Conventional and unconventional T-cell responses contribute to the prediction of clinical outcome and causative bacterial pathogen in sepsis patients.

Sepsis is characterized by a dysfunctional host response to infection culminating in life-threatening organ failure that requires complex patient management and rapid intervention. Timely diagnosis of the underlying cause of sepsis is crucial, and identifying those at risk of complications and death is imperative for triaging treatment and resource allocation. Here, we explored the potential of explainable machine learning models to predict mortality and causative pathogen in sepsis patients. By using a modelling pipeline employing multiple feature selection algorithms, we demonstrate the feasibility of identifying integrative patterns from clinical parameters, plasma biomarkers, and extensive phenotyping of blood immune cells. While no single variable had sufficient predictive power, models that combined five and more features showed a macro area under the curve (AUC) of 0.85 to predict 90-day mortality after sepsis diagnosis, and a macro AUC of 0.86 to discriminate between Gram-positive and Gram-negative bacterial infections. Parameters associated with the cellular immune response contributed the most to models predictive of 90-day mortality, most notably, the proportion of T cells among PBMCs, together with expression of CXCR3 by CD4+ T cells and CD25 by mucosal-associated invariant T (MAIT) cells. Frequencies of Vδ2+ γδ T cells had the most profound impact on the prediction of Gram-negative infections, alongside other T-cell-related variables and total neutrophil count. Overall, our findings highlight the added value of measuring the proportion and activation patterns of conventional and unconventional T cells in the blood of sepsis patients in combination with other immunological, biochemical, and clinical parameters.

The SARS-CoV2 envelope differs from host cells, exposes procoagulant lipids, and is disrupted in vivo by oral rinses.

The lipid envelope of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an essential component of the virus; however, its molecular composition is undetermined. Addressing this knowledge gap could support the design of antiviral agents as well as further our understanding of viral-host protein interactions, infectivity, pathogenicity, and innate immune system clearance. Lipidomics revealed that the virus envelope comprised mainly phospholipids (PLs), with some cholesterol and sphingolipids, and with cholesterol/phospholipid ratio similar to lysosomes. Unlike cellular membranes, procoagulant amino-PLs were present on the external side of the viral envelope at levels exceeding those on activated platelets. Accordingly, virions directly promoted blood coagulation. To investigate whether these differences could enable selective targeting of the viral envelope in vivo, we tested whether oral rinses containing lipid-disrupting chemicals could reduce infectivity. Products containing PL-disrupting surfactants (such as cetylpyridinium chloride) met European virucidal standards in vitro; however, components that altered the critical micelle concentration reduced efficacy, and products containing essential oils, povidone-iodine, or chlorhexidine were ineffective. This result was recapitulated in vivo, where a 30-s oral rinse with cetylpyridinium chloride mouthwash eliminated live virus in the oral cavity of patients with coronavirus disease 19 for at least 1 h, whereas povidone-iodine and saline mouthwashes were ineffective. We conclude that the SARS-CoV-2 lipid envelope i) is distinct from the host plasma membrane, which may enable design of selective antiviral approaches; ii) contains exposed phosphatidylethanolamine and phosphatidylserine, which may influence thrombosis, pathogenicity, and inflammation; and iii) can be selectively targeted in vivo by specific oral rinses.

Topology optimization of 3D photonic crystals with complete bandgaps.

The design of photonic crystals with complete bandgaps has recently received considerable research focus for numerous reasons. This work leverages well-known nonlinear programming techniques to alleviate the non-smoothness caused by degenerate eigenvalues such that topology optimization problems can be solved with the open-source IPOPT software. A fully-vectorial plane wave expansion technique is used with an iterative eigensolver to efficiently predict dispersion properties of candidate structures. Nonlinear programming is employed to solve the inverse problem of designing three-dimensional periodic structures that exhibit complete two-dimensional (2D) and three-dimensional (3D) photonic bandgaps. Mesh refinement is performed to alleviate the large computational burden of designing and analyzing photonic crystals, and a periodic density filter is implemented to impose a minimum feature size for manufacturability considerations.

(1)H NMR metabolomics reveals contrasting response by male and female mussels exposed to reduced seawater pH, increased temperature, and a pathogen.

Human activities are fundamentally altering the chemistry of the world's oceans. Ocean acidification (OA) is occurring against a background of warming and an increasing occurrence of disease outbreaks, posing a significant threat to marine organisms, communities, and ecosystems. In the current study, (1)H NMR spectroscopy was used to investigate the response of the blue mussel, Mytilus edulis, to a 90-day exposure to reduced seawater pH and increased temperature, followed by a subsequent pathogenic challenge. Analysis of the metabolome revealed significant differences between male and female organisms. Furthermore, males and females are shown to respond differently to environmental stress. While males were significantly affected by reduced seawater pH, increased temperature, and a bacterial challenge, it was only a reduction in seawater pH that impacted females. Despite impacting males and females differently, stressors seem to act via a generalized stress response impacting both energy metabolism and osmotic balance in both sexes. This study therefore has important implications for the interpretation of metabolomic data in mussels, as well as the impact of environmental stress in marine invertebrates in general.

Distribution of mycosporine-like amino acids along a surface water meridional transect of the Atlantic.

The composition and abundance of mycosporine-like amino acids (MAAs) were investigated in the surface waters along a 13,000-km meridional transect (52° N to 45° S) in the Atlantic Ocean (Atlantic Meridional Transect programme: Cruise AMT 18: 4/10/2008-10/11/2008). MAAs were ubiquitous along the transect, although the composition of the MAAs was variable. Highest concentrations were in the far south (below 40° S; MAA >1 µg L(-1)) and in north subtropical equatorial region (NER: 0-25° N; MAA up to 0.8 µg L(-1)). Highest MAA relative to chlorophyll-a occurred in the NER (MAA/chl-a ratio between 2 and 5). MAA/chl-a significantly correlated with the preceding month's mean daily UV dose and with UV-B/UV-A. In the far south, high MAA concentrations coincided with high phytoplankton biomass, high nutrients and a deep mixed layer associated with the austral spring. Here, the phytoplankton community was dominated by micro- and nano-eukaryotes. At the NER, the high MAA/chl-a coincided with low nutrient concentrations, a shallow mixed layer depth (20-70 m) and to a lesser extent to a shallow nitracline (40-90 m). Here, the phytoplankton consisted primarily of picophytoplankton (0-0.2 µm), dominated by the pico-cyanobacteria Synechococcus sp. and Prochlorococcus sp. and by the nitrogen fixing filamentous cyanobacterium Trichodesmium. The low nitrate concentrations (<0.1 µmol L(-1)) at the NER suggest that nitrogen fixation was required for MAA production. Specific MAAs could not easily be assigned to particular groups of phytoplankton and we could not rule out the possibility that MAAs were associated with symbiotic cyanobacteria contained within heterotrophic dinoflagellates or diatoms.

Oxylipin metabolism is controlled by mitochondrial ß-oxidation during bacterial inflammation.

Oxylipins are potent biological mediators requiring strict control, but how they are removed en masse during infection and inflammation is unknown. Here we show that lipopolysaccharide (LPS) dynamically enhances oxylipin removal via mitochondrial ß-oxidation. Specifically, genetic or pharmacological targeting of carnitine palmitoyl transferase 1 (CPT1), a mitochondrial importer of fatty acids, reveal that many oxylipins are removed by this protein during inflammation in vitro and in vivo. Using stable isotope-tracing lipidomics, we find secretion-reuptake recycling for 12-HETE and its intermediate metabolites. Meanwhile, oxylipin ß-oxidation is uncoupled from oxidative phosphorylation, thus not contributing to energy generation. Testing for genetic control checkpoints, transcriptional interrogation of human neonatal sepsis finds upregulation of many genes involved in mitochondrial removal of long-chain fatty acyls, such as ACSL1,3,4, ACADVL, CPT1B, CPT2 and HADHB. Also, ACSL1/Acsl1 upregulation is consistently observed following the treatment of human/murine macrophages with LPS and IFN-γ. Last, dampening oxylipin levels by ß-oxidation is suggested to impact on their regulation of leukocyte functions. In summary, we propose mitochondrial ß-oxidation as a regulatory metabolic checkpoint for oxylipins during inflammation.

Bioethanol Production from UK Seaweeds: Investigating Variable Pre-treatment and Enzyme Hydrolysis Parameters.

This study describes the method development for bioethanol production from three species of seaweed. Laminaria digitata, Ulva lactuca and for the first time Dilsea carnosa were used as representatives of brown, green and red species of seaweed, respectively. Acid thermo-chemical and entirely aqueous (water) based pre-treatments were evaluated, using a range of sulphuric acid concentrations (0.125-2.5 M) and solids loading contents (5-25 % [w/v]; biomass: reactant) and different reaction times (5-30 min), with the aim of maximising the release of glucose following enzyme hydrolysis. A pre-treatment step for each of the three seaweeds was required and pre-treatment conditions were found to be specific to each seaweed species. Dilsea carnosa and U. lactuca were more suited with an aqueous (water-based) pre-treatment (yielding 125.0 and 360.0 mg of glucose/g of pre-treated seaweed, respectively), yet interestingly non pre-treated D. carnosa yielded 106.4 g g-1 glucose. Laminaria digitata required a dilute acid thermo-chemical pre-treatment in order to liberate maximal glucose yields (218.9 mg glucose/g pre-treated seaweed). Fermentations with S. cerevisiae NCYC2592 of the generated hydrolysates gave ethanol yields of 5.4 g L-1, 7.8 g L-1 and 3.2 g L-1 from D. carnosa, U. lactuca and L. digitata, respectively. This study highlighted that entirely aqueous based pre-treatments are effective for seaweed biomass, yet bioethanol production alone may not make such bio-processes economically viable at large scale.

Complete Acid-Based Hydrolysis Assay for Carbohydrate Quantification in Seaweed: A Species-Specific Optimized Approach.

Accurate quantification of the carbohydrate content of biomass is crucial for many bio-refining processes. The most commonly followed protocol is typically a modification of the NREL-based assay (specifically designed for carbohydrate analysis from lignocellulosic biomass). However, this NREL protocol was revealed to be excessively thermochemically harsh for seaweed biomass. This can result in erroneously low total sugar quantification as the reaction severity can degrade a proportion of the liberated sugars to decomposition products such as furans. Here we describe an optimization of the total acid hydrolysis protocol for accurate quantification of the carbohydrate content of seaweeds. Different species of seaweed can be accurately evaluated for their carbohydrate contents by following this optimized method.

Modulation of Polar Lipid Profiles in Chlorella sp. in Response to Nutrient Limitation.

We evaluate the effects of nutrient limitation on cellular composition of polar lipid classes/species in Chlorella sp. using modern polar lipidomic profiling methods (liquid chromatography⁻tandem mass spectrometry; LC-MS/MS). Total polar lipid concentration was highest in nutrient-replete (HN) cultures with a significant reduction in monogalactosyldiacylglycerol (MGDG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE) class concentrations for nutrient-deplete (LN) cultures. Moreover, reductions in the abundance of MGDG relative to total polar lipids versus an increase in the relative abundance of digalactosyldiacylglycerol (DGDG) were recorded in LN cultures. In HN cultures, polar lipid species composition remained relatively constant throughout culture with high degrees of unsaturation associated with acyl moieties. Conversely, in LN cultures lipid species composition shifted towards greater saturation of acyl moieties. Multivariate analyses revealed that changes in the abundance of a number of species contributed to the dissimilarity between LN and HN cultures but with dominant effects from certain species, e.g., reduction in MGDG 34:7 (18:3/16:4). Results demonstrate that Chlorella sp. significantly alters its polar lipidome in response to nutrient limitation, and this is discussed in terms of physiological significance and polar lipids production for applied microalgal production systems.

Establishment of Withania somnifera hairy root cultures for the production of withanolide A.

Withania sominifera (Indian ginseng) was transformed by Agrobacterium rhizogenes. Explants from seedling roots, stems, hypocotyls, cotyledonary nodal segments, cotyledons and young leaves were inoculated with A. rhizogenes strain R1601. Hairy (transformed) roots were induced from cotyledons and leaf explants. The transgenic status of hairy roots was confirmed by polymerase chain reaction using nptII and rolB specific primers and, subsequently, by Southern analysis for the presence of nptII and rolB genes in the genomes of transformed roots. Four clones of hairy roots were established; these differed in their morphology. The doubling time of faster growing cultures was 8-14 d with a fivefold increase in biomass after 28 d compared with cultured, non-transformed seedling roots. MS-based liquid medium was superior for the growth of transformed roots compared with other culture media evaluated (SH, LS and N6), with MS-based medium supplemented with 40 g/L sucrose being optimal for biomass production. Cultured hairy roots synthesized withanolide A, a steroidal lactone of medicinal and therapeutic value. The concentration of withanolide A in transformed roots (157.4 microg/g dry weight) was 2.7-fold more than in non-transformed cultured roots (57.9 microg/g dry weight).

Selection of yeast strains for bioethanol production from UK seaweeds.

Macroalgae (seaweeds) are a promising feedstock for the production of third generation bioethanol, since they have high carbohydrate contents, contain little or no lignin and are available in abundance. However, seaweeds typically contain a more diverse array of monomeric sugars than are commonly present in feedstocks derived from lignocellulosic material which are currently used for bioethanol production. Hence, identification of a suitable fermentative microorganism that can utilise the principal sugars released from the hydrolysis of macroalgae remains a major objective. The present study used a phenotypic microarray technique to screen 24 different yeast strains for their ability to metabolise individual monosaccharides commonly found in seaweeds, as well as hydrolysates following an acid pre-treatment of five native UK seaweed species (Laminaria digitata, Fucus serratus, Chondrus crispus, Palmaria palmata and Ulva lactuca). Five strains of yeast (three Saccharomyces spp, one Pichia sp and one Candida sp) were selected and subsequently evaluated for bioethanol production during fermentation of the hydrolysates. Four out of the five selected strains converted these monomeric sugars into bioethanol, with the highest ethanol yield (13 g L-1) resulting from a fermentation using C. crispus hydrolysate with Saccharomyces cerevisiae YPS128. This study demonstrated the novel application of a phenotypic microarray technique to screen for yeast capable of metabolising sugars present in seaweed hydrolysates; however, metabolic activity did not always imply fermentative production of ethanol.

The effect of engineered iron nanoparticles on growth and metabolic status of marine microalgae cultures.

Synthetic zero-valent nano-iron (nZVI) compounds are finding numerous applications in environmental remediation owing to their high chemical reactivity and versatile catalytic properties. Studies were carried out to assess the effects of three types of industrially relevant engineered nZVI on phytoplankton growth, cellular micromorphology and metabolic status. Three marine microalgae (Pavlova lutheri, Isochrysis galbana and Tetraselmis suecica) were grown on culture medium fortified with the nano-Fe compounds for 23 days and subsequent alterations in their growth rate, size distribution, lipid profiles and cellular ultrastructure were assessed. The added nano Fe concentrations were either equimolar with the EDTA-Fe conventionally added to the generic f/2 medium (i.e. 1.17 × 10(-5)M), or factor 10 lower and higher, respectively. We provide evidence for the: (1) broad size distribution of nZVI particles when added to the nutrient rich f/2 media with the higher relative percentage of the smallest particles with the coated forms; (2) normal algal growth in the presence of all three types of nZVIs with standard growth rates, cellular morphology and lipid content comparable or improved when compared to algae grown on f/2 with EDTA-Fe; (3) sustained algal growth and normal physiology at nZVI levels 10 fold below that in f/2, indicating preference to nanoparticles over EDTA-Fe; (4) increased total cellular lipid content in T. suecica grown on media enriched with uncoated nZVI25, and in P. lutheri with inorganically coated nZVI(powder), when compared at equimolar exposures; (5) significant change in fatty acid composition complementing the nZVI(powder)-mediated increase in lipid content of P. lutheri; (6) a putative NP uptake mechanism is proposed for I. galbana via secretion of an extracellular matrix that binds nZVIs which then become bioavailable via phagocytotic membrane processes.

In vitro assessment of the bioaccessibility of tocopherol and fatty acids from sunflower seed oil bodies.

The in vitro digestibility (proteolytic and lipolytic) and bioaccessibility of nutritionally important compounds (alpha-tocopherol and fatty acids) have been studied for natural sunflower ( Helianthus annuus ) oil body suspensions in comparison to artificial emulsions emulsified with polyoxyethylene-20-sorbitan-monolaurate (Tween 20) or whey protein isolate. Proteolytic digestion of emulsions with pepsin (pH 2) promoted significant increases in mean particle size of the whey protein isolate stabilized emulsion (1.8-2.9 mum) and oil bodies (2.3-22.5 mum) but not the Tween 20 stabilized emulsions. SDS-PAGE of proteolytic digestion products suggested degradation of the stabilizing oleosin protein (ca. 18-21 kDa) in oil bodies. The rate of oil body hydrolysis with lipase was significantly slower than the lipase-catalyzed hydrolysis of the artificial emulsions and exhibited a prolonged lag phase. Results from simulated human digestion in vitro suggested that the mean bioaccessibility of alpha-tocopherol and total fatty acids from oil bodies (0.6 and 8.4%, respectively) was significantly lower than that from the Tween 20 stabilized emulsion (35 and 52%, respectively) and the whey protein isolate stabilized emulsion (17 and 33%, respectively). These in vitro results suggest that oil bodies could provide a natural emulsion in food that is digested at a relatively slow rate, the physiological consequence of which may be increased satiety.

Design of near-field irregular diffractive optical elements by use of a multiresolution direct binary search method.

A multiresolution direct binary search iterative procedure is used to design small dielectric irregular diffractive optical elements that have subwavelength features and achieve near-field focusing below the diffraction limit. Designs with a single focus or with two foci, depending on wavelength or polarization, illustrate the possible functionalities available from the large number of degrees of freedom. These examples suggest that the concept of such elements may find applications in near-field lithography, wavelength-division multiplexing, spectral analysis, and polarization beam splitters.