overview of the recent progress and achievements in 1D nanowire synthesis, working principles of nanowire-based sensors, and the applications of nanowire-based sensor electronics in chemical and biological analytes detection and recognition. In addition, some critical issues that hinder the practical applications of 1D nanowire-based sensor electronics, including device reproducibility and selectivity, stability, and power consumption, will be highlighted. Finally, challenges, perspectives, and opportunities for developing advanced and innovative nanowire-based sensor electronics in chemical and biological applications are featured.

Post-assembly Fabrication of a Functional Multicomponent Supramolecular Hydrogel Based on a Self-Sorting Double Network.

Living cells exhibit sophisticated functions because they contain numerous endogenous stimuli-responsive molecular systems that independently and cooperatively act in response to an external circumstance. On the other hand, artificial soft materials containing multiple stimuli-responsive molecular systems are still rare. Herein, we demonstrate a unique multicomponent hydrogel composed of a self-sorting double network prepared through a post-assembly fabrication (PAF) protocol. The PAF protocol allowed the construction of a well-ordered hydrogel with a dual-biomolecule response to two important biomolecules (adenosine triphosphate (ATP) and sarcosine). Such a hydrogel could not be prepared through a one-step mixing protocol. The resultant multicomponent hydrogel responded to ATP and sarcosine through gel-sol transition behavior programmed in an AND logic gate fashion. Finally, we applied the multicomponent hydrogel to the controlled release of an antibody.

Imaging-Based Study on Control Factors over Self-Sorting of Supramolecular Nanofibers Formed from Peptide- and Lipid-type Hydrogelators.

Multicomponent self-assembly is a fascinating strategy for the construction of smart soft materials. Among them, supramolecular hydrogels comprising self-sorting nanofibers have recently attracted significant attention owing to their rationally incorporated stimulus responsiveness. However, there have been limited investigations of the crucial factors that control the self-sorting phenomena. Here, we describe an imaging-based approach to evaluate the factors that control the formation of self-sorting nanofibers from peptide- and lipid-type hydrogelators. We screened a small library of hydrogelators with distinct chemical properties by direct visualization of their self-assembly behavior by using confocal laser scanning microscopy. Our systematic research identified two important factors that influence the self-sorting behavior of nanofibers: (i) the surface charge of the hydrogelators; and (ii) the hydrophobicity of the side chain on the peptide-type hydrogelators. We determined that the same net/surface charge on the hydrogelators and side chains with a lower hydrophobicity on the peptide-type hydrogelators were preferred. These findings, in combination with the previously reported kinetic factors, were used to design and successfully prepare a three-component orthogonal self-assembly composed of supramolecular nanofibers from peptide- and lipid-type hydrogelators and a cationic organorhodium complex. Our findings would be beneficial for the design of intelligent soft materials based on self-sorting phenomena.

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.

Compound identification from accurate mass MS/MS spectra is a bottleneck for untargeted metabolomics. In this study, we propose nine rules of hydrogen rearrangement (HR) during bond cleavages in low-energy collision-induced dissociation (CID). These rules are based on the classic even-electron rule and cover heteroatoms and multistage fragmentation. We evaluated our HR rules by the statistics of MassBank MS/MS spectra in addition to enthalpy calculations, yielding three levels of computational MS/MS annotation: "resolved" (regular HR behavior following HR rules), "semiresolved" (irregular HR behavior), and "formula-assigned" (lacking structure assignment). With this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in the MassBank database and 84.8% of a total of 36370 MS/MS fragment ions in the GNPS database were (semi-) resolved by predicted bond cleavages. We also introduce the MS-FINDER software for structure elucidation. Molecular formulas of precursor ions are determined from accurate mass, isotope ratio, and product ion information. All isomer structures of the predicted formula are retrieved from metabolome databases, and MS/MS fragmentations are predicted in silico. The structures are ranked by a combined weighting score considering bond dissociation energies, mass accuracies, fragment linkages, and, most importantly, nine HR rules. The program was validated by its ability to correctly calculate molecular formulas with 98.0% accuracy for 5063 MassBank MS/MS records and to yield the correct structural isomer with 82.1% accuracy within the top-3 candidates. In a test with 936 manually identified spectra from an untargeted HILIC-QTOF MS data set of human plasma, formulas were correctly predicted in 90.4% of the cases, and the correct isomer structure was retrieved at 80.4% probability within the top-3 candidates, including for compounds that were absent in mass spectral libraries. The MS-FINDER software is freely available at http://prime.psc.riken.jp/ .

A QM/MM study of the L-threonine formation reaction of threonine synthase: implications into the mechanism of the reaction specificity.

Threonine synthase catalyzes the most complex reaction among the pyridoxal-5'-phosphate (PLP)-dependent enzymes. The important step is the addition of a water molecule to the Cß-Cα double bond of the PLP-α-aminocrotonate aldimine intermediate. Transaldimination of this intermediate with Lys61 as a side reaction to form α-ketobutyrate competes with the normal addition reaction. We previously found that the phosphate ion released from the O-phospho-l-homoserine substrate plays a critical role in specifically promoting the normal reaction. In order to elucidate the detailed mechanism of this "product-assisted catalysis", we performed comparative QM/MM calculations with an exhaustive search for the lowest-energy-barrier reaction pathways starting from PLP-α-aminocrotonate aldimine intermediate. Satisfactory agreements with the experiment were obtained for the free energy profile and the UV/vis spectra when the PLP pyridine N1 was unprotonated and the phosphate ion was monoprotonated. Contrary to an earlier proposal, the base that abstracts a proton from the attacking water was the ε-amino group of Lys61 rather than the phosphate ion. Nevertheless, the phosphate ion is important for stabilizing the transition state of the normal transaldimination to form l-threonine by making a hydrogen bond with the hydroxy group of the l-threonine moiety. The absence of this interaction may account for the higher energy barrier of the side reaction, and explains the mechanism of the reaction specificity afforded by the phosphate ion product. Additionally, a new mechanism, in which a proton temporarily resides at the phenolate O3' of PLP, was proposed for the transaldimination process, a prerequisite step for the catalysis of all the PLP enzymes.

Daily Consumption of α-Linolenic Acid Increases Conversion Efficiency to Eicosapentaenoic Acid in Mice.

To maintain a beneficial concentration of eicosapentaenoic acid (EPA), the efficient conversion of its precursor, α-linolenic acid (α-LA), is important. Here, we studied the conversion of α-LA to EPA using ICR and C57BL/6 mice. A single dose of perilla oil rich-in α-LA or free α-LA had not been converted to EPA 18 h following administration. The α-LA was absorbed into the circulation, and its concentration peaked 6 h after administration, after which it rapidly decreased. In contrast, EPA administration was followed by an increase in circulating EPA concentration, but this did not decrease between 6 and 18 h, indicating that the clearance of EPA is slower than that of α-LA. After ≥1 week perilla oil intake, the circulating EPA concentration was >20 times higher than that of the control group which consumed olive oil, indicating that daily consumption, but not a single dose, of α-LA-rich oil might help preserve the physiologic EPA concentration. The consumption of high concentrations of perilla oil for 4 weeks also increased the hepatic expression of Elovl5, which is involved in fatty acid elongation; however, further studies are needed to characterize the relationship between the expression of this gene and the conversion of α-LA to EPA.

Social confrontation stress decreases hepatic fibroblast growth factor-21 expression in aged mice.

We previously showed that social stress exposure in mature adult mice increased blood corticosterone concentrations at 2 days, disrupted hepatic lipid metabolism-related pathway at 30 days, and increased the risk of overweight with hepatic hypertrophy at 90 days. To further investigate the effects of aging on the physiological responses to social stress, we conducted a study using male BALB/c mice at the ages of 2 months (mature age), 14 months (middle age) and 26 months (old age), and exposed them to confrontation stress for 2 or 7 days. Blood corticosterone concentrations were increased at 2 days of stress, and then returned to baseline concentrations. This change was observed only at 2 months of age. We further examined the effect of aging on hepatic gene expression of fibroblast growth factor-21 (Fgf21) and found that its expression was significantly decreased after 7 days of stress at 14 months of age and after 2 days of stress at 26 months of age, indicating these decreasing effects became more pronounced with age. In conclusion, our study suggests that hepatic Fgf21 expression decrease under exposure to confrontation stress at middle or more age, indicating that stress response on Fgf21 related pathway might be more pronounced with age when exposed to stress.

Interfacial Molecular Compatibility for Programming Organic-Metal Oxide Superlattices.

Artificially programming a sequence of organic-metal oxide multilayers (superlattices) by using atomic layer deposition (ALD) is a fascinating and challenging issue in material chemistry. However, the complex chemical reactions between ALD precursors and organic layer surfaces have limited their applications for various material combinations. Here, we demonstrate the impact of interfacial molecular compatibility on the formation of organic-metal oxide superlattices using ALD. The effects of both organic and inorganic compositions on the metal oxide layer formation processes onto self-assembled monolayers (SAM) were examined by using scanning transmission electron microscopy, in situ quartz crystal microbalance measurements, and Fourier-transformed infrared spectroscopy. These series of experiments reveal that the terminal group of organic SAM molecules must satisfy two conflicting requirements, the first of which is to promptly react with ALD precursors and the second is not to bind strongly to the bottom metal oxide layers to avoid undesired SAM conformations. OH-terminated phosphate aliphatic molecules, which we have synthesized, were identified as one of the best candidates for such a purpose. Molecular compatibility between metal oxide precursors and the -OHs must be properly considered to form superlattices. In addition, it is also important to form densely packed and all-trans-like SAMs to maximize the surface density of reactive -OHs on the SAMs. Based on these design strategies for organic-metal oxide superlattices, we have successfully fabricated various superlattices composed of metal oxides (Al-, Hf-, Mg-, Sn-, Ti-, and Zr oxides) and their multilayered structures.

Strain-level detection of Fusobacterium nucleatum in colorectal cancer specimens by targeting the CRISPR-Cas region.

IMPORTANCE: Fusobacterium nucleatum is one of the predominant oral bacteria in humans. However, this bacterium is enriched in colorectal cancer (CRC) tissues and may be involved in CRC development. Our previous research suggested that F. nucleatum is present in CRC tissues originating from the oral cavity using a traditional strain-typing method [arbitrarily primed polymerase chain reaction (AP-PCR)]. First, using whole-genome sequencing, this study confirmed an exemplary similarity between the oral and tumoral strains derived from each patient with CRC. Second, we successfully developed a method to genotype this bacterium at the strain level, targeting the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated system, which is hypervariable (defined as F. nucleatum-strain genotyping PCR). This method can identify F. nucleatum strains in cryopreserved samples and is significantly superior to traditional AP-PCR, which can only be performed on isolates. The new methods have great potential for application in etiological studies of F. nucleatum in CRC.

Rational Strategy for Space-Confined Atomic Layer Deposition.

Atomic layer deposition (ALD) offers excellent controllability of spatial uniformity, film thickness at the Angstrom level, and film composition even for high-aspect-ratio nanostructured surfaces, which are rarely attainable by other conventional deposition methodologies. Although ALD has been successfully applied to various substrates under open-top circumstances, the applicability of ALD to confined spaces has been limited because of the inherent difficulty of supplying precursors into confined spaces. Here, we propose a rational methodology to apply ALD growths to confined spaces (meter-long microtubes with an aspect ratio of up to 10 000). The ALD system, which can generate differential pressures to confined spaces, was newly developed. By using this ALD system, it is possible to deposit TiOx layers onto the inner surface of capillary tubes with a length of 1000 mm and an inner diameter of 100 µm with spatial deposition uniformity. Furthermore, we show the superior thermal and chemical robustness of TiOx-coated capillary microtubes for molecular separations when compared to conventional molecule-coated capillary microtubes. Thus, the present rational strategy of space-confined ALD offers a useful approach to design the chemical and physical properties of the inner surfaces of various confined spaces.

Beneficial Effects of the Consumption of Hot-Water Extracts of Thinned Immature Mangos (Mangifera indica "Irwin") on the Hypertriglyceridemia of Apolipoprotein E-Deficient Mice.

The thinned immature fruit of the mango tree (Mangifera indica "Irwin") are regarded as waste products. In this study, we evaluated the effects of daily consumption of a hot-water extract of thinned immature mango fruits (TIMEx) on the dyslipidemia of apolipoprotein E-deficient (ApoE-/-) mice. ApoE-/- mice and wild-type BALB/c mice were fed a 20% fat diet containing 0%, 0.1%, or 1.0% TIMEx for 8 weeks. Their body mass, food intake, and water consumption were unaffected by the TIMEx. The 1.0% TIMEx supplementation significantly reduced serum triglyceride, but not total cholesterol concentration. This effect was significant in ApoE-/- mice, but less marked under normal conditions in wild-type mice. In addition, the circulating concentrations of three hormones that regulate metabolism, resistin, leptin, and glucose-dependent insulinotropic polypeptide, were reduced by TIMEx consumption, which may be involved in its effect to prevent hypertriglyceridemia. However, none of the concentrations of TIMEx reduced the size of atherosclerotic plaque lesions. In conclusion, daily consumption of TIMEx ameliorates hypertriglyceridemia but not hypercholesterolemia in genetically predisposed mice.

Surface Dissociation Effect on Phosphonic Acid Self-Assembled Monolayer Formation on ZnO Nanowires.

Understanding the formation process of self-assembled monolayers (SAMs) of organophosphonic acids on ZnO surfaces is essential to designing their various applications, including solar cells, heterogeneous catalysts, and molecular sensors. Here, we report the significant effect of surface dissociation on SAM formation of organophosphonic acids on single-crystalline ZnO nanowire surfaces using infrared spectroscopy. When employing the most conventional solvent-methanol (relative permittivity εr = 32.6), the production of undesired byproducts (layered zinc compounds) on the surface was identified by infrared spectral data and microscopy. On the other hand, a well-defined SAM structure with a tridentate coordination of phosphonic acids on the surface was confirmed when employing toluene (εr = 2.379) or tert-butyl alcohol (εr = 11.22-11.50). The observation of layered zinc compounds as byproducts highlights that the degree of Zn2+ dissociation from the ZnO solid surface into a solvent significantly affects the surface coordination of phosphonic acids during the SAM formation process. Although the ZnO nanowire surface (m-plane) is hydrophilic, the present results suggest that a weaker solvent polarity is preferred to form well-defined phosphonic acid SAMs on ZnO nanowire surfaces without detrimental surface byproducts.