Estimation of the Postmortem Duration of Mouse Tissue by Electron Spin Resonance Spectroscopy

Electron spin resonance (ESR) method is a simple method for detecting various free radicals simultaneously and directly. However, ESR spin trap method is unsuited to analyze weak ESR signals in organs because of water-induced dielectric loss (WIDL). To minimize WIDL occurring in biotissues and to improve detection sensitivity to free radicals in tissues, ESR cuvette was modified and used with 5,5-dimethtyl-1-pyrroline N-oxide (DMPO). The tissue samples were mouse brain, hart, lung, liver, kidney, pancreas, muscle, skin, and whole blood, where various ESR spin adduct signals including DMPO-ascorbyl radical (AsA∗), DMPO-superoxide anion radical (OOH), and DMPO-hydrogen radical (H) signal were detected. Postmortem changes in DMPO-AsA∗ and DMPO-OOH were observed in various tissues of mouse. The signal peak of spin adduct was monitored until the 205th day postmortem. DMPO-AsA∗ in liver (y = 113.8–40.7 log (day), R1 = −0.779, R2 = 0.6, P < .001) was found to linearly decrease with the logarithm of postmortem duration days. Therefore, DMPO-AsA∗ signal may be suitable for detecting an oxidation stress tracer from tissue in comparison with other spin adduct signal on ESR spin trap method

Construction of novel metabolic pathways with artificial enzymes

Non-fossil raw materials can be utilized for the production of useful compounds by way of microbial fermentation . Sugars are obtained from carbon fixations of plants or photosynthetic microorganisms, and are used as a carbon source for the biosynthesis of useful target compounds by genetically modified microorganisms. In order for a microorganism to produce enough target compound, techniques for optimal metabolic design must include balance of energy production/consumption, redox pathways, and intracellular carbon flow. With recent innovations in genome analysis technology and information processing technology, computational design tools that can describe more than 1000 genome-scale metabolic reactions to efficiently produce target compounds have been developed worldwide. However, the established tools are not designed to search and create biosynthetic pathways for production of non-natural compounds from fossil resources. We developed BioProV and M-path, new simulation tools that enable metabolic design for the biosynthesis of unnatural compounds. By combining these tools with enzyme engineering technology, we succeeded in expanding the scope of bioproduction targets. The first example is construction of an artificial metabolic pathway to biosynthesize isoprene. Isoprene the raw material for production of synthetic rubber that can be used in automobile tires. Currently, isoprene is industrially produced as a by-product of naphtha pyrolysis. Therefore, by establishing green isoprene production technology, dependence upon petroleum can be reduced. Isoprene is a substance that can exist within cells of many organisms as a monomer of polyisoprene rubber, and also as a structural unit of secondary metabolites. It is difficult to optimize its synthentic pathway due to shortages of intracellular ATP supply, and challenges in the introduction of improved biosynthetic pathways. In nature, isoprene is produced from mevalonic acid through a five-step reaction, but the newly constructed artificial metabolic pathway consists of just two steps from mevalonic acid to isoprene. This results in a three-fold reduction in cellular energy consumption. Furthermore, we succeeded in constructing a highly active enzyme that exhibits 10,000-fold higher isoprene-producing activity relative to natural enzymes. By introducing these artificial metabolic reactions into Escherichia coli, efficient artificial isoprene production was achieved. In addition, we have developed a microbial production system for 1,3-butadiene, another alternative source for synthetic rubber. Moreover, rationally engineered enzymes from insects and plants enzymes have resulted in the construction of an artificial pathway to benzylisoquinoline alkaloids and downstream opioid analgesics

Surgical management of infants with mitral valve stenosis or atresia without diminutive ascending aorta

The surgical strategy in infants with mitral valve stenosis or atresia without diminutive ascending aorta remains to be established, including the potential for biventricular repair as a definitive operation. Our surgical experience of six infants with mitral valve stenosis (4patients) or atresia (2patients) without diminutive ascending aorta was evaluated based on three important factors:left ventricular volume;the nature of the systemic outflow obstruction; and the type of mitral valve anomaly. Two patients with systemic outflow tract diameter less than 65% of normal underwent systemic outflow tract reconstruction, and the other patients with outflow tract diameter more than 68%of normal were able to maintain systemic circulation without repair. Only one patient with mitral valve stenosis without left ventricular outflow tract obstruction underwent a successful open mitral valvotomy as a biventricular repair after first-stage palliation. The left ventricle of the other patients did not grow after first-stage palliation. Due to progressive subaortic narrowing, pulmonary artery banding should be avoided in patients with mitral atresia due to absent atrioventricular connection who are future Fontan candidates. Most patients with this lesion can be expected to become candidates for safe Fontan-type repair

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The habu genome reveals accelerated evolution of venom protein genes

Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 non-venom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole-genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type–specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI) transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA–mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our study demonstrates the utility of FAIRE-seq in providing a global view of cell type–specific regulatory elements in the genome and in identifying transcriptional regulators of adipocyte differentiation

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

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target