Characterisation of bacteriophage-host interactions in Lactococcus lactis

Lactococcus lactis is used extensively world-wide for the production of fermented dairy products. Bacteriophages (phages) infecting L. lactis can result in slow or incomplete fermentations, or may even cause total fermentation failure. Therefore, bacteriophages disrupting L. lactis fermentation are of economic concern. This thesis employed a multifaceted approach to investigate various molecular aspects of phage-host interaction in L. lactis. The genome sequence of an Irish dairy starter strain, the prophage-cured L. lactis subsp. cremoris UC509.9, was studied. The 2,250,427 bp circular chromosome represents the smallest among its sequenced lactococcal equivalents. The genome displays clear genetic adaptation to the dairy niche in the form of extensive reductive evolution. Gene prediction identified 2066 protein-encoding genes, including 104 which showed significant homology to transposase-specifying genes. Over 9 % of the identified genes appear to be inactivated through stop codons or frame shift mutations. Many pseudogenes were found in genes that are assigned to carbohydrate and amino acid transport and metabolism orthologous groups, reflecting L. lactis UC509.9’s adaptation to the lactose and casein-rich dairy environment. Sequence analysis of the eight plasmids of L. lactis revealed extensive adaptation to the dairy environment. Key industrial phenotypes were mapped and novel lactococcal plasmid-associated genes highlighted. In addition to chromosomally-encoded bacteriophage resistance systems, six functional such systems were identified, including two abortive infection systems, AbiB and AbiD1, explaining the observed phage resistance of L. lactis UC509.9 Molecular analysis suggests that the constitutive expression of AbiB is not lethal to cells, suggesting the protein is expressed in an un/inactivated form. Analysis of 936 species phage sk1-escape mutants of AbiB revealed that all such mutants harbour mutations in orf6, which encodes the major capsid protein. Results suggest that the major capsid protein is required for activation of the AbiB system, although this requires furrther investigations. Temporal transcriptomes of L. lactis UC509.9 undergoing lytic infection with either one of two distinct bacteriophages, Tuc2009 and c2, was determined and compared to the transcriptome of uninfected UC509.9 cells. Whole genome microarrays performed at various time-points post-infection demonstrated a rather modest impact on host transcription. Alterations in the UC509.9 transcriptome during lytic infection appear phage-specific, with a relatively small number of differentially transcribed genes shared between infection with either Tuc2009 or c2. Transcriptional profiles of both bacteriophages during lytic infection was shown to generally correlate with previous studies and allowed the confirmation of previously predicted promoter sequences. Bioinformatic analysis of genomic regions encoding the presumed cell wall polysaccharide (CW PS) biosynthesis gene cluster of several strains of L. lactis was performed. Results demonstrate the presence of three dominant genetic types of this gene cluster, termed type A, B and C. These regions were used for the development of a multiplex PCR to identify CW PS genotype of various lactococcal strains. Analysis of 936 species phage receptor binding protein phylogeny (RBP) and CW PS genotype revealed an apparent correlation between RBP phylogeny and CW PS type, thereby providing a partial explanation for the observed narrow host range of 936 phages. Further analysis of the genetic locus encompassing the presumed CW PS biosynthesis operon of eight strains identified as belonging to the CW PS C (geno)type, revealed the presence of a variable region among the examined strains. The obtained comparative analysis allowed for the identification of five subgroups of the C type, named C1 to C5. We purified an acidic polysaccharide from the cell wall of L. lactis 3107 (C2 subtype) and confirmed that it is structurally different from the CW PS of the C1 subtype L. lactis MG1363. Combinations of genes from the variable region of C2 subtype were amplified from L. lactis 3107 and introduced into a mutant of the C1 subtype L. lactis NZ9000 (a direct derivative of MG1363) deficient in CW PS biosynthesis. The resulting recombinant mutant synthesized a CW PS with a composition characteristic for that of the C2 subtype L. lactis 3107 and not the wildtype C1 L. lactis NZ9000. The recombinant mutant exhibited a changed phage resistance/sensitivity profile consistent with that of L. lactis 3107, which unambiguously demonstrated that L. lactis 3107 CW PS is the host cell surface receptor of two bacteriophages belonging to the P335 species as well as phages that are member of the 936 species. The research presented in this thesis has significantly advanced our understanding of L. lactis bacteriophage-host interactions in several ways. Firstly, the examination of plasmidencoded bacteriophage resistance systems has allowed inferences to be made regarding the mode of action of AbiB, thereby providing a platform for further elucidation of the molecular trigger of this system. Secondly, the phage infection transcriptome data presented, in addition to previous work, has made L. lactis a model organism in terms of transcriptomic studies of bacteriophage-host interactions. And finally, the research described in this thesis has for the first time explicitly revealed the nature of a carbohydrate bacteriophage receptor in L. lactis, while also providing a logical explanation for the observed narrow host ranges exhibited by 936 and P335 phages. Future research in discerning the structures of other L. lactis CW PS, combined with the determination of the molecular interplay between receptor binding proteins of these phages and CW PS will allow an in depth understanding of the mechanism by which the most prevalent lactococcal phages identify and adsorb to their specific host.

The Vikings in ninth-century Ireland: Sources and settlements

Archaeological excavations, particularly those of the last fifty years, have greatly advanced our understanding of Viking settlement in Ireland, and this study sets out to present a complementary analysis of the historical sources. Increasingly, evidence suggests that Viking occupation encompassed a more diverse range of settlement types than previously acknowledged. Major urban excavations such as those carried out in Dublin and Waterford, are now complemented by small scale excavations and studies of sites such as: Cherrywood, Co Dublin, a rural settlement; Beginish, Co Kerry, a maritime haven; Truska, Co Galway, a possible farmstead; longphort-settlements at Dunrally, Co Laois and Athlunkard, Co Limerick; and significant Viking settlements at Woodstown, Co Waterford and at Annagassan, Co Louth. This thesis sets out to examine patterns of Viking settlement in ninth-century Ireland; an interdisciplinary approach is adopted that attempts to combine evidence from both the extant primary sources and the archaeological evidence. It is argued that the Vikings had bases in Ireland even in the earliest period of activity 795-836, traditionally characterised as the ‘hit-and-run’ phase. The downturn discernible in Viking-related annalistic entries occurs at a time when there are increased references to Viking settlements in the Irish annals; therefore, it is proposed that this change in the ninth-century recorded pattern of Viking activity reflects their increased involvement in trade and settlement. To support this hypothesis, the evidence for settlement, settlement patterns and trade at Dublin and Waterford in the ninth century is then discussed.

Caregivers of people with neurodegenerative diseases: profile and unmet needs from a population-based survey in South Australia.

INTRODUCTION: Neurodegenerative diseases (NDD) are characterized by progressive decline and loss of function, requiring considerable third-party care. NDD carers report low quality of life and high caregiver burden. Despite this, little information is available about the unmet needs of NDD caregivers. METHODS: Data from a cross-sectional, whole of population study conducted in South Australia were analyzed to determine the profile and unmet care needs of people who identify as having provided care for a person who died an expected death from NDDs including motor neurone disease and multiple sclerosis. Bivariate analyses using chi(2) were complemented with a regression analysis. RESULTS: Two hundred and thirty respondents had a person close to them die from an NDD in the 5 years before responding. NDD caregivers were more likely to have provided care for more than 2 years and were more able to move on after the death than caregivers of people with other disorders such as cancer. The NDD caregivers accessed palliative care services at the same rate as other caregivers at the end of life, however people with an NDD were almost twice as likely to die in the community (odds ratio [OR] 1.97; 95% confidence interval [CI] 1.30 to 3.01) controlling for relevant caregiver factors. NDD caregivers reported significantly more unmet needs in emotional, spiritual, and bereavement support. CONCLUSION: This study is the first step in better understanding across the whole population the consequences of an expected death from an NDD. Assessments need to occur while in the role of caregiver and in the subsequent bereavement phase.

Bonds between fibronectin and fibronectin-binding proteins on Staphylococcus aureus and Lactococcus lactis.

Bacterial cell-wall-associated fibronectin binding proteins A and B (FnBPA and FnBPB) form bonds with host fibronectin. This binding reaction is often the initial step in prosthetic device infections. Atomic force microscopy was used to evaluate binding interactions between a fibronectin-coated probe and laboratory-derived Staphylococcus aureus that are (i) defective in both FnBPA and FnBPB (fnbA fnbB double mutant, DU5883), (ii) capable of expressing only FnBPA (fnbA fnbB double mutant complemented with pFNBA4), or (iii) capable of expressing only FnBPB (fnbA fnbB double mutant complemented with pFNBB4). These experiments were repeated using Lactococcus lactis constructs expressing fnbA and fnbB genes from S. aureus. A distinct force signature was observed for those bacteria that expressed FnBPA or FnBPB. Analysis of this force signature with the biomechanical wormlike chain model suggests that parallel bonds form between fibronectin and FnBPs on a bacterium. The strength and covalence of bonds were evaluated via nonlinear regression of force profiles. Binding events were more frequent (p < 0.01) for S. aureus expressing FnBPA or FnBPB than for the S. aureus double mutant. The binding force, frequency, and profile were similar between the FnBPA and FnBPB expressing strains of S. aureus. The absence of both FnBPs from the surface of S. aureus removed its ability to form a detectable bond with fibronectin. By contrast, ectopic expression of FnBPA or FnBPB on the surface of L. lactis conferred fibronectin binding characteristics similar to those of S. aureus. These measurements demonstrate that fibronectin-binding adhesins FnBPA and FnBPB are necessary and sufficient for the binding of S. aureus to prosthetic devices that are coated with host fibronectin.

Does improved access to diagnostic imaging results reduce hospital length of stay? A retrospective study.

BACKGROUND: One year after the introduction of Information and Communication Technology (ICT) to support diagnostic imaging at our hospital, clinicians had faster and better access to radiology reports and images; direct access to Computed Tomography (CT) reports in the Electronic Medical Record (EMR) was particularly popular. The objective of this study was to determine whether improvements in radiology reporting and clinical access to diagnostic imaging information one year after the ICT introduction were associated with a reduction in the length of patients' hospital stays (LOS). METHODS: Data describing hospital stays and diagnostic imaging were collected retrospectively from the EMR during periods of equal duration before and one year after the introduction of ICT. The post-ICT period was chosen because of the documented improvement in clinical access to radiology results during that period. The data set was randomly split into an exploratory part used to establish the hypotheses, and a confirmatory part. The data was used to compare the pre-ICT and post-ICT status, but also to compare differences between groups. RESULTS: There was no general reduction in LOS one year after ICT introduction. However, there was a 25% reduction for one group - patients with CT scans. This group was heterogeneous, covering 445 different primary discharge diagnoses. Analyses of subgroups were performed to reduce the impact of this divergence. CONCLUSION: Our results did not indicate that improved access to radiology results reduced the patients' LOS. There was, however, a significant reduction in LOS for patients undergoing CT scans. Given the clinicians' interest in CT reports and the results of the subgroup analyses, it is likely that improved access to CT reports contributed to this reduction.

Long-term changes in physical activity following a one-year home-based physical activity counseling program in older adults with multiple morbidities.

This study assessed the sustained effect of a physical activity (PA) counseling intervention on PA one year after intervention, predictors of sustained PA participation, and three classes of post-intervention PA trajectories (improvers, maintainers, and decliners) in 238 older Veterans. Declines in minutes of PA from 12 to 24 months were observed for both the treatment and control arms of the study. PA at 12 months was the strongest predictor of post-intervention changes in PA. To our surprise, those who took up the intervention and increased PA levels the most, had significant declines in post-intervention PA. Analysis of the three post-intervention PA trajectories demonstrated that the maintenance group actually reflected a group of nonresponders to the intervention who had more comorbidities, lower self-efficacy, and worse physical function than the improvers or decliners. Results suggest that behavioral counseling/support must be ongoing to promote maintenance. Strategies to promote PA appropriately to subgroups of individuals are needed.

Interleukin-15 receptor blockade in non-human primate kidney transplantation.

BACKGROUND: Interleukin (IL)-15 is a chemotactic factor to T cells. It induces proliferation and promotes survival of activated T cells. IL-15 receptor blockade in mouse cardiac and islet allotransplant models has led to long-term engraftment and a regulatory T-cell environment. This study investigated the efficacy of IL-15 receptor blockade using Mut-IL-15/Fc in an outbred non-human primate model of renal allotransplantation. METHODS: Male cynomolgus macaque donor-recipient pairs were selected based on ABO typing, major histocompatibility complex class I typing, and carboxy-fluorescein diacetate succinimidyl ester-based mixed lymphocyte responses. Once animals were assigned to one of six treatment groups, they underwent renal transplantation and bilateral native nephrectomy. Serum creatinine level was monitored twice weekly and as indicated, and protocol biopsies were performed. Rejection was defined as a increase in serum creatinine to 1.5 mg/dL or higher and was confirmed histologically. Complete blood counts and flow cytometric analyses were performed periodically posttransplant; pharmacokinetic parameters of Mut-IL-15/Fc were assessed. RESULTS: Compared with control animals, Mut-IL-15/Fc-treated animals did not demonstrate increased graft survival despite adequate serum levels of Mut-IL-15/Fc. Flow cytometric analysis of white blood cell subgroups demonstrated a decrease in CD8 T-cell and natural killer cell numbers, although this did not reach statistical significance. Interestingly, two animals receiving Mut-IL-15/Fc developed infectious complications, but no infection was seen in control animals. Renal pathology varied widely. CONCLUSIONS: Peritransplant IL-15 receptor blockade does not prolong allograft survival in non-human primate renal transplantation; however, it reduces the number of CD8 T cells and natural killer cells in the peripheral blood.

Carbon Markets: Past, Present, and Future

Carbon markets are substantial and they are expanding. There are many lessons from experiences over the past eight years: fewer free allowances, better management of market-sensitive information, and a recognition that trading systems require adjustments that have consequences for market participants and market confidence. Moreover, the emerging international architecture features separate emissions trading systems serving distinct jurisdictions. These programs are complemented by a variety of other types of policies alongside the carbon markets. This sits in sharp contrast to the integrated global trading architecture envisioned 15 years ago by the designers of the Kyoto Protocol and raises a suite of new questions. In this new architecture, jurisdictions with emissions trading have to decide how, whether, and when to link with one another, and policymakers overseeing carbon markets must confront how to measure the comparability of efforts among markets and relative to a variety of other policy approaches.

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Carbon markets: Past, present, and future

© 2014 by Annual Reviews.Carbon markets are substantial and expanding. There are many lessons from experience over the past 9 years: fewer free allowances, careful moderation of low and high prices, and a recognition that trading systems require adjustments that have consequences for market participants and market confidence. Moreover, the emerging international architecture features separate emissions trading systems serving distinct jurisdictions. These programs are complemented by a variety of other types of policies alongside the carbon markets. This architecture sits in sharp contrast to the integrated global trading architecture envisioned 15 years ago by the designers of the Kyoto Protocol and raises a suite of new questions. In this new architecture, jurisdictions with emissions trading have to decide how, whether, and when to link with one another, and policy makers must confront how to measure both the comparability of efforts among markets and the comparability between markets and a variety of other policy approaches.

Making Young Voters: The Impact of Preregistration on Youth Turnout

© 2016 by the Midwest Political Science Association.Recent research has cast doubt on the potential for various electoral reforms to increase voter turnout. In this article, we examine the effectiveness of preregistration laws, which allow young citizens to register before being eligible to vote. We use two empirical approaches to evaluate the impact of preregistration on youth turnout. First, we implement difference-in-difference and lag models to bracket the causal effect of preregistration implementation using the 2000-2012 Current Population Survey. Second, focusing on the state of Florida, we leverage a discontinuity based on date of birth to estimate the effect of increased preregistration exposure on the turnout of young registrants. In both approaches, we find preregistration increases voter turnout, with equal effectiveness for various subgroups in the electorate. More broadly, observed patterns suggest that campaign context and supporting institutions may help to determine when and if electoral reforms are effective.

Increased leptin levels correlate with thyroid autoantibodies in nonobese males.

OBJECTIVE: Leptin is an adipokine that regulates body weight and appetite. It is also an inflammatory cytokine that influences immune reactivity and autoimmunity. Leptin levels are increased in obesity and are higher in women than in men. We aimed to determine whether leptin levels, independent of sex and body mass index (BMI), are associated with thyroid autoimmunity. DESIGN: This study uses data from The Third National Health and Nutrition Examination Survey (NHANES III) to test the association of leptin and thyroid autoimmunity, independent of BMI. MEASUREMENTS: Thyroid-stimulating hormone, thyroxine, antithyroid peroxidase (TPO) antibodies and leptin levels were measured in 2902 men and 3280 women within the NHANES III population. BMI was calculated from height and weight. RESULTS: Women had significantly higher leptin levels and anti-TPO antibody titres than men. Correlation analyses demonstrated that leptin levels were associated with anti-TPO antibody levels in the total population, but when men and women were analysed separately, this association was lost. We then stratified men and women into obese (BMI > 30) or nonobese (BMI ≤ 30) subgroups and determined the association between leptin levels and anti-TPO antibody titres for each subgroup. Using regression analysis, we found that increased leptin levels correlated with thyroid autoantibodies in nonobese males, but not in obese males or in females. CONCLUSIONS: Leptin levels correlated with thyroid autoantibody titres in nonobese males. This association was not found in females. Sex and body habitus should therefore be considered in studying the role of leptin in other autoimmune conditions.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.

Immunological Signatures Identifying Different Stages of Latent Mycobacterium tuberculosis Infection and Discriminating Latent from Active Tuberculosis in Humans

Objectives: One third of the world population is considered latently infected with Mycobacterium tuberculosis(LTBI) and sterilizing this reservoir of bacteria that may reactivate is required for tuberculosis (TB) elimination. Thegroup of individuals with LTBI is heterogeneous with some of them being more at risk to develop TB disease thanothers. Improved diagnosis of subjects with LTBI is needed, allowing to differentiate subjects with LTBI from thosewith active TB, and to select among LTBI subjects those who are more at risk to develop active TB. We havecharacterized at the cellular level both the quantitative and qualitative T cell responses to different mycobacterialantigens in selected populations of infected subjects in order to identify new biomarkers that could help to identify M.tuberculosis-infected subjects and to stratify them in risk groups for reactivation of the infection.Methods: Lymphoblast frequencies and cytokine production (IFN-γ, TNF-α, IL-2) among CD4+ and CD8+ T cellswere analyzed by flow cytometry after in vitro stimulation with the latency antigen heparin-binding haemagglutinin(HBHA) or early-secreted antigen Target-6 (ESAT-6) of peripheral blood mononuclear cells from clinically wellcharacterized M. tuberculosis-infected humans (28 LTBI, 22 TB disease,12 controls). The LTBI group definedaccording to the Center for Disease Control guidelines was subdivided into QuantiFERON-TB Gold in-Tube (QFT)positive and negative subgroups.Results: Similar to TB patients, QFT+ LTBI subjects had higher proportions of HBHA-induced TNF-αsingle+ CD4+lymphocytes than QFT- LTBI subjects (p<0.05). Compared to LTBI subjects, TB patients had higher frequencies ofESAT-6-induced CD8+ lymphoblasts (p<0.001), higher proportions of ESAT-6-induced IFN-γ+TNF-α+ CD4+ Tlymphocytes (p<0.05), and lower proportions of HBHA-induced IFN-γ+TNF-α+IL-2+ (p<0.05) CD4+ T lymphocytes.Conclusions: These data provide new biomarkers to discriminate active TB from LTBI, and more interestingly,help to identify LTBI subjects with increased likelihood to develop TB disease.

Finite groups and geometries: a view on the present state and on the future

The model: groups of Lie-Chevalley type and buildingsThis paper is not the presentation of a completed theory but rather a report on a search progressing as in the natural sciences in order to better understand the relationship between groups and incidence geometry, in some future sought-after theory Τ. The search is based on assumptions and on wishes some of which are time-dependent, variations being forced, in particular, by the search itself.A major historical reference for this subject is, needless to say, Klein's Erlangen Programme. Klein's views were raised to a powerful theory thanks to the geometric interpretation of the simple Lie groups due to Tits (see for instance), particularly his theory of buildings and of groups with a BN-pair (or Tits systems). Let us briefly recall some striking features of this.Let G be a group of Lie-Chevalley type of rank r, denned over GF(q), q = pn, p prime. Let Xr denote the Dynkin diagram of G. To these data corresponds a unique thick building B(G) of rank r over the Coxeter diagram Xr (assuming we forget arrows provided by the Dynkin diagram). It turns out that B(G) can be constructed in a uniform way for all G, from a fixed p-Sylow subgroup U of G, its normalizer NG(U) and the r maximal subgroups of G containing NG(U).

Role of Landau quantization on the neutron-drip transition in magnetar crusts

The role of a strong magnetic field on the neutron-drip transition in the crust of a magnetar is studied. The composition of the crust and the neutron-drip threshold are determined numerically for different magnetic field strengths using the experimental atomic mass measurements from the 2012 Atomic Mass Evaluation complemented with theoretical masses calculated from the Brussels-Montreal Hartree-Fock-Bogoliubov nuclear mass model HFB-24. The equilibrium nucleus at the neutron-drip point is found to be independent of the magnetic field strength. As demonstrated analytically, the neutron-drip density and pressure increase almost linearly with the magnetic field strength in the strongly quantizing regime for which electrons lie in the lowest Landau level. For weaker magnetic fields, the neutron-drip density exhibits typical quantum oscillations. In this case, the neutron-drip density can be either increased by about 14% or decreased by 25% depending on the magnetic field strength. These variations are shown to be almost universal, independently of the nuclear mass model employed. These results may have important implications for the physical interpretation of timing irregularities and quasiperiodic oscillations detected in soft gamma-ray repeaters and anomalous x-ray pulsars, as well as for the cooling of strongly magnetized neutron stars.