Mutations identified in engineered with a reduced genome.

Characterizing genes that regulate cell growth and survival in model organisms is important for understanding higher organisms. Construction of strains harboring large deletions in the genome can provide insights into the genetic basis of cell growth compared with only studying wild-type strains. We have constructed a series of genome-reduced strains with deletions spanning approximately 38.

Identification of a Formate-Dependent Uric Acid Degradation Pathway in .

Purine is a nitrogen-containing compound that is abundant in nature. In organisms that utilize purine as a nitrogen source, purine is converted to uric acid, which is then converted to allantoin. Allantoin is then converted to ammonia.

Subunit Composition of Ribosome in the yqgF Mutant Is Deficient in pre-16S rRNA Processing of Escherichia coli.

Escherichia coli 16S, 23S, and 5S ribosomal RNAs (rRNAs) are transcribed as a single primary transcript, which is subsequently processed into mature rRNAs by several RNases. Three RNases (RNase III, RNase E, and RNase G) were reported to function in processing the 5'-leader of precursor 16S rRNA (pre-16S rRNA). Previously, we showed that a novel essential YqgF is involved in that processing.

Starch synthase IIIa and starch branching enzyme IIb-deficient mutant rice line ameliorates pancreatic insulin secretion in rats: screening and evaluating mutant rice lines with antidiabetic functionalities.

Diabetes mellitus is a metabolic disease spreading worldwide that has been reported to worsen the development and progression of other diseases (cancer, vascular diseases and dementia). To establish functional rice lines with anti-postprandial hyperglycaemic effects, we developed mutant rice lines, which lack one or two gene(s) related to starch synthesis, and evaluated their effects. Powder of mutant rice lines or other grains was loaded to rats fasted overnight (oral grain powder loading test).

Involvement of the ytfK gene from the PhoB regulon in stationary-phase H2O2 stress tolerance in Escherichia coli.

The Escherichia coli PhoB-PhoR two-component system responds to phosphate starvation and induces the expression of many genes. Previous studies suggested that phosphate starvation induces oxidative stress, but the involvement of the PhoB regulon in oxidative stress tolerance has not been clarified. Here, we showed that ytfK, one of the PhoB regulon genes, is involved in cell tolerance to a redox-cycling drug, menadione, and H2O2 in stationary-phase cells.

Involvement of formate dehydrogenases in stationary phase oxidative stress tolerance in Escherichia coli.

Previously, we constructed a series of reduced-genome strains of Escherichia coli by combining large-scale chromosome deletions and then tested the sensitivity of these strains to the redox-cycling drug menadione. In this study, we analyzed a deletion that increased menadione sensitivity and discovered that loss of selenocysteine synthase genes was responsible for the strain's reduced tolerance to oxidative stress. Mutants of formate dehydrogenases, which are selenocysteine-containing enzymes, were also sensitive to menadione, indicating that these enzymes are involved in oxidative stress during stationary phase, specifically under microaerobic conditions in the presence of glucose.

Systematic identification of synthetic lethal mutations with reduced-genome Escherichia coli: synthetic genetic interactions among yoaA, xthA and holC related to survival from MMS exposure.

Reduced-genome Escherichia coli strains lacking up to 38.9% of the parental chromosome have been constructed by combining large-scale chromosome deletion mutations. Functionally redundant genes involved in essential processes can be systematically identified using these reduced-genome strains.

Figure correction of a metallic ellipsoidal neutron focusing mirror.

An increasing number of neutron focusing mirrors is being adopted in neutron scattering experiments in order to provide high fluxes at sample positions, reduce measurement time, and/or increase statistical reliability. To realize a small focusing spot and high beam intensity, mirrors with both high form accuracy and low surface roughness are required. To achieve this, we propose a new figure correction technique to fabricate a two-dimensional neutron focusing mirror made with electroless nickel-phosphorus (NiP) by effectively combining ultraprecision shaper cutting and fine polishing.

Initial reduction of oxidative stress by angiotensin receptor blocker contributes long term outcomes after percutaneous coronary intervention.

Background: It remains unclear whether administration of ARB with reactive oxygen species (ROS) scavenging effects improves the prognosis of patients undergoing PCI.

Objectives: This study investigated whether the pre-intervention antioxidant effect of angiotensin receptor blocker (ARB) affects long-term outcomes in patients after successful percutaneous coronary intervention (PCI) without early adverse events.

Methods: Fifty-two patients who underwent elective PCI were randomly assigned for treatment with or without ARB, which was administered within 48 hours before PCI.

Novel essential gene Involved in 16S rRNA processing in Escherichia coli.

Biogenesis of ribosomes is a complex process mediated by many factors. While its transcription proceeds, ribosomal RNA (rRNA) folds itself into a characteristic three-dimensional structure through interaction with ribosomal proteins, during which its ends are processed. Here, we show that the essential protein YqgF, a RuvC family protein with an RNase-H-like motif, is involved in the processing of pre-16S rRNA during ribosome maturation.

New fabrication method for an ellipsoidal neutron focusing mirror with a metal substrate.

We propose an ellipsoidal neutron focusing mirror using a metal substrate made with electroless nickel-phosphorus (NiP) plated material for the first time. Electroless NiP has great advantages for realizing an ellipsoidal neutron mirror because of its amorphous structure, good machinability and relatively large critical angle of total reflection for neutrons. We manufactured the mirror by combining ultrahigh precision cutting and fine polishing to generate high form accuracy and low surface roughness.

[A novel approach to techniques in genetic testing for cancer].

In molecular targeted drug therapy, genetic screening is carried out to identify the existence of target genes that are specifically expressed in cancer cells. Conventional methods for detecting the mutation of genes in cancer cells through the use of purified DNA is time consuming, especially in the case of the enzymatic treatment of pathological specimens, and it is difficult to finish all these protocols on the same day. Also, depending on the condition of the patients, it may be difficult to perform surgery or biopsy, and pathological specimens are not always obtainable.

Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis.

Indole-3-acetic acid (IAA), an auxin plant hormone, is biosynthesized from tryptophan. The indole-3-pyruvic acid (IPyA) pathway, involving the tryptophan aminotransferase TAA1 and YUCCA (YUC) enzymes, was recently found to be a major IAA biosynthetic pathway in Arabidopsis. TAA1 catalyzes the conversion of tryptophan to IPyA, and YUC produces IAA from IPyA.

Color selectivity of surface-plasmon holograms illuminated with white light.

By using the optical frequency dependence of surface-plasmon polaritons, color images can be reconstructed from holograms illuminated with white light. We report details on the color selectivity of the color holograms. The selectivity is tuned by the thickness of a dielectric film covering a plasmonic metal film.

Effects on IS1 transposition frequency of a mutation in the ygjD gene involved in an essential tRNA modification in Escherichia coli.

The YgjD protein is essential for the synthesis of the universal tRNA modification, N(6) -threonylcarbamoyladenosine (t(6) A), which is necessary for the decoding of ANN codons. We isolated a suppressor (ygjDsup ) of the ygjD(ts) mutant by its permissive growth at high temperature in Escherichia coli. Resequencing of the ygjDsup mutant genome showed the presence of a complicated chromosome rearrangement, an inverse insertion of a large duplicated region (c.

Mutations in the essential Escherichia coli gene, yqgF, and their effects on transcription.

The Escherichia coli yqgF gene is highly conserved across a broad spectrum of bacterial genomes. The gene was first identified as being essential for cell growth during screening for targets for broad-spectrum antibiotics. YqgF is structurally similar to RuvC, a Holliday junction resolvase, but its function has not been established.

Diffuse skeletal muscles uptake of [18F] fluorodeoxyglucose on positron emission tomography in primary muscle peripheral T-cell lymphoma.

A 40-year-old man presented with weakness of neck extensor muscles. Cervical magnetic resonance imaging showed high-intensity areas in muscles of the left lateral cervical region on T2-weighted images. Fluorodeoxyglucose-positron emission tomography scan demonstrated striking fluorodeoxyglucose uptake by multiple skeletal muscles of the neck, chest, and abdominal region.

Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli.

The Escherichia coli ygjD gene is critical for the universal tRNA modification N(6)-threonylcarbamoyladenosine, together with two other essential genes, yeaZ and yjeE. This study showed that the transcription of the thr and ilv operons in ygjD mutants was increased through the inhibition of transcription attenuation and that dnaG transcription was reduced.

Oxidative stress sensitivity of engineered Escherichia coli cells with a reduced genome.

The construction of engineered bacterial cells with a reduced genome allows the investigation of molecular mechanisms that may be cryptic in wild-type strains and derivatives. Previously, a large-scale combined deletion mutant of Escherichia coli that lacked 29.7% of the parental chromosome was constructed by combining large chromosome deletions.

Surface-plasmon holography with white-light illumination.

The recently emerging three-dimensional (3D) displays in the electronic shops imitate depth illusion by overlapping two parallax 2D images through either polarized glasses that viewers are required to wear or lenticular lenses fixed directly on the display. Holography, on the other hand, provides real 3D imaging, although usually limiting colors to monochrome. The so-called rainbow holograms--mounted, for example, on credit cards--are also produced from parallax images that change color with viewing angle.

Suppression of the temperature-sensitive mutation of the bamD gene required for the assembly of outer membrane proteins by multicopy of the yiaD gene in Escherichia coli.

We isolated temperature-sensitive mutants of the Escherichia coli bamD gene, which is essential for the assembly of β-barrel outer membrane proteins. As their multicopy suppressor, we identified a novel yiaD gene encoding a putative lipoprotein, YiaD. Mutations of its OmpA domain, which is required for interaction with peptidoglycan, affected suppression, suggesting that interaction with peptidoglycan is important to YiaD function.

Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome.

Escherichia coli has dispensable genome regions and eliminating them may improve cell use by reducing unnecessary metabolic pathways and complex regulatory networks. Although several strains with reduced genomes have already been constructed, there have been no reports of strains constructed with deletions assayed for influence on growth. To retain robust growth and fundamental metabolic pathways, the growth of each deletion strain and combination effects of deletions were checked using M9 minimal medium.

Involvement of an essential gene, mviN, in murein synthesis in Escherichia coli.

We isolated a temperature-sensitive mutant with a mutation in mviN, an essential gene in Escherichia coli. At the nonpermissive temperature, mviN mutant cells swelled and burst. An intermediate in murein synthesis, polyprenyl diphosphate-N-acetylmuramic acid-(pentapeptide)-N-acetyl-glucosamine, accumulated in mutant cells.

Profiling of Escherichia coli Chromosome database.

The Profiling of Escherichia coli Chromosome (PEC) database (http://www.shigen.nig.

Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome.

Genetic information consists of protein- and RNA-coding genes that exist in a range of sizes and noncoding cis- and trans-acting sequence elements. The use of long chromosomal deletion mutations is a powerful method for identifying essential genetic information through experimental reduction of the genome to its minimal gene set. Taking advantage of recent technical advances, we constructed sequence-specific long deletion mutations of the Escherichia coli chromosome.