bluuebunny/crossref_metadata_2025 huggingface dataset:
Place field precision during an episode predicts place field fate across episodes
Authors: Chiu YuHung , Dong Can , Krishnan Seetha , Sheffield Mark E.J.
Published: June 2023

Spatial memories are represented by hippocampal place cells during navigation. This spatial code is dynamic, undergoing changes across time – known as drift – and across changes in internal state, even while navigating the same spatial environment with consistent behavior. A dynamic spatial code may be a way for the hippocampus to track distinct episodes that occur at different times or during different internal states and update spatial memories. Changes to the spatial code include place fields that remap to new locations and place fields that vanish, while others are stable. However, what determines place field fate across episodes remains unclear. We measured the lap-by-lap properties of place cells in mice during navigation for a block of trials in a rewarded virtual environment. We then had mice navigate the same spatial environment for another block of trials either separated by a day (a distinct temporal episode) or during the same session but with reward removed to change reward expectation (a distinct internal state episode). We found that, as a population, place cells with remapped place fields across episodes had lower spatial precision during navigation in the initial episode. Place cells with stable or vanished place fields generally had higher spatial precision. We conclude that place cells with less precise place fields have greater spatial flexibility, allowing them to respond to, and track, distinct episodes in the same spatial environment, while place cells with precise place fields generally preserve spatial information when their fields reappear.
The molecular prognostic score, a classifier for risk stratification of high-grade serous ovarian cancer
Authors: Sarkar Siddik , Saha Sarbar Ali , Sarkar Poulomi , Banerjee Sarthak , Mitra Pralay
Published: June 2023

The clinicopathological parameters such as residual tumor, grade, FIGO score are often used to predict the survival of ovarian cancer patients, but the 5-year survival of high grade serous ovarian cancer (HGSOC) still remains around 30%. In recent years, a gene expression based molecular prognostic score (mPS) was developed that showed improved prognosis in several cancers including ovarian cancer.

The feature extraction using LASSO-Cox regression was applied on the training data with 10-fold cross validation to obtain 20 predictor genes along with the coefficients to derive mPS. The mPS based prognosis of HGSOC patients was validated using the log-rank test and receiver operator characteristic curve.

The AUC of 20 gene-based mPS in predicting the 5-year overall survival was around 0.7 in both the training (n=491) and test datasets (n=491). It was also validated across HGSOC patients (n=7542), data collected from the Ovarian Tumor Tissue Analysis (OTTA) consortium. The mPS showed significant impact (adjusted HR = 6.1, 95% CI of HR= 3.65-10.3; p <0.001) on prognosis of HGSOC. The performance of mPS for the prognosis of survival of HGSOC was substantially better than conventional parameters: FIGO (adjusted HR=1.1, 95% CI=0.97-1.2, p=0.121), residual disease (adjusted HR=1.3, 95% CI= 1.13-1.4, p<0.001), and age (adjusted HR=1.2, 95% CI= 0.98-1.6, p=0.08). It was found that focal-adhesion, Wnt and Notch signaling pathways were significantly (p<0.001) upregulated, whereas antigen processing and presentation (p<0.001) was downregulated in high risk HGSOC cohorts based on mPS stratification.

The molecular prognostic score derived from 20-gene signature is found to be the novel robust prognostic marker of HGSOC. It could potentially be harnessed in clinical settings to determine the overall survival of ovarian cancer. The high risk HGSOC patients based on mPS stratification could be benefited from alternative therapies targeting Wnt/ Notch signaling pathways and also immune evasion.

Author summary

The 20-gene signature based molecular prognostic score (mPS) was found to be associated with risk stratification and hence, predicting the overall survival time of HGSOCs. It was applicable in all training HGSOC datasets and across RNA sequencing platforms that also includes the previous reported studies in HGSOC cohorts (Millstein et al., 2020; Talhouk et al., 2020). The 20-gene signature based mPS for the prognosis of overall survival of HGSOC outperformed conventional parameters: age, residual disease and FIGO score. The high or increased risk group of HGSOC based on our mPS stratification was found to have dysregulated pathways of Wnt, Notch, Akt signaling, and antigen presentation. Thus, treatments targeting these pathways might be beneficial for high risk HGSOC and hence anticipated to improve the over-all survival of HGSOC.
Comparative population genomics of manta rays has global implications for management
Authors: Humble Emily , Hosegood Jane , Carvalho Gary , de Bruyn Mark , Creer Simon , Stevens Guy M W , Armstrong Amelia , Bonfil Ramon , Deakos Mark , Fernando Daniel , Froman Niv , Peel Lauren R , Pollett Stephen , Ponzo Alessandro , Poquita Allan L , Stewart Joshua D , Wintner Sabine , Ogden Rob
Published: June 2023

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and thatM. birostrispopulations display higher connectivity worldwide. Through inferring modes of colonisation, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.
PI3K/AKT signalling orchestrates ICM maturation and proper epiblast and primitive endoderm specification
Authors: Geiselmann Anna , Micouin Adèle , Vandormael-Pournin Sandrine , Laville Vincent , Mella Sébastien , Navarro Pablo , Cohen-Tannoudji Michel
Published: June 2023

The inner cell mass (ICM) of early mouse embryos is specified into Epiblast (Epi) and primitive endoderm (PrE) lineages during blastocyst formation. The antagonistic transcription factors (TFs) NANOG and GATA6 in combination with FGF/ERK signalling are central actors in ICM fate choice. However, what initiates the specification of ICM progenitors and whether other factors are involved in this process is not fully understood yet. Here, we show that PI3K/AKT is constitutively active during preimplantation development. Using pharmacological inhibition, we demonstrate that PI3K/AKT enables the formation of a functional ICM capable of giving rise to both the EPI and the PrE: it maintains the expression of the TF NANOG, which specifies the EPI, and confers responsiveness to FGF4, which is essential for PrE specification. Our observations thus identify PI3K/AKT signalling as an upstream regulator orchestrating the molecular events required for both EPI and PrE specification.
Murine Gammaherpesvirus 68 Efficiently Infects Myeloid Cells Resulting In An Atypical, Restricted Form Of Infection
Authors: Vragel Gabrielle , Gomez Brittany D. , Kostelecky Rachael E. , Noell Kyra S. , Tseng Ashley , Cohen Shirli , Dalwadi Manaal , Medina Eva M. , Nail Elizabeth A. , Goodspeed Andrew , Clambey Eric T. , van Dyk Linda F.
Published: June 2023

The gammaherpesviruses (γHVs) establish a lifelong infection in their hosts, with the cellular outcome of infection intimately regulated by target cell type. Murine gammaherpesvirus 68 (MHV68), a small animal model of γHV infection, infects macrophages in vivo, resulting in a range of outcomes, from lytic replication to latent infection. Here, we have further investigated the nature of MHV68 macrophage infection using reductionist and primary in vivo infection studies. While MHV68 readily infected the J774 macrophage cell line, viral gene expression and replication were significantly impaired relative to a fully permissive fibroblast cell line. Lytic replication only occurred in a small subset of MHV68-infected J774 cells, despite the fact that these cells were fully competent to support lytic replication following pre-treatment with interleukin-4, a known potentiator of replication in macrophages. In parallel, we harvested virally-infected macrophages at 16 hours after MHV68 infectionin vivoand analyzed gene expression by single cell RNA-sequencing. Among virally infected macrophages, only rare (0.25%) cells had lytic cycle gene expression, characterized by detection of multiple lytic cycle RNAs. In contrast, ∼50% of virally-infected macrophages were characterized by expression of ORF75A, ORF75B and/or ORF75C, in the absence of other detectable viral RNAs. Selective transcription of the ORF75 locus also occurred in MHV68-infected J774 cells. In total, these studies indicate that MHV68 efficiently infects macrophages, with the majority of cells characterized by an atypical state of restricted viral transcription, and only rare cells undergoing lytic replication.

Importance

The human gammaherpesviruses Epstein-Barr virus and Kaposi’s sarcoma associated herpesvirus are DNA viruses that cause lifelong infection and are associated with multiple diseases, especially in immunocompromised individuals. Murine gammaherpesvirus 68 (MHV68) is a powerful mouse model that permits close examination of these viruses. Previous studies of MHV68 identified that macrophages are an important in vivo target of infection; how infection within these cells is regulated remains incompletely understood. Here, we demonstrate that MHV68 infection of macrophages is characterized by two divergent outcomes across a population of infected cells: while a small subset of cells undergo lytic replication, to make new virus progeny, the majority of cells are characterized by an atypical, restricted form of infection characterized by a distinct viral gene transcription program not previously reported. These studies highlight important cell-type specific outcomes of gammaherpesvirus infection and identify a potential alternate program by which these viruses usurp macrophages.
Increased error rate and delayed response to negative emotional stimuli in antisaccade task in obsessive-compulsive disorder
Authors: Khayrullina Guzal , Martynova Olga , Panfilova Elizaveta
Published: June 2023

Ample evidence links impaired inhibitory control, attentional distortions, emotional dysregulation, and obsessive-compulsive disorder (OCD). However, it remains unclear what underlies the deficit that triggers the OCD cycle. The present study used an antisaccade paradigm with emotional stimuli to compare eye movement patterns reflecting inhibitory control and attention switching in OCD and healthy control groups. Thirty-two patients with OCD and thirty healthy controls performed the antisaccade task with neutral, positive, and negative visual images. The groups differed significantly in the number of errors to negative stimuli. The latency of correct antisaccades varied between valences in OCD group when negative and neutral stimuli served as target ones. The OCD group showed more errors to negative stimuli than the control group and they also performed antisaccades more slowly to negative and neutral stimuli than positive ones. Other patterns, including mean velocity of correct antisaccades and anticipatory saccades, did not differ between groups. The mean velocity of correct antisaccades was higher for negative and positive stimuli than for neutral stimuli; however, there were more anticipatory saccades for neutral stimuli than for negative and positive stimuli in both groups. The peak velocity parameter did not show any differences either between groups or between valences. The findings support a hypothesis that an attentional bias towards threatening stimuli interferes with inhibitory control in OCD.
A transient protein folding response targets aggregation in the early phase of TDP-43-mediated disease
Authors: Gil Rebecca San , Pascovici Dana , Venturato Juliana , Brown-Wright Heledd , Mehta Prachi , Madrid San Martin Lidia , Wu Jemma , Chui Yi Kit , Bademosi Adekunle T. , Swaminathan Shilpa , Luan Wei , Berning Britt A. , Wright Amanda L. , Keating Sean S. , Lee Albert , Morsch Marco , Chung Roger S. , Lisowski Leszek , Mirzaei Mehdi , Walker Adam K.
Published: June 2023

Understanding the mechanisms that drive TDP-43 pathology is integral to combating neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). To address this, we sought to determine the timeline of proteomic alterations across disease course in TDP-43 proteinopathy. Using longitudinal quantitative proteomics analysis of cortex samples from the cytoplasmic TDP-43 rNLS8 mouse model of ALS and FTLD, we identified several distinct protein subsets characterized by temporal alterations in protein abundance across diverse biological pathways, including protein folding, intracellular transport, myelination, and neuronal synaptic function. Remarkably, neurons in the rNLS8 cortex elicited a transitory response primarily comprising protein-folding factors prior to and in the earliest stages of disease progression. This response included increased levels of DnaJ homolog subfamily B member 5, DNAJB5, and proof-of-concept studies showed that DNAJB5 over-expression decreased TDP-43 aggregation in cell and cortical neuron cultures. Conversely, knockout ofDnajb5exacerbated motor impairments caused by AAV-mediated cytoplasmic TDP-43 expression in the brains and spinal cords of mice. Lastly, the late disease proteomic signatures of rNLS8 mouse cortex strongly correlated with changes in human autopsy-derived TDP-43 proteinopathy tissues, indicating commonality of disease processes. Together, these findings reveal molecular mechanisms that regulate protein levels through distinct stages of ALS and FTLD progression, and suggest that protein folding factors that combat cytoplasmic TDP-43 protein aggregation could be protective in disease.

Highlights

The first longitudinal map of the cortex proteome throughout TDP-43-driven disease in a mouse model of cytoplasmic TDP-43 proteinopathy (rNLS8 mice).

Cytoplasmic TDP-43 accumulation drives many dynamic changes to the cortex proteome, including increases in protein folding factors prior to disease onset.

The protein folding factor DNAJB5 decreases TDP-43 aggregation in HEK293 cells and primary cortical neurons andDnajb5knockout exacerbates cytoplasmic TDP-43-associated motor impairmentsin vivo.

The proteomic signature of the rNLS8 mouse cortex correlates strongly with postmortem brain tissue from human TDP-43 proteinopathies.

A new webtool, ‘TDP-map’ (https://shiny.rcc.uq.edu.au/TDP-map/), allows comparison of transcriptomic and proteomic datasets from mouse and human TDP-43 proteinopathy.
Reduced Reverse Replay in Anxious Individuals Impairs Reward Prediction
Authors: Yu Qianqian , Luo Yuejia , Dolan Ray , Ou Jianxin , Huang Chuwen , Wang Haiteng , Xiao Zhibing , Liu Yunzhe
Published: June 2023

Anxiety traits can manifest as a tendency to overlook positive information, impacting memory and decision-making. Using EEG-based neural decoding, we examined future reward prediction in participants with varying levels of trait anxiety. In a resting period, following value learning, we found an increase in reverse replay for a task sequence that led to reward. This reward-related replay was significantly reduced within individuals exhibiting higher trait anxiety. Furthermore, this reduction correlated with a distorted neural representation of the reward-predictive sequence, an effect mirrored behaviorally in an attenuated preference for stimuli within the same sequence. These findings indicate that higher trait anxiety may impede formation of reward-predictive representations by reducing offline replay during rest. More broadly, our demonstration of sequential replay using EEG enables examination of offline learning and memory consolidation in wider populations, particularly those with psychopathology.
Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking
Authors: Jeppesen Mads , André Ingemar
Published: June 2023

AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic – tetrahedral, octahedral and icosahedral – symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 21 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.71. 15 had TM-scores of above 0.8 and were categorized as high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.
GDF15 is a Critical Renostat in the Defense Against Hypoglycemia
Authors: Li Zongyu , Zhang Xinyi , Zhu Wanling , Xu Qian , Yu Chuyue , Zhao Qiancheng , Siebel Stephan , Zhang Cuiling , Costa Lima Bruna Genisa , Li Xiruo , Israni-Winger Kavita , Nasiri Ali R. , Caplan Michael J. , Chang Rui B. , Wang Andrew , Belfort de Aguiar Renata , Hwang Janice J. , Perry Rachel J.
Published: June 2023

Episodic hypoglycemia is one of the best honed, evolutionary conserved phenomena in biology, because of the constant feast-fast cycles that have characterized most of history. The counterregulatory response to hypoglycemia, mobilizing substrate stores to produce glucose, is the primary adaptive mechanism to enable survival. Catecholamines and glucagon have long been considered the key hypoglycemia counterregulatory hormones, but here we identify a new hypoglycemia counterregulatory factor. We employed the insulin tolerance test (ITT) and hyperinsulinemic-hypoglycemic clamp to mimic the two common settings in which hypoglycemia can occur in patients: postprandial insulin overdose and elevated basal insulin administration, respectively. We found that Growth Differentiation Factor 15 (GDF15) production is induced in the S3 segment of the renal proximal tubules and its release increases hepatic gluconeogenesis by increasing intrahepatic lipolysis in a beta-adrenergic receptor-2 (Adrb2)-dependent manner. In addition, mice exposed to recurrent hypoglycemia and patients with T1D exhibit impaired GDF15 production in the setting of hypoglycemia. These data demonstrate that GDF15 acts acutely as a gluco-counterregulatory hormone and identify a critical role for kidney-derived GDF15 in glucose homeostasis under physiological and pathophysiological conditions.
Functional stress responses in Glaucophyta: evidence of ethylene and abscisic acid functions inCyanophora paradoxa
Authors: Genot Baptiste , Grogan Margaret , Yost Matthew , Iacono Gabriella , Archer Stephen D. , Burns John A.
Published: June 2023

Glaucophytes, an enigmatic group of freshwater algae, occupy a pivotal position within the Archaeplastida, providing insights into the early evolutionary history of plastids and their host cells. These algae possess unique plastids, known as cyanelles, that retain certain ancestral features, enabling a better understanding of the plastid transition from cyanobacteria. In this study, we investigated the role of ethylene, a potent hormone used by land plants to coordinate stress responses, in the glaucophyte algaCyanophora paradoxa.We demonstrate thatC. paradoxaproduces gaseous ethylene when supplied with exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor in land plants. In addition, we show that cells produce ethylene natively in response to abiotic stress, and that another plant hormone, abscisic acid (ABA), interferes with ethylene synthesis from exogenously supplied ACC, while positively regulating reactive oxygen species (ROS) accumulation. ROS synthesis also occurred following abiotic stress and ACC treatment, possibly acting as a second-messenger in stress responses. A physiological response ofC. paradoxato ACC treatment is growth inhibition. Using transcriptomics, we reveal that ACC treatment induces the upregulation of senescence-associated proteases, consistent with the observation of growth inhibition. This is the first report of hormone usage in a glaucophyte alga, extending our understanding of hormone-mediated stress response coordination into the Glaucophyta, with implications for the evolution of signaling modalities across Archaeplastida.
Identification and Characterization of CtUGT3 as the Key Player of Astragalin Biosynthesis in Safflower
Authors: Ren Chaoxiang , Xi Ziqing , Xian Bin , Chen Chao , Huang Xulong , Jiang Huajuan , Chen Jiang , Peng Cheng , Pei Jin
Published: June 2023

Safflower (Carthamus tinctoriusL.) flowers are used as a traditional Chinese medicine for a long history. Flavonoids are the main bioactive components in safflower flowers, and most of them exist in the form of flavonoid glycosides. Only few glycosyltransferases have been identified in safflower. To reveal the uridine diphosphate glycosyltransferase (UGT) involved in flavonoid glycosides biosynthesis in safflower, a metabolomics and transcriptome analysis was performed by using the flowers under different light qualities treatments. Three differentially expressedUGTgenes were screened, and their expressions were significantly related with concentrations of 9 flavonoidO-glycosides. Safflower corolla protoplasts were further used to confirm flavonoidO-glycosylation ability of UGT candidates. The astragalin (kaempferol 3-O-glucoside) content was only significantly increased when CtUGT3 was overexpressed in protoplasts. The biochemical properties and kinetic parameters of CtUGT3 were determined. CtUGT3 also showed flavonoid 3-OH and 7-OH glycosylation activitiesin vitro. Molecular modeling and site-directed mutagenesis revealed that E384 and S276 were critical catalytic residues for the 3-OH glycosylation of CtUGT3. These results demonstrate that CtUGT3 has a flavonoid 3-OH glycosylation function and is involved in the biosynthesis of astragalin in safflower. This study provides insights into the catalytic mechanisms of flavonoidO-glycosyltransferases, and makes a reference for flavonoid biosynthesis genes research in medicinal plants.
CRISPR/Cas9 gene editing to generateDrosophilaLexA lines in secondary school classes
Authors: Rankin Anne E. , Fox Elizabeth , Chisholm Townley , Lantz Nicole , Rajan Arjun , Phillips William , Griffin Elizabeth , Harper Jaekeb , Suhr Christopher , Tan Max , Wang Jason , Yang Alana , Kim Ella S. , Ankrah Naa Kwama A. , Chakraborty Praachi , Lam Alistair C. K. , Laws Madeleine E. , Lee Jackson , Park Kyle , Wesel Emily , Covert Peter H. , Kockel Lutz , Park Sangbin , Kim Seung K.
Published: June 2023

Genome editingin vivowith CRISPR/Cas9 generates powerful tools to study gene regulation and function. We developed CRISPR-based methods that permitted secondary school student scientists to convertDrosophilaGAL4 lines to LexA lines. Our novel curricula implement a new donor strain optimizing Homology-assisted CRISPR knock-in (HACK) that simplifies screening using light microscopy. Successful curricula adoption by a consortium of schools led to the generation and characterization of 16 novel LexA lines. This includes extensive comparative tissue expression analysis between the parental Gal4 and derived LexA lines. From this collaboration, we established a workflow to systematically generate LexA lines from frequently-used GAL4 lines. Modular courses developed from this effort can be tailored to specific secondary school scheduling needs, and serve as a template for science educators to innovate courses and instructional goals. Our unique collaborations highlight that resources and expertise harnessed by university-based research laboratories can transform experiential science instruction in secondary schools while addressing research needs for the community of science.
α-tubulin regulation by 5’ introns inS. cerevisiae
Authors: Wethekam Linnea C. , Moore Jeffrey K.
Published: June 2023

Across eukaryotic genomes, multiple α- and β-tubulin genes require regulation to ensure sufficient production of tubulin heterodimers. Features within these gene families that regulate expression remain underexplored. Here we investigate the role of the 5’ intron in regulating α-tubulin expression inS. cerevisiae. We find that the intron in the α-tubulin,TUB1, promotes α-tubulin expression and cell fitness during microtubule stress. The role of theTUB1intron depends on proximity to theTUB1promoter and sequence features that are distinct from the intron in the alternative α-tubulin isotype,TUB3. These results lead us to perform a screen to identify genes that act with theTUB1intron. We identified several genes involved in chromatin remodeling, α/β-tubulin heterodimer assembly, and the spindle assembly checkpoint. We propose a model where theTUB1intron promotes expression from the chromosomal locus, and that this may represent a conserved mechanism for tubulin regulation under conditions that require high levels of tubulin production.

Article Summary

α and β-tubulin proteins are encoded by families of genes that must be coordinately regulated to supply the αβ heterodimers that form microtubules. This study by Wethekam and Moore identifies a role for the early intron in the budding yeast α-tubulin, TUB1, in promoting gene function. A genetic screen reveals new tubulin regulators that act through the TUB1 intron. The results establish new layers of α-tubulin regulation that may be conserved across eukaryotes.
Overexpression of MUC1 influences the anti-proliferative effect of STAT3-inhibitor Napabucasin in epithelial cancers
Authors: Bose Mukulika , Sanders Alexa , Handa Aashna , Vora Aabha , Brouwer Cory , Mukherjee Pinku
Published: June 2023

MUC1 is a transmembrane glycoprotein that is overexpressed and aberrantly glycosylated in epithelial cancers. The cytoplasmic tail of MUC1 (MUC1 CT) aids in tumorigenesis by upregulating the expression of multiple oncogenes. Signal transducer and activator of transcription 3 (STAT3) plays a crucial role in several cellular processes and is aberrantly activated in many cancers. In this study, we focus on recent evidence suggesting that STAT3 and MUC1 regulate each other’s expression in cancer cells in an auto-inductive loop and found that their interaction plays a prominent role in mediating epithelial-to-mesenchymal transition (EMT) and drug resistance. The STAT3 inhibitor Napabucasin was in clinical trials but was discontinued due to futility. We found that higher expression of MUC1 increased the sensitivity of cancer cells to Napabucasin. Therefore, high-MUC1 tumors may have a better outcome to Napabucasin therapy. We report how MUC1 regulates STAT3 activity and provide a new perspective on repurposing the STAT3-inhibitor Napabucasin to improve clinical outcome of epithelial cancer treatment.
Stereoscopic RNA Analysis of Transcriptional and Post-transcriptional Regulation
Authors: Lee Seungha Alisa , Kwak Hojoong
Published: June 2023

Regulation of gene expression takes place at multiple stages of RNA synthesis, processing, and decay. The dynamics of RNA processing is an essential layer of RNA regulation, required for a deeper understanding of gene expression. Here, we present a streamlined analysis combining nascent RNA sequencing and poly(A) tail length sequencing methods, named Stereoscopic Analysis of Transcriptome (STOAT). Using this analysis, we were able to redefine known and unknown transcripts with high precision, and quantitatively assess RNA expression and stability. We also investigated poly(A) tail processing and their linkage to post-transcriptional features in different cell lines and identified the diversity of microRNA networks in RNA stability and opposing effects of HuR-TTP on poly(A) processing among human cell lines. This method can effectively measure promoter activity, RNA synthesis, poly(A) processing, stability, and decay, providing a comprehensive perspective of the dynamic transcriptome as well as discovering diverse transcript isoforms.

MOTIVATION

RNA sequencing (RNA-seq) enables transcriptome-wide mapping and quantitative analysis, but it only provides a static view of the transcriptome. Also, due to its lack of standardization between sequencing platforms and read depth, it compromises reproducibility, and the cost remains prohibitive. To improve these limitations, we are presenting the minimal combination of two methods, nascent RNA sequencing and poly(A) tail length sequencing, which can effectively measure promoter activity, RNA synthesis, abundance, poly(A) processing, stability, and decay, and can discover diverse undefined transcript isoforms. This streamlined analysis of transcription rate and polyadenylation status will provide a comprehensive perspective of the dynamic transcriptome.
Essential Function of Transmembrane Transcription Factor MYRF in Promoting Transcription of miRNAlin-4duringC. elegansDevelopment
Authors: Xu Zhimin , Wang Zhao , Wang Lifang , Qi Yingchuan B.
Published: June 2023

Precise developmental timing control is essential for organism formation and function, but its mechanisms are unclear. InC. elegans, the microRNAlin-4critically regulates developmental timing by post-transcriptionally downregulating the larval-stage-fate controller LIN-14. However, the mechanisms triggering the activation oflin-4expression toward the end of the first larval stage remain unknown. We demonstrate that the transmembrane transcription factor MYRF-1 is necessary forlin-4activation. MYRF-1 is initially localized on the cell membrane, and its increased cleavage and nuclear accumulation coincide withlin-4expression timing. MYRF-1 regulateslin-4expression cell-autonomously and hyperactive MYRF-1 can prematurely drivelin-4expression in embryos and young first-stage larvae. The tandemlin-4promoter DNA recruits MYRF-1GFPto form visible loci in the nucleus, suggesting that MYRF-1 directly binds to thelin-4promoter. Our findings identify a crucial link in understanding developmental timing regulation and establish MYRF-1 as a key regulator oflin-4expression.
Retrospective Evaluation of the Eye Irritation Potential of Agrochemical Formulations
Authors: Choksi Neepa , Latorre Andreia , Catalano Shadia , Grivel Arthur , Baldassari James , Pires Janaina , Corvaro Marco , Silva Mariana , Ogasawara Maryanne , Inforzato Monique , Habe Priscila , Murata Rosana , Stinchcombe Stefan , Kolle Susanne , Masinja W. , Perjessy Gisele , Daniel Amber , Allen David
Published: June 2023

While multiplein vitroeye irritation methods have been developed and adopted as OECD health effects test guidelines, only one is considered a complete replacement for thein vivorabbit eye test for classification and labelling for eye irritation hazard. Additionally, for most of the adopted methods there is a data gap on the applicability to predict the ocular irritation potential of agrochemical formulations. To overcome this data gap, a retrospective evaluation of 192 agrochemical formulations within vivo(OECD TG 405) orin vitro(OECD TG 437, 439, or 492) data was conducted to determine if thein vitromethods could accurately assign United Nations Globally Harmonized System for Classification and Labelling of Chemicals (GHS) eye irritation hazard classifications. In addition, for each of the final formulations and their individual components, we also conducted an evaluation of the GHS concentration threshold (CT) approach. The results herein suggest that the four individual methods and GHS CT approach were highly predictive of formulations that would not require classification for eye irritation hazard. Given most agrochemical formulations fall into this category, methods that accurately identify not classified mixtures could significantly reduce the use of animals for this endpoint.
hnRNPM and ELAVL1 control type I interferon induction by promoting IRF3 phosphorylation downstream of both cGAS and RIG-I
Authors: Kirchhoff Alexander , Herzner Anna-Maria , Urban Christian , Piras Antonio , Düster Robert , Wegner Julia , Grünewald Agathe , Schlee-Guimarães Thais M. , Ciupka Katrin , Leka Petro , Bootz Robert J. , de Regt Ann Kristin , Kümmerer Beate M. , Christensen Maria Hønholt , Schmidt Florian I. , Günther Claudia , Kato Hiroki , Bartok Eva , Hartmann Gunther , Geyer Matthias , Pichlmair Andreas , Schlee Martin
Published: June 2023

RIG-I and cGAS are crucial sensors of viral nucleic acids and induce type I IFNs via TBK1/IKK and IRF3. Here, we have identified hnRNPM as a novel positive regulator of IRF3 phosphorylation and type I IFN induction downstream of both cGAS and RIG-I. Combining interactome analysis and genome editing, we further identified ELAVL1 as an immune-relevant interactor of hnRNPM. Depletion of hnRNPM or ELAVL1 impaired type I IFN induction by HSV-1 and SeV. In addition, we found that hnRNPM and ELAVL1 interact with TBK1 and NF-kB p65. Confocal microscopy revealed cytosolic and perinuclear interactions between hnRNPM, ELAVL1, and TBK1. To our knowledge, hnRNPM and ELAVL1 represent the first non-redundant signaling components merging the cGAS-STING and RIG-I-MAVS pathways, thus representing a novel platform that fuels antiviral defense.
Interactive effects of salinity, temperature and food web configuration on performance and harmfulness of the raphidophyteHeterosigma akashiwo
Authors: Giesler Jakob Karl , Lemley Daniel Alan , Adams Janine Barbara , Moorthi Stefanie Devi
Published: June 2023

The cosmopolitan raphidophyteHeterosigma akashiwocommonly forms harmful algal blooms (HABs) in diverse estuaries discharging into Algoa Bay, South Africa, potentially leading to hypoxia, fish kills and a decline in key primary consumers. Despite the high environmental variability in these estuaries, little is known about how abiotic factors such as temperature and salinity constrain bloom formation and harmfulness ofH. akashiwo. The present study therefore investigates growth, competition, and grazing interactions of H. akashiwo in laboratory experiments in response to two naturally relevant levels of salinity (15, 30) and temperature (16, 22°C), respectively. Experiments were set up with the naturally co-occurring dinoflagellate competitorHeterocapsa rotundataand two estuarine microzooplankton consumers, i.e., nauplii of the copepodAcartia tonsaand the rotiferBrachionus plicatilis. In monoculture,H. akashiwogrowth was promoted at high temperature – low salinity conditions, whileH. rotundatathrived under low temperature – high salinity conditions. In polyculture,H. akashiwodominated at high temperature irrespective of the salinity regime, while at low temperature, it only dominated at low salinity and was suppressed byH. rotundataat high salinity. Grazing assays revealed highly negative effects ofH. akashiwoon copepod nauplii survival and growth as well as mucus-induced immobilization, especially at high temperatures in combination with low salinity, while the estuarine adapted rotifers showed highest mortalities at the higher salinity level. The presence ofH. rotundatasignificantly alleviated the harmful effects ofH. akashiwoon both grazers, and the selectively feeding copepod nauplii actively avoidedH. akashiwowhen non-harmful prey was present. Overall, this study demonstrates that population dynamics and harmful effects ofH. akashiwoare interactively determined by both abiotic conditions and food web configuration, implying competitor and consumer specific tolerances to the abiotic environment and their susceptibility to the harmful algaH. akashiwo.
The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genusCacajao)
Authors: Silva Felipe Ennes , Luna Leilton Willians , Batista Romina , Röhe Fabio , Gubili Chrysoula , Farias Izeni P. , Hrbek Tomas , do Amaral João Valsecchi , Ribas Camila C. , McDevitt Allan D. , Dellicour Simon , Flot Jean-François , Boubli Jean P.
Published: June 2023

Aim

Western Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia.

Location

Western Amazonia

Taxon

The uakari monkey (genusCacajao)

Methods

We performed a continuous phylogeographic analysis using 77 cytochromebsequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution ofCacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in threeCacajaospecies that were impacted by river rearrangements.

Results

Our continuous phylogeographical reconstruction points that the ancestralCacajaolineage occupied the flooded forests of the Solimões River at ∼1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure inCacajao. The demographic analysis indicates thatC. calvus, C. amuna, andC. rubicunduswent through a population decline in the last 70 Kya and have a low effective population size.

Main conclusion

Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently divergedCacajaolineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated someCacajaopopulations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.
Mitochondrial fusion and altered beta-oxidation drive muscle wasting in aDrosophilacachexia model
Authors: Dark Callum , Ali Nashia , Golenkina Sofia , Blazev Ronnie , Parker Benjamin L , Murphy Katherine , Lynch Gordon , Senapati Tarosi , Millard S Sean , Judge Sarah M , Judge Andrew R , Cheng Louise Y
Published: June 2023

Cancer cachexia is a tumour-induced wasting syndrome, characterised by extreme loss of skeletal muscle. Defective mitochondria can contribute to muscle wasting; however, the underlying mechanisms remain unclear. Using aDrosophilalarval model of cancer cachexia, we observed enlarged and dysfunctional muscle mitochondria. Morphological changes were accompanied by upregulation of beta-oxidation proteins and depletion of muscle glycogen and lipid stores. Muscle lipid stores were also decreased in Colon-26 adenocarcinoma mouse muscle samples, and expression of the beta-oxidation geneCPT1Awas negatively associated with muscle quality in cachectic patients. Mechanistically, mitochondrial defects result from reduced muscle insulin signalling, downstream of tumour-secreted insulin growth factor binding protein (IGFBP) homolog ImpL2. Strikingly, muscle-specific inhibition of Forkhead box O (FOXO), mitochondrial fusion, or beta-oxidation in tumour-bearing animals preserved muscle integrity. Finally, dietary supplementation with nicotinamide or lipids, improved muscle health in tumour-bearing animals. Overall, our work demonstrates that muscle FOXO, mitochondria dynamics/beta-oxidation and lipid utilisation are key regulators of muscle wasting in cancer cachexia.
The evolution of cooperation in the unidirectional division of labor on a tree network
Authors: Nirjhor Md Sams Afif , Nakamaru Mayuko
Published: June 2023

Division of labour on complex networks is rarely investigated using evolutionary game theory. We investigate a division of labour where divided roles are assigned to groups on the nodes of a general unidirectional finite tree graph network. From the network’s original node, a task flows and is divided along the branches. A player is randomly selected in each group of cooperators and defectors, who receives a benefit from a cooperator in the upstream group and a part of the task. A cooperator completes their part by paying a cost and then passing it downstream until the entire task is completed. Defectors do not do anything and the division of labour stops, causing all groups to suffer losses due to the incomplete task. We develop a novel method to analyse the local stability in this general tree. We discover that not the benefits but the costs of the cooperation influence the evolution of cooperation, and defections in groups that are directly related to that group’s task cause damage to players in that group. We introduce two sanction systems one of which induces the evolution of cooperation more than the system without sanctions and promote the coexistence of cooperator and defector groups.
Timecourse and source localization of abstract and concrete semantic representations
Authors: Vignali Lorenzo , Xu Yangwen , Turini Jacopo , Collignon Olivier , Crepaldi Davide , Bottini Roberto
Published: June 2023

Dual coding theories of knowledge suggest that meaning is represented in the brain by a double code, which comprises language-derived representations in the Anterior Temporal Lobe and sensory-derived representations in perceptual and motor regions. This approach predicts that concrete semantic features should activate both codes, whereas abstract features rely exclusively on the linguistic code. Using magnetoencephalography (MEG), we adopted a temporally resolved multiple regression approach to identify the contribution of abstract and concrete semantic predictors to the underlying brain signal. Results evidenced early involvement of anterior-temporal and inferior-frontal brain areas in both abstract and concrete semantic information encoding. At later stages, occipito-temporal regions showed greater responses to concrete compared to abstract features. The present findings shed new light on the temporal dynamics of abstract and concrete semantic representations in the brain and suggest that the concreteness of words processed first with a transmodal/linguistic code, housed in frontotemporal brain systems, and only after with an imagistic/sensorimotor code in perceptual and motor regions.
A weighted generative model of the human connectome
Authors: Akarca Danyal , Schiavi Simona , Achterberg Jascha , Genc Sila , Jones Derek K. , Astle Duncan E.
Published: June 2023

Probabilistic generative network models have offered an exciting window into the constraints governing the human connectome’s organization. In particular, they have highlighted the economic context of network formation and the special roles that physical geometry and self-similarity likely play in determining the connectome’s topology. However, a critical limitation of these models is that they do not consider the strength of anatomical connectivity between regions. This significantly limits their scope to answer neurobiological questions. The current work draws inspiration from the principle of redundancy reduction to develop a novel weighted generative network model. This weighted generative network model is a significant advance because it not only incorporates the theoretical advancements of previous models, but also has the ability to capture the dynamic strengthening or weakening of connections over time. Using a state-of-the-art Convex Optimization Modelling for Microstructure-Informed Tractography (COMMIT) approach, in a sample of children and adolescents (n= 88, aged 8 to 18 years), we show that this model can accurately approximate simultaneously the topology and edge-weights of the connectome (specifically, the MRI signal fraction attributed to axonal projections). We achieve this at both sparse and dense connectome densities. Generative model fits are comparable to, and in many cases better than, published findings simulating topology in the absence of weights. Our findings have implications for future research by providing new avenues for exploring normative developmental trends, models of neural computation and wider conceptual implications of the economics of connectomics supporting human functioning.
Multi-trait GWAS for diverse ancestries: Mapping the knowledge gap
Authors: Troubat Lucie , Fettahoglu Deniz , Henches Léo , Aschard Hugues , Julienne Hanna
Published: June 2023

Background

Approximately 95% of samples analyzed in univariate genome-wide association studies (GWAS) are of European ancestry. This bias toward European ancestry populations in association screening also exists for other analyses and methods that are often developed and tested on European ancestry only. However, existing data in non-European populations, which are often of modest sample size, could benefit from innovative approaches as recently illustrated in the context of polygenic risk scores.

Methods

Here, we extend and assess the potential limitations and gain of our multi-trait GWAS pipeline,JASS(JointAnalysis ofSummaryStatistics), for the analysis of non-European ancestries. To this end, we conducted the joint GWAS of 19 hematological traits and glycemic traits across five ancestries (European (EUR), admixed American (AMR), African (AFR), East Asian (EAS), South-East Asian (SAS)).

Results

We detected 367 new genome-wide significant associations in non-European populations (15 in Admixed American (AMR), 72 in African (AFR) and 280 in East Asian (EAS)). New associations detected represent 5%, 17% and 13% of associations in the AFR, AMR and EAS populations, respectively. Overall, multi-trait testing increases the replication of European associated loci in non-European ancestry by 15%. Pleiotropic effects were highly similar at significant loci across ancestries (e.g. the mean correlation between multi-trait genetic effects of EUR and EAS ancestries was 0.88). For hematological traits, strong discrepancies in multitrait genetic effects are tied to known evolutionary divergences: the ARKC1 loci, which is adaptive to overcome thep.vivaxinduced malaria.

Conclusions

Multi-trait GWAS can be a valuable tool to narrow the genetic knowledge gap between European and non-European populations.