Mutations of Francisella novicida that Alter the Mechanism of Its Phagocytosis by Murine Macrophages

Infection with the bacterial pathogen Francisella tularensis tularensis (F. tularensis) causes tularemia, a serious and debilitating disease. Francisella tularensis novicida strain U112 (abbreviated F. novicida), which is closely related to F. tularensis, is pathogenic for mice but not for man, making it an ideal model system for tularemia. Intracellular pathogens like Francisella inhibit the innate immune response, thereby avoiding immune recognition and death of the infected cell. Because activation of inflammatory pathways may lead to cell death, we reasoned that we could identify bacterial genes involved in inhibiting inflammation by isolating mutants that killed infected cells faster than the wild-type parent. We screened a comprehensive transposon library of F. novicida for mutant strains that increased the rate of cell death following infection in J774 macrophage-like cells, as compared to wild-type F. novicida. Mutations in 28 genes were identified as being hypercytotoxic to both J774 and primary macrophages of which 12 were less virulent in a mouse infection model. Surprisingly, we found that F. novicida with mutations in four genes (lpcC, manB, manC and kdtA) were taken up by and killed macrophages at a much higher rate than the parent strain, even upon treatment with cytochalasin D (cytD), a classic inhibitor of macrophage phagocytosis. At least 10-fold more mutant bacteria were internalized by macrophages as compared to the parent strain if the bacteria were first fixed with formaldehyde, suggesting a surface structure is required for the high phagocytosis rate. However, bacteria were required to be viable for macrophage toxicity. The four mutant strains do not make a complete LPS but instead have an exposed lipid A. Interestingly, other mutations that result in an exposed LPS core were not taken up at increased frequency nor did they kill host cells more than the parent. These results suggest an alternative, more efficient macrophage uptake mechanism for Francisella that requires exposure of a specific bacterial surface structure(s) but results in increased cell death following internalization of live bacteria

The SDSS-IV in 2014: a demographic snapshot

Many astronomers now participate in large international scientific collaborations, and it is important to examine whether these structures foster a healthy scientific climate that is inclusive and diverse. The Committee on the Participation of Women in the Sloan Digital Sky Survey (CPWS) was formed to evaluate the demographics and gender climate within SDSS-IV, one of the largest and most geographically distributed astronomical collaborations. In April 2014, the CPWS administered a voluntary demographic survey to establish a baseline for the incipient SDSS-IV, which began observations in July 2014. We received responses from 250 participants (46% of the active membership). Half of the survey respondents were located in the United States or Canada and 30% were based in Europe. Approximately 65% were faculty or research scientists and 31% were postdocs or graduate students. Eleven percent of survey respondents considered themselves to be an ethnic minority at their current institution. Twenty-five percent of the SDSS-IV collaboration members are women, a fraction that is consistent with the US astronomical community, but substantially higher than the fraction of women in the International Astronomical Union (16%). Approximately equal fractions of men and women report holding positions of leadership in the collaboration. When binned by academic age and career level, men and women also assume leadership roles at approximately equal rates, in a way that increases steadily for both genders with increasing seniority. In this sense, SDSS-IV has been successful in recruiting leaders that are representative of the collaboration. That said, it is clear that more progress needs to be made towards achieving gender balance and increasing diversity in the field of astronomy, and there is still room for improvement in the membership and leadership of SDSS-IV. For example, at the highest level of SDSS-IV leadership, women disproportionately assume roles related to education and public outreach. The goal of the CPWS is to use these initial data to establish a baseline for tracking demographics over time as we work to assess and improve the climate of SDSS-IV

Landau-Zener-Stuckelberg interferometry

A transition between energy levels at an avoided crossing is known as a Landau-Zener transition. When a two-level system (TLS) is subject to periodic driving with sufficiently large amplitude, a sequence of transitions occurs. The phase accumulated between transitions (commonly known as the Stuckelberg phase) may result in constructive or destructive interference. Accordingly, the physical observables of the system exhibit periodic dependence on the various system parameters. This phenomenon is often referred to as Landau-Zener-Stuckelberg (LZS) interferometry. Phenomena related to LZS interferometry occur in a variety of physical systems. In particular, recent experiments on LZS interferometry in superconducting TLSs (qubits) have demonstrated the potential for using this kind of interferometry as an effective tool for obtaining the parameters characterizing the TLS as well as its interaction with the control fields and with the environment. Furthermore, strong driving could allow for fast and reliable control of the quantum system. Here we review recent experimental results on LZS interferometry, and we present related theory.Comment: 34 single-column pages, 11 figure

Neuronal interactions between mentalizing and action systems during indirect request processing

Human communication relies on the ability to process linguistic structure and to map words and utterances onto our environment. Furthermore, as what we communicate is often not directly encoded in our language (e.g., in the case of irony, jokes, or indirect requests), we need to extract additional cues to infer the beliefs and desires of our conversational partners. Although the functional interplay between language and the ability to mentalize has been discussed in theoretical accounts in the past, the neurobiological underpinnings of these dynamics are currently not well understood. Here, we address this issue using functional imaging (fMRI). Participants listened to question-reply dialogues. In these dialogues, a reply is interpreted as a direct reply, an indirect reply, or a request for action, depending on the question. We show that inferring meaning from indirect replies engages parts of the mentalizing network (mPFC) while requests for action also activate the cortical motor system (IPL). Subsequent connectivity analysis using Dynamic Causal Modelling (DCM) revealed that this pattern of activation is best explained by an increase in effective connectivity from the mentalizing network (mPFC) to the action system (IPL). These results are an important step towards a more integrative understanding of the neurobiological basis of indirect speech processing

Community research report

University College Cork introduced its first Community-based Participatory Research (CBPR) module in 2016. The module was funded and supported by Horizon2020 funding, specifically the EnRRICH project (Enhancing Responsible Research and Innovation through Curricula in Higher Education). The module is a 5-credit module for PhD students from all disciplines in the early stages of their PhD at University College Cork. Following two fruitful partnerships in the areas of social justice / equality, community family support services and older persons, there was a keen interested to explore partnerships in markedly different areas such as environmental sustainability. A dialogue ensued with CEF where the opportunity and feasibility to collaborate on the CBPR module was explored

Psychosocial impact of undergoing prostate cancer screening for men with BRCA1 or BRCA2 mutations.

OBJECTIVES: To report the baseline results of a longitudinal psychosocial study that forms part of the IMPACT study, a multi-national investigation of targeted prostate cancer (PCa) screening among men with a known pathogenic germline mutation in the BRCA1 or BRCA2 genes. PARTICPANTS AND METHODS: Men enrolled in the IMPACT study were invited to complete a questionnaire at collaborating sites prior to each annual screening visit. The questionnaire included sociodemographic characteristics and the following measures: the Hospital Anxiety and Depression Scale (HADS), Impact of Event Scale (IES), 36-item short-form health survey (SF-36), Memorial Anxiety Scale for Prostate Cancer, Cancer Worry Scale-Revised, risk perception and knowledge. The results of the baseline questionnaire are presented. RESULTS: A total of 432 men completed questionnaires: 98 and 160 had mutations in BRCA1 and BRCA2 genes, respectively, and 174 were controls (familial mutation negative). Participants' perception of PCa risk was influenced by genetic status. Knowledge levels were high and unrelated to genetic status. Mean scores for the HADS and SF-36 were within reported general population norms and mean IES scores were within normal range. IES mean intrusion and avoidance scores were significantly higher in BRCA1/BRCA2 carriers than in controls and were higher in men with increased PCa risk perception. At the multivariate level, risk perception contributed more significantly to variance in IES scores than genetic status. CONCLUSION: This is the first study to report the psychosocial profile of men with BRCA1/BRCA2 mutations undergoing PCa screening. No clinically concerning levels of general or cancer-specific distress or poor quality of life were detected in the cohort as a whole. A small subset of participants reported higher levels of distress, suggesting the need for healthcare professionals offering PCa screening to identify these risk factors and offer additional information and support to men seeking PCa screening

Comparing Notes: Recording and Criticism

This chapter charts the ways in which recording has changed the nature of music criticism. It both provides an overview of the history of recording and music criticism, from the advent of Edison’s Phonograph to the present day, and examines the issues arising from this new technology and the consequent transformation of critical thought and practice

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.This work is supported by the UK Medical Research Council (MRC); Chinese Academy of Medical Sciences(CAMS) Innovation Fund for Medical Sciences (CIFMS), China; National Institute for Health Research (NIHR)Oxford Biomedical Research Centre, and UK Researchand Innovation (UKRI)/NIHR through the UK Coro-navirus Immunology Consortium (UK-CIC). Sequencing of SARS-CoV-2 samples and collation of data wasundertaken by the COG-UK CONSORTIUM. COG-UK is supported by funding from the Medical ResearchCouncil (MRC) part of UK Research & Innovation (UKRI),the National Institute of Health Research (NIHR),and Genome Research Limited, operating as the Wellcome Sanger Institute. T.I.d.S. is supported by a Well-come Trust Intermediate Clinical Fellowship (110058/Z/15/Z). L.T. is supported by the Wellcome Trust(grant number 205228/Z/16/Z) and by theUniversity of Liverpool Centre for Excellence in Infectious DiseaseResearch (CEIDR). S.D. is funded by an NIHR GlobalResearch Professorship (NIHR300791). L.T. and S.C.M.are also supported by the U.S. Food and Drug Administration Medical Countermeasures Initiative contract75F40120C00085 and the National Institute for Health Research Health Protection Research Unit (HPRU) inEmerging and Zoonotic Infections (NIHR200907) at University of Liverpool inpartnership with Public HealthEngland (PHE), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford.L.T. is based at the University of Liverpool. M.D.P. is funded by the NIHR Sheffield Biomedical ResearchCentre (BRC – IS-BRC-1215-20017). ISARIC4C is supported by the MRC (grant no MC_PC_19059). J.C.K.is a Wellcome Investigator (WT204969/Z/16/Z) and supported by NIHR Oxford Biomedical Research Centreand CIFMS. The views expressed are those of the authors and not necessarily those of the NIHR or MRC