Okinawa Institute of Science and Technology

About: Okinawa Institute of Science and Technology is a education organization based out in Onna Son, Japan. It is known for research contribution in the topics: Population & Gene. The organization has 1609 authors who have published 4225 publications receiving 98460 citations. The organization is also known as: Okinawa Kagaku Gijutsu Daigakuin Daigaku & OIST.

Guidelines for the use and interpretation of assays for monitoring autophagy

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.

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

Abstract: Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/ . The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.

Whole-genome analyses resolve early branches in the tree of life of modern birds

Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

A compact X-ray free-electron laser emitting in the sub-ångström region

Abstract: Researchers report sub-angstrom fundamental-wavelength lasing at the SPring-8 Angstrom Compact Free-Electron Laser in Japan. The output has a maximum power of more than 10 GW, a pulse duration of 10−14 s and a lasing wavelength of 0.634 A.

Lithium-ion batteries: outlook on present, future, and hybridized technologies

Abstract: Lithium-ion batteries (LIBs) continue to draw vast attention as a promising energy storage technology due to their high energy density, low self-discharge property, nearly zero-memory effect, high open circuit voltage, and long lifespan. In particular, high-energy density lithium-ion batteries are considered as the ideal power source for electric vehicles (EVs) and hybrid electric vehicles (HEVs) in the automotive industry, in recent years. This review discusses key aspects of the present and the future battery technologies on the basis of the working electrode. We then discuss how lithium-ion batteries evolve to meet the growing demand on high charge capacity and electrode stability. An account of a stand-alone energy device (off-grid system) that combines an energy harvesting technology with a lithium-ion battery is also provided. The main discussion is categorized into three perspectives such as the evolution from the conventional to the advanced LIBs (e.g., Li-rich transition metal oxide and Ni-rich transition metal oxide batteries), to the state-of-the-art LIBs (e.g., Li–air, Li–sulfur batteries, organic electrode batteries, solid-state batteries, and Li–CO2 batteries), and to the hybridized LIBs (e.g., metal halide perovskite batteries).