bluuebunny/crossref_metadata_2025 huggingface dataset:
tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development
Authors: Rappol Tom , Waldl Maria , Chugunova Anastasia , Hofacker Ivo L. , Pauli Andrea , Vilardo Elisa
Published: January 2024

tRNA genes exist in multiple copies in the genome of all organisms across the three domains of life. Besides the sequence differences across tRNA copies, extensive post-transcriptional modification adds a further layer to tRNA diversification. Whilst the crucial role of tRNAs as adapter molecules in protein translation is well established, whether all tRNA are actually expressed, and whether the differences across isodecoders play any regulatory role is only recently being uncovered. Here we built upon recent developments in the use of NGS-based methods for RNA modification detection and developed tRAM-seq, an experimental protocol andin silicoanalysis pipeline to investigate tRNA expression and modification. Using tRAM-seq we analysed the full ensemble of nucleo-cytoplasmic and mitochondrial tRNAs during embryonic development of the model vertebrate zebrafish. We show that the repertoire of tRNAs changes during development, with an apparent major switch in tRNA isodecoder expression and modification profile taking place around the start of gastrulation. Taken together, our findings suggest the existence of a general reprogramming of the expressed tRNA pool, possibly gearing the translational machinery for distinct stages of the delicate and crucial process of embryo development.
Fluorinated trehalose analogues for cell surface engineering and imaging ofMycobacterium tuberculosis
Authors: Guy Collette S. , Gott James A. , Ramírez-Cárdenas Jonathan , de Wolf Christopher , Furze Christopher M. , West Geoff , Muñoz-García Juan C. , Angulo Jesus , Fullam Elizabeth
Published: January 2024

The sensitive, rapid and accurate diagnosis ofMycobacterium tuberculosis(Mtb) infection is a central challenge in controlling the global tuberculosis (TB) pandemic. Yet the detection of mycobacteria is often made difficult by the low sensitivity of current diagnostic tools, with over 3.6 million TB cases missed each year. To overcome these limitations there is an urgent need for next-generation TB diagnostic technologies. Here we report the use of a discrete panel of native19F-trehalose (F-Tre) analogues to label and directly visualiseMtbby exploiting the uptake of fluorine-modified trehalose analoguesviathe mycobacterial trehalose LpqY-SugABC ATP-binding cassette (ABC) importer. We discovered the extent of modified F-Tre uptake correlates with LpqY substrate recognition and characterisation of the interacting sites by saturation transfer difference NMR coupled with molecular dynamics provides a unique glimpse into the molecular basis of fluorine-modified trehalose import inMtb. Lipid profiling demonstrated that F-Tre analogues modified at positions 2, 3 and 6 are incorporated into mycobacterial cell-surface trehalose-containing glycolipids. This rapid one-step labelling approach facilitates the direct visualisation of F-Tre-labelledMtbby focused ion beam (FIB) secondary ion mass spectrometry (SIMS), enabling pathogen specific detection. Collectively, our findings highlight that F-Tre analogues have potential as tools to probe and unravelMtbbiology and can be exploited to detect and image TB.
LSD Modulates Proteins Involved in Cell Proteostasis, Energy Metabolism and Neuroplasticity in Human Cerebral Organoids
Authors: Costa Marcelo N. , Goto-Silva Livia , Nascimento Juliana M. , Domith Ivan , Karmirian Karina , Feilding Amanda , Trindade Pablo , Martins-de-Souza Daniel , Rehen Stevens K.
Published: January 2024

Proteomic analysis of human cerebral organoids may reveal how psychedelics regulate biological processes, shedding light on drug-induced changes in the brain. This study elucidates the proteomic alterations induced by lysergic acid diethylamide (LSD) in human cerebral organoids. By employing high-resolution mass spectrometry-based proteomics, we quantitatively analyzed the differential abundance of proteins in cerebral organoids exposed to LSD. Our findings indicate changes in proteostasis, energy metabolism, and neuroplasticity-related pathways. Specifically, LSD exposure led to alterations in protein synthesis, folding, autophagy, and proteasomal degradation, suggesting a complex interplay in the regulation of neural cell function. Additionally, we observed modulation in glycolysis and oxidative phosphorylation, crucial for cellular energy management and synaptic function. In support of the proteomic data, complementary experiments demonstrated LSD’s potential to enhance neurite outgrowth in vitro, confirming its impact on neuroplasticity. Collectively, our results provide a comprehensive insight into the molecular mechanisms through which LSD may affect neuroplasticity and potentially contribute to therapeutic effects for neuropsychiatric disorders.
Decreased Left Atrial Cardiomyocyte FGF13 Expression Increases Vulnerability to Postoperative Atrial Fibrillation in Humans
Authors: Fischer Matthew A. , Arrieta Adrian , Angelini Marina , Soehalim Elizabeth , Chapski Douglas J. , Shemin Richard J. , Vondriska Thomas M. , Olcese Riccardo
Published: January 2024

Postoperative atrial fibrillation (POAF) is the most common complication after cardiac surgery and a significant cause of increased morbidity and mortality. The development of novel POAF therapeutics has been limited by an insufficient understanding of molecular mechanisms promoting atrial fibrillation. In this observational cohort study, we enrolled 28 patients without a history of atrial fibrillation that underwent mitral valve surgery for degenerative mitral regurgitation and obtained left atrial tissue samples along the standard atriotomy incision in proximity to the right pulmonary veins. We isolated cardiomyocytes and performed transcriptome analyses demonstrating 13 differentially expressed genes associated with new-onset POAF. Notably, decreased expression of fibroblast growth factor 13 (FGF13), a fibroblast growth factor homologous factor known to modulate voltage-gated sodium channel NaV1.5 inactivation, had the most significant association with POAF. To assess the functional significance of decreased FGF13 expression in atrial myocytes, we performed patch clamp experiments on neonatal rat atrial myocytes after siRNA-mediated FGF13 knockdown, demonstrating action potential prolongation. These critical findings indicate that decreased FGF13 expression promotes vulnerability to POAF.
PREFRONTAL CORRELATES OF FEAR GENERALIZATION DURING ENDOCANNABINOID DEPLETION
Authors: Rosas-Vidal Luis E. , Naskar Saptarnab , Mayo Leah M. , Perini Irene , Altemus Megan , Engelbrektsson Hilda , Jagasia Puja , Heilig Markus , Patel Sachin
Published: January 2024

Maladaptive fear generalization is one of the hallmarks of trauma-related disorders. The endocannabinoid 2-arachidonoylglycerol (2-AG) is crucial for modulating anxiety, fear, and stress adaptation but its role in balancing fear discrimination versus generalization is not known. To address this, we used a combination of plasma endocannabinoid measurement and neuroimaging from a childhood maltreatment exposed and non-exposed mixed population combined with human and rodent fear conditioning models. Here we show that 2-AG levels are inversely associated with fear generalization at the behavioral level in both mice and humans. In mice, 2-AG depletion increases the proportion of neurons, and the similarity between neuronal representations, of threat-predictive and neutral stimuli within prelimbic prefrontal cortex ensembles. In humans, increased dorsolateral prefrontal cortical-amygdala resting state connectivity is inversely correlated with fear generalization. These data provide convergent cross-species evidence that 2-AG is a key regulator of fear generalization and suggest 2-AG deficiency could represent a trauma-related disorder susceptibility endophenotype.
Synthesis and application of a photocaged L-lactate
Authors: Miyazaki Ikumi , Tsao Kelvin K. , Kamijo Yuki , Nasu Yusuke , Terai Takuya , Campbell Robert E.
Published: January 2024

l-Lactate, once considered a metabolic waste product of glycolysis, is now recognized as a vitally important metabolite and signaling molecule in multiple biological pathways. However, exploringl-lactate’s emerging intra- and extra-cellular roles is hindered by a lack of tools to locally perturbl-lactate concentration intracellularly and extracellularly. Photocaged compounds are a powerful way to introduce bioactive molecules with spatial and temporal precision using illumination. Here, we report the development of a photocaged derivative ofl-lactate, 4-methoxy-7-nitroindolinyll-lactate (MNI-l-lac), that releasesl-lactate upon UV illumination. We validated MNI-l-lac in cell culture by demonstrating that the photorelease ofl-lactate elicits a response from genetically encoded extra- and intracellularl-lactate biosensors. These results indicate that MNI-l-lac may be useful for perturbing the concentration of endogenousl-lactate in order to investigatel-lactate’s roles in metabolism and signaling pathways.
Proteasome-dependent Orc6 removal from chromatin upon S-phase entry safeguards against MCM reloading and tetraploidy
Authors: Hayashi-Takanaka Yoko , Hiratani Ichiro , Haraguchi Tokuko , Hiraoka Yasushi
Published: January 2024

DNA replication is tightly regulated to occur only once per cell cycle, as untimely re-initiation can lead to aneuploidy, which is associated with early senescence and cancer. The pre-replication complex (comprising Orc1-6, Cdc6, Cdt1, and MCM) is essential for the initiation of DNA replication, but the dynamics and function of Orc6 during the cell cycle remain elusive. Here, we demonstrate that Orc6 associates with chromatin during G1-phase and dissociates upon S-phase entry. The dissociation of Orc6 from chromatin is dependent on proteasome activity, and inhibition of the proteasome leads to the accumulation of chromatin-bound Orc6, which promotes abnormal MCM loading after S-phase entry without undergoing mitosis in human immortalized hTERT-RPE1 cells. Following release from proteasome inhibition, cells with elevated levels of chromatin-bound Orc6 and MCM proceed to the next replication phase as tetraploid cells. Our findings suggest that the proteasome-dependent dissociation of Orc6 after DNA replication is critical for preventing inappropriate MCM reloading and tetraploid formation.
Systemic inflammation accelerates neurodegeneration in a rat model of Parkinson’s disease overexpressing human alpha synuclein
Authors: Massaro Cenere Mariangela , Tiberi Marta , Paldino Emanuela , D’Addario Sebastian Luca , Federici Mauro , Giacomet Cecilia , Cutuli Debora , Matteocci Alessandro , Cossa Francesca , Zarrilli Beatrice , Casadei Nicolas , Ledonne Ada , Petrosini Laura , Berretta Nicola , Fusco Francesca Romana , Chiurchiù Valerio , Mercuri Nicola B.
Published: January 2024

Increasing efforts have been made to elucidate how genetic and environmental factors interact in Parkinson’s disease (PD). In the present study, we assessed the development of symptoms on a genetic PD rat model that overexpresses human α-synuclein (Snca+/+) at a presymptomatic age, exposed to a pro-inflammatory insult by intraperitoneal injection of lipopolysaccharide (LPS), using immunohistology, high-dimensional flow cytometry, constant potential amperometry, and behavioral analyses. A single injection of LPS into WT andSnca+/+rats triggered long-lasting increase in the activation of pro-inflammatory microglial markers, monocytes, and T lymphocytes. However, only LPSSnca+/+rats showed dopaminergic neuronal loss in thesubstantia nigra pars compacta(SNpc), associated with a reduction in the release of evoked dopamine in the striatum. No significant changes were observed in the behavioral domain.

We propose our double-hit animal as a reliable model to investigate the mechanisms whereby α-synuclein and inflammation interact to promote neurodegeneration in PD.
Gene-specific RNA homeostasis revealed by perturbation of coactivator complexes
Authors: Forouzanfar Faezeh , Plassard Damien , Furst Audrey , Moreno David F. , Oliveira Karen A. , Reina-San-Martin Bernardo , Tora László , Molina Nacho , Mendoza Manuel
Published: January 2024

Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates to maintain stable RNA levels under varying cellular conditions. Current research supports a global, non-sequence-specific connection between mRNA synthesis and degradation, but the underlying mechanisms are still unclear. In this study, we investigated changes in RNA metabolism following acute depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we demonstrate that TIP60 predominantly enhances transcription of numerous genes, while a smaller set of genes undergoes TIP60-dependent transcriptional repression. Surprisingly, transcription changes caused by TIP60 depletion were offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering mechanisms. Similarly, disruption of the unrelated ATAC coactivator complex also resulted in gene-specific transcript buffering. These findings reveal that transcript buffering functions at a gene-specific level and suggest that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.
Tapeworm infection affects sleep behavior in three-spined stickleback
Authors: Bauhus Marc , Mews Sina , Kurtz Joachim , Brinker Alexander , Peuß Robert , Anaya-Rojas Jaime
Published: January 2024

Sleep is a highly complex and conserved biological process that affects several body functions and behaviors. Recent evidence suggests that there is a reciprocal interaction between sleep and immunity. For instance, fragmented sleep can increase the probability of parasitic infections and reduce the ability of infected hosts to fight infections. It is also known, particularly in humans and other mammals, that viral and bacterial infections alter the sleep patterns of infected individuals. However, the effects of macro-parasitic infections on sleep remain largely unknown. In this study, we investigated whether macro-parasite infections could alter the sleep of their hosts. We experimentally infected three-spined sticklebacks (Gasterosteus aculeatus) with the tapewormSchistocephalus solidusand used a hidden Markov model to characterize sleep-associated behaviors in the sticklebacks. At an early time-point, 1-4 days after parasite exposure, infected fish showed no difference in sleep compared with non-exposed fish, whereas fish that were exposed but could fend off the infection slept less during the daytime. At a later time-point, 29-32 days after exposure, infected fish slept more than uninfected fish, while exposed-but-not-infected fish slept less than non-exposed fish. Using RNA-seq of brain tissue, we identified several immune- and sleep-associated genes that potentially underlie the observed behavioral changes. These results provide the first insight into the complex association between macro-parasite infection, immunity, and sleep in fish and may thus contribute to a better understanding of the reciprocal interaction between sleep and immunity.
A feather star is born: embryonic development and nervous system organization in the crinoidAntedon mediterranea
Authors: Mercurio S. , Gattoni G. , Scarì G. , Ascagni M. , Barzaghi B. , Elphick M. R. , Benito-Gutiérrez E. , Pennati R.
Published: January 2024

Background

Crinoids belong to the phylum Echinodermata, marine invertebrates with a highly derived pentaradial body plan. As the only living members of the Pelmatozoa, the sister group to other extant echinoderms, crinoids are in a key phylogenetic position to reconstruct the evolutionary history of this phylum. However, the development of crinoids has been scarcely investigated, limiting their potential for comparative studies. Many crinoids are difficult to collect in the wild and embryo manipulation is challenging. Conversely, the Mediterranean feather starAntedon mediterraneacan be found in shallow waters and has been used for experimental studies, most notably to investigate regeneration.

Results

The aim here was to establishA. mediterraneaas an experimental system for developmental biology. To accomplish this, we set up a method for culturing embryosin vitrofrom zygote to hatching larva stage that allowed us to define a developmental timeline and a standardized staging system for this species. We then optimized protocols to characterize the development of the main structures of the feather star body plan, using a combination of microscopy techniques and whole mount immunohistochemistry andin situhybridization chain reaction. Focusing on the nervous system, we show that the larval apical organ includes a combination of serotonergic, GABAergic and glutamatergic neurons that form under the influence of a conserved anterior molecular signature. The larval neural plexus is instead composed of glutamatergic neurons and develops during the formation of the ciliary bands. Larval neurons disappear at metamorphosis, and the ectoneural and entoneural components of the adult nervous system develop early in post-metamorphic stages. Furthermore, the oral ectoderm that contains the ectoneural system acquires an “anterior” signature expressingSix3/6andLhx2/9orthologs.

Conclusions

Our results deepen our knowledge on crinoid development and provide new techniques to investigate feather star embryogenesis, promoting the use ofA. mediterraneain developmental and evolutionary biology. This in turn will pave the way for the inclusion of crinoids in comparative studies to understand the origin of the echinoderm body plan and clarify many unanswered questions on deuterostome evolution.
Multiple variants of the type VII secretion system in Gram-positive bacteria
Authors: Garrett Stephen R. , Higginson Andrew B. , Palmer Tracy
Published: January 2024

Type VII secretion systems (T7SS) are found in bacteria across the Bacillota and Actinomycetota phyla and have been well described inStaphylococcus aureus,Bacillus subtilisand pathogenic mycobacteria. The T7SS from Actinomycetota and Bacillota share two common components, a membrane-bound EccC/EssC ATPase and EsxA, a small helical hairpin protein of the WXG100 family. However, they also have additional phylum-specific components, and as a result they are termed the T7SSa (Actinomycetota) and T7SSb (Bacillota), respectively. Here we identify additional organisations of the T7SS across these two phyla and describe eight additional T7SS subtypes which we have named T7SSc – T7SSj. T7SSd is found exclusively in Actinomycetota including theOlselnellaandBifodobacteriumgenus, whereas the other seven are found only in Bacillota. All of the novel subtypes contain the canonical ATPase (TsxC) and the WXG100-family protein (TsxA). Most of them also contain a small ubiquitin-related protein, TsxB, related to the T7SSb EsaB/YukB component. Protein kinases, phosphatases and forkhead associated (FHA) proteins are often encoded in the novel T7SS gene clusters. Candidate substrates of these novel T7SS subtypes include LXG-domain and RHS proteins. Predicted substrates are frequently encoded alongside genes for additional small WXG100-related proteins that we speculate serve as co-secretion partners. Collectively our findings reveal unexpected diversity in the T7SS in Gram-positive bacteria.
Supervised deep machine learning models predict forelimb movement from excitatory neuronal ensembles and suggest distinct pattern of activity in CFA and RFA networks
Authors: Latifi Shahrzad , Chang Jonathan , Pedram Mehdi , Latifikhereshki Roshanak , Thomas Carmichael S
Published: January 2024

Neuronal networks in the motor cortex are crucial for driving complex movements. Yet it remains unclear whether distinct neuronal populations in motor cortical subregions encode complex movements. Usingin vivotwo-photon calcium imaging (2P) on head- fixed grid-walking animals, we tracked the activity of excitatory neuronal networks in layer 2/3 of caudal forelimb area (CFA) and rostral forelimb area (RFA) in motor cortex. Employing supervised deep machine learning models, a support vector machine (SVM) and feed forward deep neural networks (FFDNN), we were able to decode the complex grid-walking movement at the level of excitatory neuronal ensembles. This study indicates significant differences between RFA and CFA decoding accuracy in both models. Our data demonstrate distinct temporal-delay decoding patterns for movements in CFA and RFA, as well as a selective ensemble of movement responsive neurons with higher distribution in CFA, suggesting specific patterns of activity-induced movement in these two networks.
LncRNA GAS6-AS1 contributes to 5-fluorouracil resistance in colorectal cancer
Authors: Zhu Zhonglin , Li Minghan , Weng Junyong , Li Shanbao , Guo Tianan , Guo Yang , Xu Ye
Published: January 2024

5-Fluorouracil (5-FU) resistance has always been a formidable obstacle in the adjuvant treatment of advanced colorectal cancer (CRC). In recent years, long non-coding RNAs have emerged as key regulators in various pathophysiological processes including 5-FU resistance. Here, RNA-seq combined with weighted gene correlation network analysis confirmed the close association of GAS6-AS1 with TRG grades. GAS6-AS1 expression was positively correlated with advanced clinicopathological features and poor prognosis in CRC. GAS6-AS1 increased the 50% inhibiting concentration of 5-FU, enhanced cell proliferation, and accelerated G1/S transition in CRC cells, both with and without 5-FU, both in vitro and in vivo. Mechanistically, GAS6-AS1 enhanced the stability of MCM3 mRNA by recruiting PCBP1, consequently increasing MCM3 expression. Furthermore, PCBP1 and MCM3 counteracted the effects of GAS6-AS1 on 5-FU resistance. Notably, the PDX model indicated that combining chemotherapeutic drugs with GAS6-AS1 knockdown yielded superior outcomes in vivo. Together, our findings elucidate that GAS6-AS1 directly binds to PCBP1, enhancing MCM3 expression and thereby promoting 5-FU resistance. GAS6-AS1 may serve as a robust biomarker and potential therapeutic target for combination therapy in CRC.
The role of gene duplication in facilitating divergent patterns of gene expression across a complex life cycle
Authors: DuBose James G. , de Roode Jacobus C.
Published: January 2024

Explaining the processes that facilitate divergence in the morphologies and functions expressed by organisms throughout their life cycles is fundamental for understanding life cycle evolution. Theory suggests that the expression of traits is decoupled across life stages, thus allowing for evolutionary independence. Although trait decoupling between stages has been described in many studies, explanations of how said decoupling evolves have seldom been considered. Here, we propose evolutionary divergence between duplicate genes as an important mechanism by which life cycle complexity evolves. Because the different phenotypes expressed by organisms throughout their life cycles are coded by the same genome, trait decoupling between stages must be mediated through their divergence in gene expression. Gene duplication has been identified as an important mechanism that enables divergence in gene function and expression between cells and tissues. Here, we examined the temporal changes in gene expression across the monarch butterfly (Danaus plexippus) metamorphosis. We found that within homologous groups, more phylogenetic divergent genes exhibited more distinct temporal expression patterns, and that this relationship scaled such that more phylogenetically diverse homologous groups showed more diverse patterns of gene expression. Furthermore, we found that duplicate genes showed increased stage-specificity relative to singleton genes. Overall, our findings suggest an important role of gene duplication in the evolution of trait decoupling across complex life cycles.

Significance

The proliferation of many of the world’s most diverse groups of eukaryotes is frequently attributed to their life cycle complexity. By allowing organisms to express different traits throughout their lives, complex life cycles enable individuals to utilize multiple ecological niches. However, the mechanisms that facilitate life cycle evolution are not well understood. We drew inspiration from studies on functional divergence between different tissues and examined the role of gene duplication in generating different patterns of gene expression between stages across the metamorphosis ofDanaus plexippus(the monarch butterfly). Our findings suggest that the role of gene duplication in generating differences between cell and tissue types likely extends to trait differentiation between stages within complex life cycles.
Identification of novel origins of transfer across bacterial plasmids
Authors: Ares-Arroyo Manuel , Nucci Amandine , Rocha Eduardo P.C.
Published: January 2024

Conjugative plasmids are important drivers of bacterial evolution, but most plasmids lack genes for conjugation. It is currently not known if the latter can transfer because origins of transfer by conjugation (oriT), which would allow their mobilization by conjugative plasmids, are poorly known. Here, we identify and characterize occurrences of knownoriTfamilies across thousands of plasmids confirming that most conjugative and mobilizable plasmids still lack identifiable families oforiTs. They reveal clear patterns in terms of intergenic position, distance to the relaxases, and MOB-type association. This allowed to develop a computational method to discover noveloriTs. As a proof of concept, we identify 21 noveloriTsfrom the nosocomial pathogensEscherichia coli,Klebsiella pneumoniae, andAcinetobacter baumannii, some of them responsible for the mobility of critical antimicrobial resistance genes. These 21oriTfamilies share key characteristics of the others and fill most of the missing diversity oforiTsin relaxase-encoding plasmids both in terms of frequency and phylogeny. We confirmed experimentally the function of six of them. The ability to identify noveloriTs paves the way to explore conjugation across bacterial plasmids, notably among the majority lacking conjugation-related genes.
Genetic and developmental divergence in the neural crest programme between cichlid fish species
Authors: Marconi Aleksandra , Vernaz Grégoire , Karunaratna Achira , Ngochera Maxon J. , Durbin Richard , Santos M. Emília
Published: January 2024

Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes’ cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic programme in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifiersox10(sox10aandsox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to inter-specific morphological differences. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlidsox10paralogs, with the acquisition of a novel skeletogenic function bysox10a. When compared to the teleost models zebrafish and medaka, our findings reveal thatsox10duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes – particularly those controlled bysox10s – might be involved in generating morphological diversification between species and lays the groundwork for further investigations into mechanisms underpinning vertebrate NC diversification.
A framework for reconstructing ancient food webs using functional trait data
Authors: Shaw Jack O. , Dunhill Alexander M. , Beckerman Andrew P. , Dunne Jennifer A. , Hull Pincelli M.
Published: January 2024

Food webs provide quantitative insights into the structure and dynamics of ecological communities. Previous work has shown their utility in understanding community responses to modern and ancient perturbations, including anthropogenic change and mass extinctions. However, few ancient food webs have been reconstructed due to difficulties assessing trophic interactions amongst extinct species derived from an incomplete fossil record.

We present and assess the Paleo Food web Inference Model (PFIM). PFIM uses functional trait data—predictive of interactions in modern ecosystems and commonly available for fossil organisms—to reconstruct ancient food webs. We test the model by (i) applying it to four modern ecosystems with empirical constrained food webs to directly compare PFIM-constructed networks to their empirical counterparts, (ii) by carefully comparing discrepancies between PFIM-inferred and empirical webs in one of those systems, and (iii) by comparing networks describing feasible trophic interactions (“feasible webs”) with networks to which we superimpose characteristic interaction distributions derived from modern theory (“realized webs”). As a proof of concept, we then apply the method to faunal data from two Cambrian fossil deposits to reconstruct ancient trophic systems.

PFIM-inferred feasible food webs successfully predict ∼70% of trophic interactions across four modern systems. Furthermore, inferred food webs with enforced interaction distributions (i.e., realized webs) accurately predict ∼90% of interactions. Comparisons with a global database of trophic interactions and other food web models, suggest that under sampling of empirical webs accounts for up to 21% of the remaining differences between PFIM and empirical food webs.

Food webs can be reasonably approximated by inferring trophic interactions based upon life habit traits. This study provides the foundation to use trait-based inference models across the fossil record to examine ancient food webs and community evolution.
Etiology of Craniofacial and Cardiac Malformations in a Mouse Model of SF3B4-Related Syndromes
Authors: Kumar Shruti , Bareke Eric , Lee Jimmy , Carlson Emma , Merkuri Fjodor , Schwager Evelyn E. , Maglio Steven , Fish Jennifer L. , Majewski Jacek , Jerome-Majewska Loydie
Published: January 2024

Pathogenic variants in SF3B4 are responsible for the acrofacial disorders Nager and Rodriguez Syndrome, also known as SF3B4-related Syndromes, associated with malformations in the head, face, limbs, vertebrae as well as the heart. To uncover the etiology of craniofacial malformations found in SF3B4-related syndromes, mutant mouse lines with homozygous deletion ofSf3b4in neural crest cells (NCC) were generated. Like in human patients, these embryos had craniofacial and cardiac malformations with variable expressivity and penetrance. The severity and survival ofSf3b4NCC mutants was modified by the level ofSf3b4in neighbouring non NCC. RNA sequencing analysis of heads of embryos prior to morphological abnormalities showed significant changes in expression of genes forming the NCC regulatory network, as well as an increase in exon skipping. We identified several key transcription factors and histone modifiers involved in craniofacial and cardiac development with increased exon skipping. Increased exon skipping was also associated with use of a more proximal branch point, as well as an enrichment in thymidine bases in the 50bp around the branch points. We propose that decrease inSf3b4causes changes in the expression and splicing of transcripts required for proper craniofacial and cardiac development, leading to abnormalities.
PCP Auto Count: A Novel Fiji/ImageJ plug-in for automated quantification of planar cell polarity and cell counting
Authors: Stansak Kendra L. , Baum Luke D. , Ghosh Sumana , Thapa Punam , Vanga Vineel , Walters Bradley J.
Published: January 2024

Background

During development, planes of cells give rise to complex tissues and organs. The proper functioning of these tissues is critically dependent on proper inter- and intra-cellular spatial orientation, a feature known as planar cell polarity (PCP). To study the genetic and environmental factors affecting planar cell polarity investigators must often manually measure cell orientations, which is a time-consuming endeavor.

Methodology

To automate cell counting and planar cell polarity data collection we developed a Fiji/ImageJ plug-in called PCP Auto Count (PCPA). PCPA analyzes binary images and identifies “chunks” of white pixels that contain “caves” of infiltrated black pixels. Inner ear sensory epithelia including cochleae (P4) and utricles (E17.5) from mice were immunostained for βII-spectrin and imaged on a confocal microscope. Images were preprocessed using existing Fiji functionality to enhance contrast, make binary, and reduce noise. An investigator rated PCPA cochlear angle measurements for accuracy using a 1-5 agreement scale. For utricle samples, we directly compared PCPA derived measurements against manually derived angle measurements using concordance correlation coefficients (CCC) and Bland-Altman limits of agreement. Finally, PCPA was tested against a variety of images copied from publications examining PCP in various tissues and across various species.

Results

PCPA was able to recognize and count 99.81% of cochlear hair cells (n = 1,1541 hair cells) in a sample set, and was able to obtain ideally accurate planar cell polarity measurements for over 96% of hair cells. When allowing for a <10° deviation from “perfect” measurements, PCPA’s accuracy increased to >98%. When manual angle measurements for E17.5 utricles were compared, PCPA’s measurements fell within −9 to +10 degrees of manually obtained mean angle measures with a CCC of 0.999. Qualitative examination of example images of Drosophila ommatidia, mouse ependymal cells, and mouse radial progenitors revealed a high level of accuracy for PCPA across a variety of stains, tissue types, and species. Altogether, the data suggest that the PCPA plug-in suite is a robust and accurate tool for the automated collection of cell counts and PCP angle measurements.
Casein kinase 1 controls components of a TORC2 signaling network in budding yeast
Authors: Lucena Rafael , Jasani Akshi , Anastasia Steph , Kellogg Douglas , Alcaide-Gavilan Maria
Published: January 2024

Tor kinases play diverse and essential roles in control of nutrient signaling and cell growth. Tor kinases are assembled into two large multiprotein complexes referred to as Tor Complex 1 and Tor Complex 2 (TORC1 and TORC2). In budding yeast, TORC2 controls a signaling network that relays signals regarding carbon source that strongly influence growth rate and cell size. However, the mechanisms that control TORC2 signaling are poorly understood. Activation of TORC2 requires Mss4, a phosphoinositol kinase that initiates assembly of a multi-protein complex at the plasma membrane that recruits and activates downstream targets of TORC2. Localization of Mss4 to the plasma membrane is controlled by phosphorylation and previous work suggested that yeast homologs of casein kinase 1γ, referred to as Yck1 and Yck2, control phosphorylation of Mss4. Here, we generated a new analog-sensitive allele ofYCK2and used it to test whether Yck1/2 influence signaling in the TORC2 network. We found that multiple components of the TORC2 network are strongly influenced by Yck1/2 signaling.
The integration of tandem gene repeatsviaa bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation inSaccharomyces cerevisiae
Authors: Evans Samuel , Lu Zeyu , McDonnell Liam , Anderson Will , Peralta Francisco , Watkins Tyson , Ahmed Hafna , Luna-Flores Carlos Horacio , Loan Thomas , Navone Laura , Trau Matt , Scott Colin , Speight Robert , Vickers Claudia E. , Peng Bingyin
Published: January 2024

Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms, like human diseases and microbial productivities of target bioproducts. Here, we develop a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats inSaccharomyces cerevisiaeand further visualise the evolutionary trajectories of gene repeats. We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification (ToxAmp) modules, and accidentally re-visited the high-level capacity of multi-fragment co-transformation inS. cerevisiae. This system delivered the multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection. Inducing the toxin (RelE) expressingviaa copper (II)-inducibleCUP1promoter successfully drove thein-situgene amplification of the antitoxin (RelB) module, resulting in ∼40 copies of a green fluorescence reporter (GFP) gene per copy of genome. The copy-number changes, increasing and decreasing, and stable maintenance were visualised using the GFP and blue chromoprotein AeBlue as reporters. Copy-number increasing happened spontaneously not depending on a selection pressure and was quickly enriched through toxin-antitoxin-mediated selection. In summary, the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications.

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Soma-to-germline BMP signal is essential forDrosophilaspermiogenesis
Authors: Beard Emma Kristine , Norris Rachael P. , Furusho Miki , Terasaki Mark , Inaba Mayu
Published: January 2024

In theDrosophilatestis, developing germ cells are encapsulated by somatic support cells throughout development. Soma-germline interactions are essential for successful spermiogenesis. However, it is still not fully understood what signaling events take place between the soma and the germline. In this study, we found that a Bone Morphogenetic Protein (BMP) ligand, Glass bottom boat (Gbb), secreted from somatic cyst cells (CCs), signals to differentiating germ cells to maintain proper spermiogenesis. Knockdown of Gbb in CCs or the type I BMP receptor Saxophone (Sax) in germ cells leads to a defect in sperm head bundling and decreased fertility. Our Transmission Electron Microscopy (TEM) analyses revealed that the mutant germ cells have aberrant morphology of mitochondria throughout the stages of spermiogenesis and exhibit a defect in nebenkern formation. Elongating spermatids show uncoupled nuclei and elongating mitochondrial derivatives, suggesting that improper mitochondrial development may cause the sperm bundling defect. Taken together we propose a new role of soma-derived BMP signaling, which is essential for spermiogenesis.
Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924
Authors: Lépine Sarah , Maussion Gilles , Schneider Alexandria , Nauleau-Javaudin Angela , Castellanos-Montiel María José , Ambriz Georgina Jiménez , Spiegelman Dan , Abdian Narges , Franco-Flores Anna Krystina , Haghi Ghazal , Gursu Lale , Chaineau Mathilde , Durcan Thomas Martin
Published: January 2024

A growing body of knowledge implicates perturbed RNA homeostasis in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease that currently has no cure and few available treatments. Dysregulation of the multifunctional RNA-binding protein TDP-43 is increasingly regarded as a convergent feature of this disease, evidenced at the neuropathological level by the detection of TDP-43 pathology in most patient tissues, and at the genetic level by the identification of disease-associated mutations in its coding geneTARDBP. To characterize the transcriptional landscape induced byTARDBPmutations, we performed whole-transcriptome profiling of motor neurons differentiated from two knock-in iPSC lines expressing the ALS-linked TDP-43 variants p.A382T or p.G348C. Our results show that theTARDBPmutations significantly altered the expression profiles of mRNAs and microRNAs of the 14q32 cluster in MNs. Using mutation-induced gene signatures and the Connectivity Map database, we identified compounds predicted to restore gene expression toward wild-type levels. Among top-scoring compounds selected for further investigation, the NEDD8-activating enzyme inhibitor MLN4924 effectively improved cell viability and neuronal activity, highlighting a possible role for protein post-translational modification via NEDDylation in the pathobiology of TDP-43 in ALS.
Widespread latent hyperactivity of nociceptors outlasts enhanced avoidance behavior following incision injury
Authors: Bavencoffe Alexis G. , Lopez Elia R. , Johnson Kayla N. , Tian Jinbin , Gorgun Falih M. , Shen Breanna Q. , Zhu Michael X. , Dessauer Carmen W. , Walters Edgar T.
Published: January 2024

Nociceptors with somata in dorsal root ganglia (DRGs) exhibit an unusual readiness to switch from an electrically silent state to a hyperactive state of tonic, nonaccommodating, low-frequency, irregular discharge of action potentials (APs). Ongoing activity (OA) during this state is present in vivo in rats months after spinal cord injury (SCI), and has been causally linked to SCI pain. OA induced by various neuropathic conditions in rats, mice, and humans is retained in nociceptor somata after dissociation and culturing, providing a powerful tool for investigating its mechanisms and functions. An important question is whether similar nociceptor OA is induced by painful conditions other than neuropathy. The present study shows that probable nociceptors dissociated from DRGs of rats subjected to postsurgical pain (induced by plantar incision) exhibit OA. The OA was most apparent when the soma was artificially depolarized to a level within the normal range of membrane potentials where large, transient depolarizing spontaneous fluctuations (DSFs) can approach AP threshold. This latent hyperactivity persisted for at least 3 weeks, whereas behavioral indicators of affective pain – hindpaw guarding and increased avoidance of a noxious substrate in an operant conflict test – persisted for 1 week or less. An unexpected discovery was latent OA in neurons from thoracic DRGs that innervate dermatomes distant from the injured tissue. The most consistent electrophysiological alteration associated with OA was enhancement of DSFs. Potential in vivo functions of widespread, low-frequency nociceptor OA consistent with these and other findings are to amplify hyperalgesic priming and to drive anxiety-related hypervigilance.
Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning
Authors: Niu Zijian , O’Farrell Aoife , Li Jingxin , Reffsin Sam , Jain Naveen , Dardani Ian , Goyal Yogesh , Raj Arjun
Published: January 2024

Single-molecule RNA fluorescencein situhybridization (RNA FISH)-based spatial transcriptomics methods have enabled the accurate quantification of gene expression at single-cell resolution by visualizing transcripts as diffraction-limited spots. While these methods generally scale to large samples, image analysis remains challenging, often requiring manual parameter tuning. We present Piscis, a fully automatic deep learning algorithm for spot detection trained using a novel loss function, the SmoothF1 loss, that approximates the F1 score to directly penalize false positives and false negatives but remains differentiable and hence usable for training by deep learning approaches. Piscis was trained and tested on a diverse dataset composed of 358 manually annotated experimental RNA FISH images representing multiple cell types and 240 additional synthetic images. Piscis outperforms other state-of-the-art spot detection methods, enabling accurate, high-throughput analysis of RNA FISH-derived imaging data without the need for manual parameter tuning.
Projections from thalamic nucleus reuniens to hippocampal CA1 area participate in context fear extinction by affecting extinction-induced molecular remodeling of excitatory synapses
Authors: Ziółkowska Magdalena , Sotoudeh Narges , Cały Anna , Puchalska Monika , Pagano Roberto , Śliwińska Małgorzata Alicja , Salamian Ahmad , Radwanska Kasia
Published: January 2024

The ability to extinguish contextual fear in a changing environment is crucial for animal survival. Recent data support the role of the thalamic nucleus reuniens (RE) and its projections to the dorsal hippocampal CA1 area (RE→dCA1) in this process. However, it remains poorly understood how RE impacts dCA1 neurons during contextual fear extinction (CFE). Here, we reveal that the RE→dCA1 pathway contributes to extinction of contextual fear by affecting CFE-induced molecular remodeling of excitatory synapses. Anatomical tracing and chemogenetic manipulation in mice demonstrate that RE neurons form synapses and regulate synaptic transmission in the stratum oriens (SO) and lacunosum-moleculare (SLM) of the dCA1 area, but not in the stratum radiatum (SR). We also observe CFE-specific structural changes of excitatory synapses and expression of the synaptic scaffold protein, PSD-95, in both strata innervated by RE, but not in SR. Interestingly, only the changes in SLM are specific for the dendrites innervated by RE. To further support the role of the RE→dCA1 projection in CFE, we demonstrate that brief chemogenetic inhibition of the RE→dCA1 pathway during a CFE session persistently impairs the formation of CFE memory and CFE-induced changes of PSD-95 levels in SLM. Thus, our data indicate that RE participates in CFE by regulating CFE-induced molecular remodeling of dCA1 synapses.
Electrons interacting with Goldstone modes and the rotating frame
Authors: Vasiliou Konstantinos , He Yuchi , Bultinck Nick
Published: January 2024

We consider electronic systems with a spontaneously broken continuous symmetry. The scattering vertex between electrons and Goldstone modes is calculated over the entire Brillouin zone using the random phase approximation. This calculation reveals two things: (1) electrons always couple to both ϕ and ∂tϕ, where ϕ is the Goldstone field, and (2) quasiparticles in a state with continuous symmetry breaking have to be defined in a rotating frame, which locally follows the fluctuations of the order parameter. The implications of these findings for electron spectral functions in both symmetry-broken and thermally disordered systems are discussed, and the examples of antiferromagnetism in the Hubbard model and spin spiral order in the three-band model are worked out in detail.

Published by the American Physical Society
2024