Predicted mouse peroxisome-targeted proteins and their actual subcellular locations.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: The import of most intraperoxisomal proteins is mediated by peroxisome targeting signals at their C-termini (PTS1) or N-terminal regions (PTS2). Both signals have been integrated in subcellular location prediction programs. However their present performance, particularly of PTS2-targeting did not seem fitting for large-scale screening of sequences. RESULTS: We modified an earlier reported PTS1 screening method to identify PTS2-containing mouse candidates using a combination of computational and manual annotation. For rapid confirmation of five new PTS2- and two previously identified PTS1-containing candidates we developed the new cell line CHO-perRed which stably expresses the peroxisomal marker dsRed-PTS1. Using CHO-perRed we confirmed the peroxisomal localization of PTS1-targeted candidate Zadh2. Preliminary characterization of Zadh2 expression suggested non-PPARalpha mediated activation. Notably, none of the PTS2 candidates located to peroxisomes. CONCLUSION: In a few cases the PTS may oscillate from "silent" to "functional" depending on its surface accessibility indicating the potential for context-dependent conditional subcellular sorting. Overall, PTS2-targeting predictions are unlikely to improve without generation and integration of new experimental data from location proteomics, protein structures and quantitative Pex7 PTS2 peptide binding assays

Predicted mouse peroxisome-targeted proteins and their actual subcellular locations

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The import of most intraperoxisomal proteins is mediated by peroxisome targeting signals at their C-termini (PTS1) or N-terminal regions (PTS2). Both signals have been integrated in subcellular location prediction programs. However their present performance, particularly of PTS2-targeting did not seem fitting for large-scale screening of sequences. Results We modified an earlier reported PTS1 screening method to identify PTS2-containing mouse candidates using a combination of computational and manual annotation. For rapid confirmation of five new PTS2- and two previously identified PTS1-containing candidates we developed the new cell line CHO-perRed which stably expresses the peroxisomal marker dsRed-PTS1. Using CHO-perRed we confirmed the peroxisomal localization of PTS1-targeted candidate Zadh2. Preliminary characterization of Zadh2 expression suggested non-PPARα mediated activation. Notably, none of the PTS2 candidates located to peroxisomes. Conclusion In a few cases the PTS may oscillate from "silent" to "functional" depending on its surface accessibility indicating the potential for context-dependent conditional subcellular sorting. Overall, PTS2-targeting predictions are unlikely to improve without generation and integration of new experimental data from location proteomics, protein structures and quantitative Pex7 PTS2 peptide binding assays

Loss of miR-542-3p enhances IGFBP-1 expression in decidualizing human endometrial stromal cells

Endometrial decidualization represents an essential step for the successful implantation of the embryo; however, the molecular mechanism behind this differentiation process remains unclear. This study aimed to identify novel microRNAs (miRNAs) involved in the regulation of decidual gene expression in human endometrial stromal cells (HESCs). An in vitro analysis of primary undifferentiated and decidualizing HESCs was conducted. HESCs were isolated from hysterectomy specimens from normally cycling premenopausal women with uterine fibroids, who were not on hormonal treatment at the time of surgery. Primary HESCs were expanded in culture and decidualized with 8-bromo-cyclic adenosine monophosphate and medroxyprogesterone acetate. Microarray analysis identified six miRNAs differentially expressed in response to decidualization of HESCs. All but one miRNA were downregulated upon decidualization, including miR-542-3p. We demonstrated that miR-542-3p overexpression inhibits the induction of major decidual marker genes, including IGFBP1, WNT4 and PRL. In addition, miR-542-3p overexpression inhibited the morphological transformation of HESCs in response to deciduogenic cues. A luciferase reporter assay confirmed that the 3′-untranslated region of IGFBP1 mRNA is targeted by miR-542-3p. The results suggest that miR-542-3p plays an important role in endometrial decidualization by regulating the expression of major decidual marker genes

Single-cell transcriptome atlas of Drosophila gastrula 2.0

ショウジョウバエ原腸胚における1細胞遺伝子発現アトラスを作成 --ゲノム情報による発生制御の解明に向けた基盤的リソース--. 京都大学プレスリリース. 2023-07-11.During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing accurate spatial and lineage information are still lacking. Here, we report a single-cell transcriptome atlas of Drosophila gastrulae, divided into 77 transcriptomically distinct clusters. We find that the expression profiles of plasma-membrane-related genes, but not those of transcription-factor genes, represent each germ layer, supporting the nonequivalent contribution of each transcription-factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstruct the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation

The usefulness of nifekalant for activation mapping of premature beat-triggered atrial fibrillation: Suppression of atrial fibrillation initiation without inhibiting premature beat

AbstractA 66-year-old man underwent a second ablation for atrial fibrillation (AF). Intravenous isoproterenol administration caused the atrial premature beat (APB), triggering AF. The APB originated in the right atrium and invariably initiated AF. Therefore, contact activation mapping could not be performed without frequent electrocardioversion. To prevent the initiation of AF without inhibiting the APB firing, we administered nifekalant intravenously, which facilitated precise activation mapping and ablation of the AF-triggering APB. The administration of nifekalant may improve clinical outcomes of catheter ablation for AF triggered by non-pulmonary vein APB, which invariably initiates AF

Optical and Near-Infrared Photometry of Nova V2362 Cyg : Rebrightening Event and Dust Formation

We present optical and near-infrared (NIR) photometry of a classical nova, V2362 Cyg (= Nova Cygni 2006). V2362 Cyg experienced a peculiar rebrightening with a long duration from 100 to 240 d after the maximum of the nova. Our multicolor observation indicates an emergence of a pseudophotosphere with an effective temperature of 9000 K at the rebrightening maximum. After the rebrightening maximum, the object showed a slow fading homogeneously in all of the used bands for one week. This implies that the fading just after the rebrightening maximum ( less or equal 1 week ) was caused by a slowly shrinking pseudophotosphere. Then, the NIR flux drastically increased, while the optical flux steeply declined. The optical and NIR flux was consistent with blackbody radiation with a temperature of 1500 K during this NIR rising phase. These facts are likely to be explained by dust formation in the nova ejecta. Assuming an optically thin case, we estimate the dust mass of 10^(-8) -- 10^(-10) M_solar, which is less than those in typical dust-forming novae. These results support the senario that a second, long-lasting outflow, which caused the rebrightening, interacted with a fraction of the initial outflow and formed dust grains.Comment: 6 pages, 4 figures, 2010, PASJ, 62, 1103--1108, in pres

Fe-K line probing of material around the AGN central engine with Suzaku

We systematically analyzed the high-quality Suzaku data of 88 Seyfert galaxies. We obtained a clear relation between the absorption column density and the equivalent width of the 6.4 keV line above 10$^{23}$ cm$^{-2}$, suggesting a wide-ranging column density of $10^{23-24.5}$ cm$^{-2}$ with a similar solid and a Fe abundance of 0.7--1.3 solar for Seyfert 2 galaxies. The EW of the 6.4 keV line for Seyfert 1 galaxies are typically 40--120 eV, suggesting the existence of Compton-thick matter like the torus with a column density of $>10^{23}$ cm$^{-2}$ and a solid angle of $(0.15-0.4)*4pi$, and no difference of neutral matter is visible between Seyfert 1 and 2 galaxies. An absorber with a lower column density of $10^{21-23}$ cm$^{-2}$ for Compton-thin Seyfert 2 galaxies is suggested to be not a torus but an interstellar medium. These constraints can be understood by the fact that the 6.4 keV line intensity ratio against the 10--50 keV flux is almost identical within a range of 2--3 in many Seyfert galaxies. Interestingly, objects exist with a low EW, 10--30 eV, of the 6.4 keV line, suggesting that those torus subtends only a small solid angle of $<0.2*4pi$. Ionized Fe-K$\alpha$ emission or absorption lines are detected from several percents of AGNs. Considering the ionization state and equivalent width, emitters and absorbers of ionized Fe-K lines can be explained by the same origin, and highly ionized matter is located at the broad line region. The rapid increase in EW of the ionized Fe-K emission lines at $N_{H}>10^{23}$ cm$^{-2}$ is found, like that of the cold material. It is found that these features seem to change for brighter objects with more than several $10^{44}$ erg/s such that the Fe-K line features become weak. We discuss this feature, together with the torus structure.Comment: 32 pages, 20 figures, ApJ accepte