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.

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.

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.

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.

[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.

Breath odor-based individual authentication by an artificial olfactory sensor system and machine learning.

Breath odor sensing-based individual authentication was conducted for the first time using an artificial olfactory sensor system. Using a 16-channel chemiresistive sensor array and machine learning, a mean accuracy of >97% was successfully achieved. The impact of the number of sensors on the accuracy and reproducibility was also demonstrated.

Correction: Breath odor-based individual authentication by an artificial olfactory sensor system and machine learning.

Correction for 'Breath odor-based individual authentication by an artificial olfactory sensor system and machine learning' by Chaiyanut Jirayupat et al., Chem. Commun., 2022, DOI: https://doi.org/10.1039/D1CC06384G.

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.

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.

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.

Water-Selective Nanostructured Dehumidifiers for Molecular Sensing Spaces.

Humidity and moisture effects, frequently called water poisoning, in surroundings are inevitable for various molecular sensing devices, strongly affecting their sensing characteristics. Here, we demonstrate a water-selective nanostructured dehumidifier composed of ZnO/TiO2/CaCl2 core-shell heterostructured nanowires for molecular sensing spaces. The fabricated nanostructured dehumidifier is highly water-selective without detrimental adsorptions of various volatile organic compound molecules and can be repeatedly operated. The thermally controllable and reversible dehydration process of CaCl2·nH2O thin nanolayers on hydrophilic ZnO/TiO2 nanowire surfaces plays a vital role in such water-selective and repeatable dehumidifying operations. Furthermore, the limitation of detection for sensing acetone and nonanal molecules in the presence of moisture (relative humidity ∼ 90%) was improved more than 20 times using nanocomposite sensors by operating the developed nanostructured dehumidifier. Thus, the proposed water-selective nanostructured dehumidifier offers a rational strategy and platform to overcome water poisoning issues for various molecular and gas sensors.

Impact of Lateral SnO2 Nanofilm Channel Geometry on a 1024 Crossbar Chemical Sensor Array.

We propose a rational strategy to fabricate thermally robust, highly integrated molecular and gas sensors utilizing a lateral SnO2 nanofilm channel geometry on a 1024 crossbar sensor array. The proposed lateral channel geometry substantially suppresses the detrimental effects of parasitic interconnect wire resistances compared with those of a conventional vertical sandwich-type crossbar array because of its excellent resistance controllability. A conductive oxide top-contact electrode on the lateral SnO2 nanofilm channel enhances the thermal stability at temperatures of up to 500 °C in ambient air. Integrating this lateral SnO2 nanofilm geometry with analog circuits enables the operation of a 1024 crossbar sensor array without selector devices to avoid sneak currents. The developed 1024 crossbar sensor array system detects the local spatial distribution of the molecular gas concentration. The spatial data of molecular concentrations include molecule-specific data to distinguish various volatile molecules based on their vapor pressures. Thus, this integrated crossbar sensor array system using lateral nanofilm geometry offers a platform for robust, reliable, highly integrated molecular and gas sensors.

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.

Mechanistic Approach for Long-Term Stability of a Polyethylene Glycol-Carbon Black Nanocomposite Sensor.

Polymer-carbon nanocomposite sensor is a promising molecular sensing device for electronic nose (e-nose) due to its printability, variety of polymer materials, and low operation temperature; however, the lack of stability in an air environment has been an inevitable issue. Here, we demonstrate a design concept for realizing long-term stability in a polyethylene glycol (PEG)-carbon black (CB) nanocomposite sensor by understanding the underlying phenomena that cause sensor degradation. Comparison of the sensing properties and infrared spectroscopy on the same device revealed that the oxidation-induced consumption of PEG is a crucial factor for the sensor degradation. According to the mechanism, we introduced an antioxidizing agent (i.e., ascorbic acid) into the PEG-CB nanocomposite sensor to suppress the PEG oxidation and successfully demonstrated the long-term stability of sensing properties under an air environment for 30 days, which had been difficult in conventional polymer-carbon nanocomposite sensors.

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.

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.

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.

Subchronic safety evaluation of hot-water extract from thinned immature mangos (Mangifera indica 'Irwin'): 90-days oral toxicity study in rats.

Thinned immature fruit of the mango tree (Mangifera indica 'Irwin') are handled as waste. In this study, we conducted a 90-days toxicity study in male and female Sprague Dawley rats to evaluate the safety of a hot-water extract of thinned immature mango fruits (TIMEx) administered by oral gavage at doses of 500, 1000 and 2500 mg/kg body weight/day. Treatment did not result in death or changes in the behavior or external appearance of the animals. No alterations were observed in hematological or serum chemical parameters, urinalysis, food consumption, body weight gain or organ weights at the end of the treatment period, with the exception of higher mean corpuscular volume in male rats that received high doses and lower serum creatine phosphokinase levels in female rats that received medium doses. Under the conditions of this study and based on the toxicological endpoints evaluated, the no-observed-adverse-effect level (NOAEL) for TIMEx was 2500 mg/kg/day. The findings indicate that TIMEx is safe for consumption and should be investigated as a candidate food.