| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Hansson, Magnus, et al.
(författare)
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Cyclophilin D-sensitive mitochondrial permeability transition in adult human brain and liver mitochondria.
- 2011
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Ingår i: Journal of Neurotrauma. - : Mary Ann Liebert Inc. - 1557-9042 .- 0897-7151. ; 28, s. 143-153
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Tidskriftsartikel (refereegranskat)abstract
- The mitochondrial permeability transition (mPT) is considered to be a major cause of cell death under a variety of pathophysiological conditions of the CNS and other organs. Pharmacological inhibition or genetic knock-out of the matrix protein cyclophilin D (CypD) prevents mPT and cell degeneration in several models of brain injury. Provided that findings in animal models can be translatable to human disease, pharmacological inhibition of mPT offers a promising therapeutic target. The objective of this study was to validate the presence of a CypD-sensitive mPT in adult human brain and liver mitochondria. In order to perform functional characterization of human mitochondria, fresh tissue samples were obtained during hemorrhage or tumor surgery and mitochondria were rapidly isolated. Mitochondrial calcium retention capacity, a quantitative assay for mPT, was significantly increased by the CypD inhibitor cyclosporin A in both human brain and liver mitochondria, whereas thiol-reactive compounds and oxidants sensitized mitochondria to calcium-induced mPT. Brain mitochondria underwent swelling upon calcium overload, which was reversible upon calcium removal. To further explore mPT of human mitochondria, liver mitochondria were demonstrated to exhibit several classical features of the mPT phenomenon such as calcium-induced loss of membrane potential and respiratory coupling, as well as release of the pro-apoptotic protein cytochrome c. It is concluded that adult viable human brain and liver mitochondria possess an active CypD-sensitive mPT. The present findings support the rationale of CypD and mPT inhibition as pharmacological targets in acute and chronic neurodegeneration.
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| 5. |
- Michikami, Tatsuhiro, et al.
(författare)
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Three-axial shape distributions of pebbles, cobbles and boulders smaller than a few meters on asteroid Ryugu
- 2022
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Ingår i: Icarus. - : Elsevier. - 0019-1035 .- 1090-2643. ; 381
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Tidskriftsartikel (refereegranskat)abstract
- Over a broad size range, the shapes of impact fragments from catastrophic disruptions are distributed around the mean axial ratio 2: √2: 1, irrespective of experimental conditions and target materials. Although most blocks on asteroids are likely to be impact fragments, there is not enough quantitative data for reliable statistics on their three-axial lengths and/or ratios because it is difficult to precisely estimate the heights of the blocks. In this study, we evaluate the heights of blocks on asteroid Ryugu by measuring their shadows. The three-axial ratios of ~4100 small blocks with diameters from 5.0 cm to 7.6 m in Ryugu's equatorial region are investigated using eight close-up images of narrower localities taken at altitudes below 500 m, i.e. at <5.4 cm/pixel resolution, obtained immediately before the second touch-down of the Hayabusa2 spacecraft. The purpose of this study is to investigate the block shape distribution, which is important for understanding the geological history of asteroid Ryugu. Specifically, the shape distribution is compared to laboratory impact fragments. Our observations indicate that the shape distributions of blocks smaller than 1 m on Ryugu are consistent with laboratory impact fragment shape distributions, implying that the dominant shape-determining process for blocks on Ryugu was impact fragmentation. Blocks several meters in size in the equatorial region seem to be slightly flatter than the rest, suggesting that some blocks are partly buried in a bed of regolith. In conclusion, the shape distributions of blocks from several-cm to several-m in the equatorial region of asteroid Ryugu suggest that these are mainly fragments originating from the catastrophic disruption of their parent body and/or from a later impact.
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| 6. |
- Mizutani, Anna, et al.
(författare)
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Cell type-specific target selection by combinatorial binding of Smad2/3 proteins and hepatocyte nuclear factor 4alpha in HepG2 cells
- 2011
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 286:34, s. 29848-29860
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Tidskriftsartikel (refereegranskat)abstract
- Specific regulation of target genes by transforming growth factor-β (TGF-β) in a given cellular context is determined in part by transcription factors and cofactors that interact with the Smad complex. In this study, we determined Smad2 and Smad3 (Smad2/3) binding regions in the promoters of known genes in HepG2 hepatoblastoma cells, and we compared them with those in HaCaT epidermal keratinocytes to elucidate the mechanisms of cell type- and context-dependent regulation of transcription induced by TGF-β. Our results show that 81% of the Smad2/3 binding regions in HepG2 cells were not shared with those found in HaCaT cells. Hepatocyte nuclear factor 4α (HNF4α) is expressed in HepG2 cells but not in HaCaT cells, and the HNF4α-binding motif was identified as an enriched motif in the HepG2-specific Smad2/3 binding regions. Chromatin immunoprecipitation sequencing analysis of HNF4α binding regions under TGF-β stimulation revealed that 32.5% of the Smad2/3 binding regions overlapped HNF4α bindings. MIXL1 was identified as a new combinatorial target of HNF4α and Smad2/3, and both the HNF4α protein and its binding motif were required for the induction of MIXL1 by TGF-β in HepG2 cells. These findings generalize the importance of binding of HNF4α on Smad2/3 binding genomic regions for HepG2-specific regulation of transcription by TGF-β and suggest that certain transcription factors expressed in a cell type-specific manner play important roles in the transcription regulated by the TGF-β-Smad signaling pathway.
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| 7. |
- Morokuma, Tomoki, et al.
(författare)
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Subaru FOCAS Spectroscopic Observations of High-Redshift Supernovae
- 2010
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Ingår i: Nippon Tenmon Gakkai obun kenkyu hokoku. - 0004-6264. ; 62:1, s. 19-37
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Tidskriftsartikel (refereegranskat)abstract
- We present spectra of high-redshift supernovae (SNe) that were taken with the Subaru low-resolution optical spectrograph, FOCAS. These SNe were found in SN surveys with Suprime-Cam on Subaru, the CFH12k camera on the Canada-France-Hawaii Telescope, and the Advanced Camera for Surveys on the Hubble Space Telescope. These SN surveys specifically targeted z > 1 Type la supernovae (SNe Ia). From the spectra of 39 candidates, we obtained redshifts for 32 candidates and spectroscopically identified 7 active candidates as probable SNe Ia, including one at z = 1.35, which is the most distant SN la to be spectroscopically confirmed with a ground-based telescope. An additional 4 candidates were identified as likely SNe la from the spectrophotometric properties of their host galaxies. Seven candidates are not SNe la, either being SNe of another type or active galactic nuclei. When SNe la were observed within one week of the maximum light, we found that we could spectroscopically identify most of them up to z = 1.1. Beyond this redshift, very few candidates were spectroscopically identified as SNe Ia. The current generation of super red-sensitive, fringe-free CCDs will push this redshift limit higher.
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| 8. |
- Okita, Yukari, et al.
(författare)
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The transcription factor MAFK induces EMT and malignant progression of triple-negative breast cancer cells through its target GPNMB
- 2017
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Ingår i: Science Signaling. - : AMER ASSOC ADVANCEMENT SCIENCE. - 1945-0877 .- 1937-9145. ; 10:474
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Tidskriftsartikel (refereegranskat)abstract
- Triple-negative breast cancer (TNBC) is particularly aggressive and difficult to treat. For example, the transforming growth factor-beta (TGF-beta) pathway is implicated in TNBC progression and metastasis, but its opposing role in tumor suppression in healthy tissues and early-stage lesions makes it a challenging target. Therefore, additional molecular characterization of TNBC may lead to improved patient prognosis by informing the development and optimum use of targeted therapies. We found that musculoaponeurotic fibrosarcoma (MAF) oncogene family protein K (MAFK), a member of the small MAF family of transcription factors that are induced by the TGF-beta pathway, was abundant in human TNBC and aggressive mouse mammary tumor cell lines. MAFK promoted tumorigenic growth and metastasis by 4T1 cells when implanted subcutaneously in mice. Overexpression of MAFK in mouse breast epithelial NMuMG cells induced epithelial-mesenchymal transition (EMT) phenotypes and promoted tumor formation and invasion in mice. MAFK induced the expression of the gene encoding the transmembrane glycoprotein nmb(GPNMB). Similar to MAFK, GPNMB overexpression in NMuMG cells induced EMT, tumor formation, and invasion, in mice, whereas knockdown of MAFK in tumor cells before implantation suppressed tumor growth and progression. MAFK and GPNMB expression correlated with poor prognosis in TNBC patients. These findings suggest that MAFK and its target gene GPNMB play important roles in the malignant progression of TNBC cells, offering potentially new therapeutic targets for TNBC patients.
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| 9. |
- Pham, Tuan, et al.
(författare)
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Texture Analysis and Synthesis of Malignant and Benign Mediastinal Lymph Nodes in Patients with Lung Cancer on Computed Tomography
- 2017
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Texture analysis of computed tomography (CT) imaging has been found useful to distinguish subtle differences, which are in-visible to human eyes, between malignant and benign tissues in cancer patients. This study implemented two complementary methods of texture analysis, known as the gray-level co-occurrence matrix (GLCM) and the experimental semivariogram (SV) with an aim to improve the predictive value of evaluating mediastinal lymph nodes in lung cancer. The GLCM was explored with the use of a rich set of its derived features, whereas the SV feature was extracted on real and synthesized CT samples of benign and malignant lymph nodes. A distinct advantage of the computer methodology presented herein is the alleviation of the need for an automated precise segmentation of the lymph nodes. Using the logistic regression model, a sensitivity of 75%, specificity of 90%, and area under curve of 0.89 were obtained in the test population. A tenfold cross-validation of 70% accuracy of classifying between benign and malignant lymph nodes was obtained using the support vector machines as a pattern classifier. These results are higher than those recently reported in literature with similar studies.
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| 10. |
- Sonkoly, Enikö, et al.
(författare)
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Protein kinase C-dependent upregulation of miR-203 induces the differentiation of human keratinocytes
- 2010
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Ingår i: Journal of Investigative Dermatology. - : Elsevier BV. - 0022-202X .- 1523-1747. ; 130:1, s. 124-134
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Tidskriftsartikel (refereegranskat)abstract
- Terminal differentiation of keratinocytes is a multistep process that requires a coordinated program of gene expression. We aimed to explore the possible involvement of a previously unreported class of non-coding RNA genes, microRNAs (miRNAs) in keratinocyte differentiation by using miRNA expression profiling. Out of 365 miRNAs tested, 7 showed significant change between keratinocytes cultured in low or high calcium concentration. The highest-ranked upregulated gene was miR-203, whose expression was significantly upregulated in response to calcium and other inducers of keratinocyte differentiation such as 12-O-tetradecanoylphorbol-13-acetate (TPA) and vitamin D(3). Differentiation-induced upregulation of miR-203 expression was blocked by treatment with specific inhibitors of protein kinase C (PKC), GF109203X, and Ro31-8220. Moreover, our results showed that the activator protein-1 (AP-1) proteins c-Jun and JunB regulate miR-203 expression in keratinocytes. In contrast to inducers of keratinocyte differentiation, epidermal growth factor and keratinocyte growth factor suppressed miR-203 expression in keratinocytes below the basal level. Overexpression of miR-203 in keratinocytes resulted in enhanced differentiation, whereas inhibition of miR-203 suppressed calcium-induced terminal differentiation as judged by involucrin expression. These results suggest that upregulation of miR-203 in human keratinocytes is required for their differentiation and is dependent on the activation of the PKC/AP-1 pathway.
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| 11. |
- Takeuchi, Hiroyoshi, et al.
(författare)
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Impact of Once- Versus Twice-Daily Perphenazine Dosing on Clinical Outcomes: An Analysis of the CATIE Data
- 2014
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Ingår i: Journal of Clinical Psychiatry. - : Physicians Postgraduate Press. - 0160-6689 .- 1555-2101. ; 75:5, s. 506-511
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The objective of this study was to evaluate the impact of once- versus twice-daily dosing of perphenazine, which has a plasma half-life of 8–12 hours, on clinical outcomes in patients with schizophrenia.Method: Data from phase 1 of the Clinical Antipsychotic Trial of Intervention Effectiveness (CATIE) conducted between January 2001 and December 2004 were used in this post hoc analysis. Patients with schizophrenia (DSM-IV) randomly allocated to treatment with perphenazine were also randomly assigned to once-daily (N = 133) or twice-daily (N = 124) dosing and followed over 18 months. Discontinuation rate and time to discontinuation were used as primary outcomes to compare the 2 groups. The following clinical outcomes were analyzed as secondary measures: efficacy—Positive and Negative Syndrome Scale, Clinical Global Impressions-Severity scale, Calgary Depression Scale for Schizophrenia, and Drug Attitude Inventory and safety/tolerability—Abnormal Involuntary Movement Scale, Barnes Akathisia Rating Scale, Simpson-Angus Scale, and body weight. Data on treatment-emergent adverse events, concomitant psychotropic medications, and medication adherence (pill count and clinician rating scale) were also analyzed for each group.Results: No significant differences were found in any outcome measures between the once-daily and twice-daily dosing groups, which remained the same when using the mean dose of perphenazine as a covariate.Conclusions: Perphenazine is routinely administered in a divided dosage regimen because of its relatively short plasma half-life. However, the present findings challenge such a strategy, suggesting that once-daily represents a viable treatment option. Results are discussed in the context of more recent evidence that challenges the need for high and continuous dopamine D2 receptor blockade to sustain antipsychotic response..
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| 12. |
- Uchino, Hiroyuki, et al.
(författare)
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Cyclophilin-D inhibition in neuroprotection : dawn of a new era of mitochondrial medicine
- 2013
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Ingår i: Acta Neurochirurgica. Supplementum. - Vienna : Springer Vienna. - 0065-1419. ; 118, s. 5-311
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Tidskriftsartikel (refereegranskat)abstract
- Traumatic brain injury and ischemia can result in marked neuronal degeneration and residual impairment of cerebral function. However, no effective pharmacological treatment directed at tissues of the central nervous system (CNS) for acute intervention has been developed. The detailed pathophysiological cascade leading to -neurodegeneration in these conditions has not been elucidated, but cellular calcium overload and mitochondrial dysfunction have been implicated in a wide range of animal models involving degeneration of the CNS. In particular, activation of the calcium-induced mitochondrial permeability transition (mPT) is considered to be a major cause of cell death inferred by the broad and potent neuroprotective effects of -pharmacological inhibitors of mPT, especially modulators of cyclophilin activity and, more specifically, genetic inactivation of the mitochondrial cyclophilin, cyclophilin D. Reviewed are evidence and challenges that could bring on the dawning of mitochondrial medicine aimed at safeguarding energy supply following acute injury to the CNS.
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