bluuebunny/crossref_metadata_2025 huggingface dataset:
Massively parallel mutant selection identifies genetic determinants ofPseudomonas aeruginosacolonization ofDrosophila melanogaster
Authors: Miles Jessica , Lozano Gabriel L. , Rajendhran Jeyaprakash , Stabb Eric V. , Handelsman Jo , Broderick Nichole A.
Published: November 2023

Pseudomonas aeruginosais recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing (Tn-Seq, also known as INSeq) to identify genes inP. aeruginosathat contribute to fitness during colonization ofDrosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies ofP. aeruginosaidentified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen inDrosophila, demonstrate the power of Tn-Seq in the fly model system and advance existing knowledge of intestinal pathogenesis byD. melanogaster,revealing bacterial colonization determinants that contribute to a comprehensive portrait ofP.aeruginosalifestyles across habitats.

Importance

Drosophila melanogasteris a powerful model for understanding host-pathogen interactions. Research with this system has yielded notable insights into mechanisms of host immunity and defense, many of which emerged from analysis of bacterial mutants defective for well-characterized virulence factors. These foundational studies – and advances in high-throughput sequencing of transposon mutants – support unbiased screens of bacterial mutants in the fly. To investigate mechanisms of host-pathogen interplay and exploit the tractability of this model host, we used a high-throughput, genome-wide mutant analysis to find genes that enable a pathogen,P. aeruginosa, to colonize the fly. Our analysis reveals critical mediators ofP. aeruginosaestablishment in its host, some of which are required across fly and mouse systems. These findings demonstrate the utility of massively parallel mutant analysis and provide a platform for aligning the fly toolkit with comprehensive bacterial genomics.
ICARUS v3, a massively scalable web server for single cell RNA-seq analysis of millions of cells
Authors: Jiang Andrew , Snell Russell G , Lehnert Klaus
Published: November 2023

In recent years, improvements in throughput of single cell RNA-seq have resulted in a significant increase in the number of cells profiled. The generation of single cell RNA-seq datasets comprising >1 million cells is becoming increasingly common, giving rise to demands for more efficient computational workflows. Here, we present an update to our single cell RNA-seq analysis web server application, ICARUS (available athttps://launch.icarus-scrnaseq.cloud.edu.au/) that allows effective analysis of large-scale single cell RNA-seq datasets. ICARUS v3 utilises the geometric cell sketching method to subsample cells from the overall dataset for dimensionality reduction and clustering that can be then projected to the large dataset. We then extend this functionality to select a representative subset of cells for downstream data analysis applications including differential expression analysis, gene co-expression network construction, gene regulatory network construction, trajectory analysis, cell-cell communication inference and cell cluster associations to GWAS traits. We demonstrate analysis of single cell RNA-seq datasets using ICARUS v3 of 1.3 million cells completed within the hour.
Identification of a novel papillomavirus from a New Zealand fur seal (Arctocephalus forsteri) with oral papilloma-like lesions
Authors: Mifsud Jonathon C.O. , Hall Jane , Van Brussel Kate , Rose Karrie , Parry Rhys H. , Holmes Edward C. , Harvey Erin
Published: November 2023

Despite being the predominant seal species in the Australian-New Zealand region and serving as a key indicator of marine environmental health, little is known about infectious diseases in New Zealand fur seals (Long-nosed fur seal;Arctocephalus forsteri). Several papillomaviruses have been identified in earless seals and sea lions, with the latter linked to cutaneous plaques and invasive squamous cell carcinoma. To date, no papillomaviruses have been reported in fur seals. We used traditional veterinary diagnostic techniques and metatranscriptomic sequencing of tissue samples to investigate the virome of New Zealand fur seals. We identified a novel papillomavirus, provisionally termed Arctocephalus forsteri papillomavirus 1 (AfPV1) in an animal with clinically and histologically identified oral papilloma-like lesions. RT-PCR confirmed the presence of AfPV1 only in oral papilloma samples from the affected individual. Phylogenetic analysis of the complete 7,926 bp genome of AfPV1 revealed that it clustered with taupapillomaviruses found in related Carnivora species. In addition, we identified the partial genome of a novel Gammaherpesvirus, Arctocephalus forsteri gammaherpesvirus 1 (AfGHV1), in a different individual without pathological evidence of viral infection. These findings highlight the need for further research into the disease associations and impact of undiagnosed and novel viruses on New Zealand fur seals.
“Comparative Analysis of Ovarian Transcriptome Changes Across Gestational Stages in Kari Sheep”
Authors: Ali Haidar , Ahmad Sohail
Published: November 2023

This study aimed to investigate the genetic determinants of gestation length in Kari sheep, employing RNA-Seq technology. Employing a comprehensive whole transcriptome analysis, we sought to pinpoint differentially expressed genes (DEGs) while also delving into gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway assessments. The analysis revealed the identification of a total of 19,546 genes expressed in ovary. While comparing the transcriptomes of Kari sheep with Balkhi, yielding 976 DEGs (p < 0.05, Log2fc>1, <-1). Notably, among these DEGs, an upregulation of genes was observed associated with Ubiquitin-protein transferase activity, such asCNOT4, RC3H1, andXIAP. Concurrently, DEGs likeNFAT5, EPAS1, ZNF644, RBPJ, andFOXP2exhibited associations with RNA polymerase II core promoter proximal region sequence-specific DNA binding. Conversely, downregulated genes, includingEEA1, CNOT4, FGD4, MBNL1, ZRANB2, REV3L, XIAP, ATP13A3, RPAP2, FOXP2, and ADAMTS6, were implicated in the mRNA surveillance pathway. In addition, several Gene Ontology terms, such as GO:0001228 (transcriptional activator activity) and GO:0004842, along with GO:0000978 (transcriptional activator activity), were linked to the DEGs. KEGG pathways, including “Glycosaminoglycan biosynthesis - chondroitin sulfate/dermatan sulfate” (KEGG:532) and “basal cell carcinoma” (KEGG:5217), were associated with our findings. Our principal component analysis (PCA) demonstrated a cohesive clustering of gene expression profiles among the four samples, with subtle distinctions. Protein-protein interaction (PPI) analysis indicated the functional relationships among the DEGs. Notably, genes such asABHD16BandNPBWR2exhibited strong co-expression among the down-regulated DEGs, whileDNAH7/TBC1D31andMBNL1/NOVA1displayed prominent co-expression among the up-regulated DEGs. Consequently, our study offers a comprehensive understanding of Kari sheep genetics and the pivotal genes involved in gestation length determinants. These findings carry significant genetic implications, enhancing genetic resources, furthering reproductive biology comprehension, and contributing to the advancement of sustainable sheep farming practices.
A DNA condensation code for linker histones
Authors: Watson Matthew , Sabirova Dilyara , Hardy Megan C. , Pan Yuming , Yates Henry , Wright Charlotte J. , Chan W. H. , Destan Ebru , Stott Katherine
Published: November 2023

Linker histones play an essential role in chromatin packaging by facilitating compaction of the 11-nm fibre of nucleosomal “beads on a string”. The result is a heterogeneous condensed state with local properties that range from dynamic, irregular and liquid-like, to stable and regular structures (the 30-nm fibre), which in turn impact chromatin-dependent activities at a fundamental level. The properties of the condensed state depend on the type of linker histone, particularly on the highly disordered C-terminal tail, which is the most variable region of the protein, both between species, and within the various subtypes and cell-type specific variants of a given organism. We have developed anin-vitromodel system comprising linker histone tail and linker DNA, which although very minimal, displays surprisingly complex behaviour, and is sufficient to model the known states of linker-histone-condensed chromatin: disordered “fuzzy” complexes (“open” chromatin), dense liquid-like assemblies (dynamic condensates) and higher-order structures (organised 30-nm fibres). A crucial advantage of such a simple model is that it allows the study of the various condensed states by NMR, CD and scattering methods. Moreover, it allows capture of the thermodynamics underpinning the transitions between states through calorimetry. We have leveraged this to rationalise the distinct condensing properties of linker histone subtypes and variants across species that are encoded by the amino acid content of their C-terminal tails. Three properties emerge as key to defining the condensed state: charge density, lysine/arginine ratio, and proline-free regions, and we evaluate each separately using a strategic mutagenesis approach.
Modelling low-dimensional interacting brain networks reveals organising principle in human cognition
Authors: Sanz Perl Yonatan , Geli Sebastian , Pérez-Ordoyo Eider , Zonca Lou , Idesis Sebastian , Vohryzek Jakub , Jirsa Viktor K. , Kringelbach Morten L. , Tagliazucchi Enzo , Deco Gustavo
Published: November 2023

The discovery of resting state networks shifted the focus from the role of local regions in cognitive tasks to the ongoing spontaneous dynamics in global networks. Recently, efforts have been invested to reduce the complexity of brain activity recordings through the application of nonlinear dimensionality reduction algorithms. Here, we investigate how the interaction between these networks emerges as an organising principle in human cognition. We combine deep variational auto-encoders with computational modelling to construct a dynamical model of brain networks fitted to the whole-brain dynamics measured with functional magnetic resonance imaging (fMRI). Crucially, this allows us to infer the interaction between these networks in resting state and 7 different cognitive tasks by determining the effective functional connectivity between networks. We found a high flexible reconfiguration of task-driven network interaction patterns and we demonstrate that can be used to classify different cognitive tasks. Importantly, compared to using all the nodes in a parcellation, we obtain better results by modelling the dynamics of interacting networks in both model and classification performance. These findings show the key causal role of manifolds as a fundamental organising principle of brain function, providing evidence that interacting networks are the computational engines brain during cognitive tasks.
Excitatory neurons in stratum radiatum provide an alternative pathway for excitation flow that escapes perisomatic inhibition
Authors: Lebedeva Julia , Jappy David , Nasretdinov Azat , Vazetdinova Alina , Krut’ Viktoria , Sokolov Rostislav , Dobryakova Yulia , Eliava Marina , Grinevich Valery , Rozov Andrei
Published: November 2023

For over half a century, it has been postulated that the internal excitatory circuit in the hippocampus consists of three relay stations. Excitation arrives from the entorhinal cortex to the DG granule cells, is transmitted through the mossy fibers to CA3 pyramidal cells, and is then transmitted through Schaffer collaterals to CA1 pyramidal neurons. In all three structures (DG, CA3 and CA1), the activity of the excitatory neurons involved in the synaptic transmission of excitation are under the control of inhibitory basket neurons that are recruited into network activity via feed-forward and feed-back excitation. However, in the late 90s “stratum radiatum giant cells” were described as a novel type of neuron with the anatomical features of excitatory cells. Since then, the role of these cells in the hippocampal circuitry has not been well understood. Here, using optogenetic and electrophysiological techniques we characterized the functional location of these neurons within the hippocampal network. We show that: (i) the main excitatory drive to giant excitatory neurons in stratum radiatum (ExNR) comes via Schaffer collaterals; (ii) within the CA1 field, ExNRare not directly connected with local pyramidal cells, but provide massive and efficient excitatory input to parvalbumin positive (PV+) interneurons; (iii) ExNRare reciprocally innervated by bistratified cells, but not inhibited by backet interneurons; (iv) the efficiency of ExNRexcitation to PV+ interneurons is sufficient for a single ExNRaction potential to trigger massive inhibition of downstream CA1 pyramidal cells. Taken together, our data shows that ExNRconstitute an alternative pathway of excitation for CA1 interneurons that avoids the burden of perisomatic inhibition.
Roles for CEP170 in cilia function and dynein-2 assembly
Authors: Weijman Johannes F , Vuolo Laura , Shak Caroline , Pugnetti Anna , Mukhopadhyay Aakash G , Hodgson Lorna R , Heesom Kate J , Roberts Anthony J , Stephens David J
Published: November 2023

Primary cilia are essential eukaryotic organelles required for signalling and secretion. Dynein-2 is a microtubule-motor protein complex and is required for ciliogenesis via its role in facilitating retrograde intraflagellar transport from the cilia tip to the cell body. Dynein-2 must be assembled and loaded onto IFT-trains for entry into cilia for this process to occur but how dynein-2 is assembled at the base and how it is recycled back into a cilium remain poorly understood. Here, we identify Centrosomal Protein of 170 kDa (CEP170) as a dynein-2 interacting protein. We show that loss of CEP170 perturbs intraflagellar transport, Hedgehog signalling, and alters the stability of dynein-2 holoenzyme complex. Together, our data indicate a role for CEP170 in supporting cilia function and dynein-2 assembly.

Intraflagellar transport is required for the function of primary cilia. In this work, we show that Centrosomal Protein 170 (CEP170) interacts with the IFT motor dynein-2 and loss of CEP170 causes defects in dynein-2 assembly and cilia function.
Fish Playpens – Method for raising individual juvenile zebrafish on a recirculating system for studies requiring repeated measures
Authors: Moll Tabea O.C. , Farber Steven A.
Published: November 2023

Even though many experimental approaches benefit from tracking individual larval animals, there is yet to be a commercial zebrafish rack system designed to accomplish this task. Thus, we invented playpens, an acrylic and screen container, to raise 12 individual zebrafish juveniles per standard 10 L tank on an existing recirculating fish system. During a week-long experiment, fish raised in playpens grow to the same size as conventionally raised juveniles.
Peripheral gating of pain by glial endozepine
Authors: Li Xinmeng , Prudente Arthur Silveira , Prato Vincenzo , Guo Xianchuan , Hao Han , Jones Frederick , Figoli Sofia , Mullen Pierce , Wang Yujin , Tonnello Raquel , Lee Sang Hoon , Shah Shihab , Maffei Benito , Berta Temugin , Du Xiaona , Gamper Nikita
Published: November 2023

We report that diazepam binding inhibitor (DBI) is a glial messenger mediating satellite glia-sensory neuron crosstalk in the dorsal root ganglion (DRG). DBI is highly and specifically expressed in satellite glia cells (SGCs) of mice, rat and human, but not in sensory neurons or other DRG-resident cells. Knockdown of DBI results in a robust mechanical hypersensitivity without significant effects on other sensory modalities.In vivooverexpression of DBI in SGCs reduces sensitivity to mechanical stimulation and alleviates mechanical allodynia in neuropathic and inflammatory pain models. We further show that DBI acts as a partial agonist and positive allosteric modulator at the neuronal GABAAreceptors, particularly strongly effecting those with a high-affinity benzodiazepine binding site. Such receptors are selectively expressed by a subpopulation of mechanosensitive DRG neurons and these are also more enwrapped with DBI-expressing glia, as compared to other DRG neurons, suggesting a mechanism for specific effect of DBI on mechanosensation. These findings identified a new, peripheral neuron-glia communication mechanism modulating pain signalling, which can be targeted therapeutically.
Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4
Authors: Yuan Meng , Peng Linghang , Huang Deli , Gavin Amanda , Luan Fangkun , Tran Jenny , Feng Ziqi , Zhu Xueyong , Matteson Jeanne , Wilson Ian A. , Nemazee David
Published: November 2023

Endolysosomal exonucleases PLD3 and PLD4 (phospholipases D3 and D4) are associated with autoinflammatory and autoimmune diseases. We report structures of these enzymes, and the molecular basis of their catalysis. The structures reveal an intra-chain dimer topology forming a basic active site at the interface. Like other PLD superfamily members, PLD3 and PLD4 carry HxKxxxxD/E motifs and participate in phosphodiester-bond cleavage. The enzymes digest ssDNA and ssRNA in a 5′-to-3′ manner and are blocked by 5′-phosphorylation. We captured structures in apo, intermediate, and product states and revealed a ‘link-and-release’ two-step catalysis. We also unexpectedly demonstrated phosphatase activity via a covalent 3’- phosphistidine intermediate. PLD4 contains an extra hydrophobic clamp that stabilizes substrate and could affect oligonucleotide substrate preference and product release. Biochemical and structural analysis of disease-associated mutants of PLD3/4 demonstrated reduced enzyme activity or thermostability and the possible basis for disease association. Furthermore, these findings provide insight into therapeutic design.
Combining behavior and mechanics approaches reveals the dynamics of animal impacts in mantis shrimp (Stomatopoda)
Authors: Green P.A.
Published: November 2023

Animals deliver and withstand physical impacts in diverse behavioral contexts, from competing rams clashing their antlers together to archerfish impacting prey with jets of water. Though the ability of animals to withstand impact has generally been studied by focusing on morphology, behaviors may also influence impact resistance. Mantis shrimp exchange high-force strikes on each other’s coiled, armored telsons (tailplates) during contests over territory. Prior work has shown that telson morphology has high impact resistance. I hypothesized that the behavior of coiling the telson also contributes to impact energy dissipation. By measuring impact dynamics from high-speed videos of strikes exchanged during contests between freely-moving animals, I found that over 20% more impact energy was dissipated as compared to a prior study that focused solely on morphology. This increase is likely due to behavior: because the telson is lifted off the substrate, the entire body flexes after contact, dissipating more energy than exoskeletal morphology does on its own. While variation in the degree of telson coil did not affect energy dissipation, higher velocity strikes resulted in greater energy dissipation, suggesting striking individuals may vary their behavior to affect impacts. Overall, these findings show that analysis of both behavior and morphology is crucial to understanding impact resistance, and suggest future research on the evolution of structure and function under the selective pressure of biological impacts.

Summary statement

Freely competing mantis shrimp dissipated over 90% of the energy of high-force strikes by raising their impact-resistant tailplates off the substrate; faster strikes led to greater energy dissipation.
Vaccination of cattle with a virus-vectored vaccine against a major membrane protein ofMycobacterium a. subsp.paratuberculosiselicits CD8 cytotoxic T cells that kill intracellular bacteria
Authors: Mahmoud Asmaa H. , Abdellrazeq Gaber S. , Franceschi Valentina , Schneider David A. , Bannantine John P. , Fry Lindsay M. , Hulubei Victoria , De Matteis Giovanna , Park Kun Taek , Davis William C. , Donofrio Gaetano
Published: November 2023

Infection of cattle withMycobacterium a. subsp.Paratuberculosis (Map), the causative agent of paratuberculosis, induces an immune response directed toward a 35 kD major membrane protein (MMP) ofMap. CD8 cytotoxic T cells (CTL) are elicited when peripheral blood mononuclear cells from healthy cattle are incubated ex vivo with antigen-presenting cells (APC) primed with bacterial recombinant MMP. Ex vivo development of CTL was MHC-restricted and required the presence of both CD4 and CD8 T cells. The geneMAP2121c,encoding MMP, was modified to express a modified form of MMP (p35NN) in a mammalian cell line, also capable of eliciting an ex vivo CTL response. In the present study, the modified gene for p35NN was placed into a BoHV4 vector to determine the potential use of BoHV-4AΔTK-p35NN as a peptide-based vaccine. Subcutaneous vaccination of healthy cattle with BoHV-4AΔTK-p35NN elicited a CTL recall response, as detected ex vivo. Further studies are warranted to conduct a challenge study to determine if CD8 CTL elicited by vaccination with BoHV-4AΔTK-p35NN prevents the establishment of a persistent infection byMap.
The effect of ciprofloxacin and gentamicin on wound healing inex vivosheep cornea model
Authors: Okurowska K. , Suarez D. R. Manrique , Karunakaran E.
Published: November 2023

Purpose

Our objective was to assess the efficacy of anex vivosheep corneal model as an alternative for live animal testing in screening drug cytotoxicity. In pursuit of this goal, we investigated the impact of two commonly used topical antibiotics, ciprofloxacin and gentamicin, on wound healing. Furthermore, we examined different antibiotic dosages and dosing regimens to understand their effects comprehensively.

Methods

The epithelium onex vivo sheep corneas was removed with a scalpel, and the area was treated with ciprofloxacin (0.1, 0.3, and 1 mg mL-1), gentamicin (0.25, 1, and 3 mg mL-1), or phosphate-buffered saline (control). The corneas were exposed to treatments continuously or twice daily for ten minutes. Wound closure was observed by fluorescein retention and histological staining.

Results

Untreated corneas healed within 41 hours. Continuous exposure to both ciprofloxacin and gentamicin significantly reduced the corneal healing ability in a time- and concentration-dependent manner. Overall, ciprofloxacin was found to be more toxic than gentamycin. However, this model showed that the corneal epithelium could heal effectively when both antibiotics were administered intermittently.

Conclusion

Ciprofloxacin demonstrated greater inhibition of wound healing compared to gentamicin, aligning within vivostudies. The administration of drops several times daily mitigated the toxic effects of antibiotics. Theex vivosheep wound healing model holds promise as an alternative approach toin vivotoxicity testing, enabling the swift evaluation of novel antimicrobial treatments and eye drop additives.
Phenotype projections accelerate biobank-scale GWAS
Authors: Zietz Michael , Gisladottir Undina , Brown Kathleen LaRow , Tatonetti Nicholas P.
Published: November 2023

Understanding the genetic basis of complex disease is a critical research goal due to the immense, worldwide burden of these diseases. Pan-biobank genome-wide association studies (GWAS) provide a powerful resource in complex disease genetics, generating shareable summary statistics on thousands of phenotypes. Biobank-scale GWAS have two notable limitations: they are resource-intensive to compute and do not inform about hand-crafted phenotype definitions, which are often more relevant to study. Here we present Indirect GWAS, a summary-statistic-based method that addresses these limitations. Indirect GWAS computes GWAS statistics for any phenotype defined as a linear combination of other phenotypes. Our method can reduce runtime by an order of magnitude for large pan-biobank GWAS, and it enables ultra-rapid (roughly one minute) GWAS on hand-crafted phenotype definitions using only summary statistics. Overall, this method advances complex disease research by facilitating more accessible and cost-effective genetic studies using large observational data.
MaUGT79confers drought tolerance by regulating scopolin biosynthesis in plants
Authors: Duan Zhen , Wu Fan , Yan Qi , Wang Shengsheng , Wang Yimeng , Jones Chris Stephen , Zhou Pei , Zhang Caibin , Zhang Jiyu
Published: November 2023

The coumarin scopoletin and its glycosylated form scopolin constitute a vast class of natural products that are considered to be high-value compounds, distributed widely in the plant kingdom, they help plants adapt to environmental stresses. However, the underlying molecular mechanism of how scopolin is involved in the regulation of plant drought tolerance remains largely unexplored. Here, UDP-glycosyltransferase 79 (MaUGT79) was genetically mapped as the target gene by bulk segregant analysis sequencing (BSA-seq) from twoMelilotus albusnear-isogenic lines (NILs). MaUGT79 exhibits glucosyltransferase activity toward scopoletin. The expression ofMaUGT79is induced by drought stress and it was found to mediate scopolin accumulation and reactive oxygen species (ROS) scavenging under drought stress. Moreover, the transcription ofMaUGT79was demonstrated to be directly and positively regulated by MaMYB4, which is a key integrator of both scopolin biosynthesis and drought tolerance. Collectively, this study reveals that MaMYB4 is a positive regulator in drought stress by targeting theMaUGT79promoter and activating its expression to coordinately mediate scopolin biosynthesis and drought tolerance, providing insights into the regulatory mechanism for plant growth adaption to environmental changes through accumulation of scopolin.
Acidic media promotes quiescence entry inSaccharomyces cerevisiae
Authors: Greenlaw Alison C. , Tsukiyama Toshio
Published: November 2023

Quiescence is a conserved cellular state wherein cells cease proliferation and remain poised to re-enter the cell cycle when conditions are appropriate. Budding yeast is a powerful model for studying cellular quiescence. In this work, we demonstrate that the pH of the YPD media strongly affects quiescence entry efficiency inSaccharomyces cerevisiae. Adjusting media pH to 5.5 significantly improves quiescence entry efficiency compared to unadjusted YPD media. Thermotolerance of the produced quiescence yeast are similar, suggesting the media pH influences the quantity of quiescent cells more than quality of quiescence reached.
Contiguous and complete assemblies ofBlastocystisgut microbiome-associated protists reveal evolutionary diversification to host ecology
Authors: Lind Abigail L. , McDonald Nathan A. , Gerrick Elias R. , Bhatt Ami S. , Pollard Katherine S.
Published: November 2023

Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition ofBlastocystisfrom its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure acrossBlastocystis.Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity ofBlastocystis,including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process inBlastocystisthat has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within theBlastocystisgenus, indicating different lineages ofBlastocystishave varied ecological roles in the host gut.
BRCA2 stabilises RAD51 and DMC1 nucleoprotein filaments through a conserved interaction mode
Authors: Dunce James M. , Davies Owen R.
Published: November 2023

BRCA2 is essential for DNA repair by homologous recombination in mitosis and meiosis. It interacts with recombinases RAD51 and DMC1 to facilitate the formation of nucleoprotein filaments on resected DNA ends that catalyse recombination-mediated repair. BRCA2’s BRC repeats bind and disrupt RAD51 and DMC1 filaments, whereas its PhePP motifs binds to recombinases in a manner that stabilises their nucleoprotein filaments. However, the mechanism of filament stabilisation has hitherto remained unknown. Here, we report the crystal structure of a BRCA2-DMC1 complex, revealing how PhePP motifs bind to recombinases. This novel mode of interaction is conserved for RAD51 and DMC1, which selectively bind to BRCA2’s two distinct PhePP motifs. In both cases, BRCA2 PhePP motifs enhance the stability of nucleoprotein filaments, protecting them from BRC-mediated disruption. Hence, we report the structural basis of how BRCA2’s PhePP motifs stabilise RAD51 and DMC1 nucleoprotein filaments for their essential roles in mitotic and meiotic recombination.
Sub-chronic peripheral CB1R inhibition enhances cognitive performance and induces hippocampal synaptic plasticity changes in naïve mice
Authors: Bergadà-Martínez Araceli , de los Reyes-Ramírez Lucía , Martínez-Torres Sara , Gallego Irene Martínez- , Maldonado Rafael , Rodríguez-Moreno Antonio , Ozaita Andrés
Published: November 2023

Background and Purpose

The peripheral contribution to brain function and cognitive performance is far from understood. Cannabinoid type-1 receptor (CB1R) is classically pictured in the central nervous system to have such a role. We previously demonstrated a novel mechanism where the acute peripheral CB1R inhibition in mice prolongs memory persistence. Here, we take advance of the repeated exposure to the peripherally-restricted CB1R antagonist to further reveal cognitive improvements and the hippocampal mechanisms involved.

Experimental Approach

We evaluated in young adult male and female mice the behavioural consequences of a sub-chronic treatment with AM6545. Moreover, an unbiased transcriptomic analysis, as well as electrophysiological and biochemical studies, were performed in the hippocampus of treated mice to elucidate the central cellular and molecular consequences of such peripheral approach.

Key Results

Sub-chronic inhibition of peripheral CB1R with AM6545 resulted in enhanced memory in low and high arousal conditions. Moreover, executive function was facilitated after repeated AM6545 administration, further strengthening the cognitive improving properties of peripheral CB1R inhibition. Transcriptional analysis of hippocampal synaptoneurosomes from treated male and female mice revealed a sex-dependent modulation of synaptic transcripts by AM6545. Notably, AM6545 occluded long-term potentiation in CA3-CA1 synapses while enhancing input-output relation. This was accompanied by an increase in the hippocampal expression ofBdnfandNgf.

Conclusion and Implications

Our results show that peripheral CB1R inhibition contributes to the modulation of memory persistence, executive function, and hippocampal synaptic plasticity in mice, further indicating that peripheral CB1R could act as a target for a novel class of nootropic compounds.

What is already known?

- Acute peripheral CB1R inhibition enhances object-recognition memory persistence in mice.

- Such enhancement occurs through a noradrenergic mechanism involving the vagus nerve.

What does this study add?

- Peripheral CB1R inhibition modifies synaptoneurosomal transcriptome in the hippocampus of mice.

- No tolerance and no side effects were observed after peripheral CB1R inhibition.

What is the clinical significance?

- Peripheral CB1R inhibition may function as a novel strategy for cognitive improvement.
“You cannot rely on bank loans to expand your business”: aversion to formal credit among female micro-entrepreneurs in Ghana
Authors: Ackah Charles , Torvikey Gertrude Dzifa , Obeng Adomaa Faustina , Asante Kofi Takyi
Published: November 2023

Purpose

The marginalisation of female entrepreneurs in accessing credit is well documented. Yet, how female entrepreneurs navigate through the marginalisation to gain funding is under-explored.

Design/methodology/approach

The authors address this gap using qualitative data from 30 female entrepreneurs in three neighbourhoods with varying socio-economic characteristics in Ghana's capital, Accra.

Findings

The authors find a marked aversion to bank loans among respondents. Consequently, they nurtured trust in their social circles in order to facilitate access to informal credit from internal (e.g. family and friends) and external (e.g. trade credit, associations and religious organisations) sources. This aversion to loans from formal financial institutions (FFIs) had a socio-cultural aspect, including cumbersome application procedures, a deep-rooted fear of the social consequences of defaulting and religious prohibition against interest payment for Islamic traders.

Social implications

This paper shows that providing formal access to credit is not enough to support women's entrepreneurship if the socio-cultural factors inhibiting women's access to credit from FFIs are not addressed.

Originality/value

The findings suggest that trust is an important factor that bridges the gap in female entrepreneurs' access to funding given their heavy reliance on informal sources of funding.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-02-2023-0090
The formation of municipal risk management: a comparison of seven cities
Authors: Sippola Kari , Pellinen Jukka , Rautiainen Antti , Mättö Toni , Voutilainen Vesa
Published: November 2023

Purpose

This study aims to explore the formation of municipal risk management (RM) and the reasons for the differences of RM practices between the seven biggest cities in Finland.

Design/methodology/approach

The empirical data of this comparative qualitative case study comprises 33 interviews conducted with municipal managers. Supplementary material includes documentary material on municipal rules governing RM as well as annual reports and risk tools used in the municipalities.

Findings

This study found differences in cities with respect to when, how and why RM practices had evolved. The results indicate that differences in RM practices and development paths between cities are largely explained by the differences in the original reason to initiate RM, time span since its introduction, professional and educational backgrounds of risk managers, local risk events and accounting infrastructure such as RM tools developed in a city. These findings also suggest that even within the same municipality, different functions can be at different phases regarding RM.

Originality/value

This study reports on RM as a new form of accounting in the field of Finnish municipalities. This highlights how fairly uniform considerations at the field level lead to variation in the elaboration of RM practices at the municipal level. The study finds that different paths in the development of local RM involve iterative evolution between the phases of emergence, largely explained by contextual differences. This study contributes to understanding the emergence of new accounting forms in a municipal RM context.
Effect of severity of depression on augmentation of antidepressant medication in young adults with depression
Authors: Lampela Pasi , Tanskanen Antti , Lähteenvuo Markku , Tiihonen Jari , Taipale Heidi
Published: November 2023

Background

Antipsychotics (AP) have been used to augment antidepressant (AD) medication in treatment‐resistant depression. In this study we examined factors (including severity of depression and initial antidepressant) affecting AP augmentation, as well as which APs were initiated as augmentation in young adults.

Methods

Data were extracted from Finnish nationwide registers. Of persons aged 18–29 years diagnosed with a depression during 2004–2017 we focused on incident AD users (who initiated AD 6 months before and after the diagnosis) whose severity level of depression was recorded (N = 21,966). AP augmentation was studied during 1 year after diagnosis of depression. Persons diagnosed with severe depression with psychotic features (n = 1486) were excluded from main analyses and analyzed separately.

Results

Overall, 8.4% of new antidepressant users initiated AP augmentation. Risk of augmentation increased with severity of depression as 3.9%, 5.8%, and 14.0% of persons with mild, moderate, and severe depression, respectively, initiated augmentation. Male sex, comorbid anxiety and personality disorders, substance abuse and selfharm/suicide attempt were positively associated with augmentation. Compared to citalopram, use of tricyclic antidepressant, paroxetine and venlafaxine were associated with increased risk of augmentation, while use of bupropion was associated with a decreased risk. Quetiapine and risperidone were the most common APs used in augmentation. Among persons with severe depression with psychotic features, use of sertraline was associated with AP augmentation, whereas use of fluoxetine decreased risk of augmentation.

Conclusions

Use of APs as augmentation of AD therapy was common in severe depression. Comorbidities had only a small effect to augmentation, but selection of initial AD was more closely associated to risk of augmentation. Interestingly, use of bupropion decreased risk of augmentation, which warrants further studies, as well as the decrease in risk of augmentation when fluoxetine in case of psychotic depression was used.
Vital pulp therapy for permanent teeth with diagnosis of irreversible pulpitis: biological basis and outcome
Authors: Kahler B , Taha NA , Lu J , Saoud TM
Published: November 2023

Root canal treatment (RCT) has been considered the conventional standard for the management of teeth with carious pulp exposure, particularly in mature teeth presenting with symptoms. Following a better understanding of the histopathology of deep carious lesions, the histology of the cariously exposed pulp and the healing potential of the inflamed pulp, vital pulp therapy (VPT) is increasingly adopted around the world for the management of permanent teeth with clinical signs and symptoms indicative of irreversible pulpitis. Furthermore, VPT became a recognized treatment modality by the European Society of Endodontology (ESE) and the American Association of Endodontists (AAE) by virtue of its high success rates reported in outcome studies using contemporary hydraulic calcium silicate‐based cements. However, proper case selection, strict asepsis, capping materials and good coronal seal are mandatory for success. The aim of this paper is to review the biological basis for VPT in symptomatic teeth with carious pulp exposure and to report on the outcome of pulpotomy in teeth with clinical diagnosis of irreversible pulpitis.
Fostering interdisciplinary colorectal and gynaecology surgery networks during training is crucial to maximise expertise and innovate patient care
Authors: Sarofim Mina , Sarofim Mikhail
Published: November 2023

The importance of interdisciplinary collaboration between specialties has gained significant recognition in recent years, and rightly so with notable benefits to skills acquisition and patient outcomes. Due to the scope of overlapping procedures and clinical scenarios, developing trustable networks between colorectal and gynaecology surgeons must be encouraged as a focus of trainee education. This article highlights the benefits, challenges, and recommendations for fostering such networks.
Longitudinal MRI in the context of in utero surgery for open spina bifida: A descriptive study
Authors: Mufti Nada , Aertsen Michael , Thomson Dominic , De Vloo Phillippe , Demaerel Philippe , Deprest Jan , Melbourne Andrew , David Anna L. ,   the GIFT‐Surg Imaging Working Group
Published: November 2023

Introduction

Fetal surgery for open spina bifida (OSB) requires comprehensive preoperative assessment using imaging for appropriate patient selection and to evaluate postoperative efficacy and complications. We explored patient access and conduct of fetal magnetic resonance imaging (MRI) for prenatal assessment of OSB patients eligible for fetal surgery. We compared imaging acquisition and reporting to the International Society of Ultrasound in Obstetrics and Gynecology MRI performance guidelines.

Material and methods

We surveyed access to fetal MRI for OSB in referring fetal medicine units (FMUs) in the UK and Ireland, and two NHS England specialist commissioned fetal surgery centers (FSCs) at University College London Hospital, and University Hospitals KU Leuven Belgium. To study MRI acquisition protocols, we retrospectively analyzed fetal MRI images before and after fetal surgery for OSB.

Results

MRI for fetal OSB was accessible with appropriate specialists available to supervise, perform, and report scans. The average time to arrange a fetal MRI appointment from request was 4 ± 3 days (range, 0–10), the average scan time available was 37 ± 16 min (range, 20–80 min), with 15 ± 11 min (range, 0–30 min) extra time to repeat sequences as required. Specific MRI acquisition protocols, and MRI reporting templates were available in only 32% and 18% of units, respectively. Satisfactory T2‐weighted (T2W) brain imaging acquired in three orthogonal planes was achieved preoperatively in all centers, and 6 weeks postoperatively in 96% of FSCs and 78% of referring FMUs. However, for T2W spine image acquisition referring FMUs were less able to provide three orthogonal planes presurgery (98% FSC vs. 50% FMU, p < 0.001), and 6 weeks post‐surgery (100% FSC vs. 48% FMU, p < 0.001). Other standard imaging recommendations such as T1‐weighted (T1W), gradient echo (GE) or echoplanar fetal brain and spine imaging in one or two orthogonal planes were more likely available in FSCs compared to FMUs pre‐ and post‐surgery (p < 0.001).

Conclusions

There was timely access to supervised MRI for OSB fetal surgery assessment. However, the provision of images of the fetal brain and spine in sufficient orthogonal planes, which are required for determining eligibility and to determine the reversal of hindbrain herniation after fetal surgery, were less frequently acquired. Our evidence suggests the need for specific guidance in relation to fetal MRI for OSB. We propose an example guidance for MRI acquisition and reporting.
The effects of the decentralization of collective bargaining on wages and wage dispersion: Evidence from the Finnish forest and IT industries
Authors: Kauhanen Antti
Published: November 2023

Recently, Finnish forest industries shifted from sectoral collective bargaining to firm‐level bargaining, and the IT services industry shifted to a hybrid of sector‐ and firm‐level bargaining. Using administrative data on monthly wages and the synthetic difference‐in‐differences method, I study the causal effects of collective bargaining decentralization on the level and dispersion of wages. Despite the substantial change in the level of collective bargaining, I generally find muted effects on the level and dispersion of wages. I find positive and economically and statistically significant effects on wage levels and within‐firm wage dispersion only for blue‐collar workers in the paper industry.
The role of academic health science systems in the transformation of dentistry: The Singapore experience
Authors: Poon Choy Yoke , Wong Tien Yin , Allen Finbarr
Published: November 2023

Clinicians and researchers have traditionally worked in independent silos, with limited collaboration to rapidly translate discovery into clinical practice. At institutional level, hospitals and universities have also tended to work independently with limited success in leveraging each other's strengths with a view to improving population health. The consequences include fragmentation of clinical services, poor communication between researchers and clinicians, lengthy delays in identification of clinical problems requiring innovative solutions through research and a generation of clinicians who are not well equipped with all the skills to address future health needs. Academic Health Science Systems (AHSS) have been proposed as a mechanism for driving effective collaboration between academia and clinical services. There are examples of well established AHSS and the benefits have been articulated. In Singapore, three AHSS have been established over the past 15 years. National dental specialty centres and one dental school have been embedded in AHSS and have well established multi‐disciplinary collaboration across clinical and academic domains. The aim of this commentary is to describe the concept of an AHSS and some of the areas where dentistry in Singapore has been transformed by having key dental institutions embedded in an AHSS.
Canadian food inflation: International dynamics and local agency
Authors: Nuño‐Ledesma José G. , von Massow Michael
Published: November 2023

We offer a descriptive analysis of the complexities surrounding food price inflation in Canada three years after the outbreak of COVID‐19. The Consumer Price Index and its food component have registered significant shifts since 2020 and remain elevated. This behavior is influenced by international dynamics, such as the conflict between Russia and Ukraine and the consequent commodity price surges, and domestic factors, including grocery market concentration. As external events interact with local policies, business practices, and the structure of the food retail industry, debates around market competition intensify. We posit that while the influence of international factors on local prices is undeniable, fostering domestic grocery competition remains crucial. At the same time, managing expectations of major price reductions in a small open economy like Canada's is important. In addition, we discuss some of the research and data needs that have become salient during the current inflationary episode.