University of Tsukuba

About: University of Tsukuba is a education organization based out in Tsukuba, Ibaraki, Japan. It is known for research contribution in the topics: Population & Gene. The organization has 36352 authors who have published 79483 publications receiving 1934752 citations. The organization is also known as: Tsukuba daigaku & Tsukuba University.

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.

Edge state in graphene ribbons: Nanometer size effect and edge shape dependence.

Abstract: Finite graphite systems having a zigzag edge exhibit a special edge state. The corresponding energy bands are almost flat at the Fermi level and thereby give a sharp peak in the density of states. The charge density in the edge state is strongly localized on the zigzag edge sites. No such localized state appears in graphite systems having an armchair edge. By utilizing the graphene ribbon model, we discuss the effect of the system size and edge shape on the special edge state. By varying the width of the graphene ribbons, we find that the nanometer size effect is crucial for determining the relative importance of the edge state. We also have extended the graphene ribbon to have edges of a general shape, which is defined as a mixture of zigzag and armchair sites. Examining the relative importance of the edge state for graphene ribbons with general edges, we find that a non-negligible edge state survives even in graphene ribbons with less developed zigzag edges. We demonstrate that such an edge shape with three or four zigzag sites per sequence is sufficient to show an edge state, when the system size is on a nanometer scale. The special characteristics of the edge state play a large role in determining the density of states near the Fermi level for graphite networks on a nanometer scale.

Magnetic control of ferroelectric polarization

Abstract: The magnetoelectric effect--the induction of magnetization by means of an electric field and induction of polarization by means of a magnetic field--was first presumed to exist by Pierre Curie, and subsequently attracted a great deal of interest in the 1960s and 1970s (refs 2-4). More recently, related studies on magnetic ferroelectrics have signalled a revival of interest in this phenomenon. From a technological point of view, the mutual control of electric and magnetic properties is an attractive possibility, but the number of candidate materials is limited and the effects are typically too small to be useful in applications. Here we report the discovery of ferroelectricity in a perovskite manganite, TbMnO3, where the effect of spin frustration causes sinusoidal antiferromagnetic ordering. The modulated magnetic structure is accompanied by a magnetoelastically induced lattice modulation, and with the emergence of a spontaneous polarization. In the magnetic ferroelectric TbMnO3, we found gigantic magnetoelectric and magnetocapacitance effects, which can be attributed to switching of the electric polarization induced by magnetic fields. Frustrated spin systems therefore provide a new area to search for magnetoelectric media.

The complete genome sequence of the Gram-positive bacterium Bacillus subtilis

Abstract: Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.