High-yield synthesis of 2-O-α-D-glucosyl-D-glycerate by a bifunctional glycoside phosphorylase

Osmolytes are produced by various microorganisms as a defense mechanism to protect cells and macromolecules from damage caused by external stresses in harsh environments. Due to their useful stabilizing properties, these molecules are applied as active ingredients in a wide range of cosmetics and healthcare products. The metabolic pathways and biocatalytic syntheses of glycosidic osmolytes such as 2-O-α-D-glucosyl-D-glycerate often involve the action of a glycoside phosphorylase. Here, we report the discovery of a glucosylglycerate phosphorylase from carbohydrate-active enzyme family GH13 that is also active on sucrose, which contrasts the strict specificity of known glucosylglycerate phosphorylases that can only use α-D-glucose 1-phosphate as glycosyl donor in transglycosylation reactions. The novel enzyme can be distinguished from other phosphorylases from the same family by the presence of an atypical conserved sequence motif at specificity-determining positions in the active site. The promiscuity of the sucrose-active glucosylglycerate phosphorylase can be exploited for the high-yielding and rapid synthesis of 2-O-α-D-glucosyl-D-glycerate from sucrose and D-glycerate. KEY POINTS: • A Xylanimonas protaetiae glycoside phosphorylase can use both d-glycerate and fructose as glucosyl acceptor with high catalytic efficiency • Biocatalytic synthesis of the osmolyte 2-O-α-d-glucosyl-d-glycerate • Positions in the active site of GH13 phosphorylases act as convenient specificity fingerprints.

Thermoswitchable catalysis to inhibit and promote plastic flow in vitrimers

Acid-base catalysis is a common strategy to induce covalent bond exchanges in dynamic polymer networks. Strong acids or strong bases can promote rapid network rearrangements, and are simultaneously preferred catalysts for chemical reactions where maximum efficiency at the lowest possible temperature is aimed for. However, within the context of dynamic polymer networks, the incorporation of highly active catalysts can negatively affect the longer term application potential. Network dynamicity can diminish through catalyst ageing or quenching and highly active catalysts may prematurely activate bond exchanges, leading to dimensional instability and thus low creep resistance of the polymer networks. Herein, we present several examples where we explicitly explored weak acids (carboxylic acids) as catalysts for dynamic bond exchanges, using vinylogous urethanes (VU) as a well-understood protic acid catalysed vitrimer chemistry. Surprisingly, we have found that the sought-after long-term stability offered by a weak acid does not necessarily bring lower activity at high temperature. In fact, the weak acids show a remarkable thermoswitchable catalytic behaviour, going from an inactive hydrogen bonded state to an active state where the polymer matrix is protonated, with a profound impact on the network reactivity and rheology. Carboxylic acids with different electronic or steric environments show clear reactivity trends and their fine-tuning resulted in the most thermally responsive VU vitrimers studied to date. Our findings point out that catalyst choice and design for vitrimers is only poorly informed by catalyst performance in more traditional chemical reactions (in solvent), and that a more tailored catalyst design holds great promise for the field of vitrimers.

Live Microscopy of Multicellular Spheroids with the Multimodal Near-Infrared Nanoparticles Reveals Differences in Oxygenation Gradients

Assessment of hypoxia, nutrients, metabolite gradients, and other hallmarks of the tumor microenvironment within 3D multicellular spheroid and organoid models represents a challenging analytical task. Here, we report red/near-infrared (NIR) emitting cell staining with O2-sensitive nanoparticles, which enable measurements of spheroid oxygenation on a conventional fluorescence microscope. Nanosensor probes, termed "MMIR" (multimodal infrared), incorporate an NIR O2-sensitive metalloporphyrin (PtTPTBPF) and deep red aza-BODIPY reference dyes within a biocompatible polymer shell, allowing for oxygen gradient quantification via fluorescence ratio and phosphorescence lifetime readouts. We optimized staining techniques and evaluated the nanosensor probe characteristics and cytotoxicity. Subsequently, we applied nanosensors to the live spheroid models based on HCT116, DPSCs, and SKOV3 cells, at rest, and treated with drugs affecting cell respiration. We found that the growth medium viscosity, spheroid size, and formation method influenced spheroid oxygenation. Some spheroids produced from HCT116 and dental pulp stem cells exhibited "inverted" oxygenation gradients, with higher core oxygen levels than the periphery. This contrasted with the frequently encountered "normal" gradient of hypoxia toward the core caused by diffusion. Further microscopy analysis of spheroids with an "inverted" gradient demonstrated metabolic stratification of cells within spheroids: thus, autofluorescence FLIM of NAD(P)H indicated the formation of a glycolytic core and localization of OxPhos-active cells at the periphery. Collectively, we demonstrate a strong potential of NIR-emitting ratiometric nanosensors for advanced microscopy studies targeting live and quantitative real-time monitoring of cell metabolism and hypoxia in complex 3D tissue models.

Investigation of the intrinsic cannabinoid activity of hemp-derived and semisynthetic cannabinoids with β-arrestin2 recruitment assays-and how this matters for the harm potential of seized drugs

Cultivation of industrial low-Δ9-tetrahydrocannabinol (Δ9-THC) hemp has created an oversupply of cannabidiol (CBD)-rich products. The fact that phytocannabinoids, including CBD, can be used as precursors to synthetically produce a range of THC variants-potentially located in a legal loophole-has led to a diversification of cannabis recreational drug markets. 'Hemp-compliant', 'hemp-derived' and 'semisynthetic' cannabinoid products are emerging and being advertised as (legal) alternatives for Δ9-THC. This study included a large panel (n = 30) of THC isomers, homologs, and analogs that might be derived via semisynthetic procedures. As a proxy for the abuse potential of these compounds, we assessed their potential to activate the CB1 cannabinoid receptor with a β-arrestin2 recruitment bioassay (picomolar-micromolar concentrations). Multiple THC homologs (tetrahydrocannabihexol, THCH; tetrahydrocannabiphorol, THCP; tetrahydrocannabinol-C8, THC-C8) and THC analogs (hexahydrocannabinol, HHC; hexahydrocannabiphorol, HHCP) were identified that showed higher potential for CB1 activation than Δ9-THC, based on either higher efficacy (Emax) or higher potency (EC50). Structure-activity relationships were assessed for Δ9-THC and Δ8-THC homologs encompassing elongated alkyl chains. Additionally, stereoisomer-specific differences in CB1 activity were established for various THC isomers (Δ7-THC, Δ10-THC) and analogs (HHC, HHCP). Evaluation of the relative abundance of 9(S)-HHC and 9(R)-HHC epimers in seized drug material revealed varying epimeric compositions between batches. Increased abundance of the less active 9(S)-HHC epimer empirically resulted in decreased potency, but sustained efficacy for the resulting diastereomeric mixture. In conclusion, monitoring of semisynthetic cannabinoids is encouraged as the dosing and the relative composition of stereoisomers can impact the harm potential of these drugs, relative to Δ9-THC products.

Modeled versus Experimental Salt Mixture Behavior under Variable Humidity

This study investigates the kinetics of salt mixture crystallization under relative humidity (RH) conditions, varying between 15 and 95% (at 20 °C), to inform applications in built heritage preservation, geology, and environmental sciences. We focused on commonly found, sulfate-rich and calcium-rich salt mixtures containing five to six ions, Cl-, NO3-, Na+, and K+, including or excluding less common Mg2+, and including either an excess of SO42- or Ca2+, with respect to gypsum. Using time-lapse micrographs and dynamic vapor sorption, we explore how crystallization and dissolution behavior depend on RH and mixture composition under constant temperature. A range of RH change rates were studied to simulate realistic weather events. Microstructural analyses through environmental scanning electron microscopy (ESEM) confirmed the crystal habit corresponding with RH transitions. Phases predicted from thermodynamic modeling (ECOS/RUNSALT) were confirmed using micro-Raman spectroscopy, X-ray diffraction (XRD), and elemental mapping via energy-dispersive X-ray spectroscopy (EDX). We identify a strong correlation between phase transition kinetics and RH change rates, with crystallization deviating by -15% and dissolution by +7% from modeled values under rapid (several seconds) and slow (several days) RH changes. These insights are important for preservation strategies in built heritage, salt deposition, and dissolution mechanisms in diverse geological and realistic environmental contexts, laboratory experiments, future modeling efforts, and the understanding of stone decay in general.

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

3D-Printed Shape Memory Poly(alkylene terephthalate) Scaffolds as Cardiovascular Stents Revealing Enhanced Endothelialization

Cardiovascular diseases are the leading cause of death and current treatments such as stents still suffer from disadvantages. Balloon expansion causes damage to the arterial wall and limited and delayed endothelialization gives rise to restenosis and thrombosis. New more performing materials that circumvent these disadvantages are required to improve the success rate of interventions. To this end, the use of a novel polymer, poly(hexamethylene terephthalate), is investigated for this application. The synthesis to obtain polymers with high molar masses up to 126.5 kg mol-1 is optimized and a thorough chemical and thermal analysis is performed. The polymers are 3D-printed into personalized cardiovascular stents using the state-of-the-art solvent-cast direct-writing technique, the potential of these stents to expand using their shape memory behavior is established, and it is shown that the stents are more resistant to compression than the poly(l-lactide) benchmark. Furthermore, the polymer's hydrolytic stability is demonstrated in an accelerated degradation study of 6 months. Finally, the stents are subjected to an in vitro biological evaluation, revealing that the polymer is non-hemolytic and supports significant endothelialization after only 7 days, demonstrating the enormous potential of these polymers to serve cardiovascular applications.

The association between Dioscorea sansibarensis and Orrella dioscoreae as a model for hereditary leaf symbiosis

Hereditary, or vertically-transmitted, symbioses affect a large number of animal species and some plants. The precise mechanisms underlying transmission of functions of these associations are often difficult to describe, due to the difficulty in separating the symbiotic partners. This is especially the case for plant-bacteria hereditary symbioses, which lack experimentally tractable model systems. Here, we demonstrate the potential of the leaf symbiosis between the wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae (O. dioscoreae) as a model system for hereditary symbiosis. O. dioscoreae is easy to grow and genetically manipulate, which is unusual for hereditary symbionts. These properties allowed us to design an effective antimicrobial treatment to rid plants of bacteria and generate whole aposymbiotic plants, which can later be re-inoculated with bacterial cultures. Aposymbiotic plants did not differ morphologically from symbiotic plants and the leaf forerunner tip containing the symbiotic glands formed normally even in the absence of bacteria, but microscopic differences between symbiotic and aposymbiotic glands highlight the influence of bacteria on the development of trichomes and secretion of mucilage. This is to our knowledge the first leaf symbiosis where both host and symbiont can be grown separately and where the symbiont can be genetically altered and reintroduced to the host.

Strategies for the synthesis of the osmolyte glucosylglycerate and its precursor glycerate

Glycosidic osmolytes are widespread natural compounds that protect microorganisms and their macromolecules from the deleterious effects of various environmental stresses. Their protective properties have attracted considerable interest for industrial applications, especially as active ingredients in cosmetics and healthcare products. In that regard, the osmolyte glucosylglycerate is somewhat overlooked. Glucosylglycerate is typically accumulated by certain organisms when they are exposed to high salinity and nitrogen starvation, and its potent stabilizing effects have been demonstrated in vitro. However, the applications of this osmolyte have not been thoroughly explored due to the lack of a cost-efficient production process. Here, we present an overview of the progress that has been made in developing promising strategies for the synthesis of glucosylglycerate and its precursor glycerate, and discuss the remaining challenges. KEY POINTS: • Bacterial milking could be explored for fermentative production of glucosylglycerate • Glycoside phosphorylases of GH13_18 represent attractive alternatives for biocatalytic production • Conversion of glycerol with alditol oxidase is a promising strategy for generating the precursor glycerate.

C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 contributes to GA-mediated growth and flowering by interaction with DELLA proteins

Gibberellic acid (GA) plays a central role in many plant developmental processes and is crucial for crop improvement. DELLA proteins, the core suppressors in the GA signaling pathway, are degraded by GA via the 26S proteasomal pathway to release the GA response. However, little is known about the phosphorylation-mediated regulation of DELLA proteins. In this study, we combined GA response assays with protein-protein interaction analysis to infer the connection between Arabidopsis thaliana DELLAs and the C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3), a phosphatase involved in the dephosphorylation of RNA polymerase II. We show that CPL3 directly interacts with DELLA proteins and promotes DELLA protein stability by inhibiting its degradation by the 26S proteasome. Consequently, CPL3 negatively modulates multiple GA-mediated processes of plant development, including hypocotyl elongation, flowering time, and anthocyanin accumulation. Taken together, our findings demonstrate that CPL3 serves as a novel regulator that could improve DELLA stability and thereby participate in GA signaling transduction.

Subpar reporting of pre-analytical variables in RNA-focused blood plasma studies

Extracellular RNA (cell-free RNA; exRNA) from blood-derived liquid biopsies is an appealing, minimally invasive source of disease biomarkers. As pre-analytical variables strongly influence exRNA measurements, their reporting is essential for meaningful interpretation and replication of results. The aim of this review was to chart to what extent pre-analytical variables are documented, to pinpoint shortcomings and to improve future reporting. In total, 200 blood plasma exRNA studies published in 2018 or 2023 were reviewed for annotation of 22 variables associated with blood collection, plasma preparation, and RNA purification. Our results show that pre-analytical variables are poorly documented, with only three out of 22 variables described in over half of the publications. The percentage of variables reported ranged from 4.6% to 54.6% (mean 24.84%) in 2023 and from 4.6% to 57.1% (mean 28.60%) in 2018. Recommendations and guidelines (i.e., BRISQ, ASCO-CAP, BloodPAC, PPMPT, and CEN standards) have currently not resulted in improved reporting. In conclusion, our results highlight the lack of reporting pre-analytical variables in exRNA studies and advocate for a consistent use of available standards, endorsed by funders and journals.

Transcriptional chronology reveals conserved genes involved in pennate diatom sexual reproduction

Sexual reproduction is a major driver of adaptation and speciation in eukaryotes. In diatoms, siliceous microalgae with a unique cell size reduction-restitution life cycle and among the world's most prolific primary producers, sex also acts as the main mechanism for cell size restoration through the formation of an expanding auxospore. However, the molecular regulators of the different stages of sexual reproduction and size restoration are poorly explored. Here, we combined RNA sequencing with the assembly of a 55 Mbp reference genome for Cylindrotheca closterium to identify patterns of gene expression during different stages of sexual reproduction. These were compared with a corresponding transcriptomic time series of Seminavis robusta to assess the degree of expression conservation. Integrative orthology analysis revealed 138 one-to-one orthologues that are upregulated during sex in both species, among which 56 genes consistently upregulated during cell pairing and gametogenesis, and 11 genes induced when auxospores are present. Several early, sex-specific transcription factors and B-type cyclins were also upregulated during sex in other pennate and centric diatoms, pointing towards a conserved core regulatory machinery for meiosis and gametogenesis across diatoms. Furthermore, we find molecular evidence that the pheromone-induced cell cycle arrest is short-lived in benthic diatoms, which may be linked to their active mode of mate finding through gliding. Finally, we exploit the temporal resolution of our comparative analysis to report the first marker genes for auxospore identity called AAE1-3 ("Auxospore-Associated Expression"). Altogether, we introduce a multi-species model of the transcriptional dynamics during size restoration in diatoms and highlight conserved gene expression dynamics during different stages of sexual reproduction.

Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE-mediated pediatric cow's milk allergy

BACKGROUND

IgE-mediated cow's milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies.

METHODS

We report a longitudinal in vivo murine model, in which two mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n = 6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-γ) measured, and fecal samples subjected to metabolomics. The results of the murine models were further extrapolated to fecal microbiome-metabolome data from our population of IgE-CMA (n = 22) and healthy (n = 23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes.

RESULTS

During mice sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. We confirmed microbial dysbiosis, and its associated effect on metabolic alterations in our patient cohort, through in vitro digestions and multi-omics, which was accompanied by metabolic signatures of low-grade inflammation.

CONCLUSION

Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.

Longitudinal pilot study examining the effect of punch biopsy on equine sarcoid growth dynamics

BACKGROUND

Nonexcisional tissue biopsies facilitate pre-operative confirmation of equine sarcoid yet fear of lesion deterioration currently limits its use in the diagnostic workup.

OBJECTIVES

To evaluate the effect of a single punch biopsy on tumour growth dynamics [thickness, area, circumference, viral load (VL) and Visual Analog Scale (VAS)].

ANIMALS

Six client-owned horses with 11 sarcoids of various classification.

MATERIALS AND METHODS

Growth dynamics were recorded on a weekly basis, 12 weeks pre- and 24 weeks post-biopsy. The effect of a single punch biopsy on growth dynamics was estimated by linear mixed-effect models. Spearman's rank correlation coefficient (SRCC) was calculated to investigate correlations with the number of weeks before and after the intervention.

RESULTS

While statistically significant post-biopsy changes were recorded for all parameters except VL, no parameter was consistently increased after the biopsy intervention. In two of 11 sarcoids, the VL correlation pattern revealed significant strong correlations: sarcoid 6 (pre: r = -0.66, p < 0.05; post: r = 0.81, p < 0.001), increased VL; and sarcoid 8 (pre: r = 0.85, p < 0.001; post: r = 0.17, p > 0.05), no further increase after biopsy.

CONCLUSIONS AND CLINICAL IMPORTANCE

Our results indicate that post-biopsy lesion deterioration is not a general concept that applies to all sarcoids, and both deterioration or improvement are possible outcomes over a 24-week period. Further clinical studies with a larger sample size are needed before a definitive conclusion can be made.

Development of an atrial transseptal puncture procedure in horses to access the left heart: An ultrasound-guided jugular vein and transhepatic approach

BACKGROUND

Radiofrequency ablation has been successfully applied to treat right atrial arrhythmias in horses. Ablation of left-sided arrhythmias requires a retrograde transarterial approach which is complicated. In human medicine, the left atrium is accessed through transseptal puncture (TSP) of the fossa ovalis (FO) using a caudal approach via the femoral vein.

OBJECTIVES

To develop a zero fluoroscopy TSP technique for horses using a jugular vein (cranial) and transhepatic (caudal) approach.

STUDY DESIGN

In vivo experimental study.

METHODS

Transseptal puncture was performed in 18 horses admitted for euthanasia and donated for scientific research under general anaesthesia: using a jugular vein approach (10 horses), a transhepatic approach (2 horses) or both (6 horses). Radiofrequency energy was applied on a guidewire to perforate the FO and allow sheath advancement under intracardiac and transthoracic echocardiographic guidance. Puncture lesions were inspected post-mortem.

RESULTS

Transseptal puncture was successful in 17/18 horses, of which 15/16 jugular vein approaches and 5/8 transhepatic approaches. Failure was due to technical malfunction, inability to advance the guidewire toward the heart and inability to advance the sheath through the FO. Intracardiac echocardiography was essential to safely guide the puncture process. Atrial arrhythmias caused by the TSP occurred in 13/18 horses. Puncture lesions were found in the right atrium in the FO region, and left atrium ventral to pulmonary vein ostium III.

MAIN LIMITATIONS

Because in several horses two approaches were tested consecutively, it cannot be excluded that the second TSP was performed at the previous puncture site. Due to the developmental nature of the study the approaches were not randomised and did not allow comparison.

CONCLUSION

Transseptal puncture is feasible in horses using ultrasound guidance and allows for electrophysiological exploration of the left heart. Further studies are needed to evaluate post-operative follow-up.

A guide to germ-free and gnotobiotic mouse technology to study health and disease

The intestinal microbiota has major influence on human physiology and modulates health and disease. Complex host-microbe interactions regulate various homeostatic processes, including metabolism and immune function, while disturbances in microbiota composition (dysbiosis) are associated with a plethora of human diseases and are believed to modulate disease initiation, progression and therapy response. The vast complexity of the human microbiota and its metabolic output represents a great challenge in unraveling the molecular basis of host-microbe interactions in specific physiological contexts. To increase our understanding of these interactions, functional microbiota research using animal models in a reductionistic setting are essential. In the dynamic landscape of gut microbiota research, the use of germ-free and gnotobiotic mouse technology, in which causal disease-driving mechanisms can be dissected, represents a pivotal investigative tool for functional microbiota research in health and disease, in which causal disease-driving mechanisms can be dissected. A better understanding of the health-modulating functions of the microbiota opens perspectives for improved therapies in many diseases. In this review, we discuss practical considerations for the design and execution of germ-free and gnotobiotic experiments, including considerations around germ-free rederivation and housing conditions, route and timing of microbial administration, and dosing protocols. This comprehensive overview aims to provide researchers with valuable insights for improved experimental design in the field of functional microbiota research.

Biosafety aspects of RNAi-based pests control

While the overuse of classical chemical pesticides has had a detrimental impact on the environment and human health, the discovery of RNA interference (RNAi) offered the opportunity to develop new and sustainable approaches for pest management. RNAi is a naturally occurring regulation and defense mechanism that can be exploited to effectively protect crops by silencing key genes affecting the growth, development, behavior or fecundity of pests. However, as with all technologies, there is a range of potential risks and challenges associated with the application of RNAi, such as dsRNA stability, the potential for off-target effects, the safety of non-target organisms, and other application challenges. A better understanding of the molecular mechanisms involved in RNAi and in-depth discussion and analysis of these associated safety risks, is required to limit or mitigate potential adverse effects. © 2024 Society of Chemical Industry.

Synthesis and bioactivity of psilocybin analogues containing a stable carbon-phosphorus bond

Psilocybin analogues have been synthesized comprising a non-hydrolysable P-C bond to evaluate the biological activity and the selectivity towards 5-HT2AR, 5-HT2BR and the TNAP receptor. No activity was observed towards the phosphatase, however all compounds showed good binding affinity for 5-HT2AR and 5-HT2BR and one compound showed a higher selectivity towards 5-HT2AR than psilocin.

tRNAGlu-derived fragments from embryonic extracellular vesicles modulate bovine embryo hatching

Transfer RNA-derived small RNAs (tsRNAs) have been shown to be involved in early embryo development and repression of endogenous retroelements in embryos and stem cells. However, it is unknown whether tsRNAs also regulate embryo hatching. In this study, we mined the sequencing data of a previous experiment in which we demonstrated that the microRNA (miRNA) cargo of preimplantation embryonic extracellular vesicles (EVs) influences embryo development. We thus profiled the tsRNA cargo of EVs secreted by blastocysts and non-blastocysts. The majority of tsRNAs was identified as tRNA halves originating from the 5´ ends of tRNAs. Among the 148 differentially expressed tsRNAs, the 19 nt tRNA fragment (tRF) tDR-14:32-Glu-CTC-1 was found to be significantly up-regulated in EVs derived from non-blastocysts. RT-qPCR assays confirmed its significant up-regulation in non-blastocyst embryos and their conditioned medium compared to the blastocyst group (P < 0.05). Inhibition of tDR-14:32-Glu-CTC-1 by supplementing antagomirs to the conditioned medium improved embryo hatching (P < 0.05). Transcriptomic analysis of embryos treated with tDR-14:32-Glu-CTC-1 antagomirs further showed differential expression of genes that are associated with embryo hatching and implantation. In summary, tDR-14:32-Glu-CTC-1 is up-regulated in non-blastocyst embryos and their secretions, and inhibition of tDR-14:32-Glu-CTC-1 promotes embryo hatching, while influencing embryo implantation-related genes and pathways. These results indicate that embryonic EVs containing specific tRFs may regulate preimplantation embryo development.

MAPK Cascades in Plant Microbiota Structure and Functioning

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

Contribution of combined stressors on density and gene expression dynamics of the copepod Temora longicornis in the North Sea

The impact of multiple environmental and anthropogenic stressors on the marine environment remains poorly understood. Therefore, we studied the contribution of environmental variables to the densities and gene expression of the dominant zooplankton species in the Belgian part of the North Sea, the calanoid copepod Temora longicornis. We observed a reduced density of copepods, which were also smaller in size, in samples taken from nearshore locations when compared to those obtained from offshore stations. To assess the factors influencing the population dynamics of this species, we applied generalised additive models. These models allowed us to quantify the relative contribution of temperature, nutrient levels, salinity, turbidity, concentrations of photosynthetic pigments, as well as chemical pollutants such as polychlorinated biphenyls and polycyclic aromatic hydrocarbons (PAHs), on copepod density. Temperature and Secchi depth, a proxy for turbidity, were the most important environmental variables predicting the densities of T. longicornis, followed by summed PAH and chlorophyll concentrations. Analysing gene expression in field-collected adults, we observed significant variation in metabolic and stress-response genes. Temperature correlated significantly with genes involved in proteolytic activities, and encoding heat shock proteins. Yet, concentrations of anthropogenic chemicals did not induce significant differences in the gene expression of genes involved in the copepod's fatty acid metabolism or well-known stress-related genes, such as glutathione transferases or cytochrome P450. Our study highlights the potential of gene expression biomonitoring and underscores the significance of a changing environment in future studies.

Vinylogous Urea-Urethane Vitrimers: Accelerating and Inhibiting Network Dynamics through Hydrogen Bonding

Vinylogous urethane (VUO ) based polymer networks are widely used as catalyst-free vitrimers that show rapid covalent bond exchange at elevated temperatures. In solution, vinylogous ureas (VUN ) undergo much faster bond exchange than VUO and are highly dynamic at room temperature. However, this difference in reactivity is not observed in their respective dynamic polymer networks, as VUO and VUN vitrimers prepared herein with very similar macromolecular architectures show comparable stress relaxation and creep behavior. However, by using mixtures of VUO and VUN linkages within the same network, the dynamic reactions can be accelerated by an order of magnitude. The results can be rationalized by the effect of intermolecular hydrogen bonding, which is absent in VUO vitrimers, but is very pronounced for vinylogous urea moieties. At low concentrations of VUN , these hydrogen bonds act as catalysts for covalent bond exchange, while at high concentration, they provide a pervasive vinylogous urea - urethane (VU) network of strong non-covalent interactions, giving rise to phase separation and inhibiting polymer chain dynamics. This offers a straightforward design principle for dynamic polymer materials, showing at the same time the possible additive and synergistic effects of supramolecular and dynamic covalent polymer networks.

Telechelic sequence-defined oligoamides: their step-economical synthesis, depolymerization and use in polymer networks

The application of sequence-defined macromolecules in material science remains largely unexplored due to their challenging, low yielding and time-consuming synthesis. This work first describes a step-economical method for synthesizing unnatural sequence-defined oligoamides through fluorenylmethyloxycarbonyl chemistry. The use of a monodisperse soluble support enables homogeneous reactions at elevated temperature (up to 65 °C), leading to rapid coupling times (<10 min) and improved synthesis protocols. Moreover, a one-pot procedure for the two involved iterative steps is demonstrated via an intermediate quenching step, eliminating the need for in-between purification. The protocol is optimized using γ-aminobutyric acid (GABA) as initial amino acid, and the unique ability of the resulting oligomers to depolymerize, with the formation of cyclic γ-butyrolactame, is evidenced. Furthermore, in order to demonstrate the versatility of the present protocol, a library of 17 unnatural amino acid monomers is synthesized, starting from the readily available GABA-derivative 4-amino-2-hydroxybutanoic acid, and then used to create multifunctional tetramers. Notably, the obtained tetramers show higher thermal stability than a similar thiolactone-based sequence-defined macromolecule, which enables its exploration within a material context. To that end, a bidirectional growth approach is proposed as a greener alternative that reduces the number of synthetic steps to obtain telechelic sequence-defined oligoamides. The latter are finally used as macromers for the preparation of polymer networks. We expect this strategy to pave the way for the further exploration of sequence-defined macromolecules in material science.

The relationship of affective and bodily states with goals and plans to increase physical activity: An 8-day study in students

Planning is an important tool to translate intentions into physical activity (PA) behavior. Affective and bodily states are known to influence how much PA individuals perform, but their impact on to formulation of PA plans is not yet known. The aim of the current study is to explore the effect of within- and between-subject variations in affective and bodily states on the content of PA goals and plans. Over eight consecutive days, 362 students created action and coping plans to achieve their daily PA goals. They also reported their affective and bodily states. Generalized linear mixed effect models were used to analyze the associations between these states and the content of the goals and plans. The results showed that both between- and within-subject variations in affective and bodily states were associated with goals formulated in terms of minutes, the intensity and context of planned activities, and anticipated barriers, though more effects were found for within-subject differences. Affective and bodily states impact daily PA goals and plans, highlighting the dynamic nature of planning. Our findings can be a first step toward personalized suggestions for goals, action plans, and coping strategies that are based on individual affective and bodily states.

Vagally-mediated HRV as a marker of trait rumination in healthy individuals? A large cross-sectional analysis

The tendency to ruminate (i.e., repetitive, self-referential, negative thoughts) is a maladaptive form of emotional regulation and represents a transdiagnostic vulnerability factor for stress-related psychopathology. Vagally-mediated heart rate variability (vmHRV) provides a non-invasive, surrogate measure of vagal modulation of the heart, and higher HRV is considered an indicator of susceptibility, or ability to respond to stress. Past research has suggested a link between trait rumination and vmHRV; however, inconsistent results exist in healthy individuals. In this study, we investigated the association between the tendency to ruminate, brooding, and reflection (using the Ruminative Response Scale) with vmHRV measured at baseline in a healthy population using a large cross-sectional dataset (N = 1189, 88% female; mean age = 21.55, ranging from 17 to 48 years old), which was obtained by combining samples of healthy individuals from different studies from our laboratory. The results showed no cross-sectional correlation between vmHRV and trait rumination (confirmed by Bayesian analysis), even after controlling for important confounders such as gender, age, and depressive symptoms. Also, a non-linear relationship was rejected. In summary, based on our results in a large sample of healthy individuals, vmHRV is not a marker of trait rumination (as measured by the Ruminative Response Scale).

Are All Negotiations Equally Favorable? The Role of Adolescents' Negotiation Style, Social Domain, and Mothers' Authoritarian Beliefs and Family History

Although negotiation is generally considered an adaptive means for adolescents to express disagreement in the parent-child relationship, previous research on the correlates of adolescents' negotiation has reported rather mixed results. This may be because parents do not always positively appraise and respond to adolescents' negotiation. The key aim of the present study was to better understand variability in mothers' appraisals and responses to adolescents' negotiation attempts. This was done by examining whether their appraisals and responses vary as a function of adolescents' negotiation style, social domain, and mothers' personal characteristics (i.e., authoritarian beliefs and their own history of being parented). A total of 476 mothers of 9th and 10th grade adolescents in Belgium (Mage mothers = 44.93 years old, SD = 4.07; Mage adolescents = 14.88, SD = 0.75, 51.7% boys) participated in a vignette-based experimental study. Mothers completed questionnaires assessing authoritarian beliefs and their own history of being parented, and read a vignette-based scenario depicting an adolescent's negotiation attempt. Using a between-person 2 × 2 design, adolescents' negotiation style (autonomy-supportive versus controlling) and social domain (personal versus multifaceted) were experimentally manipulated. Mothers were more likely to positively appraise and respond in more constructive ways if adolescents adopted an autonomy-supportive instead of a controlling negotiation style, and when the situation involved a personal rather than a multifaceted issue. Mothers with high authoritarian beliefs and those with a history of being parented in a psychologically controlling way, had a more negative attitude towards adolescents' negotiation. Overall, the results suggest that the success of adolescents' negotiation depends on how, about what, and with whom they negotiate.

Dual N6/C7-Substituted 7-Deazapurine and Tricyclic Ribonucleosides with Affinity for G Protein-Coupled Receptors

Various purine-based nucleoside analogues have demonstrated unexpected affinity for nonpurinergic G protein-coupled receptors (GPCRs), such as opioid and serotonin receptors. In this work, we synthesized a small library of new 7-deazaadenosine and pyrazolo[3,4-d]pyrimidine riboside analogues, featuring dual C7 and N6 modifications and assessed their affinity for various GPCRs. During the course of the synthesis of 7-ethynyl pyrazolo[3,4-d]pyrimidine ribosides, we observed the formation of an unprecedented tricyclic nucleobase, formed via a 6-endo-dig ring closure. The synthesis of this tricyclic nucleoside was optimized, and the substrate scope for such cyclization was further explored because it might avail further exploration in the nucleoside field. From displacement experiments on a panel of GPCRs and transporters, combining C7 and N6 modifications afforded noncytotoxic nucleosides with micromolar and submicromolar affinity for different GPCRs, such as the 5-hydroxytryptamine (5-HT)2B, κ-opioid (KOR), and σ1/2 receptor. These results corroborate that the novel nucleoside analogues reported here are potentially useful starting points for the further development of modulators of GPCRs and transmembrane proteins.

From Corrosion Casting to Virtual Dissection: Contrast-Enhanced Vascular Imaging using Hafnium Oxide Nanocrystals

Vascular corrosion casting is a method used to visualize the three dimensional (3D) anatomy and branching pattern of blood vessels. A polymer resin is injected in the vascular system and, after curing, the surrounding tissue is removed. The latter often deforms or even fractures the fragile cast. Here, a method is proposed that does not require corrosion, and is based on in situ micro computed tomography (micro-CT) scans. To overcome the lack of CT contrast between the polymer cast and the animals' surrounding soft tissue, hafnium oxide nanocrystals (HfO2 NCs) are introduced as CT contrast agents into the resin. The NCs dramatically improve the overall CT contrast of the cast and allow for straightforward segmentation in the CT scans. Careful design of the NC surface chemistry ensures the colloidal stability of the NCs in the casting resin. Using only 5 m% of HfO2 NCs, high-quality cardiovascular casts of both zebrafish and mice can be automatically segmented using CT imaging software. This allows to differentiate even μ $\umu$ m-scale details without having to alter the current resin injection methods. This new method of virtual dissection by visualizing casts in situ using contrast-enhanced CT imaging greatly expands the application potential of the technique.

Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease

BACKGROUND

5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs).

METHODS

We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches.

RESULTS

Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels.

CONCLUSIONS

This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.

Post-mortem feasibility of dual-energy computed tomography in the detection of bone edema-like lesions in the equine foot: a proof of concept

Introduction

In this proof-of-concept study, the post-mortem feasibility of dual-energy computed tomography (DECT) in the detection of bone edema-like lesions in the equine foot is described in agreement with the gold standard imaging technique, which is magnetic resonance imaging (MRI).

Methods

A total of five equine cadaver feet were studied, of which two were pathological and three were within normal limits and served as references. A low-field MRI of each foot was performed, followed by a DECT acquisition. Multiplanar reformations of DECT virtual non-calcium images were compared with MRI for the detection of bone edema-like lesions. A gross post-mortem was performed, and histopathologic samples were obtained of the navicular and/or distal phalanx of the two feet selected based on pathology and one reference foot.

Results

On DECT virtual non-calcium imaging, the two pathological feet showed diffuse increased attenuation corresponding with bone edema-like lesions, whereas the three reference feet were considered normal. These findings were in agreement with the findings on the MRI. Histopathology of the two pathologic feet showed abnormalities in line with bone edema-like lesions. Histopathology of the reference foot was normal.

Conclusion

DECT virtual non-calcium imaging can be a valuable diagnostic tool in the diagnosis of bone edema-like lesions in the equine foot. Further examination of DECT in equine diagnostic imaging is warranted in a larger cohort, different locations, and alive animals.

Epidemiology of Echinococcus granulosus sensu lato in the Greater Horn of Africa: A systematic review

BACKGROUND

Cystic echinococcosis (CE) is a neglected zoonotic disease that is caused by Echinococcus granulosus sensu lato (s.l.), the life cycle of which involves multiple hosts. We conducted a systematic review (SR) on E. granulosus s.l. in the Greater Horn of Africa (GHA), to provide a picture of its recent epidemiology across all hosts.

METHODS

For this SR, conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, five electronic databases, as well experts in the region were consulted to retrieve records published between 2000 and 2022, reporting the presence of E. granulosus s.l. infections in any natural host in the GHA (Djibouti, Eritrea, Ethiopia, Kenya, Sudan, Somalia, South Sudan, Tanzania and Uganda).

PRINCIPAL FINDINGS

A total of 247 records were retained, describing the presence of E. granulosus s.l. throughout the GHA, except for Djibouti. Only few population surveys on human CE were conducted in the area, with the prevalence ranging between 0.3 and 11.3%. In animals, the reported prevalence ranged up to 61.6% in camels, 88.4% in cattle; 65.2% in goats, 9.9% in pigs, 67.8% in sheep and 94.5% in dogs. In addition, E. granulosus s.l. was also reported in wildlife. A total of five species were reported in the different hosts, namely E. granulosus sensu stricto (G1, G3, GOmo), E. canadensis (G6/7), E. ortleppi (G5), E. felidis, and E. equinus (G4).

CONCLUSIONS

We confirm that E. granulosus s.l. is prevalent throughout the GHA. Nevertheless, despite our efforts to screen grey literature, an accurate assessment of the epidemiology in GHA remains challenging, due to the lack of combined host, in-depth risk factor and behavioural studies, as well as the wide diversity in subpopulations studied and diagnostic tools used. Interdisciplinary and transboundary partnerships would be essential for the design of effective control strategies, tuned to the GHA setting.

Pooled analysis of patients with inherited prion disease caused by two- to twelve-octapeptide repeat insertions in the prion protein gene (PRNP)

Inherited prion diseases caused by two- to twelve-octapeptide repeat insertions (OPRIs) in the prion protein gene (PRNP) show significant clinical heterogeneity. This study describes a family with two new cases with a 4-OPRI mutation and two asymptomatic mutation carriers. The pooled analysis summarizes all cases reported in the literature to date and describes the relation between survival, age of onset, number of OPRI and codon 129 polymorphism. MEDLINE and Google Scholar were queried from database inception up to December 31, 2022. Age of onset was compared per number of OPRI and per codon 129 polymorphism using the Kruskal-Wallis and Wilcoxon-Mann-Whitney tests, respectively. Disease duration was modeled non-parametrically by a Kaplan-Meier model and semi-parametrically by a Cox model. This study comprised 164 patients. Lower number of OPRI and presence of valine (cis-V) versus methionine (cis-M) on codon 129 were associated with an older age of onset (P < 0.001 and P = 0.025, respectively) and shorter disease duration (P < 0.001 and P = 0.003, respectively). Within patients with 5- or more OPRI codon cis-V remained significantly associated with a shorter disease duration. Codon 129 homozygosity versus heterozygosity was not significantly associated with age of onset or disease duration (P = 0.076 and P = 0.409, respectively). This study summarized the largest cohort of patients with two- to twelve-OPRI to date. Lower number of OPRI and codon 129 cis-V is associated with an older age of onset and shorter disease duration, while homozygosity or heterozygosity on codon 129 was not.

Clinical relevance of lung function trajectory clusters in middle-aged and older adults

Background

The determinants and health outcomes of lung function trajectories in adults among the general population are poorly understood. We aimed to identify and characterise clusters of lung function trajectories in adults aged ≥45 years.

Methods

Gaussian finite-mixture modelling was applied to baseline and annualised change of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC ratio z-scores in participants of the Rotterdam Study, a prospective population-based cohort study, with repeated spirometry (n=3884; mean±sd age 64.7±8.9 years). Longitudinal outcomes were all-cause mortality, respiratory outcomes (symptoms, COPD (FEV1/FVC <0.7 in absence of asthma), preserved ratio impaired spirometry (PRISm; FEV1/FVC ≥0.7 and FEV1 or FVC <80%)), smoking cessation and weight changes. Independent risk factors, including genetics, were identified by multiple logistic regression.

Results

We identified eight trajectory clusters, with the reference group having persistently normal spirometry (prevalence 42.8%). Three clusters showed higher mortality, adjusted for confounders: 1) the persistently low FEV1 cluster (prevalence 6.8%, hazard ratio (HR) 1.71, 95% CI 1.37-2.13); 2) rapid FEV1 decliners (prevalence 4.6%, HR 1.48, 95% CI 1.10-1.99); and 3) FVC decliners (prevalence 3.7%, HR 1.49, 95% CI 1.09-2.03). In contrast, FVC improvers (prevalence 6.7%, HR 0.61, 95% CI 0.41-0.90) and persistently high FEV1 (prevalence 29.2%, HR 0.82, 95% CI 0.69-0.98) were protective trajectory clusters. Clusters were characterised by differences in genetic predisposition (polygenic scores of FEV1 and FEV1/FVC), demographics, cigarette smoking, respiratory symptoms (chronic cough, wheezing and dyspnoea), cardiovascular factors (body mass index, hypertension and heart failure) and serum C-reactive protein levels. Frailty, weight changes and the development of respiratory symptoms, COPD and PRISm were significantly associated with trajectory clusters.

Conclusions

This study reveals clinically relevant lung function trajectory clusters in older adults of the general population.

Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii

Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.

MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles

Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.

Decoding immunogenic cell death from a dendritic cell perspective

Dendritic cells (DCs) are myeloid cells bridging the innate and adaptive immune system. By cross-presenting tumor-associated antigens (TAAs) liberated upon spontaneous or therapy-induced tumor cell death to T cells, DCs occupy a pivotal position in the cancer immunity cycle. Over the last decades, the mechanisms linking cancer cell death to DC maturation, have been the focus of intense research. Growing evidence supports the concept that the mere transfer of TAAs during the process of cell death is insufficient to drive immunogenic DC maturation unless this process is coupled with the release of immunomodulatory signals by dying cancer cells. Malignant cells succumbing to a regulated cell death variant called immunogenic cell death (ICD), foster a proficient interface with DCs, enabling their immunogenic maturation and engagement of adaptive immunity against cancer. This property relies on the ability of ICD to exhibit pathogen-mimicry hallmarks and orchestrate the emission of a spectrum of constitutively present or de novo-induced danger signals, collectively known as damage-associated molecular patterns (DAMPs). In this review, we discuss how DCs perceive and decode danger signals emanating from malignant cells undergoing ICD and provide an outlook of the major signaling and functional consequences of this interaction for DCs and antitumor immunity.

Successful caudal vena cava and pulmonary vein isolation in healthy horses using 3D electro-anatomical mapping and a contact force-guided ablation system

BACKGROUND

Recently, treatment of equine atrial tachycardia by three-dimensional electro-anatomical mapping (3D EAM) and radiofrequency catheter ablation (RFCA) has been described. Myocardial sleeves in the caudal vena cava and pulmonary veins are a potential trigger for initiation and perpetuation of atrial tachycardia and atrial fibrillation in the horse. Isolation of these myocardial sleeves by RFCA may be an effective treatment for these arrhythmias.

OBJECTIVES

To describe the feasibility of 3D EAM and RFCA to isolate caudal vena cava and pulmonary veins in adult horses using 3D mapping and a contact force (CF)-guided ablation system.

STUDY DESIGN

In vivo experiments.

METHODS

3D EAM and RFCA was performed in five horses without cardiovascular disease under general anaesthesia, using the CF-guided system CARTO®3. Point-by-point RFCA aimed for isolation of caudal vena cava and pulmonary veins. Radiofrequency energy was delivered in power-controlled mode with a target power of 45 W, CF between 10 and 15 g and 30 mL/min irrigation rate, until an ablation-index of 450-500 was reached.

RESULTS

In the right atrium, myocardial sleeves of the caudal vena cava were isolated (n = 5). In the left atrium, isolation of ostium II (n = 3), ostium III (n = 1) and ostium I, II and III en bloc (n = 1) was performed. Successful isolation was confirmed by entrance and exit block.

MAIN LIMITATIONS

Horses were euthanised at the end of the procedure, so long term effects such as potential reconnection of isolated veins could not be studied.

CONCLUSIONS

This is the first description of 3D EAM and RFCA with CARTO®3 in horses, thereby showing the technical feasibility and successful caudal vena cava and pulmonary vein isolation. CF measurement allowed monitoring of catheter-tissue contact, resulting in efficient acute lesion creation as confirmed by entrance and exit block. This is a promising treatment for cardiac arrhythmias in horses.

OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking

While free energy surfaces are the crux of our understanding of many chemical and biological processes, their accuracy is generally unknown. Moreover, many developments to improve their accuracy are often complicated, limiting their general use. Luckily, several tools and guidelines are already in place to identify these shortcomings, but they are typically lacking in flexibility or fail to systematically determine how to improve the accuracy of the free energy calculation. To overcome these limitations, this work introduces OGRe, a Python package for optimal grid refinement in an arbitrary number of dimensions. OGRe is based on three metrics that gauge the confinement, consistency, and overlap of each simulation in a series of umbrella sampling (US) simulations, an enhanced sampling technique ubiquitously adopted to construct free energy surfaces for hindered processes. As these three metrics are fundamentally linked to the accuracy of the weighted histogram analysis method adopted to generate free energy surfaces from US simulations, they facilitate the systematic construction of accurate free energy profiles, where each metric is driven by a specific umbrella parameter. This allows for the derivation of a consistent and optimal collection of umbrellas for each simulation, largely independent of the initial values, thereby dramatically increasing the ease-of-use toward accurate free energy surfaces. As such, OGRe is particularly suited to determine complex free energy surfaces with large activation barriers and shallow minima, which underpin many physical and chemical transformations and hence to further our fundamental understanding of these processes.

Integrated PbS Colloidal Quantum Dot Photodiodes on Silicon Nitride Waveguides

Colloidal quantum dots (QDs) have become a versatile optoelectronic material for emitting and detecting light that can overcome the limitations of a range of electronic and photonic technology platforms. Photonic integrated circuits (PICs), for example, face the persistent challenge of combining active materials with passive circuitry ideally suited for guiding light. Here, we demonstrate the integration of photodiodes (PDs) based on PbS QDs on silicon nitride waveguides (WG). Analyzing planar QDPDs first, we argue that the main limitation WG-coupled QDPDs face is detector saturation induced by the high optical power density of the guided light. Using the cladding thickness and waveguide width as design parameters, we mitigate this issue, and we demonstrate WG-QDPDs with an external quantum efficiency of 67.5% at 1275 nm that exhibit a linear photoresponse for input powers up to 400 nW. In the next step, we demonstrate a compact infrared spectrometer by integrating these WG-QDPDs on the output channels of an arrayed waveguide grating demultiplexer. This work provides a path toward a low-cost PD solution for PICs, which are attractive for large-scale production.

Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum

In synthetic biology, Fluorescent reporters are frequently used to characterize the expression levels obtained from both genetic parts such as promoters and ribosome binding sites as well as from complex genetic circuits. To this end, plate readers offer an easy and high-throughput way of characterizing both the growth and fluorescence expression levels of cell cultures. However, despite the similar mode of action used in different devices, their output is not comparable due to intrinsic differences in their setup. Additionally, the generated output is expressed using arbitrary units, limiting reliable comparison of results to measurements taken within one single experiment using one specific plate reader, hampering the transferability of data across different plate readers and laboratories. This article presents an easy and accessible calibration method for transforming the device-specific output into a standardized output expressing the amount of fluorescence per well as a known equivalent fluorophore concentration per cell for fluorescent reporters spanning the visible light spectrum. This calibration method follows a 2-fold approach determining both the estimated number of cells and the equivalent chemical fluorophore concentration per well. It will contribute to the comparison of plate reader experiments between different laboratories across the world and will therefore greatly improve the reliability and exchange of both results and genetic parts between research groups.

A protocol for a turbidimetric assay using a Saccharomyces cerevisiae thiamin biosynthesis mutant to estimate total vitamin B1 content in plant tissue samples

BACKGROUND

Understanding thiamin (thiamine; vitamin B1) metabolism in plants is crucial, as it impacts plant nutritional value as well as stress tolerance. Studies aimed at elucidating novel aspects of thiamin in plants rely on adequate assessment of thiamin content. Mass spectrometry-based methods provide reliable quantification of thiamin as well as closely related biomolecules. However, these techniques require expensive equipment and expertise. Microbiological turbidimetric assays can evaluate the presence of thiamin in a given sample, only requiring low-cost, standard lab equipment. Although these microbiological assays do not reach the accuracy provided by mass spectrometry-based methods, the ease with which they can be deployed in an inexpensive and high-throughput manner, makes them a favorable method in many circumstances. However, the thiamin research field could benefit from a detailed step-by-step protocol to perform such assays as well as a further assessment of its potential and limitations.

RESULTS

Here, we show that the Saccharomyces cerevisiae thiamin biosynthesis mutant thi6 is an ideal candidate to be implemented in a turbidimetric assay aimed at assessing the content of thiamin and its phosphorylated equivalents (total vitamer B1). An optimized protocol was generated, adapted from a previously established microbiological assay using the thi4 mutant. A step-by-step guidance for this protocol is presented. Furthermore, the applicability of the assay is illustrated by assessment of different samples, including plant as well as non-plant materials. In doing so, our work provides an extension of the applicability of the microbiological assay on top of providing important considerations upon implementing the protocol.

CONCLUSIONS

An inexpensive, user-friendly protocol, including step-by-step guidance, which allows adequate estimation of vitamer B1 content of samples, is provided. The method is well-suited to screen materials to identify altered vitamer B1 content, such as in metabolic engineering or screening of germplasm.

Ensuring valid inference for Cox hazard ratios after variable selection

The problem of how to best select variables for confounding adjustment forms one of the key challenges in the evaluation of exposure effects in observational studies, and has been the subject of vigorous recent activity in causal inference. A major drawback of routine procedures is that there is no finite sample size at which they are guaranteed to deliver exposure effect estimators and associated confidence intervals with adequate performance. In this work, we will consider this problem when inferring conditional causal hazard ratios from observational studies under the assumption of no unmeasured confounding. The major complication that we face with survival data is that the key confounding variables may not be those that explain the censoring mechanism. In this paper, we overcome this problem using a novel and simple procedure that can be implemented using off-the-shelf software for penalized Cox regression. In particular, we will propose tests of the null hypothesis that the exposure has no effect on the considered survival endpoint, which are uniformly valid under standard sparsity conditions. Simulation results show that the proposed methods yield valid inferences even when covariates are high-dimensional.

GH3-mediated auxin inactivation attenuates multiple stages of lateral root development

Lateral root (LR) positioning and development rely on the dynamic interplay between auxin production, transport but also inactivation. Nonetheless, how the latter affects LR organogenesis remains largely uninvestigated. Here, we systematically analyze the impact of the major auxin inactivation pathway defined by GRETCHEN HAGEN3-type (GH3) auxin conjugating enzymes and DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) in all stages of LR development using reporters, genetics and inhibitors in Arabidopsis thaliana. Our data demonstrate that the gh3.1/2/3/4/5/6 hextuple (gh3hex) mutants display a higher LR density due to increased LR initiation and faster LR developmental progression, acting epistatically over dao1-1. Grafting and local inhibitor applications reveal that root and shoot GH3 activities control LR formation. The faster LR development in gh3hex is associated with GH3 expression domains in and around developing LRs. The increase in LR initiation is associated with accelerated auxin response oscillations coinciding with increases in apical meristem size and LR cap cell death rates. Our research reveals how GH3-mediated auxin inactivation attenuates LR development. Local GH3 expression in LR primordia attenuates development and emergence, whereas GH3 effects on pre-initiation stages are indirect, by modulating meristem activities that in turn coordinate root growth with LR spacing.

Critical power, W' and W' reconstitution in women and men

PURPOSE

The aim of this study was to compare critical power (CP) and work capacity W', and W' reconstitution (W'REC) following repeated maximal exercise between women and men.

METHODS

Twelve women ([Formula: see text]O2PEAK: 2.53 ± 0.37 L·min-1) and 12 men ([Formula: see text]O2PEAK: 4.26 ± 0.30 L·min-1) performed a minimum of 3 constant workload tests, to determine CP and W', and 1 maximal exercise repetition test with three work bouts (WB) to failure, to quantify W'REC during 2 recovery periods, i.e., W'REC1 and W'REC2. An independent samples t test was used to compare CP and W' values between women and men, and a repeated-measures ANOVA was used to compare W'REC as fraction of W' expended during the first WB, absolute W'REC, and normalized to lean body mass (LBM).

RESULTS

CP normalized to LBM was not different between women and men, respectively, 3.7 ± 0.5 vs. 4.1 ± 0.4 W·kgLBM-1, while W' normalized to LBM was lower in women 256 ± 29 vs. 305 ± 45 J·kgLBM-1. Fractional W'REC1 was higher in women than in men, respectively, 74.0 ± 12.0% vs. 56.8 ± 9.5%. Women reconstituted less W' than men in absolute terms (8.7 ± 1.2 vs. 10.9 ± 2.0 kJ) during W'REC1, while normalized to LBM no difference was observed between women and men (174 ± 23 vs. 167 ± 31 J·kgLBM-1). W'REC2 was lower than W'REC1 both in women and men.

CONCLUSION

Sex differences in W'REC (absolute women < men; fractional women > men) are eliminated when LBM is accounted for. Prediction models of W'REC might benefit from including LBM as a biological variable in the equation. This study confirms the occurrence of a slowing of W'REC during repeated maximal exercise.

Utilisation of probiotics for disease management in giant freshwater prawn (Macrobrachium rosenbergii): Administration methods, antagonistic effects and immune response

The giant freshwater prawn (Macrobrachium rosenbergii) is a high-yielding prawn variety well-received worldwide due to its ability to adapt to freshwater culture systems. Macrobrachium rosenbergii is an alternative to shrimp typically obtained from marine and brackish aquaculture systems. However, the use of intensive culture systems can lead to disease outbreaks, particularly in larval and post-larval stages, caused by pathogenic agents such as viruses, bacteria, fungi, yeasts and protozoans. White tail disease (viral), white spot syndrome (viral) and bacterial necrosis are examples of economically significant diseases. Given the increasing antibiotic resistance of disease-causing microorganisms, probiotics have emerged as promising alternatives for disease control. Probiotics are live active microbes that are introduced into a target host in an adequate number or dose to promote its health. In the present paper, we first discuss the diseases that occur in M. rosenbergii production, followed by an in-depth discussion on probiotics. We elaborate on the common methods of probiotics administration and explain the beneficial health effects of probiotics as immunity enhancers. Moreover, we discuss the antagonistic effects of probiotics on pathogenic microorganisms. Altogether, this paper provides a comprehensive overview of disease control in M. rosenbergii aquaculture through the use of probiotics, which could enhance the sustainability of prawn culture.

A bispecific Clec9A-PD-L1 targeted type I interferon profoundly reshapes the tumor microenvironment towards an antitumor state

Despite major improvements in immunotherapeutic strategies, the immunosuppressive tumor microenvironment remains a major obstacle for the induction of efficient antitumor responses. In this study, we show that local delivery of a bispecific Clec9A-PD-L1 targeted type I interferon (AcTaferon, AFN) overcomes this hurdle by reshaping the tumor immune landscape.Treatment with the bispecific AFN resulted in the presence of pro-immunogenic tumor-associated macrophages and neutrophils, increased motility and maturation profile of cDC1 and presence of inflammatory cDC2. Moreover, we report empowered diversity in the CD8+ T cell repertoire and induction of a shift from naive, dysfunctional CD8+ T cells towards effector, plastic cytotoxic T lymphocytes together with increased presence of NK and NKT cells as well as decreased regulatory T cell levels. These dynamic changes were associated with potent antitumor activity. Tumor clearance and immunological memory, therapeutic immunity on large established tumors and blunted tumor growth at distant sites were obtained upon co-administration of a non-curative dose of chemotherapy.Overall, this study illuminates further application of type I interferon as a safe and efficient way to reshape the suppressive tumor microenvironment and induce potent antitumor immunity; features which are of major importance in overcoming the development of metastases and tumor cell resistance to immune attack. The strategy described here has potential for application across to a broad range of cancer types.

Super-Oxidizing Covalent Triazine Framework Electrocatalyst for Two-Electron Water Oxidation to H2 O2

Electrochemical two-electron water oxidation (2e WOR) is gaining surging research traction for sustainable hydrogen peroxide production. However, the strong oxidizing environment and thermodynamically competitive side-reaction (4e WOR) posit as thresholds for the 2e WOR. We herein report a custom-crafted covalent triazine network possessing strong oxidizing properties as a proof-of-concept metal-free functional organic network electrocatalyst for catalyzing 2e WOR. As the first-of-its-kind, the material shows a maximum of 89.9 % Faradaic Efficiency and 1428 μmol/h/cm2 H2 O2 production rate at 3.0 V bias potential (vs reversible hydrogen electrode, RHE), which are either better or comparable to the state-of-the-art electrocatalysts. We have experimentally confirmed a stepwise 2e WOR mechanism which was further computationally endorsed by density functional theory studies.

Differentiating airway inflammation in calves based on cluster analysis of bronchoalveolar lavage fluid cytology

BACKGROUND

Nonbronchoscopic bronchoalveolar lavage (nBAL) is routinely performed in calves, and airway cytology has great potential in airway disease diagnostics. A good reference framework for nBAL cytology is lacking.

OBJECTIVES

To distinguish different cytological profiles in nBAL from grouped housed calves using cluster analysis, and characterize these profiles on individual and herd levels.

ANIMALS

Three hundred thirty-eight group-housed calves from 60 herds (mainly dairy and beef ).

METHODS

Cross-sectional study. Differential counts of white blood cells were determined on nBAL fluid, followed by differentiation of cytological profiles by K-means-based cluster analysis. These profiles were characterized by reference values, decision tree analysis, and associations with clinical, ultrasonographic, bacteriological, and cytological features.

RESULTS

A normal (55.9%), a neutrophilic (41.1%), and an eosinophilic profile (3.0%) were identified. The normal profile was characterized by reference values of 2.3% to 47.4% neutrophils, 35.1% to 95.1% macrophages, 0.4 to 22.9% lymphocytes, and 0.0% to 0.9% eosinophils. The neutrophilic profile was characterized by ≥44.5% neutrophils, <1.6% eosinophils, and <11.5% lymphocytes. This profile was associated with the isolation of Pasteurella multocida, the presence of neutrophils with toxic granulation, and the presence of phagocytosed bacteria in neutrophils. The eosinophilic profile was characterized by eosinophils ≥1.6% (neutrophilia present) or ≥2.4% (neutrophilia absent), and associated with the presence of mast cells. On herd level, the neutrophilic and eosinophilic profiles were present in 85.0% and 15.0% of the herds, respectively.

CONCLUSIONS AND CLINICAL IMPORTANCE

This study provides a first step in the development of cytological guidelines, aiding the assessment of airway health and inflammation in calves through nBAL fluid cytology.

Biological variation of urinary protein: Creatinine ratio and urine specific gravity in cats

BACKGROUND

Laboratory results are influenced by presence and severity of disease, as well as preanalytical factors, analytical variation, and biological variation. Biological variation data for urinary protein: creatinine ratio (UPC) and urine specific gravity (USG) in cats are lacking.

OBJECTIVES

Determine the biological variation of UPC and USG in cats.

ANIMALS

Eighty healthy client-owned cats.

METHODS

Prospective study. Urine was collected on days 0, 14, and 56 from all 80 cats to investigate the persistence of borderline or overt proteinuria or suboptimal urine concentration. In 15 of these cats, urine was collected weekly from day 0 to 42 to calculate the index of individuality (II) and reference change value (RCV), and on days 56 and 57 to evaluate day-to-day variability of UPC and USG.

RESULTS

Borderline or overt proteinuria (UPC ≥0.2) was present in 18/80 (23%) cats at baseline and persisted on 3 occasions in 2 months in 8/18 (44%) cats. Urine concentration was suboptimal at inclusion (USG <1.035) in 8/80 (10%) cats and at all 3 time points during 2 months in 3/8 (38%) cats. The II of UPC and USG indicated intermediate individuality. The 1-sided RCV was 82% for UPC and 36% for USG. Proteinuria substage was identical on 2 consecutive days in 13/15 (87%) cats, and urine concentrating ability remained the same in all 15 cats.

CONCLUSIONS AND CLINICAL IMPORTANCE

A >82% increase in UPC in a healthy cat is not solely attributable to physiological and analytical variation. For USG, a decrease of >36% is considered clinically relevant.