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Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs. Although the rearrangement of DNA methylation patterns occurring in the zygote has been extensively characterized, little is known about the dynamics of DNA modifications during spermatid maturation. Here, we demonstrate that the dynamics of 5-carboxylcytosine (5caC) correlate with active transcription of LINE-1 retroelements during murine spermiogenesis. We show that the open reading frames of active and evolutionary young LINE-1s are 5caC-enriched in round spermatids and 5caC is eliminated from LINE-1s and spermiogenesis-specific genes during spermatid maturation, being simultaneously retained at promoters and introns of developmental genes. Our results reveal an association of 5caC with activity of LINE-1 retrotransposons suggesting a potential direct role for this DNA modification in fine regulation of their transcription.

Epigenetic modifications regulate gene expression in the host response to a diverse range of pathogens. The extent and consequences of epigenetic modification during macrophage responses to Streptococcus pneumoniae, and the role of pneumolysin, a key Streptococcus pneumoniae virulence factor, in influencing these responses, are currently unknown. To investigate this, we infected human monocyte derived macrophages (MDMs) with Streptococcus pneumoniae and addressed whether pneumolysin altered the epigenetic landscape and the associated acute macrophage transcriptional response using a combined transcriptomic and proteomic approach. Transcriptomic analysis identified 503 genes that were differentially expressed in a pneumolysin-dependent manner in these samples. Pathway analysis highlighted the involvement of transcriptional responses to core innate responses to pneumococci including modules associated with metabolic pathways activated in response to infection, oxidative stress responses and NFκB, NOD-like receptor and TNF signalling pathways. Quantitative proteomic analysis confirmed pneumolysin-regulated protein expression, early after bacterial challenge, in representative transcriptional modules associated with innate immune responses. In parallel, quantitative mass spectrometry identified global changes in the relative abundance of histone post translational modifications (PTMs) upon pneumococcal challenge. We identified an increase in the relative abundance of H3K4me1, H4K16ac and a decrease in H3K9me2 and H3K79me2 in a PLY-dependent fashion. We confirmed that pneumolysin blunted early transcriptional responses involving TNF-α and IL-6 expression. Vorinostat, a histone deacetylase inhibitor, similarly downregulated TNF production, reprising the pattern observed with pneumolysin. In conclusion, widespread changes in the macrophage transcriptional response are regulated by pneumolysin and are associated with global changes in histone PTMs. Modulating histone PTMs can reverse pneumolysin-associated transcriptional changes influencing innate immune responses, suggesting that epigenetic modification by pneumolysin plays a role in dampening the innate responses to pneumococci.Author summaryPneumolysin is a toxin that contributes to how Streptococcus pneumoniae, the leading cause of pneumonia, causes disease. In this study, the toxin alters gene expression in immune cells called macrophages, one of the first lines of defence against bacteria at sites of infection. Modulation involved multiple immune responses, including generation of chemical signals coordinating responses in immune cells termed cytokines. In addition, changes were observed in histone proteins that are involved in controlling gene expression in the cell. Pneumolysin reduced early production of the cytokine TNF-α and a medicine vorinostat that modifies these ‘epigenetic’ histone modifications had a similar affect, suggesting epigenetic mechanisms contribute to the ability of pneumolysin to reduce immune responses.

summary Sphagnum cuspidatum Hoffm. was collected from a remote site in N. Wales, and a polluted site in the S. Pennines. When added to artificial rainwater solution, HSO3− was oxidized to SO42−. The rate at which this oxidation occurred was modified differentially by the mosses from the two sites. S. cuspidatum from the S. Pennines promoted a rapid oxidation rate and disappearance of HSO3− was complete in 6 h. S. cuspidatum from N. Wales, on the other hand, achieved a very slow oxidation rate and HSO3− persisted in solution for more than 24 h. Prolonged exposure to HSO3− in the Welsh material caused damage to, and eventual death of, this material but not of the S. Pennine moss. The rates of HSO3− oxidation promoted by the mosses from the two sites appear to be related to the concentration of the transition metal ions, Fe(III), Mn(II), and Cu(II), present on the cell-wall cation-exchange sites. These metals, particularly Fe, present on the surface of the S. Pennine material catalysed a rapid chemical oxidation of HSO3− to SO42−. The increased levels of transition metals associated with the S. Pennine moss originate in the peat as a legacy of past pollution events at this site. Levels of Fe were approximately 100 times greater than those for Mn or Cu and 5–10 times higher on the S. Pennine moss than on that from N. Wales. Removal of these metal ions (using EDTA) from the surface of the S. Pennine material removed the HSO3− oxidizing ability of the moss, leading eventually to cell death. The ability to withstand high levels of HSO3− was conferred upon the Welsh moss by supplying Fe(m) in artificial rainwater solution under laboratory conditions. Transplanting Sphagnum from the Welsh to the S. Pennine site gave rise to a similar response. Nomenclature of mosses follows Smith (1978).

summary Shoots of Sphagnum cuspidatum Hoffm. were collected from two sites: one, a relatively unpolluted site in N. Wales, remote from pollution sources and the other, a grossly polluted site in the South Pennines.* Material from both sites was grown in the laboratory and exposed to artificial rainwater solution with and without bisulphite (HSO3) amendment (0.1 mM). Effects of exposure to HSO3 for up to 21 days on growth, photosynthesis, chlorophyll a fluorescence and chlorophyll concentrations were studied in the two Sphagnum populations. Application of HSO3 produced significantly less than maximum growth in Sphagnum from both sites. This effect was far greater, however, in the material from the unpolluted Welsh site. Photosynthesis in the Welsh material treated with HSO3 decreased steadily with time; after 21 days of exposure, photosynthetic oxygen evolution had ceased. This decrease was accompanied by a decrease in fluorescence quenching (as [(P – T)/P]), suggesting a gradual loss of water-splitting activity. In contrast, HSO3 initially stimulated photosynthesis in Sphagnum from the polluted site. Chlorophyll concentration was decreased in Spliagmtm from both sites in the presence of HSO3 Possible mechanisms of tolerance to HSO3 are discussed.

Historical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.

Manipulation of turbulence within an atmospheric boundary layer flow by application of woven wire mesh fences is investigated. Turbulence properties behind fences of different porosities and mesh opening widths were determined from velocity measurements in a wind tunnel. It is found that with the application of a fence with a porosity of 0.46, the streamwise turbulence intensity can be reduced from the inflow level of 12.5%–8.8% and the integral length scale can be reduced from 380 to 270 mm. The results show that behind the mesh fences turbulence kinetic energy decays as a power law function of the downstream distance for all wire mesh fences tested in the wind tunnel. The decay rate of turbulence kinetic energy is faster, and a larger reduction in the integral length scale is achieved for fences with porosities between 0.46 and 0.64 compared to higher porosities of between 0.73 and 0.75. Porosity of the woven wire meshes is found to be the key parameter which influences their turbulence reduction performance. In the end, application of the wire mesh fences for reduction of wind loads on solar panels and heliostats is discussed. Evaluation of wind loads based on the reduction of turbulence intensity and integral length scale shows that up to 48% and 53% reduction in peak drag and lift forces on a heliostat, respectively, can be achieved with application of mesh fences.

The critical resolved shear stress of an Al 4 wt. \% Cu alloy containing a homogeneous distribution of $��''$ precipitates was determined by means of dislocation dynamics simulations. The size distribution, shape, orientation and volume fraction of the precipitates in the alloy were obtained from transmission electron microscopy observations while the parameters controlling the dislocation/precipitate interactions (elastic mismatch, transformation strains, dislocation mobility and cross-slip probability, etc.) were calculated from atomistic simulations. The precipitates were assumed to be either impenetrable or shearable by the dislocations, the latter characterized by a threshold shear stress that has to be overcome to shear the precipitate. The predictions of the simulations in terms of the critical resolved shear stress and of the dislocation/precipitate interaction mechanisms were in good agreement with the experimental results. It was concluded that the optimum strength of this alloy is attained with a homogeneous distribution of $��''$ precipitates whose average size ($\approx$ 40 nm) is at the transition between precipitate shearing and looping. Overall, the dislocation dynamics strategy presented in this paper is able to provide quantitative predictions of precipitate strengthening in metallic alloys.

Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs. Although the rearrangement of DNA methylation patterns occurring in the zygote has been extensively characterized, little is known about the dynamics of DNA modifications during spermatid maturation. Here, we demonstrate that the dynamics of 5-carboxylcytosine (5caC) correlate with active transcription of LINE-1 retroelements during murine spermiogenesis. We show that the open reading frames of active and evolutionary young LINE-1s are 5caC-enriched in round spermatids and 5caC is eliminated from LINE-1s and spermiogenesis-specific genes during spermatid maturation, being simultaneously retained at promoters and introns of developmental genes. Our results reveal an association of 5caC with activity of LINE-1 retrotransposons suggesting a potential direct role for this DNA modification in fine regulation of their transcription., Blythe et al investigate the patterns of oxidized forms of the 5-methylcytosine DNA modification during spermatogenesis. They find that open reading frames of evolutionarily young and transcriptionally active LINE-1 retrotransposons are enriched in 5-carboxylcytosine (5caC) during spermatid maturation, suggesting a link between 5cac and LINE-1 activity.

Purpose: Infectious diseases are one of the leading causes of death among children under five (U5s) both in India and globally. This is worse in slum environments with poor access to water, sanitation and hygiene (WASH), good nutrition and a safe built environment. Globally, a One Health (i.e. human, animal and environment) approach is increasingly advocated for by the WHO-FAO-OIE tripartite to reduce infections and antimicrobial resistance. As under-5s living in peri-urban slums are exposed to household- and community-owned companion and livestock animals and pests, the CHIP consortium hypothesised that employing a One Health approach to co-produce behavioural change and slum upgrading interventions may reduce this burden where other WASH and nutrition interventions have failed. This study aimed to assess the feasibility of employing a One Health approach to assess under-5 infection and risk factor prevalence in Jaipurs peri-urban slums, prior to undertaking prospective cohort studies involving culture and culture-independent sampling of under-5s and animals across our study sites in Jaipur (Rajasthan, India), Jakarta (Indonesia) and Antofagasta (Chile). Methods: We administered a rapid household survey to 25 purposively selected households across six slums in Jaipur. The questionnaire used evaluated infection prevalence, healthseeking behaviours, the built environment, the presence of companion and livestock animals and pests, and individual- and household-level demographics. We displayed the correlations between infection incidence and a range of factors in our sample, and displayed the portion of children under 5 who experienced one or multiple episodes of ill health, categorised by a range of One Health factors. Results: Parents reported at least one recent episode of ill health for a large portion (40%) of under-5s within the last 30 days. 80% of under-5s had no access to safe drinking water; every household reported the presence of at least one kind of pest within the respondents own home; and 20% of under-5s feeding equipment was cleaned with water only. Only one household reported owning a companion or livestock animal, potentially reflecting confusion about the definition of these animals. The incidence of infection appeared to be related to WASH and socio-economic factors as expected. Conclusion: Safe drinking water, pest control and behavioural change surrounding the cleaning of under-5 feeding equipment should be given consideration in future research in this locale. Future studies should not rely solely on parent reporting of childrens symptoms cross referencing symptom reporting from multiple household members should be combined with culture and culture-independent sampling. Where possible, researchers should measure the presence of companion and livestock animals directly to avoid misinterpretation and to observe practices rather than relying on reporting alone.

Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the host&ndash, pathogen interactions during early colonisation are poorly understood. Intramammary challenge of dairy cows with S. uberis (strain 0140 J) or isogenic mutants lacking the surface-anchored serine protease, SUB1154, demonstrated that virulence was dependent on the presence and correct location of this protein. Unlike the wild-type strain, the mutant lacking SUB1154 failed to elicit IL-1&beta, from ex vivo CD14+ cells obtained from milk (bovine mammary macrophages, BMM), but this response was reinstated by complementation with recombinant SUB1154, the protein in isolation elicited no response. Production of IL-1&beta, was ablated in the presence of various inhibitors, indicating dependency on internalisation and activation of NLRP3 and caspase-1, consistent with inflammasome activation. Similar transcriptomic changes were detected in ex vivo BMM in response to the wild-type or the SUB1154 deletion mutant, consistent with S. uberis priming BMM, enabling the SUB1154 protein to activate inflammasome maturation in a transcriptionally independent manner. These data can be reconciled in a novel model of pathogenesis in which, paradoxically, early colonisation is dependent on the innate response to the initial infection.

The proposed work designs and implements a control scheme for a three phase, qZSI enabling the inverter to operate in a grid-forming role. Through PLECS simulations, the proposed control scheme is shown to operate the qZSI with inherent power sharing, when operating in parallel with other qZSIs, and tight frequency/voltage regulation capabilities. The system is benchmarked against a conventional boost-cascaded VSI system.

Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the host–pathogen interactions during early colonisation are poorly understood. Intramammary challenge of dairy cows with S. uberis (strain 0140J) or isogenic mutants lacking the surface-anchored serine protease, SUB1154, demonstrated that virulence was dependent on the presence and correct location of this protein. Unlike the wild-type strain, the mutant lacking SUB1154 failed to elicit IL-1β from ex vivo CD14+ cells obtained from milk (bovine mammary macrophages, BMM), but this response was reinstated by complementation with recombinant SUB1154; the protein in isolation elicited no response. Production of IL-1β was ablated in the presence of various inhibitors, indicating dependency on internalisation and activation of NLRP3 and caspase-1, consistent with inflammasome activation. Similar transcriptomic changes were detected in ex vivo BMM in response to the wild-type or the SUB1154 deletion mutant, consistent with S. uberis priming BMM, enabling the SUB1154 protein to activate inflammasome maturation in a transcriptionally independent manner. These data can be reconciled in a novel model of pathogenesis in which, paradoxically, early colonisation is dependent on the innate response to the initial infection.

BackgroundMigration from one environment to another often causes marked changes in developmental conditions. Here we compare epigenetic ageing and stability of the epigenetic maintenance system among British-Bangladeshi women who grew up in Bangladesh (adult migrants), where there are higher pathogen loads and poorer health care, to second-generation Bangladeshis who grew up in the UK. In our previous studies of these migrants, those who spent their childhoods in Bangladesh also had lower levels of reproductive hormones and a shorter reproductive lifespan compared to those who grew up in the UK, suggesting life history trade-offs during development. In the present study, we hypothesised that women who grew up in Bangladesh would have i) an older epigenetic/biological age compared to the women with a childhood in the UK and ii) that differences in the pace of epigenetic ageing might also be reflected by altered stability of DNA methylation marks.ResultsIllumina EPIC array methylation data from buccal tissue was used to establish epigenetic age estimates from 15 adult migrants and 11 second-generation migrants, aged 18-35 years. Using residuals from linear regression of DNA methylation-based biological age (DNAm age) on the chronological age, the results showed significant differences (p=0.016) in epigenetic age estimates: women whose childhood was in Bangladesh are on average 6.02 (± 2.34) years older, than those who grew up in London. We further investigated the efficiency of the epigenetic maintenance system which purportedly is reflected by epigenetic clocks. Methylation states of CpGs at the LHCGR/LHR locus, which contributes to Horvath’s multi tissue epigenetic clock were evaluated. Based on the Ratio of Concordance Preference (RCP) approach that uses double-stranded methylation data, we find that maintenance of epigenetic information is more stable in women who grew up in Bangladesh.ConclusionsThe work supports earlier findings that adverse childhood environments lead to phenotypic life history trade-offs. The data indicate that childhood environments can induce subtle changes to the epigenetic maintenance system that are detectable long after exposure occurred. The implication of such a finding warrants further investigation as it implies that a less flexible epigenetic memory system established early in life could reduce the capacity to respond to different environmental conditions in adult life.

Dogs develop osteosarcoma (OSA) and the disease process closely resembles that of human OSA. OSA has a poor prognosis in both species and disease-free intervals and cure rates have not improved in recent years. Gene expression in canine OSAs was compared with non-tumor tissue utilising RNA sequencing, validated by qRT-PCR and immunohistochemistry (n = 16). Polymorphic polyglutamine (polyQ) tracts in the androgen receptor (AR/NR3C4) and nuclear receptor coactivator 3 (NCOA3) genes were investigated in control and OSA patients using polymerase chain reaction (PCR), Sanger sequencing and fragment analysis (n = 1019 Rottweilers, 379 Irish Wolfhounds). Our analysis identified 1281 significantly differentially expressed genes (&gt, 2 fold change, p &lt, 0.05), specifically 839 lower and 442 elevated gene expression in osteosarcoma (n = 3) samples relative to non-malignant (n = 4) bone. Enriched pathways and gene ontologies were identified, which provide insight into the molecular pathways implicated in canine OSA. Expression of a subset of these genes (SLC2A1, DKK3, MMP3, POSTN, RBP4, ASPN) was validated by qRTPCR and immunohistochemistry (MMP3, DKK3, SLC2A1) respectively. While little variation was found in the NCOA3 polyQ tract, greater variation was present in both polyQ tracts in the AR, but no significant associations in length were made with OSA. The data provides novel insights into the molecular mechanisms of OSA in high risk breeds. This knowledge may inform development of new prevention strategies and treatments for OSA in dogs and supports utilising spontaneous OSA in dogs to improve understanding of the disease in people.

Purpose: The Ebola Virus Disease (EVD) epidemic was one of the most severe public health emergencies in modern times. The economic impact of epidemics has mostly been analysed at the macroeconomic level. Conversely, we aimed to estimate the economic costs of preventive measures of the epidemic to an extractive firm, ArcelorMittal, using data in the epidemic region from March 2014 to December 2015. ArcelorMittal is the worlds largest steel producer and particularly important in West Africa, where the extractive industry is economically crucial. Methods: Qualitative methods, in-depth interviews and focus group discussions, were used to investigate the events and channels of impact of the epidemic on the firm, as perceived by employees and contractors. Quantitative data regarding these costs was also collected. Retrospective cost analysis estimated the actual cost of preventive methods adopted. Results: Most respondents indicated the largest cost impact was suspension of Phase II expansion, a series of projects designed to increase iron ore production in Liberia. The next largest cost was the preventive measures adopted to counter disease spread. Total costs incurred for adopting preventive measures was USD 10.58-11.11 million. The overall direct costs of preventive measures adopted within the fence, meaning within the physical boundary of the firms sites, shared 30-31% of the total costs incurred. The share of external donation supporting humanitarian response was 11-12% of the total costs, followed by 7-12% of relational costs. Conclusions: The firms response during the EVD epidemic focused on its employees and operations, which was later expanded to the wider community and then in supporting the international humanitarian response.

Serratia marcescens strain BTL07, which has the ability to promote growth and suppress plant diseases, was isolated from the rhizoplane of a chili plant. The draft genome sequence data of the strain will contribute to advancing our understanding of the molecular mechanisms underlying plant growth promotion and tolerance to different stresses.

In the period from January 2013 to July 2014, three process change initiatives were undertaken at a major UK hospital to improve the patient discharge process. These initiatives were inspired by the findings of a study of the discharge process using Soft Systems Methodology. The first initiative simplified time-consuming paperwork and the second introduced more regular reviews of patient progress through daily multi-disciplinary "Situation Reports". These two initiatives were undertaken in parallel across the hospital, and for the average patient they jointly led to a 41% reduction between a patient being declared medically stable and their being discharged from the hospital. The third initiative implemented more proactive alerting of Social Care Practitioners to patients with probable social care needs at the front door, and simplified capture of important patient information (using a "SPRING" form). This initiative saw a 20% reduction in total length of stay for 88 patients on three wards where the SPRING form was used, whilst 248 patients on five control wards saw no significant change in total length of stay in the same period. Taken together, these initiatives have reduced total length of stay by 67% from 55.8 days to 18.6 days for the patients studied.

This paper investigates the effects of turbulence in the atmospheric boundary layer (ABL) on the peak wind loads on heliostats in stow position in isolation and in tandem configurations with respect to the critical scaling parameters of the heliostats. The heliostats were exposed to a part-depth ABL in a wind tunnel using two configurations of spires and roughness elements to generate a range of turbulence intensities and integral length scales. Force measurements on different-sized heliostat mirrors at a range of heights found that both peak lift and hinge moments were reduced by up to 30% on the second tandem heliostat when the spacing between the heliostat mirrors was close to the mirror chord length and converged to the isolated heliostat values when the spacing was greater than 5 times the chord length. Peak wind loads on the tandem heliostat were above those on an isolated heliostat for an integral-length-scale-to-chord-length ratio L u x / c of less than 5, whereas tandem loads were 30% lower than an isolated heliostat at L u x / c of 10. The reduced loads on the tandem heliostat corresponded to a shift to higher frequencies of the fluctuating pressure spectra, due to the break-up of large eddies by the upstream heliostat.