bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population shifts in begomoviruses associated with tomato yellow leaf curl disease in western Mediterranean countries
Authors: Granier Martine , Faize Mohamed , Passera Sandie , Urbino Cica , Peterschmitt Michel 
Published: August 2024

AbstractTomato yellow leaf curl disease (TYLCD) was reported in western Mediterranean basin since the late 1980s. Based on intensive plant samplings performed in Spain, Italy and Morocco at different periods between the 1990s and 2014, several begomoviruses (family Geminiviridae) were identified as the cause of TYLCD. They comprise the native Tomato yellow leaf curl Sardinia virus (TYLCSV), two strains of Tomato yellow leaf curl virus (TYLCV) introduced from the Middle East, and several types of TYLCV/TYLCSV recombinants including the invasive recombinant TYLCV-IS76 in which the proportion of genome inherited from TYLCSV was unusually short. Although parental and recombinant TYLCD-associated begomoviruses were present in each country, country specificities were detected with respect to their relative prevalence, the infection profiles of individual tomato plants, and the recombination patterns of TYLCV/TYLCSV recombinants. Considering geographic proximities and trade activities between these countries, and the efficient transmission of begomoviruses which are persistently transmitted by the polyphagous and tiny whitefly vectorBemisia tabaci, it was not known if these specificities would be maintained over time. To address this question, tomato samples collected in the three countries between 2015 and 2019 were analysed with PCR tests previously designed to distinguish species, strains and recombinants of TYLCD associated begomoviruses, and with an original PCR test distinguishing emerging resistance-breaking recombinants bearing short TYLCSV-inherited fragments (Srec) from formerly reported recombinants with longer TYLCSV fragments (Lrec). The results show that country specificities are still present, the most striking being the contrasted geographic distribution of Srec recombinants, with TYLCV-IS76 detected in Morocco but not in Italy, and TYLCV-IS141 and a new Srec recombinant (TYLCV-IS60) both detected in Italy and not in Morocco. Nevertheless, besides country specificities, a general population shift was revealed regarding TYLCV/TYLCSV recombinants. Indeed, all the recombinant positive samples, irrespective of their geographic origin, were Srec-positive but Lrec-negative, which suggest that the emergence of Srec recombinants occurred at the expenses of the Lrec recombinants. These results are discussed in relation to the positive selection of Srec recombinants by Ty-1 resistant tomato plants.
CarpeDeam: ADe NovoMetagenome Assembler for Heavily Damaged Ancient Datasets
Authors: Kraft Louis , Söding Johannes , Steinegger Martin , Jochheim Annika , Sackett Peter Wad , Fernandez-Guerra Antonio , Renaud Gabriel 
Published: August 2024

AbstractDe novoassembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We presentCarpeDeam, a novel damage-awarede novoassembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns,CarpeDeamrecovers longer continuous sequences and more protein sequences from both simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler,CarpeDeamopens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.
Characterization of Postsynaptic Glutamate Transporter Functionality in the Zebrafish Retinal First Synapse Across Different Wavelengths
Authors: Garbelli Marco , Niklaus Stephanie , Neuhauss Stephan C.F. 
Published: August 2024

AbstractIn the zebrafish retina, incident light undergoes wavelength-dependent processing encompassing mechanisms such as color opponency, contrast enhancement, and motion detection prior to neural transmission to the brain proper. In darkness, photoreceptors continuously release glutamate into the synaptic cleft, a process that diminishes in response to increased light intensity, thereby conveying visual signals to ON and OFF bipolar cells. Specifically, in zebrafish, the ON pathway signal transduction is mediated by metabotropic glutamate receptor 6b (mGluR6b) and Excitatory Amino Acid Transporters (EAATs). Here we demonstrate that knockout ofeaat5bandeaat7disrupts electroretinogram responses to short and long-wavelength stimuli while preserving middle-wavelength responses, suggesting wavelength-specific roles. We found differential expression of EAAT5b and EAAT7 in the outer plexiform layer, particularly in the strike zone, crucial for prey capture, supporting task specific involvement of these signaling pathways. In order to investigate this, we developed a virtual hunting assay using UV light stimuli. Such a behavioral assay targeting short and long wavelengths indicate that EAAT5b and EAAT7 influence UV-dependent prey detection and motion sensing differently. Our findings highlight the importance of EAAT5b and EAAT7 in modulating light integration dynamics in the zebrafish retina.
Hyoid bone position and upper airway patency: A computational finite element modeling study
Authors: Salman Diane , Amatoury Jason 
Published: August 2024

ABSTRACTBackground and ObjectivesThe hyoid bone’s inferior baseline position in obstructive sleep apnea (OSA) has led to surgical hyoid repositioning treatment, yet outcomes vary widely. The influence of baseline hyoid position (phenotype) and surgical hyoid repositioning on upper airway function remains unclear. We aimed to investigate their impact on the upper airway using computational modeling.MethodsA validated finite element model of the rabbit upper airway was advanced and used to simulate changes in baseline hyoid position and surgical hyoid repositioning, alone and in combination. The hyoid was displaced in cranial, caudal, anterior, anterior-cranial and anterior-caudal directions from 1-4mm. Model outcomes included upper airway collapsibility, measured using closing pressure (Pclose), cross-sectional area (CSA) and soft tissue mechanics (stress and strain).ResultsGraded baseline hyoid position increments increased Pclose for all directions, and up to 29-43% at 4mm (relative to the original baseline hyoid position). Anterior-based surgical hyoid repositioning decreased Pclose (∼-115% at 4mm) and increased ΔCSA (∼+35% at 4mm). Cranial surgical hyoid repositioning decreased ΔPclose (−29%), minimally affecting CSA. Caudal surgical hyoid repositioning increased ΔPclose (+27%) and decreased ΔCSA (−7%). Anterior-cranial and anterior-caudal surgical hyoid repositioning produced the highest stresses and strains. Surgical hyoid repositioning effects on upper airway outcomes were dependent on baseline hyoid position, with more caudal baseline hyoid positions leading to less effective surgeries.ConclusionsBaseline hyoid position (phenotype) and surgical hyoid repositioning both alter upper airway outcomes, with effects dependent on hyoid displacement direction and magnitude. Baseline hyoid position influences the effectiveness of surgical hyoid repositioning in reducing upper airway collapsibility. These findings provide further insights into the hyoid’s role in upper airway patency and suggest that considering the hyoid’s baseline position and surgical repositioning direction/increment may help improve hyoid surgeries for OSA treatment.
Seed-competent α-synuclein pathology in metachromatic leukodystrophy: the expanding spectrum of α-synucleinopathy in sphingolipidoses
Authors: Ghanem Simona , Hawksworth Jade , Thom Searlait , Hartanto Annabelle E. , O’Neill Joseph , Ponraj Janarthanan , Mansour Said , Attems Johannes , Pyle Angela , Johnson Lauren , Baines Jack , Taylor Robert W. , Outeiro Tiago F. , El-Agnaf Omar M.A. , Erskine Daniel 
Published: August 2024

ABSTRACTMetachromatic leukodystrophy (MLD) is a rare - typically paediatric - sphingolipid storage disorder resulting from bi-allelic pathogenic variants in theARSAgene, encoding the lysosomal arylsulphatase A (ASA). Heterozygous variants inARSAare associated with risk of Lewy body diseases (LBD), a group of age-associated neurodegenerative disorders characterised by the accumulation of the protein α-synuclein; however, no study has yet determined whether α-synuclein with putative pathological features is observed in MLD brain tissue. We examinedpost-mortembrain tissue from MLD cases (N=5, age 2-33) compared to matched control cases using histological approaches and α-synuclein seeding amplification assay (SAA). Juvenile-onset MLD cases exhibited granular α-synuclein deposits in neurons of regions prone to neuronal pathology in MLD, and seed-competent conformers that generated atypical short, twisted fibrils on SAA. In contrast, infantile-onset MLD cases gave only variably positive reactions on SAA. In summary, this study suggests MLD cases manifest α-synuclein pathology reminiscent of that observed in LBD, even in juvenile populations, further expanding the spectrum of sphingolipid storage disorders associated with the aggregation of α-synuclein. These findings have important implications for understanding the disease process of both LBD and MLD, potentially highlighting novel pathways for therapeutic interventions in both conditions.
Holoprosencephaly and Cyclopia inbmp7bandbmpr1baCrispant zebrafish
Authors: Kyrychenko Valentyn , Rensinghoff Philipp , Bulk Johannes , Frey Constanze , Heermann Stephan 
Published: August 2024

AbstractThe visual system is highly specialized and its function is substantially depending on the proper development of the eyes. Early eye development starts with the definition of a single eye field, which is localized within the anterior neural plate (ANP). This single eye field is split consecutively and two optic vesicles emerge at the sides. These vesicles are then transformed into optic cups, out of which the future retinae are differentiating.Holoprosencephaly (HPE) is a frequent developmental forebrain disorder, in which the splitting of ANP domains is hampered. HPE is mostly genetically linked and we recently showed that BMP antagonism is important for the eye field and the telencephalic anlage to split. Excessive BMP induction led to retinal progenitors stuck inside a dysmorphic forebrain. In this study, using the zebrafish as a model, we show with acute CRISPR/ Cas9 analysis in the F0 generation, the necessity ofbmp7bandbmpr1bafor proper forebrain development. In Crispants for both genes we found HPE phenotypes, e.g. cyclopia. Further analysis ofbmp7bCrispants indicated that predominantly the eye field is affected, rather than the telencephalic precursor domain.
Massive reduction of RyR1 in muscle spindles of mice carrying recessiveRyr1mutations alters proprioception and causes scoliosis
Authors: Ruiz Alexis , Benucci Sofia , Meier Hervé , Schultz Georg , Buczak Katarzyna , Handschin Christoph , Pena Rodrigo C. G. , Treves Susan , Zorzato Francesco 
Published: August 2024

AbstractMuscle spindles are stretch receptors lying deep within the muscle belly involved in detecting changes in muscle length and playing a fundamental role in motor control, posture and synchronized gait. They are made up of an external capsule surrounding 3-5 intrafusal muscle fibers and a nuclear bag complex. Dysfunction of muscle spindles leads to abnormal proprioceptor function, which has been linked to aberrant bone and cartilage development, scoliosis, kyphosis and joint contractures.RYR1, the gene encoding the calcium release channel of the sarcoplasmic reticulum, is the most common target of mutations linked to human congenital myopathies, a condition often accompanied by skeleton alterations and joint contractures. So far, the link betweenRYR1mutations, altered muscle spindles and skeletal defects has not been investigated. To this end, we investigated heterozygous mice carrying recessiveRyr1mutations isogenic to those present in a severely affected child. Here we show that: (i) the RyR1 protein localizes to the polar regions of intrafusal fibers and exhibits a doubled row distribution pattern, typical for junctional sarcoplasmic reticulum proteins; (ii) muscle spindles of compound heterozygous mice show structural defects; (iii) RyR1 content in intrafusal muscle fibers from dHT mice is reduced by 54%. Such a massive reduction of mutant RyR1 in intrafusal muscle fibers leads to altered expression of intrafusal fiber proteins, severe scoliosis, alteration of gait and inter limb coordination. These results support the hypothesis thatRYR1mutations not only affect the function of extrafusal muscles, but might also affect that of intrafusal muscles. The latter may be one of the underlying causes of skeletal abnormalities seen in patients affected by recessiveRYR1mutations.
Beyond neutral loci: Examining immune gene variation in tigers(Panthera tigris)
Authors: Aditi B.V. , Ramakrishnan Uma 
Published: August 2024

AbstractGenetic vulnerability of wild populations is generally assessed using neutral loci, which may not accurately reflect a population’s adaptive potential. In contrast, diversity at loci putatively involved in fitness and survival, such as immune genes, could be a better proxy for future survival. Research on immune genes in wild species has traditionally focused on the MHC loci. We investigate five families of non-MHC immune genes -Tumor Necrosis Factor, Interleukin, Toll-like Receptor, Leukocyte Immunoglobulin-Like Receptors, and Chemokine - involved in adaptive and innate immunity in the tiger(Panthera tigris), an endangered carnivore. We compare immune gene diversity to neutral diversity using publicly available resequenced whole genomes from 107 tigers representing all extant subspecies and subpopulations (within India) with different demographic histories.Immune receptor genes show high nucleotide diversity (mean: 0.0019) compared to neutral loci (0.0008) and immune signalling genes (0.0004), suggesting positive selection. However, heterozygosity of immune genes does not differ significantly from neutral loci, suggesting strong genetic drift. Populations with histories of bottleneck and inbreeding show reduced genetic diversity and high mutation load but some immune loci retain polymorphisms even in inbred populations. Genetic differentiation and site frequency spectra of immune loci correspond to patterns from neutral loci but Toll-like receptor genes show signatures associated with balancing selection. Our findings indicate that genetic drift is likely the predominant evolutionary force shaping genetic variation in bottlenecked endangered species such as tigers, even at immune loci that are typically subject to selection. However, remnants of past balancing selection might preserve important variation, potentially influencing population survival.
Sexual Dimorphism in Jump Kinematics and Choreography in Peacock Spiders
Authors: Narendra Ajay , Seibel Anna , Ramirez-Esquivel Fiorella , Joshi Pranav , McLean Donald James , Robledo-Ospina Luis , Rao Dinesh 
Published: August 2024

AbstractJumping requires a rapid release of energy to propel an animal. Terrestrial animals achieve this by relying on the power generated by muscles, or by storing and rapidly releasing elastic energy. Jumping spiders rely on hydraulic pressure and muscular action to propel their jump. Though males and females of jumping spiders vary in size, sex-specific differences in jumping have never been studied. We investigated sexual dimorphism in the jump kinematics of an Australian Peacock spider,Maratus splendens. We recorded locomotory jumps in males and females using high-speed videography (5000 frames per second). We determined the centre of mass of the animals using µCT and tracked its displacement during a jump. We found that although females weighed more than twice as much as males, both had similar accelerations and take-off velocities. Males had shorter jump take-off duration, steeper take-off angle and experienced higher g-force compared to the females. We examine the jump choreography of male and female spiders and explore the factors behind the differences in their jump kinematics.
SatXplor – A comprehensive pipeline for satellite DNA analyses in complex genome assemblies
Authors: Volarić Marin , Meštrović Nevenka , Despot-Slade Evelin 
Published: August 2024

AbstractSatellite DNAs (satDNAs) are tandemly repeated sequences that make up a significant portion of almost all eukaryotic genomes. Although satDNAs have been shown to play a very important role in genome organization and evolution, they are relatively poorly analysed even in model. One of the main reasons for the current lack of in-depth studies on satDNAs is their underrepresentation in genome assemblies. The complexity and highly repetitive nature of satDNAs make their analysis challenging, and there is a need for efficient tools that can ensure accurate annotation and analysis of satDNAs.We present a novel pipeline, named Satellite DNA Exploration (SatXplor), designed to robustly characterize satDNA elements and analyse their arrays and flanking regions. SatXplor is benchmarked against curated satDNA datasets from diverse species, showcasing its versatility across genomes with varying complexities and different satDNA profile. Component algorithms excel in the identification of tandemly repeated sequences and for the first time enable evaluation of satDNA variation and array annotation with the addition of information about surrounding genomic landscape.SatXplor is an innovative pipeline for satDNA analysis that can be paired with any tool used for satDNA detection, offering insights into the structural characteristics, array determination and genomic context of satDNA elements. By integrating various computational techniques, from sequence analysis and homology investigation to advanced clustering and graph-based methods, it provides a versatile and comprehensive approach to explore the complexity of satDNA organization and to understand the underlying mechanisms and evolutionary aspects. It is open-source and freely accessible athttps://github.com/mvolar/SatXplor.
Assessing Autophagy Flux in Glioblastoma Temozolomide Resistant Cells
Authors: Clark Courtney , Barzegar-Behrooz Amir , Cordani Marco , Shojaei Shahla , Ghavami Saeid 
Published: August 2024

AbstractAutophagy is a critical cellular process involved in the degradation and recycling of cytoplasmic components, playing a dual role in cancer by either promoting cell survival or facilitating cell death. In glioblastoma (GB), autophagy has been implicated in resistance to the chemotherapeutic agent Temozolomide (TMZ). This study presents a novel method to accurately measure autophagy flux in TMZ-resistant glioblastoma cells, combining advanced imaging techniques with biochemical assays. By quantifying key autophagy markers such as LC3-II and SQSTM1, our approach provides detailed insights into the dynamic processes of autophagosome formation and clearance under therapeutic stress. This method not only advances our understanding of autophagy in GB chemoresistance but also has significant implications for the development of autophagy-targeted therapies. The ability to monitor and manipulate autophagy flux in real-time offers a promising avenue for monitoring and understnading TMZ resistance and improving patient outcomes in glioblastoma treatment.
The genetic basis of predation resistance inPseudomonasspecies associated with the bactivorous soil amoebaDictyostelium discoideum
Authors: Steele Margaret I. , Peiser Jessica M. , Dawson Simon P. M. , Queller David C. , Strassmann Joan E. 
Published: August 2024

AbstractPredation is likely to influence the function of bacterial communities and the evolution of bacterial pathogens, because characteristics that permit escape from predators often overlap with traits used for biocontrol of plant pathogens, virulence, or even bioremediation. Soil bacteria are preyed upon by a variety of microorganisms, including the amoebaDictyostelium discoideum,which has led some strains to evolve resistance. We identified genes required for threePseudomonasspecies associated withD. discoideumto evade predation by screening more than 6,000 transposon mutants for loss of resistance. One species required a variety of genes including toxins and secondary metabolism genes, but the other two appear to have functionally redundant mechanisms of resistance, since disruption of genes with pleiotropic effects was required to render them susceptible. We determined that GacA, which positively regulates secondary metabolism, is required for resistance in all three species. Predation resistance also appears to be a social trait based on enrichment of cooperative genes in one species and rescue of mutants by wild type in another. Many genes required for resistance are conserved among both resistant and susceptible species, but several are found in few genomes and some of these have homologs in distantly related species. Gain and loss of resistance appears to be a dynamic process in which regulatory and structural genes are well conserved across species, the specific toxins they regulate may be lost in the absence of predators, and new toxins may be acquired through horizontal gene transfer.
Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB
Authors: DeAngelo Joseph D. , Maron Maxim I. , Roth Jacob S. , Silverstein Aliza M. , Gupta Varun , Stransky Stephanie , Basken Joel , Azofeifa Joey , Sidoli Simone , Gamble Matthew J. , Shechter David 
Published: August 2024

AbstractProtein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) —but not type I PRMT inhibition—leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export.