bluuebunny/crossref_metadata_2025 huggingface dataset:
Barriers and Facilitators to Community Pharmacist-Provided Injectable Naltrexone for Formerly Incarcerated Individuals During Community Reentry in Wisconsin
Authors: Chladek Jason S. , Chui Michelle A.
Published: September 2024

Medications for opioid use disorder (MOUD), including injectable naltrexone, are a key component in the treatment of opioid use disorder (OUD). These medications are especially important for individuals transitioning out of correctional facilities and back into their communities, as individuals receiving MOUD are 85% less likely to die due to drug overdose in the first month post-release and have a 32% lower risk of rearrest. Unfortunately, few formerly incarcerated individuals have access to MOUD upon reentry, incurring a 40-fold greater likelihood of overdose following release compared to the general population. While 84% of Wisconsin jails offering MOUD offer naltrexone, less than half provide linkage to community treatment for reentering individuals. In Wisconsin, community pharmacists have the authority to provide naltrexone injections. However, they have not been explored as a resource for improving access to this medication for formerly incarcerated individuals. As a first step, the goal of this study was to understand the barriers and facilitators impacting access to community pharmacist-provided injectable naltrexone for this patient population during community reentry period. The researcher conducted semi-structured interviews with 18 individuals representing five stakeholder groups. Deductive and inductive content analysis were used to identify barrier and facilitator categories across the five levels of the Socioecological Model. Overall, participants discussed factors at every level, and many barriers and facilitators confirmed findings from existing literature focused on MOUD access for formerly incarcerated individuals. Participants also identified factors more specific to community pharmacies, including 1) lack of interagency collaboration between pharmacists, prescribers, and correctional facilities and 2) lack of awareness of community pharmacist-provided MOUD services. Future research should explore interventions to address the barriers identified in this study and improve connections between community pharmacists and formerly incarcerated individuals. This work can help ensure that these individuals are given the chance to successfully reintegrate into society.
Plasma glucosylceramide levels are regulated byATP10Dand are not involved in Parkinson’s disease pathogenesis
Authors: Somerville Emma N. , James Alva , Beetz Christian , Schwieger Robert , Barrel Gal , Kandaswamy Krishna K. , Iurascu Marius I. , Bauer Peter , Ta Michael , Iwaki Hirotaka , Senkevich Konstantin , Yu Eric , Alcalay Roy N. , Gan-Or Ziv
Published: September 2024

GBA1variants and decreased glucocerebrosidase (GCase) activity are implicated in Parkinson’s disease (PD). We investigated the hypothesis that increased levels of glucosylceramide (GlcCer), one of GCase main substrates, are involved in PD pathogenesis. Using multiple genetic methods, we show thatATP10D, notGBA1, is the main regulator of plasma GlcCer levels, yet it is not involved in PD pathogenesis. Plasma GlcCer levels were associated with PD, but not in a causative manner, and are not predictive of disease status. These results argue against targeting GlcCer inGBA1-PD and underscore the need to explore alternative mechanisms and biomarkers for PD.
Covidization and decovidization of the scientific literature and scientific workforce
Authors: Ioannidis John P. A. , Collins Thomas A. , Bendavid Eran , Baas Jeroen
Published: September 2024

We examined the growth trajectory and impact of COVID-19-related papers in the scientific literature until August 1, 2024 and how the scientific workforce was engaged in this work. Scopus indexed 718,660 COVID-19-related publications. As proportion of all indexed scientific publications, COVID-19-related publications peaked in September 2021 (4.7%) remained at 4.3-4.6% for another year and then gradually declined, but was still 1.9% in July 2024). COVID-19-related publications included 1,978,612 unique authors: 1,127,215 authors had ≥5 full papers in their career and 53,418 authors were in the top-2% of their scientific subfield based on a career-long composite citation indicator. Authors with >10%, >30% and >50% of their total career citations be to COVID-19-related publications were 376,942, 201,702, and 125,523, respectively. As of August 1, 2024, 65 of the top-100 most-cited papers published in 2020 were COVID-19-related, declining to 24/100, 19/100, 7/100, and 5/100 for the most-cited papers published in 2021, 2022, 2023, and 2024, respectively. Across 174 scientific subfields, 132 had ≥10% of their active influential (top-2% by composite citation indicator) authors publish something on COVID-19 during 2020-2024. Among the 300 authors with highest composite citation indicator specifically for their COVID-19-related publications, 41 were editors or journalists/columnists and another 23 had most of their COVID-19 citations to published items other than full papers (opinion pieces/letters/notes). COVID-19 massively engaged the scientific workforce in unprecedented ways. As the pandemic ended, there has been a sharp decline in the overall volume and high impact of newly published COVID-19-related publications.

Significance statement

COVID-19 massively mobilized the scientific workforce. Between 2020 and 2024, over 700,000 papers were published on COVID-19, including 2 million different authors. Across science, almost a third of authors at the top-2% of citation impact in their subfield published on COVID-19. There was a sharp decline in the proportion of COVID-19 papers across science after 2022 and an even more sharp decline in the proportion of COVID-19 papers reaching the highest level of citations. Authors with the highest COVID-19 citation impact prominently included many who were editors, journalists/columnists and opinion writers publishing massively. While other epidemics also witnessed sharp increases and subsequent decline in interest, the magnitude of the covidization and decovidization process is unique in the scientific literature to-date.
Improving Access and Efficiency of Acute Ischemic Stroke Treatment Across Four Canadian Provinces: A Stepped-Wedge Trial
Authors: Kamal Noreen , Cora Elena A. , Alim Simone , Goldstien Judah , Volders David , Aljendi Shadi , Williams Heather , Fok Patrick T. , van der Linde Etienne , Helm-Neima Trish , Cashin Renee , Metcalfe Brian , BNSc Julie Savoie , Simpkin Wendy , Chisholm Cassie , Hill Michael D , Menon Bijoy K. , Phillips Stephen ,   the ACTEAST Collaborators
Published: September 2024

Background

The translation of standard-of-care in acute ischemic stroke reperfusion interventions into practice is well established, but multifactorial obstacles exist in the complete adoption, which has led to inequities in access and delivery of services. The objective of this study was to improve access and efficiency of ischemic stroke treatment across four Atlantic Canadian Provinces.

Methods

A stepped-wedge cluster trial was conducted over 30 months with 3 clusters covering 34 sites. The trial was conducted across all 4 Atlantic Canadian provinces: Nova Scotia (NS), New Brunswick (NB), Prince Edward Island (PE), and Newfoundland and Labrador (NL). The design was quasi-randomized, with each cluster associated with one or more provinces: cluster 1 – NS; cluster 2 – NB and PE; and cluster 3 – NL. The patient population was all ischemic stroke patients across all 4 provinces. The intervention was a 6-month modified Quality Improvement Collaborative (mQIC), which was modified from the Breakthrough Series Collaborative to be half of the 1-year period and conducted virtually. The intervention consisted of assembling an interdisciplinary improvement team, 2 full-day workshops, webinars, and virtual site visits. Suggested changes included 6 process improvement strategies.

Results

Over the trial period, 8594 ischemic stroke patients were included, out of which 1576 patients received acute treatment. The proportion of patients that received treatment did not increase significantly with the intervention [0.4% increase for patients that received thrombolysis and/or EVT (p=0.68)]. Median door-to-needle time was reduced by 9.2 minutes with the intervention (p=0.01). Cluster 3 saw the greatest improvements in both access and efficiency.

Conclusions

A mQIC intervention resulted in improvement of process measures like door-to-needle time. Quality improvement initiatives may need to be longer to allow full implementation and tailored for each health system to ensure that each system sees improvement. In-person activities might be critical to ensure fidelity of the intervention.
Introduction of cytosine-5 DNA methylation sensitizes cells to oxidative damage
Authors: Krwawicz J. , Sheeba C.J. , Hains K. , McMahon T. , Zhang Y. , Kriaucionis S. , Sarkies P.
Published: September 2024

DNA methylation at the 5 position of cytosine (5mC) is an ancient epigenetic mark in eukaryotes. The levels of total 5mC vary enormously between different species, and the DNA methyltransferases that introduce 5mC have been repeatedly lost in several independent lineages. DNA methyltransferases are a threat to genomic stability due to the increased mutagenicity of 5mC bases and the propensity of DNA methyltransferases themselves to introduce DNA alkylation damage as an off-target effect. However, whether alkylation damage explains why 5mC is frequently lost in evolution is unclear. Here we tested the fitness consequences of DNA methyltransferase-induced alkylation damage by introducing a eukaryotic-like 5mC system intoE. coli. We showed that introducing 5mC genome-wide leads to increased sensitivity to alkylating agents, which is strongly enhanced by removal of the 3mC repair enzyme AlkB. Unexpectedly, we discovered that 5mC introduction led to increased sensitivity to oxidative stress. We showed that this is due to increased formation of reactive oxygen in the presence of 5mC. We determined that reactive oxygen species led to non-enzymatic oxidation of 5mC, producing modified cytosines such as 5fC that are recognised as DNA base damage inE. coli. Overall, our work identifies increased sensitivity to oxidative stress, as well as alkylating agents, as a negative consequence of genome-wide 5mC. Oxidative stress is frequently encountered by organisms in their environment, thus offering a plausible reason for total loss of 5mC in some species.
Proof of Concept for High-Dose Cannabidiol Pretreatment to Antagonize Opioid Induced Persistent Apnea
Authors: Wiese Beth M. , Bondarenko Evgeny , Feldman Jack L.
Published: September 2024

Using a mouse equivalent of FDA-approved cannabidiol (CBD) dosing, we found high dose CBD affects opioid induced persistent apnea (OIPA), the principal cause of opioid related fatalities. CBD pretreatment mitigated respiratory depression from fentanyl in awake mice and significantly delayed OIPA onset in anesthetized mice, effective as the opioid antagonist naloxone. The powerful effect of CBD pretreatment on OIPA suggests a novel therapeutic strategy to reduce fatal opioid overdose incidence.
Neocortical and hippocampal theta oscillations track audiovisual integration and replay of speech memories
Authors: Biau Emmanuel , Wang Danying , Park Hyojin , Jensen Ole , Hanslmayr Simon
Published: September 2024

“Are you talkin’ to me?!” If you ever watched the masterpiece “Taxi driver” directed by Martin Scorsese, you certainly recall the famous monologue during which Travis Bickle rehearses an imaginary confrontation in front of a mirror. While remembering this scene, you recollect a myriad of speech features across visual and auditory senses with a smooth sensation of unified memory. The aim of this study was to investigate how brain oscillations integrate the fine-grained synchrony between coinciding visual and auditory features when forming multisensory speech memories. We developed a memory task presenting participants with short synchronous or asynchronous movie clips focusing on the face of speakers engaged in real interviews. In the synchronous condition, the natural alignment between visual and auditory onsets was kept intact. In the asynchronous condition, auditory onsets were delayed to present lip movements and speech sounds in antiphase specifically with respect to the theta oscillation synchronising them in the original movie. We recorded magnetoencephalographic (MEG) activity to investigate brain oscillations in response to audiovisual asynchrony in the theta band. Our results first showed that theta oscillations in the neocortex and hippocampus were modulated by the level of synchrony between lip movements and syllables during audiovisual speech perception. Second, the accuracy of subsequent theta oscillation reinstatement during memory recollection was decreased when lip movements and the auditory envelope were encoded in asynchrony during speech perception. We demonstrate that neural theta oscillations in the neocortex and the hippocampus integrated lip movements and syllables during natural speech. We conclude that neural theta oscillations play a pivotal role in both aspects of audiovisual speech memories, i.e., encoding and retrieval.
Sphingosine kinase 1 is induced by glucocorticoids in adipose derived stem cells and enhances glucocorticoid mediated signaling in adipose expansion
Authors: Lambert Johana , Kovilakath Anna , Jamil Maryam , Valentine Yolander , Anderson Andrea , Montefusco David , Cowart L. Ashley
Published: September 2024

Sphingosine kinase 1 (SphK1) plays a crucial role in regulating metabolic pathways within adipocytes and is elevated in the adipose tissue of obese mice. While previous studies have reported both pro- and inhibitory effects of SphK1 and its product, sphingosine-1-phosphate (S1P), on adipogenesis, the precise mechanisms remain unclear. This study explores the timing and downstream effects of SphK1/S1P expression and activation duringin vitroadipogenesis. We demonstrate that the synthetic glucocorticoid dexamethasone robustly induces SphK1 expression, suggesting its involvement in glucocorticoid-dependent signaling during adipogenesis. Notably, the activation of C/EBPδ, a key gene in early adipogenesis and a target of glucocorticoids, is diminished in SphK1-/- adipose-derived stem cells (ADSCs). Furthermore, glucocorticoid administration promotes adipose tissue expansion via SphK1 in a depot-specific manner. Although adipose expansion still occurs in SphK1-/- mice, it is significantly reduced. These findings indicate that while SphK1 is not essential for adipogenesis, it enhances early gene activation, thereby facilitating adipose tissue expansion.
Vestibular involvement in transcranial electrical stimulation: body sway as a marker of unintended stimulation
Authors: Laakso Ilkka , Nissi Janita , Kangasmaa Otto
Published: September 2024

Background

Transcranial electrical stimulation (tES) techniques are widely used to modulate brain excitability, though their mechanisms remain unclear.

Objective

We aimed to demonstrate that an alternating current applied to several commonly used tES electrode montages can influence the vestibular system.

Methods

Body-sway responses during alternating current stimulation at 4.6 or 4.8 Hz were measured in eight participants standing on a force platform. Sham and five active conditions, including common motor cortical tES electrode montages, were applied in a double-blind experiment.

Results

All active conditions increased lateral body sway compared with sham at the stimulus frequency, with very large to huge effect sizes. The sway magnitude was proportional to the montage-specific electric field within the vestibular system, obtained from a computational model. The frequency and phase of the body sway were locked to the stimulus frequency and phase. An additional experiment in three participants showed that the sway response was the largest in the lower legs, similarly for both tES with a motor cortical electrode montage and an electrical vestibular stimulation montage. Together, the results suggest a direct effect of tES on the vestibular system.

Conclusion

Unwanted vestibular effects may interfere with the interpretation of tES studies across a wide range of typical tES frequencies and current intensities.

Highlights

Alternating current stimulation produces a lateral body sway at the stimulation frequency.

Larger lateral electric field in the vestibular system produces a larger sway.

Several common tES montages can directly influence the vestibular system.

Unwanted vestibular effects may complicate the interpretation of tES studies.
Phage-phage competition and biofilms reduce the efficacy of a combination of two virulent bacteriophages againstPseudomonas aeruginosa
Authors: Bürkle Magdalena , Korf Imke H. E. , Lippegaus Anne , Krautwurst Sebastian , Rohde Christine , Weissfuss Chantal , Nouailles Geraldine , Tene Xavière Menatong , Gaborieau Baptiste , Ghigo Jean-Marc , Ricard Jean-Damien , Hocke Andreas C. , Papenfort Kai , Debarbieux Laurent , Witzenrath Martin , Wienhold Sandra-Maria , Krishnamoorthy Gopinath
Published: September 2024

Combined use of virulent bacteriophages (phages) and antibiotics reduces the severity of difficult-to-treatPseudomonas aeruginosainfections in many patients.In vitromethods that attempt to reproduce more than one physiological state of the pathogens can provide a valuable assessment of antibacterials like phages. Here, by measuring bacterial killing kinetics and individual replication in different growth conditions, including biofilms and a human lung epithelial cell line, we elucidated factors influencing the efficacy of two virulent phages againstP. aeruginosaPAO1. A single administration of phages effectively reduced theP. aeruginosaviability in planktonic conditions and infected human lung cell cultures, however, the emergence of phage-resistant variants occurred subsequently. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and meropenem. In contrast, surface-attached biofilms exhibited tolerance to phage and/or meropenem, suggesting a spatiotemporal variation in the antibacterial effect. Moreover, the phage with the shorter lysis time lysedP. aeruginosamore rapidly and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage of the combination. The sequential addition of phages resulted in their unimpeded replication with no increase in bacteriolytic activity. These findings highlight biofilm developmental stages, phage-phage competition, and phage resistance as factors restricting thein vitroefficacy of a two-phage combination. Our findings provide a framework for selecting and optimizing phage combinations for enhanced efficacy againstP. aeruginosa, a metabolically flexible pathogen that undergoes specific adaptation within the infected lung.
Beyond EEG Onset Transients: Sensitisation and Habituation of Hyper-excitation to Constant Presentation and Offset of Pattern-Glare Stimuli
Authors: Jefferis Tom , Dogan Cihan , Miller Claire E. , Karathanou Maria , Tempesta Austyn J. , Schofield Andrew J. , Bowman Howard
Published: September 2024

Pattern-glare, characterised by visual distortions, discomfort, and stress when viewing striped patterns, has been associated with cortical hyperexcitability, particularly in individuals with visually induced epilepsy, migraines, and visual stress. While previous studies have explored the onset transients of such stimuli, this research investigates the sensitisation and habituation effect to the constant presentation and offset of pattern-glare stimuli. We analysed the temporal characteristics of the Event Related Potentials (ERPs) in healthy participants to find correlates of cortical hyperexcitability over two time granularities: a fine granularity (over seconds) and a coarser granularity (across the time-course of the entire experiment). We looked for habituation and sensitization effects across these time periods. Our results suggest that brain responses to pattern-glare stimuli are correlated to participants’ sensitivity to visual discomfort with statistically significant effects observed for this factor and for its interaction with changes over time. This study improves our understanding of how the brain adapts to persistent visual stimuli and provides insights that may inform treatments for conditions like migraine and epilepsy.
An inhibitor targeting glycosome membrane biogenesis killsLeishmaniaparasites
Authors: Chou Shih-En , Kalel Vishal C. , Erdmann Ralf
Published: September 2024

Leishmaniasis is a life-threatening neglected tropical disease caused by over 20 species ofLeishmaniaparasites. Visceral leishmaniasis, also known as kala-azar, is particularly lethal, with a 95% mortality rate if left untreated. Currently, no vaccine is available, and chemotherapy remains the primary treatment option. However, these drugs have drawbacks such as high toxicities, the emergence of resistant strains, and high costs. Therefore, there is a need to develop new and safe treatments. Glycosomes are essential organelles for the survival ofLeishmaniaparasites. They are maintained by peroxin (PEX) proteins, which are responsible for glycosome biogenesis, including targeting proteins to glycosomes. Previous studies have shown that blocking the interaction between the import receptor PEX19 and the docking factor PEX3 killsTrypanosoma bruceiby disrupting glycosome biogenesis. In this study, we screened an FDA-approved drug repurposing library using an AlphaScreen based assay and identified inhibitors ofLdPEX3-LdPEX19 interactionin vitro. The inhibitor effectively killsLeishmaniaparasites, including the challenging amastigote forms contained within the infected mammalian host cells. This study validates the inhibition of glycosome biogenesis inLeishmaniaas a potential approach for developing new anti-leishmanial therapies.
Utilization and degradation of laminarin-based substrates by marine yeasts suggests their niche-specific role in microbial loop dynamics
Authors: Arslan-Gatz Berin S. , Schultz-Johansen Mikkel , Hollwedel Tom-Niklas , Niggemeier Sofie , Nimzyk Rolf , Wichels Antje , Gerdts Gunnar , Hehemann Jan-Hendrik , Harder Tilmann , Reich Marlis
Published: September 2024

In the oceans, the diversity of phytoplankton primary products supports a wide range of microbial heterotrophs, including bacteria and fungi. The organic substrate dynamics within pelagic microbial communities are strongly controlled by microorganismal interactions, resulting in a dense interactome. While the role of bacteria in the microbial loop is well documented, the degradation capacity and substrate specificity of marine fungi, as well as their role and function in metabolic guilds with bacteria, is comparatively less understood. We chose the polysaccharide laminarin, a major product of marine primary production, as well as oligomeric laminarin subunits and monomeric glucose, to study the degradation capacity of eleven marine yeast isolates from the pelagic microbial community of Helgoland Roads. Our aim was to measure yeast growth and correlate degradation yields and putative intermediate degradation products with the size of laminarin-based organic precursor substrates. We developed a reproducible, temporally resolved, high-throughput growth protocol to measure resource-specific yeast growth. Measurement of temporally fine-scaled growth kinetic models of isolates were accompanied with qualitative and quantitative chemical analyses of substrates and degradation intermediates. Our data showed that yeast growth was negatively correlated with oligomer length. Fluorophore-assisted carbohydrate electrophoresis suggested the lack of enzymatic endo-activity for laminarin in yeasts under investigation, suggesting they may occupy a niche in the microbial loop, benefitting from extracellular hydrolysis of carbohydrates by other microorganisms. In terrestrial environments, namely forest soil ecosystems, yeasts have been assigned a similar niche, supporting a prominent role of yeasts in microbial interactomes.
The XbnAb Cohort: 304 people with broadly neutralizing antibody activity to HIV-1
Authors: Pasin Chloé , Rusert Peter , Schmidt Daniel , Schanz Merle , Friedrich Nikolas , Abela Irene A. , Kusejko Katharina , Niklaus Cyrille , Sickmann Michèle , Weber Jacqueline , Huber Michael , Manrique Amapola , Rauch Andri , Calmy Alexandra , Cavassini Matthias , Stöckle Marcel , Notter Julia , Bernasconi Enos , Braun Dominique L. , Günthard Huldrych F. , Kouyos Roger D. , Trkola Alexandra ,   the Swiss HIV Cohort Study
Published: September 2024

Broadly neutralizing antibodies (bnAbs) recognizing a diversity of HIV-1 strains are widely thought to be essential for an HIV-1 vaccine. Extensive knowledge on bnAbs has been gained from studying natural HIV infection by following bnAb evolution in individual people with HIV (PWH). However, it remains essential to increase knowledge of bnAb responses in large PWH cohorts to assess the feasibility of inducing bnAb activity by vaccination. To allow a systematic analysis, we created the XbnAb cohort, a large bnAb-inducer cohort selected by screening plasma of PWH enrolled in the Swiss HIV Cohort Study (SHCS) and the Zurich Primary HIV Infection Study (ZPHI). The XbnAb cohort represents a retrospective, biobank-based cohort comprising data of 304 PWH who developed bnAb activity during HIV-1 infection. Here, we report on the characteristics of the XbnAb cohort and its potential for HIV vaccine research.
Epigenetic control and inheritance of rDNA arrays
Authors: Potapova Tamara , Kostos Paxton , McKinney Sean , Borchers Matthew , Haug Jeff , Guarracino Andrea , Solar Steven , Gogol Madelaine , Anez Graciela Monfort , de Lima Leonardo Gomes , Wang Yan , Hall Kate , Hoffman Sophie , Garrison Erik , Phillippy Adam M. , Gerton Jennifer L.
Published: September 2024

Ribosomal RNA (rRNA) genes exist in multiple copies arranged in tandem arrays known as ribosomal DNA (rDNA). The total number of gene copies is variable, and the mechanisms buffering this copy number variation remain unresolved. We surveyed the number, distribution, and activity of rDNA arrays at the level of individual chromosomes across multiple human and primate genomes. Each individual possessed a unique fingerprint of copy number distribution and activity of rDNA arrays. In some cases, entire rDNA arrays were transcriptionally silent. Silent rDNA arrays showed reduced association with the nucleolus and decreased interchromosomal interactions, indicating that the nucleolar organizer function of rDNA depends on transcriptional activity. Methyl-sequencing of flow-sorted chromosomes, combined with long read sequencing, showed epigenetic modification of rDNA promoter and coding region by DNA methylation. Silent arrays were in a closed chromatin state, as indicated by the accessibility profiles derived from Fiber-seq. Removing DNA methylation restored the transcriptional activity of silent arrays. Array activity status remained stable through the iPS cell re-programming. Family trio analysis demonstrated that the inactive rDNA haplotype can be traced to one of the parental genomes, suggesting that the epigenetic state of rDNA arrays may be heritable. We propose that the dosage of rRNA genes is epigenetically regulated by DNA methylation, and these methylation patterns specify nucleolar organizer function and can propagate transgenerationally.
Discovery and Functional analysis of a novelALPK1variant in ROSAH syndrome
Authors: Snelling Tom , Garnotel Leo O. , Jeru Isabelle , Tusseau Maud , Cuisset Laurence , Perlat Antoinette , Minard Geoffrey , Benquey Thibaut , Maucourant Yann , Wood Nicola T. , Cohen Philip , Ziegler Alban
Published: September 2024

ROSAH syndrome is an autosomal dominant autoinflammatory disorder characterised by visual disturbance caused by pathogenic variation in the protein kinase ALPK1. Only two such variants have been reported to cause ROSAH syndrome to date: 66 out of 67 patients harbour the Thr237Met variant, while a single patient carries a Tyr254Cys variant. Here we identify a family in which ROSAH syndrome is caused by a Ser277Phe variant inALPK1. The phenotypic variability in this family is high, with four of the seven individuals legally blind. Hypohidrosis, splenomegaly and arthritis were present in several family members. In contrast to wildtype ALPK1, which is activated specifically by the bacterial metabolite ADP-heptose during bacterial infection, ALPK1[Ser277Phe] was also activated by the human metabolites UDP-mannose and ADP-ribose, even more strongly than the ALPK1[Thr237Met] variant. However, unlike ALPK1[Thr237Met], ALPK1[Ser277Phe] could additionally be activated by GDP-mannose. These observations can explain why theseALPK1variants are active in cells in the absence of ADP-heptose and hence why patients have episodes of autoinflammation. Examination of the three-dimensional structure of ALPK1 revealed that the sidechains of Ser277 and Tyr254 interact but mutational analysis established that this interaction is not critical for the integrity of the ADP-heptose binding site. Instead, it is replacement of Ser277 by a large hydrophobic phenylalanine residue or the replacement of Tyr254 by a much smaller cysteine residue that is responsible for altering the specificity of the ADP-heptose-binding pocket. The characterisation ofALPK1variants that cause ROSAH syndrome suggests ways in which drugs that inhibit these disease-causing variants selectively can be developed.
Visual imagery of familiar people and places in category selective cortex
Authors: Scrivener Catriona L. , Teed Jessica A. , Silson Edward H.
Published: September 2024

Visual mental imagery is a dynamic process that involves a network of multiple brain regions. We used an electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) fusion approach to ask how the neural dynamics of category selective mental imagery in EEG related to activity within medial parietal, ventral temporal, and primary visual cortex (V1). Subjects attended separate EEG and fMRI sessions where they were asked to recall personally familiar people and place stimuli. The fMRI contrast of places versus people successfully replicated previous findings of category-selectivity in the medial parietal cortex during visual recall (Silson et al., 2019), as well as other regions including the ventral and lateral place memory areas, the fusiform face area, and frontal eye fields. Using multivariate decoding analysis in pre-defined fMRI regions of interest (ROIs), we tested the hypothesis that we would be able to decode individual stimuli within the preferred category for each region. This was largely the case in the ventral temporal ROIs, but a more complex pattern emerged in the medial parietal cortex; these regions represented information during imagery that was not restricted to their preferred category. EEG-fMRI fusion indicated that the timing of both medial parietal and ventral temporal involvement peaked early on during recall but did not clearly differ from each other. However, place-selective regions generally peaked earlier than people-selective regions, suggesting that representations of place stimuli evolved more quickly for these subjects. This mirrors the results from EEG stimuli decoding, where individual places were decodable earlier in time than people. In contrast, fusion correlations in V1 occurred later during the recall period, possibly reflecting the top-down progression of mental imagery from category-selective regions to primary visual cortex.
A Novel Rapid Host Cell Entry Pathway Determines Intracellular Fate ofStaphylococcus aureus
Authors: Rühling Marcel , Schmelz Fabio , Ulbrich Kim , Wolf Julia , Pfefferle Maximilian , Moldovan Adriana , Knoch Nadine , Iwanowitsch Andreas , Kappe Christian , Paprotka Kerstin , Arenz Christoph , Fraunholz Martin J.
Published: September 2024

Staphylococcus aureusis an opportunistic pathogen causing severe diseases. Recently,S. aureuswas recognized as intracellular pathogen with the intracellular niche promoting immune evasion and antibiotic resistance. We identified an alternative mechanism governing cellular uptake ofS. aureuswhich relies on lysosomal Ca2+, lysosomal exocytosis and occurs concurrently to other well-known entry pathways within the same host cell population. This internalization pathway is rapid and active within only few minutes after bacterial contact with host cells. Compared to slow bacterial internalization, the rapid pathway demonstrates altered phagosomal maturation as well as translocation of the pathogen to the host cytosol and ultimately results in different rates of intracellular bacterial replication and host cell death. We show that these alternative infection outcomes are caused by the mode of bacterial uptake.
Glial alterations in the glutamatergic and GABAergic signaling pathways in a mouse model of Lafora disease, a severe form of progressive myoclonus epilepsy
Authors: Viana Rosa , Rubio Teresa , Campos-Rodríguez Ángela , Sanz Pascual
Published: September 2024

Lafora disease (LD; OMIM#254780) is a rare form of progressive myoclonus epilepsy characterized by the accumulation of insoluble deposits of aberrant glycogen (polyglucosans), named Lafora bodies (LBs), in the brain but also in peripheral tissues. It is assumed that the accumulation of LBs is related to the appearance of the characteristic pathological features of the disease. In mouse models of LD, we and others have reported an increase in the levels of reactive astrocytes and activated microglia, which triggers the expression of the different pro-inflammatory mediators. Recently, we have demonstrated that the TNF and IL-6 inflammatory signaling pathways are the main mediators of the neuroinflammatory phenotype associated with the disease. In this work, we present evidence that the activation of these pathways produces a dysregulation in the levels of different subunits of the excitatory ionotropic glutamatergic receptors (phopho-GluN2B, phospho-GluA2, GluK2) and also an increase in the levels of the GABA transporter GAT1 in the hippocampus of theEpm2b-/-mice. In addition, we present evidence of the presence of activated forms of the Src and Lyn protein kinases in this area. These effects may increase the excitatory glutamatergic signaling and decrease the inhibitory GABAergic tone, leading to hyper-excitability. More importantly, the enhanced production of these subunits occurs in non-neuronal cells such as activated microglia and reactive astrocytes, pointing out a key role of glia in the pathophysiology of LD.
Profiling the physiological impact of aberrant folded-state protein filamentation in cells
Authors: Levin Tal , Garcia-Seisdedos Hector , Lobov Arseniy , Wojtynek Matthias , Alexandrov Alexander , Jona Ghil , Levi Dikla , Medalia Ohad , Levy D. Emmanuel
Published: September 2024

The formation of large polymeric structures such as cytoskeletal and enzyme filaments is crucial for normal cellular function. However, such filaments can also form due to mutations that create self-interactions at the surface of symmetric proteins. Often, the proteins forming these structures maintain a folded state and thereby differ from aggregates and amyloids that involve misfolding. We refer to this type of assemblies asagglomeratesto mark this difference. While cells have quality control mechanisms to identify, buffer, and eliminate misfolded proteins, it is unclear whether similar mechanisms exist for agglomerates, or whether agglomerates are toxic to cells. Here, we profiled the physiological impact of mutation-induced folded-state protein filamentation in yeast cells. First, we devised a simple strategy to distinguish fluorescently labeled proteins forming agglomerates versus aggregates. We then profiled exogenous protein agglomerates in terms of their recognition by known quality control mechanisms, their effects on specific cellular processes and overall fitness onS. cerevisiaecultures. We found that agglomerates do not colocalize with the proteostasis machinery and do not result in measurable fitness defects. Proteomics profiling of cells expressing the wild type protein, agglomerating or misfolded variants revealed a consistent picture, with only minor, agglomerate-size-dependent changes observed and linked to the cell-wall and plasma-membrane proteins. Overall, our findings indicate that agglomerates form mostly benign structures in cells when compared to aggregates, and thereby offer a promising route for synthetic biology applications.

Graphical Abstract
Alpha-2 agonism of the locus coeruleus impairs learning driven by negative prediction error
Authors: Lui Simon K. C. , Brink Ashleigh K. , Corbit Laura H.
Published: September 2024

Refining previous learning when environmental contingencies change is a critical adaptive function. Studies have shown that systemic noradrenaline (NA) manipulations, as well as optogenetic manipulations of the locus coeruleus (LC), the primary source of forebrain NA, can strengthen long-term retention of appetitive extinction. To determine whether the contribution of NA is specific to extinction or extends to other forms of learning where reward is less than expected, we suppressed LC activity with clonidine, an α2A-adrenergic receptor agonist, in two tasks: compound extinction, where two previously rewarded cues are paired and no longer rewarded, and overexpectation, where animals are presented with two previously rewarded cues but receive a single reward rather than the expected two. In compound extinction, we found no differences between groups in training, extinction, or a spontaneous recovery test. However, animals that received clonidine reacquired responding to the previously extinguished cue significantly faster than saline animals, suggesting weakened extinction learning. In overexpectation testing, the saline group responded significantly less to a stimulus that had undergone overexpectation relative to a control stimulus, indicating that they had recalibrated their estimation of reward magnitude following training where reward was less than expected. In contrast, clonidine-treated animals did not differ in responding to the overexpectation versus control stimuli, suggesting that clonidine impaired learning resulting from overexpectation. These results demonstrate that activity of the LC is important for learning to reduce responding in both extinction and overexpectation paradigms.
Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect between affinity and activation of ZTP riboswitch ligands
Authors: Fullenkamp Christopher R. , Mehdi Shams , Jones Christopher P. , Tenney Logan , Pichling Patricio , Prestwood Peri R. , Ferré-D’Amaré Adrian R. , Tiwary Pratyush , Schneekloth John S.
Published: September 2024

The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced stabilization, and how conformational changes influence gene expression pose significant difficulties for experimental investigation. This work employs a combination of computational and experimental methods to address these challenges. By integrating structure-informed design, crystallography, and machine learning-augmented all-atom molecular dynamics simulations (MD) we synthesized, biophysically and biochemically characterized, and studied the dissociation of a library of small molecule activators of the ZTP riboswitch, a ligand-binding RNA motif that regulates bacterial gene expression. We uncovered key interaction mechanisms, revealing valuable insights into the role of ligand binding kinetics on riboswitch activation. Further, we established that ligand on-rates determine activation potency as opposed to binding affinity and elucidated RNA structural differences, which provide mechanistic insights into the interplay of RNA structure on riboswitch activation.
Enhancer adoption by an LTR retrotransposon generates viral-like particles causing developmental limb phenotypes
Authors: Glaser Juliane , Cova Giulia , Fauler Beatrix , Prada-Medina Cesar A. , Stanislas Virginie , Phan Mai H.Q. , Schöpflin Robert , Aktas Yasmin , Franke Martin , Andrey Guillaume , Paliou Christina , Laupert Verena , Chan Wing-Lee , Wittler Lars , Mielke Thorsten , Mundlos Stefan
Published: September 2024

Mammalian genomes are scattered with transposable elements (TEs). TEs are epigenetically silenced to prevent harmful effects caused by either global activation leading to genome instability or insertional mutation disturbing gene transcription. However, whether the activation of a single element can contribute to pathological phenotypes without directly affecting gene expression is largely unknown. Here, we show that tissue-specific expression of a TE in the embryo leads to the production of viral-like particles (VLPs) which can affect organ formation. Failure to silence an LTR retrotransposon inserted upstream of theFgf8gene results in its co-expression withFgf8in the developing embryo. While local gene regulation is unaffected, the LTR retrotransposon participates in chromatin folding at the locus and adopts the expression of the regulatory domain it is located in. This drives the production of VLPs in theFgf8-expressing cells of the developing limb, triggering apoptotic cell death at the time of digit outgrowth and resulting in a limb malformation resembling human ectrodactyly. This phenotype can be rescued by knock-out or knock-in of the retrotransposon causing mutations preventing its full retroviral cycle. Insertion of the same element at other developmental loci faithfully recapitulates expression according to the neighboring regulatory activity. Our findings provide a mechanism by which TE insertion is incorporated into the local genomic regulatory landscape and show how VLP production in post-implantation embryos can interfere with organ formation.
The microbiota extends the reproductive lifespan by safeguarding the ovarian reserve
Authors: Munyoki Sarah K. , Goff Julie P. , Reshke Amanda , Wilderoter Erin , Mafarachisi Nyasha , Kolobaric Antonija , Sheng Yi , Mullett Steven J. , King Gabrielle E. , DeSchepper Jacob D. , Bookser Richard J. , Castro Carlos A. , Gelhaus Stacy L. , Grizotte-Lake Mayara , Morrison Kathleen E. , Zeleznik Anthony J. , Hand Timothy W. , Brieño-Enriquez Miguel A. , Jašarević Eldin
Published: September 2024

Infertility is a devastating condition affecting one in six people globally. In many cases, the underlying causes are unknown. Emerging evidence suggests that the microbiota influences reproduction, yet the mechanistic link between the microbiota, ovarian function, and length of the fertile lifespan remain unexplored. Here we report that the microbiota controls the length of the reproductive lifespan by maintaining the primordial follicle pool, a process mediated by microbiota-derived short chain fatty acids modulating gene regulatory networks crucial for the survival of the ovarian reserve. Dietary perturbation of the microbiota during a critical developmental window is sufficient to diminish the ovarian reserve, reduce oocyte retrieval, and impair preimplantation embryo viability, mirroring challenges in human fertility treatments. Targeted interventions to restore microbiota improve assisted reproductive outcomes, particularly when implemented early. These findings reveal a novel contribution of host-microbe interactions in mammalian reproduction and demonstrate that the microbiota impacts ovarian function and fertility.
SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots
Authors: Uruci Sidrit , Hoitsma Nicole M. , Solér-Oliva María E. , Bayona-Feliu Aleix , Gaggioli Vincent , García-Rubio María L. , Lo Calvin S.Y. , Bakker Collin , Marinello Jessica , Manolika Eleni Maria , Capranico Giovanni , Luijsterburg Martijn S. , Luger Karolin , Aguilera Andrés , Taneja Nitika
Published: September 2024

DNA replication often encounters obstacles like the stalled transcription machinery and R-loops. While ribonucleases and DNA-RNA helicases can resolve these structures, the role of chromatin remodelers remains understudied. Through a series ofin vitroandin vivoexperiments, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, is crucial for resolving nearby R-loops to maintain fork stability. SMARCAD1 directly binds R-loops via its ATPase domain and associates with the replisome through its N-terminus region. Both interactions are critical for resolving R-loops within cells. Genome-wide assays reveal that cells expressing mutant SMARCAD1 accumulate significantly more R-loops than wild-type cells, particularly in regions distinct from known fork blockage-prone sites. These R-loop-enriched regions in SMARCAD1 mutants also exhibit increased mutagenesis in germline tumors, suggesting they are mutation hotspots in cancer. Therefore, SMARCAD1 acts as an R-loop sensor and resolvase at actively progressing forks, maintaining genome stability and preventing tumorigenesis.
Diversification and conservation of DNA binding specificities of SPL family of transcription factors
Authors: Li Miaomiao , Yao Tao , Galli Mary , Lin Wanru , Zhou Yilin , Chen Jin-Gui , Gallavotti Andrea , Huang Shao-shan Carol
Published: September 2024

SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors inArabidopsis thaliana, providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins. Comparative analysis between the paralogs AtSPL9 and AtSPL15 revealed differences in their binding motifs, suggesting divergent regulatory functions. Additionally, we expanded our investigation to homologs of AtSPL9/15 inZea mays(ZmSBP8/30) andTriticum aestivum(TaSPL7/13), identifying conserved and unique DNA-binding patterns across species. These findings provide key resources for understanding the molecular mechanisms of SPL transcription factors in regulating plant development and evolution across different species.