bluuebunny/crossref_metadata_2025 huggingface dataset:
An Engineered IGF2 Mutant for Lysosomal Targeting Chimeras Development and Membrane Proteins Degradation
Authors: Pan Yanchao , Xiang Qing , Deng Kai , Anwar Muhammad , Wang Leiming , Wang Yuan , Liang Qiulian , Shen Lirou , Yang Jing , Shen Weijun
Published: February 2024

Lysosome-targeting chimeras (LYTACs) have emerged as a promising strategy for targeted degradation of membrane proteins, offering potential applications in drug development. Currently, two main methods for developing LYTACs exist: chemically modified antibodies[1-2]and wild-type insulin-like growth factor 2 (IGF2) fusion proteins (iLYTACs)[3]. However, the fusion of the IGF2 arm within iLYTACs carries the risk of activating IGF1R tyrosine kinase activity and promoting tumor development. To address this concern, we introduce eiLYTACs, a technology that employs engineered IGF2 fusion antibodies to induce degradation of endogenous membrane proteins. Compared to the wild-type IGF2, the engineered IGF2 mutant exhibited minimal binding affinity for IGF1R but demonstrated a significant 100-fold increase in its binding affinity for IGF2R. In contrast to wild-type IGF2, which promotes tumor growth, the cells incubated with the engineered IGF2 showed no stimulation of tumor growth. The eiLYTACs strategy effectively inhibits tumor cell proliferation by degrading specific targets, resulting in a significant reduction in xenograft tumor size in experimental nude mice. More interestingly, our research revealed that eiLYTACs simultaneously degrade both homo- and heterodimers of disease-relevant proteins,which offer a promising strategy to address the activation of compensatory bypass signaling pathways, drug resistance, and tumor heterogeneity.
An analysis of contractile and protrusive cell behaviours at the superficial surface of the zebrafish neural plate
Authors: Araya Claudio , Boekemeyer Raegan , Farlie Francesca , Moon Lauren , Darwish Freshta , Rookyard Chris , Allison Leanne , Vizcay-Barrena Gema , Fleck Roland , Aranda Millaray , Tada Masa , Clarke Jonathan D W
Published: February 2024

The motive forces underlying convergence and internalisation of the teleost neural plate remain unknown. To help understand this crucial morphogenetic movement we have analysed collective and individual cell behaviours at the superficial surface of the neural plate. Convergence to the midline does not rely on mediolateral cell intercalation, it is characterised by oscillatory contractile behaviours, a punctate distribution of Cdh2 and medially polarised actin-rich protrusions at the surface of the neural plate. Additionally, we characterise and discuss the intimate relationship and dynamic cell surfaces between the motile neural plate and the stationary overlying non-neural enveloping layer.
Theileria annulataInfection Promotes p53 suppression, Genomic Instability and DNA deaminase APOBEC3H upregulation leading to cancer-like phenotype in host cells
Authors: Dandesena Debabrata , Suresh Akash , Budhwar Roli , Godwin Jeffrey , Singh Sakshi , Subudhi Madhusmita , T Amruthanjali , Roy Sonti , A Vengatachala Moorthy , Bhandari Vasundhra , Sharma Paresh
Published: February 2024

Theileria annulata-infected host leukocytes display cancer-like phenotypes, though the precise mechanism is yet to be fully understood. The occurrence of cancer-like phenotypes inTheileria-infected leukocytes may be attributed to various factors, including genomic instability and acquired mutations, a crucial trait that underpins the genetic foundation of cancer. This paper presents WGS data and bioinformatic analyses to reveal point mutations and large-scale alterations in six clinically relevantT. annulata-infected cell lines. We identified 7867 exon-linked somatic mutations common to all cell lines, and cancer association analysis showed significant accumulation in oncogenes (FLT4, NOTCH2, MAP3K1, DAXX, FCGR2B, ROS1) and tumor suppressor genes (BARD1, KMT2C, GRIN2A, BAP1) implicated in established critical cancer processes. We demonstrated that a crizotinib-induced blockade of the ROS1 oncogenic protein, which harbored the most mutations, led to the death of infected leukocytes. This is consistent with the significant role of ROS1 in parasite-induced leukocyte transformation. In addition, we found somatic mutations in genes involved in genome instability and the DDR pathway. Our findings support the notion that ROS1 and Nutulin 3a are valid targets for intervention, and the suppression of TP53, a crucial tumor suppressor gene, may play a significant role in cell immortalization. We also show that upon infection with the parasite, bovine cells upregulate the expression of APOBEC3H, a DNA mutator likely responsible for the detected mutations. Our study highlights howT. annulatatransforms leukocytes to gain selective advantage via mutation, and our observations could steer future research towards a mechanistic understanding of disease pathogenesis.
Long-read sequencing reveals novel isoform-specific eQTLs and regulatory mechanisms of isoform expression
Authors: Nagura Yuya , Shimada Mihoko , Kuribayashi Ryoji , Kiyose Hiroki , Igarashi Arisa , Kaname Tadashi , Unoki Motoko , Fujimoto Akihiro
Published: February 2024

Genetic variations linked to changes in gene expression are known as expression quantitative loci (eQTLs). The identification of eQTLs provides a profound understanding of the mechanisms governing gene expression. However, prior studies have primarily utilized short-read sequencing techniques, and the analysis of eQTLs on isoforms has been relatively limited. In this study, we employed long-read sequencing technology (Oxford Nanopore) on B cells from 67 healthy Japanese individuals to explore genetic variations associated with isoform expression levels, referred to as isoform eQTLs (ieQTLs). Our analysis revealed 33,928 ieQTLs, with 69.0% remaining undetected by a gene-level analysis. Additionally, we identified ieQTLs that have significantly different effects on isoform expression levels within a gene. A functional feature analysis demonstrated a significant enrichment of ieQTLs at splice sites and specific histone marks, such as H3K36me3, H3K4me1, H3K4me3, and H3K79me3. Through an experimental validation using genome editing, we observed that a distant genomic region can modulate isoform-specific expression. Moreover, an ieQTL analysis and minigene splicing assays unveiled functionally crucial variants in splicing, which software-based predictions failed to anticipate. A comparison with GWAS data revealed a higher number of colocalizations between ieQTLs and GWAS findings compared to gene eQTLs. These findings highlight the substantial contribution of ieQTLs identified through long-read analysis in our understanding of the functional implications of genetic variations and the regulatory mechanisms governing isoforms.
Empowering Personalized Pharmacogenomics with Generative AI Solutions
Authors: Murugan Mullai , Yuan Bo , Venner Eric , Ballantyne Christie M. , Robinson Katherine M. , Coons James C. , Wang Liwen , Empey Philip E. , Gibbs Richard A.
Published: February 2024

Objective

This study evaluates an AI assistant developed using OpenAI’s GPT-4 for interpreting pharmacogenomic (PGx) testing results, aiming to improve decision-making and knowledge sharing in clinical genetics, and to enhance patient care with equitable access.

Methods

The AI assistant employs Retrieval Augmented Generation (RAG) combining retrieval and generative techniques. It employs a Knowledge Base (KB) comprising Clinical Pharmacogenetics Implementation Consortium (CPIC) data, with context-aware GPT-4 generating tailored responses to user queries from this KB, refined through prompt engineering and guardrails.

Results

Evaluated against a specialized PGx question catalog, the AI assistant showed high efficacy in addressing user queries. Compared with OpenAI’s ChatGPT 3.5, it demonstrated better performance, especially in provider-specific queries requiring specialized data and citations. Key areas for improvement include enhancing accuracy, relevancy, and representative language in responses.

Discussion

The integration of context-aware GPT-4 with RAG significantly enhanced the AI assistant’s utility. RAG’s ability to incorporate domain-specific CPIC data, including recent literature, proved beneficial. Challenges persist, such as the need for specialized genetic/PGx models to improve accuracy and relevancy and addressing ethical, regulatory, and safety concerns.

Conclusion

This study underscores generative AI’s potential for transforming healthcare provider support and patient accessibility to complex pharmacogenomic information. While careful implementation of large language models like GPT-4 is necessary, it is clear that they can substantially improve understanding of pharmacogenomic data. With further development, these tools could augment healthcare expertise, provider productivity, and the delivery of equitable, patient-centered healthcare services.
Development of an orthotopic medulloblastoma zebrafish model for rapid drug testing
Authors: van Bree Niek , Oppelt Ann-Sophie , Lindström Susanne , Zhou Leilei , Boutin Lola , Johnsen John Inge , Bräutigam Lars , Wilhelm Margareta
Published: February 2024

Medulloblastoma (MB) is one of the most common malignant brain tumors in children. Current preclinicalin vivomodel systems for MB have increased our understanding of molecular mechanisms regulating MB development; however, they may not be suitable for high-throughput screening efforts. We demonstrate here that transplantation of seven different MB cell lines or patient-derived cells into the blastula stage of zebrafish embryos leads to orthotopic tumor cell growth that can be observed within 24 hours after transplantation. Importantly, the homing of transplanted cells to the hindbrain region and the aggressiveness of tumor growth are enhanced by pre-culturing cells in a neural stem cell-like medium. The change in culture conditions rewires the transcriptome towards a more migratory and neuronal progenitor phenotype, including the expression of guidance molecules SEMA3A and EFNB1, both of which correlate with lower overall survival in MB patients. Furthermore, we highlight that the orthotopic zebrafish MB xenograft model has the potential to be used for high-throughput drug screening.

Key points

Medulloblastoma cells home to the hindbrain region in developing zebrafish embryos.

Neural stem cell culture conditions improve the homing capacity of MB tumor cells.

Medulloblastoma-transplanted zebrafish embryos can be used as a high-throughputin vivomodel for drug screening.

Importance of the Study

One of the challenges of accurately modeling medulloblastoma is the large heterogeneity in tumor characteristics. To accurately model this heterogeneous disease, patient-derived xenograft mouse models are currently the standard. However, such mouse models are labor intensive, time-consuming, and not suitable for high-throughput studies. Here, we describe a quick and straightforward zebrafish xenograft model that provides a promising alternative to these existing mouse models. We demonstrate that this model can be utilized to study tumor cell growth of several major medulloblastoma subgroups. More importantly, our model facilitates high-throughput drug testing, providing a scalable opportunity forin vivodrug screenings that will support the discovery of novel therapeutic compounds against medulloblastoma.
Metavinculin mediates differentiation cues into myogenic gene expression
Authors: Murugan Abinayaselvi , Nanjegowda Nandeesh Bevinahalli , Jothi Mathivanan
Published: February 2024

Isoform switching in deciphering differentiation signals into myogenic transcriptional output remains unexplored. Here, we report a distinct function of muscle-specific metavinculin isoform in switching canonical to non-canonical Wnt-pathways to establish skeletal muscle differentiation. Metavinculin expression is specifically associated with muscle differentiation, regeneration and absent in proliferating myoblasts. During differentiation, metavinculin-specific exon retention is facilitated by the direct binding of Rbfox1 to its downstream intron. Depletion of metavinculin impairs skeletal muscle differentiation, while its ectopic expression induces genes associated with differentiation even in proliferating myoblasts. Subsequent results revealed that pharmacological activation of canonical Wnt impedes muscle differentiation, whereas its inhibition stimulates differentiation. Canonical Wnt inhibition or ectopic non-canonical Wnt7b expression restores muscle differentiation programs in metavinculin-depleted cells. These results indicates a dynamic interplay between Rbfox1-generated metavinculin and Wnt-signaling pathways. This advancement sheds light on the intricate molecular mechanisms underlying skeletal muscle differentiation and suggests potential therapeutic targets for muscle-related disorders.
Exposure to bilingual or monolingual maternal speech during pregnancy affects the neurophysiological encoding of speech sounds in neonates differently
Authors: Arenillas-Alcón Sonia , Gorina-Careta Natàlia , Puertollano Marta , Mondéjar-Segovia Alejandro , Ijjou-Kadiri Siham , Costa-Faidella Jordi , Gómez-Roig María Dolores , Escera Carles
Published: February 2024

Exposure to maternal speech during the prenatal period shapes speech perception and linguistic preferences, allowing neonates to recognize stories heard frequently in utero and demonstrating an enhanced preference for their mother’s voice and native language. Yet, with a high prevalence of bilingualism worldwide, it remains an open question whether monolingual or bilingual maternal speech during pregnancy influence differently the fetus’ neural mechanisms underlying speech sound encoding. In the present study, the frequency-following response (FFR), an auditory evoked potential that reflects the complex spectrotemporal dynamics of speech sounds, was recorded to a two-vowel /oa/ stimulus in a sample of 131 healthy term neonates within the 1-3 days after birth. Newborns were divided into two groups according to maternal language usage during the last trimester of gestation (monolingual; bilingual). Spectral amplitudes and spectral signal-to-noise ratios (SNR) at the stimulus fundamental (F0) and first formant (F1) frequencies of each vowel were respectively taken as measures of pitch and formant structure neural encoding. Our results reveal that while spectral amplitudes at F0did not differ between groups, neonates from bilingual mothers exhibited a lower spectral SNR. Additionally, monolingually exposed neonates exhibited a higher spectral amplitude and SNR at F1frequencies. We interpret our results under the consideration that bilingual maternal speech, as compared to monolingual, is characterized by a greater complexity in the speech sound signal, rendering newborns from bilingual mothers more sensitive to a wider range of speech frequencies without generating a particularly strong response at any of them. Our results contribute to an expanding body of research indicating the influence of prenatal experiences on language acquisition and underscore the necessity of including prenatal language exposure in developmental studies on language acquisition, a variable often overlooked yet capable of influencing research outcomes.
Land-use impacts on plant functional diversity throughout Europe
Authors: Rosa Francesca , van Bodegom Peter M. , Hellweg Stefanie , Pfister Stephan , Biurrun Idoia , Boch Steffen , Chytrý Milan , Ćušterevska Renata , Dalle Fratte Michele , Damasceno Gabriella , Garbolino Emmanuel , Lenoir Jonathan , Ozinga Wim A , Penuelas Josep , Sabatini Francesco Maria , Schrodt Franziska , Uogintas Domas , Byun Chaeho , Dolezal Jiri , Dziuba Tetiana , Hérault Bruno , Martín-Forés Irene , Niinemets Ülo , Peyre Gwendolyn , Scherer Laura
Published: February 2024

Aim

Global biodiversity loss resulting from anthropogenic land-use activities is a pressing concern, requiring precise assessments of impacts at large spatial extents. Existing models mainly focus on species richness and abundance, lacking insights into ecological mechanisms and species’ roles in ecosystem functioning. To bridge this gap, we conducted an extensive analysis of the impact of human land use on vascular plant functional diversity, across diverse land-use classes and bioregions in Europe, comparing it to traditional metrics.

Location: EuropeTime period: 1992-2019Major taxa studied: Vascular plants

Methods

Integrating extensive databases of vegetation plots with spatial data on land use and land cover, we paired plots from areas actively used and modified by humans with plots from natural habitats under similar environmental conditions. Using species occurrences and traits, in each plot we computed three complementary functional diversity metrics (functional richness, evenness, and divergence), species richness and abundance. We assessed the impact of land use by comparing the metrics in the paired plots.

Results

Our findings revealed that, compared to natural habitats, anthropogenic land use exhibits lower functional richness and divergence but higher functional evenness across most land-use classes and bioregions. The response of functional richness was more marked than the other two metrics and especially pronounced in croplands and urban areas and in northern bioregions. Functional richness exhibited a pattern that did not fully overlap with the trend in species richness, providing useful complementary information.

Main conclusions

We provide a large-scale precise assessment of anthropogenic land-use impacts on functional diversity across Europe. Our findings indicate that: (i) human disturbance significantly alters plant functional diversity compared to natural habitats; (ii) this alteration goes in the direction of functional homogenization; (i) functional diversity metrics complement traditional metrics by offering deeper insights into the ecological mechanisms in response to anthropogenic land use.
DDR1 regulates RUNX1-CBFβ to control breast stem cell differentiation
Authors: Trepicchio Colin , Rauner Gat , Traugh Nicole , Parrish Meadow , Fein Daniel E.C. , Mal Youssof , Kuperwasser Charlotte
Published: February 2024

The human breast is complex and comprised of multi-lineage and multi-structural elements. Recent work has shown that epithelial stem and progenitor cells use the collagen receptor Discoidin Domain Receptor 1 (DDR1) for differentiation into both basal and luminal cell lineages, which together are necessary for both ductal and alveolar morphogenesis. We developed a next-generation single cell derived organoid model that generates miniaturized breast tissue, to study how single stem cells can give rise to multiple cell types and compound tissue structures. We show that DDR1 activation triggers stem cell differentiation via RUNX1 in turn driving multilineage differentiation as well as complex ductal-lobular development. Mechanistically, DDR1 affects the interaction and expression of RUNX1 and its cofactor CBFβ thereby regulating its activity. Together, these findings contribute to the current understanding of how the extracellular matrix component within the stem cell niche drives organogenesis and tissue regeneration.
Asiatic acid improves mitochondrial function, activates antioxidant response in the mouse brain and improves cognitive function in beta-amyloid overexpressing mice
Authors: Varada Samantha , Chamberlin Steve R , Bui Lillie , Brandes Mikah S , Gladen-Kolarsky Noah , Harris Christopher J , Hack Wyatt , Brumbach Barbara H , Quinn Joseph F , Gray Nora E
Published: February 2024

Extracts of the plantCentella asiaticacan enhance mitochondrial function, promote antioxidant activity and improve cognitive deficits. Asiatic acid (AA) is one of the constituent triterpene compounds present in the plant. In this study we explore the effects of increasing concentrations of AA on brain mitochondrial function, antioxidant response and cognition in healthy mice and a single concentration of AA in the beta-amyloid overexpressing 5xFAD mouse line. Associative memory and overall activity were assessed. Hippocampal mitochondrial bioenergetics and the expression of mitochondrial and antioxidant response genes was determined. In the 5xFAD line, total beta-amyloid plaque burden after AA treatment was also evaluated. In healthy mice, we report dose responsive effects of increasing concentrations of AA on enhanced associative memory and a dose dependent increase in basal and maximal mitochondrial respiration, mitochondrial gene expression and antioxidant gene expression. Results from the highest AA dose (1% AA) were similar to what was observed with CAW. The high AA dose was then evaluated in the context of Aβ accumulation in 5xFAD mice. Improvements in mitochondrial and antioxidant response genes were favored in females over males without significant alleviation of Aβ plaque burden.
Genetic diversity in vector populations influences the transmission efficiency of an important plant virus
Authors: Leybourne Daniel J , Whitehead Mark A , Will Torsten
Published: February 2024

The transmission efficiency of aphid-vectored plant viruses can differ between aphid populations. Intra-species diversity (genetic variation, endosymbionts) is a key determinant of aphid phenotype; however, the extent of which intra-species diversity contributes towards variation in virus transmission efficiency is unclear. Here, we use multiple populations of two key aphid species that vector barley yellow dwarf virus (BYDV) strain PAV (BYDV-PAV), the grain aphid (Sitobion avenae) and the bird cherry-oat aphid (Rhopalosiphum padi), and examine how diversity in vector populations influences virus transmission efficiency. We use Illumina sequencing to characterise genetic and endosymbiont variation in multipleS. avenaeandR. padipopulations and conduct BYDV-PAV transmission experiments to identify links between intra-species diversity in the vector and virus transmission efficiency. We observe limited variation in the transmission efficiency ofS. avenae, with transmission efficiency consistently low for this species. However, forR. padiwe observe a range of transmission efficiency and show that BYDV transmission efficiency is influenced by genetic diversity within the vector, identifying 542 SNPs that potentially contribute towards variable transmission efficiency inR. padi. Our results represent an important advancement in our understanding of the relationship between genetic diversity, vector-virus interactions, and virus transmission efficiency.
Kaempferol exerts anti-inflammatory effects by accelerating Treg development via AhR-mediated and PU.1/IRF4-dependent transactivation of theAldh1a2/RALDH2 gene in dendritic cells
Authors: Takahashi Miki , Nagata Kazuki , Watanuki Yumi , Yamaguchi Masaki , Minamikawa Natsuki , Katagiri Mayuka , Zhao Weiting , Ito Naoto , Yashiro Takuya , Nishiyama Chiharu
Published: February 2024

Retinaldehyde dehydrogenase 2 encoded in theAldh1a2gene (RALDH2) is expressed in intestinal dendritic cells (DCs) in mesenteric lymph nodes (MLNs) and plays a crucial role in Treg development by producing retinoic acid. In the present study, we screened food ingredients and identified kaempferol, a flavonoid, as the compound that most effectively up-regulated RALDH2 expression in DCs. The development of Foxp3+cells from OT-II-derived naïve CD4+T cells was enhanced by a co-culture with OVA peptide-pulsed bone marrow-derived DCs (BMDCs) in the presence of kaempferol or by a pre-treatment of BMDCs with kaempferol. The involvement of the aryl hydrocarbon receptor (Ahr) in the effects of kaempferol onAldh1a2expression was demonstrated byin vitroexperiments using siRNA and various agonistic or antagonistic compounds of AhR. AhR suppressedAldh1a2gene expression and kaempferol inhibited the AhR activity by functioning as an antagonist of AhR. The kaempferol treatment also increased the protein levels of PU.1 and IRF4, which are essential for transcription of theAldh1a2gene in DCs, and accelerated the subsequent recruitment of PU.1 to theAldh1a2gene. The kaempferol-induced increase in PU.1 protein levels occurred in an AhR-dependent and transcription-independent manner, whereas the kaempferol treatment transactivated theIrf4gene in DCs. The frequency of DCs exhibiting RALDH2 activity in the MLNs of mice was increased by the intraperitoneally (i.p.) administration of an AhR antagonist or by the oral administration of astragalin, a 3-O-glucoside of kaempferol. We also observed an increase in Tregs in the Peyer’s patches of C57BL/6 mice i.p. administered kaempferol-treated BMDCs. We utilized an OVA-induced food allergy model of Balb/c mice to examine the effects of kaempferolin vivoand confirmed that the rapid decrease in body temperature and allergic diarrhea observed just after the OVA challenge were significantly suppressed in mice administered kaempferol.
Differential colonization and succession dynamics of marine bacteria on different plastic polymers
Authors: Davidov Keren , Itzahri Sheli , Sinberger Liat Anabel , Oren Matan
Published: February 2024

During the past decades since plastic was introduced to the world, marine microorganisms have been adapted for life on marine plastic debris, forming unique plastic-attached microbial communities. To date, little is known about the colonization and succession processes that take place on plastic surfaces in marine environments and how the plastic polymer type affects the plastic-attached microbiome composition. To address this knowledge gap, we examined the colonization and succession dynamics of marine bacteria on four common plastic polymers - PE, PP, PS, and PET-compared to glass and wood in a controlled seawater system under different temperatures. Using a simple experimental design, coupled with a long-read 16S rRNA metabarcoding pipeline and a set of complementary data analyses, we characterized the temporal trends in the composition of the bacterial microbiome developed on different surfaces over 2 - 90 days. By applying weighted gene co-expression network (WGCNA) analysis, we established co-occurrence networks and identified genera with specific succession signatures, significant enrichment on specific plastic polymers and/or strong intra-genus connections. Among them, members of genusAlcanivoraxwere significantly enriched on either PE or PP plastic surfaces as early as 2 days post-inoculation.Alcanivoraxcolonization preference to polyolefins was confirmed in colonization assays with pureAlcanivoraxstrains. Our research approach presented here may contribute to understanding how plastisphere communities are being formed and help identify taxa with specific adaptations to plastic surfaces.
CD81+fibroblasts, a unique subpopulation with accelerated cellular senescence, exaggerate inflammation and activate neutrophils via C3/C3aR1 axis in periodontitis
Authors: Fu Liangliang , Yin Chenghu , Zhao Qin , Guo Shuling , Shao Wenjun , Xia Ting , Sun Quan , Chen Liangwen , Wang Min , Xia Haibin
Published: February 2024

Periodontitis, a prevalent inflammatory disease worldwide, poses a significant economic burden on society and the country. Despite numerous studies, the biological molecular mechanism underlying the development and progression of periodontitis remains unclear. Previous research has established a connection between cellular senescence and periodontitis. However, the role and mechanism of cell senescence in the progression of periodontitis have not been thoroughly investigated. This study aimed to explore the involvement of cellular senescence in the pathogenesis of periodontitis and determine the underlying mechanisms. Our findings demonstrated that senescent cells accumulated during the periodontitis progress and inhibiting cellular senescence in periodontitis via administration of metformin successfully alleviated inflammation and bone loss. Moreover, several scRNA-seq analysis suggested that gingival fibroblasts were the main cell population undergoing cellular senescence during periodontitis, which helps mitigate tissue damage and bone loss. Furthermore, we identified a high expression of CD81 in the senescent gingival fibroblast population. These cells were found to actively contribute to inflammation through their potent pro-inflammatory metabolic activity and secretion of SASP-related factors. Additionally, they recruited neutrophils via the C3/C3aR1 pathway, indirectly sustaining the inflammatory response. These results provide valuable insights into the cellular and molecular basis of periodontitis-induced tissue damage, highlighting the significance of fibroblast senescence. In conclusion, our study sheds light on the relationship between CD81 and cellular senescence, suggesting its potential as a therapeutic target for periodontitis.
High phenotypic and genotypic plasticity among strains of the mushroom-forming fungusSchizophyllum commune
Authors: Marian Ioana M. , Valdes Ivan D. , Hayes Richard D. , LaButti Kurt , Duffy Kecia , Chovatia Mansi , Johnson Jenifer , Ng Vivian , Lugones Luis G. , Wösten Han A. B. , Grigoriev Igor V. , Ohm Robin A.
Published: February 2024

Schizophyllum communeis a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related speciesSchizophyllum fasciatumwas sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes will provide a solid basis for functional genomics analyses of the strains ofS. commune.
Regulation of temporal cytokine production by co-stimulation receptors in TCR-T cells is lost in CAR-T cells
Authors: Patel Ashna , Kutuzov Mikhail A. , Dustin Michael L. , van der Merwe P. Anton , Dushek Omer
Published: February 2024

CD8+ T cells contribute to immune responses by producing cytokines when their T cell receptors (TCRs) recognise peptide antigens on major-histocompability-complex (pMHC) class I. However, excessive cytokine production can be harmful. For example, cytokine release syndrome (CRS) is a common toxicity observed in treatments that activate T cells, including chimeric antigen receptor (CAR)-T cell therapy. While engagement of costimulatory receptors is well known to enhance cytokine production, we have limited knowledge of their ability to regulate the kinetics of cytokine production by CAR-T cells. Here we compare early (0-12 hours) and late (12-20 hours) production of IFN-γ, IL-2, and TNF-α production by T cells stimulated via TCR or CARs in the presence or absence ligands for CD2, LFA-1, CD28, CD27, and 4-1BB. For T cells expressing TCRs and 1st-generation CARs, activation by antigen alone was sufficient to stimulate early cytokine production, while co-stimulation by CD2 and 4-1BB was required to maintain late cytokine production. In contrast, T cells expressing 2nd-generation CARs, which have intrinsic costimulatory signalling motifs, produce high levels of cytokines in both early and late periods in the absence of costimulatory receptor ligands. Losing the requirement for costimulation for sustained cytokine production may contribute to the effectiveness and/or toxicity of 2nd-generation CAR-T cell therapy.

Graphical abstract
Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7
Authors: Albani Simone , Bhagavath Eswaran Vishal Sudha , Piergentili Alessia , de Souza Paulo Cesar Telles , Lampert Angelika , Rossetti Giulia
Published: February 2024

Cholesterol is a major component of plasma membranes and unsurprisingly plays a significant role in actively regulating the functioning of several membrane proteins in humans. Notably, recent studies have shown that cholesterol depletion can also impact transmission of potentially painful signals in the context of peripheral inflammation, via hyperexcitability of the voltage-gated sodium channel (Nav) subtype 1.9, but the structural mechanisms underlying this regulation remain to be elucidated. In this study, we focus on the role of cholesterol depletion on Nav1.7, which is primarily expressed in the peripheral sensory neurons and linked to various chronic inherited pain syndromes. Coarse-grained molecular dynamics simulations shed light on the dynamic changes of the geometry of Nav1.7 upon membrane cholesterol depletion: A loss of rigidity at key structural motifs linked to activation and fast-inactivation is observed, as well as changes in the geometry of drug-binding regions in the channel. Loss of rigidity in cholesterol depleted conditions should allow the channel to transition between different gating states more easily.In-vitrowhole-cell patch clamp experiments on HEK293t cells expressing Nav1.7 validated these predictions madein silicoat the functional level. Hyperpolarizing shifts in the voltage-dependence of activation and fast-inactivation were observed along with an acceleration of the time to peak and onset kinetics of fast inactivation. These results underline the critical role of membrane composition, and of cholesterol in particular, in influencing Nav1.7 gating characteristics. Furthermore, our results hint to a key role of the membrane environment in affecting drug effects and in pathophysiological dysregulation, sharpening our approaches for analgesics design.

Supplementary data

https://doi.org/10.5281/zenodo.10829175
A genetically-encoded nanobody sensor reveals conformational diversity in β-arrestins orchestrated by distinct seven transmembrane receptors
Authors: Sarma Parishmita , Marková Vendula Nagy , Zaidi Nashrah , Dalal Annu , Mishra Sudha , Yadav Manish K. , Mahajan Gargi , Roy Nabarun , Miclea Paul , Lazar Josef , Shukla Arun K.
Published: February 2024

Agonist-induced interaction of G protein-coupled receptors (GPCRs) with β-arrestins (βarrs) is a critical mechanism that regulates the spatio-temporal pattern of receptor localization and downstream signaling. While the underlying mechanism governing GPCR-βarr interaction is primarily conserved and involves receptor activation and phosphorylation, there are several examples of receptor-specific fine-tuning of βarr-mediated functional outcomes. Considering the key contribution of conformational plasticity of βarrs in driving receptor-specific functional responses, it is important to develop and characterize novel sensors capable of reporting distinct βarr conformations in cellular context. Here, we design an intrabody version of a βarr-recognizing nanobody (nanobody32), referred to as intrabody32 (Ib32), in NanoLuc enzyme complementation assay format, and measure its ability to recognize βarr1 and 2 in live cells upon activation of a broad set of GPCRs. We discover that Ib32 robustly recognizes activated βarr1 and 2 in the plasma membrane as well as in the endosomes, and effectively mirrors βarr recruitment profile upon stimulation of GPCRs. We also design an Ib32 sensor for single-photon polarization microscopy with a change in linear dichroism as readout and demonstrate its utility for monitoring βarr activation upon stimulation of angiotensin receptor by its natural and biased agonists. Interestingly, when used side-by-side with a previously described sensor of βarr1 conformation known as Ib30, Ib32 uncovers distinct conformational signatures imparted on βarrs by different GPCRs, which is further corroborated using an orthogonal limited proteolysis assay. Taken together, our study presents Ib32 as a novel sensor to monitor βarr activation and leverages it to uncover conformational diversity encoded in the GPCR-βarr system with direct implications for improving the current understanding of GPCR signaling and regulatory paradigms.
SpaCCC: Large language model-based cell-cell communication inference for spatially resolved transcriptomic data
Authors: Ji Boya , Xu Liwen , Peng Shaoliang
Published: February 2024

Drawing parallels between linguistic constructs and cellular biology, large language models (LLMs) have achieved remarkable success in diverse downstream applications for single-cell data analysis. However, to date, it still lacks methods to take advantage of LLMs to infer ligand-receptor (LR)-mediated cell-cell communications for spatially resolved transcriptomic data. Here, we propose SpaCCC to facilitate the inference of spatially resolved cell-cell communications, which relies on our fine-tuned single-cell LLM and functional gene interaction network to embed ligand and receptor genes expressed in interacting individual cells into a unified latent space. The LR pairs with a significant closer distance in latent space are taken to be more likely to interact with each other. After that, the molecular diffusion and permutation test strategies are respectively employed to calculate the communication strength and filter out communications with low specificities. The benchmarked performance of SpaCCC is evaluated on real single-cell spatial transcriptomic datasets with remarkable superiority over other methods. SpaCCC also infers known LR pairs concealed by existing aggregative methods and then identifies communication patterns for specific cell types and their signalling pathways. Furthermore, spaCCC provides various cell-cell communication visualization results at both single-cell and cell type resolution. In summary, spaCCC provides a sophisticated and practical tool allowing researchers to decipher spatially resolved cell-cell communications and related communication patterns and signalling pathways based on spatial transcriptome data.
Graph analysis of the guilt network highlights associations with subclinical anxiety and self-blame
Authors: Zareba Michal Rafal , Bielski Krzysztof , Costumero Victor , Visser Maya
Published: February 2024

Maladaptive forms of guilt, such as excessive self-blame, are common characteristics of anxiety disorders. The associated network includes the superior anterior temporal lobe (sATL), underlying the conceptual representations of social meaning, and fronto-subcortical areas involved in the affective dimension of guilt. Nevertheless, despite understanding the anatomy of the guilt processing circuitry, network-level changes related to subclinical anxiety and self-blaming behaviour have not been depicted. To fill this gap, we used graph theory analyses on a resting-state functional and diffusion-weighted magnetic resonance imaging dataset of 78 healthy adults. Within the guilt network, we found increased functional contributions (higher clustering coefficient, local efficiency and strength) of the left sATL for individuals with higher self-blaming and trait-anxiety, while functional isolation (lower clustering coefficient and local efficiency) of the left pars opercularis and insula was related to higher trait-anxiety. Trait-anxiety was also linked to the structural network’s global parameters (mean clustering coefficient), with the circuitry’s architecture favouring increased local information processing in individuals with increased anxiety levels. Previous research suggests that aberrant interactions between conceptual (sATL) and affective (fronto-limbic) regions underlie maladaptive guilt and the current results align and expand on this theory by detailing network changes associated with self-blame and trait-anxiety.
Quantifying vulnerability to plant invasion across global ecosystems
Authors: Pfadenhauer William G. , Bradley Bethany A.
Published: February 2024

The widely-referenced “tens rule” in invasion ecology suggests that 10% of established, non-native species will become invasive. However, the accuracy of this estimate has been questioned, as the original analysis focused on small groups of plant species in Great Britain and Australia. Using a novel database of 9,501 established and 2,924 invasive plants, we provide a comprehensive evaluation of plant invasion rates and the first empirical analysis of how the tens rule varies across climate zones and spatial scales. We found that invasion rates ranged from 17% at the country scale to 25% at the continental scale. Tropical communities are often considered to be resistant to invasion, however our results showed significantly higher invasion rates in the tropics and especially on tropical islands, suggesting unexpectedly high vulnerability of these species-rich ecosystems. Our analysis provides improved, environment-specific estimates of invasion rates which are often twice as high as previous expectations. We recommend that practitioners reject the tens rule for plants and adjust future management practices to reflect these updated estimates of invasion risk.

Open Research Statement

The data and code that support the findings of this study are openly available on GitHub athttps://github.com/wpfadenhauer/Global-Invasion-Rates
New insights into the mechanisms of plant isotope fractionation from combined analysis of intramolecular13C and deuterium abundances inPinus nigratree-ring glucose
Authors: Wieloch Thomas , Holloway-Phillips Meisha , Yu Jun , Niittylä Totte
Published: February 2024

Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data.

To gain new insights into isotope fractionation, we analysed intramolecular13C discrimination in tree-ring glucose (Δi’,i= C-1 to C-6) and metabolic deuterium fractionation at H1and H2(εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution.

We found evidence for metabolic processes affectingΔ1’ andΔ3’ which respond to air vapour pressure deficit (VPD), and processes affectingΔ1’,Δ2’, andεmetwhich respond to precipitation but notVPD. These relationships exhibit change points dividing a period of homeostasis (1961-1980) from a period of metabolic adjustment (1983-1995). Homeostasis may result from sufficient groundwater availability. Additionally, we foundΔ5’ andΔ6’ relationships with radiation and temperature which are temporally stable and consistent with previously proposed isotope fractionation mechanisms.

Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducingΔ1’,Δ2’,Δ3’, andεmetvariability.
Development of radial frequency pattern perception in macaque monkeys
Authors: Rodríguez Deliz C. L. , Lee Gerick M. , Bushnell Brittany N. , Majaj Najib J. , Movshon J. Anthony , Kiorpes Lynne
Published: February 2024

Infant primates see poorly, and most perceptual functions mature steadily beyond early infancy. Behavioral studies on human and macaque infants show that global form perception, as measured by the ability to integrate contour information into a coherent percept, improves dramatically throughout the first several years after birth. However, it is unknown when sensitivity to curvature and shape emerges in early life. We studied the development of shape sensitivity in eighteen macaques, aged 2 months to 10 years. Using radial frequency stimuli (RFS), circular targets whose radii are modulated sinusoidally, we tested monkeys’ ability to discriminate RFS from circles as a function of the depth and frequency of sinusoidal modulation. We implemented a new 4-choice oddity task and compared the resulting data with that from a traditional 2-alternative task. Behavioral performance at all radial frequencies improved with age. Performance was better for higher radial frequencies, suggesting the developing visual system prioritizes processing of fine visual details that are ecologically relevant. By utilizing two complementary methods, we were able to capture a comprehensive developmental trajectory for shape perception.
Sensory perception of fluctuating light in Arabidopsis
Authors: Belmonte Antonela , Tissot Nicolas , Rabinovich Andrés , Ploschuk Edmundo L. , Crocco Carlos D. , Ulm Roman , Casal Jorge J.
Published: February 2024

When exposed to shade from neighbours, competitive plants modify their growth patterns to improve access to light. In dense plant stands, ranging from forests to humid grasslands and crops, shade is interrupted by sunflecks penetrating the canopy. Relatively infrequent, minute-scale interruptions can significantly contribute to the daily light input. However, given the short duration and the time gap between these low frequency sunflecks (LFS), whether plants can sense them was unknown. Here we show that phytochrome B (phyB), cryptochrome 1 (cry1), cry2, and UV RESISTANCE LOCUS 8 (UVR8) cooperatively perceive LFS to reduce hypocotyl growth inArabidopsis thaliana. LFS also enhanced the expression of photosynthetic and photo-protective genes and initiated pre-emptive acclimation to water restriction. Repeated LFS increased the nuclear abundance of cry1 and UVR8. This positive feedback enhanced the sensitivity to subsequent LFS and even to the shade between LFS. LFS reduced the nuclear abundance of the growth regulator PHYTOCHROME INTERACTING FACTOR 4 (PIF4), which only slowly recovered upon return to shade, further amplifying the signal. The dynamics of the photo-sensory system under fluctuating light helps adjust plants to the prevailing conditions.
Metadichol® induced expression of circadian clock transcription factors in human fibroblasts
Authors: Raghavan P.R.
Published: February 2024

The circadian clock genes play a significant role in various aspects of health and disease, including sleep, metabolism, inflammation, and cancer. CRY1, BMAL1, PER1, PPARGC1A, and CLOCK are key circadian clock genes that govern the daily rhythms of diverse physiological processes in mammals. These genes create a feedback loop called a transcriptional-translational feedback loop (TTFL). In this loop, the heterodimer of CLOCK and BMAL1 stimulates the production of CRY1, PER1, and other clock genes. Moreover, the CRY1 and PER1 proteins suppressed the activity of CLOCK-BMAL1. PPARGC1A is a transcription factor that regulates the expression of clock genes and metabolic genes. Only a limited number of agonists are currently known to activate these genes. In this study, we showed that treatment with metadichol, a nanoemulsion of long-chain alcohols, significantly increased the expression of the CRY1, CLOCK, and PPARGC1A genes by 4-5-fold in human fibroblasts. Additionally, 100 ng of metadichol maintained the expression of the PER1 and BMAL1 genes, as confirmed by quantitative real-time polymerase chain reaction (Q-rt-PCR) data. The lack of significant changes in PER1 and BMAL1 expression suggested that metadichol does not directly affect these genes. However, since these genes are part of the core circadian clock machinery, their normal functioning is crucial for maintaining the circadian rhythm.