Destabilization of DNA and RNA G-quadruplex structures formed by GGA repeat due to N-methyladenine modification.

N-methyladenine (mA) is the most abundant RNA modification in eukaryotic RNA. Further, mA has been identified in the genomic DNA of both eukaryotes and prokaryotes. The G-quadruplex (G4) structure is a non-canonical nucleic acid structure formed by the stacking of G:G:G:G tetrads.

Stabilization of VEGF i-motif structure by CpG methylation.

The intercalated motif (i-motif) is a non-canonical nucleic acid structure formed by intercalated hemi-protonated cytosine base pairs (C-C) under acidic conditions. The i-motif structure formation is involved in biological processes such as transcription regulation. Therefore, the identification of factors controlling i-motif formation is important in elucidating the cellular functions it controls.

Thermal Stability Changes in Telomeric G-Quadruplex Structures Due to -Methyladenine Modification.

-methyladenine modification (mdA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson-Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing the stacking interaction. In this study, the effects of mdA modification on the thermal stability of four distinct telomeric G-quadruplex (G4) structures were investigated.

Fabrication of Novel Functional Cell-Plastic Using Polyvinyl Alcohol: Effects of Cross-Linking Structure and Mixing Ratio of Components on the Mechanical and Thermal Properties.

The current system of disposal of plastic materials fabricated from petroleum-based resources causes serious environmental pollution. To solve the problem, a bioplastic called "cell-plastic" is developed, in which unicellular green algal cells serve as a fundamental resource. This approach converts CO in the atmosphere directly into plastic products by exploiting the photosynthetic-driven proliferation of algal cells.

Detection of the Metastable Ice Phase during Water Crystallization.

Background: Under atmospheric pressure, the identifiable phases of ice crystals are hexagonal (stable) and cubic (metastable).

Objective: This study aimed to test the hypothesis that water crystallizes into the cubic phase at the beginning and then changes to the hexagonal phase.

Materials And Methods: Aqueous solutions of 40% (w/w) and 50% (w/w) glucose, and 40% (w/w) ammonium hydrogen sulfate, as well as emulsified water, were investigated.

Comparison of cultured cell attachment on a temperature-responsive polymer, poly-L-lysine, and collagen using modeling curves and a thermal-controlled quartz crystal microbalance.

The characteristics of cultured cell attachment onto poly-L-lysine (PLL), collagen, and the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM) were studied using a quartz crystal microbalance (QCM). A QCM with microscope cameras enclosed in a Peltier chamber was developed to enable QCM measurements and microphotographic imaging to be conducted in a temperature-controlled CO incubator. Human hepatoma cell line HepG2 cells were cultured on the quartz crystals coated with PLL, collagen, and PNIPAM.

Effects of CpG methylation on the thermal stability of 2, *, and 1 G-quadruplex structures.

In genomic DNA, G-quadruplex (G4)-forming DNA can form either a duplex or G4 structure, suggesting that understanding the factors regulating G4 formation is important for revealing the cellular functions controlled by G4 formation. Cytosine DNA methylation in the CpG islands is known to play an important role in transcriptional regulation. Additionally, CpG methylation increases the thermal stability of G4 structures such as and G4.

Histamine H1 receptor antagonists selectively kill cisplatin-resistant human cancer cells.

Cancer therapy is often hampered by the disease's development of resistance to anticancer drugs. We previously showed that the autonomously upregulated product of fibroblast growth factor 13 gene (FGF13; also known as FGF homologous factor 2 (FHF2)) is responsible for the cisplatin resistance of HeLa cisR cells and that it is likely responsible for the poor prognosis of cervical cancer patients treated with cisplatin. Here we show that cloperastine and two other histamine H1 receptor antagonists selectively kill HeLa cisR cells at concentrations that little affect parental HeLa S cells.

Na Transporter SvHKT1;1 from a Halophytic Turf Grass Is Specifically Upregulated by High Na Concentration and Regulates Shoot Na Concentration.

We characterized an Na transporter SvHKT1;1 from a halophytic turf grass, . SvHKT1;1 mediated inward and outward Na transport in oocytes and did not complement K transporter-defective mutant yeast. SvHKT1;1 did not complement mutant , suggesting its distinguishable function from other typical HKT1 transporters.

Construction of cell-plastics as neo-plastics consisted of cell-layer provided green alga Chlamydomonas reinhardtii covered by two-dimensional polymer.

Green alga Chlamydomonas reinhardtii has gained interest as a sustainable resource because it can be easily grown using CO as a carbon source owing to its high CO assimilating activity. Although the robustness of the cell wall of C. reinhardtii makes it difficult to extract its intracellular products, such property is beneficial when using the cell as an ingredient to fabricate "cell-plastic" in this study.

Quantification of global DNA methylation level using 5-methylcytosine dioxygenase.

DNA methylation is one of the best studied epigenetic modifications. Alteration of the global DNA methylation level occurs in abnormal cells, such as those associated with cancers and Alzheimer's disease. Several assays are used to determine the global DNA methylation level, including the bisulfite-based assay, high-performance liquid chromatography (HPLC)-based assay, enzyme-linked immunosorbent assay (ELISA), and methyl acceptance assay.

Monitoring and Modeling of Living Cell Responses in the Attachment Process and Reaction to the Antitumor Reagent Cisplatin Studied by a Quartz Crystal Microbalance Combined with a Microscope.

The attachment process and response to an antitumor reagent for cultured cells were monitored with a quartz crystal microbalance (QCM) combined with a microscope. To fit the experimentally obtained curves of the resonant frequency, model equations of resonant frequency curves were built, and parameters of time constants and scale coefficients were determined. For the cell attachment process, a first-order lag response curve well fit the experimental curves.

Comprehensive histological investigation of age-related changes in dermal extracellular matrix and muscle fibers in the upper lip vermilion.

Objective: Few histological studies have directly examined age-related changes within the lips, although non-invasive investigations of such changes are increasing. Therefore, this study aimed to provide histological and molecular data on age-dependent alterations in the vermilion.

Methods: Upper vermilion specimens from 15 female Caucasian cadavers (age range, 27-78 years) were investigated histologically or immunohistochemically.

Role of polyphenol in sugarcane molasses as a nutrient for hexavalent chromium bioremediation using bacteria.

Biological methods for the removal of hexavalent chromium (Cr(VI)) from contaminated sites are safe and efficient. This is especially true because they employ microorganisms and nutrients. The use of appropriate nutrients is important for the methods to be economically feasible.

A novel biofunctionalizing peptide for metallic alloy.

Objectives: Improving biocompatibility of metallic alloy biomaterials has been of great interest to prevent implant associated-diseases, such as stent thrombosis. Herein a simple and efficient procedure was designed to biofunctionalize a biomaterial surface by isolating a SUS316L stainless steel binding peptide.

Results: After three rounds of phage panning procedure, 12 mer peptide (SBP-A; VQHNTKYSVVIR) was identified as SUS316L-binding peptide.

Destabilisation of the c-kit1 G-quadruplex structure by N-methyladenosine modification.

N-methyladenine (mdA) has been recently discovered in eukaryotic genomic DNA. However, there have been few reports on its biological roles. G-quadruplex (G4) is a non-canonical nucleic acid structure formed by the stacking of G-tetrads.

Age-related changes in the vasculature of the dermis of the upper lip vermilion.

Lip redness is unique to humans and creates an important facial impression, but this redness decreases with age. Here, using histological and immunohistological staining of human upper lip vermilion from donors of different ages, we investigated blood vessels in the upper lip dermis and age-dependent histological changes. We found that both total vessel area in the dermis and vessel number in the upper dermis decreased with aging.

G-quadruplex-forming GGA repeat region functions as a negative regulator of the enhancer.

An enhancer located upstream of the transcriptional start site of containing two GGA-rich regions and a 14-GGA repeat (GGA) region has been previously identified. Three copies of four GGA repeats in the promoter that form a tetrad:heptad:heptad:tetrad (T:H:H:T) dimerized G-quadruplex (G4) structure reportedly functions as both a transcriptional repressor and activator. Here, the secondary structures of the two GGA-rich and (GGA) regions were analyzed using circular dichroism spectral analysis, which indicated that the two GGA-rich DNAs formed parallel-type G4 structures, whereas (GGA) DNA formed the T:H:H:T dimerized G4 structure.

Model studies for isolation of G-quadruplex-forming DNA sequences through a pull-down strategy with macrocyclic polyoxazole.

G-quadruplexes (G4s) are non-B DNA structures present in guanine-rich regions of gene regulatory areas, promoters and CpG islands, but their occurrence and functions remain incompletely understood. Thus, methodology to identify G4 sequences is needed. Here, we describe the synthesis of a novel cyclic hepta-oxazole compound, L1Bio-7OTD (1), bearing a biotin affinity-tag as a tool to pull down G4 structures from mixtures of G4-forming and non G4-forming DNA sequences.

Multicolor bioluminescence resonance energy transfer assay for quantification of global DNA methylation.

Abnormal DNA methylations such as hypermethylation on tumor suppressor genes and global hypomethylation have been recognized as hallmarks of cancer. Previously, we reported a bioluminescence resonance energy transfer (BRET)-based global DNA methylation level assay using a methyl-CpG-binding domain-fused firefly luciferase (MBD-Fluc) and unmethylated CpG-binding domain-fused firefly luciferase (CXXC-Fluc). The BRET signal between MBD-Fluc and BOBO-3 DNA intercalating dye depends on the methylated CpG contents, whereas the BRET signal between CXXC-Fluc and BOBO-3 depends on the unmethylated CpG contents.

A novel transmembrane protein defines the endoplasmic reticulum stress-induced cell death pathway.

Mitochondrial membrane potential (ΔΨ) maintenance is physiologically critical in cells; its loss causes apoptotic signalling and cell death. Accumulating DNA mutations and unfolded proteins in stressed cells activate signalling pathways for cell death induction. Cancer cells often fail to die even in the presence of some death signalling proteins.

Fluorescence detection of single-nucleotide differences using aptamer-forming binary DNA probes.

We report a simple method for fluorescence detection of single-nucleotide alterations in a long target DNA, which is based on the formation of a three-way-junction-structured cholic-acid-binding DNA aptamer by the hybridization of the target with binary DNA probes. The new method was successfully exploited for SNP genotyping of human CYP2C19 gene.

Electrochemical sensing system employing fructosamine 6-kinase enables glycated albumin measurement requiring no proteolytic digestion.

Currently available enzymatic methods for the measurement of glycated proteins utilize fructosyl amino acid/peptide oxidases (FAOXs/FPOXs) as sensing elements. FAOXs/FPOXs oxidize glycated amino acids or glycated dipeptides but they are not able to accept longer glycated peptides or intact glycated proteins as substrates. Therefore, pretreatment via proteolytic digestion is unavoidable with the current enzymatic methods, and there remains a need for simpler measurement methods for glycated proteins.

shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library.

RNA interference (RNAi) screening is extensively used in the field of reverse genetics. RNAi libraries constructed using random oligonucleotides have made this technology affordable. However, the new methodology requires exploration of the RNAi target gene information after screening because the RNAi library includes non-natural sequences that are not found in genes.