Development and Application of Strategies to Generate Bacteriophage Resistant Strains for Use in Milk Fermentation Processes

End of Project ReportThe objectives of this project were firstly, the identification of natural phage resistance systems for exploitation, secondly, the development of methodologies to utilise these systems to improve the bacteriophage resistance of starter strains for use in milk fermentation processes, and thirdly, the actual application of these methodologies to improving starter strains. The main conclusions were as follows: Three new natural plasmid (DNA)-associated bacteriophage resistance systems were identified at Moorepark. The detailed genetic makeup of the phage resistance plasmid (pMRC01) was elucidated. Bacteriophages currently evolving in the industrial cheese-making environment were monitored to facilitate the judicious choice of phage resistance systems for use in commercial starter cultures which can more effectively target the documented problematic phage types. Two highly virulent phages targeting important cheese starters were identified in the industrial cheese-making environment. A reliable food-grade method to facilitate the transfer of phage resistance systems to cheese-making starter strains was developed. This is based on bacteriocin immunity-linked phage resistance. Phage resistant cheese starter cultures were developed through natural selection and by molecular manipulation using phage resistance plasmids. The phage resistance plasmid pMRC01 was introduced to 31 cheese starter strains.Department of Agriculture, Food and the Marin

Phages of non-dairy lactococci: isolation and characterization of ΦL47, a phage infecting the grass isolate Lactococcus lactis ssp. cremoris DPC6860

peer reviewedLactococci isolated from non-dairy sources have been found to possess enhanced metabolic activity when compared to dairy strains. These capabilities may be harnessed through the use of these strains as starter or adjunct cultures to produce more diverse flavor profiles in cheese and other dairy products. To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ΦL47, was isolated from a sewage sample using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. Visualization of phage virions by transmission electron microscopy established that this phage belongs to the family Siphoviridae and possesses a long tail fiber, previously unseen in dairy lactococcal phages. Determination of the lytic spectrum revealed a broader than expected host range, with ΦL47 capable of infecting 4 industrial dairy strains, including ML8, HP and 310, and 3 additional non-dairy isolates. Whole genome sequencing of ΦL47 revealed a dsDNA genome of 128, 546 bp, making it the largest sequenced lactococcal phage to date. In total, 190 open reading frames (ORFs) were identified, and comparative analysis revealed that the predicted products of 117 of these ORFs shared greater than 50% amino acid identity with those of L. lactis phage Φ949, a phage isolated from cheese whey. Despite their different ecological niches, the genomic content and organization of ΦL47 and Φ949 are quite similar, with both containing 4 gene clusters oriented in different transcriptional directions. Other features that distinguish ΦL47 from Φ949 and other lactococcal phages, in addition to the presence of the tail fiber and the genome length, include a low GC content (32.5%) and a high number of predicted tRNA genes (8). Comparative genome analysis supports the conclusion that ΦL47 is a new member of the 949 lactococcal phage group which currently includes the dairy Φ949

Properties and Detection of Spin Nematic Order in Strongly Correlated Electron Systems

A spin nematic is a state which breaks spin SU(2) symmetry while preserving translational and time reversal symmetries. Spin nematic order can arise naturally from charge fluctuations of a spin stripe state. Focusing on the possible existence of such a state in strongly correlated electron systems, we build a nematic wave function starting from a t-J type model. The nematic is a spin-two operator, and therefore does not couple directly to neutrons. However, we show that neutron scattering and Knight shift experiments can detect the spin anisotropy of electrons moving in a nematic background. We find the mean field phase diagram for the nematic taking into account spin-orbit effects.Comment: 13 pages, 11 figures. (v2) References adde

The Parkinson's progression markers initiative (PPMI) - establishing a PD biomarker cohort.

ObjectiveThe Parkinson's Progression Markers Initiative (PPMI) is an observational, international study designed to establish biomarker-defined cohorts and identify clinical, imaging, genetic, and biospecimen Parkinson's disease (PD) progression markers to accelerate disease-modifying therapeutic trials.MethodsA total of 423 untreated PD, 196 Healthy Control (HC) and 64 SWEDD (scans without evidence of dopaminergic deficit) subjects were enrolled at 24 sites. To enroll PD subjects as early as possible following diagnosis, subjects were eligible with only asymmetric bradykinesia or tremor plus a dopamine transporter (DAT) binding deficit on SPECT imaging. Acquisition of data was standardized as detailed at www.ppmi-info.org.ResultsApproximately 9% of enrolled subjects had a single PD sign at baseline. DAT imaging excluded 16% of potential PD subjects with SWEDD. The total MDS-UPDRS for PD was 32.4 compared to 4.6 for HC and 28.2 for SWEDD. On average, PD subjects demonstrated 45% and 68% reduction in mean striatal and contralateral putamen Specific Binding Ratios (SBR), respectively. Cerebrospinal fluid (CSF) was acquired from >97% of all subjects. CSF (PD/HC/SWEDD pg/mL) α-synuclein (1845/2204/2141) was reduced in PD vs HC or SWEDD (P < 0.03). Similarly, t-tau (45/53) and p-tau (16/18) were reduced in PD versus HC (P < 0.01).InterpretationPPMI has detailed the biomarker signature for an early PD cohort defined by clinical features and imaging biomarkers. This strategy provides the framework to establish biomarker cohorts and to define longitudinal progression biomarkers to support future PD treatment trials

Results of international standardised beekeeper surveys of colony losses for winter 2012-2013 : analysis of winter loss rates and mixed effects modelling of risk factors for winter loss.

This article presents results of an analysis of winter losses of honey bee colonies from 19 mainly European countries, most of which implemented the standardised 2013 COLOSS questionnaire. Generalised linear mixed effects models (GLMMs) were used to investigate the effects of several factors on the risk of colony loss, including different treatments for Varroa destructor, allowing for random effects of beekeeper and region. Both winter and summer treatments were considered, and the most common combinations of treatment and timing were used to define treatment factor levels. Overall and within country colony loss rates are presented. Significant factors in the model were found to be: percentage of young queens in the colonies before winter, extent of queen problems in summer, treatment of the varroa mite, and access by foraging honey bees to oilseed rape and maize. Spatial variation at the beekeeper level is shown across geographical regions using random effects from the fitted models, both before and after allowing for the effect of the significant terms in the model. This spatial variation is considerable

The ac magnetic response of mesoscopic type II superconductors

The response of mesoscopic superconductors to an ac magnetic field is numerically investigated on the basis of the time-dependent Ginzburg-Landau equations (TDGL). We study the dependence with frequency $\omega$ and dc magnetic field $H_{dc}$ of the linear ac susceptibility $\chi(H_{dc}, \omega)$ in square samples with dimensions of the order of the London penetration depth. At $H_{dc}=0$ the behavior of $\chi$ as a function of $\omega$ agrees very well with the two fluid model, and the imaginary part of the ac susceptibility, $\chi"(\omega)$, shows a dissipative a maximum at the frequency $\nu_o=c^2/(4\pi \sigma\lambda^2)$. In the presence of a magnetic field a second dissipation maximum appears at a frequency $\omega_p\ll\nu_0$. The most interesting behavior of mesoscopic superconductors can be observed in the $\chi(H_{dc})$ curves obtained at a fixed frequency. At a fixed number of vortices, $\chi"(H_{dc})$ continuously increases with increasing $H_{dc}$. We observe that the dissipation reaches a maximum for magnetic fields right below the vortex penetration fields. Then, after each vortex penetration event, there is a sudden suppression of the ac losses, showing discontinuities in $\chi"(H_{dc})$ at several values of $H_{dc}$. We show that these discontinuities are typical of the mesoscopic scale and disappear in macroscopic samples, which have a continuos behavior of $\chi(H_{dc})$. We argue that these discontinuities in $\chi(H_{dc})$ are due to the effect of {\it nascent vortices} which cause a large variation of the amplitude of the order parameter near the surface before the entrance of vortices.Comment: 12 pages, 9 figures, RevTex

Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates.

Zika virus (ZIKV) infection is associated with congenital defects and pregnancy loss. Here, we found that 26% of nonhuman primates infected with Asian/American ZIKV in early gestation experienced fetal demise later in pregnancy despite showing few clinical signs of infection. Pregnancy loss due to asymptomatic ZIKV infection may therefore be a common but under-recognized adverse outcome related to maternal ZIKV infection

Managed honey bee colony losses in Canada, China, Europe, Israel and Turkey, for the winters of 2008-9 and 1009-10

In 2008 the COLOSS network was formed by honey bee experts from Europe and the USA. The primary objectives set by this scientific network were to explain and to prevent large scale losses of honey bee (Apis mellifera) colonies. In June 2008 COLOSS obtained four years support from the European Union from COST and was designated as COST Action FA0803 – COLOSS (Prevention of honey bee COlony LOSSes). To enable the comparison of loss data between participating countries, a standardized COLOSS questionnaire was developed. Using this questionnaire information on honey bee losses has been collected over two years. Survey data presented in this study were gathered in 2009 from 12 countries and in 2010 from 24 countries. Mean honey bee losses in Europe varied widely, between 7-22% over the 2008-9 winter and between 7-30% over the 2009-10 winter. An important finding is that for all countries which participated in 2008-9, winter losses in 2009-10 were found to be substantially higher. In 2009-10, winter losses in South East Europe were at such a low level that the factors causing the losses in other parts of Europe were absent, or at a level which did not affect colony survival. The five provinces of China, which were included in 2009-10, showed very low mean (4%) A. mellifera winter losses. In six Canadian provinces, mean winter losses in 2010 varied between 16-25%, losses in Nova Scotia (40%) being exceptionally high. In most countries and in both monitoring years, hobbyist beekeepers (1-50 colonies) experienced higher losses than practitioners with intermediate beekeeping operations (51-500 colonies). This relationship between scale of beekeeping and extent of losses effect was also observed in 2009-10, but was less pronounced. In Belgium, Italy, the Netherlands and Poland, 2008-9 mean winter losses for beekeepers who reported ‘disappeared’ colonies were significantly higher compared to mean winter losses of beekeepers who did not report ‘disappeared’ colonies. Mean 2008-9 winter losses for those beekeepers in the Netherlands who reported symptoms similar to “Colony Collapse Disorder” (CCD), namely: 1. no dead bees in or surrounding the hive while; 2. capped brood was present, were significantly higher than mean winter losses for those beekeepers who reported ‘disappeared’ colonies without the presence of capped brood in the empty hives. In the winter of 2009-10 in the majority of participating countries, beekeepers who reported ‘disappeared’ colonies experienced higher winter losses compared with beekeepers, who experienced winter losses but did not report ‘disappeared’ colonies