bluuebunny/crossref_metadata_2025 huggingface dataset:
Copy number variation analysis of 9,482Mycobacterium tuberculosisisolates identifies lineage-specific molecular determinants
Authors: Bhalla Nikhil , Behera Anil , Gupta Ashish , Kumar Nanda Ranjan
Published: October 2024

Background

Clinical manifestations of tuberculosis (TB) caused byMycobacterium tuberculosis(Mtb) show lineage-specific differences contributed by genetic polymorphism such as phylo-single nucleotide variations (PhyloSNPs) and insertion or deletions (INDELs). Intragenomic rearrangement events, such as gene duplications and deletions, may cause gene copy number differences in Mtb, contributing to lineage-specific phenotypic variations, if any, which need better understanding.

Results

The relative gene copy number differences in high-quality publicly available whole genome sequencing datasets of 9,482 clinical Mtb isolates were determined by repurposing and modifying an RNA-seq data analysis pipeline. The pipeline included various steps, viz., alignment of reads, sorting by coordinate, GC bias correction, and variant stabilising transformation. The strategy showed maximum separation of lineage-specific clusters in two principal components, capturing ∼54% variability. Unsupervised hierarchical clustering of the top 100 genes and pairwise comparisons between Mtb lineages revealed an overlapping subset of genes (n=42) having significantly perturbed copy numbers (Benjamin Hochberg adjusted P-value < 0.05 and log2(drug-resistant/sensitive) > ± 1). These 42 genes formed multiple tandem gene clusters and are known to be involved in virulence, pathogenicity and defence response to invading phages. A separate comparison showed a significantly high copy number of phage genes and a recently reported druggable target Rv1525 in pre- and extensively drug-resistant (Pre-XDR, XDR) compared to drug-sensitive clinical Mtb isolates.

Conclusion

The identified gene sets in Mtb clinical isolates may be useful targets for lineage-specific therapeutics and diagnostics development.
A Model-Driven Meta-Analysis Supports the Emerging Consensus View that Inhibitory Neurons Dominate BOLD-fMRI Responses
Authors: Sundqvist Nicolas , Podéus Henrik , Sten Sebastian , Engström Maria , Dura-Bernal Salvador , Cedersund Gunnar
Published: October 2024

Functional magnetic resonance imaging (fMRI) is a pivotal tool for mapping neuronal activity in the brain. Traditionally, the observed hemodynamic changes are assumed to reflect the activity of the most common neuronal type: excitatory neurons. In contrast, recent experiments, using optogenetic techniques, suggest that the fMRI-signal instead reflects the activity of inhibitory interneurons. However, these data paint a complex picture, with numerous regulatory interactions, and where the different experiments display many qualitative differences. It is therefore not trivial how to quantify the relative contributions of the different cell types and to combine all observations into a unified theory. To address this, we present a new model-driven meta-analysis, which provides a unified and quantitative explanation for all data. This model-driven analysis allows for quantification of the relative contribution of different cell types: the contribution to the BOLD-signal from the excitatory cells is <20 % and 50-80 % comes from the interneurons. Our analysis also provides a mechanistic explanation for the observed experiment-to-experiment differences, e.g. a biphasic vascular response dependent on different stimulation intensities and an emerging secondary post-stimulation peak during longer stimulations. In summary, our study provides a new, emerging consensus-view supporting the larger role of interneurons in fMRI.
Unveiling the Functional Connectivity of Astrocytic Networks with AstroNet, a Graph Reconstruction Algorithm Coupled to Image Processing
Authors: Zonca L. , Bellier F.C. , Milior G. , Aymard P. , Visser J. , Rancillac A. , Rouach N. , Holcman D.
Published: October 2024

Astrocytes form extended intercellular networks, displaying complex calcium activity. However, the specific organization of these astrocytic networks and the precise extent of their functional connectivity in different brain areas remain unexplored. To unveil the functional architecture of astrocytic networks, we developed, using a data-driven methodology, a novel algorithm called AstroNet that uses two-photon calcium imaging to map temporal correlations in activation events among neighboring astro-cytes. Our approach involves reconstructing functional astrocytic networks by organizing individual astrocyte activation events chronologically. This chronological order creates activity paths that enable the extraction of local astrocyte functional correlations. Ultimately, by tallying the occurrences of direct co-activations between pairs of cells along these pathways, we construct a graph that mirrors the underlying astrocyte functional network. By applying this method to two distinct brain regions (CA1 hippocampus and motor cortex), we identified notable differences in local network organizations in sub-regions of around 20-40 astrocytes. Specifically, the cortex exhibited a lower connectivity, while astrocytes in the hippocampus displayed stronger connections. Moreover, we found that in both regions, astrocytic networks consist of smaller, tightly connected sub-networks embedded within a larger, more loosely connected one. Altogether, our innovative method enables the identification of activation paths among astrocytes, facilitates the characterization of local network functional connectivity, and quantifies distinct connectivity patterns among astrocytes from different brain regions. This approach sheds light on the heterogeneous functional organization of astrocytic networks within the brain, pointing to region-specific astrocyte connectivity.
The role of auxin-mediated gene activation in the bryophyte,Physcomitrium patens
Authors: Bascom Carlisle , Tu Danielle , Estelle Mark
Published: October 2024

Perception and response to the hormone auxin is critical to plant growth and development. Expression of auxin-response genes is tightly regulated via known mechanisms of both activation and repression. Across the plant lineage, auxin-response gene induction is performed by AUXIN-REPSONSE FACTOR (ARF) activating transcription factors. Conversely, AUXIN/INDOLE ACETIC ACID proteins repress expression. Studies of gain-of-function constitutive-repression lines andARFloss-of-function mutants have advanced the field. Yet, there is a need for a comparative study of aberrant auxin-signaling mutants to understand the developmental consequences of constitutive repression versus the absence of auxin-mediated gene induction. Using CRISPR/Cas9 gene-editing tools, we mutated each activatingARFgene in the model bryophyte,Physcomitrium patens.The resulting septuple loss-of-function mutant line (arfasept) has severe developmental phenotypes and a diminished ability to respond to exogenous auxin. However, phenotypic analysis revealed that thearfaseptline is not as severely affected as the constitutive-repression lines. Expression analysis of several auxin-response genes demonstrate that auxin-mediated gene induction is abolished in botharfaseptand constitutive-repression lines but that basal expression levels are higher in thearfaseptlines. Our results suggest that the expression of auxin-regulated genes important for developmental progression is maintained, albeit at reduced levels, in the absence of ARFs.

Highlight

Researchers used CRIPSR/Cas9 to produce a septuple Auxin Response Factor mutant in the model bryophytePhyscomitrium patensrevealing the consequences of the complete loss of auxin-mediated gene activation on development.
Biomass allocation of trees in response to mono- and heterospecific neighbourhoods
Authors: Perles-Garcia Maria D. , Fichtner Andreas , Haider Sylvia , Gu Hanjiao , Bu Wensheng , Kunz Matthias , Härdtle Werner , von Oheimb Goddert
Published: October 2024

Carbon sequestration by trees is crucial to mitigate the effects of the current climate crisis. The extent to trees sequester and allocate carbon to above- or belowground structures in turn is mediated by neighbouring species. Although many studies have demonstrated positive effects of diverse neighbourhoods on a tree’s productivity, little is known about biomass allocation responses to mono-vs. heterospecific neighbourhoods. In the present study we quantified above- and belowground biomass production and root-to-shoot ratios (RSR) of trees grown in mono- and heterospecific neighbourhoods. To this end we analysed growth of mono- and heterospecific tree species pairs (TSPs) established in a greenhouse and a field experiment. In the greenhouse experiment response variables were measured after one year of growth after sapling harvest. In the field experiment, conducted in the context of a forest biodiversity experiment in subtropical China, we analysed biomass density and RSR over three years using terrestrial laser scanner and minirhizotrons. RSR of trees in heterospecific TSPs were significantly higher than in monospecific TSPs. In the greenhouse experiment, this was related to a stronger below-than aboveground overyielding in heterospecific TSPs. In the field experiment, trees in heterospecific TSPs showed a stronger increase in aboveground investments over time than in monospecific TSPs, indicating that positive diversity effects became stronger for aboveground structures with progressing tree development. Our findings are consistent with the optimal biomass partitioning theory and highlight the importance of tree-tree interactions on biomass allocation. Higher RSR in mixtures further suggest a higher resistance or resilience of tree saplings against environmental stressors related to climate change (drought, heat waves).
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

The 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

Becker 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

Background

The 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.

Results

Ikarugamycin 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.

Conclusion

By 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

Single-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

We 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

Mutations 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 Summary

Fusions 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

In 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

Platelets 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 Points

Platelet 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 Figure

Visual abstract
CcdA chaperones CcdB against irreversible misfolding and aggregation via a cotranslational folding mechanism
Authors: Bajaj Priyanka , Kohli Pehu , Varadarajan Raghavan
Published: October 2024

Cotranslational 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 Abstract

In Brief

Using 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.

Highlights

Deep 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.
ybx1 acts upstream of atoh1a to promote the rapid regeneration of hair cells in zebrafish lateral-line neuromasts
Authors: Reagor Caleb C. , Hudspeth A. J.
Published: October 2024

Like the sensory organs of the human inner ear, the lateral-line neuromasts (NMs) of fish such as the zebrafish (Danio rerio) contain mechanosensory hair cells (HCs) that are surrounded by progenitors called supporting cells. Damaged NMs can quickly regenerate new HCs by expressing in the progenitors HC-specific genes such as atoh1a, the master regulator of HC fate. We used the supervised learning algorithm DELAY to infer regenerating NMs' early gene-regulatory network (GRN) and identify adaptations that promote the rapid regeneration of lateral-line HCs in larval zebrafish. The central hub in the network, Y-box binding protein 1 (ybx1), is highly expressed in HC progenitors and young HCs and can recognize DNA-binding motifs in cyprinids' candidate regeneration-responsive promoter elements for atoh1a. We showed that NMs from ybx1 mutant zebrafish larvae display consistent, regeneration-specific deficits in HC number and initiate both HC regeneration and atoh1a expression 20 % slower than in siblings. By demonstrating that ybx1 promotes rapid HC regeneration through early atoh1a upregulation, the results support DELAY's ability to identify key temporal regulators of gene expression.
Females drive postmating reproductive trait evolution acrossDrosophilaspecies, but not via remating rate
Authors: Peckenpaugh Brooke , Moyle Leonie C.
Published: October 2024

While 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

This 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

Antibiotic 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 Summary

Antibiotic 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.
Monitoring the Risk of Type-2 Circulating Vaccine-Derived Poliovirus Emergence during Roll-Out of Type-2 Novel Oral Polio Vaccine
Authors: Peak Corey M. , Lyons Hil , Voorman Arend , Gray Elizabeth J , Cooper Laura V , Blake Isobel M , Hawes Kaija , Bandyopadhyay Ananda S
Published: October 2024

Background/Objectives

Although wild poliovirus type 2 has been eradicated, prolonged transmission of the live-attenuated virus contained in the type-2 oral polio vaccine (OPV2) in under-immunized populations has led to emergence of circulating vaccine derived poliovirus type-2 (cVDPV2). The novel OPV2 (nOPV2) was designed to be more genetically stable and reduce the chance of cVDPV2 emergence while retaining comparable immunogenicity to the Sabin monovalent OPV2 (mOPV2). This study aims to estimate the relative reduction in the emergence risk due to use of nOPV2 instead of mOPV2.

Methods

Data on OPV2 vaccination campaigns from May 2016 to 1 August 2024 were analyzed to estimate type-2 OPV-induced immunity in children under 5 years of age. Poliovirus surveillance data were used to estimate seeding date and classify cVDPV2 emergences as Sabin- or novel-derived. The expected number of emergences if mOPV2 was used instead of nOPV2 was estimated accounting for the timing and volume of nOPV2 doses, the known emergence risk factors for emergence from mOPV2, and censoring due to the incomplete observation period for more recent nOPV2 doses.

Results

As of 1 August 2024, over 98% of the approximately 1.19 billion nOPV2 doses administered globally were in Africa. We estimate approximately 76 (95% confidence interval 69-85) index isolates of cVDPV2 emergences would be expected to be detected by 1 August 2024 if mOPV2 had been used instead of nOPV2 in Africa. The 18 observed nOPV2-derived emergences represent a 76% (74%-79%) lower risk of emergence by nOPV2 than mOPV2 in Africa. The crude global analysis produced similar results. Key limitations include the incomplete understanding of the drivers of heterogeneity in emergence risk across geographies and variance in the per-dose risk of emergence may be incompletely captured using known risk factors.

Conclusions

These results are consistent with the accumulating clinical and field evidence showing enhanced genetic stability of nOPV2 relative to mOPV2, and this approach has been implemented in near-real time to contextualize new findings during roll-out of this new vaccine. While nOPV2 has resulted in new emergences of cVDPV2, the number of cVDPV2 emergences is estimated to be approximately four-fold lower than if mOPV2 had been used instead.
DEEP LEARNING BASED DETECTION OF URETHRAL STRICTURE: SEGMENTATION & CLASSIFICATION
Authors: Gurung Nikhil , Udaya Kumar L , Chandrasekar S N , Muthukumar V Sai , Gera Darshan , Sharma Raghunatha , Shekar P Ashwin
Published: October 2024

Purpose

The retrograde urethrogram (RUG) has been a key diagnostic tool for over a century, remaining essential despite the availability of other imaging techniques for screening, diagnosis and follow up of Urethral strictures. However, interpretation of RUG images has to be done manually and needs experience on the part of the treating urologist, which calls for a common understanding of RUGs and presents a chance to improve stricture management in a practical way. Artificial intelligence (AI) algorithms present a novel way to prevent human discrepancy while concomitantly improving the accuracy of stricture identification and classification.

Methods

Dataset

We have used a balanced dataset which includes RUGs of 168 strictured cases and 178 non-strictured(healthy) cases.

Task#1

The primary requirement is to identify the Urethral region in any clinically obtained RUGs and detect the presence of stricture in it. We successfully deployed a Segmentation and Classification model to categorize the whole dataset as strictured or non-strictured RUGs.

Task#2

On obtaining superior accuracy, we effectively went on to identify the type of stricture based on their location, which is of clinical importance.

Results

With the above-mentioned available RUG dataset from 346 cases, we could train our Deep learning model and achieve a significant accuracy of 91.53% in detection and categorizing the type of stricture. At the end, a 10-fold cross-validation yielded an accuracy of about 86.66%.

Conclusion

Our attempts have successfully validated that using Deep learning (DL) tools, one could readily (i) Detect the presence of stricture in a given RUG and (ii) ultimately locate and classify these strictures effectively. Thus, these Deep learning tools could be of great clinical assistance for Urinary stricture related disease management.
Alternatives to photorespiration: A systems-level analysis reveals mechanisms of enhanced plant productivity
Authors: Smith Edward N. , van Aalst Marvin , Weber Andreas P.M. , Ebenhöh Oliver , Heinemann Matthias
Published: October 2024

Photorespiration causes a significant decrease in crop yield due to mitochondrial decarboxylation. Alternative pathways (APs) have been designed to relocate the decarboxylating step or even fix additional carbon. To improve the success of transferring those engineered APs from model species to crops we must understand how they will interact with metabolism and how the plant physiology affects their performance. Here we used multiple mathematical modelling techniques to analyse and compare existing AP designs. We show that carbon-fixing APs are the most promising candidates to replace native photorespiration in major crop species. Our results demonstrate the different metabolic routes that APs employ to increase yield and which plant physiology can profit most from them. We anticipate our results to guide the design of new APs and to help improve existing ones.

Code

https://gitlab.com/gain4crops/2024-paper
Stimulus-dependent delay of perceptual filling-in by microsaccades
Authors: Levinson Max , Pack Christopher C. , Baillet Sylvain
Published: October 2024

Perception is a function of both stimulus features and active sensory sampling. The illusion ofperceptual filling-in occurs when eye gaze is kept still: visual boundary perception may fail, causing adjacent visual features to remarkably merge into one uniform visual surface. Microsaccades–small, involuntary eye movements during gaze fixation–counteract perceptual filling-in, but the mechanisms underlying this process are not well understood. We investigated whether microsaccade efficacy for preventing filling-in depends on two boundary properties, color contrast and retinal eccentricity (distance from gaze center). Twenty-one human participants (male and female) fixated on a point until they experienced filling-in between two isoluminant colored surfaces. We found that increased color contrast independently extends the duration before filling-in but does not alter the impact of individual microsaccades. Conversely, lower eccentricity delayed filling-in only by increasing microsaccade efficacy. We propose that microsaccades facilitate stable boundary perception via a transient retinal motion signal that scales with eccentricity but is invariant to boundary contrast. These results shed light on how incessant eye movements integrate with ongoing stimulus processing to stabilize perceptual detail, with implications for visual rehabilitation and the optimization of visual presentations in virtual and augmented reality environments.

Significance Statement

To perceive, sense organs actively sample the environment—for example, by touching, sniffing, or moving the eyes. Visual sampling persists even when gaze is fixed on a single point: involuntary microsaccades continuously move the eye in small jumps. We investigated a previously documented observation that microsaccades prevent illusory fading of perceived visual boundaries during fixation. We discovered that despite being connected, microsaccades and fading are sensitive to different stimulus features. Boundaries separating surfaces with more distinct colors inherently took longer to fade. Boundaries closer to the center of vision also took longer to fade, but only because microsaccades were more effective. These findings reveal new insight into how pervasive sensory sampling delivers a stable and detailed perceptual experience.
Functional and evolutionary characterization of potential auxiliary metabolic genes (AMGs) of the global RNA virome
Authors: Zhao Yang , Zhang Zhihao , Liu Pengfei , Feng Meiling , Wen Rong , Liu Yongqin
Published: October 2024

RNA viruses play an important role in regulating their host and global biogeochemical cycling, and auxiliary metabolic genes (AMGs) are one of the main pathways by which viruses regulate hosts metabolism. However, the AMGs encoded by global RNA viruses are largely unexplored. Here, we annotated RNA viral genomes and identified AMGs from recently published global RNA virome datasets. We found 274 AMGs encoded by 243 RNA viral genomes, which accounts for only 0.008% of all 3,216,257 genomes investigated. These AMGs span 25 functional categories, the most prevalent being translation, energy metabolism, membrane transport, transcription, replication and repair, and signal transduction. Unlike DNA viruses, RNA viruses tend to encode AMGs influencing the genetic and environments information processing of their hosts, with fewer AMGs linked to nutrient cycling, such as carbon and nitrogen metabolism. In addition, RNA viruses encoding these AMGs were taxonomically diverse, spanning five established phyla, the newly proposed phylum "Taraviricota" and fourteen LucaProt supergroups. Host prediction indicated that most of these RNA viruses encoding AMGs infect eukaryotes, while only a few of them, includingLeviviricetesandVidaverviricetes, infect prokaryotes. Interestingly, the potential host phylum for most of these RNA viruses were different from the likely source phylum of their AMGs, suggesting the possibility that these RNA viruses acquired AMGs from organisms outside their predicted host range. This study provides the first comprehensive analysis of AMGs from global RNA virome, which greatly expands our understanding of their function roles, evolutionary history and virus-host interactions.
Pharmacoproteomic profiling identifies secreted markers for aberrant drug action
Authors: Knecht Sascha , Kalxdorf Mathias , Korbeń Johanna , Mathieson Toby , Sevin Daniel C. , Kuster Bernhard , Kasprowicz Richard , Sakatis Melanie Z. , Eberl H. Christian , Bantscheff Marcus
Published: October 2024

Adverse drug reactions (ADRs) contribute significantly to late-stage attrition in drug discovery due to their unpredictability and enigmatic underlying mechanisms. Here we applied mass spectrometry-based proteomics to assess the effects of 46 approved or retracted drugs with various levels of concerns for drug-induced liver injury and annotated for mitochondrial mechanisms, along with 8 tool compounds, on the secretome of a hepatocyte liver model. We observed distinct clusters of non-canonical secretion, and intracellular thermal proteome profiling linked dysregulated mechanisms to extracellular markers. Functional follow-up confirmed lysosomal alterations by cationic-amphiphilic drugs, connected damage of the respiratory chain to Rab7-dependent secretion of mitochondrial proteins, and linked drug-induced endoplasmic reticulum stress to reduced basal secretion. Perturbation of sphingolipid biosynthesis pathways specifically induced secretion of the cargo sorting protein SDF4 whilst suppressing secretion of its cargo proteins. Thermal stability changes of clusters of membrane proteins in distinct subcellular compartments suggest local accumulation as important driver for unexpected drug effects through direct and indirect interactions.
Artificial light at night enhances the defensive behavior in aquatic shredders under predation risk
Authors: Rufaida Zahira , Czarnecka Magdalena
Published: October 2024

Caddisfly larvae (Trichoptera) are mostly nocturnal aquatic invertebrates that contribute to the decomposition of coarse organic matter, such as plant litter in streams. Artificial light at night (ALAN) can interfere with their behavior, particularly in the presence of predation threat. We investigated the effects of various types of ALAN onLepidostoma hirtum, a common caddisfly species in running waters. We tested its behavior (activity and tendency to shelter) in darkness, as well as under white warm LED light and HPS (sodium lamp) light (2 lux), with and without the presence of predation cues (crushed conspecifics). We found that in darkness caddisflies did not change their behavior in the presence of predation threat. When exposed to ALAN only, caddisflies decreased their activity compared to dark nights, regardless of the type of light. The presence of both predation threat and ALAN enhanced a defensive behavior in caddisflies, especially under LED light. They not only reduced their activity, but also spent more time in shelter, compared to other treatments. This study highlights that impact of ALAN on the behavior of nocturnal aquatic invertebrates may vary depending on the spectral composition of light and may be intensified in the presence of predation threat.
PRMT5-mediated histone methylation regulates alternative splicing via MECP2-PTBP1 to promote EMT in breast cancer hypoxia
Authors: Mutnuru Srinivas Abhishek , Yadav Pooja , Kakani Parik , Dhamdhere Shruti Ganesh , Kumari Poorva , Agarwal Shruti , Samaiya Atul , Shukla Sanjeev
Published: October 2024

Tumor hypoxia induced alterations in the epigenetic landscape and alternative splicing influence cellular adaptations. PRMT5 is a type II protein arginine methyltransferase that regulates several tumorigenic events in many cancer types. However, the regulation of PRMT5 and its direct implication on aberrant alternative splicing under hypoxia remains unexplored. In this study, we observed hypoxia induced upregulation of PRMT5 via the CCCTC binding factor, CTCF. Further, PRMT5-mediated symmetric arginine dimethylation H4R3me2s and H3R8me2s directly regulated the alternative splicing of Transcription Factor 3 (TCF3). Under hypoxia, PRMT5-mediated histone dimethylation at the intronic conserved region (ICR) present betweenTCF3exon 18a and exon 18b recruits DNA methyltransferase 3A (DNMT3A), resulting in DNA methylation. DNA methylation at theTCF3-ICR is recognized and bound by Methyl CpG binding protein (MECP2) resulting in RNA-Pol II pausing, promoting the recruitment of the negative splicing factor PTBP1 to the splicing locus ofTCF3mRNA. PTBP1 promotes the exclusion of exon 18a which results in the production of the pro-invasive TCF3-18B (E47) isoform which promotes EMT and invasion of breast cancer cells under hypoxia. Collectively, our results indicate PRMT5-mediated symmetric arginine dimethylation of histones regulates alternative splicing ofTCF3gene thereby enhancing EMT and invasion in breast cancer hypoxia.