bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual Differences in the Correspondence Between Psychological and Physiological Stress Indicators
Authors: Hilger Kirsten , Talić Irma , Renner Karl-Heinz 
Published: August 2024

AbstractStress threatens physical and mental health. Reactions to acute stress comprise multiple levels, including negative thoughts, bodily symptoms and behaviors. Individuals differ in their reaction to acute stress, and importantly, also in the extent to which these levels align, with a closer correspondence between psychological and physiological stress indicators being beneficial for mental health and well-being. This preregistered study investigates such individual differences systematically by inducing psychological (social-evaluative) and physiological (cold water) stress with the Maastricht Acute Stress Test (MAST) in 149 healthy adults. Participants indicated the extent to which they perceived to be stressed and four physiological stress indicators (blood pressure, heart rate, salivary cortisol, alpha-amylase) were measured. Finally, multiple personality traits were assessed as potential moderators, including the Big Five, trait anxiety, and general cognitive ability. In line with previous research, psychological and physiological stress indicators were only weakly correlated. However, considering individual differences in personality, revealed especially conscientiousness and openness as potential moderators of the correspondence between psychological and physiological stress indicators. We propose individual differences in interoceptive abilities as another critical moderator, which deserves further investigation, and discuss how future research on individual differences in psycho-physiological correspondence can contribute to further our understanding of mental and physical diseases.Impact StatementStress has substantially increased over the last decade. A missing correspondence between self-reported stress and physiological stress measures has been related to mental illnesses and lower well-being. In revealing that specific personality traits might act as potential moderators of the psycho-physiological correspondence, our research complements recent prospects towards personalized medicine and offers starting points for the development of individualized psychological interventions and prevention programs.
Identification and structural characterization of a novel acetyl xylan esterase fromAspergillus oryzae
Authors: Yamada Chihaya , Kato Tomoe , Shiono Yoshihito , Koseki Takuya , Fushinobu Shinya 
Published: August 2024

AbstractAcetyl xylan esterase plays a crucial role in the degradation of xylan, the major plant hemicellulose, by liberating acetic acid from the backbone polysaccharides. Acetyl xylan esterase B fromAspergillus oryzae, designatedAoAXEB, was biochemically and structurally investigated. TheAoAXEB-encoding gene with a native signal peptide was successfully expressed inPichia pastorisas an active extracellular protein. The purified recombinant protein had pH and temperature optima of 8.0 and 30 °C, respectively, and was stable up to 35°C. The optimal substrate for hydrolysis by purified recombinantAoAXEB among a panel of α-naphthyl esters was α-naphthyl acetate. RecombinantAoAXEB catalyzes the release of acetic acid from wheat arabinoxylan. The release of acetic acid from wheat arabinoxylan increases synergistically with xylanase addition. No activity was detected using the methyl esters of ferulic,p-coumaric, caffeic, or sinapic acids. The crystal structures ofAoAXEB in the apo and succinate complexes were determined at resolutions of 1.75 and 1.90 Å, respectively. AlthoughAoAXEB has been classified in the Esterase_phb family in the ESTerases and alpha/beta-Hydrolase Enzymes and Relatives (ESTHER) database, its structural features partly resemble those of ferulic acid esterase in the FaeC family. Phylogenetic analysis also indicated thatAoAXEB is located between the clades of the two families. Docking analysis provided a plausible binding mode for xylotriose substrates acetylated at the 2- or 3-hydroxy position. This study expands the repertoire of side chain-degrading enzymes required for complete plant biomass degradation.
Paracrine rescue of MYR1-deficientToxoplasma gondiimutants reveals limitations of pooledin vivoCRISPR screens
Authors: Torelli Francesca , da Fonseca Diogo M. , Butterworth Simon , Young Joanna C. , Treeck Moritz 
Published: August 2024

ABSTRACTToxoplasma gondiiis an intracellular parasite that subverts host cell functions via secreted virulence factors. Up to 70% of parasite-controlled changes in the host transcriptome rely on the MYR1 protein, which is required for the translocation of secreted proteins into the host cell. Mice infected with MYR1 knock-out (KO) strains survive infection, supporting a paramount function of MYR1-dependent secreted proteins inToxoplasmavirulence and proliferation. However, we have previously shown that MYR1 mutants have no growth defect in pooledin vivoCRISPR-Cas9 screens in mice, suggesting that the presence of parasites that are wild-type at themyr1locus in pooled screens can rescue the phenotype. Here, we demonstrate that MYR1 is not required for the survival in IFN-γ-activated murine macrophages, and that parasites lacking MYR1 are able to expand during the onset of infection. While ΔMYR1 parasites have restricted growth in single-strain murine infections, we show that the phenotype is rescued by co-infection with wild-type (WT) parasitesin vivo, independent of host functional adaptive immunity or key pro-inflammatory cytokines. These data show that the major function of MYR1-dependent secreted proteins is not to protect the parasite from clearance within infected cells. Instead, MYR-dependent proteins generate a permissive niche in a paracrine manner, which rescues ΔMYR1 parasites within a pool of CRISPR mutants in mice. Our results highlight an important limitation of otherwise powerfulin vivoCRISPR screens and point towards key functions for MYR1-dependentToxoplasma-host interactions beyond the infected cell.SIGNIFICANCE STATEMENTPooled CRISPR screens are powerful tools to interrogate gene function in a high-throughput manner. Genes conferring fitness advantages or disadvantages upon disruption can be identified by sequencing. However, inToxoplasma gondiipooled CRISPR screens in mice, fitness defects for some selected mutants drastically diverge from those observed in single-strain infections. Here, we show that a growth defect of a singleToxoplasmagene deletion mutant is rescued if co-infected with wildtype parasites. These results shine light onToxoplasma’s ability to subvert the host response beyond the infected cell, and highlight an important limitation of pooled CRISPR screens in mice. This limitation is probably encountered in CRISPR screens in general where paracrine effects occur.
BGC Atlas: A Web Resource for Exploring the Global Chemical Diversity Encoded in Bacterial Genomes
Authors: Bağcı Caner , Nuhamunada Matin , Goyat Hemant , Ladanyi Casimir , Sehnal Ludek , Blin Kai , Kautsar Satria A. , Tagirdzhanov Azat , Gurevich Alexey , Mantri Shrikant , von Mering Christian , Udwary Daniel , Medema Marnix H. , Weber Tilmann , Ziemert Nadine 
Published: August 2024

AbstractSecondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology, and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35,000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides (RiPPs) are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.
Structural basis for the strict substrate specificity of β-D-galactofuranosidase fromStreptomycessp. JHA19
Authors: Fujio Noriki , Yamada Chihaya , Kashima Toma , Matsunaga Emiko , Nash Robert J. , Takegawa Kaoru , Fushinobu Shinya 
Published: August 2024

AbstractD-Galactofuranose (Galf) is widely distributed in polysaccharides and glycoconjugates of bacteria, filamentous fungi, and protozoa. The biosynthetic and degradation pathways of Galfin pathogens have attracted attention as potential targets for drug development. β-D-Galactofuranosidase (Galf-ase) releases Galffrom the non-reducing ends of glycans. Galf-ase activity is often exhibited by α-L-arabinofuranosidases, which hydrolyze a similar substrate. Several Galf-specific Galf-ases that cleave only Galfand not L-arabinofuranose (Araf) have recently been identified in the glycoside hydrolase (GH) families 2, 5, and 43. However, the structural basis of how they discriminate the substrates is unknown. ORF1110, belonging to GH2, is the first identified Galf-specific Galf-ase isolated fromStreptomycessp. JHA19. Here, we solved the crystal structure of ORF1110 in complex with a mechanism-based potent inhibitor, D-iminogalactitol (Ki= 65 μM). ORF1110 binds to the C5-C6 hydroxy groups of D-iminogalactitol with an extensive and integral hydrogen bond network. This result suggests that in the case of Araf, which lacks the C6 hydroxymethyl group, this network is not formed. The domain structure of ORF1110 is similar to that of β-glucuronidases and β-galactosidases, which belong to the same GH2 family and hydrolyze pyranose substrates. However, their active site structures were completely different. A predicted structure of the C-terminal Abf domain of ORF1110 was very similar to the carbohydrate-binding module family 42, which binds Araf, and pockets that may bind Galfwere present.
Significant and persistent carryover effects in Scots pine
Authors: Perry Annika , Beaton Joan K. , Stockan Jenni A. , Iason Glenn R. , Cottrell Joan E. , Cavers Stephen 
Published: August 2024

AbstractAfter tracking Scots pine plants from germination to 15 years old, through contrasting early life environments, we observed significant and persistent carryover effects. Groups of plants from common genetic backgrounds were raised in distinct nursery environments, and growth and phenology traits were measured repeatedly once trees had established in their field sites. Growth and phenology differences were evident for 10 and 6 years post-transplantation to the field, respectively. There was a clear interaction between site of origin and carryover effect, indicating that local adaptation also played a role. Given the increasing rate of tree planting initiatives being undertaken around the world in the name of the climate and biodiversity crises, and the strong dependence on those initiatives of nursery-grown plants, our finding of strong carryover effects of the early life environment has significant implications.
Selective enrichment of specific bacterial taxa in downy mildew-affected spinach: Comparative analysis in laboratory and field conditions
Authors: Goossens Pim , Baremans Kim , Alderkamp Marrit , Boshoven Jordi C. , van den Ackerveken Guido , Berendsen Roeland L. 
Published: August 2024

AbstractPlants host diverse microbial communities that can be influenced by their hosts to mitigate biotic stress. Previous research demonstrated that distinct laboratory cultures ofHyaloperonospora arabidopsidis(Hpa) onArabidopsis thaliana, consistently harbor nearly identical bacteria. In this study, we analyzed the bacterial phyllosphere communities of laboratory-grown spinach plants infected by the downy mildew pathogenPeronospora effusa(Pe). Using 16S amplicon sequencing, we identified 14 Amplicon Sequence Variants (ASVs), with diverse taxonomies, that were enriched in at least 3 out of 5 investigated Pe cultures. This small set of 14 ASVs occupied on average 6.9% of the total bacterial communities in healthy spinach plants, and 43.1% in Pe-inoculated plants. A specificRhodococcusand aPaenarthrobacterASV were particularly prevalent and abundant. To validate these findings outside of the laboratory, we planted a susceptible variety of spinach in 4 agricultural fields and sampled leaves from Pe-infected plants in 2 fields where this pathogen naturally occurred. Comparative microbiome analysis of diseased and healthy plants revealed significant enrichment of 16 and 31 ASVs in these 2 fields, respectively. Among these, thePaenarthrobacterASV was enriched in one field and theRhodococcusASV in the other field, suggesting that disease-associated microbiota that are abundantly detected in Pe laboratory cultures are also associated with Pe-infected field plants. Additionally, we observed an overlap of ASVs that were associated with both Pe and Hpa, indicating that similar bacteria are linked to downy mildew disease across different hosts.
Rhamnose Polysaccharide-Decorated Outer Membrane Vesicles as a Vaccine Candidate Targeting Group A Streptococcus fromStreptococcus pyogenesandStreptococcus dysgalactiaesubsp.equisimilis
Authors: Ajay Castro Sowmya , Thomson Sarah , Shaw Helen Alexandra , Zorzoli Azul , Meyer Benjamin H , Reglinski Mark , Dorfmueller Helge C. 
Published: August 2024

AbstractGroup A Streptococcus (Strep A) cause a wide range of human-exclusive infections, annually killing more than 500,000 people. Antibiotic resistance incidence of invasive Strep A tripled in the past decade and emphasises the need to develop a universal Strep A vaccine. In this study, we developed recombinant rhamnose polysaccharides (RhaPS), a validated universal Strep A vaccine candidate, presented onE. coliouter membrane vesicles (OMVs). We investigated OMV-RhaPS for their immunogenicity in the mouse and rabbit models. Through flow cytometry, ELISA, Luminex assays, and immunofluorescence microscopy, we demonstrated that RhaPS-specific antibodies recognise Strep A strains via the Group A Carbohydrate (GAC) inS. pyogenesand the newly emergedS. dysgalactiaesubsp.equisimilis. Elevated IL-17a levels from RhaPS-OMV-immunised splenocytes indicate the RhaPS-specific stimulation of long-term memory immune cells. We are the first to report the efficacy and potency of recombinant produced RhaPS inducing humoral-mediated immune responses and triggering antibodies that recognise Strep A bacteria.
SpatialLeiden - Spatially-aware Leiden clustering
Authors: Müller-Bötticher Niklas , Sahay Shashwat , Eils Roland , Ishaque Naveed 
Published: August 2024

AbstractClustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Leiden clustering is the algorithm of choice in the single-cell community. However, in the field of spatial omics, Leiden has been considered a non-spatial clustering method. Here, we show that by integrating spatial embeddings Leiden clustering is rendered into a computationally highly performant, spatially aware clustering method that compares well with state-of-the art clustering methods.
Expanding the biotechnological scope of metabolic sensors through computation-aided designs
Authors: Orsi Enrico , Schulz-Mirbach Helena , Cotton Charles A. R. , Satanowski Ari , Petri Henrik M. , Arnold Susanne L. , Grabarczyk Natalia , Verbakel Rutger , Jensen Karsten S. , Donati Stefano , Paczia Nicole , Glatter Timo , Küffner Andreas M. , Chotel Tanguy , Schillmüller Farah , De Maria Alberto , He Hai , Lindner Steffen N. , Noor Elad , Bar-Even Arren , Erb Tobias J. , Nikel Pablo I. 
Published: August 2024

AbstractMetabolic sensors are microbial strains modified so that biomass formation correlates with the availability of specific metabolites. These sensors are essential for bioengineering (e.g. in growth-coupled designs) but creating them is often a time-consuming and low-throughput process that can potentially be streamlined byin silicoanalysis. Here, we present the systematic workflow of designing, implementing, and testing versatileEscherichia colimetabolic sensor strains. Glyoxylate, a key metabolite in (synthetic) CO2fixation and carbon-conserving pathways, served as the test molecule. Through iterative screening of a compact metabolic model, we identified non-trivial growth-coupled designs that resulted in six metabolic sensors with a wide sensitivity range for glyoxylate, spanning three orders of magnitude in detected concentrations. We further adapted theseE. colistrains for sensing glycolate and demonstrated their utility in both pathway engineering (testing a key metabolic moduleviaglyoxylate) and applications in environmental monitoring (quantifying glycolate produced by photosynthetic microalgae). The versatility and ease of implementation of this workflow make it suitable for designing and building multiple metabolic sensors for diverse biotechnological applications.TeaserA streamlined workflow enables the rapid design of versatileE. colimetabolic sensors for detecting key metabolites in bioengineering and monitoring.
The knockdown of the snoRNA-jouvence blocks the cell proliferation and leads to cell death of human primary cancerous glioblastoma cells
Authors: Jaque-Cabrera Lola , Buggiani Julia , Bignon Jérôme , Daira Patricia , Bernoud-Hubac Nathalie , Martin Jean-René 
Published: August 2024

ABSTRACTCancer research aims to identify new therapeutic targets and provide patients with more effective therapies that generate fewer deleterious side effects. Previous studies have demonstrated the role of small nucleolar RNAs (snoRNAs) in many physiological and pathological cellular processes, including cancers. SnoRNAs are a group of non-coding RNAs involved in different post-transcriptional modifications of ribosomal RNAs. Recently, we have identified a new snoRNA, namedjouvence(snoRNA-jou) in humans. Here, we characterize the effect of the knockdown of the snoRNA-jouvence by sh-lentivirus on human primary glioblastoma cells. The sh-lentivirus induces a significant decrease of cell proliferation, proportional to the amount of lentivirus used. For example, with a MOI-20, a decrease of more than 50% is observed after only 72 hours, and even up to 80% after 10 days. Moreover, a EdU proliferative test confirms this decrease in cell proliferation, while a TUNEL test reveals the presence of apoptotic cells. A RNA-Seq analysis, validated by RT-qPCR, reveals that the snoRNA-jou knockdown induces a significant deregulation of several key genes involved in the cell cycle regulation, such as cyclins B1, A2 and p21, indicating a cell cycle blockage. Altogether, these results allow hypothesising that the knockdown of the snoRNA-jouvence could potentially be use as a new anti-cancer treatment (sno-Therapy).
Moult cycle and setal development of the Atlantic ditch shrimpPalaemon variansLeach, 1814 (Decapoda: Caridea: Palaemonidae)
Authors: Kim Kenneth , Antcliffe Jonathan , Daley Allison C. , Robinson-Rechavi Marc 
Published: August 2024

ABSTRACTThe Atlantic ditch shrimpPalaemon variansLeach, 1814 is a common estuarine and brackish water species on Northern Atlantic coasts.Palaemon variansis an appealing model organism for studying arthropod developmental processes, such as moulting (ecdysis). Detailed morphological information on its moult cycle is still lacking, hence we have characterised the changes in the setal features corresponding to the moult stages ofP. variansgrown under laboratory conditions. The stages of the moult cycle were differentiated and described using microscopic analysis of the setae in the uropods ofP. variansbased on Drach’s classification system. Moult stages were defined as early and late post-moult (A and B), inter-moult (C), early-, mid- and late pre-moult (D0, D1,and D2), as well as ecdysis stage (E), the actual shedding of the exuvia. Average moult cycle duration was 8.7 days, where pre-moult accounted for the longest duration of 4.4 days on average. This study provides a morphological reference for determining the moult stage ofP. varianswithout the use of invasive techniques, and thus it is well suited for repetitive observations of an individual to track the entire moulting process.
Assessing male reproductive investment in Papaveraceae using flow cytometry reveals lineage-specific trajectories to pollen-to-ovule ratio reduction
Authors: de Vos Jurriaan M. , Woudstra Yannick , Leitch Ilia J. , Hidalgo Oriane 
Published: August 2024

AbstractMale reproductive investment, in particular pollen production, is a crucial and ecologically relevant component of a plant’s phenotype and reproductive success. Its evolutionary trajectory, however, remains understudied, partly due to a lack of convenient methods to assess it. We developed a protocol for pollen quantification by flow cytometry and applied it to 107 flowers from 38 Papaveraceae species differing widely in floral traits (e.g., floral symmetry, stamen number), pollination syndromes (e.g., wind and insect pollination) and reproductive systems (e.g., degree of autogamy). We phylogenetically tested whether pollen number evolved in association with ovule, carpel, stamen and flower numbers per inflorescence, and if there were interacting effects between floral symmetry and/or self-compatibility with pollen and ovule production.Compared to manual counts, results using flow cytometry were similar, but much faster to obtain and more precise. Pollen and ovule numbers per flower varied > 39,000x and > 550x, respectively, among species. Pollen production correlated positively with ovule, carpel and stamen numbers. Lineage-specific trajectories to pollen-to-ovule ratio reduction (to values < 300) are observed. One involved increased female investment in ruderal species belonging to the subfamily Papaveroideae, while the other occurs through decreased male investment and is associated with the evolution of floral traits towards greater specialisation. The impact of reproductive systems on male and female investment is limited to ovule production in non-actinomorphic flowers.Taken together, these results revealed that the evolutionary associations between reproductive systems, floral traits, and pollen and ovule production are lineage-specific. Given the profound contrasts at the subfamily level of Papaveraceae, broader surveys across the diversity of flowering plants are clearly needed to better understand factors driving the evolution of reproductive investment. Such studies will certainly be facilitated by our new high-throughput pollen counting method outlined here.