Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide

We used N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamide as an exogenous agent to modulate the formation of DNA assemblies at specific double-stranded sequences. The concept was demonstrated on the hybridization chain reaction that forms linear DNA. Through a series of melting curve analyses, we demonstrated that the binding of Py−Im polyamide positively influenced both the HCR initiation and elongation steps. In particular, Py−Im polyamide was found to drastically stabilize the DNA duplex such that its thermal stability approached that of an equivalent hairpin structure. Also, the polyamide served as an anchor between hairpin pairs in the HCR assembly, thus improving the originally weak interstrand stability. We hope that these proof-of-concept results can inspire future use of Py−Im polyamide as a molecular tool to modulate the formation of DNA assemblies.     

Principled analytic classifier for positive-unlabeled learning via weighted integral probability metric

Machine Learning - We consider the problem of learning a binary classifier from only positive and unlabeled observations (called PU learning). Recent studies in PU learning have shown superior...     

Systematic packaging design tools integrating functional and environmental consequences on product life cycle: Case studies on laundry detergent and milk

This study presents systematic packaging design tools integrating functional and environmental consequences on product life cycle. To design packaging for sustainability, the trade-offs between functional and environmental aspects of packaging throughout the product life cycle should be considered. However, it is difficult for packaging designers to understand the overall trade-offs because the extent of the design consequences on the entire life cycle of packaging and its contents is unclear. We developed two tools for packaging design: the Life Cycle Association Matrix (LCAM) and the Function Network Diagram (FND). The following three steps, based on literature reviews and interviews with industrial experts, were applied. Firstly, we listed the product functions and design variables related to the functions as the attributes allocated to the product life cycle. Secondly, the attributes were connected appropriately based on causal relationships. Lastly, we identified the factors to support decision making in the packaging design procedure. As a result, the LCAM depicts the design consequences on the life cycle, and the FND determines the stakeholders affected by the design consequences. Two case studies were demonstrated to analyze the trade-offs by using our tools. In the case studies, a liquid laundry detergent bottle and a milk carton were redesigned. The tools identified the design consequences and stakeholders affected by the redesign of the usability and protective function for the detergent and milk cases, respectively. The results showed the significance of understanding the design consequences on the product life cycle by integrating the functional and environmental aspects.     

Short communication: Temporal changes in the skin morphology of dairy cows during the periparturient period

Management of dairy cow productivity requires monitoring of their nutritional status by visual observation. It has been suggested that changes in hair coat appearance are among the indicators of nutritional state in dairy cows. Temporal changes in the skin morphology in cows, however, have not been reported. In this study, we examined the changes in the skin of dairy cows that occur during the peripartum period. Seven pluriparous cows were used. Skin samples were collected at 28 d before the due date and 28 d and 56 d after calving for morphological examination. Hair follicle width was 108.8 ± 5.9 µm (±SD) in the dry period, 95.5 ± 5.5 µm at 28 d after calving, and 104.2 ± 5.3 µm at 56 d postpartum. The percentages of anagen hair follicles during these 3 periods were 41.4 ± 3.4, 18.5 ± 3.4, and 32.3 ± 3.3%, respectively. The corresponding sebaceous gland sizes were 8,362.0 ± 707.6, 7,800.0 ± 831.4, and 9,186.8 ± 962.6 µm², respectively. Hair follicle width was positively correlated with percentage of anagen hair follicles. The thickness of epidermal and proliferation rate of epidermal cell were also correlated. However, the hair follicle width, sebaceous gland size and cell proliferation rate, and thickness and proliferation rate of epidermal cells did not show any marked changes.     

Quantitative Elemental Analysis of a Single Cell by Using Inductively Coupled Plasma-Mass Spectrometry in Fast Time-Resolved Analysis Mode

The elemental composition of a single yeast, green alga, or red blood cell (RBC) was precisely determined by using inductively coupled plasma-mass spectrometry (ICP-MS) operating in fast time-resolved analysis (TRA) mode. The technique is known as single-cell (SC)-ICP-MS. Phosphorus, sulfur, magnesium, zinc, and iron were detected in the three types of cell. The elemental composition of yeast and green alga obtained by SC-ICP-MS was consistent with results obtained from conventional ICP-MS measurements following acid digestion of the cells. Slight differences were found in the measured values between SC-ICP-MS and the conventional ICP-MS results for RBC. However, the SC-ICP-MS results for S and Fe in RBC were closer to the estimated values for these elements that were calculated from the level of hemoglobin in RBCs. The data suggest that SC-ICP-MS is suitable for the analysis of various cell types, namely, fungus, plant, and animal cells.     

Evaluation of the Anti-Proliferative Activity of Rare Aldohexoses against MOLT-4F and DU-145 Human Cancer Cell Line and Structure-Activity Relationship of D-Idose

D-Allose (D-All), a C-3 epimer of D-glucose (D-Glc), is a naturally rare monosaccharide, which shows anti-proliferative activity against several human cancer cell lines. Unlike conventional anticancer drugs, D-All targets glucose metabolism and is non-toxic to normal cells. Therefore, it has attracted attention as a unique “seed” compound for anticancer agents. However, the anti-proliferative activities of the other rare aldohexoses have not been examined yet. In this study, we evaluated the anti-proliferative activity of rare aldohexoses against human leukemia MOLT-4F and human prostate cancer DU-145 cell lines. We found that D-All and D-idose (D-Ido) at 5 mM inhibited cell proliferation of MOLT-4F cells by 46 % and 60 %, respectively. On the other hand, the rare aldohexoses at 5 mM did not show specific anti-proliferative activity against DU-145 cells. To explore the structure–activity relationship of D-Ido, we evaluated the anti-proliferative activity of D-sorbose (D-Sor), 6-deoxy-D-Ido, and L-xylose (L-Xyl) against MOLT-4F cells and found that D-Sor, 6-deoxy-D-Ido, and L-Xyl showed no inhibitory activity at 5 mM, suggesting that the aldose structure and the C-6 hydroxy group of D-Ido are important for its activity. Cellular glucose uptake assay and western blotting analysis of thioredoxin-interacting protein (TXNIP) expression suggested that the anti-proliferative activity of D-Ido is induced by inhibition of glucose uptake via TXNIP-independent pathway.     

One Pot Cooking of Rice Grains for Preparation of Rice-Gel Samples Using a Small-Scale Viscosity Analyzer: Small-scale Rice-gel Preparation from Grains

Rice-gel prepared by the following three steps: rice grain cooking, shearing of the cooked rice, and cooling for gel formation, is expected as a novel food ingredient for modification of various food products such as bread and noodles. To meet the demand for high-throughput systems for research and developments on the new rice gels, herein we established a mini-cooking system for preparation of rice gel samples from grains using a small-scale viscosity analyzer (Rapid Visco Analyzer; RVA). Polished rice grains (4 g) were cooked with 22 mL of water in a canister, and the paddle equipped in the canister was rotated at 2,000 rpm for 30 min (80 °C was used as a representative) to shear the cooked rice. The sheared paste was cooled to 10 °C at 160 rpm, and the initial gelation property was evaluated by viscosity analysis within the RVA. Alternatively, the sheared paste was transferred to an acrylic mold and kept at 4 °C for 0, 1, 3, and 5 days for determination of the hardness with a compression test. Compressive forces required to penetrate 20 % thickness for three tested rice cultivars were measured, and the trend of the value shifts during preservation is similar to the corresponding trend obtained in 300-g grain scale laboratory tests, whereas the individual values were halved in the former. This small cooking method could offer a useful assay system for a rapid evaluation in the breeding programs and in the high-throughput screening of additives for the modification of properties.