bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflammation-like environments limit the loss of quorum sensing inPseudomonas aeruginosa
Authors: Fu Taoran , Wright Rosanna C.T. , Gifford Danna R. , Knight Christopher G. , Brockhurst Michael A. 
Published: December 2024

AbstractWithin-host environments are complex and multidimensional, making it challenging to link evolutionary responses of colonizing pathogens to causal selective drivers. Loss of quorum sensing (QS) via mutation of the master regulator,lasR, is a common adaptation ofPseudomonas aeruginosaduring chronic infections. Here, we use experimental evolution in host-mimicking media to show that loss of QS is constrained by environmental factors associated with host inflammation. Specifically, environments combining oxidative stress and abundant free amino acids limited loss of QS, whereas QS loss was rapid in the absence of oxidative stress regardless of amino acids. Under oxidative stress,lasRmutations were contingent upon first decoupling regulation of oxidative stress responses from QS via mutations in the promoter region of the primary catalase,katA, or in the oxidative stress regulator,oxyR, enabling maintenance of oxidative stress tolerance. Together, our findings suggest that host inflammatory responses likely delay the loss of QS whilst colonizers undergo stepwise evolution, first adapting to survive lethal stressors before responding to other nutritional selective drivers that favour loss of QS.Significance StatementPseudomonas aeruginosais a common cause of chronic infections characterized by persistent inflammation. Host inflammatory responses alter within-host environments, including by increasing levels of antimicrobial stressors and releasing free amino acids through proteolysis. Here, we show stepwise adaptation of experimentalP. aeruginosapopulations to inflammation-like environments, first adapting to survive lethal stress by decoupling oxidative stress responses from quorum sensing, before then adapting to the nutritional conditions, delaying the loss of quorum sensing. These results highlight the power of using laboratory evolution experiments to disentangle the multidimensional selective forces driving pathogen adaptation in complex within-host environments.
Incomplete adaptation to surface movement during hand reaching
Authors: Balestrucci Priscilla , Bianchi Matteo , Ryan Colleen P. , Daniele Giulia , Flamini Alice , Valente Fanny , Lacquaniti Francesco , Moscatelli Alessandro 
Published: December 2024

AbstractHumans can effectively adapt to changes in the environment to maintain adequate motor performance in a vast range of situations. However, residual errors tend to persist when stronga prioriassumptions about the statistical regularities of the environment are violated. In our study, we challenged the expectation that inanimate objects are usually at rest. To this end, we used a robotic interface to move a plate over which participants slid their finger while reaching towards a target. We found limited evidence of adaptation after prolonged exposure to this perturbation, and only when visual feedback about hand position was provided. Although participants were aware of the motion of the contact surface, explicit knowledge about its direction was limited. Our results provide important insights on the limits of adaptation to motion perturbation in the somatosensory system, which can inform the design of technology applications such as haptic interfaces and collaborative robots.
Barley disease screening: a multiplex digital droplet PCR approach for the detection ofRamularia collo-cygni, Rhynchosporium graminicolaandPyrenophora teres
Authors: Zia Rabisa , Popper Zoë A. , Kildea Steven 
Published: December 2024

ABSTRACTBarley is the most widely grown cereal crop in Ireland and faces substantial yield loss annually due to airborne, seed-borne, and soil-borne pathogens. The most prevalent and destructive of these include Ramularia leaf spot, Barley leaf scald and Net blotch, caused byRamularia collo-cygni, Rhynchosporium graminicolaandPyrenophora teresrespectively. Infected seeds are considered as the major source of inoculum for these diseases. The absence of varietal resistance for these fungal pathogens suggests the need for better disease management strategies. Accurate pathogen detection is one of the most widely accepted disease management strategies. Here we demonstrate two digital droplet PCR (ddPCR) assays, based on TaqMan probe chemistry, for the detection of the above pathogens. ddPCR is a third generation of PCR, relying on sample partition into thousands of droplets in which each droplet acts as a reaction unit, enabling pathogen detection at extremely low levels. We developed a multiplex assay capable of detectingR. graminicola, R.collo-cygniandP. teres. ForP. teressamples, a further assay was designed to distinguish between the two economically significant forms ofP. teresi.e.P. teresf. maculata (Ptm; spot form of Net blotch) andP. teresf. teres (Ptt; net form of Net blotch). The assay offers sensitive and selective pathogen detection from barley seeds to pico moles/µl level. Finally, the efficacy of the assay was demonstrated by screening a collection of historical barley seeds.
Marine fishes exhibit exceptional variation in biofluorescent emission spectra
Authors: Carr Emily M. , Thurman Mason M. , Martin Rene P. , Sparks Tate S. , Sparks John S. 
Published: December 2024

AbstractBiofluorescence is a phylogenetically widespread phenomenon among marine fishes, yet the phenotypic diversity in fluorescent emission wavelengths (e.g., green, red) remains poorly studied across the broad diversity of marine teleosts. In this study we investigate the fluorescent emission spectra from a diverse array of 18 teleost families and record fluorescent emission peaks over multiple body regions. Our results show that fluorescent emission spectra are remarkably diverse among teleost families, as well as within genera. Fluorescent emissions also varied across different body regions within some individuals. We show that members of the families Gobiidae, Oxudercidae, and Bothidae, exhibit at least six distinct, non-overlapping fluorescent emission peaks. Nine of the 18 families examined in this study were found to have at least four distinct and non-overlapping fluorescent emission peaks. Further, we find that several families exhibit multiple discrete emission peaks for a single fluorescent color (i.e., wavelength range), including multiple distinct peaks within the green and red portions of the spectrum. This exceptional degree of phenotypic variation in fluorescent emissions highlights the potential for a diverse, even species-specific, fluorescent signaling system in certain teleost families. The interplay between different fluorescent emission wavelengths and notable variation in the distribution of fluorescence on the body could allow for a wide array of fluorescent patterns to be produced by an individual or among closely related species. Our results reveal far more diversity in both fluorescent emission wavelengths (colors) and in the distribution of fluorescent molecules on the body than had previously been reported in the literature. We characterize this novel variation in fluorescent emissions across an array of teleost families that exhibit biofluorescence and discuss the potential functional implications of this exceptional phenotypic variability.
The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson’s disease mouse model
Authors: Morais Livia H. , Stiles Linsey , Freeman Milla , Oguienko Anastasiya D. , Hoang Jonathan D. , Jones Jeff , Quan Baiyi , Devine Jack , Bois Justin S. , Chou Tsui-Fen , Trinh Joanne , Picard Martin , Gradinaru Viviana , Mazmanian Sarkis K. 
Published: December 2024

ABSTRACTThe pathophysiology of Parkinson’s disease (PD) involves gene-environment interactions that impair various cellular processes such as autophagy, lysosomal function, or mitochondrial dysfunction. Specifically, mitochondria-associated gene mutations increase PD risk, mitochondrial respiration is altered in the PD brain, and mitochondrial-damaging toxins cause PD-like motor and gastrointestinal symptoms in animal models. The gut microbiome is altered in PD patients and represents an environmental risk, however a relationship between mitochondrial function and the microbiome in PD has not been previously established. Herein, we report that striatal mitochondria are functionally overactive in α-synuclein-overexpressing (ASO) mice, a model of PD, and that microbiome depletion restores respiration and mitochondria-associated gene expression patterns to wild-type levels. ASO mice harboring a complex microbiome produce increased reactive oxygen species in the striatum whereas germ-free counterparts express elevated levels of antioxidant proteins that may buffer against oxidative damage. Indeed, antioxidant treatment improves motor performance in ASO mice and, remarkably, blocking oxidant scavenging in germ-free mice induces α-synuclein-dependent motor deficits. Thus, the gut microbiome increases mitochondrial respiration and oxidative stress in the brain, which enhances motor symptoms in a mouse model of PD.
IMPACT OF BK POLYOMAVIRUS INFECTION IN CHILDREN AFTER KIDNEY TRANSPLANT IN A REFERENCE CENTER IN SALVADOR – BAHIA, BRAZIL
Authors: Fucs Machado Mariana Perdiz , Costa Mattoso Ricardo José 
Published: December 2024

ABSTRACTIntroductionBK Polyomavirus infection has a high incidence in the post-renal transplant phase and is considered a significant cause of premature graft failure after transplantation. Pediatric renal patients undergo relatively more potent immunosuppression; however, despite the large number of studies conducted in adult renal recipients, there is limited information on BKPyV infection in the pediatric population.ObjectiveTo estimate the incidence of BK Polyomavirus infection after kidney transplantation in pediatric patients undergoing immunosuppressive therapy at a referral center.MethodologyObservational descriptive study, with data collection based on medical records of children undergoing kidney transplantation at Hospital Ana Nery, Salvador-BA, from 2009 to 2017.ResultsForty-one children were evaluated, of which 21 (51.2%) were female. The mean age of the sample was 11 ± 3, with a higher frequency of patients in the age range of 13-17 years (43.9%). Regarding the presence of BKPyV infection, most patients were not infected (56.1%). Regarding the type of antiproliferative and calcineurin inhibitor, Mycophenolate Mofetil was used in 37 (90.2%) patients and Tacrolimus in 40 (97.6%). When comparing the groups with the presence or absence of BKPyV infection, there was no statistically significant difference between the variables: sex (p = 0.890), age (p = 0.829) and type of antiproliferative used (p = 0.187). In the analysis of renal function, an increase in creatinine was observed in 38.9% of infected patients, while among the uninfected patients, only 13% presented an increase in the period of one year. The difference between these two groups (p = 0.05) therefore demonstrated an association between worsening renal function and the presence of BKPyV infection.ConclusionThe incidence of BK Polyomavirus infection in pediatric patients undergoing kidney transplantation, in the period of one year after the surgical procedure, is almost 50%. No differences could be demonstrated between the groups with and without BKPyV infection and established risk factors, such as sex, age and immunosuppressive therapy used. Furthermore, a worsening of renal function was evidenced among infected patients, when compared to the uninfected group, in this period of one year.
Spruce hybrids show superior cumulative growth and intermediate response to climate anomalies, as compared to their ecologically divergent parental species
Authors: Reed-Métayer Edouard , Depardieu Claire , Lenz Patrick , Bousquet Jean , Perron Martin 
Published: December 2024

AbstractClimate change brings new constraints to which trees will have to adapt, including more frequent weather extremes. Black spruce and red spruce are phylogenetically close but adapted to different ecological conditions, and they form a natural hybrid zone where their distributions come into contact. Thus, they represent an interesting model to study the effect of introgressive hybridization in the context of climate change, given that interspecific gene flow could affect their capacity to adapt where their natural distributions overlap. Using a common-garden field test gathering 20-year-old progeny trees resulting from rigorous controlled crosses including previously verified genetic identity of the parents, growth patterns and wood density differences could be observed between species and between them and their F1hybrids. A dendroecological analytical approach relying on wood cores was used and revealed similar wood responses to climatic variations between species, both through lifetime climate sensitivity and through episodic stress response indexes. They were however differentially expressed in early- and latewood between black spruce and red spruce, differences likely driven by diverging cambial phenology adaptations to different growing season lengths. F1hybrids exhibited hybrid vigor for cumulative growth under the test site conditions, but showed intermediate values for traits related to climate response. These results offer new perspectives for understanding the dynamics of adaptation in hybrid zones in the context of climate change, as well as for guiding conservation and genetic improvement efforts.HighlightsF1cumulative growth is higher than their ecologically contrasted parents.Hybrids had intermediate climate responsesParental species responded similarly to climate anomalies, but in various intra-ring part.Cambial phenology likely drives divergences in wood reaction to climate anomalies
Stability through plasticity: Finding robust memories through representational drift
Authors: Natrajan Maanasa , Fitzgerald James E. 
Published: December 2024

AbstractMemories are believed to be stored in synapses and retrieved through the reactivation of neural ensembles. Learning alters synaptic weights, which can interfere with previously stored memories that share the same synapses, creating a tradeoff between plasticity and stability. Interestingly, neural representations exhibit significant dynamics, even in stable environments, without apparent learning or forgetting—a phenomenon known as representational drift. Theoretical studies have suggested that multiple neural representations can correspond to a memory, with post-learning exploration of these representation solutions driving drift. However, it remains unclear whether representations explored through drift differ from those learned or offer unique advantages. Here we show that representational drift uncovers noise-robust representations that are otherwise difficult to learn. We first define the non-linear solution space manifold of synaptic weights for a fixed input-output mapping, which allows us to disentangle drift from learning and forgetting and simulate representational drift as diffusion within this manifold. Solutions explored by drift have many inactive and saturated neurons, making them robust to weight perturbations due to noise or continual learning. Such solutions are prevalent and entropically favored by drift, but their lack of gradients makes them difficult to learn and non-conducive to further learning. To overcome this, we introduce an allocation procedure that selectively shifts representations for new information into a learning-conducive regime. By combining allocation with drift, we resolve the tradeoff between learnability and robustness.
Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities
Authors: Sereika Mantas , Mussig Aaron James , Jiang Chenjing , Knudsen Kalinka Sand , Jensen Thomas Bygh Nymann , Petriglieri Francesca , Yang Yu , Jørgensen Vibeke Rudkjøbing , Delogu Francesco , Sørensen Emil Aarre , Nielsen Per Halkjær , Singleton Caitlin Margaret , Hugenholtz Philip , Albertsen Mads 
Published: December 2024

AbstractGenomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the microbial genome catalogue of soils and sediments has been challenging due to the enormous complexity of these environments. Here, we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected across Denmark and through an optimised bioinformatics pipeline, we recovered genomes of 15,314 novel microbial species, including 4,757 high-quality genomes. The recovered microbial genomes span 1,086 novel genera and provide the first high-quality reference genomes for 612 previously known genera, expanding the phylogenetic diversity of the prokaryotic tree of life by 8 %. The long-read assemblies also enabled the recovery of thousands of complete rRNA operons, biosynthetic gene clusters and CRISPR-Cas systems, all of which were underrepresented and highly fragmented in previous terrestrial genome catalogues. Furthermore, the incorporation of the recovered MAGs into public genome databases significantly improved species-level classification rates for soil and sediment metagenomic datasets, thereby enhancing terrestrial microbiome characterization. With this study, we demonstrate that long-read sequencing and optimised bioinformatics, allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain the largest untapped source of biodiversity for expanding genome databases and filling in the gaps of the tree of life.
Identification ofSENP7andUTF1/VENTXas new loci influencing clustered protocadherin methylation across blood and brain using a genome-wide association study
Authors: Liu Yunfeng , Vukic Maja , Hannon Eilis , Mei Hailiang ,   BIOS Consortium, Mill Jonathan , Daxinger Lucia , Heijmans Bastiaan T. 
Published: December 2024

SummaryThe epigenetic regulation of clustered protocadherin (cPCDH) genes is tightly linked to their function as specific cell surface barcodes for neural self-nonself discrimination. Differential cPCDHDNA methylation in both blood and brain has been implicated in diverse human traits and diseases ranging from BMI, aging, cancer and brain disorders. However, the unique regulation of cPCDHmethylation remains poorly understood. Therefore, we performed a genome-wide association study to evaluate the association of >7 million genetic variants with DNA methylation at 607 cPCDHCpGs measured in whole blood of 3777 individuals and validated findings in prefrontal cortex samples obtained from 523 brain donors. We observed concordant cPCDHmethylation patterns in blood and prefrontal cortex, which switched between hypo-, intermediate and hypermethylation over short distances with the former overlapping with the promoter regions of each cPCDHmember. Through methylation quantitative trait locus (meQTL) analysisin trans, we first confirmed the broad effect of the candidate geneSMCHD1on cPCDHmethylation in blood which validated in prefrontal cortex. Through a genome-wide analysis, we next identified theSENP7andUTF1/VENTXloci to have widespread, subcluster-specific effects on cPCDHmethylation in blood which was validated in prefrontal cortex. WhileSENP7can indirectly affect DNA methylation through the deSUMOylation of the chromatin repressorKAP1,UTF1andVENTXare two genes involved in embryonic development not previously implicated in epigenetic regulation. Our findings shed new light on the processes involved in cPCDHmethylation that may underlie associations with disease.
Interindividual variability in flower pickiness by foraging bumblebees
Authors: Armand Mélissa , Beckenbauer Christoph , Avarguès-Weber Aurore , Lihoreau Mathieu , Czaczkes Tomer J. 
Published: December 2024

ABSTRACTPollinators navigate complex and heterogeneous “flower markets”, where floral resources vary in quality, availability, and distribution. Bumblebees, as generalist foragers, visit numerous flowers during their foraging bouts. Yet, the factors influencing their flower choices and the notable individual differences in foraging behaviour among bees are still not well understood. We hypothesised that early foraging experiences influence bees’ subsequent flower choices. To test this, we observed individualBombus terrestrisworkers forage for three consecutive bouts in two artificial flower arrays. One array simulated a favourable environment with patches alternating high- and low-quality flowers (40% vs. 20% w/w sucrose solution), while the other array presented a more challenging environment with patches of high-quality flowers alongside unrewarded flowers (40% w/w sucrose solution vs. plain water). In both arrays, bees rapidly improved their foraging efficiency, increasing sucrose intake per unit time across bouts. In the favourable array, most bees became highly selective for high-quality flowers, while some continued visiting both flower types. Their degree of pickiness was influenced by early experiences: bees initially exposed to high-quality flowers became more selective, whereas those encountering low-quality flowers first were less selective in subsequent foraging. Despite differences in pickiness and array conditions, bees achieved comparable sucrose intake rates within three bouts. This study highlights the adaptability of bee foraging behaviour and emphasizes the role of early foraging experiences in driving individual differences.Significance statementTo forage efficiently, pollinators must navigate complex “flower markets”, where floral resources vary in quality and availability. We observedBombus terrestrisworkers forage across three bouts in two artificial flower arrays: a favourable array with flower patches alternating high- and low-quality flowers (40% vs. 20% w/w sucrose solution), and an extreme array with high-quality and non-rewarding flowers (40% w/w sucrose solution vs. plain water). We found that bees initially exposed to high-quality flowers became highly selective, whereas those encountering low-quality flowers first were less picky, collecting both flower types. Despite these differences, bees rapidly improved foraging efficiency over successive bouts, achieving similar sucrose intake rates within three bouts. This study highlights the foraging flexibility of bumblebees and suggests that early experiences can have lasting effects, influencing flower choices dozens of visits later.
The use of variational autoencoders to characterise the heterogeneous subpopulations that arise due to antibiotic treatment
Authors: Bersenev Dennis , Zhang Emily 
Published: December 2024

AbstractAntimicrobial resistance (AMR) is a persistent threat to global agriculture and healthcare systems. One of the challenges towards development of robust antimicrobials to date has been the limitation posed by low resolution bacterial sequencing technologies. The recent development of Bacterial Single Cell RNA sequencing protocols has provided an unprecedented opportunity in AMR research as it now enables researchers to probe bacterial populations at single cell resolution. In this study, we apply a Bayesian Variational Autoencoder, MrVI, to data generated by one such Bacterial Single Cell RNA sequencing protocol, BacDrop, and use it characterise changes in gene expression levels before and after antibiotic perturbation. Through the use of MrVI, we were able to find distinct DNA damage and heat shock response subpopulations. We also determined that each of the subpopulations could be mapped back to its respective antibiotic treatments, providing more precise insight into their mechanisms of resistance. These preliminary results indicate the potential that this new window into intracellular bacterial communication provides, and motivate the continued exploration of models to unveil the mechanisms underlying AMR.