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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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- Milillo, A., et al.
(author)
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Investigating Mercury's Environment with the Two-Spacecraft BepiColombo Mission
- 2020
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In: Space Science Reviews. - : Springer Science and Business Media LLC. - 0038-6308 .- 1572-9672. ; 216:5
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Research review (peer-reviewed)abstract
- The ESA-JAXA BepiColombo mission will provide simultaneous measurements from two spacecraft, offering an unprecedented opportunity to investigate magnetospheric and exospheric dynamics at Mercury as well as their interactions with the solar wind, radiation, and interplanetary dust. Many scientific instruments onboard the two spacecraft will be completely, or partially devoted to study the near-space environment of Mercury as well as the complex processes that govern it. Many issues remain unsolved even after the MESSENGER mission that ended in 2015. The specific orbits of the two spacecraft, MPO and Mio, and the comprehensive scientific payload allow a wider range of scientific questions to be addressed than those that could be achieved by the individual instruments acting alone, or by previous missions. These joint observations are of key importance because many phenomena in Mercury's environment are highly temporally and spatially variable. Examples of possible coordinated observations are described in this article, analysing the required geometrical conditions, pointing, resolutions and operation timing of different BepiColombo instruments sensors.
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| 6. |
- Sugita, S., et al.
(author)
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The geomorphology, color, and thermal properties of Ryugu: Implications for parent-body processes
- 2019
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In: Science. - : AAAS. - 0036-8075 .- 1095-9203. ; 364:6437
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Journal article (peer-reviewed)abstract
- Asteroids fall to Earth in the form of meteorites, but these provide little information about their origins. The Japanese mission Hayabusa2 is designed to collect samples directly from the surface of an asteroid and return them to Earth for laboratory analysis. Three papers in this issue describe the Hayabusa2 team's study of the near-Earth carbonaceous asteroid 162173 Ryugu, at which the spacecraft arrived in June 2018 (see the Perspective by Wurm). Watanabeet al.measured the asteroid's mass, shape, and density, showing that it is a “rubble pile” of loose rocks, formed into a spinning-top shape during a prior period of rapid spin. They also identified suitable landing sites for sample collection. Kitazatoet al.used near-infrared spectroscopy to find ubiquitous hydrated minerals on the surface and compared Ryugu with known types of carbonaceous meteorite. Sugitaet al.describe Ryugu's geological features and surface colors and combined results from all three papers to constrain the asteroid's formation process. Ryugu probably formed by reaccumulation of rubble ejected by impact from a larger asteroid. These results provide necessary context to understand the samples collected by Hayabusa2, which are expected to arrive on Earth in December 2020.Science, this issue p.268, p.272, p.eaaw0422; see also p.230
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| 7. |
- Sakatani, N., et al.
(author)
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Anomalously porous boulders on (162173) Ryugu as primordial materials from its parent body
- 2021
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In: Nature Astronomy. - : Springer Nature. - 2397-3366. ; 5:8, s. 766-774
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Journal article (peer-reviewed)abstract
- Planetesimals—the initial stage of the planetary formation process—are considered to be initially very porous aggregates of dusts1,2, and subsequent thermal and compaction processes reduce their porosity3. The Hayabusa2 spacecraft found that boulders on the surface of asteroid (162173) Ryugu have an average porosity of 30–50% (refs. 4,5,6), higher than meteorites but lower than cometary nuclei7, which are considered to be remnants of the original planetesimals8. Here, using high-resolution thermal and optical imaging of Ryugu’s surface, we discovered, on the floor of fresh small craters (<20 m in diameter), boulders with reflectance (~0.015) lower than the Ryugu average6 and porosity >70%, which is as high as in cometary bodies. The artificial crater formed by Hayabusa2’s impact experiment9 is similar to these craters in size but does not have such high-porosity boulders. Thus, we argue that the observed high porosity is intrinsic and not created by subsequent impact comminution and/or cracking. We propose that these boulders are the least processed material on Ryugu and represent remnants of porous planetesimals that did not undergo a high degree of heating and compaction3. Our multi-instrumental analysis suggests that fragments of the highly porous boulders are mixed within the surface regolith globally, implying that they might be captured within collected samples by touch-down operations10,11.
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| 9. |
- Amm, O., et al.
(author)
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Towards understanding the electrodynamics of the 3-dimensional high-latitude ionosphere : present and future
- 2008
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In: Annales Geophysicae. - : Copernicus GmbH. - 0992-7689 .- 1432-0576. ; 26:12, s. 3913-3932
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Research review (peer-reviewed)abstract
- Traditionally, due to observational constraints, ionospheric modelling and data analysis techniques have been devised either in one dimension (e. g. along a single radar beam), or in two dimensions (e. g. over a network of magnetometers). With new upcoming missions like the Swarm ionospheric multi-satellite project, or the EISCAT 3-D project, the time has come to take into account variations in all three dimensions simultaneously, as they occur in the real ionosphere. The link between ionospheric electrodynamics and the neutral atmosphere circulation which has gained increasing interest in the recent years also intrinsically requires a truly 3-dimensional (3-D) description. In this paper, we identify five major science questions that need to be addressed by 3-D ionospheric modelling and data analysis. We briefly review what proceedings in the young field of 3-D ionospheric electrodynamics have been made in the past to address these selected question, and we outline how these issues can be addressed in the future with additional observations and/or improved data analysis and simulation techniques. Throughout the paper, we limit the discussion to high-latitude and mesoscale ionospheric electrodynamics, and to directly data-driven (not statistical) data analysis.
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| 13. |
- Soares, C. G, et al.
(author)
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Damage Assessment After Accidental Events : Report of Committee V.1
- 2009. - 1
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In: Proceedings of the 17<sup>th</sup> International Ship and Offshore Structures Congress. - Seoul, Korea : Seoul National University. ; , s. 1-72
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Book chapter (other academic/artistic)abstract
- This paper contains the report of the Committee, which is a new one that was created todeal with the methods to assess damage and residual strength after accidental events.The name of the committee, being a short one may give a wrong impression about itsscope as it mentions damage assessment while the mandate refers that there should beconcern for the extent of damage and local and global residual strength of shipstructures, after accidental events. Therefore the contents of the report deal also withmethods to determine local and global residual strength, including the specification ofthe appropriate loads.It starts by providing a description of the type of damages that can be found in thevarious accidental events. Representative scenarios are described and the typicaldamages that results from the specific accidents are indicated. Next section describeshow in real situations the damaged state is perceived. Thus, inspection methods aredescribed as well as the available approaches to derive information about the status ofthe structure from indirect measurements.Loads on the structure are treated afterwards, including the loads that are generatedduring the accidental situation itself and also after the accident when the ship is indamaged state, often listed and with non symmetric sections. The loads are used todetermine ship strength using the assessment methods described in section 5, whichdeals with various types of components.If the ship is considered not having enough strength for temporary voyage to repairyard local repairs are necessary. Otherwise she will travel to a repair shipyard and berepaired there. The various types of problems raised in repair are dealt with in thefollowing section.Finally last section deals with salvage and recovery strategies which are necessary inthe cases of very large damage in ships.
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| 14. |
- Yabuta, Hikaru, et al.
(author)
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Macromolecular organic matter in samples of the asteroid (162173) Ryugu
- 2023
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In: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 379:6634
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Journal article (peer-reviewed)abstract
- Samples of the carbonaceous asteroid (162173) Ryugu were collected and brought to Earth by the Hayabusa2 spacecraft. We investigated the macromolecular organic matter in Ryugu samples and found that it contains aromatic and aliphatic carbon, ketone, and carboxyl functional groups. The spectroscopic features of the organic matter are consistent with those in chemically primitive carbonaceous chondrite meteorites that experienced parent-body aqueous alteration (reactions with liquid water). The morphology of the organic carbon includes nanoglobules and diffuse carbon associated with phyllosilicate and carbonate minerals. Deuterium and/or nitrogen-15 enrichments indicate that the organic matter formed in a cold molecular cloud or the presolar nebula. The diversity of the organic matter indicates variable levels of aqueous alteration on Ryugus parent body.
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| 15. |
- Zeichner, Sarah S., et al.
(author)
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Polycyclic aromatic hydrocarbons in samples of Ryugu formed in the interstellar medium
- 2023
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In: Science. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075 .- 1095-9203. ; 382:6677, s. 1411-1415
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Journal article (peer-reviewed)abstract
- Polycyclic aromatic hydrocarbons (PAHs) contain less than or similar to 20% of the carbon in the interstellar medium. They are potentially produced in circumstellar environments (at temperatures greater than or similar to 1000 kelvin), by (similar to 10 kelvin) interstellar clouds, or by processing of carbon-rich dust grains. We report isotopic properties of PAHs extracted from samples of the asteroid Ryugu and the meteorite Murchison. The doubly-C-13 substituted compositions (Delta 2x(13)C values) of the PAHs naphthalene, fluoranthene, and pyrene are 9 to 51 parts per thousand higher than values expected for a stochastic distribution of isotopes. The Delta 2x(13)C values are higher than expected if the PAHs formed in a circumstellar environment, but consistent with formation in the interstellar medium. By contrast, the PAHs phenanthrene and anthracene in Ryugu samples have Delta 2x(13)C values consistent with formation by higher-temperature reactions.
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| 16. |
- Montero, Angeles M., et al.
(author)
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Clinicopathological significance of the expression of PD-L1 in Non-Small Cell Lung Cancer
- 2021
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In: Annals of Diagnostic Pathology. - : Elsevier BV. - 1092-9134 .- 1532-8198. ; 51, s. 151701-
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Journal article (peer-reviewed)abstract
- Introduction: PD1/PD-L1 pathway targeting therapies are nowadays an established treatment option for patients with NSCLC. We assessed whether PD-L1 expression in NSCLC tumor cells was associated with specific clinical features or overall survival using four different clones. Methods and results: A retrospective study included formalin-fixed paraffin embedded (FFPE) surgical tumors from 482 patients. PD-L1 status was assessed with immunohistochemistry in tumor cells on tissue microarrays using clones 28-8, 22C3, SP263 and SP142. Associations with OS were assessed by Kaplan-Meier and multivariate Cox's regression analysis. Patients' median age: 68 years (39–86); histology: adenocarcinoma (AdCa) 61%, squamous-cell carcinoma (SqCC) 33%, and large cell carcinoma (LCC) 6%; p-stage: IA (46%), IB (30%), IIA (10%), IIB (11,4%), IIIA (1,2%), IIIB – IV (0,4%). PD-L1 positivity (≥1%) in NSCLC for clones 28-8, 22C3, SP263, SP142 was 41.5%, 34.2%, 42.7%, 10.4%, respectively (Pearson Chi-square p < 0.0001). PD-L1 expression was correlated with histology, tumor size and grading. Statistically significant association between PD-L1 expression and OS in NSCLC and Non-AdCa was observed with clone SP142 (log-rank p = 0.045 and p = 0.05, respectively). Statistically significant association between PD-L1 expression and OS in LCC was observed with clones 22C3 (log-rank p = 0.009) and SP263 (log-rank p = 0.050). Conclusions: Overexpression of the PD-L1 clone SP142 was associated with poor overall survival in NSCLC and Non-AdCa. Clones 22C3 and SP263 were associated with poor prognosis in LCC. PD-L1 status might serve as a prognostic marker in NSCLC.
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| 17. |
- Nilsson, Jessica, et al.
(author)
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Bis- and tris(pyridyl)amine-oxidovanadium complexes: characteristics and insulin-mimetic potential.
- 2009
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In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9234 .- 1477-9226. ; :38, s. 7902-7911
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Journal article (peer-reviewed)abstract
- Two novel vanadium complexes, [V(IV)O(bp-O)(HSO4)] (1) and [V(IV)O(bp-OH)Cl2] x CH3OH (2 x CH3OH), where bp-OH is 2-{[bis(pyrid-2-yl)methyl]amine}methylphenol, were prepared and structurally characterised. EPR spectra of methanol solutions of 2 suggest exchange of Cl- for CH3OH and partial conversion to [VO(bp-OH)(CH3OH)3]2+. Speciation studies on the VO2+-bpOH system in a water/dmso mixture (4:1 v/v) revealed [VO(bp-O)(H2O)n]+ as the dominating species in the pH range 2-7. The insulin-mimetic properties of 1 and 2, [V(IV)O(SO4)tpa] (3), [V(IV)O(pic-trpMe)2] (5) and the new mixed-ligand complexes [V(V)O(pic-trpH)tpa]Cl2 (4Cl2) and [V(V)O(pic-OEt)tpa]Cl2 (6Cl2), tpa = tris(pyrid-2-yl)methylamine, picH-trpH = 2-carboxypyridine-5-(L-tryptophan)carboxamide (picH-trpMe is the respective tryptophanmethyl ester), pic-OEt = 5-carboethoxypyridine-2-carboxylic acid, were evaluated with rat adipocytes, employing two lipolysis assays (release of glycerol and free fatty acids (FFA)), respectively and a lipogenesis assay (incorporation of glucose into lipids). The IC50 values for the inhibition of lipolysis in the FFA assay vary between 0.41 (+/-0.03) (5) and 21.2 (+/-0.6) mM (2), as compared to 0.81 (+/-0.2) mM for VOSO4.
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| 21. |
- Yamauchi, M., et al.
(author)
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Plasma-neutral gas interactions in various space environments : Assessment beyond simplified approximations as a Voyage 2050 theme
- 2022
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In: Experimental astronomy. - : Springer Nature. - 0922-6435 .- 1572-9508.
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Journal article (peer-reviewed)abstract
- In the White Paper, submitted in response to the European Space Agency (ESA) Voyage 2050 Call, we present the importance of advancing our knowledge of plasma-neutral gas interactions, and of deepening our understanding of the partially ionized environments that are ubiquitous in the upper atmospheres of planets and moons, and elsewhere in space. In future space missions, the above task requires addressing the following fundamental questions: (A) How and by how much do plasma-neutral gas interactions influence the re-distribution of externally provided energy to the composing species? (B) How and by how much do plasma-neutral gas interactions contribute toward the growth of heavy complex molecules and biomolecules? Answering these questions is an absolute prerequisite for addressing the long-standing questions of atmospheric escape, the origin of biomolecules, and their role in the evolution of planets, moons, or comets, under the influence of energy sources in the form of electromagnetic and corpuscular radiation, because low-energy ion-neutral cross-sections in space cannot be reproduced quantitatively in laboratories for conditions of satisfying, particularly, (1) low-temperatures, (2) tenuous or strong gradients or layered media, and (3) in low-gravity plasma. Measurements with a minimum core instrument package (< 15 kg) can be used to perform such investigations in many different conditions and should be included in all deep-space missions. These investigations, if specific ranges of background parameters are considered, can also be pursued for Earth, Mars, and Venus.
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| 22. |
- Yoshimi, N., et al.
(author)
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Cerebrospinal fluid metabolomics identifies a key role of isocitrate dehydrogenase in bipolar disorder: evidence in support of mitochondrial dysfunction hypothesis
- 2016
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In: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 21:11, s. 1504-1510
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Journal article (peer-reviewed)abstract
- Although evidence for mitochondrial dysfunction in the pathogenesis of bipolar disorder (BD) has been reported, the precise biological basis remains unknown, hampering the search for novel biomarkers. In this study, we performed metabolomics of cerebrospinal fluid (CSF) from male BD patients (n = 54) and age-matched male healthy controls (n = 40). Subsequently, postmortem brain analyses, genetic analyses, metabolomics of CSF samples from rats treated with lithium or valproic acid were also performed. After multivariate logistic regression, isocitric acid (isocitrate) levels were significantly higher in the CSF from BD patients than healthy controls. Furthermore, gene expression of two subtypes (IDH3A and IDH3B) of isocitrate dehydrogenase (IDH) in the dorsolateral prefrontal cortex from BD patients was significantly lower than that of controls, although the expression of other genes including, aconitase (ACO1, ACO2), IDH1, IDH2 and IDH3G, were not altered. Moreover, protein expression of IDH3A in the cerebellum from BD patients was higher than that of controls. Genetic analyses showed that IDH genes (IDH1, IDH2, IDH3A, IDH3B) and ACO genes (ACO1, ACO2) were not associated with BD. Chronic (4 weeks) treatment with lithium or valproic acid in rats did not alter CSF levels of isocitrate, and mRNA levels of Idh3a, Idh3b, Aco1 and Aco2 genes in the rat brain. These findings suggest that abnormality in the metabolism of isocitrate by IDH3A in the mitochondria plays a key role in the pathogenesis of BD, supporting the mitochondrial dysfunction hypothesis of BD. Therefore, IDH3 in the citric acid cycle could potentially be a novel therapeutic target for BD.
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