bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficiency and novelty of using environmental swabs for dry surface biofilm recovery.
Authors: Watson Fergus , Wilks Sandra , Chewins John , Keevil Bill
Published: July 2023

Studies on the epidemiology of dry surface biofilms within healthcare has shown an almost universal distribution across frequently touched items.  Despite a growing body of evidence for dry surface biofilms in hospitals little attention has been paid to the recovery capacity of techniques used to detect these microbial communities. Biofilms are inherently difficult to remove from surfaces due to adhesive substances within their matrix and may act as sources of infection but to what extent is largely unknown. In this study we evaluate the recovery efficiencies of commonly used environmental swabs against dry surface biofilms containing 7.24-Log10 Acinetobacter baumannii/cm2, using a drip flow reactor and desiccation cycle. Biofilm presence was visually confirmed using episcopic differential interference contrast microscopy combined with epifluorescence and quantified using sonicated viable plate counts. The swab materials used comprised of foam, viscose and cotton, all of which were pre-moistened using a buffer solution. The surfaces were vigorously swabbed by each material type and the resultant microbe populations for both swabs and remaining dry surface biofilms were quantified. Our results found foam tipped swabs to be superior, detecting on average 30% of the original dry surface biofilm contamination; followed by viscose (6%) and cotton (3%). However, no distinct difference was revealed in the concentration of microbes remaining on the surface after swabbing for each swab type suggesting there is variation in the capacity for each swab to release biofilm associated microorganisms. We conclude whilst environmental swabs do possess the ability to detect biofilms on dry surfaces; the reduced efficiencies are likely to cause an underestimation of the microbes present and should be considered during clinical application.
Immune-Epithelial Dynamics and Tissue Remodeling in Chronically Inflamed Nasal Epithelium via Multi-scaled Transcriptomics
Authors: Liao Guanrui , Nakayama Tsuguhisa , Lee Ivan T. , Zhu Bokai , Bravo Dawn. T. , Overdevest Jonathan B. , Yan Carol H. , Zarabanda David , Gall Philip A. , Dholakia Sachi S. , Borchard Nicole A. , Yang Angela , Kim Dayoung , Patel Zara M. , Hwang Peter H. , Wagh Dhananjay , Coller John , Phillips Katie , Chang Michael T. , Lechner Matt , Ma Qin , Li Zihai , Nolan Garry , Barouch Dan H. , Nayak Jayakar V. , Jiang Sizun
Published: July 2023

Chronic rhinosinusitis (CRS) is a common inflammatory disease of the sinonasal cavity that affects millions of individuals worldwide. The complex pathophysiology of CRS remains poorly understood, with emerging evidence implicating the orchestration between diverse immune and epithelial cell types in disease progression. We applied single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to both dissociated and intact, freshly isolated sinonasal human tissues to investigate the cellular and molecular heterogeneity of CRS with and without nasal polyp formation compared to non-CRS control samples. Our findings reveal a mechanism for macrophage-eosinophil recruitment into the nasal mucosa, systematic dysregulation of CD4+ and CD8+ T cells, and enrichment of mast cell populations to the upper airway tissues with intricate interactions between mast cells and CD4 T cells. Additionally, we identify immune-epithelial interactions and dysregulation, particularly involving understudied basal progenitor cells and Tuft chemosensory cells. We further describe a distinct basal cell differential trajectory in CRS patients with nasal polyps (NP), and link it to NP formation through immune-epithelial remodeling. By harnessing stringent patient tissue selection and advanced technologies, our study unveils novel aspects of CRS pathophysiology, and sheds light onto both intricate immune and epithelial cell interactions within the disrupted CRS tissue microenvironment and promising targets for therapeutic intervention. These findings expand upon existing knowledge of nasal inflammation and provide a comprehensive resource towards understanding the cellular and molecular mechanisms underlying this uniquely complex disease entity, and beyond.
Predicting non-response to ketamine for depression: a symptom-level analysis of real-world data
Authors: Miller Eric A. , Afshar Houtan Totonchi , Mishra Jyoti , Ramanathan Dhakshin
Published: July 2023

Background

Ketamine helps some patients with treatment resistant depression (TRD), but reliable methods for predicting which patients will, or will not, respond to treatment are lacking.

Methods

This is a retrospective analysis of PHQ-9 item response data from 120 military veterans with TRD who received repeated doses of intravenous racemic ketamine or intranasal eskatamine in a real-world clinic. Regression models were fit to individual patients’ symptom trajectories and model parameters were analyzed to characterize how different symptoms responded to treatment. Logistic regression classifiers were used to predict treatment response using patients’ baseline depression symptoms alone. Finally, by parametrically adjusting the classifier decision thresholds, the full space of models was searched to identify the best models for predicting non-response with very high negative predictive value.

Results

Model slopes indicated progressive improvement on all nine symptoms, but the symptom of depressed mood improved faster than the symptom of low energy. The first principal component (PC) represented a data-driven measurement of overall treatment response, while the second PC divided the symptoms into affective and somatic subdomains. Logistic regression classifiers predicted response better than chance using baseline symptoms, but these models achieved only 60.2% predictive value. Using threshold tuning, we identified models that can predict non-response with a negative predictive value of 96.4%, while retaining a specificity of 22.1%, suggesting we could successfully identify 22% of individuals who would not respond purely based on baseline symptom scores.

Conclusions

We developed an approach for identifying a subset of patients with TRD who will likely not respond to ketamine. This could inform rational treatment recommendations to avoid additional treatment failures.
Simultaneous Mapping of DNA Binding and Nucleosome Positioning with SpLiT-ChEC
Authors: Banks Orion G. B. , Harms Michael J. , McKnight Jeffrey. N. , McKnight Laura E.
Published: July 2023

The organization of chromatin – including the positions of nucleosomes and the binding of other proteins to DNA – helps define transcriptional profiles in eukaryotic organisms. While techniques like ChIP-Seq and MNase-Seq can map protein-DNA and nucleosome localization separately, assays designed to simultaneously capture nucleosome positions and protein-DNA interactions can produce a detailed picture of the chromatin landscape. Most assays that monitor chromatin organization and protein binding rely on antibodies, which often exhibit nonspecific binding, and/or the addition of bulky adducts to the DNA-binding protein being studied, which can affect their expression and activity. Here, we describe SpyCatcher Linked Targeting of Chromatin Endogenous Cleavage (SpLiT-ChEC), where a 13-amino acid SpyTag peptide, appended to a protein of interest, serves as a highly-specific targeting moiety for in situ enzymatic digestion. The SpyTag/SpyCatcher system forms a covalent bond, linking the target protein and a co-expressed MNase-SpyCatcher fusion construct. SpyTagged proteins are expressed from endogenous loci, whereas MNase-SpyCatcher expression is induced immediately before harvesting cultures. MNase is activated with high concentrations of calcium, which primarily digests DNA near target protein binding sites. By sequencing the DNA fragments released by targeted MNase digestion, we found that this method recovers information on protein binding and proximal nucleosome positioning. SpLiT-ChEC provides precise temporal control that we anticipate can be used to monitor chromatin under various conditions and at distinct points in the cell cycle.
Artificial Intelligence for Anatomical Structure Identification on Ultrasound in Regional Anaesthesia: A Scoping Review Protocol
Authors: Bowness James S , Metcalfe David , El-Boghdadly Kariem , Thurley Neal , Noble J Alison , Higham Helen
Published: July 2023

Background

Ultrasound is the most common form of guidance for regional anaesthesia. There is increasing interest in developing supporting technology, particularly in the form of artificial intelligence (AI), to aid in the acquisition and interpretation of optimal ultrasound views for these procedures. However, this is a broad field, with academia, clinical practice, and industry all providing disparate contributions. We will undertake a scoping review of publicly-available data, to assess methods of evaluation for accuracy and utility of such systems.

Methods

We will perform searches in multiple databases, including ACM Digital Library, CINAHL, EMBASE, IEEE Explore, and OVID MEDLINE. We will search the International Committee of Medical Journal Editors approved clinical trial registries and the World Health Organisation (WHO) clinical trials registry for studies registered in this field. Grey literature will be searched through the online library of doctoral theses (http://ethos.bl.uk/Home.do), regulatory authority registries and competent authority websites of North America and the UK, the websites of international learned societies in regional anaesthesia, and material from commercial organisations with products in the field.

The primary goal is to summarise the approaches used to evaluate accuracy and utility of these devices. A secondary goal is to assess the standardisation of reporting in this field, with particular reference to whether reporting guidelines have been followed.

Discussion

To the best of our knowledge, this is the first scoping review of this type. Synthesis of the available evidence will enable us to make recommendations on standardised evaluation approaches of assessment, to allow robust and relevant evaluation which can be compared to similar evaluations of other devices.
Polygenic risk score analysis reveals shared genetic burden between epilepsy and psychiatric comorbidities
Authors: Campbell C. , Lewis-Smith D. , Leu C. , Martins H. , Wolking S. , Krause R. , O’Brien T. , Sill G. , Zara F. , Koeleman B. , Depondt C. , Marson A. , Stefánnson H. , Stefánnson K. , Craig J. , Johnson MR. , Striano P. , Jorgensen A. , Lerche H. , Delanty N. ,   The EpiPGX Consortium, Sisodiya S.M. , Thomas R. H. , Cavalleri G. L.
Published: July 2023

Background

One in three people with epilepsy experiences psychiatric comorbidity, with higher rates in people with drug-resistant epilepsy. Despite their high heritabilities, finding genetic links between epilepsy and psychiatric disorders has proven difficult. We used polygenic risk scoring (PRS) to test whether people with epilepsy have an increased polygenic burden of common genetic variants for depression, anxiety, psychosis, and attention deficit/hyperactivity disorder (ADHD), and examined whether such polygenic burden influences the response to pharmacological treatment of epilepsy.

Methods

Phenotype data in the UK Biobank were assessed to identify people with 1) epilepsy (n=8 488), 2) depression (n=143 440), 3) psychosis (n=2 357), 4) ADHD (n=89), and 5) anxiety (n=18 222. Using genotype data and restricting to Caucasian-ancestry samples (n=409 634), PRS for each psychiatric trait were calculated and multinomial regression was used to compare 1) population controls, 2) people with epilepsy and no psychiatric illness, 3) people with epilepsy and the psychiatric trait of interest, and 4) people with the psychiatric trait of interest and no epilepsy. Fixed-effect meta-analysis was used to compare psychiatric PRS in drug-resistant and drug-responsive epilepsy samples from the UK Biobank (n=1 640) and the EpiPGX consortium (n=3 449).

Results

After correction for multiple testing, people with epilepsy showed elevated PRS for depression (p<2 x10−16), psychosis (p=0.04) and ADHD (p<0.001). Patients with drug-resistant epilepsy had an increased PRS for psychosis (p=0.002) and depression (p=0.0004) relative to responsive cases.

Conclusion

We present evidence that the common genetic basis of epilepsy overlaps with that of psychiatric conditions which are frequently comorbid in people with epilepsy. Common genetic variants that drive psychiatric illness are enriched in people with drug-resistant epilepsy. These results further our understanding of the genetic architecture of epilepsy and suggest a potential future role for polygenic interpretation of common variants in prognostic stratification, both for seizure-treatment outcomes and non-seizure comorbidities.
Feasibility, acceptability, and cognitive benefits of a theory-informed intervention to increase Mediterranean diet adherence and physical activity in older adults at risk of dementia: the MedEx-UK randomised controlled trial
Authors: Jennings A , Shannon OM , Gillings R , Lee V , Elsworthy R , Rao G , Hanson S , Hardeman W , Paddick S-M , Siervo M , Aldred S , Mathers JC , Hornberger M , Minihane AM
Published: July 2023

Background

Despite an urgent need for multi-domain lifestyle interventions to reduce dementia risk there is a lack of interventions which are informed by theory- and evidence- based behaviour change strategies and no interventions in this domain have investigated the feasibility or effectiveness of behaviour change maintenance.

Objectives

We tested the feasibility, acceptability, and cognitive effects of MedEx-UK, a personalised theory-based 24-week intervention to improve Mediterranean-diet (MD) adherence alone, or in combination with physical activity (PA), in older-adults at risk of dementia, defined using a cardiovascular risk-score of >10%.

Design

104 participants (74% female, 57–76 years) were randomised to three parallel intervention arms: 1) control, 2) MD, or 3) MD+PA for 24-weeks and invited to an additional 24-week follow-up period with no active intervention. Behaviour change was supported using personalised targets, a web-based intervention, group sessions and food provision.

Results

The intervention was feasible and acceptable with the intended number of ‘at risk’ participants completing the study. Participant engagement with group sessions and food provision components was high. There was improved MD adherence in the two MD groups compared with control at 24-weeks (3.7 points on a 14-point scale (95% CI 2.9, 4.5, p <0.01) and 48-weeks (2.7 points (95% CI 1.6, 3.7) p<0.01). Intervention did not change objectively measured PA. Improvements in general cognition (0.22 (95% CI 0.05, 0.35, p =0.01), memory (0.31 (95% CI 0.10, 0.51, p <0.01), and select cardiovascular outcomes captured as underpinning physiological mechanisms were observed in the MD groups at 24-weeks.

Conclusion

The intervention was successful in initiating and maintaining dietary behaviour change for up to 12-months, which was likely due to the intense early support provided which resulted in cognitive benefits. These results will inform larger-scale complex behaviour change interventions with health and well-being endpoints.
The association between family structure and adolescent physical activity levels: A systematic review of literature published since 2010
Authors: Mylona Elena , Kletter Maartje , Jones Helen M , Murphy Marie , Lampard Richard , Oyebode Oyinlola
Published: July 2023

Background

Adolescent physical activity is influenced by biological, psychological, sociocultural, and environmental factors; however, no review has yet explored the effect of family structure (usually defined based on the relationships between people living in a household) on adolescent physical activity levels.

Methods

Databases MEDLINE, EMBASE, Web of Science, PsycINFO, CINAHL, and Sociological Abstracts were searched for peer-reviewed studies with a quantitative component published since 2010, with no restrictions on language, country, and year of data collection. Study screening, data extraction, and quality assessment occurred in duplicate. SWiM guidelines guided the narrative synthesis. PROSPERO protocol CRD42020221090.

Results

Thirty studies met inclusion criteria: 17 looked at global physical activity, 13 at leisure physical activity, and sport participation. All studies used cross-sectional designs and 27 assessed outcomes through a survey. Sixteen (10 of good quality) reported a significant association between family structure and adolescent physical activity. Of these, three did not specify the direction of this association while nine found adolescents in ‘traditional’ (two-parent) families were more physically active compared with other family structures. This association was stronger in studies of leisure- time physical activity. Two studies reported that adolescents with single mothers achieve more physical activity than adolescents living with neither parent. Two studies, focused on school physical exercise classes and active transport, found adolescents in single-parent households engaged in more physical activity than those living with two parents.

Conclusion

High-quality accelerometery, time diary, and longitudinal studies are needed to investigate the effect of family structure on adolescent physical activity and health sequelae. An improved understanding of social determinants of adolescent physical activity could inform health promotion strategies.
Cortical Adaptation in the Delta Band in People with Post-Stroke Aphasia during Picture Naming
Authors: Renaud-D’Ambra Malo , Aksenov Alexandre , Mesnildrey Quentin , Hartwigsen Gesa , Volpert Vitaly , Beuter Anne
Published: July 2023

Abstract

This study explores differences in spatiotemporal cortical dynamics between five people with chronic post-stroke aphasia and five healthy subjects. Electroencephalography was recorded during picture naming in both groups.

Frequency-specific Global Field Power (GFP) results showed that the delta band has higher power to discriminate between healthy subjects and people with aphasia (PWA) than theta and alpha bands. EEG topologies computed at the time of GFP peaks in the delta band revealed strong activation oscillating between posterior and anterior areas in PWA. On the other hand, EEG topologies from healthy subjects were variable.

Then, Spatial ERP (S-ERP) were developed to add spatial resolution to classical ERP analysis. S-ERP and associated analyses confirmed the previously observed oscillatory pattern in the delta frequency band among PWA during picture naming. This oscillating pattern was alternating between occipital and prefrontal areas with almost opposite phases, a characteristic not observed in healthy subjects. In addition, all PWA performed well on the picture naming task, suggesting that this oscillating pattern may be a cortical adaptation mechanism enabling them to succeed.

The observation of large-scale oscillating delta activity across the scalp in all post-stroke subjects who have substantially recovered from aphasia holds the potential to inspire innovative rehabilitation methods employing non-invasive brain stimulation techniques such as transcranial alternating current stimulation (tACS).
New variants in the Chloroplast Genome Sequence of two Colombian individuals of the Cedar timber species (Cedrela odorataL.), using long read Oxford Nanopore Technology
Authors: Simbaqueba Jaime , Garzón-Martínez Gina A. , Castano Nicolas
Published: July 2023

The plant speciesCedrela odoratahas been largely exploited in the timber industry due to the high demand of its wood. Therefore,C. odorata, has been considered as a vulnerable species since 1994, with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).C. odoratais one of the key timber species included in the management and conservation plans in Colombia. These plans include the study of local populations by developing genetic resources for the species. In this study, two novel chloroplast (cp) genomes have been generated using the MinION long read sequencing technology. The new cp assemblies were compared with other cp genomes for the species, supporting previous hypothesis of intraspecific diversity associated to their place of origin. Furthermore, the cp genomes were screened for sequence variants (SV) and a total of 16 SNPs were identified, presumably unique to populations of the amazon region in Colombia. Here, the first cp genome sequences ofC. odoratafrom Colombian individuals represent novel and valuable genomic resources for the species suitable for DNA fingerprinting and DNA barcoding applications.
Alzheimer’s disease associated isoforms of human CD33 distinctively modulate microglial cell responses in 5XFAD mice
Authors: Eskandari-Sedighi Ghazaleh , Crichton Madeline , Zia Sameera , Gomez Erik , St. Laurent Chris D. , Cortez Leonardo M. , Patel Zain H. , Sidhu Gaurav , Sarkar Susmita , Aghanya Vivian , Sim Valerie L. , Tan Qiumin , Julien Olivier , Plemel Jason R. , Macauley Matthew S.
Published: July 2023

Microglia play diverse pathophysiological roles in Alzheimer’s disease (AD), with genetic susceptibility factors skewing microglial cell function to influence AD risk. CD33 is an immunomodulatory receptor associated with AD susceptibility through a single nucleotide polymorphism that modulates mRNA splicing, skewing protein expression from a long protein isoform (CD33M) to a short isoform (CD33m). Understanding how human CD33 isoforms differentially impact microglial cell functionin vivohas been challenging due to functional divergence of CD33 between mice and humans. We address this challenge by studying transgenic mice expressing either of the human CD33 isoforms crossed with the 5XFAD mouse model of amyloidosis and find that human CD33 isoforms have opposing effects on the response of microglia to amyloid-β (Aβ) deposition. Mice expressing CD33M have increased Aβ levels, mo7re diffuse plaques, fewer disease-associated microglia, and more dystrophic neurites compared to control 5XFAD mice. Conversely, CD33m promotes plaque compaction and microglia-plaque contacts, and minimizes neuritic plaque pathology, highlighting an AD protective role for this isoform. Protective phenotypes driven by CD33m are detected at an earlier timepoint compared to the more aggressive pathology in CD33M mice that appears at a later timepoint, suggesting that CD33m has a more prominent impact on microglia cell function at earlier stages of disease progression. In addition to divergent roles in modulating phagocytosis, scRNAseq and proteomics analyses demonstrate that CD33m+microglia upregulate nestin, an intermediate filament involved in cell migration, at plaque contact sites. Overall, our work provides new functional insights into how CD33, as a top genetic susceptibility factor for AD, modulates microglial cell function.
Distinct features of the regenerating heart uncovered through comparative single-cell profiling
Authors: Carey Clayton M. , Hollins Hailey L. , Schmid Alexis V. , Gagnon James A.
Published: July 2023

Adult humans respond to heart injury by forming a permanent scar, yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians, the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features, we compared cardiac injury responses in zebrafish and medaka, two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single-cell transcriptional profiling to create a time-resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach, we identified several key features that distinguish cardiac injury response in the non-regenerating medaka heart. By comparing immune responses to injury, we found altered cell recruitment and a distinct pro-inflammatory gene program in medaka leukocytes, and an absence of the injury-induced interferon response seen in zebrafish. In addition, we found a lack of pro-regenerative signals, including nrg1 and retinoic acid, from medaka endothelial and epicardial cells. Finally, we identified alterations in the myocardial structure in medaka, where they lack embryonic-like primordial layer cardiomyocytes, and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka, demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates.
ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data
Authors: Siggel Marc , Jensen Rasmus K. , Mahamid Julia , Kosinski Jan
Published: July 2023

Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular resolution. To enable quantitative analysis of the complex shapes and morphologies of lipid membranes, the noisy three-dimensional (3D) volumes must be segmented. Despite recent advances, this task often requires considerable user intervention to curate the resulting seg-mentations. Here, we present ColabSeg, a Python-based tool for processing, visualizing, cleaning, and fitting membrane segmentations from cryo-ET data for downstream analysis. ColabSeg makes many well-established algorithms for point-cloud processing easily available to the broad community of structural biologists for applications in cryo-ET through its graphical user interface (GUI). We demonstrate the usefulness of the tool with a range of use cases and biological examples. Finally, for a largeMycoplasma pneumoniaedataset of 50 tomograms, we show how ColabSeg enables high-throughput membrane segmentation, which can be used as valuable training dataset for fully automated convolutional neural network (CNN)-based segmentation.
Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects
Authors: Plavskin Yevgeniy , de Biase Maria Stella , Ziv Naomi , Janská Libuše , Zhu Yuan O. , Hall David W. , Schwarz Roland F. , Tranchina Daniel , Siegal Mark L.
Published: July 2023

The fitness effects of new mutations determine key properties of evolutionary processes. Beneficial mutations drive evolution, yet selection is also shaped by the frequency of small-effect deleterious mutations, whose combined effect can burden otherwise adaptive lineages and alter evolutionary trajectories and outcomes in clonally evolving organisms such as viruses, microbes, and tumors. The small effect sizes of these important mutations have made accurate measurements of their rates difficult. In microbes, assessing the effect of mutations on growth can be especially instructive, as this complex phenotype is closely linked to fitness in clonally evolving organisms. Here, we perform high-throughput time-lapse microscopy on cells from mutation-accumulation strains to precisely infer the distribution of mutational effects on growth rate in the budding yeast,Saccharomyces cerevisiae. We show that mutational effects on growth rate are overwhelmingly negative, highly skewed towards very small effect sizes, and frequent enough to suggest that deleterious hitchhikers may impose a significant burden on evolving lineages. By using lines that accumulated mutations in either wild-type or slippage repair-defective backgrounds, we further disentangle the effects of two common types of mutations, single-nucleotide substitutions and simple sequence repeat indels, and show that they have distinct effects on yeast growth rate. Although the average effect of a simple sequence repeat mutation is very small (∼0.3%), many do alter growth rate, implying that this class of frequent mutations has an important evolutionary impact.
Systemic Lupus Erythematosus Serum Stimulation of Human Intestinal Organoids Induces Changes in Goblet Cell Differentiation and Mitochondrial Fitness
Authors: Hensel Inga Viktoria , Éliás Szabolcs , Steinhauer Michelle , Stoll Bilgenaz , Benfatto Salvatore , Merkt Wolfgang , Krienke Stefan , Lorenz Hanns-Martin , Haas Jürgen , Wildeman Brigitte , Resnik-Docampo Martin
Published: July 2023

Human intestinal epithelial cells are the interface between potentially harmful luminal content and basally residing immune cells. Their role is not only nutrient absorption but also the formation of a tight monolayer that constantly secrets mucus creating a multi-layered protective barrier. Alterations in this barrier can lead to increased gut permeability which is frequently seen in individuals with chronic extraintestinal autoimmune diseases, such as Systemic Lupus Erythematosus (SLE). Despite recent advances in identifying alterations in gut microbiota composition in SLE patients, not much attention has been given to the epithelial barrier itself. To date, it remains largely unexplored which role and function intestinal epithelial cells have in SLE pathology. Here, we present a unique near-physiologicin vitromodel specifically designed to examine the effects of SLE on the epithelial cells. We utilize human colon organoids that are stimulated with serum obtained from SLE patients. Combining bulk and scRNA transcriptomic analysis with functional assays revealed that SLE serum stimulation induced a unique expression profile marked by a type I interferon gene signature. Additionally, organoids exhibited decreased mitochondrial fitness, alterations in mucus composition and imbalanced cellular composition. Similarly, transcriptomic analysis of SLE human colon biopsies revealed a downregulation of epithelial secretory markers. Our work uncovers a crucial connection between SLE and intestinal homeostasis that might be promotedin vivothrough the blood, offering insights into the causal connection of barrier dysfunction and autoimmune diseases.
Mimicking of tau hyperphosphorylation in GABAergic motoneurons ofC. elegansinduces severe peripheral and neuronal alterations
Authors: Labarre Audrey , Schramm Émilien , Pilliod Julie , Boyer Samuel , Lapointe Marianne , Maios Claudia , Leclerc Nicole , Parker J. Alex
Published: July 2023

In several neurodegenerative diseases including Alzheimer’s disease (AD), tau, a microtubule-associated protein (MAP) enriched in the axon, becomes hyperphosphorylated, detaches from microtubules, redistributes to the somato-dendritic compartment and self-aggregates. The mechanisms leading to neuronal dysfunction and death by tau pathology remain to be fully elucidated.C. eleganshas been successfully used by several groups including ours to identify mechanisms involved in neurodegeneration. We generated three strains, one overexpressing wild-type human tau (WT Tau), one a tau mutant mimicking hyperphosphorylation (hyperP Tau) and one preventing phosphorylation (hypoP Tau) in GABA motor neurons. A significant reduction of body size and egg laying was noted in these tau strains. Starting at day 1, we found that the worms overexpressing hyperP Tau were smaller than the N2 control strain and the worms either overexpressing WT Tau or hypoP Tau. Starting at day 5, the worms overexpressing WT Tau were smaller than control and the worms overexpressing hypoP Tau. Egg laying was reduced in both hyperP Tau and WT Tau worms. Survival was only decreased in WT Tau worms. Motility deficits were also observed. For age-dependent paralysis, a difference was noted between control and hyperP Tau. Swimming activity and speed were increased in hypoP Tau and decreased in hyperP Tau strains. Axonal integrity was altered in all tau strains. In the case of synaptic activity, at day 1, it was increased in the hypoP Tau strain and decreased in the hyperP Tau one. Collectively, our data revealed that overexpression of tau exerted neuronal and peripheral defects indicating that tau dysfunction could affect cell-cell communication.
Mapping interactions between disordered regions reveals promiscuity in biomolecular condensate formation
Authors: Gilat Atar , Dubrueil Benjamin , Levy Emmanuel D.
Published: July 2023

Intrinsically-disordered regions (IDRs) promote intracellular phase separation and the formation of biomolecular condensates through interactions encoded in their primary sequence. While these condensates form spatially distinct assemblies in cells, it is unclear whether such specificity can be conferred by IDRs alone. Indeed, IDRs exhibit high conformational flexibility whereas specificity in protein recognition is generally associated with well-defined 3D structures. To characterize IDR-IDR interactions and assess their ability to mediate self-specific partitioning, we developed a synthetic system of Multivalent IDRs forming Constitutive DROPlets (micDROP). We investigated ten natural IDRs that underwent phase separation inmicDROP. These IDRs exhibited a wide range of saturation concentrationsin vivo, which correlated well with their total sequence stickiness. We then probed IDR-IDR specificity by co-expressing pairs of IDRs fused to homologous scaffolds that did not co-assemble. We observed a high degree of promiscuity, particularly among IDRs from the proteins Ddx4, DYRK3, ERα, FUS, hnRNPA1, HspB8, RBM14 and TAF15, whereas TDP43 and UBQ2 formed spatially distinct condensates regardless of their partner. Further investigation revealed the short and conserved α-helical segment of TDP43’s IDR was governing its specific self-recognition. Our findings imply that IDRs can tune their phase separation propensity through sequence composition, while their formation of discrete condensates likely requires additional cellular or structural determinants.

Abstract Figure
Strengthening E-cadherin adhesion via antibody mediated binding stabilization
Authors: Xie Bin , Xu Shipeng , Schecterson Leslayann , Gumbiner Barry M. , Sivasankar Sanjeevi
Published: July 2023

E-cadherins (Ecads) are a crucial cell-cell adhesion protein with tumor suppression properties. Ecad adhesion can be enhanced by the monoclonal antibody 66E8, which has potential applications in inhibiting cancer metastasis. However, the biophysical mechanisms underlying 66E8 mediated adhesion strengthening are unknown. Here, we use molecular dynamics simulations, site directed mutagenesis and single molecule atomic force microscopy experiments to demonstrate that 66E8 strengthens Ecad binding by stabilizing the primary Ecad adhesive conformation: the strand-swap dimer. By forming electrostatic interactions with Ecad, 66E8 stabilizes the swapped β-strand and its hydrophobic pocket and impedes Ecad conformational changes, which are necessary for rupture of the strand-swap dimer. Our findings identify fundamental mechanistic principles for strengthening of Ecad binding using monoclonal antibodies.
Modeling the Correlation betweenZandBin an X-ray Crystal Structure Refinement
Authors: Buscagan Trixia M. , Rees Douglas C.
Published: July 2023

We have examined how the refinedB-factor changes as a function ofZ(the atomic number of a scatterer) at the sulfur site of the [4Fe:4S] cluster of the nitrogenase iron protein by refinement. A simple model is developed that quantitatively captures the observed relationship betweenZandB, based on a Gaussian electron density distribution with a constant electron density at the position of the scatterer. From this analysis, the fractional changes inBandZare found to be similar. The utility ofB-factor refinement to potentially distinguish atom types reflects theZdependence of X-ray atomic scattering factors; the weaker dependence of electron atomic scattering factors onZimplies that distinctions between refined values ofBin an electron scattering structure will be less sensitive to the atomic identity of a scatterer than for the case with X-ray-diffraction. This behavior provides an example of the complementary information that can be extracted from different types of scattering studies.
Replication Protein A1 is essential for DNA damage repair during mammalian oogenesis
Authors: Miao Xiaosu , Guo Rui , Williams Andrea , Lee Catherine , Ma Jun , Wang P. Jeremy , Cui Wei
Published: July 2023

Persistence of unrepaired DNA damage in oocytes is detrimental and may cause genetic aberrations, miscarriage, and infertility. RPA, an ssDNA-binding complex, is essential for various DNA-related processes. Here we report that RPA plays a novel role in DNA damage repair during postnatal oocyte development after meiotic recombination. To investigate the role of RPA during oogenesis, we inactivated RPA1 (replication protein A1), the largest subunit of the heterotrimeric RPA complex, specifically in oocytes using two germline-specificCredrivers (Ddx4-CreandZp3-Cre). We find that depletion of RPA1 leads to the disassembly of the RPA complex, as evidenced by the absence of RPA2 and RPA3 in RPA1-deficient oocytes. Strikingly, severe DNA damage occurs in RPA1-deficient GV-stage oocytes. Loss of RPA in oocytes triggered the canonical DNA damage response mechanisms and pathways, such as activation of ATM, ATR, DNA-PK, and p53. In addition, the RPA deficiency causes chromosome misalignment at metaphase I and metaphase II stages of oocytes, which is consistent with altered transcript levels of genes involved in cytoskeleton organization in RPA1-deficient oocytes. Absence of the RPA complex in oocytes severely impairs folliculogenesis and leads to a significant reduction in oocyte number and female infertility. Our results demonstrate that RPA plays an unexpected role in DNA damage repair during mammalian folliculogenesis.
MEILB2-BRME1 forms a V-shaped DNA clamp upon BRCA2-binding in meiotic recombination
Authors: Gurusaran Manickam , Zhang Jingjing , Zhang Kexin , Shibuya Hiroki , Davies Owen R.
Published: July 2023

DNA double-strand break repair by homologous recombination has a specialised role in meiosis by generating crossovers that enable the formation of haploid germ cells. This requires meiosis-specific MEILB2-BRME1, which interacts with BRCA2 to facilitate loading of recombinases onto resected DNA ends. Here, we report the crystal structure of the MEILB2-BRME1 2:2 core complex, revealing a parallel four-helical assembly that recruits BRME1 to meiotic double-strand breaksin vivo. It forms an N-terminal β-cap that binds to DNA, and a MEILB2 coiled-coil that bridges to C-terminal ARM domains. Upon BRCA2-binding, MEILB2-BRME1 2:2 complexes dimerize into a V-shaped 2:4:4 complex, with rod-like MEILB2-BRME1 components arranged at right-angles. The β-caps located at the tips of the MEILB2-BRME1 limbs are separated by 25 nm, allowing them to bridge between DNA molecules. Thus, we propose that BRCA2 induces MEILB2-BRME1 to function as a DNA clamp, connecting resected DNA ends or homologous chromosomes to facilitate meiotic recombination.
Circuits in the Motor Cortex Explain Oscillatory Responses to Transcranial Magnetic Stimulation
Authors: Haggie Lysea , Besier Thor , McMorland Angus
Published: July 2023

Transcranial Magnetic Stimulation (TMS) is a popular method used to investigate brain function. Stimulation over the motor cortex evokes muscle contractions known as motor evoked potentials (MEPs) and also high frequency volleys of electrical activity measured in the cervical spinal cord. The physiological mechanisms of these experimentally derived responses remain unclear, but it is thought that the connections between circuits of excitatory and inhibitory neurons play a vital role. Using a spiking neural network model of the motor cortex, we explained the generation of waves of activity, so called ‘I-waves’, following cortical stimulation. The model reproduces a number of experimentally known responses including direction of TMS, increased inhibition and changes in strength. Using populations of thousands of neurons in a model of cortical circuitry we showed that the cortex generated transient oscillatory responses without any tuning, and that neuron parameters such as refractory period and delays influenced the pattern and timing of those oscillations. By comparing our network with simpler, previously proposed circuits, we explored the contributions of specific connections and found that recurrent inhibitory connections are vital in producing later waves which significantly impact the production of motor evoked potentials in downstream muscles (Thickbroom, 2011). This model builds on previous work to increase our understanding of how complex circuitry of the cortex is involved in the generation of I-waves.
Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia
Authors: Bhuiyan Shamsuddin A. , Xu Mengyi , Yang Lite , Semizoglou Evangelia , Bhatia Parth , Pantaleo Katerina I. , Tochitsky Ivan , Jain Aakanksha , Erdogan Burcu , Blair Steven , Cat Victor , Mwirigi Juliet M. , Sankaranarayanan Ishwarya , Tavares-Ferreira Diana , Green Ursula , McIlvried Lisa A. , Copits Bryan A. , Bertels Zachariah , Del Rosario John S. , Widman Allie J. , Slivicki Richard A. , Yi Jiwon , Woolf Clifford J. , Lennerz Jochen K. , Whited Jessica L. , Price Theodore J. , Gereau Robert W. , Renthal William
Published: July 2023

Peripheral sensory neurons in the dorsal root ganglion (DRG) and trigeminal ganglion (TG) are specialized to detect and transduce diverse environmental stimuli including touch, temperature, and pain to the central nervous system. Recent advances in single-cell RNA-sequencing (scRNA-seq) have provided new insights into the diversity of sensory ganglia cell types in rodents, non-human primates, and humans, but it remains difficult to compare transcriptomically defined cell types across studies and species. Here, we built cross-species harmonized atlases of DRG and TG cell types that describe 18 neuronal and 11 non-neuronal cell types across 6 species and 19 studies. We then demonstrate the utility of this harmonized reference atlas by using it to annotate newly profiled DRG nuclei/cells from both human and the highly regenerative axolotl. We observe that the transcriptomic profiles of sensory neuron subtypes are broadly similar across vertebrates, but the expression of functionally important neuropeptides and channels can vary notably. The new resources and data presented here can guide future studies in comparative transcriptomics, simplify cell type nomenclature differences across studies, and help prioritize targets for future pain therapy development.
Deletion of VPS50 protein in mice brain impairs synaptic function and behavior
Authors: Ahumada-Marchant Constanza , Ancatén-Gonzalez Carlos , Haensgen Henny , Arancibia Felipe , Brauer Bastian , Droste Rita , Horvitz H. Robert , Constantine-Paton Martha , Arriagada Gloria , Chávez Andrés E , Bustos Fernando J
Published: July 2023

VPS50, is an accessory protein, involved in the synaptic and dense core vesicle acidification and its alterations produce behavioral changes inC.elegans. Here, we produce the mosaic knock out (mKO) of VPS50 using CRISPR/Cas9 system in both cortical cultured neurons and whole animals to evaluate the effect of VPS50 in regulating mammalian brain function and behavior. While mKO of VPS50 does not change the number of synaptic vesicles, it produces a mislocalization of the V-ATPase pump that likely impact in vesicle acidification and vesicle content to impair synaptic and neuronal activity in cultured neurons. In mice, mKO of VPS50 in the hippocampus, alter synaptic transmission and plasticity, and generated robust cognitive impairments associate to memory formation. We propose that VPS50 is an accessory protein that aids the correct recruitment of the V-ATPase pump to synaptic vesicles, thus having a crucial role controlling synaptic vesicle acidification and hence synaptic transmission.
Chromatin attachment to the nuclear matrix represses hypocotyl elongation inArabidopsis thaliana
Authors: Xu Linhao , Zheng Shiwei , Witzel Katja , Van De Slijke Eveline , Baekelandt Alexandra , Mylle Evelien , Van Damme Daniel , Cheng Jinping , Jaeger Geert De , Inze Dirk , Jiang Hua
Published: July 2023

The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we showed that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known asSMALL AUXIN UP RNAs(SAURs) inArabidopsis thaliana. The transcriptional repression ofSAURsdepends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contained matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to theSAURloci. This leads to the removal of H3 acetylation at theSAURloci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a novel mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
Primordial germ cell DNA demethylation and development require DNA translesion synthesis
Authors: Shah Pranay , Hill Ross , Clark Stephen , Dion Camille , Abakir Abdulkadir , Arends Mark , Leitch Harry , Reik Wolf , Crossan Gerry
Published: July 2023

Mutations in DNA damage response (DDR) factors are associated with human infertility, which affects up to 15% of the population. It remains unclear if the role of DDR is solely in meiosis. One pathway implicated in human fertility is DNA translesion synthesis (TLS), which allows replication impediments to be bypassed. We find that TLS is essential for pre-meiotic germ cell development in the embryo. Loss of the central TLS component, REV1, significantly inhibits the induction of human PGC-like cells (hPGCLCs). This is recapitulated in mice, where deficiencies in TLS initiation (Rev1-/-orPcnaK164R/K164R) or extension (Rev7-/-) result in a >150-fold reduction in the number of primordial germ cells (PGCs) and complete sterility. In contrast, the absence of TLS does not impact the growth, function, or homeostasis of somatic tissues. Surprisingly, we find a complete failure in both activation of the germ cell transcriptional program and in DNA demethylation, a critical step in germline epigenetic reprogramming. Our findings show that for normal fertility, DNA repair is required not only for meiotic recombination but for progression through the earliest stages of germ cell development in mammals.