bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting the evolution and function of NIP2 parologs in theRhynchosporium spp.complex
Authors: Darma Reynaldi , Yu Daniel S. , Outram Megan A. , Sung Yi-Chang , Hill Erin H. , Croll Daniel , Williams Simon J. , Ovenden Ben , Milgate Andrew , Solomon Peter S. , McDonald Megan C. 
Published: October 2024

AbstractThe fungusRhynchosporium commune,the causal agent of barley scald disease, contains a paralogous effector gene family calledNecrosis-Inducing Protein 2(NIP2) andNIP2-like protein(NLP). However, the function and full genomic context of these paralogs remains uncharacterised. Here we present a highly contiguous long-read assembly ofR. communeWAI453. Using this assembly, we show that the duplication of theNIP2andNLPgene families is distributed throughout the genome and pre-dates the speciation ofR. communefrom its sister species. SomeNIP2paralogs have subsequently been lost or are absent in the sister species. The diversity of these paralogs was examined fromR. communeglobal populations and their expression was analysed duringin plantaandin vitrogrowth to analyse the importance of these genes during infection. The majority ofNIP2andNLPparalogs in WAI453 genome were significantly upregulated during plant infection suggesting that theNIP2andNLPgenes harbour virulence roles. An attempt to further characterise function of NIP2.1 by infiltrating purified protein into barley leaves did not induce necrosis questioning its previously reported role as an inducer of host cell death. Together these results suggest that theNIP2effector family does play a role during infection of barley, however the exact function ofNIP2, like many effectors, remains uncharacterised.
Becker muscular dystrophy mice showed site-specific decay of type IIa fibers with capillary change in skeletal muscle
Authors: Miyazaki Daigo , Sato Mitsuto , Shiba Naoko , Yoshizawa Takahiro , Nakamura Akinori 
Published: October 2024

AbstractBecker muscular dystrophy (BMD), an X-linked muscular dystrophy, is mostly caused by an in-frame deletion ofDMD. BMD severity varies from asymptomatic to severe, associated with the genotype ofDMD. However, the underlying mechanisms remain unclear.We established BMD mice carrying three representative exon deletions: ex45–48 del., ex45–47 del., and ex45–49 del. (d45–48, d45–47 and d45–49), with high frequencies and different severities in the human BMD hotspot. All three BMD mice showed muscle weakness, muscle degeneration, and fibrosis, but these changes appeared at different times for each exon deletion, consistent with the severities obtained by the natural history study of BMD. BMD mice showed site-specific muscle changes, unlikemdxmice, which showed diffuse muscle changes, and we demonstrated selective type IIa fiber reduction in BMD mice. Furthermore, BMD mice showed sarcolemmal neuronal nitric oxide synthase (nNOS) reduction and morphological capillary changes around type IIa fibers.These results suggest that capillary changes caused by nNOS reduction may be associated with the mechanism of skeletal muscle degeneration and type IIa fiber reduction in BMD mice. BMD mice may be useful in elucidating the pathomechanisms and developing vascular targeted therapies for human BMD.
A Plug-and-Play System for Polycyclic Tetramate Macrolactam Expression and Functionalization
Authors: Glöckle Anna , Schuler Sebastian , Einsiedler Manuel , Gulder Tobias A. M. 
Published: October 2024

AbstractBackgroundThe biosynthesis of the natural product family of the polycyclic tetramate macrolactams (PoTeMs) employs an uncommon iterative polyketide synthase/non-ribosomal peptide synthetase (iPKS/NRPS). This machinery produces a universal PoTeM biosynthetic precursor that contains a tetramic acid moiety connected to two unsaturated polyene side chains. The enormous structural and hence functional diversity of PoTeMs is enabled by pathway-specific tailoring enzymes, particularly cyclization-catalyzing oxidases that process the polyene chains to form distinct ring systems, and further modifying enzymes.ResultsIkarugamycin is the first discovered PoTeM and is formed by the three enzymes IkaABC. Utilizing the iPKS/NRPS IkaA, we established a genetic plug-and-play system by screening eight different strong promoters downstream ofikaAto facilitate high-level heterologous expression of PoTeMs in differentStreptomyceshost systems. Furthermore, we applied the system on three different PoTeM modifying genes (ptmD, ikaD, andcftA), showing the general utility of this approach to study PoTeM post PKS/NRPS processing of diverse tailoring enzymes.ConclusionBy employing our plug-and-play system for PoTeMs, we reconstructed the ikarugamycin biosynthesis and generated five derivatives of ikarugamycin. This platform will generally facilitate the investigation of new PoTeM biosynthetic cyclization and tailoring reactions in the future.
Interactive design and validation of antibody panels using single-cell RNA-seq atlases
Authors: Watson Matthew , Latour Simon , Abazari Golnaz , Geuenich Michael J , Poon Eunice , Cao Ruonan , Mrkonjic Miralem , McGuigan Alison P. , Jackson Hartland W. , Campbell Kieran R. 
Published: October 2024

AbstractSingle-cell RNA-sequencing holds promise for identifying novel markers of cellular variation for antibody-based technologies. However, antibody panel design is often difficult due to multiple experimental and biological constraints. We introduce Cytomarker, an interactive platform enabling human-in-the-loop design of antibody panels from single-cell transcriptomic data. We use Cytomarker to spatially profile human mammary tissue subpopulations and develop a novel antibody screening approach to validate granular subpopulation predictions across >3.5M cells.
Increase trajectories of tendon micro vibration intensity during ankle plantar flexion: A longitudinal data analysis using latent curve models
Authors: Matsumoto Tatsuhiko , Kano Yutaka 
Published: October 2024

AbstractWe focus on fine vibrations originating from tendons (Mechanotendography: MTG) as a novel method for quantifying muscle activity. Quantifying muscle activity using MTG can enable daily and long-term continuous measurements, which have been challenging for electromyography (EMG) and mechanomyography (MMG). However, the detailed trajectory of MTG increase relative to exerted muscle strength has not been clarified, nor has the mechanism of MTG generation. Our research has two objectives. The first is to clarify the detailed relationship between exerted muscle strength levels and MTG through statistical modeling. The second is to establish a highly accurate hypothesis concerning the mechanism of MTG generation based on the modeling results and physiological knowledge. We focused on the Achilles tendon to study these two objectives. Experiments were conducted on 62 participants, and MTG data were obtained at various levels of exerted muscle strength. The obtained data were structured into a longitudinal data format representing the trajectory of MTG increase with increasing exerted muscle strength. We used latent curve models (LCM) to identify this structure. By applying various LCMs to explore an optimal model, we found that the quadratic LCM received the best fit for females, while the piecewise linear LCM with a breakpoint at 50% exerted muscle strength received the best fit for males. Notably, a significant sex difference was observed in the rate of increase in MTG at low levels of exerted muscle strength. These results suggest that MTG is caused by fine vibrations generated by muscle fiber contractions, and these fine vibrations are transmitted to the tendons connected to the muscles, where they are observed. Future research will focus on verifying this hypothesis through increased time points and physiological experiments.
Convergent evolution of epigenome recruited DNA repair across the Tree of Life
Authors: Monroe J. Grey , Lee Chaehee , Quiroz Daniela , Lensink Mariele , Oya Satoyo , Davis Matthew , Long Evan , Bird Kevin A. , Pierce Alice , Zhao Kehan , Runcie Daniel 
Published: October 2024

AbstractMutations fuel evolution while also causing diseases like cancer. Epigenome-targeted DNA repair can help organisms protect important genomic regions from mutation. However, the adaptive value, mechanistic diversity, and evolution of epigenome-targeted DNA repair systems across the tree of life remain unresolved. Here, we investigated the evolution of histone reader domains fused to the DNA repair protein MSH6 (MutS Homolog 6) across over 4,000 eukaryotes. We uncovered a paradigmatic example of convergent evolution: MSH6 has independently acquired distinct histone reader domains; PWWP (metazoa) and Tudor (plants), previously shown to target histone modifications in active genes in humans (H3K36me3) and Arabidopsis (H3K4me1). Conservation in MSH6 histone reader domains shows signatures of natural selection, particularly for amino acids that bind specific histone modifications. Species that have gained or retained MSH6 histone readers tend to have larger genome sizes, especially marked by significantly more introns in genic regions. These patterns support previous theoretical predictions about the co-evolution of genome architectures and mutation rate heterogeneity. The evolution of epigenome-targeted DNA repair has implications for genome evolution, health, and the mutational origins of genetic diversity across the tree of life.Short SummaryFusions between histone reader domains and the mismatch repair protein MSH6 have evolved multiple times across Eukaryotes and show evidence of selection, providing mechanistic and theoretical insight into the forces shaping genomic mutation rate heterogeneity.
Application of a Bayesian model based on probability of occurrence to evaluate the effect of an environmental gradient on the turnover of aquatic insect genera in Cerrado streams
Authors: Godoy BS , Lodi S , Oliveira LG 
Published: October 2024

AbstractIn ecology, understanding and quantifying the species turnover rates among different locations is essential for a more concise and predictive science. However, little is known about how the turnover occurs among environmentally similar locations and how it may be related to habitat integrity. Using the communities of Ephemoptera, Plecoptera, and Trichoptera sampled from streams in the Brazilian Cerrado, we tested the following hypotheses: a) genus turnover between similar streams will higher in more preserved streams; b) the relationship between proportional genus turnover and the environment is influenced by the taxonomic group. We estimated parameters related to the number of potentials, observed, and alternation of these genera across a habitat integrity gradient in 101 observed streams using a model with Bayesian inference. Genera turnover among environmentally similar sites was directly related to the environmental integrity of the stream. Only the genera Plecoptera showed a pattern similar to the hypothesis we elaborated, showing an increased turnover among well-preserved streams. For the other orders, the turnover presented two peaks in the environmental gradient, one in impacted sites and the other in preserved ones.
The First Comprehensive Description of the Platelet Single Cell Transcriptome
Authors: Wolfsberger Walter , Dietz Chase , Foster Caitlin , Oleksyk Taras , Washington A. Valance , Lynch Donald 
Published: October 2024

AbstractPlatelets are derived from megakaryocytes, either in peripheral or pulmonic circulation. The transcriptome of megakaryocytes has been studied, while the platelet transcriptome is thought to be a reflection of their parent cells; it has not yet been investigated. Although platelets lack nuclei, they inherit RNA from their parent megakaryocytes, while only about 10% of them are believed to contain enough RNA for meaningful analysis. This study explores the potential of single-cell RNA sequencing to analyze the platelet transcriptome, aiming to expand our understanding of platelets beyond their traditional role in coagulation. Using acridine orange staining and antibody-based sequencing, we successfully sequenced RNA from seven healthy donors. Results revealed significant heterogeneity in gene expression, with common platelet markers, such asITGA2Band GP1B, being less abundant than expected. Interestingly, immune markers associated with lung megakaryocytes were not strongly represented in peripheral platelets. Comparison with current algorithms for cell identification suggests that platelets are often misclassified as other blood cell types, highlighting limitations of existing pipelines in platelet annotation. This misclassification may have led to misrepresentation of platelet transcriptomics in previous studies. These findings underscore the need for tailored sequencing methods to accurately profile platelets and set the foundation for further exploration of platelet biology and immune function, potentially opening avenues for therapeutic interventions in immune modulation, drug delivery, and the use of platelets as disease biomarkers in cancer and other conditions.Key PointsPlatelet single cell sequencing can be implemented with appropriate technical refinements to ensure optimal isolation without exogenous activation. In comparison to bulk sequencing techniques, single cell analysis affords the ability to exclude contaminating cells enabling examination of the authentic platelet transcriptome. This is critically important as contaminating cells contain far more RNA ultimately skewing results of transcriptomic analysis.Most platelets do not contain significant levels of commonly expected transcripts such as ITGA2B, GP1B, TREML1. In the context of recent data, our single cell transcriptomic data supports the intradividual and interindividual heterogeneity of the platelet transcriptome. The lung megakaryocyte signature is not disguisable in peripheral platelets. Further studies are needed to understand sources of RNA within platelets and the impact of the platelet microenvironment.Abstract FigureVisual abstract
CcdA chaperones CcdB against irreversible misfolding and aggregation via a cotranslational folding mechanism
Authors: Bajaj Priyanka , Kohli Pehu , Varadarajan Raghavan 
Published: October 2024

ABSTRACTCotranslational subunit assembly is thought to be a prominent feature throughout the proteome, but in bacteria, there are only a limited number of experimentally confirmed examples and most involve addition of extraneous tag sequences for experimental convenience. CcdA and CcdB are the antitoxin and toxin components, respectively, of theccdABoperon. They assemble in a hetero-multimeric complexin vivo. Mutant phenotypes in a saturation mutagenesis library of CcdB were inferred from deep sequencing in two contexts, one when CcdB is expressed alone, and the other when CcdB is present in an operonic context downstream of its cognate antitoxin, CcdA. When expressed in the absence of CcdA, charged and polar mutations in the CcdB core cause the protein to misfold. However, many such deleterious mutations are rescued when expressed along with CcdA in the native operon. CcdA thus acts as a chaperone and relieves the folding defect in CcdBcotranslationally. Assembly efficiency and efficacy decreases when CcdA and CcdB are expressed from separate mRNAs relative to when they are expressed from the same polycistronic mRNA. Gene organisation in operons in bacteria may thus reflect a fundamental cotranslational mechanism that is important for effective assembly of protein complexes and can potentially buffer substantial genetic variation.Graphical AbstractIn BriefUsing the CcdAB Type II Toxin-Antitoxin system, the authors show that the antitoxin is able to suppress folding defects of the toxin, likely by processes involving cotranslational assembly.HighlightsDeep mutational scanning is used to assess and compare the foldability of buried-site CcdB mutants in the absence and presence of CcdA.Folding defects of CcdB mutants are rescued in the presence of CcdA when expressed in an operonic context.CcdAB complex formation is enhanced when both the toxin and antitoxin components are synthesized from the same polycistronic mRNA, relative to synthesis from separate mRNAs.CcdA acts as chaperone both to assist correct folding, and to buffer mutations in CcdB, likely via cotranslational assembly mechanisms.
Females drive postmating reproductive trait evolution acrossDrosophilaspecies, but not via remating rate
Authors: Peckenpaugh Brooke , Moyle Leonie C. 
Published: October 2024

AbstractWhile traits that contribute to premating sexual interactions are known to be wildly diverse, much less is known about the diversity of postmating (especially female) reproductive traits and the mechanisms shaping this diversity. To assess the rate, pattern, and potential drivers of postmating reproductive trait evolution, we analyzed male and female traits across up to 30Drosophilaspecies within a phylogenetic comparative framework. In addition to postmating reproductive morphology (e.g., sperm length, reproductive tract length and mass), we also quantified mating behaviors including female remating rate—a common proxy for the strength of postmating sexual selection. We found evidence for strong coevolution between male and female postmating traits (specifically sperm length and sperm storage organ size). However, remating rate was not associated with the rate of evolution or exaggeration of either male or female postmating reproductive morphology, once phylogenetic relatedness was accounted for. We infer that female-mediated and intersexual selection predominantly drive the evolution of our postmating morphological traits, including via divergent male and female interests in controlling paternity. In comparison, remating rate has a complex and likely secondary role in shaping this evolution, in part because this trait can be both a driver and a product of postmating selection.
Using Fisher Information Matrix to predict uncertainty in covariate effects and power to detect their relevance in Non-Linear Mixed Effect Models in pharmacometrics
Authors: Fayette Lucie , Brendel Karl , Mentré France 
Published: October 2024

AbstractThis work focuses on design of experiments for Pharmacokinetic (PK) and Pharmacodynamic (PD) studies. Non-Linear Mixed effects Models (NLMEM) modeling allows the identification and quantification of covariates that explain inter-individual variability (IIV). The Fisher Information Matrix (FIM), computed by linearization, has already been used to predict uncertainty on covariate parameters and the power of a test to detect statistical significance. A covariate effect on a parameter is deemed statistically significant if it is different from 0 according to a Wald comparison test and clinically relevant if the ratio of change it causes in the parameter is relevant according to two one-sided tests (TOST) as in bioequivalence studies. FIM calculation was extended by computing its expectation on the joint distribution of the covariates, discrete and continuous. Three methods were proposed: using a provided sample of covariate vectors, simulating covariate vectors, based on provided independent distributions or on estimated copulas. Thereafter, CI of ratios, power of tests and number of subjects needed to achieve desired confidence were derived. Methods were implemented in a working version of the R packagePFIM. A simulation study was conducted under various scenarios, including different sample sizes, sampling points, and IIV. Overall, uncertainty on covariate effects and power of tests were accurately predicted. The method was applied to a population PK model of the drug cabozantinib including 27 covariate relationships. Despite numerous relationships, limited representation of certain covariates, PFIM correctly predicted uncertainty, and is therefore suitable for rapidly computing number of subjects needed to achieve given powers.
CombiANT Reader - Deep learning-based automatic image processing and measurement of distances to robustly quantify antibiotic interactions
Authors: Hallström Erik , Fatsis-Kavalopoulos Nikos , Bimpis Manos , Hast Anders , Andersson Dan I. 
Published: October 2024

AbstractAntibiotic resistance is a severe danger to human health, and combination therapy with several antibiotics has emerged as a viable treatment option for multi-resistant strains. CombiANT is a recently developed agar plate-based assay where three reservoirs on the bottom of the plate create a diffusion landscape of three antibiotics that allows testing of the efficiency of antibiotic combinations. This test, however, requires manually assigning nine reference points to each plate, which can be prone to errors, especially when plates need to be graded in large batches and by different users. In this study, an automated deep learning-based image processing method is presented that can accurately segment bacterial growth and measure more than 150 distances from key points on the CombiAnt assay at sub-millimeter precision. The software was tested on 100 plates using photos captured by three different users with their mobile phone cameras, comparing the automated analysis with the human scoring. The result indicates significant agreement between the users and the software. Moreover, the automated analysis remains consistent when applied to different photos of the same assay despite varying photo qualities and lighting conditions. The software can easily be integrated into a potential smartphone application. Integrating deep learning-based smartphone image analysis with simple agar-based tests like CombiANT could unlock powerful tools for combating antibiotic resistance.Author SummaryAntibiotic resistance is a significant problem worldwide with increasing prevalence of multi-resistant bacteria that may require the simultaneous administration of several different antibiotics. With the right antibiotics and concentration, such combination therapy may treat a strain that is otherwise resistant to each antibiotic individually. CombiANT is a novel test that can be used to identify suitable or inappropriate antibiotic combinations. However, it requires the human evaluator to grade each plate manually, which is time-consuming, and errors can easily be made, especially if the human evaluator needs to grade many plates in succession. In this study, an image processing pipeline is developed using a deep neural network to grade CombiANT test assays automatically.