Role of DiaA and SeqA homologues in the deep-sea adapted growth of photobacterium profundum SS9

The mechanism of high pressure-adapted growth in the deep-sea bacterium Photobacterium profundum SS9 is poorly understood. To gain further insights, two P. profundum SS9R mutants were investigated. FL23 (pbpra3229::m-Tn10) and FL28 (pbpra1039::m-Tn10) had been previously characterised as high pressuresensitive and pressure-enhanced, respectively. FL23 had a growth defect at atmospheric pressure but failed to show high pressure-adapted growth on solid agar. Pbpra3229 is 75 % identical to E. coli DiaA (stimulator of DNA replication and critical for the timely initiation of replication) and 45% identical to E. coli GmhA (essential for lipopolysaccharide core biosynthesis), which led to an investigation into whether either process was affected in FL23. However, the lipopolysaccharide of FL23 and its parent strain were identical, which suggests that Pbpra3229 is not a GmhA homologue. In contrast, the pbpra3229 and E. coli diaA genes were functionally interchangeable and both restored the timing of DNA replication in an E. coli diaA mutant. FL28 had growth and morphological defects at high pressure, but both phenotypes were exacerbated at atmospheric pressure. Pbpra1039 is 55% identical to E. coli SeqA, which is a negative regulator of DNA replication and also essential for timely initiation. Pbpra1039 was shown to be a functional homologue of E. coli SeqA, as pbpra1039 partially complemented the DNA replication defect of an E. coli seqA mutant. Combined, these findings provide evidence that Pbpra3229 is a DiaA homologue, whereas Pbpra1039 is a cold adapted SeqA homologue, and that both positive and negative regulation of initiation of DNA replication are essential for the ability of P. profundum SS9 to adapt to deep-sea conditions. A marine metagenomic library was also screened for clones that produced novel cell envelope polysaccharides and tools were developed to identify cell envelope polysaccharides in P. profundum SS9

Data Oblivious ISA Extensions for Side Channel-Resistant and High Performance Computing

Blocking microarchitectural (digital) side channels is one of the most pressing challenges in hardware security today. Recently, there has been a surge of effort that attempts to block these leakages by writing programs data obliviously. In this model, programs are written to avoid placing sensitive data-dependent pressure on shared resources. Despite recent efforts, however, running data oblivious programs on modern machines today is insecure and low performance. First, writing programs obliviously assumes certain instructions in today\u27s ISAs will not leak privacy, whereas today\u27s ISAs and hardware provide no such guarantees. Second, writing programs to avoid data-dependent behavior is inherently high performance overhead. This paper tackles both the security and performance aspects of this problem by proposing a Data Oblivious ISA extension (OISA). On the security side, we present ISA design principles to block microarchitectural side channels, and embody these ideas in a concrete ISA capable of safely executing existing data oblivious programs. On the performance side, we design the OISA with support for efficient memory oblivious computation, and with safety features that allow modern hardware optimizations, e.g., out-of-order speculative execution, to remain enabled in the common case. We provide a complete hardware prototype of our ideas, built on top of the RISC-V out-of-order, speculative BOOM processor, and prove that the OISA can provide the advertised security through a formal analysis of an abstract BOOM-style machine. We evaluate area overhead of hardware mechanisms needed to support our prototype, and provide performance experiments showing how the OISA speeds up a variety of existing data oblivious codes (including ``constant time\u27\u27 cryptography and memory oblivious data structures), in addition to improving their security and portability

Selection at a single locus leads to widespread expansion of toxoplasma gondii lineages that are virulent in mice

The determinants of virulence are rarely defined for eukaryotic parasites such as T. gondii, a widespread parasite of mammals that also infects humans, sometimes with serious consequences. Recent laboratory studies have established that variation in a single secreted protein, a serine/threonine kinase known as ROPO18, controls whether or not mice survive infection. Here, we establish the extent and nature of variation in ROP18among a collection of parasite strains from geographically diverse regions. Compared to other genes, ROP18 showed extremely high levels of diversification and changes in expression level, which correlated with severity of infection in mice. Comparison with an out-group demonstrated that changes in the upstream region that regulates expression of ROP18 led to an historical increase in the expression and exposed the protein to diversifying selective pressure. Surprisingly, only three atypically distinct protein variants exist despite marked genetic divergence elsewhere in the genome. These three forms of ROP18 are likely adaptations for different niches in nature, and they confer markedly different virulence to mice. The widespread distribution of a single mouse-virulent allele among geographically and genetically disparate parasites may have consequences for transmission and disease in other hosts, including humans

Photobacterium profundum under Pressure:A MS-Based Label-Free Quantitative Proteomics Study

Photobacterium profundum SS9 is a Gram-negative bacterium, originally collected from the Sulu Sea. Its genome consists of two chromosomes and a 80 kb plasmid. Although it can grow under a wide range of pressures, P. profundum grows optimally at 28 MPa and 15°C. Its ability to grow at atmospheric pressure allows for both easy genetic manipulation and culture, making it a model organism to study piezophily. Here, we report a shotgun proteomic analysis of P. profundum grown at atmospheric compared to high pressure using label-free quantitation and mass spectrometry analysis. We have identified differentially expressed proteins involved in high pressure adaptation, which have been previously reported using other methods. Proteins involved in key metabolic pathways were also identified as being differentially expressed. Proteins involved in the glycolysis/gluconeogenesis pathway were up-regulated at high pressure. Conversely, several proteins involved in the oxidative phosphorylation pathway were up-regulated at atmospheric pressure. Some of the proteins that were differentially identified are regulated directly in response to the physical impact of pressure. The expression of some proteins involved in nutrient transport or assimilation, are likely to be directly regulated by pressure. In a natural environment, different hydrostatic pressures represent distinct ecosystems with their own particular nutrient limitations and abundances. However, the only variable considered in this study was atmospheric pressure

Is Violent Radicalisation Associated with Poverty, Migration, Poor Self-Reported Health and Common Mental Disorders?

BACKGROUND: Doctors, lawyers and criminal justice agencies need methods to assess vulnerability to violent radicalization. In synergy, public health interventions aim to prevent the emergence of risk behaviours as well as prevent and treat new illness events. This paper describes a new method of assessing vulnerability to violent radicalization, and then investigates the role of previously reported causes, including poor self-reported health, anxiety and depression, adverse life events, poverty, and migration and socio-political factors. The aim is to identify foci for preventive intervention. METHODS: A cross-sectional survey of a representative population sample of men and women aged 18-45, of Muslim heritage and recruited by quota sampling by age, gender, working status, in two English cities. The main outcomes include self-reported health, symptoms of anxiety and depression (common mental disorders), and vulnerability to violent radicalization assessed by sympathies for violent protest and terrorist acts. RESULTS: 2.4% of people showed some sympathy for violent protest and terrorist acts. Sympathy was more likely to be articulated by the under 20s, those in full time education rather than employment, those born in the UK, those speaking English at home, and high earners (>£75,000 a year). People with poor self-reported health were less likely to show sympathies for violent protest and terrorism. Anxiety and depressive symptoms, adverse life events and socio-political attitudes showed no associations. CONCLUSIONS: Sympathies for violent protest and terrorism were uncommon among men and women, aged 18-45, of Muslim heritage living in two English cities. Youth, wealth, and being in education rather than employment were risk factors

Regional variation and determinants of vitamin D status in sunshine-abundant Thailand

<p>Abstract</p> <p>Background</p> <p>Vitamin D insufficiency is highly prevalent. Most of the studies concerning vitamin D status were generated from countries situated at temperate latitudes. It is less clear what the extent of vitamin D insufficiency is in countries situated in the tropics and how geographical regions within country would affect vitamin D status. In the present study, we investigated vitamin D status in Thais according to geographical regions and other risk factors.</p> <p>Methods</p> <p>Subjects consisted of 2,641 adults, aged 15 - 98 years, randomly selected from the Thai 4th National Health Examination Survey (2008-9) cohort. Serum 25 hydroxyvitamin D were measured by liquid chromatography/tandem mass spectrometry. Data were expressed as mean ± SE.</p> <p>Results</p> <p>Subjects residing in Bangkok, the capital city of Thailand, had lower 25(OH)D levels than other parts of the country (Bangkok, central, northern, northeastern and southern regions: 64.8 ± 0.7, 79.5 ± 1.1, 81.7 ± 1.2, 82.2 ± 0.8 and 78.3 ± 1.3 nmol/L, respectively; <it>p </it>< 0.001). Within each region, except for the northeastern part of the country, subjects living inside municipal areas had lower circulating 25(OH)D (central, 77.0 ± 20.9 nmol/L vs 85.0 ± 22.1 nmol/L, <it>p </it>< 0.001; north 79.3 ± 22.1 nmol/L vs 86.8 ± 21.8 nmol/L, <it>p </it>< 0.001; northeast 84.1 ± 23.3 nmol/L vs 87.3 ± 20.9 nmol/L, <it>p </it>= 0.001; south, 76.6 ± 20.5 nmol/L vs 85.2 ± 24.7 nmol/L, <it>p </it>< 0.001). Overall, the prevalence of vitamin D insufficiency was 64.6%, 46.7%, and 33.5% in Bangkok, municipal areas except Bangkok, and outside municipal area in other parts of the country, respectively. In addition, the prevalence of vitamin D insufficiency according to geographical regions was 43.1%, 39.1%, 34.2% and 43.8% in the central, north, northeast and south, respectively. After controlling for covariates in multiple linear regression analysis, the results showed that low serum 25(OH)D levels were associated with being female, younger age, living in urban and Bangkok.</p> <p>Conclusions</p> <p>Vitamin D insufficiency is common and varies across geographical regions in Thailand.</p

Increased Aβ pathology in aged Tg2576 mice born to mothers fed a high fat diet

Maternal obesity is associated with increased risk of developing diabetes, obesity and premature death in adult offspring. Mid-life diabetes, hypertension and hypercholesterolaemia are risk factors for the development of sporadic Alzheimer's disease (AD). A key pathogenic feature of AD is the accumulation of β-amyloid (Aβ) in the brain. The purpose of this study was to investigate the effect of high fat diet feeding during early life on Aβ pathology in the Tg2576 mouse model of AD. Female mice were fed a standard (C) or high fat (HF) diet before mating and during gestation and lactation. At weaning, male offspring were fed a C diet. Significantly higher levels of guanidine-soluble Aβ and plaque loads were observed in the hippocampi of 11-month old Tg2576 mice born to mothers fed a HF diet. Changes in the extracellular matrix led to increased retention of Aβ within the parenchyma. These data support a role for maternal and gestational health on the health of the aged brain and pathologies associated with AD and may provide a novel target for both the prevention and treatment of AD

Helicobacter pylori, persistent infection burden and structural brain imaging markers

Persistent infections, whether viral, bacterial or parasitic, including Helicobacter pylori infection, have been implicated in non-communicable diseases, including dementia and other neurodegenerative diseases. In this cross-sectional study, data on 635 cognitively normal participants from the UK Biobank study (2006–21, age range: 40–70 years) were used to examine whether H. pylori seropositivity (e.g. presence of antibodies), serointensities of five H. pylori antigens and a measure of total persistent infection burden were associated with selected brain volumetric structural MRI (total, white, grey matter, frontal grey matter (left/right), white matter hyperintensity as percent intracranial volume and bi-lateral sub-cortical volumes) and diffusion-weighted MRI measures (global and tract-specific bi-lateral fractional anisotropy and mean diffusivity), after an average 9–10 years of lag time. Persistent infection burden was calculated as a cumulative score of seropositivity for over 20 different pathogens. Multivariable-adjusted linear regression analyses were conducted, whereby selected potential confounders (all measures) and intracranial volume (sub-cortical volumes) were adjusted, with stratification by Alzheimer’s disease polygenic risk score tertile when exposures were H. pylori antigen serointensities. Type I error was adjusted to 0.007. We report little evidence of an association between H. pylori seropositivity and persistent infection burden with various volumetric outcomes (P &gt; 0.007, from multivariable regression models), unlike previously reported in past research. However, H. pylori antigen serointensities, particularly immunoglobulin G against the vacuolating cytotoxin A, GroEL and outer membrane protein antigens, were associated with poorer tract-specific white matter integrity (P &lt; 0.007), with outer membrane protein serointensity linked to worse outcomes in cognition-related tracts such as the external capsule, the anterior limb of the internal capsule and the cingulum, specifically at low Alzheimer’s disease polygenic risk. Vacuolating cytotoxin A serointensity was associated with greater white matter hyperintensity volume among individuals with mid-level Alzheimer’s disease polygenic risk, while among individuals with the highest Alzheimer’s disease polygenic risk, the urease serointensity was consistently associated with reduced bi-lateral caudate volumes and the vacuolating cytotoxin A serointensity was linked to reduced right putamen volume (P &lt; 0.007). Outer membrane protein and urease were associated with larger sub-cortical volumes (e.g. left putamen and right nucleus accumbens) at middle Alzheimer’s disease polygenic risk levels (P &lt; 0.007). Our results shed light on the relationship between H. pylori seropositivity, H. pylori antigen levels and persistent infection burden with brain volumetric structural measures. These data are important given the links between infectious agents and neurodegenerative diseases, including Alzheimer’s disease, and can be used for the development of drugs and preventive interventions that would reduce the burden of those diseases

Identification of a New Rhoptry Neck Complex RON9/RON10 in the Apicomplexa Parasite Toxoplasma gondii

Apicomplexan parasites secrete and inject into the host cell the content of specialized secretory organelles called rhoptries, which take part into critical processes such as host cell invasion and modulation of the host cell immune response. The rhoptries are structurally and functionally divided into two compartments. The apical duct contains rhoptry neck (RON) proteins that are conserved in Apicomplexa and are involved in formation of the moving junction (MJ) driving parasite invasion. The posterior bulb contains rhoptry proteins (ROPs) unique to an individual genus and, once injected in the host cell act as effector proteins to co-opt host processes and modulate parasite growth and virulence. We describe here two new RON proteins of Toxoplasma gondii, RON9 and RON10, which form a high molecular mass complex. In contrast to the other RONs described to date, this complex was not detected at the MJ during invasion and therefore was not associated to the MJ complex RON2/4/5/8. Disruptions of either RON9 or RON10 gene leads to the retention of the partner in the ER followed by subsequent degradation, suggesting that the RON9/RON10 complex formation is required for proper sorting to the rhoptries. Finally, we show that the absence of RON9/RON10 has no significant impact on the morphology of rhoptry, on the invasion and growth in fibroblasts in vitro or on virulence in vivo. The conservation of RON9 and RON10 in Coccidia and Cryptosporidia suggests a specific relation with development in intestinal epithelial cells

Proteomic Analysis of Fractionated Toxoplasma Oocysts Reveals Clues to Their Environmental Resistance

Toxoplasma gondii is an obligate intracellular parasite that is unique in its ability to infect a broad range of birds and mammals, including humans, leading to an extremely high worldwide prevalence and distribution. This work focuses on the environmentally resistant oocyst, which is the product of sexual replication in felids and an important source of human infection. Due to the difficulty in producing and working with oocysts, relatively little is known about how this stage is able to resist extreme environmental stresses and how they initiate a new infection, once ingested. To fill this gap, the proteome of the wall and sporocyst/sporozoite fractions of mature, sporulated oocysts were characterized using one-dimensional gel electrophoresis followed by LC-MS/MS on trypsin-digested peptides. A combined total of 1021 non-redundant T. gondii proteins were identified in the sporocyst/sporozoite fraction and 226 were identified in the oocyst wall fraction. Significantly, 172 of the identified proteins have not previously been identified in Toxoplasma proteomic studies. Among these are several of interest for their likely role in conferring environmental resistance including a family of small, tyrosine-rich proteins present in the oocyst wall fractions and late embryogenesis abundant domain-containing (LEA) proteins in the cytosolic fractions. The latter are known from other systems to be key to enabling survival against desiccation