Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization

Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.

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.

On subjective measures of decision quality

In times of person-centered care, it is all the more important to support patients in making good decisions about their care. One way to offer such support to patients is by way of Patient Decision Aids (PDAs). Ranging from patient brochures to web-based tools, PDAs explicitly state the decisions patients face, inform them about their medical options, help them to clarify and discuss their values, and ultimately make a decision. However, lingering discussions surround effectiveness research on PDAs. In this article, I focus on two subjective measures of decision quality that are widely used as outcome measures in effectiveness research on PDAs (i.e., the Decisional Conflict Scale (DCS) and measures of regret). Although these measurement instruments have attracted critical attention in the scientific literature, bioethicists have hardly engaged with them. Therefore, I set myself to analyze the relationship between (the different subscales of) the DCS and measures of regret, on the one hand, and ethical principles such as beneficence and autonomy, on the other hand. In light of that analysis, I will clarify some discussions regarding the use of these measures of decision quality in effectiveness research on PDAs. This should help us to align the way we evaluate PDAs with ethical principles and avoid that our attempts to support patients in making good decisions about their care that is so central to person-centered care point in unethical directions.

Exploring indicators of natural recovery from alcohol and drug use problems: findings from the life in recovery survey in Flanders

INTRODUCTION

Research has established natural recovery (NR) as an important pathway to substance use recovery. Studies investigating correlates of NR have mainly focused on demographic and substance use variables rather than life circumstances. This study seeks to better understand the phenomenon of natural recovery by (i) validating the international scientific literature concerning demographic and substance use indicators of NR in Flanders and (ii) assessing the additional explanatory power of recovery strengths and barriers during active addiction, controlling for demographic and substance use covariates.

METHODS

A total of 343 persons in recovery from alcohol or drug use problems (≥ 3 months) completed an online cross-sectional survey in Flanders. Participants in NR and in recovery after following treatment were compared using multivariate linear regression models. Reasons for not following treatment were analyzed using inductive thematic analysis.

RESULTS

Higher education level, lower severity of dependence, and cannabis use as the main problem substance (vs. alcohol) were statistically significant (p < 0.05) correlates of NR. When scores for the number of barriers and strengths associated with active addiction were added, barriers (but not strengths) were significantly associated with NR. When barrier items were individually tested, having untreated emotional or mental health problems, having a driver's license revoked and damaging property were statistically significant correlates. The most reported reason for not entering treatment was not experiencing any need to do so.

CONCLUSION

The results highlight the importance of a holistic approach to recovery support across multiple life domains. Limitations and opportunities for further research are discussed.

Selenium reduction pathways in the colloidal synthesis of CdSe nanoplatelets

Several established procedures are now available to prepare zinc blende CdSe nanoplatelets. While these protocols allow for detailed control over both thickness and lateral dimensions, the chemistry behind their formation is yet to be unraveled. In this work, we discuss the influence of the solvent on the synthesis of nanoplatelets. We confirmed that the presence of double bonds, as is the case for 1-octadecene, plays a key role in the evolution of nanoplatelets, through the isomerization of the alkene, as confirmed by nuclear magnetic resonance spectroscopy and mass spectrometry. Consequently, 1-octadecene can be replaced as a solvent (or solvent mixture), however, only by one that also contains α protons to CC double bonds. We confirm this via synthesis of nanoplatelets in hexadecane spiked with a small amount of 1-octadecene, and in the aromatic solvent 1,2,3,4-tetrahydronaphthalene (tetralin). At the same time, the chemical reaction leading to the formation of nanoplatelets occurs to some extent in saturated solvents. A closer examination revealed that an alternative formation pathway is possible, through interaction of carboxylic acids, such as octanoic acid, with selenium. Next to shedding more light on the synthesis of CdSe nanoplatelets, fundamental understanding of the precursor chemistry paves the way to use optimized solvent admixtures as an additional handle to control the nanoplatelet synthesis, as well as to reduce potential self-polymerization hurdles observed with 1-octadecene.

Variability in Hemispheric Functional Segregation Phenotypes: A Review and General Mechanistic Model

Many functions of the human brain are organized asymmetrically and are subject to strong population biases. Some tasks, like speaking and making complex hand movements, exhibit left hemispheric dominance, whereas others, such as spatial processing and recognizing faces, favor the right hemisphere. While pattern of preference implies the existence of a stereotypical way of distributing functions between the hemispheres, an ever-increasing body of evidence indicates that not everyone follows this pattern of hemispheric functional segregation. On the contrary, the review conducted in this article shows that departures from the standard hemispheric division of labor are routinely observed and assume many distinct forms, each having a different prevalence rate. One of the key challenges in human neuroscience is to model this variability. By integrating well-established and recently emerged ideas about the mechanisms that underlie functional lateralization, the current article proposes a general mechanistic model that explains the observed distribution of segregation phenotypes and generates new testable hypotheses.

Transitioning from Methanol to Olefins (MTO) toward a Tandem CO2 Hydrogenation Process: On the Role and Fate of Heteroatoms (Mg, Si) in MAPO-18 Zeotypes

The tandem CO2 hydrogenation to hydrocarbons over mixed metal oxide/zeolite catalysts (OXZEO) is an efficient way of producing value-added hydrocarbons (platform chemicals and fuels) directly from CO2via methanol intermediate in a single reactor. In this contribution, two MAPO-18 zeotypes (M = Mg, Si) were tested and their performance was compared under methanol-to-olefins (MTO) conditions (350 °C, PCH3OH = 0.04 bar, 6.5 gCH3OH h-1 g-1), methanol/CO/H2 cofeed conditions (350 °C, PCH3OH/PCO/PH2 = 1:7.3:21.7 bar, 2.5 gCH3OH h-1 g-1), and tandem CO2 hydrogenation-to-olefin conditions (350 °C, PCO2/PH2 = 7.5:22.5 bar, 1.4-12.0 gMAPO-18 h molCO2-1). In the latter case, the zeotypes were mixed with a fixed amount of ZnO:ZrO2 catalyst, well-known for the conversion of CO2/H2 to methanol. Focus was set on the methanol conversion activity, product selectivity, and performance stability with time-on-stream. In situ and ex situ Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), solid-state nuclear magnetic resonance (NMR), sorption experiments, and ab initio molecular dynamics (AIMD) calculations were performed to correlate material performance with material characteristics. The catalytic tests demonstrated the better performance of MgAPO-18 versus SAPO-18 at MTO conditions, the much superior performance of MgAPO-18 under methanol/CO/H2 cofeeds, and yet the increasingly similar performance of the two materials under tandem conditions upon increasing the zeotype-to-oxide ratio in the tandem catalyst bed. In situ FT-IR measurements coupled with AIMD calculations revealed differences in the MTO initiation mechanism between the two materials. SAPO-18 promoted initial CO2 formation, indicative of a formaldehyde-based decarboxylation mechanism, while CO and ketene were the main constituents of the initiation pool in MgAPO-18, suggesting a decarbonylation mechanism. Under tandem CO2 hydrogenation conditions, the presence of high water concentrations and low methanol partial pressure in the reaction medium led to lower, and increasingly similar, methanol turnover frequencies for the zeotypes. Despite both MAPO-18 zeotypes showing signs of activity loss upon storage due to the interaction of the sites with ambient humidity, they presented a remarkable stability after reaching steady state under tandem reaction conditions and after steaming and regeneration cycles at high temperatures. Water adsorption experiments at room temperature confirmed this observation. The faster activity loss observed in the Mg version is assigned to its harder Mg2+-ion character and the higher concentration of CHA defects in the AEI structure, identified by solid-state NMR and XRD. The low stability of a MgAPO-34 zeotype (CHA structure) upon storage corroborated the relationship between CHA defects and instability.

Genomic mining of Vibrio parahaemolyticus highlights prevalence of antimicrobial resistance genes and new genetic markers associated with AHPND and tdh + /trh + genotypes

BACKGROUND

Acute Hepatopancreatic Necrosis Disease (AHPND) causes significant mortality in shrimp aquaculture. The infection is primarily instigated by Vibrio parahaemolyticus (Vp) strains carrying a plasmid encoding the binary toxin PirAB. Yet, comprehension of supplementary virulence factors associated with this relatively recent disease remains limited. Furthermore, the same holds for gastroenteritis in humans caused by other Vp genotypes. Additionally, given the prevalent use of antibiotics to combat bacterial infections, it becomes imperative to illuminate the presence of antimicrobial resistance genes within these bacteria.

RESULTS

A subsampled number of 1,036 Vp genomes was screened for the presence of antimicrobial resistance genes, revealing an average prevalence of 5 ± 2 (SD) genes. Additional phenotypic antimicrobial susceptibility testing of three Vp strains (M0904, TW01, and PV1) sequenced in this study demonstrated resistance to ampicillin by all tested strains. Additionally, Vp M0904 showed multidrug resistance (against ampicillin, tetracycline, and trimethoprim-sulfamethoxazole). With a focus on AHPND, a screening of all Vibrio spp. for the presence of pirA and/or pirB indicates an estimated prevalence of 0.6%, including four V. campbellii, four V. owensii, and a Vibrio sp. next to Vp. Their pirAB-encoding plasmids exhibited a highly conserved backbone, with variations primarily in the region of the Tn3 family transposase. Furthermore, an assessment of the subsampled Vp genomes for the presence of known virulence factors showed a correlation between the presence of the Type 3 Secretion System 2 and tdh, while the presence of the Type 6 Secretion System 1 was clade dependent. Furthermore, a genome-wide association study (GWAS) unveiled (new) genes associated with pirA, pirB, tdh, and trh genotypes. Notable associations with the pirAB genotype included outer membrane proteins, immunoglobulin-like domain containing proteins, and toxin-antitoxin systems. For the tdh + /trh + genotypes (containing tdh, trh, or both genes), associations were found with T3SS2 genes, urease-related genes and nickel-transport system genes, and genes involved in a 'minimal' type I-F CRISPR mechanism.

CONCLUSIONS

This study highlights the prevalence of antimicrobial resistance and virulence genes in Vp, identifying novel genetic markers associated with AHPND and tdh + /trh + genotypes. These findings contribute valuable insights into the genomic basis of these genotypes, with implications for shrimp aquaculture and food safety.

Leaf growth - complex regulation of a seemingly simple process

Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.

Image Denoising of Low-Dose PET Mouse Scans with Deep Learning: Validation Study for Preclinical Imaging Applicability

PURPOSE

Positron emission tomography (PET) image quality can be improved by higher injected activity and/or longer acquisition time, but both may often not be practical in preclinical imaging. Common preclinical radioactive doses (10 MBq) have been shown to cause deterministic changes in biological pathways. Reducing the injected tracer activity and/or shortening the scan time inevitably results in low-count acquisitions which poses a challenge because of the inherent noise introduction. We present an image-based deep learning (DL) framework for denoising lower count micro-PET images.

PROCEDURES

For 36 mice, a 15-min [18F]FDG (8.15 ± 1.34 MBq) PET scan was acquired at 40 min post-injection on the Molecubes β-CUBE (in list mode). The 15-min acquisition (high-count) was parsed into smaller time fractions of 7.50, 3.75, 1.50, and 0.75 min to emulate images reconstructed at 50, 25, 10, and 5% of the full counts, respectively. A 2D U-Net was trained with mean-squared-error loss on 28 high-low count image pairs.

RESULTS

The DL algorithms were visually and quantitatively compared to spatial and edge-preserving denoising filters; the DL-based methods effectively removed image noise and recovered image details much better while keeping quantitative (SUV) accuracy. The largest improvement in image quality was seen in the images reconstructed with 10 and 5% of the counts (equivalent to sub-1 MBq or sub-1 min mouse imaging). The DL-based denoising framework was also successfully applied on the NEMA-NU4 phantom and different tracer studies ([18F]PSMA, [18F]FAPI, and [68 Ga]FAPI).

CONCLUSION

Visual and quantitative results support the superior performance and robustness in image denoising of the implemented DL models for low statistics micro-PET. This offers much more flexibility in optimizing preclinical, longitudinal imaging protocols with reduced tracer doses or shorter durations.

Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP

α-1 acid glycoprotein (AGP) is one of the most abundant plasma proteins. It fulfills two important functions: immunomodulation, and binding to various drugs and receptors. These different functions are closely associated and modulated via changes in glycosylation and cancer missense mutations. From a structural point of view, glycans alter the local biophysical properties of the protein leading to a diverse ligand-binding spectrum. However, glycans can typically not be observed in the resolved X-ray crystallography structure of AGP due to their high flexibility and microheterogeneity, so limiting our understanding of AGP's conformational dynamics 70 years after its discovery. We here investigate how mutations and glycosylation interfere with AGP's conformational dynamics changing its biophysical behavior, by using molecular dynamics (MD) simulations and sequence-based dynamics predictions. The MD trajectories show that glycosylation decreases the local backbone flexibility of AGP and increases the flexibility of distant regions through allosteric effects. We observe that mutations near the glycosylation site affect glycan's conformational preferences. Thus, we conclude that mutations control glycan dynamics which modulates the protein's backbone flexibility directly affecting its accessibility. These findings may assist in the drug design targeting AGP's glycosylation and mutations in cancer.

Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection

In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.

Surface Reconstructions in II-VI Quantum Dots

Although density functional theory (DFT) calculations have been crucial in our understanding of colloidal quantum dots (QDs), simulations are commonly carried out on QD models that are significantly smaller than those generally found experimentally. While smaller models allow for efficient study of local surface configurations, increasing the size of the QD model will increase the size or number of facets, which can in turn influence the energetics and characteristics of trap formation. Moreover, core-shell structures can only be studied with QD models that are large enough to accommodate the different layers with the correct thickness. Here, we use DFT calculations to study the electronic properties of QDs as a function of size, up to a diameter of ∼4.5 nm. We show that increasing the size of QD models traditionally used in DFT studies leads to a disappearance of the band gap and localization of the HOMO and LUMO levels on facet-specific regions of the QD surface. We attribute this to the lateral coupling of surface orbitals and the formation of surface bands. The introduction of surface vacancies and their a posteriori refilling with Z-type ligands leads to surface reconstructions that widen the band gap and delocalize both the HOMO and LUMO. These results show that the surface geometry of the facets plays a pivotal role in defining the electronic properties of the QD.

Relating different perspectives on how outcomes of behavior influence behavior

Many researchers have tackled the question of how behavior is influenced by its outcomes. Some have adopted a nonmechanistic (functional) perspective that attempts to describe the influence of outcomes on behavior. Others have adopted a mechanistic (cognitive) perspective that attempts to explain the influence of outcomes on behavior. Orthogonal to this distinction, some have focused on the influence of outcomes that a behavior had in the past, whereas others also consider the influence of outcomes that a behavior might have in the future. In this article, we relate these different perspectives with the goal of reducing misunderstandings and fostering collaborations between researchers who adopt different perspectives on the common question of how behavior is influenced by its outcomes.

A comprehensive metabolite fingerprint of fibrostenosis in patients with Crohn's disease

Intestinal fibrostenosis in patients with Crohn's disease (CD) is a common and untreatable comorbidity that is notoriously difficult to monitor. We aimed to find metabolites associated with the presence of fibrostenosis in patients with CD using targeted and untargeted metabolomics analyses of serum and primary cell cultures using hyphenated ultra-high performance liquid chromatography high-resolution mass spectrometry. Targeted metabolomics revealed 11 discriminating metabolites in serum, which were enriched within the arginine and proline metabolism pathway. Based on untargeted metabolomics and discriminant analysis, 166 components showed a high predictive value. In addition, human intestinal fibroblasts isolated from stenotic tissue were characterized by differential levels of medium-chain dicarboxylic acids, which are proposed as an energy source through beta-oxidation, when oxidative phosphorylation is insufficient. Another energy providing pathway in such situations is anaerobic glycolysis, a theory supported by increased expression of hexokinase 2 and solute carrier family 16 member 1 in stenotic fibroblasts. Of interest, four (unannotated) metabolic components showed a negative correlation with hexokinase 2 gene expression. Together, this study provides a discriminative metabolic fingerprint in the serum and in intestinal fibroblasts of stenotic and non-stenotic patients with CD suggestive for increased production of building blocks for collagen synthesis and increased glycolysis.

Reaching the Tumor: Mobility of Polymeric Micelles Inside an In Vitro Tumor-on-a-Chip Model with Dual ECM

Degradable polymeric micelles are promising drug delivery systems due to their hydrophobic core and responsive design. When applying micellar nanocarriers for tumor delivery, one of the bottlenecks encountered in vivo is the tumor tissue barrier: crossing the dense mesh of cells and the extracellular matrix (ECM). Sometimes overlooked, the extracellular matrix can trap nanoformulations based on charge, size, and hydrophobicity. Here, we used a simple design of a microfluidic chip with two types of ECM and MCF7 spheroids to allow "high-throughput" screening of the interactions between biological interfaces and polymeric micelles. To demonstrate the applicability of the chip, a small library of fluorescently labeled polymeric micelles varying in their hydrophilic shell and hydrophobic core forming blocks was studied. Three widely used hydrophilic shells were tested and compared, namely, poly(ethylene glycol), poly(2-ethyl-2-oxazoline), and poly(acrylic acid), along with two enzymatically degradable dendritic hydrophobic cores (based on hexyl or nonyl end groups). Using ratiometric imaging of unimer:micelle fluorescence and FRAP inside the chip model, we obtained the local assembly state and dynamics inside the chip. Notably, we observed different micelle behaviors in the basal lamina ECM, from avoidance of the ECM structure to binding of the poly(acrylic acid) formulations. Binding to the basal lamina correlated with higher uptake into MCF7 spheroids. Overall, we proposed a simple microfluidic chip containing dual ECM and spheroids for the assessment of the interactions of polymeric nanocarriers with biological interfaces and evaluating nanoformulations' capacity to cross the tumor tissue barrier.

The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions

BACKGROUND

It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in overexploitation and depletion of resources, and environmental degradation. In this context, microbial biomass has emerged as a promising sustainable protein alternative. Nevertheless, often no consideration is given on the fact that the cultivation conditions affect the composition of microbial cells, and hence their quality and nutritional value. Apart from the properties and nutritional quality of the produced microbial food (ingredient), this can also impact its sustainability. To qualitatively assess these aspects, here, we investigated the link between substrate availability, growth rate, cell composition and size of Cupriavidus necator and Komagataella phaffii.

RESULTS

Biomass with decreased nucleic acid and increased protein content was produced at low growth rates. Conversely, high rates resulted in larger cells, which could enable more efficient biomass harvesting. The proteome allocation varied across the different growth rates, with more ribosomal proteins at higher rates, which could potentially affect the techno-functional properties of the biomass. Considering the distinct amino acid profiles established for the different cellular components, variations in their abundance impacts the product quality leading to higher cysteine and phenylalanine content at low growth rates. Therefore, we hint that costly external amino acid supplementations that are often required to meet the nutritional needs could be avoided by carefully applying conditions that enable targeted growth rates.

CONCLUSION

In summary, we demonstrate tradeoffs between nutritional quality and production rate, and we discuss the microbial biomass properties that vary according to the growth conditions.

Chemical induction of hypocotyl rooting reveals extensive conservation of auxin signalling controlling lateral and adventitious root formation

Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca2+ signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.

Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform

BACKGROUND

Thermography is a popular tool to assess plant water-use behavior, as plant temperature is influenced by transpiration rate, and is commonly used in field experiments to detect plant water deficit. Its application in indoor automated phenotyping platforms is still limited and mainly focuses on differences in plant temperature between genotypes or treatments, instead of estimating stomatal conductance or transpiration rate. In this study, the transferability of commonly used thermography analysis protocols from the field to greenhouse phenotyping platforms was evaluated. In addition, the added value of combining thermal infrared (TIR) with hyperspectral imaging to monitor drought effects on plant transpiration rate (E) was evaluated.

RESULTS

The sensitivity of commonly used TIR indices to detect drought-induced and genotypic differences in water status was investigated in eight maize inbred lines in the automated phenotyping platform PHENOVISION. Indices that normalized plant temperature for vapor pressure deficit and/or air temperature at the time of imaging were most sensitive to drought and could detect genotypic differences in the plants' water-use behavior. However, these indices were not strongly correlated to stomatal conductance and E. The canopy temperature depression index, the crop water stress index and the simplified stomatal conductance index were more suitable to monitor these traits, and were consequently used to develop empirical E prediction models by combining them with hyperspectral indices and/or environmental variables. Different modeling strategies were evaluated, including single index-based, machine learning and mechanistic models. Model comparison showed that combining multiple TIR indices in a random forest model can improve E prediction accuracy, and that the contribution of the hyperspectral data is limited when multiple indices are used. However, the empirical models trained on one genotype were not transferable to all eight inbred lines.

CONCLUSION

Overall, this study demonstrates that existing TIR indices can be used to monitor drought stress and develop E prediction models in an indoor setup, as long as the indices normalize plant temperature for ambient air temperature or relative humidity.

Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time

BACKGROUND

Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME.

RESULTS

Transit time was identified as the single most important driver of microbial cell concentrations (52%), metabolic activity (45%) and quantitative (24%) and proportional (22%) community composition. Deceleration of transit was characterised by a significant decrease of specific Bifidobacterium and Veillonella spp. and increase of specific fibre degrading bacteria and nutrient specialists, such as Bacteroides, Prevotella, Ruminococcus, Bilophila and Akkermansia spp. These microbial communities reached a higher population density and net carbohydrate fermentation, leading to an increased SCFA production at longer transit times. In contrast, the carbohydrate-to-biomass production efficiency was increased at shorter transits, particularly in well-adapted faecal microbiomes from donors with short in vivo transit. Said adaptation was also reflected in the carbohydrate-to-SCFA conversion efficiency which varied with donor, but also colon region and SCFA chain length. A long transit time promoted propionate production, whereas butyrate production and butyrate producers were selectively enriched in the proximal colon at medium transit time.

CONCLUSION

Microbial growth rates and nutrient utilisation efficiency mediate the species-specific gut microbiota response to in vitro transit time variation, which is the main driver of in vitro microbial load, metabolism and community composition. Given the in vivo transit time variation within and between individuals, the personalisation of in vitro transit time based on in vivo data is required to accurately study intra- and inter-individual differences in gut microbiome structure, functionality and interactions with host and environmental modulators. Video Abstract.

Syntaxin 18 Defects in Human and Zebrafish Unravel Key Roles in Early Cartilage and Bone Development

SNARE proteins comprise a conserved protein family responsible for catalyzing membrane fusion during vesicle traffic. Syntaxin18 (STX18) is a poorly characterized endoplasmic reticulum (ER)-resident t-SNARE. Recently, together with TANGO1 and SLY1, its involvement was shown in ER to Golgi transport of collagen II during chondrogenesis. We report a fetus with a severe osteochondrodysplasia in whom we identified a homozygous substitution of the highly conserved p.Arg10 to Pro of STX18. CRISPR/Cas9-mediated Stx18 deficiency in zebrafish reveals a crucial role for Stx18 in cartilage and bone development. Furthermore, increased expression of multiple components of the Stx18 SNARE complex and of COPI and COPII proteins suggests that Stx18 deficiency impairs antero- and retrograde vesicular transport in the crispant stx18 zebrafish. Taken together, our studies highlight a new candidate gene for a recessive form of osteochondrodysplasia, thereby possibly broadening the SNAREopathy phenotypic spectrum and opening new doors toward future research avenues. © 2023 American Society for Bone and Mineral Research (ASBMR).

An information-theoretic approach to basis-set fitting of electron densities and other non-negative functions

The numerical ill-conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater-type functions is overcome by using the (extended) Kullback-Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non-negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non-negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non-negative basis functions. We present a fixed-point iteration method for optimizing the Kullback-Leibler divergence and compare it to conventional gradient-based optimization methods. These algorithms are released through the free and open-source BFit package, which also includes a L2-norm squared optimization routine applicable to any square-integrable scalar function.

Proximity-Induced Ligation and One-Pot Macrocyclization of 1,4-Diketone-Tagged Peptides Derived from 2,5-Disubstituted Furans upon Release from the Solid Support

1,4-Dione-containing peptides are generated during the cleavage of 2,5-disubstituted furan-containing systems. The generated electrophilic systems then react with α-effect nucleophiles, following a Paal-Knorr-like mechanism, for the generation of macrocyclic peptides, occurring after simple resuspension of the crude peptide in water. Conveniently, the in situ generation of the electrophile from a stable furan ring avoids the complications associated with the synthesis of carbonyl-containing peptides. Detailed investigation of the reaction characteristics was first performed on supramolecular coiled-coil systems.

STE20 kinase TAOK3 regulates type 2 immunity and metabolism in obesity

Healthy adipose tissue (AT) contains ST2+ Tregs, ILC2s, and alternatively activated macrophages that are lost in mice or humans on high caloric diet. Understanding how this form of type 2 immunity is regulated could improve treatment of obesity. The STE20 kinase Thousand And One amino acid Kinase-3 (TAOK3) has been linked to obesity in mice and humans, but its precise function is unknown. We found that ST2+ Tregs are upregulated in visceral epididymal white AT (eWAT) of Taok3-/- mice, dependent on IL-33 and the kinase activity of TAOK3. Upon high fat diet feeding, metabolic dysfunction was attenuated in Taok3-/- mice. ST2+ Tregs disappeared from eWAT in obese wild-type mice, but this was not the case in Taok3-/- mice. Mechanistically, AT Taok3-/- Tregs were intrinsically more responsive to IL-33, through higher expression of ST2, and expressed more PPARγ and type 2 cytokines. Thus, TAOK3 inhibits adipose tissue Tregs and regulates immunometabolism under excessive caloric intake.

Detailed whole-body nutrient analysis identifies differences in feeding ecology between related fish species: The case of Orestias native Andean killifish in Lake Titicaca

Body nutrient profiles in ecological studies allow for relating the nutritional status of consumers and their effects on the movement and retention of elements in ecosystems, as well as reflecting feeding conditions and habitat quality. This study compared the detailed whole-body nutrient composition (macronutrients, minerals, fatty acids and amino acids) of two omnivorous natives Orestias killifish from Lake Titicaca (Orestias agassizii and Orestias luteus, Valenciennes), the largest lake in the Andes, as an indirect tool to understand differences in their feeding ecology. Although both species are usually described as omnivorous fish, both have amphipods (Hyalella spp) as their main food source. Our results showed that both killifish had a comparable macronutrient composition, and the mineral concentrations of Mg, P and Ca (reflecting bony structures) differed between them. Many of the saturated fatty acids were significantly lower in O. luteus, and O. agassizii had higher concentrations of cis-vaccenic acid (18:1n11 (cis)), supporting the idea of a higher algal contribution to the diet of this fish. The lower histidine and higher taurine concentrations in O. agassizii compared with O. luteus (independent of body size) may reflect its ubiquitous behaviour and plasticity. This study shows how whole-body nutrient analysis can identify differences in feeding ecology and feeding behaviour between related species.

Operando Modeling of Zeolite-Catalyzed Reactions Using First-Principles Molecular Dynamics Simulations

Within this Perspective, we critically reflect on the role of first-principles molecular dynamics (MD) simulations in unraveling the catalytic function within zeolites under operating conditions. First-principles MD simulations refer to methods where the dynamics of the nuclei is followed in time by integrating the Newtonian equations of motion on a potential energy surface that is determined by solving the quantum-mechanical many-body problem for the electrons. Catalytic solids used in industrial applications show an intriguing high degree of complexity, with phenomena taking place at a broad range of length and time scales. Additionally, the state and function of a catalyst critically depend on the operating conditions, such as temperature, moisture, presence of water, etc. Herein we show by means of a series of exemplary cases how first-principles MD simulations are instrumental to unravel the catalyst complexity at the molecular scale. Examples show how the nature of reactive species at higher catalytic temperatures may drastically change compared to species at lower temperatures and how the nature of active sites may dynamically change upon exposure to water. To simulate rare events, first-principles MD simulations need to be used in combination with enhanced sampling techniques to efficiently sample low-probability regions of phase space. Using these techniques, it is shown how competitive pathways at operating conditions can be discovered and how broad transition state regions can be explored. Interestingly, such simulations can also be used to study hindered diffusion under operating conditions. The cases shown clearly illustrate how first-principles MD simulations reveal insights into the catalytic function at operating conditions, which could not be discovered using static or local approaches where only a few points are considered on the potential energy surface (PES). Despite these advantages, some major hurdles still exist to fully integrate first-principles MD methods in a standard computational catalytic workflow or to use the output of MD simulations as input for multiple length/time scale methods that aim to bridge to the reactor scale. First of all, methods are needed that allow us to evaluate the interatomic forces with quantum-mechanical accuracy, albeit at a much lower computational cost compared to currently used density functional theory (DFT) methods. The use of DFT limits the currently attainable length/time scales to hundreds of picoseconds and a few nanometers, which are much smaller than realistic catalyst particle dimensions and time scales encountered in the catalysis process. One solution could be to construct machine learning potentials (MLPs), where a numerical potential is derived from underlying quantum-mechanical data, which could be used in subsequent MD simulations. As such, much longer length and time scales could be reached; however, quite some research is still necessary to construct MLPs for the complex systems encountered in industrially used catalysts. Second, most currently used enhanced sampling techniques in catalysis make use of collective variables (CVs), which are mostly determined based on chemical intuition. To explore complex reactive networks with MD simulations, methods are needed that allow the automatic discovery of CVs or methods that do not rely on a priori definition of CVs. Recently, various data-driven methods have been proposed, which could be explored for complex catalytic systems. Lastly, first-principles MD methods are currently mostly used to investigate local reactive events. We hope that with the rise of data-driven methods and more efficient methods to describe the PES, first-principles MD methods will in the future also be able to describe longer length/time scale processes in catalysis. This might lead to a consistent dynamic description of all steps-diffusion, adsorption, and reaction-as they take place at the catalyst particle level.

Crosstalk between glucocorticoid and mineralocorticoid receptors boosts glucocorticoid-induced killing of multiple myeloma cells

The glucocorticoid receptor (GR) is a crucial drug target in multiple myeloma as its activation with glucocorticoids effectively triggers myeloma cell death. However, as high-dose glucocorticoids are also associated with deleterious side effects, novel approaches are urgently needed to improve GR action in myeloma. Here, we reveal a functional crosstalk between GR and the mineralocorticoid receptor (MR) that plays a role in improved myeloma cell killing. We show that the GR agonist dexamethasone (Dex) downregulates MR levels in a GR-dependent way in myeloma cells. Co-treatment of Dex with the MR antagonist spironolactone (Spi) enhances Dex-induced cell killing in primary, newly diagnosed GC-sensitive myeloma cells. In a relapsed GC-resistant setting, Spi alone induces distinct myeloma cell killing. On a mechanistic level, we find that a GR-MR crosstalk likely arises from an endogenous interaction between GR and MR in myeloma cells. Quantitative dimerization assays show that Spi reduces Dex-induced GR-MR heterodimerization and completely abolishes Dex-induced MR-MR homodimerization, while leaving GR-GR homodimerization intact. Unbiased transcriptomics analyses reveal that c-myc and many of its target genes are downregulated most by combined Dex-Spi treatment. Proteomics analyses further identify that several metabolic hallmarks are modulated most by this combination treatment. Finally, we identified a subset of Dex-Spi downregulated genes and proteins that may predict prognosis in the CoMMpass myeloma patient cohort. Our study demonstrates that GR-MR crosstalk is therapeutically relevant in myeloma as it provides novel strategies for glucocorticoid-based dose-reduction.

Interplay between uncertainty intolerance, emotion regulation, cognitive flexibility, and psychopathology during the COVID-19 pandemic: a multi-wave study

The COVID-19 pandemic has created a significant mental health burden on the global population. Studies during the pandemic have shown that risk factors such as intolerance of uncertainty and maladaptive emotion regulation are associated with increased psychopathology. Meanwhile, protective factors such as cognitive control and cognitive flexibility have been shown to protect mental health during the pandemic. However, the potential pathways through which these risk and protective factors function to impact mental health during the pandemic remain unclear. In the present multi-wave study, 304 individuals (18 years or older, 191 Males), residing in the USA during data collection, completed weekly online assessments of validated questionnaires across a period of five weeks (27th March 2020-1st May 2020). Mediation analyses revealed that longitudinal changes in emotion regulation difficulties mediated the effect of increases in intolerance of uncertainty on increases in stress, depression, and anxiety during the COVID-19 pandemic. Further, individual differences in cognitive control and flexibility moderated the relationship between intolerance of uncertainty and emotion regulation difficulties. While intolerance of uncertainty and emotion regulation difficulties emerged as risk factors for mental health, cognitive control and flexibility seems to protect against the negative effects of the pandemic and promote stress resilience. Interventions aimed at enhancing cognitive control and flexibility might promote the protection of mental health in similar global crises in the future.

Ulva: An emerging green seaweed model for systems biology

Green seaweeds exhibit a wide range of morphologies and occupy various ecological niches, spanning from freshwater to marine and terrestrial habitats. These organisms, which predominantly belong to the class Ulvophyceae, showcase a remarkable instance of parallel evolution toward complex multicellularity and macroscopic thalli in the Viridiplantae lineage. Within the green seaweeds, several Ulva species ("sea lettuce") are model organisms for studying carbon assimilation, interactions with bacteria, life cycle progression, and morphogenesis. Ulva species are also notorious for their fast growth and capacity to dominate nutrient-rich, anthropogenically disturbed coastal ecosystems during "green tide" blooms. From an economic perspective, Ulva has garnered increasing attention as a promising feedstock for the production of food, feed, and biobased products, also as a means of removing excess nutrients from the environment. We propose that Ulva is poised to further develop as a model in green seaweed research. In this perspective, we focus explicitly on Ulva mutabilis/compressa as a model species and highlight the molecular data and tools that are currently available or in development. We discuss several areas that will benefit from future research or where exciting new developments have been reported in other Ulva species.

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

The analysis of extracellular vesicles (EV) in blood samples is under intense investigation and holds the potential to deliver clinically meaningful biomarkers for health and disease. Technical variation must be minimized to confidently assess EV-associated biomarkers, but the impact of pre-analytics on EV characteristics in blood samples remains minimally explored. We present the results from the first large-scale EV Blood Benchmarking (EVBB) study in which we systematically compared 11 blood collection tubes (BCT; six preservation and five non-preservation) and three blood processing intervals (BPI; 1, 8 and 72 h) on defined performance metrics (n = 9). The EVBB study identifies a significant impact of multiple BCT and BPI on a diverse set of metrics reflecting blood sample quality, ex-vivo generation of blood-cell derived EV, EV recovery and EV-associated molecular signatures. The results assist the informed selection of the optimal BCT and BPI for EV analysis. The proposed metrics serve as a framework to guide future research on pre-analytics and further support methodological standardization of EV studies.

Facts and fears that limit digital transformation in farming: Exploring barriers to the outreach of wireless sensor networks in Southwest Iran

Wireless sensor networks (WSNs) are considered part of an environmentally friendly technology leading to more timely and cost-effective production and management of farms. Despite the potential of WSNs to agricultural development in the global South, outreach is still very limited, also in Iran. Therefore, in order to facilitate the adoption of WSNs, it is necessary to identify the factors influencing and challenging the adoption of this technology. This exploratory study uses a qualitative approach to identify the main barriers WSN outreach is facing. In the results, we distinguish facts that we define as issues or barriers that were identified by others from fears that are not supported by evidence so far, at the level of the farmers, the government actors as well as the technology itself. Facts include communication barriers such as internet access, farmers' knowledge levels and rigidity to change as well as the government's top-down organisation of the extension programme and support levels. Fears are mainly expressed on the technology itself and relate to costs, a lack of access, the complexity of use and reliability of the data. We provide a nuanced view of how fears need to be acknowledged and facts are to be tackled.

Characterising different molecular landscapes in dynamic covalent networks

Dynamic covalent networks present a unique opportunity to exert molecular-level control on macroscopic material properties, by linking their thermal behaviour to the thermodynamics and kinetics of the underlying chemistry. Yet, existing methods do not allow for the extraction and analysis of the influence of local differences in chemical reactivity caused by available reactants, catalysts, or additives. In this context, we present a rheological paradigm that allows us to correlate the composition of a reactive polymer segment to a faster or slower rate of network rearrangement. We discovered that a generalised Maxwell model could separate and quantify the dynamic behaviour of each type of reactive segment individually, which was crucial to fully comprehend the mechanics of the final material. More specifically, Eyring and Van 't Hoff analysis were used to relate possible bond catalysis and dissociation to structural changes by combining statistical modelling with rheology measurements. As a result, precise viscosity changes could be measured, allowing for accurate comparison of various dynamic covalent network materials, including vitrimers and dissociative networks. The herein reported method therefore facilitated the successful analysis of virtually any type of rate-enhancing effect and will allow for the design of functional and fast (re)processable materials, as well as improve our ability to predict and engineer their properties for future applications.

Recent progress in diagnosis and treatment of Human African Trypanosomiasis has made the elimination of this disease a realistic target by 2030

Human African Trypanosomiasis (HAT) is caused by unicellular flagellated protozoan parasites of the genus Trypanosoma brucei. The subspecies T. b. gambiense is mainly responsible for mostly chronic anthroponotic infections in West- and Central Africa, accounting for roughly 95% of all HAT cases. Trypanosoma b. rhodesiense results in more acute zoonotic infections in East-Africa. Because HAT has a two-stage pathogenesis, treatment depends on clinical assessment of patients and the determination whether or not parasites have crossed the blood brain barrier. Today, ultimate confirmation of parasitemia is still done by microscopy analysis. However, the introduction of diagnostic lateral flow devices has been a major contributor to the recent dramatic drop in T. b. gambiense HAT. Other techniques such as loop mediated isothermal amplification (LAMP) and recombinant polymerase amplification (RPA)-based tests have been published but are still not widely used in the field. Most recently, CRISPR-Cas technology has been proposed to improve the intrinsic diagnostic characteristics of molecular approaches. This will become crucial in the near future, as preventing the resurgence of HAT will be a priority and will require tools with extreme high positive and negative predicted values, as well as excellent sensitivity and specificity. As for treatment, pentamidine and suramin have historically been the drugs of choice for the treatment of blood-stage gambiense-HAT and rhodesiense-HAT, respectively. For treatment of second-stage infections, drugs that pass the blood brain barrier are needed, and melarsoprol has been effectively used for both forms of HAT in the past. However, due to the high occurrence of post-treatment encephalopathy, the drug is not recommended for use in T. b. gambiense HAT. Here, a combination therapy of eflornithine and nifurtimox (NECT) has been the choice of treatment since 2009. As this treatment requires IV perfusion of eflornithine, efforts were launched in 2003 by the drugs for neglected disease initiative (DNDi) to find an oral-only therapy solution, suitable for rural sub-Saharan Africa treatment conditions. In 2019 this resulted in the introduction of fexinidazole, with a treatment regimen suitable for both the blood-stage and non-severe second-stage T. b. gambiense infections. Experimental treatment of T. b. rhodesiense HAT has now been initiated as well.

Quantitative mapping of mercury and selenium in mushroom fruit bodies with laser ablation-inductively coupled plasma-mass spectrometry

This work describes the development of a novel method for quantitative mapping of Hg and Se in mushroom fruit body tissues with laser ablation coupled to inductively coupled plasma-mass spectrometry (LA-ICP-MS). Different parameters of the protocol for preparation of the standards used for quantification via external calibration were assessed, e.g., the dissolution temperature of gelatin standards and the addition of chitosan and L-cysteine as additives to the gelatin-based calibration droplets to better match the sample matrix. While chitosan was not suited for this purpose, the presence of L-cysteine considerably improved the figures of merit of the calibration, leading to limits of detection of 0.006 and 0.3 µg g-1 for Hg and Se, respectively, at a pixel size of 20 × 20 µm. Further, an in-house reference material, ideally suited for the validation of the method for application to mushroom samples, was successfully prepared from a paste of Boletus edulis. The newly developed method was used to investigate the distribution of Hg and Se in tissue sections of five porcini mushroom individuals of three different species (Boletus edulis, Boletus aereus, and Boletus pinophilus) and one sample of a parasol mushroom (Macrolepiota procera). For one sample, additional areas were ablated at higher spatial resolution, with a laser spot size down to 5 µm, which allows a detailed investigation of the spatial distribution of Hg and Se in mushrooms.

Whole genome duplication of wild-type and CINNAMYL ALCOHOL DEHYDROGENASE1-downregulated hybrid poplar reduces biomass yield and causes a brittle apex phenotype in field-grown wild types

The potential of whole genome duplication to increase plant biomass yield is well-known. In Arabidopsis tetraploids, an increase in biomass yield was accompanied by a reduction in lignin content and, as a result, a higher saccharification efficiency was achieved compared with diploid controls. Here, we evaluated whether the results obtained in Arabidopsis could be translated into poplar and whether the enhanced saccharification yield upon alkaline pretreatment of hairpin-downregulated CINNAMYL ALCOHOL DEHYDROGENASE1 (hpCAD) transgenic poplar could be further improved upon a whole genome duplication. Using a colchicine treatment, wild-type (WT) Populus tremula x P. alba cv. INRA 717-1B4, a commonly used model clone in tree biotechnology research, and hpCAD tetraploids were generated and grown in the greenhouse. In parallel, WT tetraploid poplars were grown in the field. In contrast to Arabidopsis, a whole genome duplication of poplar had a negative impact on the biomass yield of both greenhouse- and field-grown trees. Strikingly, field-grown WT tetraploids developed a brittle apex phenotype, i.e., their tip broke off just below the apex. In addition, the chromosome doubling altered the biomass composition of field-grown, but not of greenhouse-grown tetraploid poplars. More specifically, the lignin content of field-grown tetraploid poplars was increased at the expense of matrix polysaccharides. This increase in lignin deposition in biomass is likely the cause of the observed brittle apex phenotype, though no major differences in stem anatomy or in mechanical properties could be found between di- and tetraploid WT poplars grown in the field. Finally, without biomass pretreatment, the saccharification efficiency of greenhouse- and field-grown WT diploids was not different from that of tetraploids, whereas that of greenhouse-grown hpCAD tetraploids was higher than that of greenhouse-grown diploids. Upon alkaline pretreatment, the saccharification yield of diploids was similar to that of tetraploids for all genotypes and growth conditions tested. This study showed that a whole genome duplication in hybrid WT and hpCAD poplar did neither result in further improvements in biomass yield, nor in improved biomass composition and, hence, saccharification performance.

RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

High-risk neuroblastoma, a pediatric tumor originating from the sympathetic nervous system, has a low mutation load but highly recurrent somatic DNA copy number variants. Previously, segmental gains and/or amplifications allowed identification of drivers for neuroblastoma development. Using this approach, combined with gene dosage impact on expression and survival, we identified ribonucleotide reductase subunit M2 (RRM2) as a candidate dependency factor further supported by growth inhibition upon in vitro knockdown and accelerated tumor formation in a neuroblastoma zebrafish model coexpressing human RRM2 with MYCN. Forced RRM2 induction alleviates excessive replicative stress induced by CHK1 inhibition, while high RRM2 expression in human neuroblastomas correlates with high CHK1 activity. MYCN-driven zebrafish tumors with RRM2 co-overexpression exhibit differentially expressed DNA repair genes in keeping with enhanced ATR-CHK1 signaling activity. In vitro, RRM2 inhibition enhances intrinsic replication stress checkpoint addiction. Last, combinatorial RRM2-CHK1 inhibition acts synergistic in high-risk neuroblastoma cell lines and patient-derived xenograft models, illustrating the therapeutic potential.

A construction heuristic for the capacitated Steiner tree problem

Many real-life problems boil down to a variant of the Minimum Steiner Tree Problem (STP). In telecommunications, Fiber-To-The-Home (FTTH) houses are clustered so they can be connected with fiber as cost-efficiently as possible. The cost calculation of a fiber installment can be formulated as a capacitated STP. Often, STP variants are solved with integer linear programs, which provide excellent solutions, though the running time costs increase quickly with graph size. Some geographical areas require graphs of over 20000 nodes—typically unattainable for integer linear programs. This paper presents an alternative approach. It extends the shortest path heuristic for the STP to a new heuristic that can construct solutions for the capacitated STP: the Capacitated Shortest Path Heuristic (CSPH). It is straightforward to implement, allowing many extensions. In experiments on realistic telecommunications datasets, CSPH finds solutions on average in time O(|V|²), quadratic in the number of nodes, making it possible to solve 50000 node graphs in under a minute.

A Hepatitis C virus genotype 1b post-transplant isolate with high replication efficiency in cell culture and its adaptation to infectious virus production in vitro and in vivo

Hepatitis C virus (HCV) is highly diverse and grouped into eight genotypes (gts). Infectious cell culture models are limited to a few subtypes and isolates, hampering the development of prophylactic vaccines. A consensus gt1b genome (termed GLT1) was generated from an HCV infected liver-transplanted patient. GLT1 replicated to an outstanding efficiency in Huh7 cells upon SEC14L2 expression, by use of replication enhancing mutations or with a previously developed inhibitor-based regimen. RNA replication levels almost reached JFH-1, but full-length genomes failed to produce detectable amounts of infectious virus. Long-term passaging led to the adaptation of a genome carrying 21 mutations and concomitant production of high levels of transmissible infectivity (GLT1cc). During the adaptation, GLT1 spread in the culture even in absence of detectable amounts of free virus, likely due to cell-to-cell transmission, which appeared to substantially contribute to spreading of other isolates as well. Mechanistically, genome replication and particle production efficiency were enhanced by adaptation, while cell entry competence of HCV pseudoparticles was not affected. Furthermore, GLT1cc retained the ability to replicate in human liver chimeric mice, which was critically dependent on a mutation in domain 3 of nonstructural protein NS5A. Over the course of infection, only one mutation in the surface glycoprotein E2 consistently reverted to wildtype, facilitating assembly in cell culture but potentially affecting CD81 interaction in vivo. Overall, GLT1cc is an efficient gt1b infectious cell culture model, paving the road to a rationale-based establishment of new infectious HCV isolates and represents an important novel tool for the development of prophylactic HCV vaccines.

Ocean-Liner Ceramics: A Red Star Line Assemblage in Antwerp, Belgium

In contrast to what films such as Titanic would have people believe, scientific knowledge about ocean liners is fairly limited. These boats and their material culture, however, functioned as symbols of modernity par excellence and thus allow a better understanding of the advent of a new world at the turn of the 20th century. The focus of this article is a ceramic assemblage from the Red Star Line, the shipping company that transported some two million migrants from Antwerp (Belgium) to the United States between 1873 and 1934. The analysis of this material provides new insights into the furnishings and daily life aboard these ships. Moreover, the possible reuse of these maritime objects ashore forms a basis for a discussion of the ways in which ordinary people entered into the modern world using material culture and to what extent they might have embraced the values associated with these mass-produced goods.

Two-stage lot quality assurance sampling framework for monitoring and evaluation of neglected tropical diseases, allowing for imperfect diagnostics and spatial heterogeneity

Background

Monitoring and evaluation (M&E) is a key component of large-scale neglected tropical diseases (NTD) control programs. Diagnostic tests deployed in these M&E surveys are often imperfect, and it remains unclear how this affects the population-based program decision-making.

Methodology

We developed a 2-stage lot quality assurance sampling (LQAS) framework for decision-making that allows for both imperfect diagnostics and spatial heterogeneity of infections. We applied the framework to M&E of soil-transmitted helminth control programs as a case study. For this, we explored the impact of the diagnostic performance (sensitivity and specificity), spatial heterogeneity (intra-cluster correlation), and survey design on program decision-making around the prevalence decisions thresholds recommended by WHO (2%, 10%, 20% and 50%) and the associated total survey costs.

Principal findings

The survey design currently recommended by WHO (5 clusters and 50 subjects per cluster) may lead to incorrect program decisions around the 2% and 10% prevalence thresholds, even when perfect diagnostic tests are deployed. To reduce the risk of incorrect decisions around the 2% prevalence threshold, including more clusters (≥10) and deploying highly specific diagnostic methods (≥98%) are the most-cost saving strategies when spatial heterogeneity is moderate-to-high (intra-cluster correlation >0.017). The higher cost and lower throughput of improved diagnostic tests are compensated by lower required sample sizes, though only when the cost per test is <6.50 US$ and sample throughput is ≥3 per hour.

Conclusion/Significance

Our framework provides a means to assess and update M&E guidelines and guide product development choices for NTD. Using soil-transmitted helminths as a case study, we show that current M&E guidelines may severely fall short, particularly in low-endemic and post-control settings. Furthermore, specificity rather than sensitivity is a critical parameter to consider. When the geographical distribution of an NTD within a district is highly heterogeneous, sampling more clusters (≥10) may be required.

Tree Species Diversity and Forest Edge Density Jointly Shape the Gut Microbiota Composition in Juvenile Great Tits (Parus major)

Despite the microbiome’s key role in health and fitness, little is known about the environmental factors shaping the gut microbiome of wild birds. With habitat fragmentation being recognised as a major threat to biological diversity, we here determined how forest structure influences the bacterial species richness and diversity of wild great tit nestlings (Parus major). Using an Illumina metabarcoding approach which amplifies the 16S bacterial ribosomal RNA gene, we measured gut microbiota diversity and composition from 49 great tit nestlings, originating from 23 different nests that were located in 22 different study plots across a gradient of forest fragmentation and tree species diversity. Per nest, an average microbiome was determined on which the influence of tree species (composition and richness) and forest fragmentation (fragment area and edge density) was examined and whether this was linked to host characteristics (body condition and fledging success). We found an interaction effect of edge density with tree species richness or composition on both the microbial richness (alpha diversity: Chao1 and Shannon) and community structure (beta diversity: weighted and unweighted UniFrac). No significant short-term impact was observed of the overall faecal microbiome on host characteristics, but rather an adverse effect of specific bacterial genera on fledging success. These results highlight the influence of environmental factors on the microbial richness as well as the phylogenetic diversity during a life stage where the birds’ microbiota is shaped, which could lead to long-term consequences for host fitness.

Mechanistic Characterization of Zeolite-Catalyzed Aromatic Electrophilic Substitution at Realistic Operating Conditions

Zeolite-catalyzed benzene ethylation is an important industrial reaction, as it is the first step in the production of styrene for polymer manufacturing. Furthermore, it is a prototypical example of aromatic electrophilic substitution, a key reaction in the synthesis of many bulk and fine chemicals. Despite extensive research, the reaction mechanism and the nature of elusive intermediates at realistic operating conditions is not properly understood. More in detail, the existence of the elusive arenium ion (better known as Wheland complex) formed upon electrophilic attack on the aromatic ring is still a matter of debate. Temperature effects and the presence of protic guest molecules such as water are expected to impact the reaction mechanism and lifetime of the reaction intermediates. Herein, we used enhanced sampling ab initio molecular dynamics simulations to investigate the complete mechanism of benzene ethylation with ethene and ethanol in the H-ZSM-5 zeolite. We show that both the stepwise and concerted mechanisms are active at reaction conditions and that the Wheland intermediate spontaneously appears as a shallow minimum in the free energy surface after the electrophilic attack on the benzene ring. Addition of water enhances the protonation kinetics by about 1 order of magnitude at coverages of one water molecule per Brønsted acidic site. In the fully solvated regime, an overstabilization of the BAS as hydronium ion occurs and the rate enhancement disappears. The obtained results give critical atomistic insights in the role of water to selectively tune the kinetics of protonation reactions in zeolites.

Sensitivity of candling as routine method for the detection and recovery of ascaridoids in commercial fish fillets

Ascaridoids are one of the main parasitic hazards in commercial fish. Candling is the current industrial screening method whereby visible ascaridoid larvae are detected on a light table and manually removed. The aim of this study was to assess the sensitivity (Se) and negative predictive value (NPV) of this method. To make targeted recommendations to the fish industry, the Se was calculated per fish part, larval genus, and fish species. All fish parts (n = 615) were first candled, and larvae were collected, followed by enzymatic digestion to recover the remaining larvae. A fish part was considered positive if at least one larva was detected using candling and/or enzymatic digestion, with both methods combined as reference standard. The overall Se of candling was 31% (95% CI 23-41%) and NPV was 87% (95% CI 85-90%). The Se increased with higher numbers of larvae/100 g infected muscle. A low NPV was found for the belly flaps, therefore we either advise the removal or proper freezing of this part. Lastly, the Se and larval recovery was the highest for the darker and larger Pseudoterranova spp. larvae. Due to the low overall efficacy of candling, further assessment of its cost-benefit and impact on consumers' health risk should be conducted.

Do Psychological Needs Play a Role in Times of Uncertainty? Associations with Well-Being During the COVID-19 Crisis

Across the world, measures were taken to contain the spreading of the COVID-19 virus. Many of these measures caused a sudden rupture in people's daily routines, thereby eliciting considerable uncertainty and potentially also hampering the satisfaction of individuals' psychological needs for autonomy, relatedness, and competence. Drawing upon Maslow's Hierarchical Need Theory and Self-Determination Theory, this study examined the unique role of felt insecurity and the psychological needs, as well as their dynamic interplay, in the prediction of mental health. A large and heterogeneous sample of adults (N = 5118; Mage = 43.45 years) was collected during the first ten days of the lockdown period in Flanders, Belgium. A subsample (N = 835, Mage = 41.39) participated during a second wave one week later. Hierarchical regression analyses indicated that felt insecurity, need satisfaction and need frustration all independently predicted various positive (life satisfaction, sleep quality) and negative indicators depressive symptoms, anxiety) of mental health, with little systematic evidence for interactions between the predictors. The pattern of findings obtained concurrently largely held in the longitudinal analyses. Finally, results showed that associations between felt insecurity and lower concurrent and prospective mental health were partially mediated by need satisfaction and frustration, with especially psychological need frustration predicting changes in mental health over time. Overall, the findings suggest that satisfaction of the psychological needs for autonomy, competence, and relatedness is not just a 'luxury good'. Satisfaction of these needs is important also in times of insecurity, while need frustration represents a risk factor for maladjustment during such times.

Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe

CONTEXT

Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.

OBJECTIVES

We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.

METHODS

We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.

RESULTS

Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.

CONCLUSIONS

Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation per se. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10980-021-01376-7.

The Fine-Structure Constant as a Ruler for the Band-Edge Light Absorption Strength of Bulk and Quantum-Confined Semiconductors

Low-dimensional semiconductors have found numerous applications in optoelectronics. However, a quantitative comparison of the absorption strength of low-dimensional versus bulk semiconductors has remained elusive. Here, we report generality in the band-edge light absorptance of semiconductors, independent of their dimensions. First, we provide atomistic tight-binding calculations that show that the absorptance of semiconductor quantum wells equals mπα (m = 1 or 2 with α as the fine-structure constant), in agreement with reported experimental results. Then, we show experimentally that a monolayer (superlattice) of quantum dots has similar absorptance, suggesting an absorptance quantum of mπα per (confined) exciton diameter. Extending this idea to bulk semiconductors, we experimentally demonstrate that an absorptance quantum equal to mπα per exciton Bohr diameter explains their widely varying absorption coefficients. We thus provided compelling evidence that the absorptance quantum πα per exciton diameter rules the band-edge absorption of all direct semiconductors, regardless of their dimension.

Cyan Emission in Two-Dimensional Colloidal Cs2CdCl4:Sb3+ Ruddlesden-Popper Phase Nanoplatelets

Metal halide perovskites are one of the most investigated materials in optoelectronics, with their lead-based counterparts being renowned for their enhanced optoelectronic performance. The 3D CsPbX₃ structure has set the standard with many studies currently attempting to substitute lead with other metals while retaining the properties of this material. This effort has led to the fabrication of metal halides with lower dimensionality, wherein particular 2D layered perovskite structures have captured attention as inspiration for the next generation of colloidal semiconductors. Here we report the synthesis of the Ruddlesden-Popper Cs₂CdCl₄:Sb³⁺ phase as colloidal nanoplatelets (NPs) using a facile hot injection approach under atmospheric conditions. Through strict adjustment of the synthesis parameters with emphasis on the ligand ratio, we obtained NPs with a relatively uniform size and good morphological control. The particles were characterized through transmission electron microscopy, synchrotron X-ray diffraction, and pair distribution function analysis. The spectroscopic characterization revealed most strikingly an intense cyan emission under UV excitation with a measured PLQY of ∼20%. The emission was attributed to the Sb³⁺-doping within the structure.

The impact of strict measures as a result of the COVID-19 pandemic on the spatial pattern of the demand for police: case study Antwerp (Belgium)

COVID-19 impacts the daily lives of millions of people. This radical change in our daily activities affected many aspects of life, but acted as well as a natural experiment for research into the spatial distribution of 911 calls. We analyse the impact of the COVID-19 measures on the spatial pattern of police interventions. Crime is not uniformly distributed across street segments, but how does COVID-19 affect these spatial patterns? To this end, Gini coefficients are calculated and a proportion differences spatial point pattern test is applied to compare the similarity of the patterns of incidents before, during, and after the first lockdown in Antwerp, Belgium. With only essential mobility being allowed, the emergency call pattern has not significantly changed before, during or after this lockdown, however, a qualitative shift in police officer's daily work may have had an effect on the daily operation of the Antwerp police force.

Development of Lignin-Based Mesoporous Carbons for the Adsorption of Humic Acid

There is an increasing urge to make the transition toward biobased materials. Lignin, originating from lignocellulosic biomass, can be potentially valorized as humic acid (HA) adsorbents via lignin-based mesoporous carbon (MC). In this work, these materials were synthesized for the first time starting from modified lignin as the carbon precursor, using the soft-template methodology. The use of a novel synthetic approach, Claisen rearrangement of propargylated lignin, and a variety of surfactant templates (Pluronic, Kraton, and Solsperse) have been demonstrated to tune the properties of the resulting MCs. The obtained materials showed tunable properties (BET surface area: 95-367 m²/g, pore size: 3.3-36.6 nm, V _BJH pore volume: 0.05-0.33 m³/g, and carbon and oxygen content: 55.5-91.1 and 3.0-12.2%, respectively) and good performance in terms of one of the highest HA adsorption capacities reported for carbon adsorbents (up to 175 mg/g).

Luminescence lifetime imaging of three-dimensional biological objects

A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.