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Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements

Watabe M, Arjunan SNV, Chew WX, Kaizu K, Takahashi K

Phys Rev E, 2019 Jul;100(1-1):010402.
PMID: 31499827 DOI: 10.1103/PhysRevE.100.010402

We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring the biological cooperativity of molecular binding networks, in particular, ligand molecules binding to cell-surface receptor proteins. Our results show how the nonstatistical uncertainties lead to invalid identifications of the measured cooperativity. Through this computational scheme, the biological interpretation can be more objectively evaluated and understood under a specific experimental configuration of interest.
High performance photoanodic catalyst prepared from an active organic photovoltaic cell - high potential gain from visible light

Nagai K, Kuwabara T, Ahmad MF, Nakano M, Karakawa M, Taima T, et al.

Chem Commun (Camb), 2019 Oct 15;55(83):12491-12494.
PMID: 31573004 DOI: 10.1039/c9cc04759j

Photoelectrochemical oxidation of thiols was enhanced with a threshold potential of -0.35 V vs. Ag/AgCl by the use of a ZnPc/PCBM:P3HT/ZnO electode, which was prepared by removing the PEDOT:PSS/Au electrode of an inverted OPV device and coating it with ZnPc. A co-photocatalysis property of ZnPc was observed in the photoelectrochemistry and scanning Kelvin probe microscopy.
Fulltext Taxon- and Growth Phase-Specific Antioxidant Production by Chlorophyte, Bacillariophyte, and Haptophyte Strains Isolated From Tropical Waters

Rahman NA, Katayama T, Wahid MEA, Kasan NA, Khatoon H, Yamada Y, et al.

Front Bioeng Biotechnol, 2020;8:581628.
PMID: 33330417 DOI: 10.3389/fbioe.2020.581628

Antioxidants found in microalgae play an essential role in both animals and humans, against various diseases and aging processes by protecting cells from oxidative damage. In this study, 26 indigenous tropical marine microalgae were screened. Out of the 26 screened strains, 10 were selected and were further investigated for their natural antioxidant compounds which include carotenoids, phenolics, and fatty acids collected in their exponential and stationary phases. The antioxidant capacity was also evaluated by a total of four assays, which include ABTS, DPPH, superoxide radical (O2•-) scavenging capacity, and nitric oxide (•NO-) scavenging capacity. This study revealed that the antioxidant capacity of the microalgae varied between divisions, strains, and growth phase and was also related to the content of antioxidant compounds present in the cells. Carotenoids and phenolics were found to be the major contributors to the antioxidant capacity, followed by polyunsaturated fatty acids linoleic acid (LA), eicosapentaenoic acid (EPA), arachidonic acid (ARA), and docosahexaenoic acid (DHA) compared to other fatty acids. The antioxidant capacity of the selected bacillariophytes and haptophytes was found to be positively correlated to phenolic (R2-value = 0.623, 0.714, and 0.786 with ABTS, DPPH, and •NO-) under exponential phase, and to carotenoid fucoxanthin and β-carotene (R2 value = 0.530, 0.581 with ABTS, and 0.710, 0.795 with O2•-) under stationary phase. Meanwhile, antioxidant capacity of chlorophyte strains was positively correlated with lutein, β-carotene and zeaxanthin under the exponential phase (R2 value = 0.615, 0.615, 0.507 with ABTS, and R2 value = 0.794, 0.659, and 0.509 with •NO-). In the stationary phase, chlorophyte strains were positively correlated with violaxanthin (0.755 with •NO-), neoxanthin (0.623 with DPPH, 0.610 with •NO-), and lutein (0.582 with •NO-). This study showed that antioxidant capacity and related antioxidant compound production of tropical microalgae strains are growth phase-dependent. The results can be used to improve the microalgal antioxidant compound production for application in pharmaceutical, nutraceutical, food, and feed industry.
Large-scale distribution and composition of floating plastic debris in the transition region of the North Pacific

Miyazono K, Yamashita R, Miyamoto H, Ishak NHA, Tadokoro K, Shimizu Y, et al.

Mar Pollut Bull, 2021 Sep;170:112631.
PMID: 34175698 DOI: 10.1016/j.marpolbul.2021.112631

Floating plastic debris was investigated in the transition region in the North Pacific between 141°E and 165°W to understand its transportation process from Asian coast to central subtropical Pacific. Distribution was influenced primarily by the current system and the generation process of the high concentration area differed between the western and eastern areas. West of 180°, debris largely accumulated around nearshore convergent area and was transported by eddies and quasi-stationary jet from south to the subarctic region. The average was 15% higher than that previously reported in 1989, suggesting an increase in plastic debris in 30 years. East of 180°, debris concentrated in the calm water downstream of the Kuroshio Extension Bifurcation with considerably high concentration (505,032 ± 991,989 pieces km-2), due to the accumulation of small transparent film caused by calm weather conditions, suggesting a further investigation on small plastic (<1 mm) in the subsurface depth in the subtropical North Pacific.
Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization

Watabe M, Arjunan SNV, Chew WX, Kaizu K, Takahashi K

Phys Rev E, 2019 Dec;100(6-1):062407.
PMID: 31962468 DOI: 10.1103/PhysRevE.100.062407

While cooperativity in ligand-induced receptor dimerization has been linked with receptor-receptor couplings via minimal representations of physical observables, effects arising from higher-order oligomer, e.g., trimer and tetramer, formations of unobserved receptors have received less attention. Here we propose a dimerization model of ligand-induced receptors in multivalent form representing physical observables under basis vectors of various aggregated receptor states. Our simulations of multivalent models not only reject Wofsy-Goldstein parameter conditions for cooperativity, but show that higher-order oligomer formations can shift cooperativity from positive to negative.
Normative Data and Associations of OCT Angiography Measurements of the Macula: The Singapore Malay Eye Study

Teo ZL, Sun CZ, Chong CCY, Tham YC, Takahashi K, Majithia S, et al.

Ophthalmol Retina, 2022 Nov;6(11):1080-1088.
PMID: 35580772 DOI: 10.1016/j.oret.2022.05.010

OBJECTIVE: To describe the normative quantitative parameters of the macular retinal vasculature, as well as their systemic and ocular associations using OCT angiography (OCTA).
DESIGN: Population-based, cross-sectional study.
SUBJECTS: Adults aged > 50 years were recruited from the third examination of the population-based Singapore Malay Eye Study.
METHODS: All participants underwent a standardized comprehensive examination and spectral-domain OCTA (Optovue) of the macula. OCT angiography scans that revealed pre-existing retinal disease, revealed macular pathology, and had poor quality were excluded.
MAIN OUTCOME MEASURES: The normative quantitative vessel densities of the superficial layer, deep layer, and foveal avascular zone (FAZ) were evaluated. Ocular and systemic associations with macular retinal vasculature parameters were also evaluated in a multivariable analysis using linear regression models with generalized estimating equation models.
RESULTS: We included 1184 scans (1184 eyes) of 749 participants. The mean macular superficial vessel density (SVD) and deep vessel density (DVD) were 45.1 ± 4.2% (95% confidence interval [CI], 37.8%-51.4%) and 44.4 ± 5.2% (95% CI, 36.9%-53.2%), respectively. The mean SVD and DVD were highest in the superior quadrant (48.7 ± 5.9%) and nasal quadrant (52.7 ± 4.6%), respectively. The mean FAZ area and perimeter were 0.32 ± 0.11 mm2 (95% CI, 0.17-0.51 mm) and 2.14 ± 0.38 mm (95% CI, 1.54-2.75 mm), respectively. In the multivariable regression analysis, female sex was associated with higher SVD (β = 1.25, P ≤ 0.001) and DVD (β = 0.75, P = 0.021). Older age (β = -0.67, P < 0.001) was associated with lower SVD, whereas longer axial length (β = -0.42, P = 0.003) was associated with lower DVD. Female sex, shorter axial length, and worse best-corrected distance visual acuity were associated with a larger FAZ area. No association of a range of systemic parameters with vessel density was found.
CONCLUSIONS: This study provided normative macular vasculature parameters in an adult Asian population, which may serve as reference values for quantitative interpretation of OCTA data in normal and disease states.
Fulltext High possibility of hepatocarcinogenesis in HBV genotype C1 infected Cambodians is indicated by 340 HBV C1 full-genomes analysis from GenBank

Chuon C, Takahashi K, Matsuo J, Katayama K, Yamamoto C, Ko K, et al.

Sci Rep, 2019 08 21;9(1):12186.
PMID: 31434918 DOI: 10.1038/s41598-019-48304-z

Approximately 75% of hepatocellular carcinomas (HCC) occur in Asia; core promoter mutations are associated with HCC in HBV genotype C, the dominant genotype in Cambodia. We analyzed these mutations in Cambodian residents and compared them with HBV full genomes registered in GenBank. We investigated the characteristics of 26 full-length HBV genomes among 35 residents positive for hepatitis B surface antigen in Siem Reap province, Cambodia. Genotype C1 was dominant (92.3%, 24/26), with one case of B2 and B4 each. Multiple mutations were confirmed in 24 Cambodian C1 isolates, especially double mutation at A1762T/G1764A in 18 isolates (75.0%), and combination mutation at C1653T and/or T1753V and A1762T/G1764A in 14 isolates (58.3%). In phylogenetic analysis, 16 of 24 isolates were located in the cluster with Laos, Thailand, and Malaysia. In 340 GenBank-registered C1 strains, 113 (33.2%) had combination mutation amongst which 16.5%, 34.2%, and 95.2% were found in ASC, chronic hepatitis, and liver cirrhosis (LC)/HCC respectively (P
Fulltext Transfer free graphene growth on SiO2 substrate at 250 °C

Vishwakarma R, Rosmi MS, Takahashi K, Wakamatsu Y, Yaakob Y, Araby MI, et al.

Sci Rep, 2017 03 02;7:43756.
PMID: 28251997 DOI: 10.1038/srep43756

Low-temperature growth, as well as the transfer free growth on substrates, is the major concern of graphene research for its practical applications. Here we propose a simple method to achieve the transfer free graphene growth on SiO2 covered Si (SiO2/Si) substrate at 250 °C based on a solid-liquid-solid reaction. The key to this approach is the catalyst metal, which is not popular for graphene growth by chemical vapor deposition. A catalyst metal film of 500 nm thick was deposited onto an amorphous C (50 nm thick) coated SiO2/Si substrate. The sample was then annealed at 250 °C under vacuum condition. Raman spectra measured after the removal of the catalyst by chemical etching showed intense G and 2D peaks together with a small D and intense SiO2 related peaks, confirming the transfer free growth of multilayer graphene on SiO2/Si. The domain size of the graphene confirmed by optical microscope and atomic force microscope was about 5 μm in an average. Thus, this approach will open up a new route for transfer free graphene growth at low temperatures.