bluuebunny/crossref_metadata_2025 huggingface dataset:
Intracranial electroencephalography reveals effector-independent evidence accumulation dynamics in multiple human brain regions
Authors: Gherman Sabina , Markowitz Noah , Tostaeva Gelana , Espinal Elizabeth , Mehta Ashesh D. , O’Connell Redmond G. , Kelly Simon P. , Bickel Stephan
Published: April 2023

Neural representations of perceptual decision formation that are abstracted from specific motor requirements have previously been identified in humans using non-invasive electrophysiology, however, it is currently unclear where these originate in the brain. Here, we capitalized on the high spatiotemporal precision of intracranial EEG to localize such abstract decision signals. Presurgical epilepsy patients judged the direction of random-dot stimuli and responded either with a speeded button press (N=23), or vocally, after a randomized delay (N=11). We found a widely distributed motor-independent network of regions where high-frequency activity exhibited key characteristics consistent with evidence accumulation, including a gradual build-up that was modulated by the strength of the sensory evidence, and an amplitude that predicted subjects’ choice accuracy and response time. Our findings offer a new view on the brain networks governing human decision making.
A transcriptome analysis ofOsNAC02Ko-mutant during vegetative endosperm development
Authors: Yan Mei , Jiao Guiai , Shao Gaoneng , Chen Ying , Zhu Maodi , Yang Lingwei , Xie Lihong , Hu Peisong , Tang Shaoqing
Published: April 2023

The Ko-Osnac02mutant matured earlier than the wild type (WT) in 15 days obviously. The result showed that theKo-Osnac02chalky with white-core and white-belly mature endosperm. The seed filling rate plays a major role in determining the yield and quality of rice (Oryza sativa L. versus japonica). Interestingly, in the Ko-Osnac02seeds, higher amylose content (AC) was observed in vegetative endosperm (5DAP), while lower amylose content (AC) and higher soluble sugar content were observed in the mature endosperm. RNA-Seq analysis of N2/N3 seed (3DAPs) and the WT revealed that among the top differentially expressed genes (DEGs), the OsBAM2 (LOC_Os10g32810) expressed significantly high which involved in starch degradation. In addition, seven genes were expressed at a lower-level in pro-pro interactions inducing the chalky endosperm formation in N2 mutant seeds (3 DAP), which could be verified by heatmap diagrams based on DEGs of N2 versus WT. The cell cycler controlling the Tubulin genes downregulated their expression together with the MCM family genes MCM4 ( ↓ ), MCM7 ( ↑ ), which may cause white-core in the early endosperm development. In conclusion, the developing period shorten significantly in the Ko-Osnac02mutants may cause the chalkiness in seeds during the early endosperm development.

ONE SENTENCE SUMMARY

The geneOsNAC02which controls a great genetic co-network for cell cycle regulation in early development, and Ko-Osnac02mutant shows prematurity and white-core in endosperm.
Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience
Authors: Blaszczak Joanna R. , Yackulic Charles B. , Shriver Robert K. , Hall Robert O.
Published: April 2023

Directly observing autotrophic biomass at ecologically relevant frequencies is difficult in many ecosystems, hampering our ability to predict productivity through time. Since disturbances can impart distinct reductions in river productivity through time by modifying underlying standing stocks of biomass, mechanistic models fit to productivity time series can infer underlying biomass dynamics. We incorporated biomass dynamics into a river ecosystem productivity model for six rivers to identify disturbance flow thresholds and understand the resilience of primary producers. The magnitude of flood necessary to disturb biomass and thereby reduce ecosystem productivity was consistently lower than the more commonly used disturbance flow threshold of the flood magnitude necessary to mobilize river bed sediment. The estimated daily maximum percent increase in biomass (a proxy for resilience) ranged from 5% to 42% across rivers. Our latent biomass model improves understanding of disturbance thresholds and recovery patterns of autotrophic biomass within river ecosystems.
Evidence for Involvement ofWDPCPGene in Alcohol Consumption, Lipid Metabolism, and Liver Cirrhosis
Authors: O’Farrell Felix , Aleyakpo Benjamin , Mustafa Rima , Jiang Xiyun , Pinto Rui Climaco , Elliott Paul , Tzoulaki Ioanna , Dehghan Abbas , Loh Samantha H. Y. , Barclay Jeff W. , Martins L. Miguel , Pazoki Raha
Published: April 2023

Alcohol consumption continues to cause a significant health burden globally. The advent of genome-wide association studies has unraveled many genetic loci associated with alcohol consumption. However, the biological effect of these loci and the pathways involved in alcohol consumption and its health consequences such as alcohol liver disease (ALD) remain to be elucidated. We combined human studies with model organismsDrosophila melanogasterandCaenorhabditis elegansto shed light on the molecular mechanisms underlying alcohol consumption and the health outcomes caused by alcohol intake. Using genetics and metabolite data within the Airwave study, a sample of police forces in the UK, we performed several analyses to identify changes in circulating metabolites that are triggered by alcohol consumption. We selected a set of genes annotated to genetic variants that are (1) known to be implicated in alcohol consumption, (2) are linked to liver function, and (3) are associated with expression (cis-eQTL) of their annotated genes. We used mutations and/or RNA interference (RNAi) to suppress the expression of these genes inC. elegansandDrosophila. We examined the effect of this suppression on ethanol consumption and on the sedative effects of ethanol. We also investigated the alcohol-induced changes in triacylglycerol (TGA) levels inDrosophilaand tested differences in locomotion ofC. elegansafter acute exposure to ethanol. In human population, we found an enrichment of the alcohol-associated metabolites within the linoleic acid (LNA) and alpha linolenic acid (ALA) metabolism pathway. We further showed the effect ofACTR1BandMAPTon locomotionin C. elegansafter exposure to ethanol. We demonstrated that three genes namelyWDPCP, TENM2andGPN1modify TAG levels inDrosophila. Finally, we showed that gene expression ofWDPCPin human population is linked to liver fibrosis and liver cirrhosis. Our results underline the impact of alcohol consumption on metabolism of lipids and pinpointsWDPCPas a gene with potential impact on fat accumulation upon exposure to ethanol suggesting a possible pathway to ALD.
Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profilesin silico
Authors: Williams Avery S. , Wilk Elizabeth J. , Fisher Jennifer L. , Lasseigne Brittany N.
Published: April 2023

Preclinical models like cancer cell lines and patient-derived xenografts (PDXs) are vital for studying disease mechanisms and evaluating treatment options. It is essential that they accurately recapitulate the disease state of interest to generate results that will translate in the clinic. Prior studies have demonstrated that preclinical models do not recapitulate all biological aspects of human tissues, particularly with respect to the tissue of origin gene expression signatures. Therefore, it is critical to assess how well preclinical model gene expression profiles correlate with human cancer tissues to inform preclinical model selection and data analysis decisions. Here we evaluated how well preclinical models recapitulate human cancer and non-diseased tissue gene expression patternsin silicowith respect to the full gene expression profile as well as subsetting by the most variable genes, genes significantly correlated with tumor purity, and tissue-specific genes by using publicly available gene expression profiles across multiple sources. We found that using the full gene set improves correlations between preclinical model and tissue global gene expression profiles, confirmed that GBM PDX global gene expression correlation to GBM tumor global gene expression outperforms GBM cell line to GBM tumor global gene expression correlations, and demonstrated that preclinical models in our study often failed to reproduce tissue-specific expression. While including additional genes for global gene expression comparison between cell lines and tissues decreases the overall correlation, it improves the relative rank between a cell line and its tissue of origin compared to other tissues. Our findings underscore the importance of using the full gene expression set measured when comparing preclinical models and tissues and confirm that tissue-specific patterns are better preserved in GBM PDX models than in GBM cell lines. Future studies can build on these findings to determine the specific pathways and gene sets recapitulated by particular preclinical models to facilitate model selection for a given study design or goal.
Sidestream bio-P and mainstream anammox in a BNR process with upstream carbon capture
Authors: McCullough Kester , Klaus Stephanie , Wilson Christopher , Vanrolleghem Peter A. , Gu April Z. , Bott Charles
Published: April 2023

The integration of biological phosphorus removal (bio-P) and shortcut nitrogen removal (SNR) processes is challenging because of the conflicting demands on influent carbon: SNR allows for upstream carbon diversion but this reduction of influent carbon (especially volatile fatty acids (VFA) prevents or limits bio-P The objective of this study was to achieve SNR, either via partial nitritation/anammox (PNA) or partial denitrification/anammox (PdNA), simultaneously with biological phosphorus removal in a process with upstream carbon capture. This study took place in a pilot scale A/B process with a sidestream bio-P reactor and tertiary anammox polishing. Despite low influent rbCOD concentrations from the A-stage effluent, bio-P occurred in the B-stage thanks to the addition of A-stage WAS fermentate to the sidestream reactor. Nitrite accumulation occurred in the B-stage via partial denitrification and partial nitritation (NOB out-selection), depending on operational conditions, and was removed along with ammonia by the tertiary anammox MBBR, with the ability to achieve effluent TIN less than 2 mg/L.
Conformational dynamics of lipid transfer domains provide a general framework to decode their functional mechanism
Authors: Srinivasan Sriraksha , Di Luca Andrea , John Peter Arun T. , Gehin Charlotte , Lone Museer A. , Hornemann Thorsten , D’Angelo Giovanni , Vanni Stefano
Published: April 2023

Lipid Transfer Proteins (LTPs) are key players in cellular homeostasis and regulation, as they coordinate the exchange of lipids between different cellular organelles. Despite their importance, our mechanistic understanding of how LTPs function at the molecular level is still in its infancy, mostly due to the large number of existing LTPs and to the low degree of conservation at the sequence and structural level. In this work, we use molecular simulations to characterize dynamical and mechanistic aspects of a representative dataset of Lipid Transport Domains (LTDs) of 12 LTPs that belong to 8 distinct families. We find that LTDs display common dynamical, rather than structural, features despite no sequence homology nor structural conservation. These dynamical features correlate with their mechanistic mode of action, allowing to interpret and design experimental strategies to further dissect their mechanism. Our findings indicate the existence of a conserved, fold-independent mechanism of lipid transfer across LTPs of various families and offer a general framework for understanding their functional mechanism.
A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation
Authors: Amico Tommaso , Dada Samuel , Lazzari Andrea , Brezinova Michaela , Trovato Antonio , Vendruscolo Michele , Fuxreiter Monika , Maritan Amos
Published: April 2023

Many proteins have been recently shown to undergo a process of phase separation that leads to the formation of biomolecular condensates. Intriguingly, it has been observed that some of these proteins form dense droplets of sizeable dimensions already below the critical concentration, which is the concentration at which phase separation occurs. To understand this phenomenon, which is not readily compatible with classical nucleation theory, we investigated the properties of the droplet size distributions as a function of protein concentration. We found that these distributions can be described by a scale-invariant log-normal function with an average that increases progressively as the concentration approaches the critical concentration from below. The results of this scaling analysis suggest the existence of a universal behaviour independent of the sequences and structures of the proteins undergoing phase separation. While we refrain from proposing a theoretical model here, we suggest that any model of protein phase separation should predict the scaling exponents that we reported here from the fitting of experimental measurements of droplet size distributions. Furthermore, based on these observations, we show that it is possible to use the scale invariance to estimate the critical concentration for protein phase separation.
Computational Screen for Sex-Specific Drug Effects in a Cardiac Fibroblast Network Model
Authors: Watts Kelsey M. , Nichols Wesley , Richardson William J.
Published: April 2023

Heart disease is the leading cause of death in both men and women. Cardiac fibrosis is the uncontrolled accumulation of extracellular matrix proteins which can exacerbate the progression of heart failure, and there are currently no drugs approved specifically to target matrix accumulation in the heart. Computational signaling network models (SNMs) can be used to facilitate discovery of novel drug targets. However, the vast majority of SNMs are not sex-specific and/or are developed and validated using data skewed towards male in vitro and in vivo samples. Biological sex is an important consideration in cardiovascular health and drug development. In this study, we integrate a previously constructed cardiac fibroblast SNM with estrogen signaling pathways to create sex-specific SNMs. The sex-specific SNMs maintained previously high validation when compared toin vitroexperimental studies in the literature. A sex-specific perturbation analysis and drug screen uncovered several potential pathways that warrant further study in the pursuit of sex-specific treatment recommendations for cardiac fibrosis.

Author Summary

Heart failure is a leading cause of death for both men and women, but we still do not have adequate therapies to prevent or reverse this disease. One factor that contributes to heart failure is scarring of cardiac tissue, also known as fibrosis. Computer models can help find new heart failure drugs by simulating hundreds of biological reactions that regulate fibrosis at the molecular level. Unfortunately, the differences in male and female patients are not usually considered for these drug discovery simulations, which can result in drugs that work well for some individuals but not for other individuals. In our study, we added sex-specific biological reactions to a computer model in order to identify drugs that could treat fibrosis differently in male and female patients. Our simulations also predicted why premenopausal women may generally develop less fibrosis than men, while post-menopausal women may develop similar levels of fibrosis as men.
A comparison between Greengenes, SILVA, RDP, and NCBI reference databases in four published microbiota datasets
Authors: Ceccarani Camilla , Severgnini Marco
Published: April 2023

Inaccurate bacterial taxonomic assignment in 16S-based microbiota experiments could have deleterious effects on research results, as all downstream analyses heavily rely on the accurate assessment of microbial taxonomy: a bias in the choice of the reference database can deeply alter microbiota biodiversity (alpha-diversity), composition (beta-diversity), and taxa profile (bacterial relative abundances).

In this paper, we explored the influence of the reference 16S rRNA collection by performing a classification against four of the main databases used by the scientific community (i.e. Greengenes, SILVA, RDP, NCBI); the consequences of database clustering at 97% were also explored. To investigate the effects of the database choice on real and representative microbiome samples from different ecosystems, we performed a comparative analysis on four already published datasets from various sources: stools from a mouse model experiment, bovine milk, human gut microbiota stool samples, and swabs from the human vaginal environment. We took into consideration the computational time needed to perform the taxonomic classification as well.

Although values in both alpha- and beta-diversity varied a lot, sometimes even statistically, according to the dataset chosen and the eventual clustering, the final outcome of the analysis was a concordance in the capability to retrieve the original experimental group differences over the various datasets. However, in the taxonomy classification, we found several inconsistencies with taxonomies correctly assigned in only some of the four databases. The degree of concordance among the databases was related to both the complexity of the environment and its degree of completeness in the reference databases.

IMPORTANCE

16S rRNA sequencing is, nowadays, the most commonly used strategy for microbiota profiling in many different ecosystems, ranging from human-associated to animal models, food matrices, and environmental samples. The ability of this kind of analysis to correctly capture differences in the microbiota composition is related to the taxonomic classification of the fragments obtained from sequencing and, thus, to the choice of the best reference database. This paper deals with four of the most popular microbial databases, which were evaluated in their ability to reproduce the experimental evidence from four already published datasets. The knowledge of the advantages and drawbacks of the database choice can be pivotal for planning future experiments in the field, making researchers aware of the repercussions of such a choice according to the different environments under scrutiny.

Moreover, this work can also shed new light upon past results, partially explaining discordant evidence.
Plasmodium falciparumexploits CD44 as a co-receptor for erythrocyte invasion
Authors: Baro-Sastre Barbara , Kim Chi Yong , Lin Carrie , Kongsomboonvech Angel K. , Tetard Marilou , Salinas Nichole D. , Tolia Niraj H. , Egan Elizabeth S.
Published: April 2023

The malaria parasitePlasmodium falciparuminvades and replicates asexually within human erythrocytes. CD44 expressed on erythrocytes was previously identified as an important host factor forP. falciparuminfection through a forward genetic screen, but little is known about its regulation or function in these cells, nor how it may be utilized by the parasite. We found that CD44 can be efficiently deleted from primary human hematopoietic stem cells using CRISPR/Cas9 genome editing, and that the efficiency of ex-vivo erythropoiesis to enucleated cultured red blood cells (cRBCs) is not impacted by lack of CD44. However, the rate ofP. falciparuminvasion was substantially reduced in CD44-null cRBCs relative to isogenic wild-type (WT) control cells, validating CD44 as an important host factor for this parasite. We identified twoP. falciparuminvasion ligands as binding partners for CD44, Erythrocyte Binding Antigen-175 (EBA-175) and EBA-140, and demonstrated that their ability to bind to human erythrocytes relies primarily on their canonical receptors-glycophorin A and glycophorin C, respectively. We further show that EBA-175 induces phosphorylation of erythrocyte cytoskeletal proteins in a CD44-dependent manner. Our findings support a model whereP. falciparumexploits CD44 as a co-receptor during invasion of human erythrocytes, stimulating CD44-dependent phosphorylation of host cytoskeletal proteins that alter host cell deformability and facilitate parasite entry.
Disulfide bridge-dependent dimerization triggers FGF2 membrane translocation into the extracellular space
Authors: Lolicato F , Steringer JP , Saleppico R , Beyer D , Fernandez-Sobaberas J , Unger S , Klein S , Riegerová P , Wegehingel S , Müller HM , Schmitt XJ , Kaptan S , Freund C , Hof M , Šachl R , Chlanda P , Vattulainen I , Nickel W
Published: April 2023

Fibroblast Growth Factor 2 (FGF2) exits cells by direct translocation across the plasma membrane, a type I pathway of unconventional protein secretion. This process is initiated by PI(4,5)P2-dependent formation of highly dynamic FGF2 oligomers at the inner plasma membrane leaflet, inducing the formation of lipidic membrane pores. Cell surface heparan sulfate chains linked to glypican-1 (GPC1) capture FGF2 at the outer plasma membrane leaflet, completing FGF2 membrane translocation into the extracellular space. While the basic steps of this pathway are well understood, the molecular mechanism by which FGF2 oligomerizes on membrane surfaces remains unclear. In the current study, we demonstrate the initial step of this process to depend on C95-C95 disulfide-bridge-mediated FGF2 dimerization on membrane surfaces, producing the building blocks for higher FGF2 oligomers that drive the formation of membrane pores. We find FGF2 with a C95A substitution to be defective in oligomerization, pore formation, and membrane translocation. Consistently, we demonstrate a C95A variant of FGF2 to be characterized by a severe secretion phenotype. By contrast, while also important for efficient FGF2 secretion from cells, a second cysteine residue on the molecular surface of FGF2 (C77) is not involved in FGF2 oligomerization. Rather, we find C77 to be part of the protein-protein interaction interface through which FGF2 binds to the α1 subunit of the Na,K-ATPase, the landing platform for FGF2 at the inner plasma membrane leaflet. Using cross-linking mass spectrometry, atomistic molecular dynamics simulations combined with a machine learning analysis and cryo-electron tomography, we provide insights into a FGF2 dimerization interface that brings C95 residues in close proximity, resulting in disulfide bridged FGF2 dimers. We propose a mechanism by which they bind with high avidity to PI(4,5)P2on membrane surfaces. We further propose a tight coupling between FGF2 secretion and the formation of ternary signaling complexes on cell surfaces, hypothesizing that C95-C95 bridged FGF2 dimers are functioning as the molecular units triggering autocrine and paracrine FGF2 signaling.
Antioxidant Activity via Free Radical Scavenging of Pitavastatin and Its Hydroxylated Metabolites. A Quantum Chemical Attempt Aiming to Assist Drug Development
Authors: Bâldea Ioan
Published: April 2023

Statins form a class of drugs often administered in a variety of cardiovascular diseases, for which their antioxidant capacity appears particularly relevant. Although experiments have long provided empirical evidence that statins can suppress various oxidation pathways, theoretical attempts to quantify the antioxidant activity of statins (read, atorvastatin ATV, because this is the only one studied so far) were not published until last year. Molecular and clinical differences of stains trace back to the ring attached to the statin’s active moiety. This can be, e.g., a pyrrole, as the case of the aforementioned ATV or a quinoline, as the case of pitavastatin (PVT), which represents the focus of the present work. Extensive results reported here for PVT and derivative include the thermodynamic antioxidant descriptors (bond dissociation enthalpy BDE, adiabatic ionization potential IP, proton dissociation enthalpy PDE, proton affinity PA, and electron transfer enthalpy ETE) related to the three antioxidant mechanisms (hydrogen atom transfer HAT, stepwise electron transfer proton transfer SETPT, sequential proton loss electron transfer SPLET). Our particular emphasis is on the PVT’s hydroxylated derivatives wherein a hydroxy group replaces a hydrogen atom either on the quinoline core (Q-hydroxylated metabolites) or on the fluorophenyl ring (F-hydroxylated metabolites). Our calculations indicate that both the Q- and F-hydroxylated metabolites possess antioxidant properties superior to the parent PVT molecule. Given the fact that, to the best of our knowledge, no experimental data for the antioxidant potency of PVT and its hydroxylated derivatives exist, this is a theoretical prediction, and we Given the fact that, to the best of our knowledge, no experimental data for the antioxidant potency of PVT and its hydroxylated derivatives exist, this is a theoretical prediction for the validation of which we aim hereby to stimulate companion experimental in vivo and in vitro investigations and inspire pharmacologists in further drug developments.
Eupatilin improves cilia defects in human CEP290 ciliopathy models
Authors: Corral-Serrano JC , Sladen PE , Ottaviani D , Rezek FO , Jovanovic K , Athanasiou D , van der Spuy J , Mansfield BC , Cheetham ME
Published: April 2023

The photoreceptor outer segment is a highly specialized primary cilium essential for phototransduction and vision. Biallelic pathogenic variants in the cilia-associated geneCEP290cause non-syndromic Leber congenital amaurosis 10 (LCA10) and syndromic diseases, where the retina is also affected. While RNA antisense oligonucleotides and gene editing are potential treatment options for the common deep intronic variant c.2991+1655A>G inCEP290, there is a need for variant-independent approaches that could be applied to a broader spectrum of ciliopathies. Here, we generated several distinct human models ofCEP290-related retinal disease and investigated the effects of the flavonoid eupatilin as a potential treatment. Eupatilin improved cilium formation and length in CEP290 LCA10 patient-derived fibroblasts, in gene-editedCEP290knockout (CEP290 KO) RPE1 cells, and in both CEP290 LCA10 and CEP290 KO iPSCs-derived retinal organoids. Furthermore, eupatilin reduced rhodopsin retention in the outer nuclear layer of CEP290 LCA10 retinal organoids. Eupatilin altered gene transcription in retinal organoids, by modulating the expression of rhodopsin, and by targeting cilia and synaptic plasticity pathways. This work sheds light into the mechanism of action of eupatilin, and supports its potential as a variant-independent approach forCEP290-associated ciliopathies.

Abstract Figure
Hippocampal subfield vulnerability to α-synuclein pathology precedes neurodegeneration and cognitive dysfunction
Authors: Dues Dylan J. , Nguyen An Phu Tran , Becker Katelyn , Ma Jiyan , Moore Darren J.
Published: April 2023

Cognitive dysfunction is a salient feature of Parkinson’s disease (PD) and Dementia with Lewy bodies (DLB). The onset of dementia reflects the spread of Lewy pathology throughout forebrain structures. The mere presence of Lewy pathology, however, provides limited indication of cognitive status. Thus, it remains unclear whether Lewy pathology is the de facto substrate driving cognitive dysfunction in PD and DLB. Through application of α-synuclein fibrilsin vivo, we sought to examine the influence of pathologic inclusions on cognition. Following stereotactic injection of α-synuclein fibrils within the mouse forebrain, we measured the burden of α-synuclein pathology at 1-, 3-, and 6-months post-injection within subregions of the hippocampus and cortex. Under this paradigm, the hippocampal CA2/3 subfield was especially susceptible to α- synuclein pathology. Strikingly, we observed a drastic reduction of pathology in the CA2/3 subfield across time-points, consistent with the consolidation of α-synuclein pathology into dense somatic inclusions followed by neurodegeneration. Silver-positive degenerating neurites were observed prior to neuronal loss, suggesting that this might be an early feature of fibril-induced neurotoxicity and a precursor to neurodegeneration. Critically, mice injected with α-synuclein fibrils developed progressive deficits in spatial learning and memory. These findings support that the formation of α-synuclein inclusions in the mouse forebrain precipitate neurodegenerative changes that recapitulate features of Lewy-related cognitive dysfunction.

Highlights

Mice injected with α-synuclein fibrils develop hippocampal and cortical α- synuclein pathology with a dynamic regional burden at 1-, 3-, and 6-months post-injection.

Silver-positive neuronal processes are an early and enduring degenerative feature of the fibril model, while extensive neurodegeneration of the hippocampal CA2/3 subfield is detected at 6-months post-injection.

Mice exhibit progressive hippocampal-dependent spatial learning and memory deficits.

Forebrain injection of α-synuclein fibrils may be used to model aspects of Lewy-related cognitive dysfunction.
Crosstalk between the tRNA methyltransferase Trm1 and RNA chaperone La influences eukaryotic tRNA maturation
Authors: Porat Jennifer , Vakiloroayaei Ana , Remnant Brittney M. , Talebi Mohammadaref , Cargill Taylor , Bayfield Mark A.
Published: April 2023

tRNAs undergo an extensive maturation process involving post-transcriptional modifications often associated with tRNA structural stability and promoting the native fold. Impaired post-transcriptional modification has been linked to human disease, likely through defects in translation, mitochondrial function, and increased susceptibility to degradation by various tRNA decay pathways. More recently, evidence has emerged that bacterial tRNA modification enzymes can act as tRNA chaperones to guide tRNA folding in a manner independent from catalytic activity. Here, we provide evidence that the fission yeast tRNA methyltransferase Trm1, which dimethylates nuclear– and mitochondrial-encoded tRNAs at G26, can also promote tRNA functionality in the absence of catalysis. We show that wild type and catalytic-dead Trm1 are active in anin vivotRNA-mediated suppression assay and possess RNA strand annealing and dissociation activityin vitro, similar to previously characterized RNA chaperones. Trm1 and the RNA chaperone La have previously been proposed to function synergistically in promoting tRNA maturation, yet we surprisingly demonstrate that La binding to nascent pre-tRNAs decreases Trm1 tRNA dimethylationin vivoandin vitro. Collectively, these results support the hypothesis for tRNA modification enzymes that combine catalytic and non-catalytic activities to promote tRNA maturation, as well as expand our understanding of how La function can influence tRNA modification.
Efficient self-organization of blastoids solely from mouse ESCs is facilitated by transient reactivation of 2C gene network
Authors: Jana Debabrata , Singh Priya , Sailasree Purnima , Kumar Nithyapriya , Vishnu Vijay V , Kale Hanuman T , Lakshmi Jyothi , Kumari Asha , Sowpati Divya Tej , Shekar P Chandra
Published: April 2023

Human pluripotent stem cells (hPSCs) can self-organize into a blastocyst-like structure (blastoid) by virtue of their full developmental potential. The pluripotent mouse embryonic stem cells (mESC) are considered to lack this potential and hence can form blastoids only when combined with trophoblast stem cells. We performed a small molecule and cytokine screen to demonstrate that mESC have full potential to efficiently self-organize themselves into E-blastoids (ESC-blastoids). The morphology, cell lineages and the transcriptome of these blastoids resemble the mouse blastocyst. The E-blastoids undergo implantation andin uterodevelopment in mice. The transient reactivation of the 2C-gene network by retinoid signaling is essential for E-blastoid generation. GSK3β activity is critical for retinoid signaling and consequent 2C gene network activation. Collectively, the mESC possess full developmental potential to generate blastoids similar to hPSCs and other mammals. The plasticity of PSCs to self-organize into blastoids is not exclusive to humans or larger mammals; rather, it could be a general feature shared by most mammals, including rodents.
PGSbuilder: An end-to-end platform for human genome association analysis and polygenic risk score predictions
Authors: Lee Ko-Han , Lee Yi-Lun , Hsieh Tsung-Ting , Chang Yu-Chuan , Wang Su-Shia , Fann Geng-Zhi , Lin Wei-Che , Chang Hung-Ching , Chen Ting-Fu , Li Peng-Husan , Kuo Ya-Ling , Chen Pei-Lung , Juan Hsueh-Fen , Tsai Huai-Kuang , Chen Chien-Yu , Huang Jia-Hsin
Published: April 2023

Understanding the genetic basis of human complex diseases is increasingly important in the development of precision medicine. Over the last decade, genome-wide association studies (GWAS) have become a key technique for detecting associations between common diseases and single nucleotide polymorphisms (SNPs) present in a cohort of individuals. Alternatively, the polygenic risk score (PRS), which often applies results from GWAS summary statistics, is calculated for the estimation of genetic propensity to a trait at the individual level. Despite many GWAS and PRS tools being available to analyze a large volume of genotype data, most clinicians and medical researchers are often not familiar with the bioinformatics tools and lack access to a high-performance computing cluster resource. To fill this gap, we provide a publicly available web server, PGSbuilder, for the GWAS and PRS analysis of human genomes with variant annotations. The user-friendly and intuitive PGSbuilder web server is developed to facilitate the discovery of the genetic variants associated with complex traits and diseases for medical professionals with limited computational skills. For GWAS analysis, PGSbuilder provides the most renowned analysis tool PLINK 2.0 package. For PRS, PGSbuilder provides six different PRS methods including Clumping and Thresholding, Lassosum, LDPred2, GenEpi, PRS-CS, and PRSice2. Furthermore, PGSbuilder provides an intuitive user interface to examine the annotated functional effects of variants from known biomedical databases and relevant literature using advanced natural language processing approaches. In conclusion, PGSbuilder offers a reliable platform to aid researchers in advancing the public perception of genomic risk and precision medicine for human disease genetics. PGSbuilder is freely accessible athttp://pgsb.tw23.org.
Association between the skin microbiome and MHC class II diversity in an amphibian
Authors: Cortazar-Chinarro M , Richter-Boix A , Rodin-Mörch P , Halvarsson P , Logue JB , Laurila A , Höglund J
Published: April 2023

It has become clear that the microbiome plays an important role in determining host health, diseases, and phenotypic variation. There is increasing evidence that the microbiome influences host fitness and its adaptation to the environment is changing our thinking on host-microbe interactions. However, it remains unclear how a host genotype shapes its microbiome. Here, we explored how genetic background and evolutionary history influence associated microbiome in amphibian populations. We studied how skin bacterial diversity is associated with the Major Histocompatibility Complex (MHC) class II exon 2 diversity in 12 moor frog populations belonging to two geographical clusters that show signatures of past and ongoing differential selection patterns. We found that bacterial alpha-diversity remained similar between the two clusters, while MHC haplotype-supertypes and genetic diversity differed between the clusters. Bacterial alpha-diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. We also found that bacterial community composition differed significantly between the two geographic clusters and between specific MHC supertypes. These findings further suggest that population historical demographic events influence hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
Plant recognition byTrichoderma harzianumelicits upregulation of a novel secondary metabolite cluster required for colonization
Authors: Schalamun Miriam , Li Guofen , Hinterdobler Wolfgang , Großkinsky Dominik K. , Compant Stéphane , Dreux-Zigha Assia , Gerke Jennifer , Cox Russell , Schmoll Monika
Published: April 2023

Trichoderma harzianumis a filamentous ascomycete frequently applied as biocontrol agent in agriculture. While mycoparasitism and antagonism ofTrichodermaspp. against fungal pathogens are well known, early fungal responses to the presence of a plant await broader investigation. Analyzing early stages of plant-fungus communication we show thatT. harzianumB97 chemotropically responds to a plant extract and that both plant and fungus alter secondary metabolite secretion upon recognition. We developed a strategy for omics-analysis simulating conditions of early plant recognition eliciting a chemotropic response in the fungus and found 102 genes to be differentially regulated, including nitrate and nitrite reductases. Additionally, the previously uncharacterizedPlantCommunicationAssociated (PCA) gene cluster was strongly induced upon recognition of the plant, comprises a palindromic DNA motif and was essential for plant colonization. The PCA-cluster is only present in the Harzianum clade ofTrichodermaand closely related to a homologous cluster inMetarhiziumspp. Horizontal gene transfer (HGT) was detected for PCA-cluster genes by plants, while the cluster inT. harzianumis likely under balancing or positive selection.

Hence, the PCA-cluster mediates early fungus-plant chemical communication and may be responsible for the high potential ofT. harzianumand closely related species for biocontrol applications.

Plain language summary

Interactions of plants with fungi – beneficial or pathogenic – are crucial for the ecological function of both partners. Yet, the chemical “language” they use and how or when they use it is still insufficiently known. We describe discovery of a novel gene cluster, which is strongly induced upon plant recognition and essential for plant-fungal interkingdom interaction in the biocontrol-agentTrichoderma harzianum.
G-quadruplexe as a structural modulator of Intron Retention upon viral infection
Authors: Lejault Pauline , Terrier Michel-Pierre , Vannutelli Anaïs , Bolduc François , Brand Carolin , Perreault Martin Bisaillon Jean Pierre
Published: April 2023

Amongst the wide array of alternative splicing events (ASE), the intrinsic mechanisms of intron retention have remained elusive. This particular type of ASE has long been characterized as an artifact, but recent studies have shown its implication in numerous diseases. It has also been revealed that numerous viruses choose to disrupt alternative splicing to escape cellular immune response and further their proliferation. The main focus of this study was to investigate the G-quadruplex role in Alternative Splicing Events (ASEs) that occur following Flavivirus infections. After having demonstrated that G-quadruplexes structures are mainly formed in Intron Retained Transcripts by RNA-seq, our attention turned toward the ULK3 gene, coding for a serine/threonine kinase regulating autophagy, an essential mechanism in the cellular response to stress and even pathogen infections. In this study, we revealed the presence of a G-quadruplex in the first intron of the ULK3 gene near the 3 ’ splice site. Furthermore, we assayed the formation and stability of this G-quadruplex in vitro and showed that its formation affects IR, as demonstrated by comparisons between wild-type and mutant transfected mini-genes. Finally, we identified the specific RNA-binding protein signature for this G-quadruplex, thereby uncovering the novel role of G-quadruplexes in Alternative Splicing.
Carcinoma-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment
Authors: Wrenn Emma D. , Apfelbaum April A. , Rudzinski Erin R. , Deng Xuemei , Jiang Wei , Sud Sudha , Van Noord Raelene A. , Newman Erika A. , Garcia Nicolas M. , Hoglund Virginia J. , Bhise Shruti S. , Kanaan Sami B. , Waltner Olivia G. , Furlan Scott N. , Lawlor Elizabeth R.
Published: April 2023

Tumor heterogeneity is a major driver of cancer progression. In epithelial-derived malignancies, carcinoma-associated fibroblasts (CAFs) contribute to tumor heterogeneity by depositing extracellular matrix (ECM) proteins that dynamically remodel the tumor microenvironment (TME). Ewing sarcomas (EwS) are histologically monomorphous, mesenchyme-derived tumors that are devoid of CAFs. Here we identify a previously uncharacterized subpopulation of transcriptionally distinct EwS tumor cells that deposit pro-tumorigenic ECM. Single cell analyses revealed that these CAF-like cells differ from bulk EwS cells by their upregulation of a matrisome-rich gene signature that is normally repressed by EWS::FLI1, the oncogenic fusion transcription factor that underlies EwS pathogenesis. Further, our studies showed that ECM-depositing tumor cells express the cell surface marker CD73, allowing for their isolation ex vivo and detection in situ. Spatial profiling of tumor xenografts and patient biopsies demonstrated that CD73+EwS cells and tumor cell-derived ECM are prevalent along tumor borders and invasive fronts. Importantly, despite loss of EWS::FLI1-mediated gene repression, CD73+EwS cells retain expression of EWS::FLI1 and the fusion-activated gene signature, as well as tumorigenic and proliferative capacities. Thus, EwS tumor cells can be reprogrammed to adopt CAF-like properties and these transcriptionally and phenotypically distinct cell subpopulations contribute to tumor heterogeneity by remodeling the TME.
Enhanced nonenzymatic RNA copying within-situactivation of short oligonucleotides
Authors: Ding Dian , Zhang Stephanie J. , Szostak Jack
Published: April 2023

The nonenzymatic copying of RNA is thought to have been necessary for the transition between prebiotic chemistry and ribozyme-catalyzed RNA replication in the RNA World. We have previously shown that a potentially prebiotic nucleotide activation pathway based on phospho-Passerini chemistry can lead to the efficient synthesis of 2-aminoimidazole activated mononucleotides when carried out under freeze-thaw cycling conditions. Such activated nucleotides react with each other to form 5′-5′ 2-aminoimidazolium bridged dinucleotides, enabling template-directed primer extension to occur within the same reaction mixture. However, mononucleotides linked to oligonucleotides by a 5′-5′ 2-aminoimidazolium bridge are superior substrates for nonenzymatic primer extension, due to their higher intrinsic reactivity and their higher template affinity. Here we show that eutectic phase phospho-Passerini chemistry efficiently activates short oligonucleotides and promotes the formation of monomer-bridged-oligonucleotide species during freeze-thaw cycles. We then demonstrate thatin-situgenerated monomer-bridged-oligonucleotides lead to efficient nonenzymatic template copying in the same reaction mixture. Our findings pave the way for future research into the activation of complex mixtures of mono- and oligonucleotides for the enhanced copying and potentially the replication of arbitrary RNA sequences.
Cryo-EM structures of tau filaments from SH-SY5Y cells seeded with brain extracts from cases of Alzheimer’s disease and corticobasal degeneration
Authors: Tarutani Airi , Lövestam Sofia , Zhang Xianjun , Kotecha Abhay , Robinson Andrew C. , Mann David M.A. , Saito Yuko , Murayama Shigeo , Tomita Taisuke , Goedert Michel , Scheres Sjors H.W. , Hasegawa Masato
Published: April 2023

The formation of amyloid filaments through templated seeding is believed to underlie the propagation of pathology in most human neurodegenerative diseases. A widely used model system to study this process is to seed amyloid filament formation in cultured cells using human brain extracts. Here, we report the electron cryo-microscopy (cryo-EM) structures of tau filaments from undifferentiated seeded SH-SY5Y cells, that transiently expressed N-terminally HA-tagged 1N3R or 1N4R human tau, using brain extracts from individuals with AD or CBD. Although the resulting filament structures differed from those of the brain seeds, some degree of structural templating was observed. Studying templated seeding in cultured cells, and determining the structures of the resulting filaments, can thus provide insights into the cellular aspects underlying neurodegenerative diseases.
inserexs: reflection choice software for resonant elastic X-ray scattering
Authors: Peña Corredor Antonio , Viart Nathalie , Lefevre Christophe
Published: April 2023

This paper presents inserexs, an open-source computer program that aims to pre-evaluate the different reflections for resonant elastic X-ray scattering (REXS) diffraction experiments. REXS is an extremely versatile technique that can provide positional and occupational information about the atoms present in a crystal. inserexs was conceived to help REXS experimentalists know beforehand which reflections to choose to determine a parameter of interest. Prior work has already proven this to be useful in the determination of atomic positions in oxide thin films. inserexs allows generalization to any given system and aims to popularize resonant diffraction as an alternative technique to improve the resolution of crystalline structures.
Corporate governance and bank performance: evidence from banking sector of Pakistan
Authors: Athar Muhammad , Chughtai Sumayya , Rashid Abdul
Published: April 2023

Purpose

The aim of this study is to understand how board structure, size of audit committee (AC), gender diversity and ownership structure influence banks’ performance in Pakistan. This study also aims to examine how various dimensions of governance differently affect the different measures of bank performance.

Design/methodology/approach

This study used panel estimation techniques to quantify the impact of various elements of corporate governance on bank performance by taking annual data of 19 Pakistani banks for the period 2013–2020. The corporate governance is measured by board size, CEO duality, AC size, ownership structure and gender diversity. To get the robust results, this study measures bank performance by considering different indicators, namely, return on assets, earning per share, technical efficiency (TE) and total factor productivity. The empirical investigation is based on several well-known and well-accepted governance theories such as the agency theory, the stewardship theory, the tokenism/critical mass theory and the information asymmetry theory.

Findings

The findings of the study reveal that the size of board and ACs both significantly improve profitability and productivity, whereas they decrease TE. Further, the findings suggest that most of the indicators of gender diversity significantly deteriorate the performance of banks. However, ownership structure significantly improves banks’ earnings per share and TE. This study further illustrates that CEO’s duality does not have any significant impact on bank performance. This finding holds true for all the performance measures considered for this study.

Practical implications

The findings are of great importance to various stakeholders, especially to policymakers to know about the factors influencing different measures of performance. Specifically, based on these findings, they can devise the result-oriented strategies to enhance the financial and real performance of banks. The findings also suggest that both investors and owners should take into consideration the governance indicators while evaluating banks’ performance by using accounting, market-based, efficiency and productivity measures.

Originality/value

This research adds to the vast body of existing knowledge about the effectiveness of corporate governance by investigating how the different dimensions of corporate governance and gender diversity influence bank performance in a developing country, namely, Pakistan. Further, this study elaborates the domestic rules/regulations, governance theories and governance framework and practices and tries to link the empirical findings with them for better understanding the role of governance in determining the performance of the banking sector of Pakistan.