Biology subjects

Takeuchi, T.

Publications and source records attributed to Takeuchi, T..

6 recordsLinked to original sources

bioRxiv2018

A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology

Urodele amphibian newts have unique biological properties, notably including prominent regeneration ability. Iberian ribbed newt, Pleurodeles waltl, is a promising model newt along with the successful development of the easy breeding system and efficient transgenic and genome editing methods. However, genetic information of P. waltl was limited. In the present study, we conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build gene models and annotate them. We generated 1.2 billion Illumina reads from a wide variety of samples across 11 different tissues and 9 time points during embryogenesis. They were assembled into 202,788 non-redundant contigs that appear to cover nearly complete (~98%) P. waltl protein-coding genes. Using the gene set as a reference, our gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Ortholog analyses with other vertebrates revealed the gene repertoire evolution of amphibians which includes urodele-specific loss of bmp4 and duplications of wnt11b. Our transcriptome resource will enhance future research employing this emerging model animal for regeneration research as well as other areas such as developmental biology, stem cell biology, cancer research, ethology and toxico-genomics. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).

genomics↗

bioRxiv2018

A transgenic mutant mouse line accompanied by the complete deletion of interleukin-33 showed insulin and leptin resistances

Interleukin (IL) -33 has been identified as a member of the IL-1 family. Members of the IL-1 family have been reported to be involved in the regulation of energy homeostasis and glucose metabolism. Homozygous transgenic mutant mice of FLP14 line, that we previously generated, unexpectedly developed mature-onset obesity and diabetes. Through genetic investigations, we found that insertion of the transgenes had resulted in complete deletion of the Il33 gene. These obese male homozygous mutant mice exhibited hyperphagia with hyperleptinemia and insulin resistance caused by increased hepatic gluconeogenesis and decreased glucose uptake in skeletal muscle. As a result of examining preobese male homozygous mutant mice to investigate with the exclusion of the effect of obesity, hyperphagia with hyperleptinemina and insulin resistance caused by decreased glucose uptake in skeletal muscle were already observed, but the increased hepatic glucose production was not. To investigate whether the insulin resistance was caused by deletion of the Il33 gene, we treated these preobese homozygous mutant mice with recombinant IL-33 protein and noted a significant improvement in insulin resistance. Thus, insulin resistance in these homozygous mutant mice was caused, at least in part, by IL-33 deficiency, suggesting a favorable role of IL-33 for glucose metabolism in the skeletal muscle.

molecular biology↗

bioRxiv2018

Prospective randomized controlled study directly comparing tadalafil and tamsulosin for male patients with lower urinary tract symptoms.

Lower urinary tract symptoms are widespread in elderly men and often suggestive of benign prostatic hyperplasia (LUTS/BPH). A randomized, prospective, and open-labeled trial directly comparing the effects of tadalafil (a phosphodiesterase 5 inhibitor) 5 mg once daily and tamsulosin (an 1-blocker) 0.2 mg once daily for 12 weeks in LUTS/BPH patients was conducted. Data were recorded before randomization as well as at 4, 8, and 12 weeks after medication. Fifteen patients allocated tadalafil and 20 allocated tamsulosin completed 12 weeks of medication. Total IPSS, IPSS voiding, and IPSS-QOL scores declined with medication, but there was no difference between drugs. IPSS storage scores reduced more in the tamsulosin group than tadalafil group. OABSS did not decline significantly with medication. IIEF5 was maintained in the tadalafil group, but declined in the tamsulosin group. The maximum flow rate and post-void residual urine volume did not significantly change with medication. Daytime, night-time, and 24-hour urinary frequencies as well as the mean and largest daytime, night-time, and 24-hour voiding volumes per void did not significantly change with medication. In conclusion, tamsulosin was more effective to reduce storage symptoms than tadalafil. Tadalafil had the advantage of maintaining the erectile function.

clinical trials↗

bioRxiv2018

Prediction of prostate cancer by deep learning with multilayer artificial neural network.

ObjectivesTo predict the rate of prostate cancer detection on prostate biopsy more accurately, the performance of deep learning utilizing a multilayer artificial neural network was investigated.\n\nMaterials and methodsA total of 334 patients who underwent multiparametric magnetic resonance imaging before ultrasonography-guided transrectal 12-core prostate biopsy were enrolled in the analysis. Twenty-two non-selected variables as well as selected ones by least absolute shrinkage and selection operator (Lasso) regression analysis and by stepwise logistic regression analysis were input into the constructed multilayer artificial neural network (ANN) programs. 232 patients were used as training cases of ANN programs, and the remaining 102 patients were for the test to output the probability of prostate cancer existence, accuracy of prostate cancer prediction, and area under the receiver operating characteristic (ROC) curve with the learned model.\n\nResultsWith any prostate cancer objective variable, Lasso and stepwise regression analyses selected 12 and 9 explanatory variables from 22, respectively. In common between them, age at biopsy, findings on digital rectal examination, findings in the peripheral zone on MRI diffusion-weighted imaging, and body mass index were positively influential variables, while numbers of previous prostatic biopsy and prostate volume were negatively influential. Using trained ANNs with multiple hidden layers, the accuracy of predicting any prostate cancer in test samples was about 5-10% higher compared with that with logistic regression analysis (LR). The AUCs with multilayer ANN were significantly larger on inputting variables that were selected by the stepwise logistic regression compared with the AUC with LR. The ANN had a higher net-benefit than LR between prostate cancer probability cut-off values of 0.38 and 0.6.\n\nConclusionANN accurately predicted prostate cancer without biopsy marginally better than LR. However, for clinical application, ANN performance may still need improvement.

bioinformatics↗

bioRxiv2017

Prediction error induced motor contagions in human behaviors

Motor contagions refer to implicit effects on ones actions induced by observation of others actions. Motor contagions are believed to be induced simply by action observation and cause an observers action to become similar to the observed action. In contrast, here we report a new motor contagion that is induced only when the observation is accompanied by prediction errors-differences between actions one observes and those he/she predicts or expects. Moreover, this contagion may not manifest as a similarity between ones own and observed actions. In our experiment, observation of the same action induced distinct motor contagions, depending on whether prediction errors are present or not. In the absence of prediction errors, similarly to previous reports, participants actions changed to become similar to the observed action, while in the presence of prediction errors, their actions changed to diverge away from it. Our results suggest distinct effects of action observation and action prediction on human actions.

neuroscience↗

bioRxiv2017

Introduction of single nucleotide variations into the promoter region of the mouse kidney anion exchanger 1 gene downstream of a TATA box changes its transcriptional activity.

(Introduction) Distal renal tubular acidosis (dRTA) is characterized by an impairment of urine acidification and can be caused by variations in genes functioning in -intercalated cells such as anion exchanger 1 (AE1). AE1 encodes the Cl-/HCO3- exchanger in erythrocytes (eAE1) and -intercalated cells (kAE1). We previously reported that in human erythroid intron 3 containing the promoter region of human kAE1, a SNP (rs999716) 39 base pairs downstream of the TATA box showed a higher minor allele A frequency in incomplete dRTA patients and such a promoter region showed reduced activities, leading to the hypothesis that those with the A allele may express less kAE1, developing incomplete dRTA. Here, single nucleotide variations were introduced downstream of the TATA box in the murine erythroid intron 3 to investigate changes in the promoter activity for murine kAE1 mRNA. (Methods) The erythroid intron 3 of C57BL/6 was subcloned into the pGL4.17 reporter vector, leading to mu kAE1Pro-pGL4.17. Three types of G to A substitutions were introduced 33, 35, and 36 base pairs downstream of the TATA box in the murine kAE1 promoter region by inverse PCR (Var1, Var2, and Var3, respectively). The HEK 293 cells were transfected with vectors. After 24 hours, the firefly luciferase activity was determined. (Results and Discussion) The promoter activity of Var1, as well as that of Var2 to a lesser extent, was reduced compared with that of the wild-type. The introduction of variations such as Var1 and Var2 into the murine genome by genome editing may help to establish mouse models of incomplete dRTA.

genomics↗