bluuebunny/crossref_metadata_2025 huggingface dataset:
An ornithological survey of Fergusson Island, D’Entrecasteaux Archipelago, Papua New Guinea, reveals new island records and noteworthy natural history observations
Authors: Boersma Jordan , Gregg Jason , Nason Doka , Malesa Eli , Le Breton Cosmo , Ketaloya Serena , Iova Bulisa , Mittermeier John C.
Published: July 2024

Fergusson Island lies off the southeastern end of New Guinea and is the largest landmass in the D’Entrecasteaux and Trobriand Island Endemic Bird Area. We conducted audiovisual and camera trapping surveys in eastern Fergusson in September 2022 and recorded 97 bird species, documenting breeding and vocalizations for several of the EBA’s endemic taxa. Notably, we provide the first confirmed documentation of the “lost”insularissubspecies of Pheasant PigeonOtidiphaps nobilis(often recognized as a distinct species, Black-naped Pheasant-pigeon), in 126 years, observations of eight bird species not previously recorded from Fergusson, and nesting of Goldie’s Bird-of-ParadiseParadisea decoraand the endemiccrookshankitaxon of Capped White-eyeZosterops fuscicapilla(or Oya Tabu White-eye). Our new distributional records were mostly either migratory species or species found in open habitats, highlighting the value of surveying across seasons and habitats. We summarise our results and provide comments on distributional records, breeding behaviour, and vocalizations.
Deciphering thecis-regulatory landscape of natural yeast Transcript Leaders
Authors: Akirtava Christina , May Gemma , McManus C. Joel
Published: July 2024

Protein synthesis is a vital process that is highly regulated at the initiation step of translation. Eukaryotic 5’ transcript leaders (TLs) contain a variety ofcis-regulatory features that influence translation and mRNA stability. However, the relative influences of these features in natural TLs are poorly characterized. To address this, we used massively parallel reporter assays (MPRAs) to quantify RNA levels, ribosome loading, and protein levels from 11,027 natural yeast TLsin vivoand systematically compared the relative impacts of their sequence features on gene expression. We found that yeast TLs influence gene expression over two orders of magnitude. While a leaky scanning model using Kozak contexts and uAUGs explained half of the variance in expression across transcript leaders, the addition of other features explained ∼70% of gene expression variation. Our analyses detected keycis-acting sequence features, quantified their effects in vivo, and compared their roles to motifs reported from anin vitrostudy of ribosome recruitment. In addition, our work quantitated the effects of alternative transcription start site usage on gene expression in yeast. Thus, our study provides new quantitative insights into the roles of TL cis-acting sequences in regulating gene expression.
The role of ER exit sites in maintaining P-body organization and transmitting ER stress response duringDrosophila melanogasteroogenesis
Authors: Milano Samantha N. , Bayer Livia V. , Ko Julie J. , Casella Caroline E. , Bratu Diana P.
Published: July 2024

Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidatedin vitro, a nuanced understanding of how their assembly is regulatedin vivoremains elusive. Here, we investigate the potential link between ER exit sites and P-bodies inDrosophila melanogasteregg chambers. Employing a combination of live and super-resolution imaging, we found that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies which are more mature than their cytoplasmic counterparts. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch) suggesting a potential role for ER exit sites in P-body organization. We further show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA,oskar, are reduced. Finally, we show that ER stress is communicated to P-bodies via ER exit sites, highlighting the pivotal role of ER exit sites as a bridge between membrane-bound and membrane-less organelles in ER stress response. Together, our data unveils the significance of ER exit sites not only in governing P-body organization, but also in facilitating inter-organellar communication during stress, potentially bearing implications for a variety of disease pathologies.
Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes
Authors: Rossetto Isaac H. , Ludington Alastair J. , Simões Bruno F. , Van Cao Nguyen , Sanders Kate L.
Published: July 2024

The photopigment-encoding visual opsin genes that mediate colour perception show great variation in copy number and adaptive function across vertebrates. An open question is how this variation has been shaped by the interaction of lineage-specific structural genomic architecture and ecological selection pressures. We contribute to this issue by investigating the expansion dynamics and expression of the duplicated Short-Wavelength-Sensitive-1 opsin (SWS1) in sea snakes (Elapidae). We generated one new genome, 45 resequencing datasets, 10 retinal transcriptomes, and 81 SWS1 exon sequences for sea snakes, and analysed these alongside 16 existing genomes for sea snakes and their terrestrial relatives. Our analyses revealed multiple independent transitions in SWS1 copy number in the marineHydrophisclade, with at least three lineages having multiple intact SWS1 genes: the previously studiedHydrophis cyanocinctusand at least two close relatives of this species;H. atriceps-H. fasciatus;and an individualH. curtus. In each lineage, gene copy divergence at a key spectral tuning site resulted in distinct UV and Violet/Blue-sensitive SWS1 subtypes. Both spectral variants were simultaneously expressed in the retinae ofH. cyanocinctusandH. atriceps,providing the first evidence that these SWS1 expansions confer novel phenotypes. Finally, chromosome annotation for nine species revealed shared structural features in proximity to SWS1 regardless of copy number. If these features are associated with SWS1 duplication, expanded opsin complements could be more common in snakes than is currently recognised. Alternatively, selection pressures specific to aquatic environments could favour improved chromatic distinction in just some lineages.

Significance

Secondary transitions to marine environments are commonly accompanied by pseudogenisation of the visual opsin genes which mediate colour perception. Conversely, a species of fully-marine hydrophiid snake has functionally expanded its short-wavelength-sensitive opsin repertoire following a terrestrial ancestry. The current study explores this further by mapping opsin copy number across the hydrophiid phylogeny and by quantifying expression of SWS1 subtypes within sea snake retinae. Despite few reports of opsin expansions in tetrapods, we provide evidence for the occurrence of multiple expansion events throughoutHydrophis. Most intriguingly, retinal expression of spectrally-divergent copies implies a functionally-significant phenotype; possibly even trichromacy.
Species distribution modeling of the castor bean tick,Ixodes ricinus(Linnaeus, 1758), under current and future climates, with a special focus on Ukraine and Latvia
Authors: Tytar Volodymyr , Kozynenko Iryna , Pupins Mihails , Škute Arturs , Čeirāns Andris , Nekrasova Oksana
Published: July 2024

This study assesses the impact of climate change on the distribution ofIxodes ricinusticks, that is transmitting Lyme disease, a growing public health concern. Utilizing ensemble models from the R package flexsdm and climate data from WorldClim, ENVIREM, and CliMond, we project habitat suitability changes for the focus species. The models, validated against Lyme disease incidence rates, predicted a 1.5-fold increase in suitable habitats in Latvia opposite to a 4.5-fold decrease in suitable habitats within Ukraine over the coming decades. SHAP values were analyzed to determine the most influential climatic features affecting tick distribution, providing insights for future vector control and disease prevention strategies: here name the drivers in decreasing order. This implies an increased presence of ticks in Scandinavian countries (Sweden, Norway, Finland), Baltic states (Estonia, Latvia, Lithuania), Denmark, and Belarus. These findings largely coincide with our projections regarding bioclimatic suitability for ticks in Ukraine and Latvia. These shifts reflect broader patterns of vector redistribution driven by global warming, with potential expansions in higher altitudes and latitudes. Our findings highlight the urgent need to adapt public health planning to the evolving landscape of vector-borne diseases under climate change.
Effectiveness of Video Teletherapy in Treating Child and Adolescent Obsessive-Compulsive Disorder with Exposure and Response Prevention: a Retrospective Longitudinal Observational Study
Authors: Feusner Jamie D. , Farrell Nicholas R. , Nuñez Mia C. , Lume Nicholas , MacDonald Catherine W. , McGrath Patrick B. , Trusky Larry , Smith Stephen , Rhode Andreas
Published: July 2024

Background

An effective primary treatment for obsessive-compulsive disorder (OCD) in children and adolescents as well as adults is exposure and response prevention, a form of cognitive-behavioral therapy. Despite strong evidence supporting the efficacy and effectiveness of exposure and response prevention from studies in research and real-world settings, its clinical use remains limited. This underuse is often attributed to access barriers such as the scarcity of properly trained therapists, geographical constraints, and costs. Some of these barriers may be addressed with virtual behavioral health, providing exposure and response prevention for OCD through video teletherapy and supplemented by app-based therapeutic tools and messaging support between sessions. While studies of teletherapy exposure and response prevention in adults with OCD have shown benefits in research and real-world settings in both small and large samples, studies in children and adolescents thus far have been in small samples and limited to research settings.

Objective

This study reports on the real-world effectiveness of teletherapy exposure and response prevention for OCD in the largest sample (N=2173) of child and adolescent patients to date.

Methods

Children and adolescents with OCD were treated with live, face-to-face video teletherapy sessions, with parent/caregiver involvement, using exposure and response prevention. Assessments were conducted at baseline, after 7-11 weeks, and after 13-17 weeks. Additionally, longitudinal assessments of OCD symptoms were performed at weeks 18-30, 31-42, and 43-54.

Results

Treatment resulted in a median 37.3% decrease in OCD symptoms at 13-17 weeks, and 53.4% of youth met full response criteria at this point. In addition, there were significant reductions in the severity of depression, anxiety, and stress symptoms. The median amount of therapist involvement was 13 appointments and 11.5 hours. Further, symptom improvements were maintained, or improved upon, in the longitudinal assessment period.

Conclusions

These results show that remote ERP treatment, assisted by technology, can effectively improve symptoms in children and adolescents with OCD in a real-world setting. Notable outcomes were achieved in a relatively small amount of therapist time, demonstrating its efficiency. These findings have implications for widespread dissemination of accessible, evidence-based care for children and adolescents with OCD.
Population dynamics after pancreatitis dictates long-lasting epigenetic reprogramming and mediates tumor predisposition
Authors: Fantuz Marco , Liebig Johannes , Fontana Giovanni , Iebba Valerio , Carbone Carmine , Lukassen Sören , Conrad Christian , Carrer Alessandro
Published: July 2024

Local inflammation in the pancreas is transient but imprints a durable epigenetic memory on epithelial cells, making them more amenable to oncogenic transformation. However, it is unclear whether epithelial cell heterogeneity is impacted by acute pancreatitis (AP) or whether population dynamics during regeneration contributes to the establishment of inflammation memory.

To tackle those questions, we deployed experimental pancreatitis in mice and performed paired sequencing of transcriptomic and chromatin accessibility profiles at single nucleus resolution. We documented cell type abundance but also applied integrative analyses to infer phenotypically-distinct clusters of mesenchymal and exocrine cells. We found that AP perturbs a subset of “idling” acinar cells, which separate from more canonical “secretory” acini based on a more diversified proteome, which include elevated expression of signal transduction receptors. We linked acinar cell heterogeneity to epigenetic differences that also endow idling cells with superior plasticity. These constitute about 40% of acinar cells but can proliferate and skew their phenotype in response to AP. This leads to a remarkable recovery of pancreas histology and function, but also to the dissemination of idling-like features across the exocrine parenchyma. Mechanistically, idling acinar cells are characterized by enhanced transcriptional activity and protein synthesis. After recovery from pancreatitis, acini show elevation of both and establishment of chronic Unfolded Protein Response (UPR). We finally demonstrated that AP-primed pancreata show signs of elevated UPR and that ER stress promotes acinar cell metaplasia.

Our data interrogate phenotypical dynamics during tissue regeneration to identify cell states amenable to epigenetic imprinting. They also suggest that UPR-alleviating strategies might curtail the risk of developing pancreatic cancer for individuals who experiences AP.
Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users
Authors: Jannasch Anett , Tulok Silke , Okafornta Chukwuebuka William , Kugel Thomas , Bortolomeazzi Michele , Boissonnet Tom , Schmidt Christian , Vogelsang Andy , Dittfeld Claudia , Tugtekin Sems-Malte , Matschke Klaus , Paliulis Leocadia , Thomas Carola , Lindemann Dirk , Fabig Gunar , Müller-Reichert Thomas
Published: July 2024

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multi-dimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universität Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardized group-specific naming convention, metadata curation with tagging and Key-Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.
Pre-cancerous Niche Remodelling Dictates Nascent Tumour Survival
Authors: Skrupskelyte G. , Rojo Arias J. E. , Dang Y. , Han S. , Bejar M. T. , Colom B. , Fowler J. C. , Jones P. H. , Rulands S. , Simons B. D. , Alcolea M. P.
Published: July 2024

Interactions between mutant cells and their environment play a key role in determining cancer susceptibility. However, our understanding of how the pre-cancer microenvironment contributes to early tumorigenesis remains limited. Here, we show that newly emerging tumours at their most incipient stages shape their microenvironment in a critical process that determines their survival. Analysis of nascent squamous tumours in the upper gastrointestinal tract of the mouse reveals that the stress response of early tumour cells instructs the underlying mesenchyme to form a supportive “pre-cancer niche”, which dictates the long-term outcome of epithelial lesions. Stimulated fibroblasts beneath emerging tumours activate a wound healing response that triggers a dramatic remodelling of the underlying extracellular matrix, resulting in the formation of a fibronectin-rich stromal scaffold that promotes tumour growth. Functional heterotypic 3D culture assays and in vivo grafting experiments, combining carcinogen-free healthy epithelium and tumour-derived stroma, demonstrate that the pre-cancerous niche alone is sufficient to confer tumour properties to healthy epithelial cells. We propose a model where both mutations and the stromal response to genetic stress defines the likelihood of early tumours to survive and progress towards more advanced disease stages.
Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction
Authors: Kim Jungeun , Blazyte Asta , Choi Jae-Pil , Kim Changjae , Sharko Fedor , Jeon Sungwon , Kim Eun-Mi , Sohn Hawsun , Lee Jong Hee , Kim Hyun Woo , Yoo Mi Hyun , Lee Kyunglee , Nedoluzhko Artem , Bhak Jong
Published: July 2024

Background

The Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea and known as the Japanese sea lion, was endemic to the Northwest Pacific coast before becoming extinct in the 1950s. Little is known about its origins, speciation compared to otherOtariidaespecies or how the rapid decline affected the species’ genetic diversity.

Results

To raise the Dokdo sea lion from this relative obscurity, we sequenced DNA from 16Z. japonicus’ bone fragments, obtained from Dokdo and Ulleungdo islands in Korea. Our analysis establishesZ. japonicusas the earliest diverged species within its genus, significantly redefining its evolutionary relationship with the California (Z. californianus) and Galapagos (Z. wollebaeki) sea lions. This genome-scale analysis clarifies the phylogeny ofZ. japonicus, shedding light on its speciation and the evolutionary pathways that shaped its genetic diversity before its extinction. In addition, we discovered, population decline of theZ. japonicusstarted already 1,000 years ago, however,Z. japonicusgenome maintained a relatively high heterozygosity despite, nearing extinction.

Conclusions

Our genome-scale analysis eliminated ambiguity inZ. japonicusphylogeny, and shed light on the evolutionary pathways underlying its speciation. This study highlights the importance of the genome-scale analysis for extinct species to understand their complex evolutionary histories and conservation status.
Instantly Reversible Enzyme Regulation via Dichromatic Irradiation of Incorporated Azobenzene
Authors: Lahmy Ranit , Hiefinger Caroline , Zeqiri Fjoralba , Mandl Sabrina , Stockerl Willibald , Gschwind Ruth M. , König Burkhard , Hupfeld Andrea
Published: July 2024

Azobenzene is a widely recognized tool for achieving artificial spatiotemporal control of enzyme activity using light. Photocontrol reversibility is typically based on photostationary states with varyingEandZisomer compositions achieved through irradiation at specific wavelengths. Here, we report an alternative mechanism for azobenzene based enzyme regulation, discovered through simultaneous irradiation with two wavelengths. Using two engineered variants of imidazole glycerol phosphate synthase, in which azobenzene was incorporated as an unnatural amino acid to enable reversible control under monochromatic irradiation, we uncovered unique behavior under dichromatic irradiation. Notably, a distinct spectroscopic signal from the azobenzene moiety emerged during simultaneous irradiation at 365 nm and 420 nm and vanished upon return to the dark. Intriguingly, dichromatic irradiation triggered a reproducible two-fold increase in catalytic activity and an instantaneous return to baseline activity in the dark for one variant. In contrast, the other variant and the wild-type enzyme maintained their baseline activity under the same conditions. These findings reveal an unexplored avenue for azobenzene photoswitching, offering a novel approach to photocontrol with potential applications in sequentially regulating multiple enzymes, especially when combined with monochromatic irradiation strategies.
Anti-snake behavior and snake discrimination in vervet monkeys
Authors: Schad Lukas , van de Waal Erica , Fischer Julia
Published: July 2024

Anti-predator behavior allows to investigate how animals classify potential threats in their environment and which cognitive mechanisms might be involved in risk assessment. Snakes are common predators for many primate species, yet most of our knowledge on primate anti-snake behavior stems from predator model experiments. Few studies have investigated natural predator-prey interactions. Here, we combine an observational study on anti-snake behavior in free-ranging vervet monkeys,Chlorocebus pygerythrus,with an experimental study of snake classification, to achieve an integrated understanding of the monkeys’ responses to and classification of snakes. Over 25 months, we gathered data from over 200 individuals in five groups and recorded natural encounters between vervet monkeys and five different species of snakes. We assessed whether the time that monkeys spent inspecting snakes from close by varied with the encountered species. We further examined whether age and sex classes differed in their propensity to inspect snakes or alarm call. Pythons were associated with higher average inspection durations and were more likely to elicit inspection responses. While adult males were less likely to approach and inspect snakes, we found no effect of age or sex on alarm calling probability. Alarm calling appeared to be restricted to individuals in close proximity to snakes, suggesting that recruitment of nearby group members is an essential function of this call type. In the experiments, we tested whether vervet monkeys discriminated snake models by length and/or diameter, but found no effect of model size on the intensity of anti-snake behavior. While the experimental data showed the same trends as data from natural encounters, responses towards model pythons were much stronger than responses towards real pythons. These results point to a potential sampling bias in predator model experiments that needs to be taken into account when assessing data from experiments alone.
Cybernetic control of a natural microbial co-culture
Authors: Lee Ting An , Morlock Jan , Allan John , Steel Harrison
Published: July 2024

A key obstacle in the widespread application of microbial co-cultures in bioprocesses is their compositional instability, as faster-growing species outcompete and dominate the culture. While several synthetic biology approaches have demonstrated control over co-culture composition, there has been an increased interest in computer-based cybernetic control approaches that can offload burdensome genetic control circuitry to computers and enable dynamic control and real-time noise rejection. This work extends that approach, demonstrating a cybernetic control method that is not reliant on any genetic engineering, instead interfacing cells with computers by exploiting their natural characteristics to measure and actuate the composition. We apply this to aPseudomonas putida(P. putida) andEscherichia coli(E. coli) co-culture grown in Chi.Bio bioreactors, first showing how composition estimates calculated from different bioreactor measurements can be combined with a system model using an extended Kalman filter to generate accurate estimates of a noisy system. We also demonstrate that because the species have different optimal temperature niches, adjusting the temperature of the culture can drive the composition in either direction. By using a proportional-integral control algorithm to calculate the temperature that would bring the measured composition towards the desired composition, we are able to track dynamic references and stabilised the co-culture for 7 days (∼250 generations), with the experiment ending before the cells could adapt out of the control. This cybernetic framework is broadly applicable, with different microbes’ unique features and specific growth niches enabling robust control over diverse co-cultures.
Influenza A defective viral genome production is altered by metabolites, metabolic signaling molecules, and cyanobacteria extracts
Authors: Agu Ilechukwu , José Ivy R. , Díaz-Muñoz Samuel L.
Published: July 2024

RNA virus infections are composed of a diverse mix of viral genomes that arise from low fidelity in replication within cells. The interactions between “defective” and full-length viral genomes have been shown to shape pathogenesis, leading to intense research into employing these to develop novel antivirals. In particular, Influenza A defective viral genomes (DVGs) have been associated with milder clinical outcomes. Yet, the full potential of DVGs as broad-spectrum antivirals remains untapped due to the unknown mechanisms of theirde novoproduction. Much of the research into the factors affecting defective viral genome production has focused on the virus, while the role of the host has been neglected. We recently showed that altering host cell metabolism away from pro-growth pathways using alpelisib increased the production of Influenza A defective viral genomes. To uncover other drugs that could induce infections to create more DVGs, we subjected active influenza infections of the two circulating human subtypes (A/H1N1 & A/H3N2) to a screen of metabolites, metabolic signaling molecules, and cyanobacteria-derived biologics, after which we quantified the defective viral genomes (specifically deletion-containing viral genomes, DelVGs) and total viral genomes using third generation long-read sequencing. Here we show that metabolites and signaling molecules of host cell central carbon metabolism can significantly alter DelVG production early in Influenza A infection. Adenosine, emerged as a potent inducer of defective viral genomes, significantly amplifying DelVG production across both subtypes. Insulin had similar effects, albeit subtype-specific, predominantly enhancing polymerase segment DVGs in TX12 infections. Tricarboxylic Acid (TCA) cycle inhibitors 4-octyl itaconate and UK5099, along with the purine analog favipiravir, increased total viral genome production across subtypes. Cyanobacterial extracts primarily affected DVG and total viral genome production in TX12, with a specific, almost complete shutdown of influenza antigenic segments. These results underscore the influence of host metabolic pathways on DVG production and suggest new avenues for antiviral intervention, including PI3K-AKT and Ras-MAPK signaling pathways, TCA cycle metabolism, purine-pyrimidine metabolism, polymerase inhibition, and cyanotherapeutic approaches. More broadly, our findings suggest that the social interactions observed between defective and full-length viral genomes, depend not only on the viral actors, but can be altered by the stage provided by the host. Our study advances our fundamental understanding of DVG production mechanisms and highlights the potential of targeting host metabolism to develop broad-spectrum influenza therapeutics.
Molecular and cellular rhythms in excitatory and inhibitory neurons in the mouse prefrontal cortex
Authors: Burns Jennifer N. , Jenkins Aaron K. , Yin RuoFei , Zong Wei , Vadnie Chelsea A. , DePoy Lauren M. , Petersen Kaitlyn A , Tsyglakova Mariya , Scott Madeline R. , Tseng George C. , Huang Yanhua H. , McClung Colleen A.
Published: July 2024

Previous studies have shown that there are rhythms in gene expression in the mouse prefrontal cortex (PFC); however, the contribution of different cell types and potential variation by sex has not yet been determined. Of particular interest are excitatory pyramidal cells and inhibitory parvalbumin (PV) interneurons, as interactions between these cell types are essential for regulating the excitation/inhibition balance and controlling many of the cognitive functions regulated by the PFC. In this study, we identify cell-type specific rhythms in the translatome of PV and pyramidal cells in the mouse PFC and assess diurnal rhythms in PV cell electrophysiological properties. We find that while core molecular clock genes are conserved and synchronized between cell types, pyramidal cells have nearly twice as many rhythmic transcripts as PV cells (35% vs. 18%). Rhythmic transcripts in pyramidal cells also show a high degree of overlap between sexes, both in terms of which transcripts are rhythmic and in the biological processes associated with them. Conversely, in PV cells, rhythmic transcripts from males and females are largely distinct. Moreover, we find sex-specific effects of phase on action potential properties in PV cells that are eliminated by environmental circadian disruption. Together, this study demonstrates that rhythms in gene expression and electrophysiological properties in the mouse PFC vary by both cell type and sex. Moreover, the biological processes associated with these rhythmic transcripts may provide insight into the unique functions of rhythms in these cells, as well as their selective vulnerabilities to circadian disruption.

Significance statement

This is the first study to examine translatomic rhythms in the mouse PFC with cell-type specificity. We find that the core molecular clock cycles in phase across cell types, indicating that previously described daily oscillations in the cortical excitation/inhibition balance are not the consequence of a phase offset between PV and pyramidal cells. Nevertheless, rhythmic transcripts and their associated biological processes differ by both sex and cell type, suggesting that molecular rhythms may play a unique role in different cell types and between sexes. Therefore, our results, such as the enrichment of transcripts associated with mitochondrial function in PV cells from males, point towards possible cell and sex-specific mechanisms that could contribute to psychiatric and cognitive diseases upon rhythm disruption.
Insights into gene conversion and crossing-over processes from long-read sequencing of human, chimpanzee and gorilla testes and sperm
Authors: Porsborg Peter Soerud , Charmouh Anders Poulsen , Singh Vinod Kumar , Winge Sofia Boeg , Hvilsom Christina , Pelizzola Marta , Laurentino Sandra , Neuhaus Nina , Hobolth Asger , Bataillon Thomas , Almstrup Kristian , Besenbacher Søren , Schierup Mikkel Heide
Published: July 2024

Homologous recombination rearranges genetic information during meiosis to generate new combinations of variants. Recombination also causes new mutations, affects the GC content of the genome and reduces selective interference. Here, we use HiFi long-read sequencing to directly detect crossover and gene conversion events from switches between the two haplotypes along single HiFi-reads from testis tissue of humans, chimpanzees and gorillas as well as human sperm samples. Furthermore, based on DNA methylation calls, we classify the cellular origin of reads to either somatic or germline cells in the testis tissue. We identify 1692 crossovers and 1032 gene conversions in nine samples and investigate their chromosomal distribution. Crossovers are more telomeric and correlate better with recombination maps than gene conversions. We show a strong concordance between a human double-strand break map and the human samples, but not for the other species, supporting different PRDM9-programmed double-strand break loci. We estimate the average gene conversion tract lengths to be similar and very short in all three species (means 40-100 bp, fitted well by a geometric distribution) and that 95-98% of non-crossover events do not involve tracts intersecting with polymorphism and are therefore not detectable. Finally, we detect a GC bias in the gene conversion of both single and multiple SNVs and show that the GC-biased gene conversion affects SNVs flanking crossover events. This implies that gene conversion events associated with crossover events are much longer (estimated above 500 bp) than those associated with non-crossover events. Highly accurate long-read sequencing combined with the classification of reads to specific cell types provides a new, powerful way to make individual, detailed maps of gene conversion and crossovers for any species.
Transovarial transmission in field caught mosquitoes identifies a mechanism for the establishment of Usutu virus in a temperate country
Authors: Schilling Mirjam , Lawson Becki , Spiro Simon , Jagdev Madhujot , Vaux Alexander G.C. , Bruce Robert C. , Johnston Colin J. , Abbott Anthony J. , Wrigglesworth Ethan , Pearce-Kelly Paul , Cunningham Andrew A. , Medlock Jolyon M. , Johnson Nicholas , Folly Arran J.
Published: July 2024

Usutu virus (USUV) is an emerging zoonotic flavivirus in Europe, and the first zoonotic mosquito-borne virus to be confirmed in animal hosts in the United Kingdom (UK). Phylogenetic analysis of USUV in the three years following its initial detection in 2020 indicated that the virus is overwintering in the UK. In 2023, USUV was identified outside Greater London for the first time. Therefore, USUV should now be considered endemic within southeast England. Surveillance of avian hosts and mosquito vectors has been insufficient to elucidate the mechanism by which USUV has persisted through temperate winters. It is likely that mosquitoes play a significant role in facilitating the establishment of USUV in temperate areas, as is the case for related mosquito-borne viruses. Here we undertake enhanced targeted vector surveillance at the index site to investigate the role of mosquitoes in facilitating USUV establishment in the UK.

Between 2021 and 2024 inclusive, we detected USUV in host-seeking adult femaleCulex pipienss.l. (n = 8/554 pools), a key vector of the virus in Europe. During 2023, enhanced surveillance detected transovarial transmission of USUV in wildCx. pipienss.l. (n = 1/202 pools), by screening adults following captive rearing of mosquito larvae collected from the field. This is, to our knowledge, the first description of vertical transmission of USUV in an arthropod vector. Consequently, transovarial transmission should be considered a viable mechanism for the persistence of USUV in temperate areas. Our results highlight the importance of undertaking detailed vector surveillance, across life stages, to inform the epidemiology of vector-borne viruses.
A general Bioluminescence Resonance Energy Transfer (BRET) protocol to measure and analyze protein interactions in mammalian cells
Authors: Duval Carla Jane , Steffen Candy Laura , Pavic Karolina , Abankwa Daniel Kwaku
Published: July 2024

Bioluminescence resonance energy transfer (BRET) allows to quantitate protein interactions in intact cells. Here we provide a step-by-step protocol for measuring BRET due to transient interactions of oncogenic K-RasG12V in plasma membrane nanoclusters of HEK293-EBNA cells. We describe how to seed, transfect and replate cells, followed by their preparation for BRET-measurements on a microplate reader and detailed data analysis steps. For details on how to apply this protocol, please refer to Steffen et al., 20241.

Graphical abstract
Glycoengineering with neuraminic acid analogs to label lipooligosaccharides and detect native sialyltransferase activity in Gram-negative bacteria
Authors: Alvarado Melendez Erianna I. , de Jong Hanna , Hartman Jet E. M. , Ong Jun Yang , Wösten Marc M. S. M. , Wennekes Tom
Published: July 2024

Lipooligosaccharides (LOS) are the most abundant cell surface glycoconjugates on the outer membrane of Gram-negative bacteria. They play important roles in host-microbe interactions. Certain Gram-negative pathogenic bacteria cap their LOS with the sialic acid,N-acetylneuraminic acid (Neu5Ac), to mimic host glycans that among others protects these bacteria from recognition by the hosts immune system. This process of molecular mimicry is not fully understood and remains under investigated. To explore the functional role of sialic acid-capped lipooligosaccharides (LOS) at the molecular level, it is important to have tools readily available for the detection and manipulation of both Neu5Ac on glycoconjugates and the involved sialyltransferases, preferably in live bacteria. We and others have shown that the native sialyltransferases of some Gram-negative bacteria can incorporate extracellular unnatural sialic acid nucleotides onto their LOS. We here report on the expanded use of native bacterial sialyltransferases to incorporate neuraminic acids analogs with a reporter group into the LOS of a variety of Gram-negative bacteria. We show that this approach offers a quick strategy to screen bacteria for the expression of functional sialyltransferases and the ability to use exogenous CMP-Neu5Ac to decorate their glycoconjugates. For selected bacteria we also show this strategy complements two other glycoengineering techniques, Metabolic Oligosaccharide Engineering (MOE) and Selective Exo-Enzymatic Labelling (SEEL), and that together they provide tools to modify, label, detect and visualize sialylation of bacterial LOS.
Glia control experience-dependent plasticity in an olfactory critical period
Authors: Leier Hans C. , Foden Alexander J. , Jindal Darren A. , Wilkov Abigail J. , Costello Paola Van der Linden , Vanderzalm Pamela J. , Coutinho-Budd Jaeda C. , Tabuchi Masashi , Broihier Heather T.
Published: July 2024

Sensory experience during developmental critical periods has lifelong consequences for circuit function and behavior, but the molecular and cellular mechanisms through which experience causes these changes are not well understood. The Drosophila antennal lobe houses synapses between olfactory sensory neurons (OSNs) and downstream projection neurons (PNs) in stereotyped glomeruli. Many glomeruli exhibit structural plasticity in response to early-life odor exposure, indicating a general sensitivity of the fly olfactory circuitry to early sensory experience. We recently found that glia shape antennal lobe development in young adults, leading us to ask if glia also drive experience-dependent plasticity during this period. Here we define a critical period for structural and functional plasticity of OSN-PN synapses in the ethyl butyrate (EB)-sensitive glomerulus VM7. EB exposure for the first two days post-eclosion drives large-scale reductions in glomerular volume, presynapse number, and post-synaptic activity. Crucially, pruning during the critical period has long-term consequences for circuit function since both OSN-PN synapse number and spontaneous activity of PNs remain persistently decreased following early-life odor exposure. The highly conserved engulfment receptor Draper is required for this critical period plasticity as ensheathing glia upregulate Draper, invade the VM7 glomerulus, and phagocytose OSN presynaptic terminals in response to critical-period EB exposure. Loss of Draper fully suppresses the morphological and physiological consequences of critical period odor exposure, arguing that phagocytic glia engulf intact synaptic terminals. These data demonstrate experience-dependent pruning of synapses and argue that Drosophila olfactory circuitry is a powerful model for defining the function of glia in critical period plasticity.
An adaptor for feedback regulation of heme biosynthesis by the mitochondrial protease CLPXP
Authors: Cottle Thomas , Joh Lydia , Posner Cori , DeCosta Adam , Kardon Julia R.
Published: July 2024

Heme biosynthesis is tightly coordinated such that essential heme functions including oxygen transport, respiration, and catalysis are fully supplied without overproducing toxic heme precursors and depleting cellular iron. The initial heme biosynthetic enzyme, ALA synthase (ALAS), exhibits heme-induced degradation that is dependent on the mitochondrial AAA+ protease complex CLPXP, but the mechanism for this negative feedback regulation had not been elucidated. By biochemical reconstitution, we have discovered that POLDIP2 serves as a heme-sensing adaptor protein to deliver ALAS for degradation. Similarly, loss of POLDIP2 strongly impairs ALAS turnover in cells. POLDIP2 directly recognizes heme-bound ALAS to drive assembly of the degradation complex. The C-terminal element of ALAS, truncation of which leads to a form of porphyria (XLDPP), is dispensable for interaction with POLDIP2 but necessary for degradation. Our findings establish the molecular basis for heme-induced degradation of ALAS by CLPXP, establish POLDIP2 as a substrate adaptor for CLPXP, and provide mechanistic insight into two forms of erythropoietic protoporphyria linked to CLPX and ALAS.
Healthcare professionals’ attitudes towards digital health interventions and perspectives on digital health inequalities: a qualitative study
Authors: Ramasawmy Mel , Sunkersing David , Poole Lydia , Blandford Ann , Gill Paramjit , Khunti Kamlesh , Modha Shivali H , Patel Kiran , Potts Henry WW , Sajid Madiha , Khan Nushrat , Banerjee Amitava
Published: July 2024

Background

Use of Digital Health Interventions (DHIs) for the management of cardiometabolic diseases has increased, but may exacerbate existing health inequalities. Healthcare professionals (HCPs) play a vital role in recommending and supporting patients to use these tools. There is a need to understand the role of HCPs in managing the implementation of digital health in communities at risk of health inequalities.

Objective

To explore the views of health care professionals about digital health and its impact on health inequalities, focusing on cardiometabolic diseases and the South Asian population in the UK.

Methods

Online interviews and focus-groups with HCPs (n=18), exploring participants’ experiences and attitudes towards digital health, perceptions of patients’ barriers and facilitators to use, whether they perceived any populations to be particularly at risk of digital inequalities, and the impact of the COVID-19 pandemic on their practice in relation to digital health. After informed consent, transcription and coding, a reflexive thematic approach was taken to analysis.

Results

HCPs recognised the potential benefits of DHIs to improve access and delivery of care and patient outcomes, but described several barriers to successful implementation. HCPs demonstrated a good understanding of the challenges their patients face in relation to wider inequalities, barriers to health behaviours and healthcare access, and digital health. Of particular concern was the impact of increasing reliance of digital interventions in health care on the exclusion of some patient groups. Participants recommended improvement of the design and implementation of DHIs offered to patients through working with at-risk populations throughout the process. Finally, participants emphasised the importance of ensuring non-digital services remained available to ensure equitable access to health and social care.

Conclusions

HCPs described the complexities of delivering care to underserved communities. DHIs were identified as a potential way to improve health outcomes for some, while over-reliance risked exacerbating inequalities. Participant recommendations related to design, implementation, and engaging target populations providing practical examples to address digital health inequalities, such as working with other sectors to take a community approach.
How a year of pandemic and related public health measures impacted youth and young adults and the foundations they build upon: Qualitative interviews in Ontario Canada
Authors: Austin Laurel C. , Gomes Makayla Nunes , Chavez Sebastian , Degano Celina
Published: July 2024

Introduction

During youth and young adult (YYA) years education, employment, relationships with family and friends, and important rituals representing transition to new phases of life are foundations on which personal identity and future well-being are established. These were shaken by the COVID-19 pandemic. We explore how Ontario YYAs and the foundations they build upon (education, employment, relationships, transitional events) were impacted by over a year of pandemic and public health responses to prevent spread.

Methods

In-depth semi-structured interviews with 19 Ontario YYAs age 16-21 were conducted during April - June 2021. Reflexive thematic analysis aided by MAXQDA software was used to iteratively engage with data to search for patterns and shared meaning.

Results

Thirteen themes were identified, organized into four meta-themes: impacts on self, impacts on foundations (educational, employment, transitional events/rituals), impacts on relationships, and coping responses. Many, especially those living with loved ones believed to risk a fatal outcome from COVID-19, felt the weight of needing to avoid the virus to protect loved ones. YYAs who were in their last year of secondary school in spring 2020 or 2021 missed important transitional endings, e.g., graduation. Those graduating in 2020 and going on to post-secondary school also missed transitional beginnings, e.g., experiencing in-person on-campus higher education classrooms, living in residence, and meeting new friends. Perceived negative impacts on education quality and professional development were common. Virtual learning models and changes to in-person schooling, hastily introduced and evolving over the next year, did not measure up to traditional learning models.

Conclusions

All of these impacts took a toll. Respondents routinely volunteered concerns about stress, loneliness, and their mental health. There is need for further research to assess long-term impacts of these experiences, especially among YYAs who had family members at severe risk, and those finishing secondary school in spring of 2020.
Co-option of mitochondrial nucleic acid sensing pathways by HSV-1 UL12.5 for reactivation from latent Infection
Authors: Cuddy Sean R. , Flores Matthew E. , Krakowiak Patryk A. , Whitford Abigail L. , Dochnal Sara A. , Babnis Aleksandra , Miyake Tsuyoshi , Tigano Marco , Engel Daniel A. , Cliffe Anna. R
Published: July 2024

Although viruses subvert innate immune pathways for their replication, there is evidence they can also co-opt anti-viral responses for their benefit. The ubiquitous human pathogen, Herpes Simplex Virus-1 (HSV-1), encodes a protein (UL12.5) that induces the release of mitochondrial nucleic acid into the cytosol, which activates immune sensing pathways and reduces productive replication in non-neuronal cells. HSV-1 establishes latency in neurons and can reactivate to cause disease. We found that UL12.5 is required for HSV-1 reactivation in neurons and acts to directly promote viral lytic gene expression during initial exit from latency. Further, the direct activation of innate immune sensing pathways triggered HSV reactivation and compensated for a lack of UL12.5. Finally, we found that the induction of HSV-1 lytic genes during reactivation required intact RNA and DNA sensing pathways, demonstrating that HSV-1 can both respond to and active antiviral nucleic acid sensing pathways to reactivate from a latent infection.