Showing papers by "Osaka University published in 2013"

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Abstract: We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

Abstract: Manipulation of the gut microbiota holds great promise for the treatment of inflammatory and allergic diseases. Although numerous probiotic microorganisms have been identified, there remains a compelling need to discover organisms that elicit more robust therapeutic responses, are compatible with the host, and can affect a specific arm of the host immune system in a well-controlled, physiological manner. Here we use a rational approach to isolate CD4(+)FOXP3(+) regulatory T (Treg)-cell-inducing bacterial strains from the human indigenous microbiota. Starting with a healthy human faecal sample, a sequence of selection steps was applied to obtain mice colonized with human microbiota enriched in Treg-cell-inducing species. From these mice, we isolated and selected 17 strains of bacteria on the basis of their high potency in enhancing Treg cell abundance and inducing important anti-inflammatory molecules--including interleukin-10 (IL-) and inducible T-cell co-stimulator (ICOS)--in Treg cells upon inoculation into germ-free mice. Genome sequencing revealed that the 17 strains fall within clusters IV, XIVa and XVIII of Clostridia, which lack prominent toxins and virulence factors. The 17 strains act as a community to provide bacterial antigens and a TGF-β-rich environment to help expansion and differentiation of Treg cells. Oral administration of the combination of 17 strains to adult mice attenuated disease in models of colitis and allergic diarrhoea. Use of the isolated strains may allow for tailored therapeutic manipulation of human immune disorders.

An ultra-lightweight design for imperceptible plastic electronics

Abstract: Electronic devices have advanced from their heavy, bulky origins to become smart, mobile appliances. Nevertheless, they remain rigid, which precludes their intimate integration into everyday life. Flexible, textile and stretchable electronics are emerging research areas and may yield mainstream technologies. Rollable and unbreakable backplanes with amorphous silicon field-effect transistors on steel substrates only 3 μm thick have been demonstrated. On polymer substrates, bending radii of 0.1 mm have been achieved in flexible electronic devices. Concurrently, the need for compliant electronics that can not only be flexed but also conform to three-dimensional shapes has emerged. Approaches include the transfer of ultrathin polyimide layers encapsulating silicon CMOS circuits onto pre-stretched elastomers, the use of conductive elastomers integrated with organic field-effect transistors (OFETs) on polyimide islands, and fabrication of OFETs and gold interconnects on elastic substrates to realize pressure, temperature and optical sensors. Here we present a platform that makes electronics both virtually unbreakable and imperceptible. Fabricated directly on ultrathin (1 μm) polymer foils, our electronic circuits are light (3 g m(-2)) and ultraflexible and conform to their ambient, dynamic environment. Organic transistors with an ultra-dense oxide gate dielectric a few nanometres thick formed at room temperature enable sophisticated large-area electronic foils with unprecedented mechanical and environmental stability: they withstand repeated bending to radii of 5 μm and less, can be crumpled like paper, accommodate stretching up to 230% on prestrained elastomers, and can be operated at high temperatures and in aqueous environments. Because manufacturing costs of organic electronics are potentially low, imperceptible electronic foils may be as common in the future as plastic wrap is today. Applications include matrix-addressed tactile sensor foils for health care and monitoring, thin-film heaters, temperature and infrared sensors, displays, and organic solar cells.

Catalytic Functionalization of C(sp2) ? H and C(sp3) ? H Bonds by Using Bidentate Directing Groups

Abstract: C-H bonds are ubiquitous in organic compounds. It would, therefore, appear that direct functionalization of substrates by activation of C-H bonds would eliminate the multiple steps and limitations associated with the preparation of functionalized starting materials. Regioselectivity is an important issue because organic molecules can contain a wide variety of C-H bonds. The use of a directing group can largely overcome the issue of regiocontrol by allowing the catalyst to come into proximity with the targeted C-H bonds. A wide variety of functional groups have been evaluated for use as directing groups in the transformation of C-H bonds. In 2005, Daugulis reported the arylation of unactivated C(sp(3))-H bonds by using 8-aminoquinoline and picolinamide as bidentate directing groups, with Pd(OAc)2 as the catalyst. Encouraged by these promising results, a number of transformations of C-H bonds have since been developed by using systems based on bidentate directing groups. In this Review, recent advances in this area are discussed.

Autophagy in infection, inflammation and immunity

Abstract: It is increasingly understood that autophagy is an ancient defence mechanism that has become incorporated into numerous immunological pathways. As discussed in this Review, its immunological roles include the elimination of microorganisms, the control of inflammation, the regulation of antigen presentation and lymphocyte homeostasis, and the secretion of immune mediators.

Autophagosomes form at ER–mitochondria contact sites

Abstract: This study shows that autophagosomes form at sites of contact between the endoplasmic reticulum and mitochondria, and that formation requires the SNARE protein syntaxin 17.

Topological Insulator Materials

Abstract: Topological insulators represent a new quantum state of matter which is characterized by peculiar edge or surface states that show up due to a topological character of the bulk wave functions. This review presents a pedagogical account on topological insulator materials with an emphasis on basic theory and materials properties. After presenting a historical perspective and basic theories of topological insulators, it discusses all the topological insulator materials discovered as of May 2013, with some illustrative descriptions of the developments in materials discoveries in which the author was involved. A summary is given for possible ways to confirm the topological nature in a candidate material. Various synthesis techniques as well as the defect chemistry that are important for realizing bulk-insulating samples are discussed. Characteristic properties of topological insulators are discussed with an emphasis on transport properties. In particular, the Dirac fermion physics and the resulting peculiar qu...

The autophagosome: origins unknown, biogenesis complex

Abstract: Autophagosome biogenesis starts at the isolation membrane (also called the phagophore). Our understanding of the molecular processes that initiate the isolation membrane, the membrane sources from which this membrane originates and how it is expanded to the autophagosome membrane by autophagy-related (ATG) proteins and the vesicular trafficking machinery, is increasing.

Topological Insulator Materials

Abstract: Topological insulators represent a new quantum state of matter which is characterized by peculiar edge or surface states that show up due to a topological character of the bulk wave functions. This review presents a pedagogical account on topological insulator materials with an emphasis on basic theory and materials properties. After presenting a historical perspective and basic theories of topological insulators, it discusses all the topological insulator materials discovered as of May 2013, with some illustrative descriptions of the developments in materials discoveries in which the author was involved. A summary is given for possible ways to confirm the topological nature in a candidate material. Various synthesis techniques as well as the defect chemistry that are important for realizing bulk-insulating samples are discussed. Characteristic properties of topological insulators are discussed with an emphasis on transport properties. In particular, the Dirac fermion physics and the resulting peculiar quantum oscillation patterns are discussed in detail. It is emphasized that proper analyses of quantum oscillations make it possible to unambiguously identify surface Dirac fermions through transport measurements. The prospects of topological insulator materials for elucidating novel quantum phenomena that await discovery conclude the review.

Bruxism defined and graded: an international consensus

Abstract: To date, there is no consensus about the definition and diagnostic grading of bruxism. A written consensus discussion was held among an international group of bruxism experts as to formulate a definition of bruxism and to suggest a grading system for its operationalisation. The expert group defined bruxism as a repetitive jaw-muscle activity characterised by clenching or grinding of the teeth and/or by bracing or thrusting of the mandible. Bruxism has two distinct circadian manifestations: it can occur during sleep (indicated as sleep bruxism) or during wakefulness (indicated as awake bruxism). For the operationalisation of this definition, the expert group proposes a diagnostic grading system of 'possible', 'probable' and 'definite' sleep or awake bruxism. The proposed definition and grading system are suggested for clinical and research purposes in all relevant dental and medical domains.

Microtubule-driven spatial arrangement of mitochondria promotes activation of the NLRP3 inflammasome

Abstract: NLRP3 forms an inflammasome with its adaptor ASC, and its excessive activation can cause inflammatory diseases. However, little is known about the mechanisms that control assembly of the inflammasome complex. Here we show that microtubules mediated assembly of the NLRP3 inflammasome. Inducers of the NLRP3 inflammasome caused aberrant mitochondrial homeostasis to diminish the concentration of the coenzyme NAD(+), which in turn inactivated the NAD(+)-dependent α-tubulin deacetylase sirtuin 2; this resulted in the accumulation of acetylated α-tubulin. Acetylated α-tubulin mediated the dynein-dependent transport of mitochondria and subsequent apposition of ASC on mitochondria to NLRP3 on the endoplasmic reticulum. Therefore, in addition to direct activation of NLRP3, the creation of optimal sites for signal transduction by microtubules is required for activation of the entire NLRP3 inflammasome.

Layer V cortical neurons require microglial support for survival during postnatal development

Abstract: Neurons require trophic support during neural circuit formation; however, how the cellular milieu contributes to neuronal survival remains unclear. We found that layer V cortical neurons require support from microglia for survival during postnatal development. Specifically, we found that microglia accumulated close to the subcerebral and callosal projection axons in the postnatal brain. Inactivation of microglia by minocycline treatment or transient ablation of microglia in CD11b-DTR transgenic mice led to increased apoptosis, specifically in layer V subcerebral and callosal projection neurons. CX3CR1 in microglia was required for the survival of layer V neurons. Microglia consistently promoted the survival of cortical neurons in vitro. In addition, we identified microglia-derived IGF1 as a trophic factor that maintained neuronal survival. Our results highlight a neuron-glia interaction that is indispensable for network formation during a specific period in the developing brain.

Anti-CCR4 mAb selectively depletes effector-type FoxP3+CD4+ regulatory T cells, evoking antitumor immune responses in humans

Abstract: CD4+ Treg cells expressing the transcription factor FOXP3 (forkhead box P3) are abundant in tumor tissues and appear to hinder the induction of effective antitumor immunity. A substantial number of T cells, including Treg cells, in tumor tissues and peripheral blood express C-C chemokine receptor 4 (CCR4). Here we show that CCR4 was specifically expressed by a subset of terminally differentiated and most suppressive CD45RA−FOXP3hiCD4+ Treg cells [designated effector Treg (eTreg) cells], but not by CD45RA+FOXP3loCD4+ naive Treg cells, in peripheral blood of healthy individuals and cancer patients. In melanoma tissues, CCR4+ eTreg cells were predominant among tumor-infiltrating FOXP3+ T cells and much higher in frequency compared with those in peripheral blood. With peripheral blood lymphocytes from healthy individuals and melanoma patients, ex vivo depletion of CCR4+ T cells and subsequent in vitro stimulation of the depleted cell population with the cancer/testis antigen NY-ESO-1 efficiently induced NY-ESO-1–specific CD4+ T cells. Nondepletion failed in the induction. The magnitude of the responses was comparable with total removal of FOXP3+ Treg cells by CD25+ T-cell depletion. CCR4+ T-cell depletion also augmented in vitro induction of NY-ESO-1–specific CD8+ T cells in melanoma patients. Furthermore, in vivo administration of anti-CCR4 mAb markedly reduced the eTreg-cell fraction and augmented NY-ESO-1–specific CD8+ T-cell responses in an adult T-cell leukemia-lymphoma patient whose leukemic cells expressed NY-ESO-1. Collectively, these findings indicate that anti-CCR4 mAb treatment is instrumental for evoking and augmenting antitumor immunity in cancer patients by selectively depleting eTreg cells.

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

Abstract: The functional roles of SNPs within the 8q24 gene desert in the cancer phenotype are not yet well understood. Here, we report that CCAT2, a novel long noncoding RNA transcript (lncRNA) encompassing the rs6983267 SNP, is highly overexpressed in microsatellite-stable colorectal cancer and promotes tumor growth, metastasis, and chromosomal instability. We demonstrate that MYC, miR-17-5p, and miR-20a are up-regulated by CCAT2 through TCF7L2-mediated transcriptional regulation. We further identify the physical interaction between CCAT2 and TCF7L2 resulting in an enhancement of WNT signaling activity. We show that CCAT2 is itself a WNT downstream target, which suggests the existence of a feedback loop. Finally, we demonstrate that the SNP status affects CCAT2 expression and the risk allele G produces more CCAT2 transcript. Our results support a new mechanism of MYC and WNT regulation by the novel lncRNA CCAT2 in colorectal cancer pathogenesis, and provide an alternative explanation of the SNP-conferred cancer risk.

Regulatory T cells: recommendations to simplify the nomenclature

Abstract: c o rr e s p o n d e n c e npg © 2013 Nature America, Inc. All rights reserved. Regulatory T cells: recommendations to simplify the nomenclature To the Editor: Regulatory T cells (T reg cells) have attracted much interest from both basic and clinical immunologists. Although questions remain about their fundamental biology and their clinical potential has yet to be fully realized, considerable advances have been made in the under- standing of the differentiation, homeostasis and function of T reg cells. This new knowledge has led to a substantial increase in the number of Foxp3 + T reg cell subpopulations described in the literature and conse- quently to an increase in the use of new abbreviations and terminology. Furthermore, as the understanding of T reg cell biology has grown, so too has the realization that some aspects of the original terminology are no longer accurate, and its use has become less stringent. At the Third International Conference on Regulatory T Cells and Th Subsets and Clinical Application in Human Diseases held in Shanghai, China, on 13–16 October 2012, a small workshop was convened to discuss T reg cell nomenclature and to develop several recommendations. We hasten to add that this is simply a list of recommendations, and it remains the prerogative of journals to develop their own editorial preferences and for the authors to use the nomenclature they feel best suits their manuscript. However, we support the recommendations noted below. There were three general issues that provided the momentum for this workshop. First, the terms used for the principal Foxp3 + T reg cell populations—those that differentiate in the thymus, those that differ- entiate in the periphery and those generated in vitro—are not ideal, as these are, to some extent, inaccurate, ambiguous and/or uninformative. For example, the widely used term ‘natural T reg cell’ is misleading and ambiguous, as it indicates that all other Foxp3 + T reg cell populations are ‘unnatural’. It also does not convey any useful or accurate information. One feature of these Foxp3 + T reg cell populations that is more informa- tive is the anatomical location of their differentiation. Instead, use of the terms ‘thymus’, ‘periphery’ and ‘in vitro’ provides a clear indica- tion of whence the Foxp3 + T reg cells in question are derived. Thus, we would recommend that ‘natural Foxp3 + T reg cells’ instead be referred to as ‘thymus-derived T reg cells’ (Box 1). Consistent with the rationale above, we would recommend that Foxp3 + T reg cells that differentiate in the periphery be referred to as ‘peripherally derived T reg cells’ rather than ‘induced or adaptive T reg cells’ (Box 1). In this context, we noted that terms used to define a T reg cell subpopulation, such as ‘induced T reg cells’, are often used when the location of their differentiation is unclear. Thus, we would suggest that the newly recommended terms ‘thymus-derived T reg cells’ and ‘peripherally derived T reg cells’ be used only when the anatomical location of their differentiation has been clearly demonstrated. When the origin of the T reg cell being studied is unclear, the general term ‘Foxp3 + T reg cell’ would be more appropriate. Finally, to clearly distinguish between Foxp3 + T reg cell populations that are generated in vivo versus those generated in vitro, we would suggest nature immunology volume 14 number 4 april 2013 that the term ‘in vitro–induced T reg cells’ be used for all Foxp3 + T reg cell populations generated ex vivo, such as those generated through the use of transforming growth factor-b (Box 1). Second, there has been a growing tendency to use terms such as ‘T reg cells’ or ‘iT reg cells’ when confirmation of such identity is lacking. The frequent use of the term ‘T reg cells’ has been a particular problem in studies focusing on human T reg cells, as activated conventional T cells can also express Foxp3. The term ‘T reg cell’ should be used only when it is clear that the cells have (or had) suppressive ability or have a transcriptional, epigenetic and/or protein-expression signature that suggests that the cells in question are, beyond a reasonable doubt, Foxp3 + T reg cells (Box 1). Also, as indicated above, the terms ‘thymus- derived T reg cell’ and ‘peripherally derived T reg cells’ should be used only when the anatomical location of their development has been clearly demonstrated. Third, there has been progressive growth in the development and use of new T reg cell terminology that is likely to lead to more confusion and the further ‘jargonization’ of immunology. Until a new popula- tion has been extensively demonstrated to be unique, distinct from other populations and stable, we would recommend not coining new terms for such subpopulations (Box 1). Instead, we would encourage investigators to identify them through the use of prominent aspects of their expression pattern, such as a transcription factor or cytokine. Although the focus of this Correspondence has been CD4 + Foxp3 + T reg cell populations, many CD4 – Foxp3 – T reg cell populations have been described, and we would similarly recommend that new terms be used to describe these only when their identity and stability have been clearly defined. Box 1 T reg cell nomenclature recommendations 1. ‘Thymus-derived T reg cell (tT reg cell)’ should be used instead of ‘natural T reg cell (nT reg cell)’. 2. ‘Peripherally derived T reg cell (pT reg cell)’ should be used instead of ‘induced or adaptive T reg cell (iT reg cell or aT reg cell)’. 3. ‘In vitro–induced T reg cell (iT reg cell)’ should be used to clearly distinguish between those T reg cell populations generated in vivo versus those generated in vitro. 4. T reg cell terms should be used only when there is definitive evidence justifying their use. 5. The development and use of new T reg cell terminology should be limited, especially for subpopulations.

Preorganized hydrogel: self-healing properties of supramolecular hydrogels formed by polymerization of host-guest-monomers that contain cyclodextrins and hydrophobic guest groups

Abstract: Supramolecular hydrogels formed by a host-guest interaction show self-healing properties. The cube-shaped hydrogels with β-cyclodextrin and adamantane guest molecules mend after being broken. The hydrogels sufficiently heal to form a single gel, and the initial strength is restored. Although contact between a freshly cut and uncut surface does not mend the gels, two freshly cut surfaces selectively mend.

Improved luminosity determination in pp collisions at root s=7 TeV using the ATLAS detector at the LHC

Abstract: The luminosity calibration for the ATLAS detector at the LHC during pp collisions at root s = 7 TeV in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at root s = 7 TeV. A luminosity uncertainty of delta L/L = +/- 3.5 % is obtained for the 47 pb(-1) of data delivered to ATLAS in 2010, and an uncertainty of delta L/L = +/- 1.8 % is obtained for the 5.5 fb(-1) delivered in 2011.

Review of lattice results concerning low-energy particle physics

Abstract: We review lattice results related to pion, kaon, D- and B-meson physics with the aim of making them easily accessible to the particle physics community. More specifically, we report on the determination of the light-quark masses, the form factor f+(0), arising in semileptonic K -> pi transition at zero momentum transfer, as well as the decay constant ratio fK/fpi of decay constants and its consequences for the CKM matrix elements Vus and Vud. Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of SU(2)LxSU(2)R and SU(3)LxSU(3)R Chiral Perturbation Theory and review the determination of the BK parameter of neutral kaon mixing. The inclusion of heavy-quark quantities significantly expands the FLAG scope with respect to the previous review. Therefore, for this review, we focus on D- and B-meson decay constants, form factors, and mixing parameters, since these are most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. In addition we review the status of lattice determinations of the strong coupling constant alpha_s.

Conjugated organic framework with three-dimensionally ordered stable structure and delocalized π clouds

Abstract: Covalent organic frameworks can utilize π-stacking interactions for the formation of ordered, layered frameworks. Here, the authors report an ordered framework with tailored π-interactions resulting in periodic ordering in three dimensions, which leads to enhanced stability and electronic properties.