An update on the human and animal enteric pathogen Clostridium perfringens

Clostridium perfringens, a rapid-growing pathogen known to secrete an arsenal of >20 virulent toxins, has been associated with intestinal diseases in both animals and humans throughout the past century. Recent advances in genomic analysis and experimental systems make it timely to re-visit this clinically and veterinary important pathogen. This Review will summarise our understanding of the genomics and virulence-linked factors, including antimicrobial potentials and secreted toxins of this gut pathogen, and then its up-to-date clinical epidemiology and biological role in the pathogenesis of several important human and animal-associated intestinal diseases, including pre-term necrotising enterocolitis. Finally, we highlight some of the important unresolved questions in relation to C. perfringens-mediated infections, and implications for future research directions

Proximate Kitaev quantum spin liquid behaviour in a honeycomb magnet.

Quantum spin liquids (QSLs) are topological states of matter exhibiting remarkable properties such as the capacity to protect quantum information from decoherence. Whereas their featureless ground states have precluded their straightforward experimental identification, excited states are more revealing and particularly interesting owing to the emergence of fundamentally new excitations such as Majorana fermions. Ideal probes of these excitations are inelastic neutron scattering experiments. These we report here for a ruthenium-based material, α-RuCl3, continuing a major search (so far concentrated on iridium materials) for realizations of the celebrated Kitaev honeycomb topological QSL. Our measurements confirm the requisite strong spin-orbit coupling and low-temperature magnetic order matching predictions proximate to the QSL. We find stacking faults, inherent to the highly two-dimensional nature of the material, resolve an outstanding puzzle. Crucially, dynamical response measurements above interlayer energy scales are naturally accounted for in terms of deconfinement physics expected for QSLs. Comparing these with recent dynamical calculations involving gauge flux excitations and Majorana fermions of the pure Kitaev model, we propose the excitation spectrum of α-RuCl3 as a prime candidate for fractionalized Kitaev physics.Research using ORNL’s HFIR and SNS facilities was sponsored by the US Department of Energy, Office of Science, Basic Energy Sciences (BES), Scientific User Facilities Division. A part of the synthesis and the bulk characterization performed at ORNL was supported by the US Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division (C.A.B. and J.-Q.Y.). The work at University of Tennessee was funded in part by the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4416 (D.G.M. and L.L.). The work at Dresden was in part supported by DFG grant SFB 1143 (J.K. and R.M.), and by a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD) (J.K.). D.L.K. is supported by EPSRC Grant No. EP/M007928/1. The collaboration as a whole was supported by the Helmholtz Virtual Institute ‘New States of Matter and their Excitations’ initiative.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nmat460

Excitations in the field-induced quantum spin liquid state of α-RuCl3

The celebrated Kitaev quantum spin liquid (QSL) is the paradigmatic example of a topological magnet with emergent excitations in the form of Majorana Fermions and gauge fluxes. Upon breaking of time-reversal symmetry, for example in an external magnetic field, these fractionalized quasiparticles acquire non-Abelian exchange statistics, an important ingredient for topologically protected quantum computing. Consequently, there has been enormous interest in exploring possible material realizations of Kitaev physics and several candidate materials have been put forward, recently including α-RuCl3. In the absence of a magnetic field this material orders at a finite temperature and exhibits low-energy spin wave excitations. However, at moderate energies, the spectrum is unconventional and the response shows evidence for fractional excitations. Here we use time-of-flight inelastic neutron scattering to show that the application of a sufficiently large magnetic field in the honeycomb plane suppresses the magnetic order and the spin waves, leaving a gapped continuum spectrum of magnetic excitations. Our comparisons of the scattering to the available calculations for a Kitaev QSL show that they are consistent with the magnetic field induced QSL phase.The work at ORNL’s Spallation Neutron Source and the High Flux Isotope Reactor was supported by the United States Department of Energy (US-DOE), Office of Science - Basic Energy Sciences (BES), Scientific User Facilities Division. Part of the research was supported by the US-DOE, Office of Science - BES, Materials Sciences and Engineering Division (P.K., C.A.B. and J-Q.Y.). D.M. and P.K. acknowledge support from the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4416. The work at Dresden was in part supported by DFG grant SFB 1143 (J.K. and R.M.). J.K. is supported by the Marie Curie Programme under EC Grant agreements No.703697

Generation of Induced Pluripotent Stem Cells from CD34+ Cells across Blood Drawn from Multiple Donors with Non-Integrating Episomal Vectors

The methodology to create induced pluripotent stem cells (iPSCs) affords the opportunity to generate cells specific to the individual providing the host tissue. However, existing methods of reprogramming as well as the types of source tissue have significant limitations that preclude the ability to generate iPSCs in a scalable manner from a readily available tissue source. We present the first study whereby iPSCs are derived in parallel from multiple donors using episomal, non-integrating, oriP/EBNA1-based plasmids from freshly drawn blood. Specifically, successful reprogramming was demonstrated from a single vial of blood or less using cells expressing the early lineage marker CD34 as well as from unpurified peripheral blood mononuclear cells. From these experiments, we also show that proliferation and cell identity play a role in the number of iPSCs per input cell number. Resulting iPSCs were further characterized and deemed free of transfected DNA, integrated transgene DNA, and lack detectable gene rearrangements such as those within the immunoglobulin heavy chain and T cell receptor loci of more differentiated cell types. Furthermore, additional improvements were made to incorporate completely defined media and matrices in an effort to facilitate a scalable transition for the production of clinic-grade iPSCs

Baseline Levels of Influenza-Specific CD4 Memory T-Cells Affect T-Cell Responses to Influenza Vaccines

BACKGROUND: Factors affecting immune responses to influenza vaccines have not been studied systematically. We hypothesized that T-cell and antibody responses to the vaccines are functions of pre-existing host immunity against influenza antigens. METHODOLOGY/PRINCIPAL FINDINGS: During the 2004 and 2005 influenza seasons, we have collected data on cellular and humoral immune reactivity to influenza virus in blood samples collected before and after immunization with inactivated or live attenuated influenza vaccines in healthy children and adults. We first used cross-validated lasso regression on the 2004 dataset to identify a group of candidate baseline correlates with T-cell and antibody responses to vaccines, defined as fold-increase in influenza-specific T-cells and serum HAI titer after vaccination. The following baseline parameters were examined: percentages of influenza-reactive IFN-gamma(+) cells in T and NK cell subsets, percentages of influenza-specific memory B-cells, HAI titer, age, and type of vaccine. The candidate baseline correlates were then tested with the independent 2005 dataset. Baseline percentage of influenza-specific IFN-gamma(+) CD4 T-cells was identified as a significant correlate of CD4 and CD8 T-cell responses, with lower baseline levels associated with larger T-cell responses. Baseline HAI titer and vaccine type were identified as significant correlates for HAI response, with lower baseline levels and the inactivated vaccine associated with larger HAI responses. Previously we reported that baseline levels of CD56(dim) NK reactivity against influenza virus inversely correlated with the immediate T-cell response to vaccination, and that NK reactivity induced by influenza virus depended on IL-2 produced by influenza-specific memory T-cells. Taken together these results suggest a novel mechanism for the homeostasis of virus-specific T-cells, which involves interaction between memory helper T-cells, CD56(dim) NK and DC. SIGNIFICANCE: These results demonstrate that assessment of baseline biomarkers may predict immunologic outcome of influenza vaccination and may reveal some of the mechanisms responsible for variable immune responses following vaccination and natural infection

Roles of glial cells in synapse development

Brain function relies on communication among neurons via highly specialized contacts, the synapses, and synaptic dysfunction lies at the heart of age-, disease-, and injury-induced defects of the nervous system. For these reasons, the formation—and repair—of synaptic connections is a major focus of neuroscience research. In this review, I summarize recent evidence that synapse development is not a cell-autonomous process and that its distinct phases depend on assistance from the so-called glial cells. The results supporting this view concern synapses in the central nervous system as well as neuromuscular junctions and originate from experimental models ranging from cell cultures to living flies, worms, and mice. Peeking at the future, I will highlight recent technical advances that are likely to revolutionize our views on synapse–glia interactions in the developing, adult and diseased brain

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research