Aerobic and Anaerobic Biotransformation of Bile Acids by Escherichia coli (III)

The oxidation/reduction reactions of bile acids by Escherichia coli (E. coli) K-12 were examined in both Davis and brain-heart infusion (BHI) media under aerobic and anaerobic conditions. The pH in the Davis medium changed by almost the same amount, around pH 6.5?7.0 in both aerobic and anaerobic cultures, but the pH in the BHI medium was different in both cultures, that is, about pH 9.0 in the aerobic culture but only about 6.5 in the anaerobic culture. The growth curve of E. coli in the Davis medium showed a similar pattern in both conditions. Cholic acid (CA) was oxidized to 3α12α-dihydroxy-7-oxo-5β-cholanoic acid (3α12α7=O) in both cultures, but the reaction in the anaerobic culture was somewhat slower than that in the aerobic culture. On the other hand, reduction of 3α12α7=O to CA did not occur in the aerobic culture, but about 10% reduction was observed in the anaerobic culture after 4 days. These data suggest that the oxidation/reduction reaction of E. coli was oxidative in aerobic culture but reductive in anaerobic culture and these characteristics were not due to the changes in the pH of the medium. The reactions of CA and glycocholic acid to crude 7α-HSDH prepared from E. coli were examined and it was found that both free and conjugated CA as a substrate for the 7α-HSDH showed similar Km values

DNA Amplification and Nucleotide Sequence Determination of a Region of Mitochondrial DNA in the Sea Snake, Laticauda Semifasciata

We determined the nucleotide sequence of a region of the 12S ribosomal RNA (rRNA) gene in the mitochondrial DNA (mtDNA) of the sea snake, Laticauda semifasciata, using the polymerase chain reaction (PCR). We synthesized oligonucleotide primers according to the nucleotide sequence of human mt DNA 12S rRNA gene and found that the target sequence (386bp) of the sea snake mtDNA could be amplified with these primers. The nucleotide sequence of the amplified region of the sea snake mt DNA was determined on six separate plasmid clones for each individual snake DNA and matched completely among the DNA samples of three sea snakes. The sequence homology in the region of the mtDNA 12S rRNA gene between L. semifasciata and human is 69.1%

Biotransformation of Bile Acids by Bacteroides sp. Strain T-40 Isolated from Human Microflora

The effects of Bacteroides sp. strain T-40 isolated from human feces on the biotransformation of bile acids were examined in an anaerobic culture system. Bacteroides sp. T-40 oxidized cholic acid (CA) and chenodeoxycholic acid (CDCA) to 3α,12α-dihydroxy-7-oxo-5β-cholanoic acid and 3α-hydroxy-7-oxo-5β-cholanoic acid, and reduced these oxo-bile acids to CA and CDCA, respectively. However, the reduction activities were lower than the oxidation activities. Hyocholic acid was dehydrogenated, but to a lesser extent than CA or CDCA. On the other hand, α-muricholic acid, which has a hydroxyl group at the position of 7α, was not dehydrogenated. Glycocholic acid was converted to free 3α,12α-dihydroxy-7-oxo-5β-cholanoic acid but any glycine conjugated 7-oxo product was not detected. These data indicate that Bacteroides sp. T-40 possesses bile acid hydrolase and 7α-hydroxysteroid dehydrogenase, by which conjugated bile acids are initially deconjugated, and then undergo oxidization of the 7α-hydroxy group

Molecular Analysis of Common Types ofﾎｱ-Thalassemia Associated with(ﾎｲ-Thalassemia in Northern Thailand

We applied PCR strategies to detect the common types of ﾎｱ- thalassemia determinants which were associated with ﾎｲ- thalassemia in northern Thailand. Two types of deletions in the ﾎｱ-globin gene locus;the 18 kb deletion of Southeast Asian type(-ﾎｱSEA)and the 3.7 kb rightward deletion(-ﾎｱ3.7), and the most prevalent non-deletion mutation, Hb Constant Spring(ﾎｱC8, TAA to CAA at the codon 141)were investigated in 22 cases of ﾎｲ-thalassemia. Nine ﾎｲ-thalassemia patients were found to be associated with one or two of these defective ﾎｱ-globin gene determinants and the mean hemoglobin concentration in these patients was 6.3 ﾂｱ 1.1 g/dl whereas it was 5.6ﾂｱ.0.8 g/dl in 12 ﾎｲ-thalassemia patients without ﾎｱ- globin gene abnormalities ; the difference is statistically insignificant (p = 0.08). The level of anemia was severe in the ﾎｲ-thalassemia patients carrying a single ﾎｱ-globin gene abnormality in the heterozygous compounds ; whereas the (ﾎｲ-thalassemias withﾎｱ-globin gene defects in both alleles showed less severe anemia. A patient carrying the ﾎｱ ・｣8 determinant in homozygous compound showed the highest hemoglobin level among these ﾎｲ-thalassemia patients

Establishment of a reborn MMV-microarray technology: realization of microbiome analysis and other hitherto inaccessible technologies

BACKGROUND: With the accelerating development of bioscience, the problem of research cost has become important. We previously devised and developed a novel concept microarray with manageable volumes (MMV) using a soft gel. It demonstrated the great potential of the MMV technology with the examples of 1024-parallel-cell culture and PCR experiments. However, its full potential failed to be expressed, owing to the nature of the material used for the MMV chip. RESULTS: In the present study, by developing plastic-based MMVs and associated technologies, we introduced novel technologies such as C2D2P (in which the cells in each well are converted from DNA to protein in 1024-parallel), NGS-non-dependent microbiome analysis, and other powerful applications. CONCLUSIONS: The reborn MMV-microarray technology has proven to be highly efficient and cost-effective (with approximately 100-fold cost reduction) and enables us to realize hitherto unattainable technologies

The ASTRO-H X-ray Observatory

The joint JAXA/NASA ASTRO-H mission is the sixth in a series of highly successful X-ray missions initiated by the Institute of Space and Astronautical Science (ISAS). ASTRO-H will investigate the physics of the high-energy universe via a suite of four instruments, covering a very wide energy range, from 0.3 keV to 600 keV. These instruments include a high-resolution, high-throughput spectrometer sensitive over 0.3-2 keV with high spectral resolution of Delta E < 7 eV, enabled by a micro-calorimeter array located in the focal plane of thin-foil X-ray optics; hard X-ray imaging spectrometers covering 5-80 keV, located in the focal plane of multilayer-coated, focusing hard X-ray mirrors; a wide-field imaging spectrometer sensitive over 0.4-12 keV, with an X-ray CCD camera in the focal plane of a soft X-ray telescope; and a non-focusing Compton-camera type soft gamma-ray detector, sensitive in the 40-600 keV band. The simultaneous broad bandpass, coupled with high spectral resolution, will enable the pursuit of a wide variety of important science themes.Comment: 22 pages, 17 figures, Proceedings of the SPIE Astronomical Instrumentation "Space Telescopes and Instrumentation 2012: Ultraviolet to Gamma Ray

Hitomi (ASTRO-H) X-ray Astronomy Satellite

The Hitomi (ASTRO-H) mission is the sixth Japanese x-ray astronomy satellite developed by a large international collaboration, including Japan, USA, Canada, and Europe. The mission aimed to provide the highest energy resolution ever achieved at E  >  2  keV, using a microcalorimeter instrument, and to cover a wide energy range spanning four decades in energy from soft x-rays to gamma rays. After a successful launch on February 17, 2016, the spacecraft lost its function on March 26, 2016, but the commissioning phase for about a month provided valuable information on the onboard instruments and the spacecraft system, including astrophysical results obtained from first light observations. The paper describes the Hitomi (ASTRO-H) mission, its capabilities, the initial operation, and the instruments/spacecraft performances confirmed during the commissioning operations for about a month

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection