bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seed coating with phages for sustainable plant biocontrol of plant pathogens and influence of the seed coat mucilage
Authors: Erdrich Sebastian H. , Schurr Ulrich , Frunzke Julia , Arsova Borjana 
Published: January 2024

AbstractPathogens resistant to classical control strategies are on the rise and cause significant damage in crop yield production with seeds as one major transmission route. Bacteriophages are specialized viruses of bacteria and their interaction with seeds holds great potential as targeted and sustainable solution to this problem. In this study, we isolated and characterized two novel phages, Athelas and Alfirin, infectingPseudomonas syringaeandAgrobacterium tumefaciens, respectively, and included the recently published phage Pfeifenkraut infectingXanthomonas translucens. The three phages were tested for their interaction with the seed coat mucilage. Phage binding onArabidopsisseeds, which exude the mucilage as a polysaccharide-polymer-matrix, was assessed by comparison to seeds with removed mucilage. Two of the three phages were dependant on mucilage for seed binding, and podophage Athelas showed the highest dependency. Further podoviruses of theAutographiviridaeobtained from the systematicE. coli(BASEL) phage collection were tested and showed a similar dependency on the mucilage for seed adhesion. Comparative analysis using a set ofArabidopsisseed coat mutants revealed the diffusible cellulose fraction as important component for phage binding. Long-term activity tests revealed a high stability of phages on seed surfaces and phage coating effectively increased the survival rate of plant seedling in the presence of the pathogen. Utilization of non-virulent host strains was further successfully applied to boost the presence of infectious phage particles on seed surfaces. Altogether, our study highlights the high potential of phage-based applications as sustainable biocontrol strategy on the seed level.
PyLossless: A non-destructive EEG processing pipeline
Authors: Huberty Scott , Desjardins James , Collins Tyler , Elsabbagh Mayada , O’Reilly Christian 
Published: January 2024

AbstractEEG recordings are typically long and contain large amounts of data, making manual cleaning a time-consuming and error-prone task. Automated pre-processing pipelines can facilitate the efficient and objective extraction of artifacts, enabling standardized and reproducible analyses. However, automated pre-processing pipelines typically remove data considered artifact, and return a subset of irreversibly transformed signals. This approach obfuscates pre-processing decisions, and often makes it impossible to recover the original data or modify the pre-processing steps. Further, it complicates collaboration between research teams working on a common dataset, because different analyses may require specific pre-processing routines. Given the large amount of resources that are devoted to collecting EEG, tools that can help efficiently and transparently pre-process data are greatly needed. PyLossless addresses this need by creating a non-destructive, automated pre-processing pipeline that maintains the continuous EEG structure. It offers a user-friendly API, it is well documented, tested through continuous integration, easily deployable, and integrates with the popular MNE-Python environment. The pipeline further provides a browser-based quality control review (QCR) dashboard that allows researchers to visualize and edit the automated artifact annotations on sensors, time-periods, and independent components. The end product of PyLossless is a lossless annotated data state that can be shared and used with analysis-specific artifact rejection policies, allowing for an optimal balance between flexibility and standardization.
Seasonal dynamics and drivers of microbial communities in a temperate dimictic lake: insights from metabarcoding and machine learning
Authors: Michał Karlicki , Anna Bednarska , Paweł Hałakuc , Kacper Maciszewski , Anna Karnkowska 
Published: January 2024

AbstractMicrobial communities, consisting of prokaryotes and protists, play a central role in ecological processes in aquatic environments. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and to track spatio-temporal dynamics in both marine and freshwater environments. While previous research has primarily focused on marine ecosystems, it is important to study microbial communities in freshwater environments, which are characterised by high diversity and susceptibility to rapid environmental change. In temperate lakes, despite extensive research on temporal changes in physico-chemical factors and microscopic studies of plankton, there is a notable research gap regarding their eukaryotic microbial communities. Our study fills this gap by investigating the diversity and seasonal changes of prokaryotic and eukaryotic communities in Lake Roś (Poland), a representative temperate lake characterised by two mixing episodes in spring and autumn and pronounced stratification in summer. Our metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. To decipher the drivers of the seasonal communities, we used machine learning and statistical methods and identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the community composition in Lake Roś are temperature, oxygen and silicon concentration. Understanding these community structures and the underlying factors is crucial in the context of climate change, which might affect mixing patterns and lead to prolonged stratification. Given the pronounced seasonal shifts observed in these communities, we can anticipate that climate change will profoundly impact the functioning of temperate dimictic lakes.
Altered firing output of VIP interneurons and early dysfunctions in CA1 hippocampal circuits in the 3xTg mouse model of Alzheimer’s disease
Authors: Michaud Felix , Francavilla Ruggiero , Topolnik Dimitry , Iloun Parisa , Tamboli Suhel , Calon Frederic , Topolnik Lisa 
Published: January 2024

AbstractAlzheimer’s disease (AD) leads to progressive memory decline, and alterations in hippocampal function are among the earliest pathological features observed in human and animal studies. GABAergic interneurons (INs) within the hippocampus coordinate network activity, among which type 3 interneuron-specific (I-S3) cells expressing vasoactive intestinal polypeptide and calretinin play a crucial role. These cells provide primarily disinhibition to principal excitatory cells (PCs) in the hippocampal CA1 region, regulating incoming inputs and memory formation. However, it remains unclear whether AD pathology induces changes in the activity of I-S3 cells, impacting the hippocampal network motifs. Here, using young adult 3xTg-AD mice, we found that while the density and morphology of I-S3 cells remain unaffected, there were significant changes in their firing output. Specifically, I-S3 cells displayed elongated action potentials and decreased firing rates, which was associated with a reduced inhibition of CA1 INs and their higher recruitment during spatial decision-making and object exploration tasks. Furthermore, the activation of CA1 PCs was also impacted, signifying early disruptions in CA1 network functionality. These findings suggest that altered firing patterns of I-S3 cells might initiate early-stage dysfunction in hippocampal CA1 circuits, potentially influencing the progression of AD pathology.SignificanceThis study examines VIP interneurons in the CA1 hippocampus affected by Alzheimer’s disease (AD) pathology. While these cells maintain their structural integrity, they exhibit altered firing patterns in young adult 3xTg-AD mice. These changes might correlate with enhanced CA1 inhibition and impact the activation of principal cells. These findings shed light on early dysfunction in hippocampal circuits as a potential mechanism of AD pathology and offer insights into prospective therapeutic targets.
Different outcomes of endurance and resistance exercise in skeletal muscles of Oculopharyngeal muscular dystrophy
Authors: Boulinguiez Alexis , Dhiab Jamila , Crisol Barbara , Muraine Laura , Gaut Ludovic , Rouxel Corentin , Flaire Justine , Mouigni Hadidja-Rose , Lemaitre Mégane , Giroux Benoit , Audoux Lucie , SaintPierre Benjamin , Ferry Arnaud , Mouly Vincent , Butler-Browne Gillian , Negroni Elisa , Malerba Alberto , Trollet Capucine 
Published: January 2024

ABSTRACTBackgroundExercise is widely considered to have beneficial impact on skeletal muscle aging. In addition, there are also several studies demonstrating a positive effect of exercise on muscular dystrophies. Oculopharyngeal muscular dystrophy (OPMD) is a late-onset autosomal dominant inherited neuromuscular disorder caused by mutations in thePAPBN1gene. These mutations consist in short (1-8) and meiotically stable GCN trinucleotide repeat expansions in its coding region responsible for the formation of PAPBN1 intranuclear aggregates. This study aims to characterize the effects of two types of chronic exercise, resistance and endurance, on the OPMD skeletal muscle phenotype using a relevant murine model of OPMD.MethodsIn this study, we tested two protocols of exercise. In the first, based on endurance exercise, FvB (wild-type) and A17 (OPMD) mice underwent a 6-week-long motorized treadmill protocol consisting in 3 sessions per week of running 20cm/s for 20 minutes. In the second protocol, based on resistance exercise generated by chronic mechanical overload (OVL), surgical removal of gastrocnemius and soleus muscles was performed, inducing hypertrophy of the plantaris muscle. In both types of exercise, muscles of A17 and FvB mice were compared to those of respective sedentary mice. For all the groups, force measurement, muscle histology and molecular analyses were conducted.ResultsFollowing the endurance exercise protocol, we did not observe any major changes in the muscle physiological parameters, but an increase in the number of PABPN1 intranuclear aggregates and enhanced collagen deposition in the exercised A17 OPMD mice. In the resistance overload protocol, we also observed an increased collagen deposition in the A17 OPMD mice which was associated with larger muscle mass and fiber cross sectional area and increased absolute maximal force as well as a reduction in PABPN1 aggregate number.ConclusionsRunning exercise and mechanical overload led to very different outcome in skeletal muscles of A17 mice. Both types of exercise enhanced collagen deposition but while the running protocol increased aggregates, the OVL reduced them. More importantly OVL reversed muscle atrophy and maximal force in the A17 mice. Our study performed in a relevant model gives an indication of the effect of different types of exercise on OPMD muscle which should be further evaluated in humans for future recommendations as a part of the lifestyle of individuals with OPMD.
Single residues in the complexin N-terminus exhibit distinct phenotypes in synaptic vesicle fusion
Authors: Toulme Estelle , Murach Jacqueline , Bärfuss Simon , Kroll Jana , Malsam Jörg , Trimbuch Thorsten , Herman Melissa A. , Söllner Thomas H. , Rosenmund Christian 
Published: January 2024

AbstractThe release of neurotransmitters at central synapses is dependent on a cascade of protein interactions, specific to the presynaptic compartment. Amongst those dedicated molecules the cytosolic complexins play an incompletely defined role as synaptic transmission regulators. Complexins are multidomain SNARE complex binding proteins which confer both inhibitory and stimulatory functions. Using systematic mutagenesis and combining reconstitutedin vitromembrane fusion assays with electrophysiology in neurons, we deciphered the function of the N-terminus of complexin II (Cpx). The N-terminus (amino acid 1 - 27) starts with a region enriched in hydrophobic amino acids (1-12), which can lead to lipid binding. In contrast to mutants which maintain the hydrophobic character and the stimulatory function of Cpx, non-conservative exchanges largely perturbed spontaneous and evoked exocytosis. Mutants in the downstream region (amino acid 11-18) show differential effects. Cpx-A12W increased spontaneous release without affecting evoked release whereas replacing D15 with amino acids of different shapes or hydrophobic properties (but not charge) not only increased spontaneous release, but also impaired evoked release and surprisingly reduced the size of the readily releasable pool, a novel Cpx function, unanticipated from previous studies. Thus, the exact amino acid composition of the Cpx N-terminus fine tunes the degree of spontaneous and evoked neurotransmitter release.Significance StatementWe describe in this work the importance of the N-terminal domain of the small regulatory cytosolic protein complexin in spontaneous and evoked glutamatergic neurotransmitter release at hippocampal mouse neurons. We show using a combination of biochemical, imaging and electrophysiological techniques that the binding of the proximal region of complexin (amino acids 1-10) to lipids is crucial for spontaneous synaptic vesicular release. Furthermore, we identify a single amino acid at position D15 which is structurally important since it not only is involved in spontaneous release but, when mutated, also decreases drastically the readily releasable pool, a function that was never attributed to complexin.
Wnt target gene Ascl4 is dispensable for skin appendage development
Authors: Papagno Verdiana , Sulic Ana-Marija , Satta Jyoti P. , Hoshiar Aida Kaffash , Kumar Vinod , Jernvall Jukka , Mikkola Marja L. 
Published: January 2024

AbstractThe development of skin appendages, including hair follicles, teeth and mammary glands is initiated through the formation of the placode – a local thickening of the epithelium. The Wnt/β-catenin signaling cascade is an evolutionary conserved pathway with an essential role in placode morphogenesis, but its downstream targets and their exact functions remain ill defined. In this study, we identifyAchaete-scute complex-like 4(Ascl4) as a novel target of the Wnt/β-catenin pathway and demonstrate its expression pattern in the signaling centers of developing hair follicles and teeth. Ascl transcription factors belong to the superfamily of basic helix-loop-helix transcriptional regulators involved in cell fate determination in many tissues. However, their specific role in the developing skin remains largely unknown. We report thatAscl4null mice have no overt phenotype. Absence of Ascl4 did not impair hair follicle morphogenesis or hair shaft formation suggesting that it is non-essential for hair follicle development. No tooth or mammary gland abnormalities were detected either. We suggest that other transcription factors may functionally compensate for the absence of Ascl4, but further research is warranted to assess this possibility.
Identification, structure and function of the methyltransferase involved in the biosynthesis of the dithiolopyrrolone antibiotic xenorhabdin
Authors: Su Li , Huber Eva M. , Westphalen Margaretha , Gellner Jonas , Bode Edna , Köbel Tania , Grün Peter , Alanjary Mohammad M. , Glatter Timo , Schindler Daniel , Groll Michael , Bode Helge B. 
Published: January 2024

AbstractXenorhabdins (XRDs) are produced byXenorhabdusspecies and are members of the dithiopyrrolone (DTP) class of natural products that have potent antibacterial, antifungal and anticancer activity. The amide moiety of their DTP core can be methylated or not to fine-tune the bioactivity properties. However, the enzyme responsible for the amideN-methylation remained elusive. Here, we identified and characterized the amide methyltransferase XrdM that is encoded nearly 600 kb away from the XRD gene cluster using proteomic analysis, methyltransferase candidate screening, gene deletion, and allied approaches. In addition, crystallographic analysis and site-directed mutagenesis proved that XrdM is completely distinct from the recently reported DTP methyltransferase DtpM, and that both have been tailored in a species-specific manner for DTP biosynthesis in Gram-negative/positive organisms. Our study expands the limited knowledge of post-NRPS amide methylation in DTP biosynthesis and reveals the evolution of two structurally completely different enzymes for the same reaction in different organisms.
Urban greenspace aerobiomes are shaped by soil conditions and land cover type
Authors: Brame Joel E. , Liddicoat Craig , Abbott Catherine A. , Cando-Dumancela Christian , Robinson Jake M. , Breed Martin F. 
Published: January 2024

ABSTRACTGrowing evidence suggests that exposure to microbial biodiversity is important for human immunoregulation and health. Urban greenspaces harbour airborne bacterial communities (aerobiomes) with the potential to transfer beneficial bacteria to humans. However, limited studies have examined the ecological influences of soil, vegetation, and rainfall on aerobiomes in urban greenspaces. Here, we utilised 16S rRNA amplicon sequence data to analyse the effects of land cover, soil abiotic characteristics, surrounding vegetation diversity, and rainfall on aerobiome diversity and composition from 33 urban greenspace sites in Adelaide, South Australia. We sampled air and soil from two urban greenspace land cover types: highly-managed sports fields (n= 11) and minimally-managed nature parks (n= 22). Sports field aerobiomes had a distinct aerobiome community composition and higher alpha diversity than nature parks. Aerobiome alpha diversity was shaped more by soil abiotic characteristics, particularly soil pH and iron levels, than woody plant species diversity. Rainfall prior to sampling also had strong effects on the aerobiome community composition and associated with decreased alpha diversity. These findings point toward soil iron and pH management as pathways to increase aerobiome bacterial diversity. Our study shows that, with additional research, there is potential for greenspace managers and urban planners to target specific soil abiotic characteristics in urban greenspaces to improve microbiome-mediated urban health.
Dysregulated expanded endocannabinoid system as therapeutic targets of amyotrophic lateral sclerosis
Authors: Ito Daisuke , Iida Madoka , Iguchi Yohei , Hashizume Atsushi , Yamada Shinichiro , Kishimoto Yoshiyuki , Komori Shota , Shimamura Teppei , Takemoto Yuto , Nakatochi Masahiro , Akashi Tomohiro , Hinohara Kunihiko , Lee-Okada Hyeon-Cheol , Niwa Junichi , Sobue Gen , Tanaka Shinji , Takashina Ken , Yokomizo Takehiko , Katsuno Masahisa 
Published: January 2024

AbstractAmyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the selective loss of upper and lower motor neurons. ALS patients often manifest systemic metabolic abnormalities such as glucose intolerance. Herein, to elucidate the systemic metabolic changes related to ALS progression, we performed metabolomics analysis on the serum of ALS patients and identified several metabolites associated with the disease progression, including metabolites involved in the expanded endocannabinoid system (ECS). In particular, the levels of N-acyl taurines (NAT) were correlated with the longitudinal change in the revised ALS functional rating scale (ALSFRS-R) rating. In vitro experiments with ALS cell models and in vivo studies with SOD1G93Atransgenic mice revealed that PF-04457845, a fatty amide acid hydrolase (FAAH) inhibitor, up-regulated the expanded ECS, particularly the levels of NATs and N-acyl ethanolamine and ameliorates motor neuron degeneration through the regulation of microglial polarization, synapse plasticity, and neuronal development. Our study indicates that dysregulation of the expanded ECS is associated with ALS progression and a target for novel disease-modifying therapies.
Differential tissue deformability underlies shape divergence of the embryonic brain and spinal cord under fluid pressure
Authors: McLaren Susannah B.P. , Xue Shi-Lei , Ding Siyuan , Winkel Alex , Baldwin Oscar , Dwarakacherla Shreya , Franze Kristian , Hannezo Edouard , Xiong Fengzhu 
Published: January 2024

ABSTRACTAn expanded brain enables the complex behaviours of vertebrates that promote their adaptation in diverse ecological niches1–3. Initial morphological differences between the brain and spinal cord emerge as the antero-posteriorly patterned neural plate folds to form the neural tube4–7during embryonic development. Following neural tube closure, a dramatic expansion of the brain diverges its shape from the spinal cord8, setting their distinct morphologies for further development9,10. How the brain and the spinal cord expand differentially remains unclear. Here, using the chicken embryo as a model, we show that the hindbrain expands through dorsal tissue thinning under a positive hydrostatic pressure from the neural tube lumen11,12while the dorsal spinal cord shape resists the same pressure. Using magnetic droplets and atomic force microscopy, we reveal that the dorsal tissue in the hindbrain is more fluid than in the spinal cord. The dorsal hindbrain harbours more migratory neural crest cells13and exhibits reduced apical actin and a disorganised laminin matrix compared to the dorsal spinal cord. Blocking the activity of neural crest-associated matrix metalloproteinases inhibited dorsal tissue thinning, leading to abnormal brain morphology. Transplanting early dorsal hindbrain cells to the spinal cord was sufficient to create a region with expanded brain-like morphology including a thinned-out roof. Our findings open new questions in vertebrate head evolution and neural tube defects, and suggest a general role of mechanical pre-pattern in creating shape differences in epithelial tubes.
The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells
Authors: Sugiyama Kota , Yoshioka Kazuma , Hayakawa Nao , Marutani Miyu , Masuda Ryo , Abadi Selma Alamanda , Ichisakino Maki , Seki Yoshiyuki 
Published: January 2024

AbstractAfter fertilization, maternally deposited mRNA is cleared, andde novomRNA is transcribed from the zygotic genome through zygotic genome activation (ZGA), which is called maternal- to-zygotic transition (MZT) occurring in the mouse at 2-cell (2C) stage. 2C-like cells (2CLCs) marked by MERVL expression and transcriptionally similar to 2C embryos spontaneously emerge from mouse embryonic stem cells (mESCs). Although the emergence of 2CLCs completely depends on DUX function, a recent knockout study clearly showed that DUX is dispensable for mouse embryos, suggesting that DUX-independent molecular pathways are not recapitulated in 2CLCs. We present here that the disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates DUX-dependent and -independent molecular pathway associated with the development of early mouse embryos mediated by the upregulation of Preferentially expressed antigen of melanoma family-like 7 (PRAMEL7). Furthermore, the abnormality of the gene expression profile caused byDuxKO is partially rescued by the overexpression of PRAMEL7 in mESCs. Our study provides new insights into the DUX-independent molecular pathway for developing early mouse embryos.