bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying transcriptome turnover on phylogenies by modeling gene expression as a binary trait
Authors: Thompson Ammon , May Michael R. , Hopkins Ben , Riedl Nerisa , Barmina Olga , Liebeskind Benjamin J. , Zhao Li , Begun David , Kopp Artyom
Published: October 2024

Changes in gene expression are a key driver of phenotypic evolution, leading to a persistent interest in the evolution of transcriptomes. Traditionally, gene expression is modeled as a continuous trait, leaving qualitative transitions largely unexplored. In this paper, we detail the development of new Bayesian inference techniques to study the evolutionary turnover of organ-specific transcriptomes, which we define as instances where orthologous genes gain or lose expression in a particular organ. To test these techniques, we analyze the transcriptomes of two male reproductive organs, testes and accessory glands, across 11 species of the Drosophila melanogaster species group. We first discretize gene expression states by estimating the probability that each gene is expressed in each organ and species. We then define a phylogenetic model of correlated transcriptome evolution in two or more organs and fit it to the expression state data. Inferences under this model show that many genes have gained and lost expression in each organ, and that the two organs experienced accelerated transcriptome turnover on different branches of the Drosophila phylogeny.
CMTM4 is an adhesion modulator that regulates skeletal patterning and primary mesenchyme cell migration in sea urchin embryos
Authors: Descoteaux Abigail E. , Radulovic Marko , Alburi Dona , Bradham Cynthia A.
Published: October 2024

MARVEL proteins, including those of the CMTM gene family, are multi-pass transmembrane proteins that play important roles in vesicular trafficking and cell migration; however, little is understood about their role in development, and their role in skeletal patterning is unexplored. CMTM4 is the only CMTM family member found in the developmental transcriptome of the sea urchinLytechinus variegatus. Here, we validate that LvCMTM4 is a transmembrane protein and show that perturbation of CMTM4 expression via zygotic morpholino or mRNA injection perturbs skeletal patterning, resulting in loss of secondary skeletal elements and rotational defects. We also demonstrate that normal levels of CMTM4 are required for normal PMC migration and filopodial organization, and that these effects are not due to gross mis-specification of the ectoderm. Finally, we show that CMTM4 is sufficient to mediate PMC cell-cell adhesion. Taken together, these data suggest that CMTM4 controls PMC migration and biomineralization via adhesive regulation during sea urchin skeletogenesis. This is the first discovery of a functionally required adhesive gene in this skeletal patterning system.

Graphical Abstract
Muscle-specific Keap1 deletion enhances force production but does not prevent inactivity-induced muscle atrophy in mice
Authors: Miranda Edwin R. , Shahtout Justin L. , Watanabe Shinya , Milam Norah , Karasawa Takuya , Rout Subhasmita , Atkinson Donald L. , Holland William L. , Drummond Micah J. , Funai Katsuhiko
Published: October 2024

Immobilization-associated muscle atrophy and weakness appear to be driven in part by oxidative stress. Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) is a critical redox rheostat that regulates oxidative stress responses, and its deletion is known to accelerate muscle atrophy and weakness during aging (sarcopenia) or denervation. Conversely, pharmacologic activation of NRF2 extends mouse lifespan and attenuates sarcopenia. Similarly, deletion of Kelch-like ECH-associated Protein 1 (Keap1), negative regulator of NRF2, enhances exercise capacity. The purpose of this study was to determine whether muscle-specific Keap1 deletion is sufficient to prevent muscle atrophy and weakness in mice following 7-days of hindlimb unloading (HU). To test this hypothesis, control (Ctrl) and tamoxifen inducible, muscle-specific Keap1 knockout (mKO) mice were subjected to either normal housing (Sham) or HU for 7 days. Activation of NRF2 in muscle was confirmed by increased mRNA of NRF2 targets thioredoxin 1 (Txn1) and NAD(P)H quinone dehydrogenase 1 (NQO1) in mKO mice. Keap1 deletion had an effect to increase force-generating capacity at baseline. However, muscle masses, cross sectional area, andex vivoforce were not different between mKO and Ctrl HU mice. In addition, muscle 4-hydroxynonenal-modified proteins and protein carbonyls were unaffected by Keap1 deletion. These data suggest NRF2 activation improves muscle force production during ambulatory conditions but is not sufficient prevent muscle atrophy or weakness following 7-days of HU.

Graphical Abstract
Long deletion signatures in repetitive genomic regions track somatic evolution and enable sensitive detection of microsatellite instability
Authors: Guo Qingli , Househam Jacob , Lakatos Eszter , Nowinski Salpie , Al Bakir Ibrahim , Grant Heather , Balarajah Vickna , Hughes Christine S. , Zapata Luis , Kocher Hemant M , Sottoriva Andrea , Baker Ann-Marie , Mustonen Ville , Graham Trevor A.
Published: October 2024

Deficiency in the mismatch repair system (MMRd) causes microsatellite instability (MSI) in cancers and determines eligibility for immunotherapy. Here, we show that MMRd tumours harbour long-deletion signatures (≥2-5+ base pairs deleted in repetitive regions), which provide new insights into MSI evolution and enable sensitive MSI detection particularly in challenging clinical samples. Long deletions, accumulated through stepwise DNA slippage errors, are significantly more prevalent in metastatic MMRd tumours compared to primary tumours. Importantly, we show that long-deletion signatures harbour features that are distinct from background noise, making them robustly detectable even in shallow whole genome sequencing (sWGS, ∼0.1X coverage) of formalin-fixed samples. We constructed a machine learning classifier that uses these distinct features to detect Microsatellite Instability in LOw-quality (MILO) samples. MILO achieved 100% accuracy in detecting MSI in sWGS data with only 2%-15% tumour purity and demonstrated promise in identifying MMRd clones in precancerous intestinal lesions. We propose that MILO could be clinically used for the sensitive monitoring of MMRd cancer evolution from early to late stages, using minimal sequencing data from both archival and fresh-frozen samples with low tumour content.

Significance

Mutational signatures characterised by long deletions in repetitive genomic regions provide a sensitive route to detect and track MMRd clone evolution, even with low purity shallow whole genome sequencing data.
Regulation of REM Sleep Onset and Homeostasis by Preoptic Glutamatergic Neurons
Authors: Mondino Alejandra , Jadidian Amir , Toth Brandon , Hambrecht-Wiedbusch Viviane S. , Floran-Garduno Leonor , Li Duan , York A. Kane , Torterolo Pablo , Pal Dinesh , Burgess Christian , Mashour George A. , Vanini Giancarlo
Published: October 2024

The preoptic area of the hypothalamus is key for the control of sleep onset and sleep homeostasis. Although traditionally considered exclusively somnogenic, recent studies identified a group of preoptic glutamatergic neurons that promote wakefulness. Specifically, our previous investigations demonstrated that chemogenetic stimulation of glutamatergic neurons within the medial-lateral preoptic area (MLPO_VGLUT2) promotes wakefulness, fragments non-rapid eye movement sleep (NREMs), and suppresses REM sleep (REMs). This evidence is further supported by recent work showing that preoptic glutamatergic neurons are activated during microarousals that fragment sleep in response to stress, and optogenetic stimulation of these neurons promotes microarousals and wakefulness. Thus, while the wake-promoting function of MLPO_VGLUT2 is clear, their role in sleep homeostasis has not been assessed. We tested the hypothesis that MLPO_VGLUT2 are wake-active, and their activation will increase wakefulness and disrupt sleep homeostasis via projections to arousal-promoting systems. Using fiber photometry, we found that MLPO_VGLUT2 were highly active during REMs, wakefulness and brief arousals, and remained minimally active during NREMs. Chemogenetic stimulation of MLPO_VGLUT2 inhibited REMs onset and suppressed the REMs homeostatic response after total sleep deprivation. Chemogenetic inhibition of MLPO_VGLUT2 increased REMs time (during the light phase only) but did not influence REMs and NREMs homeostasis. Anterograde projection mapping revealed that MLPO_VGLUT2 innervate central regions that promote wakefulness and inhibit REMs. We conclude that MLPO_VGLUT2 powerfully suppress REMs and that exogenous —and possibly pathologic— activation of these neurons disrupts REMs recovery, presumably by directly or indirectly activating REMs-inhibitory mechanisms.

SIGNIFICANCE STATEMENT

The preoptic area of the hypothalamus has been extensively studied and its role in sleep regulation is well-established. Importantly, recent work identified a group of preoptic glutamatergic neurons (MLPO_VGLUT2) that are wake-active and promote wakefulness. However, whether these neurons influence sleep homeostasis remains unknown. We demonstrate that MLPO_VGLUT2 are maximally active during REM sleep (REMs), wakefulness and brief arousals from sleep, and innervate wake-promoting and REMs-inhibitory regions. MLPO_VGLUT2 stimulation inhibits REMs and REMs rebound after sleep deprivation, whereas their inactivation increases REMs but does not alter REMs homeostatic response. We thus identified a preoptic mechanism that powerfully suppresses REMs, which we propose may engage during normal sleep-to-wake transitions to block REMs intrusions into subsequent wakefulness.
STRUCT: a statistical approach to identify RNA secondary structures from raw sequencing data, bypassing multiple sequence alignment
Authors: Wang Julie Fangran , Rustagi Arjun , Salzman Julia
Published: October 2024

RNA secondary and tertiary structures are essential to life. Experimental methods to detect RNA structure, such as X-ray crystallography and chemical probing, are incisive but suffer from low throughput and dimensionality. Computational approaches, leveraging evolutionary signals from correlated mutations, provide an alternative means to infer RNA structures. However, these methods require assembly and face challenges due to statistical biases inherent in multiple sequence alignment (MSA). Furthermore, these methods cannot exploit a given RNA element’s full spectrum of natural sequence variations. Here, we introduce STRUCT (StatisticalTesting ofRNAUnits withCovariationTraits), an assembly-free, MSA-free, and metadata-free statistical method for identifying conserved RNA structures from raw sequencing data, quantifying base-pair covariations or stem variation exclusion in the putative RNA structures. We show STRUCT rediscovers known HIV structural elements and identifies conserved rRNA structures in metatranscriptomics samples. Moreover, STRUCT finds viral structures in mosquito metatranscriptomics samplesde novo, including previously unannotated viral genomes, highlighting the method’s potential for viral discovery. STRUCT is an ultra-fast, easy-to-use, and robust tool that excels in high-throughput RNA structure prediction and hypothesis generation, presenting a novel approach for discovering structural RNA elements.
Test-retest reliability of perturbation-evoked cortical activity reflects stable individual differences in reactive balance control
Authors: Mirdamadi Jasmine L. , Poorman Alex , Munter Gaetan , Jones Kendra , Ting Lena H. , Borich Michael R. , Payne Aiden M.
Published: October 2024

There is a growing interest in measuring cortical activity during balance control for understanding mechanisms of impaired balance with aging and neurological dysfunction. The most well-characterized electrophysiological signal elicited by a balance disturbance is the perturbation-evoked N1 potential that peaks 100-200 msec post-perturbation and is thought to reflect error processing. We previously found associations between the N1 and individual differences in balance ability, suggesting it may be a potential biomarker of balance health. However, a potential biomarker of balance function will be limited by its reliability and clinical feasibility, which has yet to be established. Here, we characterized the reliability of the N1 elicited by standing balance perturbations within and between sessions over a one-week interval in 10 younger and 14 older adults. A subset of older adults (n=12) completed a session approximately one year prior to the main experiment. We extracted N1 amplitude and latency from the Cz electrode using an advanced, computationally-intensive approach that relies on large amounts of data (e.g., 64 channels, many trials), Test-retest reliability was assessed using the intra-class correlation coefficient (ICC). Internal consistency was quantified by split-half reliability using the Spearman correlation coefficient. N1s varied across individuals (amplitude:12-82µV, latency: 142-282ms), yet within individuals, the N1 showed excellent test-retest reliability (ICC>0.9) across a one-week and one-year time span. N1 amplitude reached excellent internal reliability for each session and group (r>0.9), that generally plateaued within 6 trials, while more trials were needed to reliably measure N1 latency. Similar results were obtained when quantifying N1s using a minimal approach performed with only three electrodes and simple preprocessing. Overall, the N1 is stable within and across sessions, and is largely independent of approach suggesting it could be a clinically-feasible biomarker of balance function. Characterizing reliability in populations with neurologic dysfunction and in different environmental contexts will be necessary to enhance our understanding of the N1, optimize experimental design, and determine its predictive validity of clinical outcomes (e.g., falls risk).
More cells, more doublets in sample-barcoded single-cell data
Authors: Howitt George , Dixit Gunjan , Aharon Rotem , Streeton-Cook Victoria , Ling Ling , Hickey Peter F. , Amann-Zalcenstein Daniela , Gubbels Liam , Shanthikumar Shivanthan , Ranganathan Sarath , Neeland Melanie R. , Maksimovic Jovana , Oshlack Alicia
Published: October 2024

Sample-specific barcoding of each molecule in single-cell RNA-sequencing experiments allows deconvolution of RNA from different cells captured together within a droplet. However, this is only possible when each cell comes from a different sample. As the number of cells in a droplet increases, the probability of two or more cells coming from the same sample increases rapidly. We show that the number of these unresolvable multiplets is greater than previously estimated in the 10X Flex scRNA-seq protocol, and provide a formula for estimating the fraction of multiplets in a data set given a measured average droplet occupancy and number of unique samples in a pool. We also show that existing doublet detection tools should be applied to Flex data to identify these multiplets, and demonstrate that filtering out barcodes identified by these tools improves downstream analysis.
MDA5 variants trade antiviral activity for protection from autoimmune disease
Authors: Wallace Chris , Singh Rahul , Modis Yorgo
Published: October 2024

Loss-of-function variants in MDA5, a key sensor of double-stranded RNA from viruses and retroelements, have been associated with protection from type 1 diabetes (T1D) in genome-wide association studies (GWAS). MDA5 loss-of-function variants have also been reported to increase the risk of inflammatory bowel disease (IBD). Whether these associations are linked or extend to other diseases remains unclear. Here, fine-mapping analysis of four large GWAS datasets shows that T1D-protective loss-of-function MDA5 variants also protect against psoriasis and hypothyroidism, while increasing the risk of IBD. The degree of autoimmune protection and IBD risk were linearly proportional. The magnitudes of the odds ratios for autoimmune protection and IBD risk were larger for rare MDA5 variants than for common variants, which were differentially expressed in different geographic populations. Our analysis suggests MDA5 genetic variants offer a direct fitness trade-off between viral clearance and autoimmune tissue damage.
Monosynaptic ventral tegmental area glutamate projections to the locus coeruleus enhance aversive processing
Authors: Parker Kyle E. , Kuo Chao-Cheng , Buckley Alex R. , Patterson Abigail P. , Duong Vincent , Hunter Sarah C. , McCall Jordan G.
Published: October 2024

Distinct excitatory synaptic inputs to the locus coeruleus (LC) modulate behavioral flexibility. Here we identify a novel monosynaptic glutamatergic input to the LC from the ventral tegmental area (VTA). We show robust VTA axonal projections provide direct glutamatergic transmission to LC. Despite weak synaptic summation, optogenetic activation of these axons enhances LC tonic firing and facilitates real-time and conditioned aversive behaviors. We hypothesized this projection may modulate synaptic integration with other excitatory inputs. We then used coincident VTA-LC photostimulation with local electrical stimulation and observed enhanced LC burst induction. To determine whether this integration also occursin vivo, we took an analogous approach measuring reward-seeking behavior during unpredictable probabilistic punishment. Here, glutamatergic VTA-LC photostimulation during a concurrent noxious stimulus did not delay reward-seeking behavior, but increased probability of task failure. Together, we identified a novel VTA-LC glutamatergic projection that drives concurrent synaptic summation during salient stimuli to promote behavioral avoidance.
Germplasm stability in zebrafish requires maternal Tdrd6a and Tdrd6c
Authors: Consorte Alessandro , El Sherif Yasmin , Kielisch Fridolin , Wittkopp Nadine , Ketting René F.
Published: October 2024

Germ cell specification is driven, in many species, by germplasm: a collection of phase-separation-based structures in the embryo, formed by RNA and proteins that derive from the cytoplasm of the oocytes. How the formation of germplasm is regulated, especially in vertebrates, remains unclear. In this study, we show that two multi-Tudor proteins, Tdrd6a and Tdrd6c, together are necessary for the stability of germplasm in zebrafish, while the related Balbiani body in the oocyte is largely unaffected. Combined lack of maternal Tdrd6a and Tdrd6c still allows the initial germplasm formation but causes its dispersal during the first hours of development. This results in the absence of primordial germ cells during later development and in sterility of the resulting adult animals. Furthermore, our study suggests that the Prion-like domain of Tdrd6c is relevant for Tdrd6c self-interaction as well as for its interaction with Bucky ball, the organizer of germplasm in zebrafish and that these dynamics are modulated by Tdrd6c Tudor domains. The identification of Tdrd6a and Tdrd6c as required for germplasm stability is an important step in our understanding of how this phase-separated structure is controlled during development.

Author Summary

We show that maternal Tdrd6a and Tdrd6c proteins interact with Bucky Ball and are essential for embryonic germplasm stability, germ cell specification and fertility in zebrafish.
Representation of verbal thought in motor cortex and implications for speech neuroprostheses
Authors: Kunz Erin M. , Meschede-Krasa Benyamin , Kamdar Foram , Avansino Donald , Nason-Tomaszewski Samuel R. , Card Nicholas S. , Jacques Brandon , Bechefsky Payton , Hahn Nick , Iacobacci Carrina , Hochberg Leigh R. , Brandman David M. , Stavisky Sergey D. , AuYong Nicholas , Pandarinath Chethan , Druckmann Shaul , Henderson Jaimie M. , Willett Francis R.
Published: October 2024

Speech brain-computer interfaces show great promise in restoring communication for people who can no longer speak1–3, but have also raised privacy concerns regarding their potential to decode private verbal thought4–6. Using multi-unit recordings in three participants with dysarthria, we studied the representation of inner speech in the motor cortex. We found a robust neural encoding of inner speech, such that individual words and continuously imagined sentences could be decoded in real-time This neural representation was highly correlated with overt and perceived speech. We investigated the possibility of "eavesdropping" on private verbal thought, and demonstrated that verbal memory can be decoded during a non-speech task. Nevertheless, we found a neural "overtness" dimension that can help to avoid any unintentional decoding. Together, these results demonstrate the strong representation of verbal thought in the motor cortex, and highlight important design considerations and risks that must be addressed as speech neuroprostheses become more widespread.
Integrating Artificial Intelligence and Bioinformatics Methods to Identify Disruptive STAT1 Variants Impacting Protein Stability and Function
Authors: Kamal Ebtihal , Kaddam Lamis A. , Ahmed Mehad , Alabdulkarim Abdulaziz
Published: October 2024

The Signal Transducer and Activator of Transcription1 (STAT1)gene is an essential component of the JAK-STAT signalling pathway. This pathway has a pivotal role in regulating different cellular processes, including immune responses, cell growth, and apoptosis. Mutations in theSTAT1gene contribute to various body pathologies [OMIM #600555], including immune system dysfunction.

In the current study, we used eighteen online computational approaches. Six pathogenic variants (R602W, I648T, V642D, L600P, I578N, and W504C) were predicted to significantly disrupt protein stability and function. These findings highlight the potential of approaches to pinpoint pathogenic single nucleotide polymorphisms, providing a time and cost effective alternative to experimental approaches. Up to the best of our knowledge, this is the original inclusive study, where we analyzeSTAT1gene variants using both bioinformatics and artificial intelligence based model tools.
Single-cell RNA sequencing on formalin-fixed and paraffin-embedded (FFPE) tissue identified multi-ciliary cells in breast cancer
Authors: González-Martínez Silvia , Carretero-Barrio Irene , Pérez-Mies Belén , Fernández-Lanza Val , García-Cosío Mónica , Caniego-Casas Tamara , Hardisson David , Esteban-Rodríguez Isabel , Cortés Javier , Palacios José
Published: October 2024

The purpose of this study was to evaluate the suitability of paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA sequencing (scRNAseq). To this end, we compared whether single-cell profiles from FFPE and matched FF tissue samples from one invasive carcinoma of no especial type carcinoma (invasive ductal carcinoma –IDC) and one invasive lobular carcinoma (ILC) were similar when captured using the common immunohistochemical (IHC) and immune features of the tumors.

FF and FFPE tissue derived libraries showed high-quality parameters. The cell heterogeneity obtained was similar, although, there were some differences in the number of cells captured, but there were no specific cell populations captured exclusively by one of the two different approaches. The combined analysis of the four samples identified six types of epithelial cells (normal basal cells, four subpopulations of neoplastic cells in the IDC and one in the ILC), and different tumoral microenvironment populations.

scRNAseq results from epithelial neoplastic cells were concordant with common IHC markers. In addition, after quantitative assessment of the whole slide images using QuPath, the proportion of immune cells identified by IHQ in FFPE sections were similar to those obtained by scRNAseq. Confirming the suitability of scRNAseq using FFPE tissue, this technique identified one subpopulation of neoplastic cells present only in the IDC, characterized by the expression of genes related with multi-ciliated cell (MCC) differentiation (FOXJ1, ROPN1L, TPPP3, CFAP45). IHC analysis ofFOXJ1expression confirmed the presence of positive cells only in the IDC in a similar proportion to that obtained by scRNAseq. Analysis ofFOXJ1in a cohort of 214 ER-positive invasive carcinomas demonstrated protein expression in at least 1% of cells in 33% of tumors, suggesting frequent focal MCC differentiation. Our results support the suitability of scRNAseq analysis using FFPE tissue and identified a subpopulation of neoplastic MCC in breast cancer.
Leveraging clinical sleep data across multiple pediatric cohorts for insights into neurodevelopment: the Retrospective Analysis of Sleep in Pediatric (RASP) cohorts study
Authors: Gong Naihua N. , Mahat Aditya , Ahmad Samya , Glaze Daniel , Maletic-Savatic Mirjana , McGinley Matthew , Morse Anne Marie , Rodriguez Alcibiades J. , Thurm Audrey , Redline Susan , Maski Kiran , Purcell Shaun , Buckley Ashura
Published: October 2024

Sleep disturbances are prominent across neurodevelopmental disorders (NDDs) and may reflect specific abnormalities in brain development and function. Overnight polysomnography (PSG) allows for detailed investigation of sleep architecture, offering a unique window into neurocircuit function. A better understanding of sleep in NDDs compared to typically developing children could therefore define mechanisms underlying abnormal development in NDDs and provide avenues for the development of therapeutic interventions to improve sleep quality and developmental outcomes. Here, we introduce and characterize a collection of 1527 pediatric overnight PSGs across five different sites. We first developed an automated stager trained on independent pediatric sleep data, which yielded better performance compared to a stager trained on adults. Using consistent staging across cohorts, we derived a panel of EEG micro-architectural features. This unbiased approach replicated broad trajectories previously described in typically developing sleep architecture. Further, we found sleep architecture disruptions in children with Down’s Syndrome (DS) that were consistent across independent cohorts. Finally, we built and evaluated a model to predict age from sleep EEG metrics, which recapitulated our previous findings of younger predicted brain age in children with DS. Altogether, by creating a resource pooled from existing clinical data we expanded the available datasets and computational resources to study sleep in pediatric populations, specifically towards a better understanding of sleep in NDDs. This Retrospective Analysis of Sleep in Pediatric (RASP) cohorts dataset, including staging annotation derived from our automated stager, will be deposited athttps://sleepdata.org.

Statement of significance

We introduce the RASP cohorts, a collection of 1527 clinical pediatric overnight polysomnographies that includes typically developing and neurodevelopmental disorder cases. As a first step towards addressing the analytic bottleneck inherent in manual sleep staging, we developed and validated a pediatric-specific sleep stager. Leveraging the retrospective RASP cohorts dataset, we redemonstrated known developmental trajectories in sleep architecture. To summarize changes in brain function reflected in sleep, we developed a model to predict brain age from sleep measures. We recapitulate younger predicted age in RASP Down’s Syndrome cases. This work not only enhances our understanding of sleep disturbances in NDDs, but also provides a valuable resource for future research and underscores the utility of existing clinical polysomnography studies.
Stress-hardening behaviour of biofilm streamers
Authors: Savorana Giovanni , Redaelli Tommaso , Truzzolillo Domenico , Cipelletti Luca , Secchi Eleonora
Published: October 2024

Bacteria’s ability to withstand mechanical challenges is enhanced in their biofilm lifestyle, where they are encased in a viscoelastic polymer matrix [1]. Under fluid flow, biofilms can form as streamers – slender filaments tethered to solid surfaces and suspended in the flowing fluid [2, 3]. Streamers thrive in environments subjected to intense hydrodynamic stresses, such as medical devices and water filters, often resulting in catastrophic clogging [4]. Their colonisation success may depend on a highly adaptable mechanical response to varying stress conditions, though the evidence and underlying mechanisms of this adaptation remain elusive. Here, we demonstrate that biofilm streamers exhibit a stress-hardening behaviour, with both differential elastic modulus and effective viscosity increasing linearly with external stress. This stress-hardening is consistent across biofilms with different matrix compositions, formed by various bacterial species, and under diverse growth conditions. We further demonstrated that this mechanical response originates from the properties of extracellular DNA (eDNA) molecules [5], which constitute the structural backbone of the streamers. Our findings reveal an instantaneous, purely physical mechanism enabling streamers to adapt to hydrodynamic stresses. Given the ubiquity of eDNA in biofilms [1, 6], this discovery prompts a re-evaluation of its functional role in biofilm mechanics. Moreover, the stress-hardening behaviour may have broad implications for biofilm development, survival, and ecology, paralleling its role in tissues where it regulates processes such as morphogenesis, cancer formation and wound healing [7, 8].
A single nucleotide polymorphism genotyping panel for efficient genetic stock identification of the Teno river Atlantic salmon (Salmo salar) population complex
Authors: Johansson Helena , Erkinaro Jaakko , Falkegard Morten , Foldvik Anders , Orell Panu , Primmer Craig R , Pritchard Victoria L
Published: October 2024

A new single nucleotide polymorphism (SNP) panel for genetic stock identification in the Teno River Atlantic salmon fishery was developed, with a view to improving on an existing microsatellite panel. Twenty-two genetically differentiated reporting units were proposed based on population genetic analyses of 1212 individuals collected at 37 locations in the river and genotyped for > 33,000 genome-wide SNPs. A small subset of these SNPs was selected for GSI using an iterative process that considered their diversity and differentiation across reporting units. A genotyping-by-sequencing assay was developed to simultaneously genotype 180 of these GSI SNPs plus a sexing marker. This new SNP panel showed comparative GSI power to the microsatellite panel, with anticipated improvements in terms of cost, speed, and robustness and transferability across laboratories and genotyping platforms. Mixed stock analysis of the 2018 Teno River salmon catch using the new panel inferred all 22 reporting units to contribute to the fishery. Estimated catch proportions positively scaled with an independent estimate of reporting unit productivity: target spawning female biomass. This demonstrates the usefulness and efficiency of the 180 SNP panel for Atlantic salmon GSI in the Teno River system. If conducted on a regular basis, GSI can enable fine-tuning of management strategies to promote sustainable fishing.
Mammalian chemosensory bile acid detection supports species and gut microbiome evaluation
Authors: Haran Varun , Morimoto Mari , Rouyer Leena S. F. , McDonald Jeffrey G. , Wang Jinxin , Meeks Julian P.
Published: October 2024

Long abstract

The rodent accessory olfactory system (AOS) detects environmental chemosignals and guides social and survival-oriented behaviors. Fecal bile acids activate neurons in the AOS, potentially serving as mammalian pheromones and kairomones, but few molecules in this large class have been evaluated thus far. We used live volumetric Ca2+imaging to screen naturally occurring bile acids for their capacity to activate peripheral vomeronasal sensory neurons (VSNs). We found that taurine-conjugated bile acids (tauro-BAs), including taurine-conjugates of cholic acid, deoxycholic acid, lithocholic acid, and chenodeoxycholic acid (TCA, TDCA, TLCA, TCDCA, respectively) activate large populations of VSNs at sub-micromolar concentrations. Tauro-BA-sensitive VSNs rarely responded to unconjugated (CA, CDCA, DCA, LCA), glycine-conjugated (GCA, GDCA, GLCA, GCDCA), or keto-conjugated (7-keto DCA, 12-keto DCA, 7-keto LCA) bile acids. Tauro-BA-sensitive VSNs were also insensitive to well-studied sulfated steroids, suggesting tauro-BAs activate vomeronasal receptors that have not yet been de-orphaned. Among the tauro-BAs, TDCA displayed particularly strong potency, activating many VSNs at sub-micromolar concentrations. Tauro-BAs were not detectable in mouse fecal extracts by mass spectrometry, but were found in reptile fecal extracts and germ-free mouse fecal extracts. VSN responses to germ-free and conventional mouse fecal extracts, conjugated bile acids, and tauro-BAs revealed that non-overlapping populations of VSNs respond to germ-free and conventional mouse feces. A subset of VSNs that were activated by germ-free mouse fecal extracts responded to tauro-BAs, whereas VSNs responsive to conventionally fecal extracts responded to unconjugated bile acids.In vivoexposure to TDCA alone, and to mouse fecal extracts spiked with TDCA, elicited mild aversion and stress-associated behaviors in a non-social context (avoidance, digging, grooming, etc.). These studies establish tauro-BAs as a novel class of aversive vomeronasal ligands that vary in feces across species and gut microbiomes.

Short abstract

The rodent accessory olfactory system (AOS) detects environmental chemosignals and guides social and survival-oriented behaviors. Fecal bile acids activate neurons in the AOS, but the full repertoire of bile acids that activate VSNs is not known. A live Ca2+imaging screen revealed that VSNs were highly activated by taurine-conjugated bile acids (tauro-BAs) at sub-micromolar concentrations. Tauro-BAs were undetectable in conventionally raised mouse fecal extracts, but were found in reptile fecal extracts and germ-free mouse fecal extracts. VSN activity to tauro-BAs overlapped that of germ-free mouse fecal extracts, suggesting a link between bile acid chemosensation and the gut microbiome. When mice were exposed to taurodeoxycholic acidin vivo, they displayed mild aversion and stress-associated behaviors.
Melanocyte differentiation and mechanosensation are differentially modulated by distinct extracellular matrix proteins
Authors: Luthold Carole , Didion Marie , Benedum Emilio , Burkhart Ann-Kathrin , Demmerle Nina , Gunaratnam Gubesh , Rácz Vanessa Samira , Bischoff Markus , Ridzal Annika , Iden Sandra
Published: October 2024

Dysfunctions in melanocytes can lead to pigmentation disorders, such as albinism, or contribute to the development of melanoma, the most aggressive form of skin cancer. Epidermal melanocytes typically interact with the collagen IV-rich basement membrane, but upon injury or in pathological conditions, they can encounter environments rich in collagen I or fibronectin. While alterations in ECM composition and stiffness are known to impact cell behavior, the specific roles of each of these cues for melanocyte functions remain unclear. To explore the impact of these extrinsic cues, we here exposed murine melanocytes to different ECM proteins as well as varying substrate stiffnesses. This study identified MITF, a key regulator of melanocyte differentiation and function, as an ECM- and mechanosensitive transcription factor. We further revealed that distinct ECM proteins and substrate stiffness engage a MEK/ERK/MITF signaling axis to control melanocyte functions. Exposure of melanocytes to collagen I restricted ERK activation, promoting high nuclear MITF levels associated with melanocyte proliferation and differentiation. Conversely, fibronectin elicited elevated ERK activation, leading to low nuclear MITF, correlating with a dedifferentiated and motile phenotype. Importantly, inhibiting ERK activity in melanocytes cultured on fibronectin led to increased MITF nuclear localization, MITF target gene expression and enhanced melanogenesis. Additionally, we uncovered that melanocyte mechanoresponses differ depending on the specific ECM environment. Together, these findings reveal a synergistic effect of extrinsic cues on melanocyte function, with a context-dependent MITF regulation downstream of ERK, offering new perspectives for our understanding of melanocyte-related pathologies.
Universal rules govern plasmid copy number
Authors: Ramiro-Martínez Paula , de Quinto Ignacio , Gama João Alves , Rodríguez-Beltrán Jerónimo
Published: October 2024

Plasmids –autonomously replicating DNA molecules– are pervasive in the microbial world, where they fuel evolution as key vehicles for gene transfer. Plasmids are as diverse as their hosts and exhibit a broad range of replication and mobility strategies, genetic repertoires, host ranges, sizes, and copies per cell. While most of these features have been extensively characterized, the determinants of plasmid copy number (PCN) remain poorly understood. Here, we leveraged extensive DNA sequencing data to comprehensively analyze the copy number of thousands of diverse bacterial plasmids. We found that the copy number of natural plasmids is highly variable, spanning nearly three orders of magnitude, and that it is intrinsically robust against changes in genomic context. We further show that PCN variability is tightly associated with plasmid lifestyles and develop the concept of replicon dominance to explain interactions in widespread multi-replicon plasmids. Finally, we uncover a universal scaling law that links copy number and plasmid size across phylogenetic boundaries, indicating that pervasive constraints orchestrate the PCN-size trade-off. Altogether, our work pioneers large-scale analyses of PCN while uncovering the fundamental rules that govern plasmid biology.
An active matter model captures the spatial dynamics of actomyosin oscillations during morphogenesis
Authors: Mackay Euan D. , Bebbington Aimee , Januschke Jens , Kursawe Jochen , Bischoff Marcus , Sknepnek Rastko
Published: October 2024

The apicomedial actomyosin network is crucial for generating mechanical forces in cells. Oscillatory behaviour of this contractile network is commonly observed before or during significant morphogenetic events. For instance, during the development of theDrosophilaadult abdominal epidermis, larval epithelial cells (LECs) undergo pulsed contractions before being replaced by histoblasts. These contractions involve the formation of contracted regions of concentrated actin and myosin. However, the emergence and control of pulsed contractions are not fully understood. Here, we combined in vivo 4D microscopy with numerical simulations of an active elastomer model applied to realistic cell geometries and boundary conditions to study LEC actomyosin dynamics. The active elastomer model was able to reproduce in vivo observations quantitatively. We also characterised the relationship between cell shape, cell polarity, and actomyosin network parameters with the spatiotemporal characteristics of the contractile network both in vivo and in simulations. Our results show that cell geometry, accompanied by boundary conditions which reflect the cells’ polarity, is essential to understand the dynamics of the apicomedial actomyosin network. Moreover, our findings support the notion that spatiotemporal oscillatory behaviour of the actomyosin network is an emergent property of the actomyosin network, rather than driven by upstream signalling.
A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments
Authors: Wallenius A.J. , Venetz J. , Zygadlowska O.M. , Lenstra W.K. , van Helmond N.A.G.M. , Dalcin Martins P. , Slomp C.P. , Jetten M.S.M.
Published: October 2024

Coastal areas are responsible for over 75% of global marine methane emissions and this proportion is predicted to grow due to an increase in anthropogenically induced eutrophication and deoxygenation. Prolonged periods of low oxygen and high organic matter input have been put forward to cause an imbalanced microbial methane cycle, as methane oxidation cannot keep up with methane production. However, it is still unclear what factors affect each process and which microorganisms are responsible. Here we show that methanogenic processes dominate microbial methane cycling in the anoxic sediments of marine Lake Grevelingen (NL) after summer stratification with bottom water anoxia. We observed a shallow and narrow sulfate-methane transition zone between 5 and 15 cm depth, with high methane concentrations (> 5 mM) below this zone. Methanogenesis was dominant over methanotrophy in all investigated layers as active methanogenesis potential was detected down to 60 cm below sea floor, but methane oxidation was only observed in a narrow section of the sulfate-methane transition zone. Based on amplicon sequencing and sediment incubations, we uncovered a metabolically and phylogenetically diverse methanogenic community with distinct niche separation in different sediment layers. ANME archaea and their putative syntrophic sulfate-reducing bacteria were restricted to a narrow zone and were co-occurring with the detected methane oxidation activity. Our results suggest that eutrophication and deoxygenation will further contribute to rising methane emissions in coastal areas, as the microbial methane cycle will be tilted towards increased methanogenesis while the efficiency of the microbial methane filter is expected to decline.
Systems genetic dissection of Alzheimer’s disease brain gene expression networks
Authors: Zhao Pinghan , Fadel Omar El , Le Anh , Mangleburg Carl Grant , Dhindsa Justin , Wu Timothy , Zhao Jinghan , Huang Meichen , Amoh Bismark , Marella Aditi Sai , Li Yarong , Seyfried Nicholas T. , Levey Allan I. , Liu Zhandong , Al-Ramahi Ismael , Botas Juan , Shulman Joshua M
Published: October 2024

In Alzheimer’s disease (AD), changes in the brain transcriptome are hypothesized to mediate the impact of neuropathology on cognition. Gene expression profiling from postmortem brain tissue is a promising approach to identify causal pathways; however, there are challenges to definitively resolve the upstream pathologic triggers along with the downstream consequences for AD clinical manifestations. We have functionally dissected 30 AD-associated gene coexpression modules using a cross-species strategy in fruit fly (Drosophila melanogaster) models. Integrating longitudinal RNA-sequencing and behavioral phenotyping, we interrogated the unique and shared transcriptional responses to amyloid beta (Aβ) plaques, tau neurofibrillary tangles, and/or aging, along with potential links to progressive neuronal dysfunction. Our results highlight hundreds of conserved, differentially expressed genes mapping to human AD regulatory networks. To confirm causal modules and pinpoint AD network drivers, we performed systematicin vivogenetic manipulations of 357 conserved, prioritized targets, identifying 141 modifiers of Aβ- and/or tau-induced neurodegeneration. We discover an up-regulated network that is significantly enriched for both AD risk variants and markers of immunity / inflammation, and which promotes Aβ and tau-mediated neurodegeneration based on fly genetic manipulations in neurons. By contrast, a synaptic regulatory network is strongly downregulated in human brains with AD and is enriched for loss-of-function suppressors of Aβ/tau inDrosophila. Additional experiments suggest that this human brain transcriptional module may respond to and modulate Aβ-induced glutamatergic hyperactivation injury. In sum, our cross-species, systems genetic approach establishes a putative causal chain linking AD pathology, large-scale gene expression perturbations, and ultimately, neurodegeneration.
Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia
Authors: Sen Arko , Xu Zhichao , Tyndale Sélène T. , Yasis Jean , Cho Chae Yun , Bump Rosalind , Chandran Sahaana , Luo Linda , Fu Yi , Petersen Lillian Kay , Shokhirev Max , Kuo Dennis J. , McVicker Graham , Dixon Jesse R.
Published: October 2024

B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric malignancy. Based on gene expression profiling, B-ALL can be classified into distinct transcriptional subtypes with differing disease outcomes. Many of these transcriptional subtypes are defined by mutations in transcription factors and chromatin-modifying enzymes, but how such diverse mutations lead to distinct transcriptional subtypes remains unclear. To illuminate the chromatin regulatory landscape in B-ALL, we analyzed 3D genome organization, open chromatin, and gene expression in 53 primary patient samples. At the level of 3D genome organization, we identified chromatin interactions that vary across transcriptional subtypes. These sites of variable 3D chromatin interactions correlate with local gene expression changes and are enriched for core drivers of B-ALL observed in genome-wide CRISPR knock-out screens. Sites of variable 3D genome interactions are frequently shared across multiple transcriptional subtypes and are enriched for open chromatin sites found in normal B-cell development but repressed in mature B-cells. Within an individual patient sample, the chromatin landscape can resemble progenitor chromatin states at some loci and mature B-cell chromatin at others, suggesting that the chromatin in B-ALL patient tumor cells is in a partially arrested immature state. By analyzing transcriptomic data from large cohorts of B-ALL patients, we identify gene expression programs that are shared across transcriptional subtypes, associated with B-cell developmental stages, and predictive of patient survival. In combination, these results show that the 3D genome organization of B-ALL reflects B-cell developmental stages and helps illustrate how B-cell developmental arrest interacts with transcriptional subtypes to drive B-ALL.
α-Copaene is a potent repellent against the Asian Citrus PsyllidDiaphorina citri
Authors: Magnani Rodrigo Facchini , Volpe Haroldo Xavier Linhares , Luvizotto Rejane Angélica Grigio , Mulinari Tatiana Aparecida , Agostini Thiago Trevisoli , Bastos Jairo Kenupp , Ribeiro Victor Pena , Carmo-Sousa Michele , Wulff Nelson Arno , Peña Leandro , Leal Walter S.
Published: October 2024

The Asian Citrus Psyllid (ACP),Diaphorina citri, severely threatens citrus production worldwide by transmitting the greening(= Huanglongbing)-causing bacteriumCandidatusLiberibacter asiaticus. There is growing evidence that the push-pull strategy is suitable to partially mitigate HLB by repelling ACP with transgenic plants engineered to produce repellents and attracting the vector to plants with a minimal disease transmission rate. Species that pull ACP away from commercial citrus plants have been identified, and transgenic plants that repel ACP have been developed. The concept of a repellent-producing plant was first demonstrated with anArabidopsisline engineered to overexpress a gene controlling the synthesis of β-caryophyllene and other sesquiterpenes. We have analyzed the volatile organic compounds released by thisArabidopsisline and identified α-humulene, α-copaene, and trace amounts of β-elemene, in addition to β-caryophyllene. Behavioral measurements demonstrated that α-copaene repels ACP at doses ca. 100x lower than those needed for β-caryophyllene repellence. In contrast, α-humulene is innocuous at the level emitted by the transgenic plant. We confirmed that a mixture of the three sesquiterpenes in the ratio 100:10:1 repels ACP. Likewise, a commercial sample of refined copaiba oil containing the three sesquiterpenes, in a proportion similar to that in the transgenic plant, repelled ACP.