bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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.SignificanceSecondary 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

AbstractThis 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

AbstractBackgroundAn 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.ObjectiveThis 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.MethodsChildren 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.ResultsTreatment 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.ConclusionsThese 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

AbstractLocal 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

AbstractModern 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

SummaryInteractions 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

AbstractBackgroundThe 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.ResultsTo 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.ConclusionsOur 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

AbstractAzobenzene 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

AbstractAnti-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

AbstractA 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

AbstractRNA 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.