bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractNeuronal 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

Abstract5-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

AbstractExplaining 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.SignificanceThe 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

ABSTRACTConjugative 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

AbstractNeural 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

ABSTRACTFood 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

SUMMARYPathogenic 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

AbstractBackgroundDuring 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.MethodologyTo 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.ResultsPCPA 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

AbstractTor 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

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

AbstractIn 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

AbstractA 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

AbstractNociceptors 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.