Correlation of ex vivo and in vivo ammonia production with L-asparaginase biological activity in adults with lymphoid malignancies.

Silent inactivation of L-asparaginase (L-Asp) represents rapid clearance of L-Asp by anti-L-Asp IgG antibodies without clinical symptoms. Measurement of L-Asp activity is the gold standard for diagnosis of silent inactivation, but this test is not commercially available in Japan as of 2023. We evaluated ex vivo and in vivo ammonia production in relation to L-Asp activity.

Prdm12 regulates inhibitory neuron differentiation in mouse embryonal carcinoma cells.

The epigenetic regulatory system significant influences the fate determination of cells during developmental processes. Prdm12 is a transcriptional regulator that modulates gene expression epigenetically. The gene has been shown to be expressed in neural tissues, specifically during development, but its detailed function is not fully understood.

Accuracy of BIS monitoring using a novel interface device connecting conventional needle-electrodes and BIS sensors during frontal neurosurgical procedures.

Background: Bispectral index (BIS) monitoring is a widely used non-invasive method to monitor the depth of anesthesia. However, in the event of surgeries requiring a frontal approach, placement of the electrode may be impossible at the designated area to achieve a proper BIS measurement.

Methods: We developed an investigational interface device to connect needle-electrodes to BIS sensors.

Chairside fabrication of provisional crowns on FDM 3D-printed PVA model.

Purpose: The purpose of this study was to evaluate the dimensional accuracy of crowns fabricated using a polyvinyl alcohol (PVA) dental model.

Methods: An intraoral scanner (LAVA TDS) was used to scan a prepared molar abutment as a master model. The STL file obtained from the scanning process was transferred into the FDM 3D printer (Value 3D Magix MF-1000) and then models were fabricated with PVA filament.

Representations of female body weight in the media: An update of Playboy magazine from 2000 to 2014.

Most content analyzes of Playboy magazine have reported a trend toward increased thinness over time. However, recent research suggests that this trend may be reversing. The current study updates this research by examining changes in the body mass index (BMI) of Playboy models from 2000 to 2014.

Transcriptomic features associated with energy production in the muscles of Pacific bluefin tuna and Pacific cod.

Bluefin tuna are high-performance swimmers and top predators in the open ocean. Their swimming is grounded by unique features including an exceptional glycolytic potential in white muscle, which is supported by high enzymatic activities. Here we performed high-throughput RNA sequencing (RNA-Seq) in muscles of the Pacific bluefin tuna (Thunnus orientalis) and Pacific cod (Gadus macrocephalus) and conducted a comparative transcriptomic analysis of genes related to energy production.

Haptoglobin promoter polymorphism rs5472 as a prognostic biomarker for peptide vaccine efficacy in castration-resistant prostate cancer patients.

Personalized peptide vaccination (PPV) is an attractive approach to cancer immunotherapy with strong immune-boosting effects conferring significant clinical benefit. However, as with most therapeutic agents, there is a difference in clinical efficacy among patients receiving PPV. Therefore, a useful biomarker is urgently needed for prognosticating clinical outcomes to preselect patients who would benefit the most from PPV.

The Effects of Annealing Temperatures on Composition and Strain in SiGe Obtained by Melting Growth of Electrodeposited Ge on Si (100).

The effects of annealing temperatures on composition and strain in SiGe, obtained by rapid melting growth of electrodeposited Ge on Si (100) substrate were investigated. Here, a rapid melting process was performed at temperatures of 1000, 1050 and 1100 °C for 1 s. All annealed samples show single crystalline structure in (100) orientation.

Crystallization of Electrodeposited Germanium Thin Film on Silicon (100).

We report the crystallization of electrodeposited germanium (Ge) thin films on n-silicon (Si) (100) by rapid melting process. The electrodeposition was carried out in germanium (IV) chloride: propylene glycol (GeCl₄:C₃H₈O₂) electrolyte with constant current of 50 mA for 30 min. The measured Raman spectra and electron backscattering diffraction (EBSD) images show that the as-deposited Ge thin film was amorphous.

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology.

Identification and classification of a two-component system based on domain structures in bacteria and differences in domain structure between Gram-positive and Gram-negative bacteria.

Genome sequencing has revealed many pairs of proteins termed two-component systems (TCSs) in bacteria. Each pair consists of a sensor or histidine kinase (HK) and an effector or response regulator (RR). The HK is usually a membrane-spanning protein that senses specific environmental parameters and communicates this information to the cytoplasmic RR protein through phosphotransfer reactions to cope with a variety of environmental stresses, including osmotic pressure, nitrogen lack, phosphoric acid lack, and the presence of oxygen.

Deciphering cellular functions of protein phosphatases by comparison of gene expression profiles in Saccharomyces cerevisiae.

Expression profiles of protein phosphatase (PPase) disruptants were analyzed by use of Pearson's correlation coefficient to find profiles that correlated with those of 316 Reference Gene (RG) disruptants harboring deletions in genes with known functions. Twenty-six Deltappase disruptants exhibited either a positive or negative correlation with 94 RG disruptants when the p value for Pearson's correlation coefficient was >0.2.

[Plasma cell leukemia presenting with cleaved nuclei and a monocytoid appearance].

A 74-year-old man presented with anemia, thrombocytopenia and leukocytosis with 41% abnormal cells having cleaved and monocytoid nuclei. The bone marrow was infiltrated with 43.6% abnormal cells that were negative for peroxidase staining and positive for PAS staining.

Properties of a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae.

We characterized a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae, TFL20, that has a mutation in the LEU4 gene. We monitored the concentration of extracellular i-AmOH and intracellular amino acids, and compared the ratios of gene expression in TFL20 with the wild-type strain, K30. We found that the LEU1, LEU2, and BAT1 genes were up-regulated in TFL20 for metabolism, and that TFL20 simultaneously produced as much i-AmOH and leucine as K30 does.

Construction of enzyme-substrate complexes between hen egg-white lysozyme and N-acetyl-D-glucosamine hexamer by systematic conformational search and molecular dynamics simulation.

We constructed the complexes between HEWL and (GlcNAc)6 oligomer in order to investigate the amino acid residues related to substrate binding in the productive and nonproductive complexes, and the relationship between the distortion of the GlcNAc residue D and the formation of the productive complexes. We obtained 49 HEWL-(GlcNAc)6 complexes by a systematic conformational search and classified the each one to the three binding modes; left side, center, or right side. Furthermore we performed the molecular dynamics simulation against 20 HEWL-(GlcNAc)6 complexes (8: chair model, 12 : half-chair model) selected from the 49 complexes to investigate the interaction between HEWL and (GlcNAc)6.

Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases.

Microarrays are often used to identify target genes that trigger specific diseases, to elucidate the mechanisms of drug effects, and to check SNPs. However, data from microarray experiments are well known to contain biases resulting from the experimental protocols. Therefore, in order to elucidate biological knowledge from the data, systematic biases arising from their protocols must be removed prior to any data analysis.

Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades.

We developed an extensive yeast gene expression library consisting of full-genome cDNA array data for over 500 yeast strains, each with a single-gene disruption. Using this data, combined with dose and time course expression experiments with the oral antifungal agent griseofulvin, whose exact molecular targets were previously unknown, we used Boolean and Bayesian network discovery techniques to determine the gene expression regulatory cascades affected directly by this drug. Using this method we identified CIK1 as an important affected target gene related to the functional phenotype induced by griseofulvin.

Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries.

Gene regulatory networks elucidated from strategic, genome-wide experimental data can aid in the discovery of novel gene function information and expression regulation events from observation of transcriptional regulation among genes of known and unknown biological function. To create a reliable and comprehensive data set for the elucidation of transcription regulation networks, we conducted systematic genome-wide disruption expression experiments of yeast on 118 genes with known involvement in transcription regulation. We report several novel regulatory relationships between known transcription factors and other genes with previously unknown biological function discovered with this expression library.

[Drug discovery based on microarray].

Gene regulatory networks developed from full genome expression libraries from gene perturbation variant cell lines can be used to quickly and efficiently identify the molecular mechanism of action of drugs or lead compound molecules. We developed an extensive yeast gene expression library consisting of full-genome cDNA array data for over 500 yeast strains each with a single gene disruption. Using this data, combined with dose and time course expression experiments with the oral antifungal agent, we used Boolean network discovery techniques to determine the genes whose expression was most profoundly affected by this drug.

Changes at the floor of the peptide-binding groove induce a strong preference for proline at position 3 of the bound peptide: molecular dynamics simulations of HLA-A*0217.

We report on molecular dynamics simulations of major histocompatibility complex (MHC)-peptide complexes. Class I MHC molecules play an important role in cellular immunity by presenting antigenic peptides to cytotoxic T cells. Pockets in the peptide-binding groove of MHC molecules accommodate anchor side chains of the bound peptide.

Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide.

In our model system, we generated T cell clones specific for the HLA-DR4 (DRB1*0405)-index peptide (YWALEAAAD) complex. Based on response patterns of the T cell clones, analogue peptides containing single amino acid substitutions of the index peptide were classified into three types, agonists, antagonists or null peptides (non-agonistic and non-antagonistic peptides). Subtle structural changes induced by the antagonists in the T-cell receptor (TCR) binding regions have already been explained using the root mean square (r.

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.

Protein-protein interactions play pivotal roles in various aspects of the structural and functional organization of the cell, and their complete description is indispensable to thorough understanding of the cell. As an approach toward this goal, here we report a comprehensive system to examine two-hybrid interactions in all of the possible combinations between proteins of Saccharomyces cerevisiae. We cloned all of the yeast ORFs individually as a DNA-binding domain fusion ("bait") in a MATa strain and as an activation domain fusion ("prey") in a MATalpha strain, and subsequently divided them into pools, each containing 96 clones.

The hydrophobic cores of proteins predicted by wavelet analysis.

Motivation: In the process of protein construction, buried hydrophobic residues tend to assemble in a core of a protein. Methods used to predict these cores involve use or no use of sequential alignment. In the case of a close homology, prediction was more accurate if sequential alignment was used.

Streptomyces ATP nucleotide 3'-pyrophosphokinase-gene cloning and sequence analysis.

Streptomyces ATP nucleotide 3'-pyrophosphokinase is an extracellular enzyme that transfers 5'-beta, gamma-pyrophosphoryl groups of ATP to a variety of nucleotides at the 3'-OH site. The enzyme gene was cloned from partially Sau3AI-digested chromosomal DNA of S. morookaensis in S.