Environmental Institute

Diel vertical migrations in the ocean play a key role in predator-prey dynamics and the functioning of the biological carbon pump. However, changes in ocean conditions including warming and deoxygenation threaten to significantly perturb vertical migration patterns over the twenty-first century. Specifically, vertical migrations over regions of critically low oxygen, known as oxygen minimum zones (OMZs), are likely to be most sensitive to changes in temperature and oxygen. In this study, we apply a simplified prognostic ecosystem model (APECOSM-1D) to changing conditions in the Pacific Ocean OMZ as simulated by 13 Earth System Models from the Coupled Model Intercomparison Project Phase 6 (CMIP6). We find that modeled fish migration depths at a given location in the region may deepen or shoal by over 100 m by the end of the century; however, there are large uncertainties across the CMIP6 ensemble for the geographic pattern of migration depth changes. To reconcile this, we adopt a water mass based approach which aggregates changes into regions defined by their vertical oxygen minimum value. In this framework, we find that fish migration depths over the lowest oxygen core of the OMZ remain stable due to compensating changes in temperature and oxygen. Meanwhile, away from the OMZ core, ocean warming and deoxygenation together drive shallower migration depths in projected conditions.

Abstract Background Increased intake of ultra-processed food (UPF) links to higher risk of inflammatory bowel disease (IBD)1, while its biological mechanism remains unclear. Our previous work implied gene-diet interaction modulates the risk of IBD, especially in those with higher IBD susceptibility2,3. This study is to unveil UPF’s effect on IBD via circulating metabolites, localize key component, and explore its mechanism linking UPF to IBD. Methods We aim to find the mechanism of UPF on incident IBD through key metabolite and related gene. Analyses involved two parts: a. construct UPF metabolic signature in UK Biobank (UKB) discovery cohort (n = 10,229), with internal (n = 91,306) and external validation (Whitehall II [WHII], n = 7,893); b. identify and validate key metabolite in UPF-IBD association and its mechanism in Western and Eastern (n = 752) cohorts. UPF metabolic signature was developed by elastic net regression of metabolites (assayed by high-throughput metabolomic platforms) on UPF intake (measured by repeated dietary recalls). We applied Cox regression to assess the metabolic signature on IBD risk. Weighted gene co-expression network analysis (WGCNA) was used to identify metabolite clusters in the signature. We combined linear model, elastic net regression, survival analysis, mediation analysis, and WGCNA to identify key metabolites. Further validation was performed in an Eastern multi-center cohort, ONE-IBD. Mendelian randomisation (MR), colocalization, and gene-environment (G-E) interaction analyses were used to address potential causality and genetic locus (Fig 1). Results A UPF metabolic signature of 73 metabolites was constructed (Fig 2A) and validated in UKB and WHII (Spearman ρ: 0.20-0.25). More pronounced UPF metabolic signature was associated with higher risk of IBD and CD (IBD: HRper SD=1.72, 95% CI 1.32-2.24; CD: HRper SD=2.65, 95% CI 1.57-4.48 Fig 2B). WGCNA revealed a cluster rich in fatty acids inversely associated with CD (HRper SD=0.66, 95% CI 0.45-0.98, Fig 2C), in which docosahexaenoic acid (DHA) was pinpointed as key metabolite (mediated proportion=12.5%, Fig 2D-E). External validation in ONE-IBD supported DHA as the metabolite most strongly associated with UPF and CD (Fig 2F). MR and colocalization revealed rs174546 in FADS1 gene as a shared variant linking DHA with CD (Fig 2G-H). G-E analysis showed UPF’s effect on CD was pronounced in individuals with FADS1 variant (T allele carriers, linking to lower DHA), while metabolic signature’s effect on CD was weakened, stressing the central role of metabolites (Fig 2I). Conclusion Our study reveals the critical role of metabolites linking UPF and IBD risk, especially in CD, with consistent evidence identifying DHA and FADS1 gene as personalised targets in IBD precision prevention.

SARS-CoV-2 induces delayed type-I/III interferon production, allowing it to escape the early innate immune response. The delay has been attributed to a deficiency in the ability of cells to sense viral replication upon infection, which in turn hampers activation of the antiviral state in bystander cells. Here, we introduce a cellular automaton model to investigate the spatiotemporal spreading of viral infection as a function of virus and host-dependent parameters. The model suggests that the considerable person-to-person heterogeneity in SARS-CoV-2 infections is a consequence of high sensitivity to slight variations in biological parameters near a critical threshold. It further suggests that within-host viral proliferation can be curtailed by the presence of remarkably few cells that are primed for IFN production. Thus, the observed heterogeneity in defense readiness of cells reflects a remarkably cost-efficient strategy for protection.

<strong class="journal-contentHeaderColor">Abstract.</strong> Ocean CO₂ uptake and acidification in response to human activities are driven primarily by the rise in atmospheric CO₂, but are also modulated by climate change. Existing work suggests that this `climate effect' influences the uptake and storage of anthropogenic carbon and acidification via the global increase in ocean temperature, although some regional responses have been attributed to changes in circulation or biological activity. Here, we investigate spatial patterns in the climate effect on surface-ocean acidification (and the closely related carbonate chemistry) in an Earth System Model under a rapid CO<sub>2</sub>-increase scenario, and identify another culprit. We show that the amplification of the hydrological cycle, a robustly simulated feature of climate change, is largely responsible for the spatial patterns in this climate effect at the sea surface. This `hydrological effect' can be understood as a subset of the total climate effect which includes warming, hydrological cycle amplification, circulation and biological changes. We demonstrate that it acts through two primary mechanisms: (i) directly diluting or concentrating dissolved ions by adding or removing freshwater and (ii) altering the sea surface temperature, which influences the solubility of dissolved inorganic carbon (DIC) and acidity of seawater. The hydrological effect opposes acidification in salinifying regions, most notably the subtropical Atlantic, and enhances acidification in freshening regions such as the western Pacific. Its single strongest effect is to dilute the negative ions that buffer the dissolution of CO₂, quantified as `Alkalinity'. The local changes in Alkalinity, DIC, and pH linked to the pattern of hydrological cycle amplification are as strong as the (largely uniform) changes due to warming, explaining the weak increase in pH and DIC seen in the climate effect in the subtropical Atlantic Ocean.

To investigate the efficiency of silver nanoparticles synthesized by the green method, and evaluate their antibacterial activity. The green method was used to synthesize silver nanoparticles (Ag NPs) from silver nitrate salt, and pomegranate peel extract (P) as a reducing agent. The synthesized Ag NPs were characterized by UV–visible spectrophotometer (UV–Vis), X-ray diffraction pattern (XRD), Fourier transform infrared (FT-IR), and scanning electron microscopy (SEM). The UV–Vis spectra displayed a resonance peak at 386 nm, equivalent to P-Ag NPs, and the FT-IR spectra confirmed the association of biological molecules from the extract in the synthesis process. The SEM image data confirmed the round and circular nature of Ag NPs. The EDX data presented the elemental configuration with a solid peak at 65 KeV that matched the silver. The antibacterial study of the synthesized nanoparticles was investigated by the agar diffusion method. We examined the antibacterial activity of biologically medicated silver nanoparticles against microbial strains of E. coli. The findings indicate that different doses (5, 10, and 15 μg) of Ag NPs synthesized by silver nitrate aided by pomegranate peel extract demonstrate vigorous antibacterial activity against E. coli bacteria. At a dose of 5 μg, the inhibition zone was neglected, but at doses of 10, 15 μg there was significant bacterial growth inhibition around the Ag NPs. Bacterial growth was effectively inhibited by the Ag NPs produced.

African horse sickness (AHS) is a highly infectious and often fatal disease caused by 9 serotypes of the orbivirus African horse sickness virus (AHSV). In March 2020, an AHS outbreak was reported in Thailand in which AHSV serotype 1 was identified as the causative agent. Trivalent live attenuated vaccines serotype 1, 3, and 4 were used in a targeted vaccination campaign within a 50-km radius surrounding the infected cases, which promptly controlled the spread of the disease. However, AHS-like symptoms in vaccinated horses required laboratory diagnostic methods to differentiate infected horses from vaccinated horses, especially for postvaccination surveillance. We describe a real-time reverse transcription PCR-based assay for rapid characterization of the affecting field strain. The development and validation of this assay should imbue confidence in differentiating AHS-vaccinated horses from nonvaccinated horses. This method should be applied to determining the epidemiology of AHSV in future outbreaks.

Monitoring data from apex predators were key drivers in the development of early chemicals legislations due to the population declines of many species during the twentieth century, which was linked to certain persistent organic pollutants (POPs). Besides triggering the development of global treaties (e.g. the Stockholm Convention), chemical monitoring data from apex predators have been particularly important for identifying compounds with bioaccumulative properties under field conditions. Many apex predators are protected species and only a few environmental specimen banks (ESBs) regularly collect samples as many ESBs were established during the 1980–1990s when apex predators were scarce. Today, many POPs have been banned, which contributed to the recovery of many apex predator populations. As a consequence, apex predator samples are now available in research collections (RCs) and natural history museums (NHMs). These samples can be used for routine analysis as well as for screening studies using novel analytical techniques and advanced data treatment workflows, such as suspect and non-target screening. The LIFE APEX project has demonstrated how these samples can be used in a cost-efficient way to generate data on legacy compounds and contaminants of emerging concern. Furthermore, it has described quality assurance/control measures to ensure high quality and comparable data, with a view to uses in chemicals risk assessment and management. To increase the visibility of available sample collections and monitoring data from apex predators we developed accessible online database systems. Additionally, the acquired high-resolution mass spectrometric data were stored in a digital sample freezing platform that allows retrospective suspect screening in previously analysed samples for substances that may be of concern/under assessment in the future. These databases provide open access to a wide range of chemical data, for use by regulators, researchers, industry and the general public, and contribute to a stronger link between science and policy.

A large number of apex predator samples are available in European research collections, environmental specimen banks and natural history museums that could be used in chemical monitoring and regulation. Apex predators bioaccumulate pollutants and integrate contaminant exposure over large spatial and temporal scales, thus providing key information for risk assessments. Still, present assessment practices under the different European chemical legislations hardly use existing chemical monitoring data from top predators. Reasons include the lack of user-specific guidance and the fragmentation of data across time and space. The European LIFE APEX project used existing sample collections and applied state-of-the-art target and non-target screening methods, resulting in the detection of > 4,560 pollutants including legacy compounds. We recommend establishing infrastructures that include apex predators as an early warning system in Europe. Chemical data of apex species from freshwater, marine and terrestrial compartments should become an essential component in future chemical assessment and management across regulations, with the purpose to (1) validate registration data with ‘real world’ measurements and evaluate the predictability of current models; (2) identify and prioritise hazardous chemicals for further assessment; (3) use data on food web magnification as one line of evidence to assess biomagnification; (4) determine the presence of (bio)transformations products and typical chemical mixtures, and (5) evaluate the effectiveness of risk management measures by trend analysis. We highlight the achievements of LIFE APEX with regard to novel trend and mixture analysis tools and prioritisation schemes. The proposed advancements complement current premarketing regulatory assessments and will allow the detection of contaminants of emerging concern at an early stage, trigger risk management measures and evaluations of their effects with the ultimate goal to protect humans and the environment. This is the second policy brief of the LIFE APEX project.