bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring age-dependent viscoelastic properties of organelles, cells and organisms via Time-Shared Optical Tweezer Microrheology
Authors: Català-Castro Frederic , Ortiz-Vásquez Santiago , Martínez-Fernández Carmen , Pezzano Fabio , Garcia-Cabau Carla , Fernández-Campo Martín , Sanfeliu-Cerdán Neus , Jiménez-Delgado Senda , Salvatella Xavier , Ruprecht Verena , Frigeri Paolo-Antonio , Krieg Michael
Published: October 2023

Recording the mechanical response of biological samples, the cell’s interior and complex fluids in general, would enable deeper understanding of cellular differentiation, ageing and drug discovery. Here, we present a time-shared optical tweezer microrheology (TimSOM) pipeline to determine the frequency- and age-dependent viscoelastic properties of biological materials. Our approach consists in splitting a single laser beam into two near-instantaneous time-shared optical traps to carry out simultaneous force and displacement measurements with sub-nanometer and sub-picoNewton accuracy during sinusoidal perturbations. Leveraging numerical and analytical models, we find solutions to commonly encountered deviations, to build a practical and robust nanorheometer. We demonstrate the versatility of the technique by 1) measuring the phase transitions of an ageing biomolecular condensate, 2) quantifying the complex viscoelastic properties of three intracellular compartments of zebrafish progenitor cells, and, 3) usingCaenorhabditis elegans, we uncover how mutations causing nuclear envelopathies soften the cytosol of intestinal cells during organismal age. Together, our advances afford rapid phenotyping of material properties inside cells and proteins blends, opening avenues for biomedical and drug screening applications.
Distinguishing mutants that resist drugs via different mechanisms by examining fitness tradeoffs
Authors: Schmidlin  , Apodaca  , Newell  , Sastokas  , Kinsler  , Geiler-Samerotte
Published: October 2023

There is growing interest in designing multidrug therapies that leverage tradeoffs to combat resistance. Tradeoffs are common in evolution and occur when, for example, resistance to one drug results in sensitivity to another. Major questions remain about the extent to which tradeoffs are reliable, specifically, whether the mutants that provide resistance to a given drug all suffer similar tradeoffs. This question is difficult because the drug-resistant mutants observed in the clinic, and even those evolved in controlled laboratory settings, are often biased towards those that provide large fitness benefits. Thus, the mutations (and mechanisms) that provide drug resistance may be more diverse than current data suggests. Here, we perform evolution experiments utilizing lineage-tracking to capture a fuller spectrum of mutations that give yeast cells a fitness advantage in fluconazole, a common antifungal drug. We then quantify fitness tradeoffs for each of 774 evolved mutants across 12 environments, finding these mutants group into 6 classes with characteristically different tradeoffs. Their unique tradeoffs may imply that each group of mutants affects fitness through different underlying mechanisms. Some of the groupings we find are surprising. For example, we find some mutants that resist single drugs do not resist their combination, while others do. And some mutants to the same gene have different tradeoffs than others. These findings, on one hand, demonstrate the difficulty in relying on consistent or intuitive tradeoffs when designing multidrug treatments. On the other hand, by demonstrating that hundreds of adaptive mutations can be reduced to a few groups with characteristic tradeoffs, our findings may yet empower multidrug strategies that leverage tradeoffs to combat resistance. More generally speaking, by grouping mutants that likely affect fitness through similar underlying mechanisms, our work guides efforts to map the phenotypic effects of mutation.
A deep learning model embedded framework to distinguish DNA and RNA mutations directly from RNA-seq
Authors: Fu Zhi-Can , Gao Bao-Qing , Nan Fang , Ma Xu-Kai , Yang Li
Published: October 2023

We develop a stepwise computational framework, called DEMINING, to directlydetectexpressed DNA and RNAmutations in RNA deep sequencingdata. DEMINING incorporates a deep learning model named DeepDDR, which facilitates the separation of expressed DNA mutations from RNA mutations after RNA-seq read mapping and pileup. When applied in RNA-seq of acute myeloid leukemia patients, DEMINING uncovered previously-underappreciated DNA and RNA mutations, some associated with the upregulated expression of host genes or the production of neoantigens. Finally, we demonstrate that DEMINING could precisely classify DNA and RNA mutations in RNA-seq data from non-primate species through the utilization of transfer learning.
A syngeneic spontaneous zebrafish model oftp53-deficient, EGFRvIII, and PI3KCAH1047R-driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo
Authors: Weiss Alex , D’Amata Cassandra , Pearson Bret J. , Hayes Madeline N.
Published: October 2023

High-throughput vertebrate animal model systems for the study of patient-specific biology and new therapeutic approaches for aggressive brain tumors are currently lacking, and new approaches are urgently needed. Therefore, to build a patient-relevantin vivomodel of human glioblastoma, we expressed common oncogenic variants including activated human EGFRvIIIand PI3KCAH1047Runder the control of the radial glial-specific promoterher4.1in syngeneictp53loss-of-function mutant zebrafish. Robust tumor formation was observed prior to 45 days of life, and tumors had a gene expression signature similar to human glioblastoma of the mesenchymal subtype, with a strong inflammatory component. Within early stage tumor lesions, and in anin vivoand endogenous tumor microenvironment, we visualized infiltration of phagocytic cells, as well as internalization of tumor cells bympeg1.1:EGFP+ microglia/macrophages, suggesting negative regulatory pressure by pro-inflammatory cell types on tumor growth at early stages of glioblastoma initiation. Furthermore, CRISPR/Cas9-mediated gene targeting of master inflammatory transcription factorsirf7orirf8led to increased tumor formation in the primary context, while suppression of phagocyte activity led to enhanced tumor cell engraftment following transplantation into otherwise immune-competent zebrafish hosts. Altogether, we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging, high-throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation, with important future opportunities for therapeutic discovery and optimizations.
Enhanced local cooling effects of forests across the globe
Authors: Verbiest William W. M. , Smith Gabriel Reuben , Mirzagholi Leila , Lauber Thomas , Zohner Constantin M. , Maynard Daniel S. , Schemm Sebastian , Crowther Thomas W.
Published: October 2023

Forests cool the land surface in warm regions and warm the land surface in cool regions. Because these local temperature buffering effects depend on background climate1,2, increasingly large areas might experience forest cooling effects as the climate warms3–5. Here, using statistical modeling, we quantified changes in the sensitivity of land surface temperatures6to forest cover change7from 1988 – 2016, across 15 million km2of land area. Forests had a local cooling effect on day and night surface temperatures in 86.3% (72 million km2) and 61.6% (5,108 million km2) of the forest area, respectively. This area has increased by 0.3% (0.2 million km2) at day and 4.7% (2 million km2) at night over recent decades. Our study indicates that climate change is enhancing the cooling effect of forests in the short term, underscoring the importance of protecting natural, diverse forest ecosystems in the face of rising global temperatures that threaten ecosystems8,9, human health10,11, and food production12.
Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells
Authors: Kocanova Silvia , Raynal Flavien , Goiffon Isabelle , Oksuz Betul Akgol , Baú Davide , Kamgoué Alain , Cantaloube Sylvain , Zhan Ye , Lajoie Bryan , Marti-Renom Marc A. , Dekker Job , Bystricky Kerstin
Published: October 2023

The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen responsive genes in human breast cancer cell lines following hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene (PGR) expression occurs in the context of pre-existing, cell type specific chromosomal architectures encompassing the 90 kb PGR coding region and an enhancer-spiked 5’ 300 kb upstream genomic region. In response to estradiol, interactions between estrogen-receptor α (ERα) bound regulatory elements are re-enforced. While initial enhancer – gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ER accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de-novo extensive rewiring of long-range chromatin interactions.
Maximizing Efficiency in SedaDNA Analysis: A Novel Extract Pooling Approach
Authors: Oberreiter Victoria , Gelabert Pere , Brück Florian , Franz Stefan , Zelger Evelyn , Szedlacsek Sophie , Cheronet Olivia , Tenorio Cano Fernanda , Exler Florian , Zagorc Brina , Karavanić Ivor , Banda Marko , Gasparyan Boris , Straus Lawrence Guy , Gonzalez Morales Manuel R. , Kappelman John , Stahlschmidt Mareike , Rattei Thomas , Kraemer Stephan M. , Sawyer Susanna , Pinhasi Ron
Published: October 2023

In recent years, the field of ancient DNA (aDNA) has taken a new direction toward studying human population dynamics through sedimentary DNA (sedaDNA), enabling the study of past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing method. Our approach involves combining multiple extracts, allowing users to parallelize laboratory procedures early in the sample preparation pipeline while effectively screening for the presence of aDNA. Pooled samples that exhibit aDNA signals can then undergo detailed analysis, while empty pools are discarded. We have successfully applied our extract pooling method to various sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
Niche Availability and Competitive Facilitation Control Proliferation of Bacterial Strains Intended for Soil Microbiome Interventions
Authors: Čaušević Senka , Dubey Manupriyam , Morales Marian , Salazar Guillem , Sentchilo Vladimir , Carraro Nicolas , Ruscheweyh Hans-Joachim , Sunagawa Shinichi , van der Meer Jan Roelof
Published: October 2023

Microbiome engineering, the rational manipulation of microbial communities and their habitats, is considered a crucial strategy to revert dysbiosis. However, the concept is in its infancy and lacks experimental support. Here we study the ecological factors controlling the proliferation of focal bacterial inoculants into taxa-complex soil communities and their impact on resident microbiota. We demonstrate using standardized soil microbiomes with different growth phases that the proliferation of typical soil inoculants depends on niche competition. By adding an artificial, inoculant selective niche to soil we improve inoculant proliferation and show by metatranscriptomics to give rise to a conjoint metabolic network in the soil microbiome. Furthermore, using random paired growth assays we demonstrate that, in addition to direct competition, inoculants lose competitiveness with soil bacteria because of metabolite sharing. Thus, the fate of inoculants in soil is controlled by niche availability and competitive facilitation, which may be manipulated by selective niche generation.

Teaser

Typical bacterial inoculants for soil microbiome engineering suffer from facilitating growth of native resident microorganisms
SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes
Authors: Yang Jianyu , Yen Kuangyu , Mahony Shaun
Published: October 2023

Genome-wide nucleosome profiles are predominantly characterized using MNase-seq, which involves extensive MNase digestion and size selection to enrich for mono-nucleosome-sized fragments. Most available MNase-seq analysis packages assume that nucleosomes uniformly protect 147bp DNA fragments. However, some nucleosomes with atypical histone or chemical compositions protect shorter lengths of DNA. The rigid assumptions imposed by current nucleosome analysis packages ignore variation in nucleosome lengths, potentially blinding investigators to regulatory roles played by atypical nucleosomes.

To enable the characterization of different nucleosome types from MNase-seq data, we introduce the Size-based Expectation Maximization (SEM) nucleosome calling package. SEM employs a hierarchical Gaussian mixture model to estimate the positions and subtype identity of nucleosomes from MNase-seq fragments. Nucleosome subtypes are automatically identified based on the distribution of protected DNA fragment lengths at nucleosome positions. Benchmark analysis indicates that SEM is on par with existing packages in terms of standard nucleosome-calling accuracy metrics, while uniquely providing the ability to characterize nucleosome subtype identities.

Using SEM on a low-dose MNase H2B MNase-ChIP-seq dataset from mouse embryonic stem cells, we identified three nucleosome types: short-fragment nucleosomes, canonical nucleosomes, and dinucleosomes. The short-fragment nucleosomes can be divided further into two subtypes based on their chromatin accessibility. Interestingly, the subset of short-fragment nucleosomes in accessible regions exhibit high MNase sensitivity and display distribution patterns around transcription start sites (TSSs) and CTCF peaks, similar to the previously reported “fragile nucleosomes”. These SEM-defined accessible short-fragment nucleosomes are found not just in promoters, but also in enhancers and other regulatory regions. Additional investigations reveal their co-localization with the chromatin remodelers Chd6, Chd8, and Ep400.

In summary, SEM provides an effective platform for distinguishing various nucleosome subtypes, paving the way for future exploration of non-standard nucleosomes.
Population variability in X-chromosome inactivation across 9 mammalian species
Authors: Werner Jonathan M. , Hover John , Gillis Jesse
Published: October 2023

One of the two X chromosomes in female mammals is epigenetically silenced in embryonic stem cells by X chromosome inactivation (XCI). This creates a mosaic of cells expressing either the maternal or the paternal X allele. The XCI ratio, the proportion of inactivated parental alleles, varies widely among individuals, representing the largest instance of epigenetic variability within mammalian populations. While various contributing factors to XCI variability are recognized, namely stochastic and/or genetic effects, their relative contributions are poorly understood. This is due in part to limited cross-species analysis, making it difficult to distinguish between generalizable or species-specific mechanisms for XCI ratio variability. To address this gap, we measured XCI ratios in nine mammalian species (9,143 individual samples), ranging from rodents to primates, and compared the strength of stochastic models or genetic factors for explaining XCI variability. Our results demonstrate the embryonic stochasticity of XCI is a general explanatory model for population XCI variability in mammals, while genetic factors play a minor role.
A multiscale model of immune surveillance in micrometastases: towards cancer patient digital twins
Authors: Rocha Heber L. , Aguilar Boris , Getz Michael , Shmulevich Ilya , Macklin Paul
Published: October 2023

Metastasis is the leading cause of death in patients with cancer, driving considerable scientific and clinical interest in immunosurveillance of micrometastases. We investigated this process by creating a multiscale mathematical model to study the interactions between the immune system and the progression of micrometastases in general epithelial tissue. We analyzed the parameter space of the model using high-throughput computing resources to generate over 100,000 virtual patient trajectories. We demonstrated that the model could recapitulate a wide variety of virtual patient trajectories, including uncontrolled growth, partial response, and complete immune response to tumor growth. We classified the virtual patients and identified key patient parameters with the greatest effect on the simulated immunosurveillance. We highlight the lessons derived from this analysis and their impact on the nascent field of cancer patient digital twins (CPDTs). While CPDTs could enable clinicians to systematically dissect the complexity of cancer in each individual patient and inform treatment choices, our work shows that key challenges remain before we can reach this vision. In particular, we show that there remain considerable uncertainties in immune responses, dysfunctional data stratification, and unpredictable personalized treatment. Nonetheless, we also show that in spite of these challenges, patient-specific models suggest strategies to increase control of clinically undetectable micrometastases even without complete parameter certainty.
Scale-dependent hierarchical resolution: applications to atomic resolution and model validation in cryoEM
Authors: Ray Korak Kumar , Kinz-Thompson Colin D.
Published: October 2023

The recent cryoEM resolution revolution has had a tremendous impact on our ability to investigate biomolecular structure and function. However, outstanding questions about the reliability of using a cryoEM-derived molecular model for interpreting experiments and building further hypotheses limit its full impact. Significant amounts of research have been focused on developing metrics to assess cryoEM model quality, yet no consensus exists. This is in part because the meaning of cryoEM model quality is not well defined. In this work, we formalize cryoEM model quality in terms of whether a cryoEM map is better described by a model with localized atomic coordinates or by a lower-resolution model that lacks atomic-level information. This approach emerges from a novel, quantitative definition of image resolution based upon the hierarchical structure of biomolecules, which enables computational selection of the length scale to which a biomolecule is resolved based upon the available evidence embedded in the experimental data. In the context of cryoEM, we develop a machine learning-based implementation of this framework, called hierarchical atomic resolution perception (HARP), for assessing local atomic resolution in a cryoEM map and thus evaluating cryoEM model quality in a theoretically and statistically well-defined manner. Finally, using HARP, we perform a meta-analysis of the cryoEM-derived structures in the Protein Data Bank (PDB) to assess the state of atomic resolution in the field and quantify factors that affect it.

Significance Statement

Information about biomolecular structure is very useful to researchers investigating the mechanistic basis of biomolecular function. To enable researchers to assess the reliability of biomolecular structural information that is derived from experimental data, a new theoretical definition of atomic resolution has been developed. This definition forms the basis of a machine learning-based tool called HARP that can be used to measure the local atomic resolution of cryoEM maps, as well as the quality of the biomolecular structural models derived from such cryoEM maps. To demonstrate the power and utility of these conceptually novel approaches, this work demonstrates how they may be used to investigate the scientific and social factors that have historically affected the quality of cryoEM experiments.
Skimming genomes for systematics and DNA barcodes of corals
Authors: Quattrini Andrea M. , McCartin Luke J. , Easton Erin E. , Horowitz Jeremy , Wirshing Herman H. , Bowers Hailey , Mitchell Kenneth , Sei Makiri , McFadden Catherine S. , Herrera Santiago
Published: October 2023

1:

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage whole genome sequencing) remains a low-cost, promising method to not only extract high-copy loci, but also 100s to 1000s of phylogenetically informative single-copy nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and historical museum samples. The subphylum Anthozoa, which includes important ecosystem engineers (e.g., stony corals, black corals, anemones and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach.

2:

Genome skimming was conducted on 242 hexacorals and octocorals collected from 1890 to 2022. Using previously developed target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. We also extracted partial to whole mitogenomes and nuclear rRNA genes from the skim data.

3:

The mean number of UCE and exon loci extracted from the genome skimming data was 1,837 ± 662 SD for octocorals and 1,422 ± 720 loci for hexacorals; phylogenetic relationships were well resolved within each class. A mean of 1,422 ± 720 loci were obtained from the historical museum specimens, with 1,253 loci recovered from the oldest specimen collected in 1886 and 1,336 loci recovered from a holotype. The nuclearrRNAgenes and the majority of mitochondrial genes were successfully obtained from >95% of samples. Out of 99 circularized mitogenomes, 88% were recovered in samples from which we obtained >15M paired-end (PE) reads (>30M total reads); there was more variability in whether mitogenomes were circularized or not in samples with <15M PE reads.

4:

Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.
Building RNA Backbone in Constant Time by Numerical Approximation
Authors: Thibault Philippe , Major François
Published: October 2023

We present a numerical approximation method designed to swiftly create RNA ribose conformations in constant time. The method’s parameterization relies on the atomic coordinates of a given base along with its two neighboring phosphate groups. Such a parameterization suits three dimensional modeling engines that determine the RNA conformational search space using base operations instead of backbone sampling. These engines consider phosphate groups as part of the base rigid bodies. Reconstructing ribose conformations result in less than 1 Å of RMSD (root-mean-square deviation) compared to original conformations derived from high-resolution X-ray crystallographic structures. By incorporating this ribose construction method intoMC-Sym, a well-established RNA three dimensional modeling software, we streamline the modeling process into two phases. This enhances the search algorithm’s speed and improves model consistency and precision. Additionally, we employed the method to pinpoint 27 irregular ribose stereoisomers in high-resolution RNA X-ray crystal structures.
TARO: tree-aggregated factor regression for microbiome data integration
Authors: Mishra Aditya K. , Mahmud Iqbal , Lorenzi Philip L. , Jenq Robert R. , Wargo Jennifer A. , Ajami Nadim J. , Peterson Christine B.
Published: October 2023

Motivation

Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns.

Results

We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the phylogenetic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances.

Availability and implementation

The R packageTAROimplementing the proposed methods is available online athttps://github.com/amishra-stats/taro-package.
Universal signatures of transposable element compartmentalization across eukaryotic genomes
Authors: Gozashti Landen , Hartl Daniel L. , Corbett-Detig Russ
Published: October 2023

The evolutionary mechanisms that drive the emergence of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the massive accumulation of genome assemblies spanning phylogenetic diversity. Transposable elements (TEs) are a rich source of large-effect mutations since they directly and indirectly drive genomic structural variation and changes in gene expression. Here, we demonstrate universal patterns of TE compartmentalization across eukaryotic genomes spanning ~1.7 billion years of evolution, in which TEs colocalize with gene families under strong predicted selective pressure for dynamic evolution and involved in specific functions. For non-pathogenic species these genes represent families involved in defense, sensory perception and environmental interaction, whereas for pathogenic species, TE-compartmentalized genes are highly enriched for pathogenic functions. Many TE-compartmentalized gene families display signatures of positive selection at the molecular level. Furthermore, TE-compartmentalized genes exhibit an excess of high-frequency alleles for polymorphic TE insertions in fruit fly populations. We postulate that these patterns reflect selection for adaptive TE insertions as well as TE-associated structural variants. This process may drive the emergence of a shared TE-compartmentalized genome architecture across diverse eukaryotic lineages.
Resting state changes in aging and Parkinson’s disease are shaped by underlying neurotransmission – a normative modeling study
Authors: Kasper Jan , Caspers Svenja , Lotter Leon D. , Hoffstaedter Felix , Eickhoff Simon B. , Dukart Juergen
Published: October 2023

Human healthy and pathological aging is linked to a steady decline in brain resting state activity and connectivity measures. The neurophysiological mechanisms underlying these changes remain poorly understood. Making use of recent developments in normative modeling and availability of in vivo maps for various neurochemical systems, we test in the UK Biobank cohort (N=25,917) if and how age- and Parkinson’s disease related resting state changes in commonly applied local and global activity and connectivity measures co-localize with underlying neurotransmitter systems. We find the distributions of several major neurotransmitter systems including serotonergic, dopaminergic, noradrenergic and glutamatergic neurotransmission to explain age-related changes as observed across functional activity and connectivity measures. Co-localization patterns in Parkinson’s disease deviate from normative aging trajectories for these, as well as for cholinergic and GABAergic neurotransmission. The deviation from normal co-localization of brain function and GABAa correlates with disease duration. These findings provide new insights into molecular mechanisms underlying age- and Parkinson’s related brain functional changes. Combining normative modeling and neurotransmitter mapping may aid future research and drug development through deeper understanding of neurophysiological mechanisms underlying specific clinical conditions.
Neuronal activity modulates the incorporation of newly translated PSD-95 into a robust structure as revealed by STED and MINFLUX
Authors: Gürth Clara-Marie , do Rego Barros Fernandes Lima Maria Augusta , Palacios Victor Macarrón , Hubrich Jasmine , Cereceda Delgado Angel Rafael , Mougios Nikolaos , Opazo Felipe , D’Este Elisa
Published: October 2023

The postsynaptic density component PSD-95 undergoes activity-dependent plasticity mechanisms that rely on protein synthesis and structural remodeling. How synaptic activity can influence these dynamics at the single synapse level remains unclear. Here we combine genome-editing, pulse-chase experiments, STED and 3D MINFLUX nanoscopy on hippocampal neuronal cultures to study the integration of newly translated PSD-95 molecules at postsynaptic sites and their rearrangement within individual clusters at near-molecular resolution. We show that the amount of newly translated PSD-95 recruited to individual synapses scales with synaptic size, and modulates in a bidirectional manner, resulting in less new protein following excitatory and more new protein following inhibitory stimulation. Furthermore, we show that within synaptic clusters PSD-95 has a dispersed organization that is largely robust to long-lasting changes in activity. Altogether, this work sheds new light on the mechanisms underlying plasticity at the single synapse level, adding previously inaccessible information.
Comparative transcriptomics of Hirschfeldia incana and relatives highlights differences in photosynthetic pathways
Authors: Garassino Francesco , Luoni Sofia Bengoa , Cumerlato Tommaso , Marquez Francisca Reyes , Harbinson Jeremy , Aarts Mark G. M. , Nijveen Harm , Smit Sandra
Published: October 2023

Photosynthesis is the only yield-related trait that has not yet been substantially improved by plant breeding. The limited results of previous attempts to increase yield via improvement of photosynthetic pathways suggest that more knowledge is still needed to achieve this goal. To learn more about the genetic and physiological basis of high photosynthetic light-use efficiency (LUE) at high irradiance, we studyHirschfeldia incana. Here, we compare the transcriptomic response to high light ofH. incanawith that of three other members of the Brassicaceae,Arabidopsis thaliana, Brassica rapa, andBrassica nigra, which have a lower photosynthetic LUE.

First, we built a high-light, high-uniformity growing environment in a climate-controlled room. Plants grown in this system developed normally and showed no signs of stress during the whole growth period. Then we compared gene expression in low and high-light conditions across the four species, utilizing a panproteome to group homologous proteins efficiently. As expected, all species actively regulate genes related to the photosynthetic process. An in-depth analysis on the expression of genes involved in three key photosynthetic pathways revealed a general trend of lower gene expression in high-light conditions. However,H. incanadistinguishes itself from the other species through higher expression of certain genes in these pathways, either through constitutive higher expression, as forLHCB8, ordinary differential expression, as forPSBE, or cumulative higher expression obtained by simultaneous expression of multiple gene copies, as seen forLHCA6.

These differentially expressed genes in photosynthetic path-ways are interesting leads to further investigate the exact relationship between gene expression, protein abundance and turnover, and ultimately the LUE phenotype. In addition, we can also exclude thousands of genes from “explaining” the phenotype, because they do not show differential expression between both light conditions. Finally, we deliver a transcriptomic resource of plant species fully grown under, rather than briefly exposed to, a very high irradiance, supporting efforts to develop highly efficient photosynthesis in crop plants.
The genetic evolution of acral melanoma
Authors: Wang Meng , Fukushima Satoshi , Sheen Yi-Shuan , Ramelyte Egle , Pacheco Noel Cruz , Shi Chenxu , Liu Shanshan , Banik Ishani , Aquino Jamie D. , Acosta Martin Sangueza , Levesque Mitchell , Dummer Reinhard , Liau Jau-Yu , Chu Chia-Yu , Shain A. Hunter , Yeh Iwei , Bastian Boris C.
Published: October 2023

Acral melanoma is an aggressive type of melanoma with unknown origins, arising on the sole, palm, or nail apparatus. It is the most common type of melanoma in individuals with dark skin and is notoriously challenging to treat. Our study examined exome sequencing data from 139 tissue samples, spanning different progression stages, collected from 37 patients. We found that 78.4% of the melanomas displayed one or more clustered copy number transitions with focal amplifications, recurring predominantly on chromosomes 5, 11, 12, and 22. These genomic “hailstorms” were typically shared across all progression stages within individual patients. Genetic alterations known to activateTERTalso arose early. By contrast, mutations in the MAP- kinase pathway appeared later during progression, often leading to different tumor areas harboring non-overlapping driver mutations. We conclude that the evolutionary trajectories of acral melanomas substantially diverge from those of melanomas on sun-exposed skin, where MAP-kinase pathway activation initiates the neoplastic cascade followed by immortalization later. The punctuated formation of hailstorms, paired with earlyTERTactivation, suggests a unique mutational mechanism underlying the origins of acral melanoma. Our findings highlight an essential role for telomerase, likely in re-stabilizing tumor genomes after hailstorms have initiated the tumors. The marked genetic heterogeneity, in particular of MAP-kinase pathway drivers, may partly explain the limited success of targeted and other therapies in treating this melanoma subtype.
Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan
Authors: Bomba-Warczak Ewa K. , Velez Karen M. , Zhou Luhan T , Guillermier Christelle , Edassery Seby , Steinhauser Matthew L. , Savas Jeffrey N. , Duncan Francesca E.
Published: October 2023

The mechanisms contributing to age-related deterioration of the female reproductive system are complex, however aberrant protein homeostasis is a major contributor. We elucidated exceptionally stable proteins, structures, and macromolecules that persist in mammalian ovaries and gametes across the reproductive lifespan. Ovaries exhibit localized structural and cell-type specific enrichment of stable macromolecules in both the follicular and extrafollicular environments. Moreover, ovaries and oocytes both harbor a panel of exceptionally long-lived proteins, including cytoskeletal, mitochondrial, and oocyte-derived proteins. The exceptional persistence of these long-lived molecules suggest a critical role in lifelong maintenance and age-dependent deterioration of reproductive tissues.

One sentence summary

Exceptionally long-lived macromolecules in mammalian ovaries and oocytes as pillars for lifelong reproductive health span.
Perturbation-response analysis ofin silicometabolic dynamics in nonlinear regime: Hard-coded responsiveness in the cofactors and network sparsity
Authors: Himeoka Yusuke , Furusawa Chikara
Published: October 2023

Homeostasis is a fundamental characteristic of living systems. Unlike rigidity, homeostasis necessitates that systems respond flexibly to diverse environments. Understanding the dynamics of biochemical systems when subjected to perturbations is essential for the development of a quantitative theory of homeostasis. In this study, we analyze the response of bacterial metabolism to externally imposed perturbations using kinetic models ofEscherichia coli’s central carbon metabolism in nonlinear regimes. We found that three distinct kinetic models consistently display strong responses to perturbations; In the strong responses, minor initial discrepancies in metabolite concentrations from steady-state values amplify over time, resulting in significant deviations. This pronounced responsiveness is a characteristic feature of metabolic dynamics, especially since such strong responses are seldom seen in toy models of the metabolic network. Subsequent numerical studies show that adenyl cofactors consistently influence the responsiveness of the metabolic systems across models. Additionally, we examine the impact of network structure on metabolic dynamics, demonstrating that as the metabolic network becomes denser, the perturbation response diminishes—a trend observed commonly in the models. To confirm the significance of cofactors and network structure, we constructed a simplified metabolic network model, underscoring their importance. By identifying the structural determinants of responsiveness, our findings offer implications for bacterial physiology, the evolution of metabolic networks, and the design principles for robust artificial metabolism in synthetic biology and bioengineering.
cMYC-mediated immune repression is reversed by inhibition of H3K9/H3K27 methylation maintenance
Authors: Dye Isabel , Laing Sarah , Garner Ian , Mirza Hasan B. , Iyer Nayana , Brady Nicola , Spiliopoulou Pavlina , Spear Sarah , Robinson James , Fiorentino Francesca , Fuchter Matthew J. , Murphy Daniel J. , McNeish Iain A. , Brown Robert
Published: October 2023

Aberrant cMYC activity is a key driver of cancer, involved in several hallmark processes. Alongside the canonical hallmark of proliferation, cMYC represses immune signalling in a cell-intrinsic manner. The histone methyltransferases EZH2 and G9a interact with cMYC to modulate gene expression, including repression of immune genes via H3K27 and H3K9 histone methylation. Analyses of 565 cell lines derived from solid cancers demonstrated that greater cMYC-G9a/EZH2-mediated repression correlates with lower immune gene scores in a cell-intrinsic manner (innate, Type I and Type II IFN response), an effect most evident inMYC-amplified cell lines. In ovarian high-grade serous carcinoma (HGSC) cell lines and anin vivomurine model of HGSC, HKMTi-1-005, an inhibitor of H3K27/H3K9 methylation maintenance, relieved cMYC-G9a/EZH2 repression whilst inducing an immune response. A 7-gene immune signature (7ISG), related to viral mimicry signalling, is at the core of the HGSC immune response to HKMTi-1-005. InMYC-amplified HGSC patients, a low 7ISG score was associated with poor survival. Additionally,MYC-amplified cell lines were significantly more sensitive to HKMTi-1-005, whilst a low 7ISG score was associated with greater HKMTi-1-005 sensitivity, effects that were independent of canonical cMYC transcriptional activation. Examining the effects of HKMTi-1-005 treatment in aMYC-deregulated lung adenocarcinoma (LuAd) revealed induction of an immune responsein vitroand prolonged survivalin vivo.This suggests that inhibition of H3K27/H3K9 methylation maintenance will have efficacy in cMYC-deregulated tumours with low 7ISG scores, via disruption of cMYC-mediated repression of cell autonomous immune signalling and induction of an anti-tumour immune response.

Statement of significance

Over 70% of cancers are cMYC-deregulated. We show that inhibition of H3K27/H3K9 methylation maintenance relieves cMYC-dependent immune repression and prolongs survival of animal tumour models, suggesting a novel approach to treating cMYC-deregulated tumours.
Nearly half of all bacterial gene families are biased toward specific chromosomal positions
Authors: Hu Xiao-Pan , Lercher Martin J.
Published: October 2023

Many bacterial genes encoding components of the translation and transcription machinery occupy genomic positions close to the origin of genome replication. These positional biases are thought to result from selection for high expression levels, as genes close to the origin are the first to be duplicated after the initiation of DNA replication. However, recent work indicates that positional biases of RNA genes involved in translation have evolved to support optimal growth rate dependence of expression levels rather than high expression per se. We hypothesized that, more generally, natural selection may have favored the location of different genes at specific chromosomal positions to optimize the growth rate dependence of their relative gene copy numbers. Here we show that 49% of bacterial gene families are preferentially localized to specific chromosomal regions, with most families biased toward either the origin or the terminus of replication. From our hypothesis, we derive six specific predictions regarding the genes’ chromosomal positioning and functional categories, as well as the minimum cellular doubling times. All six predictions are robustly supported by comparative genomic analyses of 773 bacterial species and by proteomics data fromEscherichia coliandBacillus subtilis. Our findings reveal a complex relationship between bacterial growth, resource allocation and genome organization, and they provide new insights into the physiological significance and potential functions of a large number of gene families.
The structural OFF and ON states of myosin can be decoupled from the biochemical super-relaxed and disordered-relaxed states
Authors: Ma Weikang , Jani Vivek P. , Song Taejeong , Gao Chengqian , Gong Henry , Sadayappan Sakthivel , Kass David A. , Irving Thomas C.
Published: October 2023

There is a growing awareness that both thick filament and classical thin filament regulation play central roles in modulating muscle contraction. Myosin ATPase assays have demonstrated that under relaxed conditions, myosin may reside in either a high energy-consuming disordered-relaxed (DRX) state available for binding actin to generate force, or in an energy-sparing super-relaxed (SRX) state unavailable for actin binding. X-ray diffraction studies have shown the majority of myosin heads are in a quasi-helically ordered OFF state in a resting muscle and that this helical ordering is lost when myosin heads are turned ON for contraction. It has been assumed that myosin heads in SRX and DRX states are equivalent to the OFF and ON state respectively and the terms have been used interchangeably. Here, we use X-ray diffraction and ATP turnover assays to track the structural and biochemical transitions of myosin heads respectively induced with either omecamtiv mecarbil (OM) or piperine in relaxed porcine myocardium. We find that while OM and piperine induce dramatic shifts of myosin heads from the OFF to ON states, there are no appreciable changes in the population of myosin heads in the SRX and DRX states in both unloaded and loaded preparations. Our results show that biochemically defined SRX and DRX can be decoupled from structurally-defined OFF and ON states. In summary, while SRX/DRX and OFF/ON transitions can be correlated in some cases, these two phenomena are measured using different approaches, do not necessarily reflect the same properties of the thick filament and should be investigated and interpreted separately.

Significance

Myosin based thick filament regulation is now known to be critical for muscle contraction with myosin dysregulation found in hypertrophic and dilated cardiomyopathies. While previously thought to be synonymous, this study finds that biochemical and structural thick filament disengagement are distinct properties and should be investigated as independent phenomena. Understanding the details of thick filament regulation will be of great relevance to defining sarcomere-level dysfunction in myopathies and understanding and better designing and testing sarcomere therapies aimed at reversing them for treatment of cardiomyopathy.
The type of carbon source not the growth rate it supports can determine diauxie
Authors: Huo Yu , Danecka Weronika , Farquhar Iseabail , Mailliet Kim , Moses Tessa , Wallace Edward W. J. , Swain Peter S.
Published: October 2023

How cells choose between potential carbon sources is a classic example of cellular decision-making, and we know that many organisms prioritise glucose. Yet there has been little investigation of whether other sugars are also preferred, blinkering our view of carbon sensing. Here we study eukaryotic budding yeast and its growth on mixtures of palatinose, an isomer of sucrose, with other sugars. We find that yeast prioritise galactose over palatinose, but not sucrose or fructose, despite all three of these sugars being able to support faster growth than palatinose. Our results therefore disfavour carbon flux-sensing as the sole mechanism. By using genetic perturbations and transcriptomics, we show that repression is active and through Gal4, the master regulator of the GAL regulon. Cells enforce their preference for galactose over palatinose by preventing runaway positive feedback in the MAL regulon, whose genes enable palatinose catabolism. They do so both by repressing MAL11, the gene encoding the palatinose transporter, and by first expressing the isomaltases, IMA1 and IMA5, which cleave palatinose and so prevent its intracellular concentration becoming enough to induce further MAL expression. Our results demonstrate that budding yeast actively maintain a preference for carbon sources other than glucose and that such preferences have been selected by more than differences in growth rates. They imply that carbon-sensing strategies even in unicellular organisms are more complex than previously thought.