bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving properties of chitosan/polyvinyl alcohol films using cashew nut testa extract: potential applications in food packaging
Authors: Dang Thuy Tien , Nguyen Lam Anh Thy , Dau Duc Tien , Nguyen Quy Sinh , Le Thao Nhien , Nguyen Thi Quynh Ngoc
Published: December 2024

Cashew nut testa, a by-product of cashew nut processing, is abundant in phenolic compounds and exhibits strong antioxidant properties, making it a potential additive for enhancing the antioxidant properties of biodegradable films used in food packaging. This study explores the fabrication of biodegradable chitosan/polyvinyl alcohol films incorporating varying concentrations of cashew nut testa extract (CNTE; 0, 1, 2 and 3% v/v) and evaluates their physical, structural, mechanical, optical and antioxidant properties. The results demonstrate that increasing extract concentration generally increased the thickness, tensile strength, Young's modulus, thermal stability and antioxidant capacity of the films, while reducing the moisture content, swelling degree, elongation at break, and light transmittance. Specifically, the film with 3% extract showed approximately 11% lower moisture content and 31% lower swelling degree compared with the plain film. It also displayed the highest tensile strength and Young's modulus at 28.63 and 147.35 MPa, respectively. Microstructural analysis revealed that the incorporation of CNTE resulted in a smoother and slightly denser film structure. Antioxidant activity, determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging assay, was not detected in the plain film but increased with increasing extract concentration. The film with 3% CNTE exhibited the highest antioxidant activity of 58.93 µmol Trolox equivalents (TE) g
−1
film. This study highlights the potential of CNTE as an effective edible additive for developing antioxidant and ultraviolet barrier films with improved mechanical strength and water resistance for food packaging applications.
Identification of subwavelength microstructural information from macroscopic boundary measurements in elastodynamics
Authors: Lochner Tanja , Peter Malte A.
Published: December 2024

We present a method to obtain microstructural information from macroscopic boundary measurements exploiting scattering governed by the wave equation in a bounded linearly elastic domain in the long-wavelength regime. Applying a force to the outer boundary of the body on the macroscopic scale while measuring the resulting boundary displacement, we solve the inverse problem of identifying the geometry of the microstructure in the context of periodic homogenization minimizing a tracking-type objective functional as long as the geometry of the microstructure is parameterized by a finite set of parameters. Shape calculus is used to characterize the Gâteaux derivative of the objective function facilitating the use of gradient-based algorithms, and we present numerical experiments for a generic non-destructive testing problem for ellipsoidal microstructures showcasing the functioning of the identification method.
Heterogeneous mosquito exposure increases
Plasmodium vivax
and
Plasmodium falciparum
co-infections: a modelling study
Authors: Grimée Mathilde , Taylor Aimee R. , White Michael T.
Published: December 2024

In malaria-endemic regions,
Plasmodium vivax
and
Plasmodium falciparum
coexist and may interact. For instance, fevers induced by
P. falciparum
might activate dormant
P. vivax
parasites and concurrent radical cure of both species has been proposed to prevent relapses. Heterogeneous mosquito exposure may contribute to the dependence of both parasites. We conducted a literature review on their respective prevalence and that of co-infections. The data revealed a positive correlation between
P. vivax
and
P. falciparum
prevalence, and co-infection prevalences exceeding expectations assuming infections occur independently. We used the review data to fit a compartmental model of co-infections that features heterogenous mosquito exposure. The fit suggests that heterogeneous exposure sufficiently explains the observed departure from independence. Finally, we performed simulations under the model assessing the impact on
P. vivax
prevalence of the activation-by-fever hypothesis and the radical cure proposition. We demonstrated a moderate impact of allowing
P. falciparum
fevers to reactivate
P. vivax
and a substantial impact of treating
P. falciparum
cases with radical cure. Our model highlights dependence between
P. falciparum
and
P. vivax
and emphasizes the influence of heterogeneous mosquito exposure. This simple framework can inform the design of more complex models assessing integrated malaria control strategies in coendemic regions.
Managing the tradeoff between reproduction and survival requires flexibility in behaviour and gene regulation in three-spined stickleback
Authors: Barbasch Tina A. , Abuwa Victoria I. , Carswell Beth , Bell Alison M.
Published: December 2024

Predators exert a powerful selective force, however, predator avoidance can conflict with other important activities such as attracting mates. Decisions over whether to court mates versus avoiding predators are vital to fitness, yet the mechanistic underpinnings of how animals manage such tradeoffs are poorly understood. Here, we investigate the flexibility of behaviour and gene regulation in response to a tradeoff between avoiding predators (survival) and courting potential mates (reproduction) in three-spined stickleback (
Gasterosteus aculeatus
). We compared behavioural and transcriptomic responses of male sticklebacks faced with a courtship opportunity and cues of a predator simultaneously with the responses of males faced with a courtship opportunity or cues of a predator alone, and found that males behaviourally compromised courtship in favour of predator avoidance when faced with a tradeoff between them. The need to manage this tradeoff elicited dynamic changes in brain gene expression, and sets of functionally connected genes were organized into discrete modules based on co-expression. Additionally, we found that behavioural flexibility in response to tradeoffs corresponded to flexibility in gene regulatory network structure. Combined, these results uncover the coordinated response by the brain to a fundamental ecological tradeoff, providing insight into the structure and function of genetic networks underpinning how animals make fitness-influencing decisions.
Extensive locomotor versatility across a global sample of hunter–gatherer societies
Authors: Brill George , Mirazon-Lahr Marta , Dyble Mark
Published: December 2024

Studies of hunter–gatherer locomotion inform a wide range of academic fields, from human behavioural ecology and hominin evolution to sports science and evolutionary health. Despite celebrated ethnographic examples of hunter–gatherer locomotor proficiency in running, climbing, swimming and diving, there has been limited systematic analysis of cross-cultural variation in hunter–gatherer locomotor versatility. We conducted a systematic cross-cultural analysis of hunter–gatherer locomotion, coding locomotor behaviour from over 900 ethnographic documents. Our results indicated that high levels of locomotor versatility are common among hunter–gatherers, and that proficiency of running, climbing, swimming and diving is found in societies across the geographical and ecological breadth of the sample. Each locomotor modality was found to be relevant not only to food acquisition but also in leisure, ritual and violent conflict. Our results also indicated the prevalence of both male and female engagement within each locomotor modality, with climbing being the only modality to possess a notable bias towards male engagement in a substantial proportion of societies. The widespread habituality and functional significance of diverse locomotor proficiency in hunter–gatherers suggests that locomotor versatility represents a dimension of human adaptive lability, playing a major role in the ability of hunter–gatherers to thrive in almost every global ecology.
EsoDetect: Computational Validation and Algorithm Development of a Novel Diagnostic and Prognostic Tool for Dysplasia in Barrett’s Esophagus
Authors: Miskinyte Migla , Pondeca Benilde , Pereira-Leal José B. , Cardoso Joana
Published: December 2024

Barrett’s esophagus (BE) is the only known precursor to esophageal adenocarcinoma (EAC), a malignancy with increasing incidence and unfavorable prognosis. This study endeavors to identify BE biomarkers capable of diagnosing low-grade dysplasia (LGD) in BE, as well as biomarkers that can predict the progression from BE to EAC to be subsequently integrated into diagnostic and prognostic algorithms.

Datasets containing gene expression data from metaplastic and dysplastic BE, as well as EAC tissue samples, were collected from public databases and used to explore gene expression patterns that differentiate between non-dysplastic (ND) and LGD BE (for diagnostic purposes) and between non-progressed and progressed BE (for prognostic purposes). Specifically, for the diagnostic application, three RNAseq datasets were employed, while for the prognostic application, nine microarray datasets were identified, and 25 previously described genes were validated. A Thresholding Function was applied to each gene to determine the optimal gene expression threshold for group differentiation. All analyzed genes were ranked based on the F1-score metrics. Following the identification of genes with superior performance, different classifiers were trained. Subsequently, the best algorithms for diagnostic and prognostic applications were selected.

In evaluating the value of gene expression for diagnosis and prognosis, the analyzed datasets allowed for the ranking of biomarkers, resulting in eighteen diagnostic genes and fifteen prognostic genes that were used for further algorithm development. Ultimately, a linear support vector machine algorithm incorporating ten genes was identified for diagnostic application, while a radial basis function support vector machine algorithm, also utilizing ten genes, was selected for prognostic prediction. Notably, both classifiers achieved recall and specificity scores exceeding 0.90.

The identified algorithms, along with their associated biomarkers, hold significant potential to aid in the early management of malignant progression of BE. Their strengths lie in their development using multiple independent datasets and their ability to demonstrate recall and specificity levels superior to those reported in the existing literature. Ongoing experimental and clinical validation is essential to further substantiate their utility and effectiveness, and to ensure that these tools can be reliably integrated into clinical practice to improve patient outcomes.
Implementing the mhGAP-HIG: The process and outcome of supervising trained primary health care workers in Khyber Pakhtunkhwa, Pakistan
Authors: Humayun Asma , Najmussaqib Arooj , Muneeb Noor ul Ain
Published: December 2024

Background

The province of Khyber Pakhtunkhwa (KP), grappling with frequent humanitarian and conflict challenges, faces significant gaps in mental health services marked by limited resources and inequitable distribution of services. To strengthen these services in nine districts in the province, 105 PHCWs were trained to identify and treat psychological conditions and were subsequently supervised for three months. This study examined the efficacy of remote supervision and analyzed the clinical data gathered during the supervision period.

Methods

A mixed-method approach was used to collect clinical data during supervision. Supervision covered assessment, management (including pharmacological and psychosocial interventions), and referral needs in all cases. Both qualitative and quantitative feedback were analyzed. Additionally, clinical data were examined to identify reported stressors and clinical presentations.

Results

Out of 105 registered trainees, 53 (50.34%) participants (including 38 PCPs and 15 CPs) submitted 413 cases through the application during three months of supervision following the initial training. The most frequently reported condition was depression (56.9%). Commonly reported stressors include health challenges or caregiver burden, marital or domestic challenges, bereavement, and socio-economic difficulties. Supervision was crucial in adjusting diagnoses in nearly a quarter of cases and management plans in 38.25% of cases. Participants expressed a preference for remote supervision and found it beneficial for assessment/diagnosis (61.1%), management interventions (72.2%), and referral guidance (44.4%).

Conclusion

Effective capacity building of PHCWs depends on remote supervision for an extended period, continuous monitoring of assessment and intervention skills, and the establishment of structured referral pathways. The collection of clinical data is crucial for improving the training programs. Systematic support from provincial governments is essential to scale up this initiative.
Bulk Transcriptomic Analysis with InMoose, the Integrated Multi-Omic Open-Source Environment in Python
Authors: Colange Maximilien , Appé Guillaume , Meunier Léa , Weill Solène , Johnson W. Evan , Nordor Akpéli , Behdenna Abdelkader
Published: December 2024

We introduce InMoose, an open-source Python environment aimed at omic data analysis. We illustrate its capabilities for bulk transcriptomic data analysis.

Due to its wide adoption, Python has grown as ade factostandard in fields increasingly important for bioinformatic pipelines, such as data science, machine learning, or artificial intelligence (AI). As a general-purpose language, Python is also recognized for its versatility and scalability. InMoose aims at bringing state-of-the-art tools, historically written in R, to the Python ecosystem. Our intent is to provide a drop-in replacement for R tools, so our approach focuses on the faithfulness to the original tools outcomes. The first development phase has focused on bulk transcriptomic data, with current capabilities encompassing data simulation, batch effect correction, and differential analysis and meta-analysis.
Knowledge Graph and Machine Learning Help the Research of Drugs Aimed at Neurological Diseases
Authors: Menestrina Luca , Recanatini Maurizio
Published: December 2024

In this study, we present PATHOS (PATHologies of HOmo Sapiens), a semantically rich knowledge graph constructed by integrating diverse datasets spanning multiple biomedical entity types. PATHOS provides a comprehensive resource for representing and exploring the intricate relationships underlying human diseases. To leverage this resource, we developed LOGOS (Learning Optimized Graph-based representations of Object Semantics), a graph embedding model capable of generating predictions relevant to drug research. The PATHOS-LOGOS framework was validated through three neurological case studies: drug repurposing for Alzheimer’s disease, phenotype selection for Huntington’s disease, and protein target identification in multiple sclerosis. The results demonstrate the potential of this approach to advance therapeutic insights and inform biomedical research.
Rebuilding the autoimmune-damaged corneal stroma through topical lubrication
Authors: Efraim Yael , Ting Chen Feeling Yu , Niknezhad Seyyed Vahid , Pham Dylan , Cheong Ka Neng , An Luye , Sinada Hanan , McNamara Nancy A. , Knox Sarah M.
Published: December 2024

Corneal lubrication is the most common treatment for relieving the signs and symptoms of dry eye and is considered to be largely palliative with no regenerative functions. Here we challenge this notion by demonstrating that wetting the desiccated cornea of an aqueous-deficient mouse model with the simplest form of lubrication, a saline-based solution, is sufficient to rescue the severely disrupted collagen-rich architecture of the stroma, the largest corneal compartment that is essential to transparency and vision. At the single cell level we show that stromal keratocytes responsible for maintaining stromal integrity are converted from an inflammatory state into unique reparative cell states by lubrication alone, thus revealing the extensive plasticity of these cells and the regenerative function of lubricating the surface. We further show that the generation of a reparative phenotype is due, in part, to disruption of an IL1β autocrine amplification loop promoting chronic inflammation. Thus, our study uncovers the regenerative potential of topical lubrication in dry eye and represents a paradigm shift in our understanding of its therapeutic impact.
PD-L1 expression is mediated by microRNA processing, Wnt/β-catenin signaling, and chemotherapy in Wilms tumor
Authors: Desai Kavita , Tiburcio Patricia D.B. , Warne Austin , Nabbi Arash , Zhou Serena , Reiff Sean D. , Campbell Matthew E. , Chen Kenneth S.
Published: December 2024

Inhibition of immune checkpoint proteins is effective in adult cancers but has shown limited efficacy in pediatric cancers. While factors regulating expression of immune checkpoint proteins such as PD-L1 are well-documented in adult cancers, their regulation is poorly understood in pediatric cancers. Here, we show that PD-L1 is upregulated in distinct subsets of Wilms tumor, the most common pediatric kidney cancer. Specifically, chemotherapy-exposed Wilms tumor specimens exhibited higher levels of PD-L1 expression, and common chemotherapeutics upregulated PD-L1 in childhood cancer cell linesin vitro. Furthermore, mutations inCTNNB1andDROSHA, the two most commonly mutated genes in Wilms tumor, correlated with higher PD-L1. Activation of Wnt/β-catenin signaling and knockdown ofDROSHAorDICER1both increase PD-L1in vitro. Lastly, in adult cancers,DICER1alterations are associated with immune gene expression signatures and improved survival in response to immune checkpoint inhibitors. Together, our results identify clinical and biological properties regulating PD-L1 in Wilms tumor that may inform precision therapy approaches in pediatric immuno-oncology.
FCRL4 and exhausted B cell signature in tumor infiltrating B cells from lung cancer
Authors: Bryushkova EA , Shchoka EV , Lukyanov DK , Gikalo MB , Mushenkova N , Laktionov K.K. , Kazakov A.M. , Khalmurzaev O.A , Matveev V.B. , Chudakov DM , Serebrovskaya EO
Published: December 2024

Our understanding of the heterogeneity of tumor-infiltrating B cells (TIBs) evolves in parallel with the advances in high-dimensional flow cytometry and single-cell RNA sequencing (scRNA-seq). Subpopulations of TIBs have been described with diverse and even opposite roles in tumor control, based on surface molecule, cytokine and transcriptional factor expression. Furthermore, recently the predictive role of IgA and IgG expression in tumors was shown for melanoma and KRAS-mutated, but not KRAS wild type, lung adenocarcinoma. This may imply that B cells producing different immunoglobulin isotypes also acquire different functional characteristics that have unequal effects on tumor microenvironment (TME) and differentially affect tumor progression. To address this question, we performed comparative bulk transcriptome analysis of tumor-infiltrating surface-IgA+ (sIgA+) and sIgG+ memory B cells from lung adenocarcinoma (LUAD) tumors. We identified FCRL4, PDCD1 and RUNX2 among genes overexpressed in IgA+ B cells, which suggests exhausted, chronically antigen-stimulated phenotype. Using public scRNA-seq data, we showed that FCRL4-expressing memory TIBs form a distinct cluster of cells with transcriptomic profile characterized by upregulation of genes involved in IFNγ and IFNα responses. sIgG+ B cells, on the other hand, overexpress IL5RA, consistent with the role of IL-5 in class-switch recombination to IgG isotype. Moreover, based on the analysis of the TCGA LUAD cohort, we found that FCRL4 to CD20 expression ratio correlates with lower overall survival, further strengthening the view on FCRL4 as a marker of exhausted dysfunctional TIBs. Our findings support the initial hypothesis that IgA/IgG ratio in tumors is not merely an indication of cytokine environment in the TME, but also reflects the difference in the functional characteristics of the respective B cell populations.
Vaginal Microbiome and Inflammation Among Chinese Women
Authors: Yichan Zhang , Ina Schuppe-Koistinen , Huarui Wang , Vicente Pelechano Garcia , Xiangyang Tian , Wei-Hua Chen , Guolan Gao , Juan Du
Published: December 2024

Human papillomavirus (HPV) infection, cervical intraepithelial neoplasia (CIN), pelvic organ prolapse (POP), cervical polyps (CP), abnormal uterine bleeding (AUB), and vaginitis are common conditions encountered in gynecological practice. In this study, we collected vaginal secretions from patients diagnosed with these diseases (n = 310) and from healthy donors (n = 112) to analyze their vaginal microbiome using 16S rRNA sequencing and cytokine expression using a cytometric bead array (CBA). Our findings revealed that the vaginal microbiome in POP patients exhibited higher complexity compared to other groups. Regarding cytokine expression, levels of IL-1α, IL-1β, IL-6, IL-8, MCP-1, and MIG were significantly elevated in HPV and CIN patients. Analysis of microbial associations showed thatLactobacillus crispatusandLactobacillus inerswere significantly negatively correlated with IL-1α and IL-1β expression. In contrast, non-Lactobacillusbacteria, includingBifidobacterium breve, Prevotella bivia, Gardnerella vaginalis, Sneathia amnii, Sneathia sanguinegens, Prevotella amnii, Escherichia coli,andChlamydia trachomatis, were positively correlated with IL-1α, IL-1β, IL-6, IL-8, MCP-1, and MIG levels. Furthermore,Lactobacillus inersexhibited a significant negative effect in the HPV and CIN patient groups.
Temporal Lobe Epilepsy is dominated by Region Specific Interictal Cortical Inhibition
Authors: Kienitz Ricardo , Strzelczyk Adam , Spyrantis Andrea , Konczalla Jürgen , Rosenow Felix , Strüber Michael
Published: December 2024

Epilepsy is typically characterized by excessive neuronal excitability, manifesting as seizures and interictal epileptiform discharges (IEDs) in the EEG. However, the dynamics of excitation and inhibition (E/I balance) remain poorly understood. Here, we leverage the aperiodic exponent of the EEG power spectrum—a marker indicative of synaptic inhibition—to investigate shifts in E/I balance during antiseizure medication (ASM) tapering in patients with mesial temporal lobe epilepsy (TLE). We analyzed EEG data from 28 TLE patients and 25 controls with non-epileptic episodes (NEE) undergoing presurgical video EEG monitoring. Unexpectedly, TLE patients showed a localized increase in the aperiodic exponent in the ipsilesional temporal lobe during ASM tapering, absent in controls. This inhibition increase correlated with seizure latency and predicted seizure occurrence. Intracranial recordings from 10 TLE patients revealed higher aperiodic exponents in the lateral temporal cortex compared to the hippocampus, suggesting stronger inhibition in the lateral cortex. Notably, hippocampal IEDs triggered transient inhibitory responses in the lateral cortex, accompanied by increased high-frequency activity and disrupted hippocampus-to-lateral connectivity. These findings suggest that TLE likely involves complex inhibitory mechanisms beyond the epileptic focus in the interictal period, with neocortical inhibition potentially containing epileptic activity, and offers a new tool to map epileptic brain regions.
Does domestication trade-off stress tolerance for leaf growth? A search for evidence across eight Pooideae grass species
Authors: Yun Jie , Yuan Chenyang , Irelan Katherine , Kabongo MJ , Urkumbayev Eldar , Des Marais David L.
Published: December 2024

Plant domestication is thought to create trade-offs between high yield and stress tolerance, raising concerns about yield stability in future climates. Previous studies have found limited direct evidence for such trade-offs, often focusing on weakened defenses associated with higher growth rates. However, trade-offs can also occur when traits (such as yield in agriculture) optimized for favorable conditions perform less efficiently in stressful conditions. Deciphering the mechanisms driving these trade-offs is crucial for maintaining yield in changing environments. We examine leaf growth, a key trait influencing carbon assimilation, in eight species of grasses. We use a machine learning pipeline to automatically extract cell dimensions and positions from leaf microscope images to study cell kinematics, finding that domesticated plants generally have longer leaves, larger division zones and higher cell production rates. We found no clear evidence of trade-off between domestication and drought response in final leaf length. However, a trade-off is observed in development as wild species exhibited a smaller decrease in elongation zone size under drought than their domesticated counterparts. These nuanced trade-offs associated with domestication highlight the importance of examining physiological traits and mechanisms in greater detail, possibly informing breeding strategies to enhance crop resilience in the face of climate change.

Highlight

This study uses a high throughput pipeline to characterize leaf elongation responding to drought stress across eight species including barley, wheat, oat and wild relatives.
Pheno-Morphological Characterization and Genetic Diversity Assessment of Grain and Vegetable Soybean (Glycine max. (L.) Merrill) Lines for Breeding Advancements
Authors: Saha Madhumita , Chavan Mohan , Onkarappa T , Ravikumar R L , Das Uddalak
Published: December 2024

This study presents for the first time, a thorough pheno-morphological characterization of ten soybean [Glycine max(L.) Merrill] lines (four grain type and six vegetable type). The vegetable soybean, also called asEdamame, and the grain type soybean, which underpin considerable genetic variation across traits such as flowering and pod-setting times, plant height, and seed size. Analyses of variance and clustering reveal obvious differentiation between vegetable and grain-type soybeans, particularly in traits such as height at the R7 stage, pod length, and branching patterns. The vegetable type exhibited faster plant development throughout reproductive stages and tended to be taller than the grain type. The study found characteristics, including test weight, plant height, and pods per plant, had higher phenotypic and genotypic coefficient of variation and, therefore, may serve as good candidates for selection breeding since these characteristics are based on a strong genetic constitution and to a lesser extent on environmental influences. The traits like number of pods per plant and test weight had high heritability and genetic advance and thus held great promise for improvement of productivity through selection. Important PCA explained traits were the plant height at the R7 stage, number of branches, and number of pods per cluster, which have high values for the breeding program. Hierarchical clustering also clumped the genotypes from other morphological characteristics which grouped them into clear distinct classification for the genetic diversity of this germplasm. In relation to this, one realizes that these soybean lines have genetic variability for significant breeding programs concerning increases in yield, adaptability, and resistance to stresses: biotic and abiotic.
RGnet: Recessive Genotype Network in a Large Mendelian Disease Cohort
Authors: Ai Fandi , Kang Lu , Zeng Jiayi , He Mingmin , Zhong Mingjun , Cheng Jing , Lu Yu , Yuan Huijun , Bu Fengxiao
Published: December 2024

Recessive genotypes, including compound heterozygotes and homozygotes formed by rare variants that impact gene function, affect both alleles and were linked to numerous diseases and traits. However, the underlying patterns and interconnections of these recessive genotypes in large cohorts have rarely been studied. To address this gap, the Recessive Genotype Network (RGnet) was developed. This network model maps variant and genotype features to visualize and analyze recessive genotype patterns within large cohorts. Additionally, it uses permutation-based analyses to assess the enrichment of these genotypes in relation to specific phenotypes. Demonstrated through its application to the genetic deafness geneSLC26A4in 22,125 cases affected by hearing loss, RGnet successfully identified pathogenic variants with high connectivity, providing a reliable method for exploring the pathogenic mechanisms underlying recessive disorders or traits.

Availability and Implementation

RGnet is available from GitHub athttps://github.com/jiayiiiZeng/RGnet

Contact

bufengxiao@wchscu.cn

Supplementary information

Supplementary data are available at Bioinformatics online.
CrGEF1, CrGAP1, and CrGDI2 function as key regulators of ROP-GTPase mediated modulation of alkaloid biosynthesis inCatharanthus roseus
Authors: Sharma Anuj , Mohan Sruthi , Gupta Priyanka , Parihar Durgesh , Nagegowda Dinesh A.
Published: December 2024

ROP-GTPase Regulatory Proteins (RGRPs) have been shown to control plant morphogenesis, development and immunity, however, their role in specialized metabolism is hitherto not known. Here, we demonstrate that specific RGRPs control monoterpene indole alkaloid (MIA) biosynthesis by interacting with distinct Rho of Plants (ROP) inCatharanthus roseus. Among the five Guanine nucleotide Exchange Factors (GEFs), four GTPase-activating proteins (GAPs), and two GDP dissociation inhibitors (GDIs) identified in theC. roseusgenome, only CrGEF1, CrGAP1, and CrGDI2 specifically interacted with CrROP3 and CrROP5. These RGRPs displayed distinct cytosolic and/or membrane localization patterns, with their transcripts predominantly expressed in aerial tissues. Functional studies revealed thatCrGEF1acts as a positive regulator of MIA biosynthesis, as its silencing led to a reduction in MIA production, while overexpression enhanced MIA levels. Conversely, CrGAP1 and CrGDI2 function as negative regulators, with their silencing resulting in increased MIA production and their overexpression causing reduced MIA levels. Notably, terminal truncated forms of these RGRPs showed interaction with CrROP3 or CrROP5 but failed to influence MIA biosynthesis, underscoring the importance of these domains in their regulatory functions. Overall, our findings uncover a previously unexplored mechanism by which distinct RGRPs coordinate with specific ROPs to regulate transcription factors and fine-tune MIA biosynthesis inC. roseus.

Significance

Plants fine-tune their metabolic pathways to adapt to environmental and physiological cues, balancing primary and specialized metabolism. Here, we uncover a feedback regulatory mechanism by which ROP-GTPase regulatory proteins (RGRPs) control alkaloid biosynthesis inCatharanthus roseus. We found that CrGEF1, CrGAP1, and CrGDI2 specifically interact with ROP-GTPases CrROP3 and CrROP5, modulating the monoterpene indole alkaloid (MIA) pathway. This RGRP-ROP module plays a crucial role in dynamically regulating MIA levels, where CrGEF1 promotes MIA production while CrGAP1 and CrGDI2 act as negative regulators. These findings highlight the importance of RGRP-ROP circuitry in control of alkaloid biosynthesis inC. roseus, and specialized metabolism in plants.
Retrotransposon LINE1 trans-inhibiting differentiation maintains embryonic stem cell identity
Authors: Ren Likun , Teng Yue , Xu Wenqiu , Hou Jingya , Lu Mengyue , Shi Feitong , Ren Jie , Zheng Caihong , Cai Jun
Published: December 2024

Long Interspersed Nuclear Elements-1s (LINE1s) are one of the >17% most abundant Retrotransposons in mammalian genomes. LINE1 RNA is high expression during early embryonic development, meanwhile is under tight epigenetic control. Some studies have confirmed LINE1 play a critical role in early embryo development and ESC identity. Previous studies focused on the role of LINE1 in cis-regulation, however, the function of L1 RNA in tans-regulation remains largely unknown. In this study, we performed a high-throughput proximity MARGI (pxMARGI) experiment found transposon LINE1 RNA trans-regulated prefer to young LINE1 subfamily, and in hybrid and non-hybrid two different manner repress ESC to dual progress of 2C-like cells and differentiation. In differentiation process, LINE1 RNA as a scaffold recruit polycomb core subunits combine three core pluripotent factors maintain ESC identity. In 2C process, LINE1 RNA in a sequence-specific manner recruit Kap1 to old L1 subfamily, and recruit ELL3 to RE 5‘UTR maintain ESC self-renewal. Our data point to LINE1 transcriptions more detail trans-regulation mechanism to orchestrate developmental progression for the self-renewal of embryonic stem cells (ESCs). LINE1 RNA may be potential biomarker for noninvasive embryo selection.
Cell-Cell Fusion in NSCLC Confers a Fitness Benefit Under Drug Selection
Authors: Shultes Paulameena V. , Tadele Dagim S. , Durmaz Arda , Weaver Davis T. , Barker-Clarke Rowan , Dinh Mina N. , Liu Siqing , Alemu Endalkachew A. , Rayner Simon , Scott Jacob G.
Published: December 2024

Cell-cell fusion has been implicated in various physiological and pathological processes, including cancer progression. This study investigated the role of cell-cell fusion in non-small cell lung cancer (NSCLC), focusing on its contribution to chemoresistance and tumor evolution. By co-culturing drug-sensitive and drug-resistant NSCLC cell lines, we observed spontaneous cell-cell fusion events, particularly under gefitinib selection. These fused cells exhibited enhanced fitness and a higher degree of chemoresistance compared to parental lines across a panel of 12 chemotherapeutic agents. Further analysis, including fluorescence imaging and cell cycle analysis, confirmed nuclear fusion and increased DNA content in the fused cells. Bulk RNA sequencing revealed genomic heterogeneity in fused cells, including enrichment of gene sets associated with cell cycle progression and epithelial-mesenchymal transition, hallmarks of cancer malignancy. These findings demonstrate that cell-cell fusion contributes significantly to therapeutic resistance and the promotion of aggressive phenotypes in NSCLC, highlighting its potential as a therapeutic target.
Toward AI-Resilient Screening of Nucleic Acid Synthesis Orders: Process, Results, and Recommendations
Authors: Wittmann Bruce J. , Alexanian Tessa , Bartling Craig , Beal Jacob , Clore Adam , Diggans James , Flyangolts Kevin , Gemler Bryan T. , Mitchell Tom , Murphy Steven T. , Wheeler Nicole E. , Horvitz Eric
Published: December 2024

Fast-moving advances in AI-assisted protein engineering are enabling breakthroughs in the life sciences that promise numerous beneficial applications. At the same time, these new capabilities are creating potential biosecurity challenges by providing new pathways to intentional or accidental synthesis of genes that encode hazardous proteins. The synthesis of nucleic acids is a key choke point in the AI-assisted protein engineering pipeline as it is where digital designs are transformed into physical instructions that can produce potentially harmful proteins. Thus, one focus for efforts to enhance biosecurity in the face of new AI-enabled capabilities is on bolstering the screening of orders by nucleic acid synthesis providers. We describe a multistakeholder, cross-sector effort to address biosecurity challenges with uses of AI-powered biological design tools to reformulate naturally occurring proteins of concern to createsynthetic homologsthat have low sequence identity to the wild-type proteins. We evaluated the abilities of traditional nucleic acid biosecurity screening tools to detect these synthetic homologs and found that, of tools tested, not all could previously detect such AI-redesigned sequences reliably. However, as we report, patches were built and deployed to improve detection rates over the course of the project, resulting in a final mean detection rate over tools of 97% of the synthetic homologs that were determined, using in-silico metrics, to be more likely to retain wild-type-like function. Finally, we make recommendations on approaches for studying and addressing the rising risk of adversarial AI-assisted protein engineering attacks like the one we identified and worked to mitigate.
Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1
Authors: Legal Thibault , Joachimiak Ewa , Parra Mireya , Peng Wang , Tam Amanda , Black Corbin , Valente-Paterno Melissa , Brouhard Gary , Gaertig Jacek , Wloga Dorota , Bui Khanh Huy
Published: December 2024

Motile cilia are unique organelles with the ability to autonomously move. Force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet microtubules and a central pair (CP) with a distinct structure at the tip. In this study, we present a high-resolution structure of the CP in the ciliary tip of the ciliateTetrahymena thermophilaand identify several tip proteins that bind and form unique patterns on both microtubules of the tip CP. Two of those proteins that contain tubulin polymerization-promoting protein (TPPP)-like domains, TLP1 and TLP2, bind to high curvature regions of the microtubule. TLP2, which contains two TPPP-like domains, is an unusually long protein that wraps laterally around half a microtubule and forms the bridge between the two microtubules. Moreover, we found that the conserved protein SPEF1 binds to both microtubule seams.In vitro, human SPEF1 not only binds to the microtubule seam but also crosslinks two parallel microtubules. Single-molecule microtubule dynamics assays indicate that SPEF1 stabilizes microtubulesin vitro. Together, these data show that the proteins in the tip CP maintain stable microtubule structure and probably play important roles in maintaining the integrity of the axoneme.
Expanding GABAergic Neuronal Diversity in iPSC-Derived Disease Models
Authors: Hu Ruiqi , Boshans Linda L. , Zhu Bohan , Cai Peiwen , Tao Yiran , Youssef Mark , Girrbach Gizem Inak , Song Yingnan , Wang Xuran , Tsankov Alexander , Buxbaum Joseph D. , Ma Sai , Yang Nan
Published: December 2024

GABAergic interneurons play a critical role in maintaining neural circuit function, and their dysfunction is implicated in various neurodevelopmental and psychiatric disorders. Traditional approaches for differentiating human pluripotent stem cells (PSCs) into neuronal cells often face challenges such as incomplete neural differentiation, prolonged culture periods, and variability across PSC lines. To address these limitations, we developed a new strategy that integrates overexpression of transcription factors ASCL1 and DLX2 with dual-SMAD and WNT inhibition, efficiently driving the differentiation of human PSCs into diverse, region-specific GABAergic neuronal types. Using single-cell sequencing, we characterized the cellular heterogeneity of GABAergic induced neurons (iNs) generated with the patterning factors (patterned iNs) and those derived solely with transcription factors (PSC-derived iNs), uncovering the regulatory mechanisms that govern their fate specification. Patterned iNs exhibited gene expression features corresponding to multiple brain regions, particularly ganglionic eminence (GE) and neocortex, while GABAergic PSC-derived iNs predominantly resembled hypothalamic and thalamic neurons. Both iN types were enriched for genes relevant to neurodevelopmental and psychiatric disorders, with patterned iNs more specifically linked to neural lineage genes, highlighting their utility for disease modeling. We further applied this protocol to investigate the impact of an ADNP syndrome-associated mutation (p.Tyr719* variant) on GABAergic neuron differentiation, revealing that this mutation disrupts GABAergic fate specification and synaptic transmission. Overall, this study expands the toolkit for disease modeling by demonstrating the complementary advantages of GABAergic PSC-derived iNs and patterned iNs in representing distinct GABAergic neuron subtypes, brain regions, and disease contexts. These approaches offer a powerful platform for elucidating the molecular mechanisms underlying various neurodevelopmental and psychiatric disorders.
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues
Authors: Quake Stephen R ,   The Tabula Sapiens Consortium
Published: December 2024

The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from nine new donors, doubles the number of cells in Tabula Sapiens, and adds four new tissues. This new data includes four donors with multiple organs contributed, thus providing a unique data set in which genetic background, age, and epigenetic effects are controlled for. We analyzed the combined Tabula Sapiens data for expression of transcription factors, thereby providing putative cell type specificity for nearly every human transcription factor and as well as new insights into their regulatory roles. We analyzed the molecular phenotypes of senescent cells across the entire data set, providing new insight into both the universal attributes of senescence as well as those aspects of human senescence that are specific to particular organs and cell-types. Similarly, we analyzed sex-specific gene expression across all of the identified cell types and discovered which cell types and genes have the most distinct sex based gene expression profiles. Finally, to enable accessible analysis of the voluminous medical records of Tabula Sapiens donors, we created a web application powered by a large language model that allows users to ask general questions about the health history of the donors.
Trehalose supports the growth ofAedes aegypticells and modifies gene expression and dengue virus replication
Authors: Marten Andrew D. , Haslitt Douglas P. , Martin Chad A. , Swanson Daniel H. , Kalera Karishma , Johnson Ulysses G. , Swarts Benjamin M. , Conway Michael J.
Published: December 2024

Trehalose is a non-reducing disaccharide that is the major sugar found in insect hemolymph fluid. Trehalose provides energy, and promotes growth, metamorphosis, stress recovery, chitin synthesis, and insect flight. Trehalase is the only enzyme responsible for the hydrolysis of trehalose, which makes it an attractive molecular target. Here we show thatAedes aegypti(Aag2) cells express trehalase and that they can grow on trehalose-containing cell culture media. Trehalase activity was confirmed by treating Aag2 cells with trehalase inhibitors, which inhibited conversion of trehalose to glucose and reduced cell proliferation. Cell entry of a fluorescent trehalose probe was dependent on trehalose concentration, suggesting that trehalose moves across the cell membrane via passive transport. Culturing Aag2 cells with trehalose-containing cell culture media led to significant changes in gene expression, intracellular lipids, and dengue virus replication and specific infectivity, and increased their susceptibility to trehalase inhibitors. These data describe anin vitromodel that can be used to rapidly screen novel trehalase inhibitors and probes and underscores the importance of trehalose metabolism inAe. aegyptiphysiology and transmission of a mosquito-borne virus.
Tmbim5 loss causes muscle atrophy in zebrafish without exacerbating mcu or slc8b1 knockout phenotypes
Authors: Wasilewska Iga , Adamek-Urbańska Dobrochna , Baranykova Sofiia , Majewski Łukasz , Methner Axel
Published: December 2024

Mitochondria generate ATP by creating a proton gradient across the inner membrane. This gradient also drives calcium uptake by the mitochondrial calcium uniporter (MCU) complex, while NCLX, encoded bySLC8B1,facilitates efflux. Mcu deficiency in various species does not result in obvious phenotypes, suggesting the existence of additional calcium transport systems. We here generated zebrafish lacking Tmbim5, a potential bidirectional mitochondrial calcium transporter, and Slc8b1, the probable NCLX ortholog.tmbim5knockout fish exhibited impaired growth, muscle atrophy, increased brain cell death, and reduced mitochondrial membrane potential, but no significant changes in steady-state mitochondrial calcium levels. Slc8b1-deficient fish had increased larval mortality but were otherwise normal. Double knockouts oftmbim5/mcuandtmbim5/slc8b1were viable with normal Mendelian distribution, indicating robust compensatory mechanisms maintain calcium homeostasis.tmbim5knockout rescued the increased mortality in Slc8b1-deficient fish, and the NCLX inhibitor CGP-37157 lost its effect on behavior in Tmbim5-deficient but not Slc8b1-deficient zebrafish, implying shared, possibly antagonistic pathways. These findings suggest alternative pathways for mitochondrial calcium transport compensate for the loss of these proteins, enabling zebrafish survival.
Intermittent suppressive posaconazole therapy is ineffective at mitigating cardiac and digestive tract pathologies in an experimental model of chronic Chagas disease
Authors: Jayawardhana Shiromani , Olmo Francisco , Fortes Francisco Amanda , Khan Archie A. , Lewis Michael D. , Taylor Martin C. , Kelly John M.
Published: December 2024

Infections withTrypanosoma cruzicause Chagas disease, a chronic condition that can give rise to debilitating cardiac and/or gastrointestinal damage. However, it is unclear why only ∼30% of individuals progress to symptomatic pathology, why this can take decades to become apparent, and why there is such a wide range of disease outcomes. Disease pathology is a long-term cumulative process resulting from collateral damage caused by inflammatory immune responses that continually eliminate transient parasite infections in the heart and/or gastrointestinal tract. The guiding principle behind anti-parasitic drug development is that sterile cure is required to prevent progression to symptomatic pathology. Evidence suggests that the cumulative damage required to reach the symptomatic threshold is determined by a number of factors, including host and parasite genetics, which govern the intensity and location(s) of infection. Therefore, an alternative therapeutic strategy could involve long-term intermittent treatment, which may not confer sterile cure, but is able to suppress the parasite burden to a level where the disease does not become symptomatic within the life-time of the infected individual. To test this hypothesis, we used an experimental murine model that displays both cardiac and digestive tract pathology. Mice were given intermittent treatment with posaconazole, under conditions that reduced the parasite burden by >99%, but did not confer sterile clearance. Our results show that this did not provide long-term protection against the key cardiac or gastrointestinal manifestations of Chagas disease, and that sterile cure should remain the single goal of the drug development community.