Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na-Driven Flagella.

The flagellar motor protein complex consists of rotor and stator proteins. Their interaction generates torque of flagellum, which rotates bidirectionally, clockwise (CW) and counterclockwise. FliG, one of the rotor proteins, consists of three domains: N-terminal (FliG), middle (FliG), and C-terminal (FliG).

Establishment of S100A8 Transgenic Rats to Understand Innate Property of S100A8 and Its Immunological Role.

The innate properties of S100A8 as a regulator in acute inflammation have not yet been elucidated in detail. Our aims are to newly establish S100A8 transgenic rats (Tg-S100A8) and to elucidate the immunological functions of S100A8. Following the treatment with 5% dextran sulfate sodium for 1 week, the body weight in Tg-S100A8 weakly decreased after the start; however, that in Japanese Wistar rats (WT) significantly decreased in the end.

Time-series oligonucleotide count to assign antiviral siRNAs with long utility fit in the big data era.

Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes.

A fourth subtype of retinoic acid receptor-related orphan receptors is activated by oxidized all- retinoic acid in medaka ().

Background: The three known subtypes of the retinoic acid receptor-related orphan receptor (ROR) have been implicated in the control of immunity, brain function, and circadian rhythm in mammals. Here, we demonstrate by phylogenetic analysis that there were originally four subtypes of RORs in vertebrates. One of the novel paralogs, ( in the Ensembl database), is conserved among teleosts, but absent in mammals.

Human Metapneumovirus M2-2 Protein Acts as a Negative Regulator of Alpha Interferon Production by Plasmacytoid Dendritic Cells.

Human metapneumovirus (HMPV) has the ability to inhibit Toll-like receptor 7 (TLR7)- and TLR9-dependent alpha interferon (IFN-α) production by plasmacytoid dendritic cells (pDCs). However, the inhibition mechanism remains largely unknown. To identify viral proteins responsible for this inhibition, we performed a screening of HMPV open reading frames (ORFs) for the ability to block TLR7/9-dependent signaling reconstituted in HEK293T cells by transfection with myeloid differentiation factor 88 (MyD88), tumor necrosis factor receptor-associated factor 6 (TRAF6), IKKα, and IFN regulatory factor 7 (IRF7).

DNA hypomethylation circuit of mouse rDNA repeats in the germ cell lineage.

DNA methylation is dynamically reprogrammed at two developmental periods, in primordial germ cells and pre-implantation embryos, via distinct phases of DNA demethylation and de novo methylation. Here we show that ribosomal DNA (rDNA) promoters are hypomethylated in sperm and oocytes; this hypomethyaltion was maintained during pre-implantation development. A DNA methylation analysis of embryonic and extra-embryonic cells on embryonic day 7.

Chlorophyll-Based Organic-Inorganic Heterojunction Solar Cells.

Solid-state chlorophyll solar cells (CSCs) employing a carboxylated chlorophyll derivative, methyl trans-3 -carboxypyropheophorbide a, as a light-harvesting dye sensitizer chlorophyll (DSC) deposited on mesoporous TiO , on which four zinc hydroxylated chlorophyll derivatives were spin-coated for hole transporter chlorophylls (HTCs), are described. Key parameters, including the effective carrier mobility of the HTC films, as determined by the space charge-limited current method, and the frontier molecular orbitals of these DSCs and HTCs, as estimated from cyclic voltammetry and electronic absorption spectra, suggest that both charge separation and carrier transport are favorable. The power conversion efficiencies (PCEs) of the present CSCs with fluorine-doped tin oxide (FTO)/TiO /DSC/HTCs/Ag were determined to follow the order of HTC-1>HTC-2>HTC-3>HTC-4, which coincided perfectly with the order of their hole mobilities.

The forkhead-like transcription factor (Fhl1p) maintains yeast replicative lifespan by regulating ribonucleotide reductase 1 (RNR1) gene transcription.

In eukaryotes, numerous genetic factors contribute to the lifespan including metabolic enzymes, signal transducers, and transcription factors. As previously reported, the forkhead-like transcription factor (FHL1) gene was required for yeast replicative lifespan and cell proliferation. To determine how Fhl1p regulates the lifespan, we performed a DNA microarray analysis of a heterozygous diploid strain deleted for FHL1.

Effects of Mild and Severe Vitamin B Deficiencies on the Meiotic Maturation of Mice Oocytes.

We investigated the effects of vitamin B deficiency on the meiosis maturation of oocytes. Female Crl:CD1 (ICR) mice were fed a 20% casein diet (control group) or a vitamin B-free diet (test group). The vitamin B concentration in ovary was approximately 30% lower in the test group than in the control group.

Generation of monoclonal antibodies against mitocryptide-2: toward a new strategy to investigate the biological roles of cryptides.

We recently identified a novel family of neutrophil-activating peptides including mitocryptide-1 and mitocryptide-2 (MCT-2) that are endogenously produced from various mitochondrial proteins. Among them, MCT-2 is an N-formylated pentadecapeptide derived from mitochondrial cytochrome b and is found to promote neutrophilic migration and phagocytosis efficiently. Signaling mechanisms of neutrophil activation by MCT-2 have been investigated at the cellular level, and MCT-2 has been demonstrated to be an endogenous specific ligand for formyl peptide receptor-2 (also referred to as formyl peptide receptor-like 1).

Asymmetrically reduced expression of hand1 homeologs involving a single nucleotide substitution in a cis-regulatory element.

During vertebrate evolution, whole genome duplications resulted in a number of duplicated genes, some of which eventually changed their expression patterns and/or levels via alteration of cis-regulatory sequences. However, the initial process involved in such cis-regulatory changes remains unclear. Therefore, we investigated this process by analyzing the duplicated hand1 genes of Xenopus laevis (hand1.

An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data.

Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions.

Exonuclease processivity of archaeal replicative DNA polymerase in association with PCNA is expedited by mismatches in DNA.

Family B DNA polymerases comprise polymerase and 3' ->5' exonuclease domains, and detect a mismatch in a newly synthesized strand to remove it in cooperation with Proliferating cell nuclear antigen (PCNA), which encircles the DNA to provide a molecular platform for efficient protein-protein and protein-DNA interactions during DNA replication and repair. Once the repair is completed, the enzyme must stop the exonucleolytic process and switch to the polymerase mode. However, the cue to stop the degradation is unclear.

Molecular mechanism and structural basis of gain-of-function of STAT1 caused by pathogenic R274Q mutation.

Gain-of-function (GOF) mutations in the gene are critical for the onset of chronic mucocutaneous candidiasis (CMC) disease. However, the molecular basis for the gain of STAT1 function remains largely unclear. Here, we investigated the structural features of GOF residues to better understand the impact of these pathogenic mutations.

Substitution at the C-3 Position of Catechins Has an Influence on the Binding Affinities against Serum Albumin.

It is known that catechins interact with the tryptophan (Trp) residue at the drug-binding site of serum albumin. In this study, we used catechin derivatives to investigate which position of the catechin structure strongly influences the binding affinity against bovine serum albumin (BSA) and human serum albumin (HSA). A docking simulation showed that (-)-epigallocatechin gallate (EGCg) interacted with both Trp residues of BSA (one at drug-binding site I and the other on the molecular surface), mainly by π-π stacking.

Molecular mechanisms of insulin resistance in 2 cases of primary insulin receptor defect-associated diseases.

Background: Defects of the insulin receptor gene ( INSR ) cause wide spectra of congenital insulin resistance. Monoallelic defects result in milder insulin-resistant diabetes mellitus with acanthosis nigricans (IRAN, type A). Whereas, leprechaunism (Donahue syndrome), the most severe condition with lethality during the infantile period is caused by biallelic defects of INSR .

Effects of Normothermic Conditioned Microwave Irradiation on Cultured Cells Using an Irradiation System with Semiconductor Oscillator and Thermo-regulatory Applicator.

We investigated the effects of microwave irradiation under normothermic conditions on cultured cells. For this study, we developed an irradiation system constituted with semiconductor microwave oscillator (2.45 GHz) and thermos-regulatory applicator, which could irradiate microwaves at varied output powers to maintain the temperature of cultured cells at 37 °C.

Frameshift Mutation Confers Function as Virulence Factor to Leucine-Rich Repeat Protein from .

Many plant pathogens inject type III (T3SS) effectors into host cells to suppress host immunity and promote successful infection. The bacterial pathogen causes brown stripe symptom in many species of monocotyledonous plants; however, individual strains of each pathogen infect only one host species. T3SS-deleted mutants of K1 (virulent to rice) or N1141 (virulent to finger millet) caused no symptom in each host plant, suggesting that T3SS effectors are involved in the symptom formation.

Calcitonin-typical suppression of osteoclastic activity by amphioxus calcitonin superfamily peptides and insights into the evolutionary conservation and diversity of their structures.

Calcitonin (CT) is a hormone that decreases serum calcium level by suppressing osteoclastic activity in the vertebrate bone. In vertebrates, the structure-function relationship of CTs has been studied extensively. We recently identified three CT superfamily peptides, Bf-CTFP1 to 3, and clarified the molecular and functional characteristics of their receptor and receptor activity-modifying protein in amphioxus, Branchiostoma floridae.

Analysis to Estimate Genetic Variations in the Idarubicin-Resistant Derivative MOLT-3.

Gene alterations are a well-established mechanism leading to drug resistance in acute leukemia cells. A full understanding of the mechanisms of drug resistance in these cells will facilitate more effective chemotherapy. In this study, we investigated the mechanism(s) of drug resistance in the human acute leukemia cell line MOLT-3 and its idarubicin-resistant derivative MOLT-3/IDR through complete mitochondrial and nuclear DNA analyses.

Classification of ligand molecules in PDB with graph match-based structural superposition.

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set.