Structural feature of N-glycans of bamboo shoot glycoproteins: useful source of plant antigenic N-glycans

An effective method to prepare plant complex type (PCT) N-glycans in large amounts has been required to evaluate their immunological activity. In this study, we found that glycoproteins in bamboo shoots predominantly carry PCT N-glycans including the Lewis a epitope-containing ones, suggesting that bamboo shoot is an excellent source for the plant antigenic glycans to synthesize immunoactive neoglycopolymers

日本語教師の学び合いの場を協働構築する意義-マレーシア人教師と日本人教師による社会的実践活動の分析から-

早大学位記番号:新8252早稲田大

Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections

Photo-isolation chemistry (PIC) enables isolation of transcriptome information from locally defined areas by photo-irradiation. Here, we present an optimized PIC protocol for formalin-fixed frozen and paraffin mouse sections and fresh-frozen mouse sections. We describe tissue section preparation and permeabilization, followed by in situ reverse transcription using photo-caged primers. We then detail immunostaining and UV-mediated uncaging to the target areas, followed by linear amplification of uncaged cDNAs, library preparation, and quantification. This protocol can be applied to various animal tissue types

Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

京の伝統野菜ミブナの育種の歴史を解明. 京都大学プレスリリース. 2021-06-02.Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna

High-depth spatial transcriptome analysis by photo-isolation chemistry

光照射を用いた超高解像度な遺伝子解析技術の開発に成功 --組織内に潜むがん細胞の病理診断などに応用可能--. 京都大学プレスリリース. 2021-07-27.In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8, 000 genes were detected with 7 × 10⁴ unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions

Nitroprusside increases intracellular Zn2+ concentration without affecting cellular thiol content : A model experiment using rat thymocytes and FluoZin-3

Nitric oxide (NO) is cytotoxic under some conditions although it has physiological roles. It is recently proposed that the cytotoxicity of NO is resulted from its interaction with glutathione and zinc. Since we have revealed that a decrease in cellular content of non-protein thiols, presumably glutathione, induces intracellular Zn2+ release, there is a possibility that the cytotoxicity of nitroprusside, a donor of NO, is resulted from the interaction of NO with cellular thiols, leading to an increase in intracellular Zn2+ concentration. To test the possibility, the effects of nitroprusside on cell lethality, intracellular thiol content, and intracellular Zn2+ concentration were examined in rat thymocytes by using a flow cytometer with propidium iodide and FluoZin-3. Nitroprusside at concentrations of 0.3 mM or more (up to 10 mM) significantly augmented FluoZin-3 fluorescence, indicating an increase in intracellular Zn2+ concentration. It was also the case under external Zn2+-free condition, suggesting nitroprusside-induced release of intracellular Zn2+. However, nitroprusside at 10 mM did not affect cell lethality and cellular thiol content. Thus, it can be concluded that nitroprusside-induced increase in intracellular Zn2+ concentration is not related to its cytotoxicity

Tetracaine decreases intracellular Zn2+ concentration by inhibiting Zn2+ influx in rat thymocytes

In this study to examine the cytotoxic property of tetracaine, we cytometrically examined the effect of tetracaine on intracellular Zn2+ concentration by the use of FluoZin-3, a fluorescent indicator of intracellular Zn2+. Lidocaine was used as a reference drug. The incubation of rat thymocytes with tetracaine decreased the intensity of FluoZin-3 fluorescence while that with lidocaine increased the intensity. The incubation with 10 μM DTPA, a chelator for extracellular Zn2+, attenuated the tetracaine-induced decrease in fluorescence intensity. The application of ZnCl2 augmented FluoZin-3 fluorescence. The augmentation by ZnCl2 was a temperature-sensitive. Tetracaine attenuated the ZnCl2-induced augmentation of FluoZin-3 fluorescence. Taken together, the results suggest that tetracaine attenuates membrane Zn2+ influx, resulting in a decrease in intracellular Zn2+ concentration in rat thymocytes. Although the cells in this study are not targets for actions of local anesthetics, the result may give one clue to explain the difference between the cytotoxicity of local anesthetics since the action of tetracaine on FluoZin-3 fluorescence was opposite to that of lidocaine

Evaluation of transporter-mediated hepatobiliary transport of newly developed ¹⁸F-labeled pitavastatin derivative, PTV-F1, in rats by PET imaging

Quantitative evaluations of the functions of uptake and efflux transporters directly in vivo is desired to understand an efficient hepatobiliary transport of substrate drugs. Pitavastatin is a substrate of organic anion transporting polypeptides (OATPs) and canalicular efflux transporters; thus, it can be a suitable probe for positron-emission tomography (PET) imaging of hepatic transporter functions. To characterize the performance of [¹⁸F]PTV-F1, an analogue of pitavastatin, we investigated the impact of rifampicin (a typical OATP inhibitor) coadministration or Bcrp (breast cancer resistance protein) knockout on [¹⁸F]PTV-F1 hepatic uptake and efflux in rats by PET imaging. After intravenous administration, [¹⁸F]PTV-F1 selectively accumulated in the liver, and the radioactivity detected in plasma, liver, and bile mainly derived from the parent PTV-F1 during the PET study (∼40 min). Coadministration of rifampicin largely decreased the hepatic uptake of [¹⁸F]PTV-F1 by 73%. Because of its lower clearance in rats, [¹⁸F]PTV-F1 is more sensitive for monitoring changes in hepatic OATP1B function that other previously reported OATP1B PET probes. Rifampicin coadministration also significantly decreased the biliary excretion of radioactivity by 65%. Bcrp knockout did not show a significant impact on its biliary excretion.[¹⁸F]PTV-F1 enables quantitative analysis of the hepatobiliary transport system for organic anions

Replication study of the association of SNPs in the LHX3-QSOX2 and IGF1 loci with adult height in the Japanese population; wide-ranging comparison of each SNP genotype distribution

Adult height is a highly heritable trait involving multiple genes. Recent genome-wide association studies have identified that SNP rs12338076 in the LHX3-QSOX2 locus, and rs1457595 and rs17032362 in the IGF1 locus are associated with human height in the Japanese population (Okada et al. (2010)[9]). We performed a replication study to examine the associations between these three SNPs and adult height in the Japanese population based on autopsy cases. However, it was not possible to confirm that all these SNPs influenced adult height in the study population. We first conducted a wide-ranging survey of these three SNPs in the above genes using nine different populations including Asians, Africans and Caucasians, and demonstrated that the genotypes of rs12338076 and rs17032362 were distributed in an ethnicity-dependent manner; even within Asian populations, the genotype distributions of the SNPs differed widely. Although there are differences in height distribution between different populations, possibly due to genetic factors and/or gene-environmental interactions, the contradictory results of the association study and ethnic differences in genotype distribution allow us to assume that these height-related SNPs in the genes may contribute to adult height to a slight extent, at least in the Japanese population. It is anticipated that the present information will be useful for developing a reliable tool for personal identification through elucidation of the genetic basis of human height