Variability in the durability of CRISPR-Cas immunity

This is the author accepted manuscript. The final version is available from Royal Society via the DOI in this record.The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria Streptococcus thermophilus against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.Natural Environment Research Council (NERC)Biotechnology & Biological Sciences Research Council (BBSRC)European CommissionEuropean Molecular Biology Organization (EMBO)Leverhulme TrustNatural Sciences and Engineering Research Council of Canad

Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity

This is the final version of the article. Available from Elsevier via the DOI in this record.Some phages encode anti-CRISPR (acr) genes, which antagonize bacterial CRISPR-Cas immune systems by binding components of its machinery, but it is less clear how deployment of these acr genes impacts phage replication and epidemiology. Here, we demonstrate that bacteria with CRISPR-Cas resistance are still partially immune to Acr-encoding phage. As a consequence, Acr-phages often need to cooperate in order to overcome CRISPR resistance, with a first phage blocking the host CRISPR-Cas immune system to allow a second Acr-phage to successfully replicate. This cooperation leads to epidemiological tipping points in which the initial density of Acr-phage tips the balance from phage extinction to a phage epidemic. Furthermore, both higher levels of CRISPR-Cas immunity and weaker Acr activities shift the tipping points toward higher initial phage densities. Collectively, these data help elucidate how interactions between phage-encoded immune suppressors and the CRISPR systems they target shape bacteria-phage population dynamics.M.L. was supported by funding from the Wellcome Trust (https://wellcome.ac.uk) (109776/Z/15/Z), which was awarded to E.R.W. E.R.W. further acknowledges the Natural Environment Research Council (https://nerc.ukri.org) (NE/M018350/1), the BBSRC (BB/N017412/1), and the European Research Council (https://erc.europa.eu) (ERC-STG-2016-714478 - EVOIMMECH) for funding. S.v.H. acknowledges funding from the People Programme (Marie Curie Actions; https://ec.europa.eu/research/mariecurieactions/) of the European Union’s Horizon 2020 (REA grant agreement no. 660039) and from the BBSRC (BB/R010781/1). S.G. acknowledges funding (Visiting Professorship) from the Leverhulme Trust. A.B. acknowledges funding from the Royal Society. The authors thank Olivier Fradet for experimental contributions and Adair Borges and Joe Bondy-Denomy (UCSF) for providing DMS3mvir-AcrIF4 and phage JBD26

Evolutionary emergence of infectious diseases in heterogeneous host populations

This is the final version. Available from Public Library of Science via the DOI in this record.The emergence and re-emergence of pathogens remains a major public health concern. Unfortunately, when and where pathogens will (re-)emerge is notoriously difficult to predict, as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here, we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that the probability of pathogen emergence rapidly declines with the diversity of resistance in the host population. Experimental tests using lytic bacteriophages infecting their bacterial hosts containing Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR-Cas) immune defenses confirm these theoretical predictions. These results suggest effective strategies for cross-species spillover and for the management of emerging infectious diseases.Natural Environment Research Council (NERC)Wellcome TrustBiotechnology & Biological Sciences Research Council (BBSRC)European CommissionMarie Curie ActionsNatural Sciences and Engineering Research Council of CanadaLeverhulme Trus

Review: ‘Gimme five’: future challenges in multiple sclerosis. ECTRIMS Lecture 2009

This article is based on the ECTRIMS lecture given at the 25th ECTRIMS meeting which was held in Düsseldorf, Germany, from 9 to 12 September 2009. Five challenges have been identified: (1) safeguarding the principles of medical ethics; (2) optimizing the risk/benefit ratio; (3) bridging the gap between multiple sclerosis and experimental autoimmune encephalitis; (4) promoting neuroprotection and repair; and (5) tailoring multiple sclerosis therapy to the individual patient. Each of these challenges will be discussed and placed in the context of current research into the pathogenesis and treatment of multiple sclerosis

Nanoindentation study of the mechanical and damage behaviour of suspension plasma sprayed TiO2 coatings

TiO2 coatings can be used as self-cleaning surfaces owing to their photocatalytic and hydrophilic properties. Suspension plasma spray (SPS) has proven to be a feasible and cheap technique for producing self-cleaning surfaces with acceptable photo-activity. This paper presents a nanoindentation study of the mechanical properties (hardness. Young's modulus and scratch resistance) of photoactive layers of suspension plasma sprayed TiO2 coatings applied on to glass substrates. Microstructure observation showed that the rutile grains were surrounded by fine anatase crystals. Under the same spraying conditions, the resulting anatase/rutile concentrations varied depending on the cooling rate (the substrate being either cooled with water or in air). The results showed that higher concentrations of anatase, which is softer than rutile, reduced the scratch damage and increased the friction coefficient. (C) 2011 Elsevier B.V. All rights reserved.The study was financially supported by the Spanish Ministry of Science and Innovation (PID-600200-2009-5 and MAT2009-14144-C03-01 -02).Rayón Encinas, E.; Bonache Bezares, V.; Salvador Moya, MD.; Bannier, E.; Sánchez, E.; Denoirjean, A.; Ageorges, H. (2012). Nanoindentation study of the mechanical and damage behaviour of suspension plasma sprayed TiO2 coatings. Surface and Coatings Technology. 206(10):2655-2660. doi:10.1016/j.surfcoat.2011.11.010S265526602061

Small Heat Shock Protein αA-Crystallin Prevents Photoreceptor Degeneration in Experimental Autoimmune Uveitis

The small heat shock protein, αA-crystallin null (αA−/−) mice are known to be more prone to retinal degeneration than the wild type mice in Experimental Autoimmune Uveoretinitis (EAU). In this report we demonstrate that intravenous administration of αA preserves retinal architecture and prevents photoreceptor damage in EAU. Interestingly, only αA and not αB-crystallin (αB), a closely related small heat shock protein works, pointing to molecular specificity in the observed retinal protection. The possible involvement of αA in retinal protection through immune modulation is corroborated by adaptive transfer experiments, (employing αA−/− and wild type mice with EAU as donors and Rag2−/− as the recipient mice), which indicate that αA protects against the autoimmune challenge by modulating the systemic B and T cell immunity. We show that αA administration causes marked reduction in Th1 cytokines (TNF-α, IL-12 and IFN-γ), both in the retina and in the spleen; notably, IL-17 was only reduced in the retina suggesting local intervention. Importantly, expression of Toll-like receptors and their associated adaptors is also inhibited suggesting that αA protection, against photoreceptor loss in EAU, is associated with systemic suppression of both the adaptive and innate immune responses

Association of narcolepsy-cataplexy with HLA-DRB1 and DQB1 in Mexican patients: A relationship between HLA and gender is suggested

<p>Abstract</p> <p>Background</p> <p>Narcolepsy-cataplexy is characterized by excessive daytime sleepiness with recurrent episodes of irresistible sleep, cataplexy, hallucinations and sleep paralysis. Its aetiology is unknown, but it is positively associated with the human leukocyte antigens (HLA) in all studied populations. The purpose of the present study was to investigate the association of HLA class II <it>DRB1</it>/<it>DQB1 </it>alleles with narcolepsy-cataplexy in Mexican Mestizo patients.</p> <p>Methods</p> <p>This is a case-control study of consecutive patients and ethnically matched controls. We included 32 patients diagnosed with typical narcolepsy-cataplexy, of the National Institute of Neurology, of the Institute of Psychiatry and at the Center of Narcolepsy at Stanford University. As healthy controls, 203 Mexican Mestizos were included. <it>DRB1 </it>alleles were identified using sequence based typing. A PCR-SSOP reverse dot blot was used for <it>DQB1 </it>typing. Allele frequency was calculated by direct counting and the significance of the differences was assessed using the Yates Chi square. Odds ratio and confidence intervals were evaluated.</p> <p>Results</p> <p>HLA-<it>DRB1</it>*1501 (OR = 8.2; pc < 0.0001) and <it>DQB1</it>*0602 (OR = 8.4; pc < 0.0001) were found positively associated with narcolepsy. When deleting <it>DQB1</it>*0602+ patients from the analysis, <it>DQB1</it>*0301 was also found increased (OR = 2.7; p = 0.035; pc = NS). <it>DQB1</it>*0602/<it>DQB1</it>*0301 genotype was present in 15.6% of the cases (OR = 11.5; p = 0.00035), conferring a high risk. <it>DRB1</it>*0407 (OR = 0.2; p = 0.016 pc = NS) and <it>DQB1</it>*0302(OR = 0.4; p = 0.017, pc = NS) were found decreased in the patients. The gender stratification analysis showed a higher risk in females carrying <it>DRB1</it>*1501 (OR = 15.8, pc < 0.0001) and <it>DQB1</it>*0602 (OR = 19.8, pc < 0.0001) than in males (OR = 5.0 for both alleles; p = 0.012, pc = NS for <it>DRB1 </it>& p = 0.0012, pc = 0.017 for <it>DQB1</it>). The susceptibility alleles found in Mexicans with narcolepsy are also present in Japanese and Caucasians; <it>DRB1</it>*04 linked protection has also been shown in Koreans. A stronger HLA association is suggested in females, in accordance with the sexual dimorphism claimed previously.</p> <p>Conclusion</p> <p>This knowledge may contribute to a better understanding of the disease pathogenesis in different populations. The evaluation of the risk to develop narcolepsy-cataplexy in carriers of the described alleles/genotypes may also be possible. A larger sample should be analysed in Mexican and in other Hispanic patients to confirm these results.</p

Anomalous Hypothalamic Responses to Humor in Cataplexy

Cataplexy is observed in a subset of patients with narcolepsy and affects approximately 1 in 2,000 persons. Cataplexy is most often triggered by strong emotions such as laughter, which can result in transient, yet debilitating, muscle atonia. The objective of this study was to examine the neural systems underlying humor processing in individuals with cataplexy.While undergoing functional Magnetic Resonance Imaging (fMRI), we showed ten narcolepsy-cataplexy patients and ten healthy controls humorous cartoons. In addition, we examined the brain activity of one subject while in a full-blown cataplectic attack. Behavioral results showed that participants with cataplexy rated significantly fewer humorous cartoons as funny compared to controls. Concurrent fMRI showed that patients, when compared to controls and in the absence of overt cataplexy symptoms, showed pronounced activity in the emotional network including the ventral striatum and hypothalamus while viewing humorous versus non-humorous cartoons. Increased activity was also observed in the right inferior frontal gyri--a core component of the inhibitory circuitry. In comparison, the one subject who experienced a cataplectic attack showed dramatic reductions in hypothalamic activity.These findings suggest an overdrive of the emotional circuitry and possible compensatory suppression by cortical inhibitory regions in cataplexy. Moreover, during cataplectic attacks, the hypothalamus is characterized by a marked decrease in activity similar to that observed during sleep. One possible explanation for these findings is an initial overdrive and compensatory shutdown of the hypothalamus resulting in full cataplectic symptoms

Generalized shrinkage F-like statistics for testing an interaction term in gene expression analysis in the presence of heteroscedasticity

<p>Abstract</p> <p>Background</p> <p>Many analyses of gene expression data involve hypothesis tests of an interaction term between two fixed effects, typically tested using a residual variance. In expression studies, the issue of variance heteroscedasticity has received much attention, and previous work has focused on either between-gene or within-gene heteroscedasticity. However, in a single experiment, heteroscedasticity may exist both within and between genes. Here we develop flexible shrinkage error estimators considering both between-gene and within-gene heteroscedasticity and use them to construct <it>F</it>-like test statistics for testing interactions, with cutoff values obtained by permutation. These permutation tests are complicated, and several permutation tests are investigated here.</p> <p>Results</p> <p>Our proposed test statistics are compared with other existing shrinkage-type test statistics through extensive simulation studies and a real data example. The results show that the choice of permutation procedures has dramatically more influence on detection power than the choice of <it>F </it>or <it>F</it>-like test statistics. When both types of gene heteroscedasticity exist, our proposed test statistics can control preselected type-I errors and are more powerful. Raw data permutation is not valid in this setting. Whether unrestricted or restricted residual permutation should be used depends on the specific type of test statistic.</p> <p>Conclusions</p> <p>The <it>F</it>-like test statistic that uses the proposed flexible shrinkage error estimator considering both types of gene heteroscedasticity and unrestricted residual permutation can provide a statistically valid and powerful test. Therefore, we recommended that it should always applied in the analysis of real gene expression data analysis to test an interaction term.</p