bluuebunny/crossref_metadata_2025 huggingface dataset:
Drosophila melanogasterToll-9 elicits antiviral immunity againstDrosophilaC virus
Authors: Chauhan Manish , Martinak Peter E. , Hollenberg Benjamin M. , Goodman Alan G.
Published: June 2024

The Toll pathway plays a pivotal role in innate immune responses against pathogens. The evolutionary conserved pathogen recognition receptors (PRRs), including Toll like receptors (TLRs), play a crucial role in recognition of pathogen associated molecular patterns (PAMPs). TheDrosophilagenome encodes nine Toll receptors that are orthologous to mammalian TLRs. While mammalian TLRs directly recognize PAMPs, mostDrosophilaTolls recognize the proteolytically cleaved ligand Spätzle to activate downstream signaling cascades. In this study, we demonstrated that Toll-9 is crucial for antiviral immunity againstDrosophilaC virus (DCV), a natural pathogen ofDrosophila. A transposable element insertion in theToll-9gene renders the flies more susceptible to DCV. The stable expression of Toll-9 in S2 cells confers resistance against DCV infection by upregulation of the RNAi pathway. Toll-9 promotes the dephosphorylation of AKT, resulting in the induction of antiviral RNAi genes to inhibit DCV replication. Toll-9 localizes to the endosome where it binds dsRNA, suggesting its role to detect viral dsRNA. Toll-9 also induces apoptosis during DCV infection, contributing to its antiviral role. Together, this work identifies the role of Toll-9 in antiviral immunity against DCV infection through its ability to bind dsRNA and induce AKT-mediated RNAi antiviral immunity.

IMPORTANCE

Insects rely on innate immunity and RNA interference (RNAi) to combat viral infections. Our study underscores the pivotal role ofDrosophilaToll-9 in antiviral immunity, aligning with findings inBombyx mori, where Toll-9 activation upregulates the RNAi componentDicer2. We demonstrate thatDrosophilaToll-9 functions as a pattern recognition receptor (PRR) for double-stranded RNA (dsRNA) duringDrosophila Cvirus (DCV) infection, akin to mammalian TLRs. Toll-9 activation leads to the upregulation of key RNAi components,Dicer2andArgonaute2, and dephosphorylation of AKT triggers apoptosis via induction of proapoptotic genesHidandReaper. This study also reveals that Toll-9 localizes in endosomal compartments where it interacts with dsRNA. These insights enhance our understanding ofDrosophilainnate immune mechanisms, reflecting the evolutionary conservation of immune responses across diverse species and providing impetus for further research into the conserved roles of TLRs across the animal kingdom.
A Habitat Selection Multiverse Reveals Largely Consistent Results Despite a Multitude of Analysis Options
Authors: Marshall Benjamin Michael , Duthie Alexander Bradley
Published: June 2024

Researchers are intrinsically part of the research process. While we may strive for objectivity, there are always judgement calls required during research. When you ask ten researchers to answer the same question with the same dataset, you will likely receive ten different answers. This variation in answers has been linked to several disciplines’ replication crises. Here, we explore whether answers from movement ecology, specifically habitat selection, vary as a result of differing analytical choices. We conducted a multiverse analysis on around 400 synthetic animal movement datasets, exploring a multitude of analysis pathways to determine habitat selection, resulting in approximately half a million unique estimates of selection. By using simulated virtual animals with a known preference, we were able to show which decisions during analysis could lead to more variable estimates of habitat selection. The multiverse revealed that data quantity (i.e., tracking frequency and duration) was more important to obtaining consistent answers than any analysis choice. Overall, the pattern of estimates shows the majority of analysis pathways provide similar final results, particularly for modern analysis methods. The pattern reflects findings from other disciplines, indicating that while movement ecology is not immune to issues of non-replicability stemming from researcher choice, it is also not at any greater risk than other disciplines.
RSG-YOLO: Detection of rice seed germination rate based on enhanced YOLOv8 and multi-scale attention feature fusion
Authors: Li Huikang , Liu Longbao , Li Qi , Liao Juan , Liu Lu , Zhang Yujun , Tang Qixing , Rao Yuan , Gao Yanwei
Published: June 2024

The lack of obvious difference between germinated seeds and non-germinated seeds will cause the low accuracy of detecting rice seed germination rate, remains a challenging issue in the field. In view of this, a new model named Rice Seed Germination-YOLO (RSG-YOLO) is proposed in this paper. This model initially incorporates CSPDenseNet to streamline computational processes while preserving accuracy. Furthermore, the BRA, a dynamic and sparse attention mechanism is integrated to highlight critical features while minimizing redundancy. The third advancement is the employment of a structured feature fusion network, based on GFPN, aiming to reconfigure the original Neck component of YOLOv8, thus enabling efficient feature fusion across varying levels. An additional detection head is introduced, improving detection performance through the integration of variable anchor box scales and the optimization of regression losses. This paper also explores the influence of various attention mechanisms, feature fusion techniques, and detection head architectures on the precision of rice seed germination rate detection. Experimental results indicate that RSG-YOLO achieves a mAP50of 0.981, marking a 4% enhancement over the mAP50of YOLOv8 and setting a new benchmark on the RiceSeedGermination dataset for the detection of rice seed germination rate.
Factors influencing the adoption of health education for Schistosomiasis control in Luangwa, Zambia
Authors: Chinoya Rabecca , Zulu Professor Joseph , Halwiindi Dr Hikabansa , Silumbwe Mr Adam , Maritim Ms Patricia
Published: June 2024

Implementation of health education with mass drug administration is advised so as to induce better decision among various populations through uptake of the health messages. However, this disease remains a problem in Luangwa despite implementation of health education. The study was thus conducted to assess the factors influencing the adoption of health education for schistosomiasis control in Luangwa district of Zambia. It was specifically aimed at assessing the scope of health education and strategies being employed in delivery of health education for schistosomiasis in Luangwa. Additionally, it explored the barriers and facilitators in delivering health education for schistosomiasis in Luangwa and finally revealed perceptions of key stakeholders towards health education messages for schistosomiasis in Luangwa.

This case study qualitatively explored various factors influencing adoption of health education in Luangwa district. Three Key Informant Interviews, six In-depth Interviews and eight Focus Group Discussions were performed with implementers, health educators and recipients of the health education respectively. The recipients of the health education included school going children, members of the community and mothers who attended under-five clinic sessions.

The Factors that were seen to facilitate acceptability of health education include adaptability of health education, community engagement, use of locally acceptable venues to deliver health education, use of teaching aids and learning from others. On the other hand, factors that inhibited acceptability of health education were poor road network, unreached areas, beliefs and myths surrounding bilharzia, the fishing cultural orientation, inadequate income and human resources, busy work schedules and poor access to clean water.

The framework used in the study was found to reveal critical aspects of Health education adoption in Luangwa district. However, there still exists a need to conduct further research as well as focus on improving the structural characteristics as are illustrated in this study.
MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards
Authors: Mosca Ettore , Ulaszewska Marynka , Alavikakhki Zahrasadat , Bellini Edoardo Niccolò , Mannella Valeria , Frigerio Gianfranco , Drago Denise , Andolfo Annapaola
Published: June 2024

Short Structured Abstract

Untargeted metabolomics by mass spectrometry technologies generates huge numbers of metabolite signals, requiring computational analyses for post-acquisition processing and databases for metabolite identification. Web-based data processing solutions frequently include only a part of the entire workflow thus requiring the use of different platforms. The R package “margheRita” enhances fragment matching accuracy and addresses the complete workflow for metabolomic profiling in untargeted studies based on liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS), especially in the case of data-independent acquisition, where all MS/MS spectra are acquired with high quantitative accuracy.

Availability and Implementation

source code and documentation are available athttps://github.com/emosca-cnr/margheRita.

Contact

ettore.mosca@itb.cnr.it,andolfo.annapaola@hsr.it
Metabolic analysis in intact human-derived cerebral organoids by high-resolution magic-angle spinning NMR spectroscopy
Authors: Castilla Bolanos Maria Alejandra , Chinchalongporn Vorapin , Biswas Rajshree Ghosh , Bailey Colleen , Wu Maggie , Soong Ronald , Saleh Fermisk , Simpson Andre , Schuurmans Carol , Near Jamie
Published: June 2024

Human-derived cerebral organoids (COs) are an emerging model system for the study of human neural development and physiology. Here, we describe the assessment of metabolism in human-derived CO’s using high-resolution magic-angle spinning (HR-MAS) NMR spectroscopy. Metabolic changes during development are assessed by studying COs at various stages of maturity. Our results suggest that COs exhibit a metabolic profile similar toin vivohuman brain metabolism, albeit with a few notable metabolic differences.
Comparison of the CDC2-like kinase family across eukaryotes highlights the functional conservation of these unique biological thermometers
Authors: Ogle Rachel A. , Netherton Jacob K. , Robinson Benjamin R. , Heyd Florian , Zhang Xu Dong , Baker Mark A.
Published: June 2024

The family of CDC2-like kinases (CLKs) play a crucial role in regulating alternative splicing (AS), a process fundamental to eukaryotic gene expression and adaptation. Of particular interest, these enzymes exhibit unique responsiveness to minor temperature shifts, enabling them to modulate AS accordingly. Dysregulated CLK expression is linked to a wide variety of human diseases, establishing them as promising therapeutic targets. Despite the importance of CLKs, limited research has explored the genetic and functional diversification of this gene family. This report investigates the evolutionary origins, diversification, and functional implications of CLKs across major eukaryotic lineages through phylogenetic and structural comparisons. Our data demonstrate these kinases are prevalent throughout eukaryotes, with the original gene (which shares orthology to human CLK2), dating back to the Last Eukaryotic Common Ancestor. We identified three key duplication events in vertebrates, highlighting how this gene family has expanded and diversified in complex metazoans. Despite two instances of CLK paralog loss in vertebrate lineages, CLKs remain prevalent throughout metazoans, suggesting they are essential for complex eukaryotic life. Structural comparisons across diverse eukaryotes demonstrate kinase domain conservation, which is in line with their maintained function in AS regulation. While their N-terminal regions vary significantly in amino acid sequence, the function of this domain to regulate phosphorylation of AS factors is conserved, albeit in a species-specific manner. CLKs exhibit unique thermo-sensitive properties across diverse species, challenging conventional enzymatic behaviour. This temperature regulation, mediated by their kinase activation segment, is characterised by increased activity at lower physiological temperatures. The conservation of this structure, and a thermo-sensitive amino acid motif within it, suggests this was an ancient adaptation for responding to environmental cues. Species-specific temperature profiles highlight the adaptive evolution of CLKs, enabling organisms to thrive in diverse environmental conditions including extreme temperatures. Our analysis expands the understanding of CLK biology across diverse eukaryotes and connects insights from model organisms to human biology.
Essentiality of LD-Transpeptidation inAgrobacterium tumefaciens
Authors: Aliashkevich Alena , Guest Thomas , Alvarez Laura , Gilmore Michael C. , Amstutz Jennifer , Mateus André , Schiffthaler Bastian , Ruiz Iñigo , Typas Athanasios , Savitski Mikhail M. , Brown Pamela J. B. , Cava Felipe
Published: June 2024

Peptidoglycan (PG), a mesh-like structure which is the primary component of the bacterial cell wall, is crucial to maintain cell integrity and shape. While most bacteria rely on penicillin binding proteins (PBPs) for crosslinking, some species employ LD-transpeptidases (LDTs). Unlike PBPs, the essentiality and biological functions of LDTs remain largely unclear. The Hyphomicrobiales order of the Alphaproteobacteria, known for their polar growth, have PG which is unusually rich in LD-crosslinks, suggesting that LDTs may play a more significant role in PG synthesis in these bacteria. Here, we investigated LDTs in the plant pathogenAgrobacterium tumefaciensand found that LD-transpeptidation, resulting from at least one of 14 putative LDTs present in this bacterium, is essential for its survival. Notably, a mutant lacking a distinctive group of 7 LDTs which are broadly conserved among the Hyphomicrobiales exhibited reduced LD-crosslinking and tethering of PG to outer membrane β-barrel proteins. Consequently, this mutant suffered severe fitness loss and cell shape rounding, underscoring the critical role played by these Hyphomicrobiales-specific LDTs in maintaining cell wall integrity and promoting elongation. Tn-sequencing screens further revealed non-redundant functions forA. tumefaciensLDTs. Specifically, Hyphomicrobiales-specific LDTs exhibited synthetic genetic interactions with division and cell cycle proteins, and a single LDT from another group. Additionally, our findings demonstrate that strains lacking all LDTs except one displayed distinctive phenotypic profiles and genetic interactions. Collectively, our work emphasizes the critical role of LD-crosslinking inA. tumefacienscell wall integrity and growth and provides insights into the functional specialization of these crosslinking activities.
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Authors: Schulte Douwe , Šiborová Marta , Käll Lukas , Snijder Joost
Published: June 2024

Antibodies are a major component of adaptive immunity against invading pathogens. Here we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in convalescent serum. This approach aims to perform simultaneous antibody sequencing and epitope mapping using a combination of single particle cryo-electron microscopy (cryoEM) and bottom-up proteomics techniques based on mass spectrometry (LC-MS/MS). We evaluate the performance of the deep-learning tool ModelAngelo in determiningde novoantibody sequences directly from reconstructed 3D volumes of antibody-antigen complexes. We demonstrate that while map quality is a critical bottleneck, it is possible to sequence antibody variable domains from cryoEM reconstructions with accuracies of up to 80-90%. While the rate of errors exceeds the typical levels of somatic hypermutation, we show that the ModelAngelo-derived sequences can be used to assign the used V-genes. This provides a functional guide to assemblede novopeptides from LC-MS/MS data more accurately and improves the tolerance to a background of polyclonal antibody sequences. Following this proof-of-principle, we discuss the feasibility and future directions of this approach to characterize antigen-specific antibody repertoires.
Mono-allelic epigenetic regulation of bi-directional silencing of RNA Polymerase II polycistronic transcription initiation inTrypanosoma brucei
Authors: Kieft Rudo , Cliffe Laura , Yan Haidong , Schmitz Robert J. , Hajduk Stephen L. , Sabatini Robert
Published: June 2024

Unique for a eukaryote, protein-coding genes in trypanosomes are arranged in polycistronic units (PTUs). This genome arrangement has led to a model where Pol II transcription of PTUs is unregulated and that changes in gene expression are entirely post-transcriptional. Trypanosoma brucei brucei is unable to infect humans because of its susceptibility to an innate immune complex, trypanosome lytic factor (TLF) in the circulation of humans. The initial step in TLF mediated lysis ofT.b.bruceirequires high affinity haptoglobin/hemoglobin receptor (HpHbR) binding. Here we demonstrate that byin vitroselection with TLF, resistance is obtained in a stepwise process correlating with loss of HpHbR expression at an allelic level. RNA-seq, Pol II ChIP and run-on analysis indicate HpHbR silencing is at the transcriptional level, where loss of Pol II binding at the promoter region specifically shuts down transcription of the HpHbR containing gene cluster and the adjacent opposing gene cluster. Reversible transcriptional silencing of the divergent PTUs correlates with DNA base J modification of the shared promoter region. Therefore, we show that epigenetic mechanisms, including base J modification, are involved in regulating gene expression via Pol II transcription initiation of gene clusters in a mono-allelic fashion. These findings suggest epigenetic chromatin-based regulation of gene expression is deeply conserved among eukaryotes, including early divergent eukaryotes that rely on polycistronic transcription.

IMPORTANCE

The single-cell parasiteTrypanosoma bruceicauses lethal diseases in both humans and livestock.T. bruceiundergoes multiple developmental changes to adapt in different environments during its digenetic life cycle. With protein-coding genes organized as polycistronic transcription and apparent absence of promoter-mediated regulation of transcription initiation, it is believed that developmental gene regulation in trypanosomes is essentially post-transcriptional. In this study, we found reversible Pol II transcriptional silencing of two adjacent polycistronic gene arrays that correlates with the novel DNA base J modification of the shared promoter region. Our findings support epigenetic regulation of Pol II transcription initiation as a viable mechanism of gene expression control inT. brucei. This has implications for our understanding how trypanosomes utilize polycistronic genome organization to regulate gene expression during its life cycle.
NMR structures of small molecules bound to a model of an RNA CUG repeat expansion
Authors: Chen Jonathan L. , Taghavi Amirhossein , Frank Alexander J. , Fountain Matthew A. , Choudhary Shruti , Roy Soma , Childs-Disney Jessica L. , Disney Matthew D.
Published: June 2024

Trinucleotide repeat expansions fold into long, stable hairpins and cause a variety of incurable RNA gain-of-function diseases such as Huntington’s disease, the myotonic dystrophies, and spinocerebellar ataxias. One approach for treating these diseases is to bind small molecules to the structured RNAs. Both Huntington’s disease-like 2 (HDL2) and myotonic dystrophy type 1 (DM1) are caused by a r(CUG) repeat expansion, or r(CUG)exp. The RNA folds into a hairpin structure with a periodic array of 1×1 nucleotide UU loops (5’CUG/3’GUC; where the underlined nucleotides indicate the Us in the internal loop) that sequester various RNA-binding proteins (RBP) and hence the source of its gain-of-function. Here, we report NMR-refined structures of single 5’CUG/3’GUC motifs in complex with three different small molecules, a diguandinobenzoate (1), a derivative of1where the guanidino groups have been exchanged for imidazole (2), and a quinoline with improved drug-like properties (3). These structures were determined using nuclear magnetic resonance (NMR) spectroscopy and simulated annealing with restrained molecular dynamics (MD). Compounds1,2, and3formed stacking and hydrogen bonding interactions with the 5’CUG/3’GUC motif. Compound3also formed van der Waals interactions with the internal loop. The global structure of each RNA-small molecule complexes retains an A-form conformation, while the internal loops are still dynamic but to a lesser extent compared to the unbound form. These results aid our understanding of ligand-RNA interactions and enable structure-based design of small molecules with improved binding affinity for and biological activity against r(CUG)exp. As the first ever reported structures of RNA r(CUG) repeats bound to ligands, these structures can enable virtual screening campaigns combined with machine learning assistedde novodesign.
Molecular Structure and Enzymatic Mechanism of the Human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1
Authors: De Marco Matteo , Rai Sristi Raj , Scietti Luigi , Mattoteia Daiana , Liberi Stefano , Pinnola Alberta , Forneris Federico
Published: June 2024

During biosynthesis, collagen lysine residues undergo extensive post-translational modifications essential for the stability and functions of collagen supramolecular assemblies. In the endoplasmic reticulum, two distinct metal ion dependent enzyme families (i.e., multifunctional lysyl hydroxylases-glucosyltransferases LH/PLODs and galactosyltransferases GLT25D/COLGALT) alternatively operate on collagen lysine side chains ultimately generating the highly conserved α-(1,2)-glucosyl-β-(1,O)-galactosyl-5-hydroxylysine pattern. Malfunctions in the collagen lysine post-translational modification machinery is linked to multiple developmental pathologies as well as extracellular matrix alterations causing enhanced cellular proliferation and invasiveness of several solid tumors, prompting for an in-depth characterization of LH/PLOD and GLT25D/COLGALT enzyme families. Here, we present an integrative molecular study of GLT25D1/COLGALT, highlighting an elongated head-to-head homodimeric assembly characterized by an N-terminal segment of each monomer wrapping around its dimerization partner. Each monomer encompasses two Rossman fold-type domains (GT1 and GT2) separated by an extended linker. Both domains were found capable of binding Mn2+cofactors and UDP-α-galactose donor substrates, resulting in four candidate catalytic sites per dimer. Site-directed mutagenesis and biochemical studies identify the C-terminal GT2 domain as the functional GLT25D1/COLGALT1 catalytic site, highlighting an unprecedented Glu-Asp-Asp motif critical for metal ion binding, and suggesting structural roles for the N-terminal GT1 essential for correct quaternary structure assembly. Conversely, dimerization was not a requirement for GLT25D1/COLGALT1 enzymatic activityin vitro, suggesting that the elongated enzyme homodimer assembly, resembling that of LH/PLOD binding partners, could represent a functional hallmark for correct recognition and successful processing of collagen lysine residues.
A genome resource for the marine annelidPlatynereis dumerilii
Authors: Mutemi Kevin Nzumbi , Simakov Oleg , Pan Leslie , Santangeli Luca , Null Ryan , Handberg-Thorsager Mette , Vellutini Bruno Cossermelli , Peterson Kevin J. , Fromm Bastian , Larsson Tomas , Savage Emily , Lopez Mireia Osuna , Hercog Rajna , Provaznik Jan , Ordoñez-Rueda Diana , Azevedo Nayara , Gazave Eve , Vervoort Michel , Tomancak Pavel , Tan Wenhua , Winkler Sylke , Benes Vladimir , Hui Jerome , Helm Conrad , Özpolat B. Duygu , Arendt Detlev
Published: June 2024

The marine annelidPlatynereis dumeriliiis a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes ofP. dumerilii(laboratory culture reference and a single individual assembly) and of the closely relatedP. massiliensisandP. megalops(single individual assembly) to facilitate comparative genomic approaches and help explorePlatynereisbiology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ∼1.47 Gbp forP. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation (∼3% heterozygosity) within thePlatynereisspecies complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development ofPlatynereisgenomic resources.
VERICIGUAT RESCUES CYCLIC GUANOSINE MONOPHOSPHATE PRODUCTION IN HUMAN AORTIC VASCULAR SMOOTH MUSCLE CELLS AND AUGMENTS VASORELAXATION IN AORTIC RINGS EXPOSED TO HIGH GLUCOSE
Authors: Polhemus David , Almodiel Diego , Harb Tarek , Ziogos Efthymios , Amat-Codina Nuria , Ranek Mark , Santhanam Lakshmi , Gerstenblith Gary , Leucker Thorsten
Published: June 2024

Background

Normal endothelial cell dependent vascular smooth muscle cell function is mediated by nitric oxide (NO), which stimulates soluble guanylyl cyclase (sGC) production of the second messenger, cyclic guanosine monophosphate (cGMP) leading to increased protein kinase G (PKG) activity and vascular smooth muscle relaxation. NO bioavailability is impaired in inflammatory settings, such as high glucose (HG). We examined whether the direct sGC sensitizer/stimulator vericiguat, augments cGMP production in human vascular smooth muscle cells (HVSMC) exposed to high glucose and explored its effect on vasorelaxation.

Methods

Aortic HVSMCs were exposed to HG for 24h. In the treatment group, cells also received 1uM vericiguat for 24h. After incubation, cGMP and PKG activity were measured. Additionally, thoracic murine aortas were exposed to HG or to normal glucose (NG) control. The rings were then placed in an organ chamber bath and dose response curves to increasing doses of acetylcholine (Ach) and sodium nitroprusside were constructed for three groups: control (normal glucose), HG alone, and HG + vericiguat.

Results

HVSMCs exposed to HG produced significantly less cGMP than those exposed to NG. cGMP production in the presence of HG was rescued when treated with 1uM vericiguat. Additionally, PKG activity was impaired in the presence of HG and enzyme activity was restored with vericiguat. In isolated mouse aortic rings, ACh mediated relaxation was impaired following treatment with HG, but was improved when a HG group was treated with vericiguat.

Conclusions

The sGC sensitizer/stimulator vericiguat restored cGMP production and PKG activity in the setting of HG. Vericiguat enhanced ACh-mediated vasorelaxation in the setting of HG. The findings suggest clinical studies are warranted to investigate the potential of sGC sensitization/stimulation as a therapeutic intervention to improve vascular endothelial-dependent function that is impaired in pro-inflammatory settings that are associated with the development of atherosclerotic disease.
In- & Out-Cloning: Plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly
Authors: de Vries Stijn T. , Köbel Tania S. , Sanal Ahmet , Schindler Daniel
Published: June 2024

Golden Gate cloning has become one of the most important DNA assembly strategies. The construction of standardized and reusable part libraries, their assembly into transcription units, and the subsequent assembly of multigene constructs is highly reliable and sustainable. Researchers can quickly construct derivatives of their assemblies or entire pathways, and importantly, the standardization of Golden Gate assemblies is compatible with laboratory automation. Most Golden Gate strategies rely on four nucleotide overhangs generated by commonly used Type IIS enzymes. However, reduction to three nucleotide overhangs allows the use of codons as fusion sites and reduces potential scar sequences. This is particularly important when studying biological functions, as additional nucleotides may alter the structure or stability of the transcribed RNA. To address this issue we use SapI, a Type IIS enzyme generating three nucleotide overhangs, for transcription unit assembly, allowing for codon-based fusion in coding sequences. We created a corresponding plasmid toolbox for basic part generation and transcription unit assembly, a workflow we termIn-Cloning. In-Cloningis downstream compatible with the Modular Cloning standard developed by Sylvestre Marillonnet’s group for standardized assembly of multigene constructs. However, the multigene construct plasmids may not be compatible for use with the model organism of choice. Therefore, we have developed a workflow calledOut-Cloningto rapidly generate Golden Gate acceptor plasmids.Out-Cloninguses standardized plasmid parts that are assembled into Golden Gate acceptor plasmids using flexible linkers. This allows the systematic construction of acceptor plasmids needed to transfer assembled DNA into the organism of interest.
Biogenesis of DNA-carrying extracellular vesicles by the dominant human gut methanogenic archaeon
Authors: Baquero Diana P. , Borrel Guillaume , Gazi Anastasia , Martin-Gallausiaux Camille , Cvirkaite-Krupovic Virginija , Commere Pierre-Henri , Pende Nika , Tachon Stéphane , Sartori-Rupp Anna , Douché Thibaut , Matondo Mariette , Gribaldo Simonetta , Krupovic Mart
Published: June 2024

Extracellular vesicles (EVs) are membrane-bound particles secreted by cells from all domains of life and implicated in a variety of important processes, from intercellular communication to pathogenesis. Here, we characterize EVs produced by the dominant human gut methanogen,Methanobrevibacter smithii, which, unlike most archaea, contains a peptidoglycan cell wall. Using quantitative proteomics, we show thatM. smithiiEVs are enriched in various proteins responsible for chromatin structure, including histones, and DNA repair. Consistently, theM. smithiiEVs carry DNA, with fragments covering the entire cellular chromosome. Notably, the EVs are strongly enriched in extrachromosomal circular DNA (eccDNA) molecules which originate from excision of a 2.9-kb chromosomal fragment and a proviral genome. The eccDNA encodes two of the key methanogenesis enzymes and could boost their expression inside the cells through the gene dosage effect. Furthermore, four of the top ten most abundant EV proteins are implicated in methanogenesis. Cryo-electron tomography (Cryo-ET) suggests that EVs are formed by budding from the cell membrane and are trapped under the cell wall prior to liberation through local disruptions in the cell wall. Collectively, our results reveal parallels with EV biogenesis in bacteria and suggest thatM. smithiiEVs facilitate the export of both cellular and viral DNA as well as key metabolic proteins in the gut environment, with potential impact on methane production.
Proteomic and Metabolomic Profiling of Archaeal Extracellular Vesicles from the Human Gut
Authors: Weinberger Viktoria , Darnhofer Barbara , Mertelj Polona , Stentz Regis , Thapa Himadri B , Jones Emily , Grabmann Gerlinde , Mohammadzadeh Rokhsareh , Shinde Tejus , Juodeikis Rokas , Pernitsch Dominique , Hingerl Kerstin , Zurabishvili Tamara , Kumpitsch Christina , Kuehnast Torben , Kolb Dagmar , Gotts Kathryn , Weichhart Thomas , Köcher Thomas , Köfeler Harald , Carding Simon R. , Schild Stefan , Moissl-Eichinger Christine
Published: June 2024

One potential mechanism for microbiome-host, and microbiome constituents’ interaction and communication involves extracellular vesicles (EVs). Here, for the first time, we report the capability of two M. smithii strains (ALI and GRAZ-2), Candidatus M. intestini, and Methanosphaera stadtmanae, as underrepresented components of the gut microbiome, to produce EVs. Interesting, size, morphology, and composition of AEVs were comparable to bacterial EVs, as indicated by ultrastructure, composition, proteomic and metabolomic analyses; however, EVs were substantially less prevalent in the studied Archaea. When looking at the proteomics more precisely, although AEVs from M. smithii ALI and M. intestini were found to be carrying unique proteins (n=135 and n=30, respectively), the shared proteins in AEVs within this genus (n=229), were mostly adhesins(/like) proteins, or proteins with IG-like domains. One remarkable observation was the uptake of AEVs obtained from Methanosphaera stadtmanae and the studied Methanobrevibacter species by human monocytes and the subsequent IL-8 secretion.
Quantum Interference between Quasi-2D Fermi Surface Sheets in
UTe2
Authors: Weinberger T. I. , Wu Z. , Graf D. E. , Skourski Y. , Cabala A. , Pospíšil J. , Prokleška J. , Haidamak T. , Bastien G. , Sechovský V. , Lonzarich G. G. , Vališka M. , Grosche F. M. , Eaton A. G.
Published: June 2024

UTe2 is a spin-triplet superconductor candidate for which high quality samples with long mean free paths have recently become available, enabling quantum oscillation measurements to probe its Fermi surface and effective carrier masses. It has recently been reported that UTe2 possesses a 3D Fermi surface component []. The distinction between 2D and 3D Fermi surface sections in triplet superconductors can have important implications regarding the topological properties of the superconductivity. Here we report the observation of oscillatory components in the magnetoconductance of UTe2 at high magnetic fields. We find that these oscillations are well described by quantum interference between quasiparticles traversing semiclassical trajectories spanning magnetic breakdown networks. Our observations are consistent with a quasi-2D model of this material’s Fermi surface based on prior dHvA-effect measurements. Our results strongly indicate that UTe2—which exhibits a multitude of complex physical phenomena—possesses a remarkably simple Fermi surface consisting exclusively of two quasi-2D cylindrical sections.

Published by the American Physical Society
2024
Quasi-Isodynamic Stellarators with Low Turbulence as Fusion Reactor Candidates
Authors: Goodman Alan G. , Xanthopoulos Pavlos , Plunk Gabriel G. , Smith Håkan , Nührenberg Carolin , Beidler Craig D. , Henneberg Sophia A. , Roberg-Clark Gareth , Drevlak Michael , Helander Per
Published: June 2024

The stellarator is a type of fusion energy device that—if properly designed—could provide clean, safe, and abundant energy to the grid. To generate this energy, a stellarator must keep a hot mixture of charged particles (known as a plasma) sufficiently confined by using a fully shaped magnetic field. If this is achieved, the heat from fusion reactions within the plasma can be harvested as energy. We present a novel method for designing reactor-relevant stellarator magnetic fields, which combine several key physical properties. These include plasma stability, excellent confinement of the fast-moving particles generated by fusion reactions, and reduction of the turbulence that is known to limit the performance of the most advanced stellarator experiment in the world, Wendelstein 7-X.

Published by the American Physical Society
2024
TomoPyUI: a user-friendly tool for rapid tomography alignment and reconstruction
Authors: Welborn Samuel S. , Preefer Molleigh B. , Nelson Weker Johanna
Published: June 2024

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.
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3-edge X-ray spectroscopy of rhodium and palladium compounds
Authors: Suarez Orduz Hugo Alexander , Bugarin Luca , Heck Sarina-Lena , Dolcet Paolo , Casapu Maria , Grunwaldt Jan-Dierk , Glatzel Pieter
Published: June 2024

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3-edge high-energy-resolution fluorescence-detection X-ray absorption near-edge structure (XANES) spectra for palladium and rhodium compounds are presented, with focus on their electronic structures. The data are compared with transmission XANES spectra recorded at the K-edge. A correlation between the absorption edge energy and the metal ion oxidation state is not observed. Despite the different filling of the 4d orbitals and different local coordination, the Rh and Pd compounds show remarkably similar spectral shapes. Calculation of the density of states and of the L
3-XANES data reproduce the experimental results.
Make it real, make it useful! The impact of AR social experience on brand positivity and information sharing
Authors: Shaheen Riziq , Aljarah Ahmad , Ibrahim Blend , Hazzam Joe , Ghasemi Matina
Published: June 2024

Purpose

This study investigated the impact of the perceived Augmented Reality (AR) social experience of restaurant menus on two types of prosocial behaviors: brand positivity and brand information sharing.

Design/methodology/approach

This study adopts the expectancy-value model as a framework, drawing on the cognitive load, self-determination, and media richness theories. Using a sample of 879 participants from the United States, the research model was tested using structural equation modeling (PLS-SEM).

Findings

The findings indicate that the social experience derived from using AR menus significantly predicts brand positivity and brand information sharing. The perceived usefulness of AR mediates this relationship. Moreover, AR reality congruence acts as a significant mediator between perceived AR social experience and brand positivity but not brand information sharing. The positive relationship between AR social experience, brand positivity, and brand information sharing is sequentially mediated by AR reality congruence and AR usefulness.

Originality/value

This groundbreaking research pioneers a fresh perspective, delving into the impact of AR social experiences on consumers' prosocial behaviors, specifically brand positivity and information sharing. Unravels intricate mechanisms, shedding light on how and under what circumstances AR social experiences foster positive behaviors within the dynamic realm of food services and restaurant settings. This study provides valuable insights for restaurant managers and marketers to leverage AR technology to create engaging and immersive customer-dining experiences, a concept that has not been thoroughly explored in previous studies.
Human social responsibility from challenges to achievements: discursive empowerment of women innovators across organizational borders
Authors: Maier Carmen Daniela
Published: June 2024

Purpose

The paper explains how challenges and achievements of human social responsibility (HSR) are addressed by women innovators across the organizational borders of various industries. More precisely, this qualitative study’s goal is to clarify the empowering roles of discursive strategies employed by Women in Innovation (WIN) organization when communicating about women innovators’ demanding realities and about their collaborative initiatives meant to generate changes related to gender, diversity and intersectionality. The WIN members include women leaders in the innovation space with extensive professional, advisory and international experience.

Design/methodology/approach

The paper proposes an approach that brings together perspectives upon empowerment, perspectives on social, intellectual and symbolic capital and a social semiotic perspective on discourse. The WIN blogs are investigated to facilitate: first, an understanding of how discursive strategies recontextualize the women innovators’ identities and actions and second, an understanding of how these discursive strategies contribute to sustaining and legitimizing dynamic social capital while building new intellectual capital and symbolic capital across organizational borders.

Findings

The WIN discourses both disclose contemporary gender, diversity and intersectionality challenges across organizational borders as well as promote ways of breaking the barriers that prevent women innovators from thriving. The discursive strategies recontextualize women innovators as resourceful social actors with multiple identities. Their social actions are discursively recontextualized as collaborative challenge-solving enterprises. These recurrent discursive strategies accomplish empowering functions at individual, relational and collective well-being levels through materializing new intellectual and symbolic capital when revealing the manifestations of bridging and bonding social capital.

Originality/value

This paper provides a novel integrative approach to explaining in detail the complexity of empowering discourses at several levels of analytical delicacy. It responds to the needs of HSR research and practice for gaining more insights into the challenges of communicating effectively about how to create a more socially responsible world.
Seeking relief or reward? A utilitarian-hedonic journey perspective on escapism
Authors: Ponsignon Frederic , Bauman Matthew , Lunardo Renaud
Published: June 2024

Purpose

This paper aims to explores the escapist journey that consumers embark on to reduce self-discrepancy, from the motivation to satisfy personal goals to the fulfilment of these goals. Escapism is a powerful concept for understanding why and how people resolve a perceived self-discrepancy. Previous research has provided rich and diverse insights into the motivations and goals, experience contexts and outcomes that are associated with escapism. However, these notions have been explored in an independent, piecemeal fashion that has hampered the development of cohesive theoretical foundations.

Design/methodology/approach

The authors conduct a qualitative study, relying on 33 journeys derived from 20 in-depth interviews, to understand and explain how escapism is initiated, formed and relived.

Findings

The findings document the existence of a predominantly utilitarian and a predominantly hedonic model, articulating why and how consumers pursue distinctly different types of escapist journeys. Utilitarian escapism is primarily concerned with the need to avoid negative emotional states, prompting consumers to decide impulsively to engage into routinised experience contexts to find relief. Hedonic escapism is primarily concerned with the desire to achieve positive emotional states. It involves lengthy and thoughtful anticipation, promotes consumers to pursue experiences in out of the ordinary contexts, and is realised when consumers obtain reward.

Research limitations/implications

This study’s contributions present significant opportunities for further knowledge development.

Practical implications

The research findings have substantial practical ramifications for industry.

Social implications

Understanding people’s needs to avoid the stress of everyday life (i.e. utilitarian escapism) and their desires to seek out excitement and pleasure (i.e. hedonic escapism) has important societal implications.

Originality/value

This research provides a robust theoretical foundation for escapism, one that is applicable across multiple settings. Findings are anchored within existing theory to articulate the notions of utilitarian and hedonic escapism, explaining why and how consumers engage in markedly different escapist journeys.
Examining the influence of international organizations in globalizing education policy in Kuwait: a qualitative study
Authors: Alazmi Ayeshah Ahmed
Published: June 2024

Purpose

Globalization, and more specifically international organizations, has had a major effect upon national education systems worldwide. Understandably, the academic literature covering this phenomenon has expanded at a prolific rate. This study contributes to this body of knowledge by examining how the international organizations affect global education policy, as seen via the lens of a Kuwaiti context.

Design/methodology/approach

The study employed a qualitative data collection approach using semi-structured interviews with 27 key figures involved in policymaking at national educational institutions in Kuwait. Each interview was coded for recurring themes.

Findings

Three main themes emerged from data analysis: (1) policy adoption and reformulation, (2) curriculum and pedagogical changes and (3) evaluation and accountability mechanisms. This study’s findings demonstrated that globalization processes and international organizations have profoundly affected Kuwait’s national educational policies.

Originality/value

This research forms the foundation for further investigations into how international organizations have affected national and subnational educational decision-making and reforms.
Children’s rights and agency: promoting participative capabilities through self-directed education
Authors: DeCesare Tony
Published: June 2024

Purpose

The purpose of this paper is to connect emerging conceptions of childhood in the capabilities approach (CA) literature to models of self-directed education in hopes of articulating and defending the educational goal of promoting children's participative capabilities.

Design/methodology/approach

This paper offers a conceptual and theoretical exploration of childhood from a CA perspective and seeks to connect it to self-directed education.

Findings

The author argues that self-directed education, especially democratic schools in the model of the Sudbury Valley School, is well-suited to the task of promoting children's participative capabilities and that people should, therefore, consider this the kind of education to which children have a right.

Originality/value

By applying the CA framework to self-directed education, this paper makes an original contribution in two directions: first, it offers a new set of theoretical tools for self-directed education scholars; second, it offers capabilities theorists interested in promoting children's participative capabilities with a new model of education.