Functional Analysis Research Articles

Abstract 6147: Genome-wide association study identifies new genetic susceptibility loci for multiple primary cancers

Abstract Objectives: Genetic susceptibility is thought to contribute to the development of multiple primary cancers (MPC), often called secondary cancers. Although rare variants contribute to risk, these only account for a small fraction of MPC cases. The contribution of common variants to risk is unknown. Methods: To identify common genetic variants associated with the risk of MPC, we conducted a trans-ancestry meta-analysis of genome-wide association studies (GWAS), including 7,360 MPC cases and 138,684 controls from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and UK Biobank (UKBB). Association analyses were performed separately by genetic ancestry, genotype platform, and study, adjusting for age, sex, and principal components, and the results were meta-analyzed together using a fixed effects model. Genome-wide SNP heritability was estimated using GCTA. Pathway and functional enrichment analyses were conducted to gain insights into potential biological mechanisms underlying discovered loci. Results: We identified one novel locus at chromosome 3q26.2 (LRRC34, rs7621631) that was associated with MPC risk (P=1.16x10-8). Variants in this region have been previously associated with telomere length, suggesting a possible underlying mechanism. In sex-stratified analyses, we identified an additional locus at chromosome 12q24.33 (intergenic, rs10466868) associated with MPC in men (P= 7.76x10-8), but not women. Although the risk associated with these two discovered loci was small, the genome-wide SNP heritability was estimated to be 12%, suggesting that there are likely more common variants to be discovered for MPC risk. Conclusions: Our study demonstrates that common genetic variation contributes to the risk of multiple primary cancers and suggests additional loci are likely to be identified with larger studies. Citation Format: Shisi He, James Perry, Shengchao Li, Braxton D. Mitchell, Yuji Zhang, Shuo Chen, Laura Beane-Freeman, Kathryn Hughes Barry, Sonja I. Berndt. Genome-wide association study identifies new genetic susceptibility loci for multiple primary cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6147.

Transcriptome profiling of MYB-overexpressed transgenic lines provides crucial molecular insights into anthocyanin and remodel the biosynthesis regulatory network in Nicotiana tabacum

Anthocyanin is an important pigment in plants and one of the most powerful antioxidants for the food industry. In plants, anthocyanin biosynthesis is controlled by several structural genes and regulated by MYB transcription factors. However, the molecular mechanism and regulation of anthocyanin biosynthesis and the explicit role of MYB in pigmentation and stress responses have not been elucidated yet. In this study, we conducted transcriptomic profiling of MYB overexpressed transgenic lines, unveiling differentially expressed genes (DEGs) likely involved in anthocyanin biosynthesis and abiotic stress responses. Over-expression of two peanut MYB genes, Arahy.J3K16K (JK) and Arahy.CD1PG8 (C8), individually, as well as their co-expression (CJ), led to alterations in anthocyanin content in tobacco. Notably, JK over-expression line exhibited superior maintenance of growth indices, chlorophyll pigments, and anthocyanin content. Transcriptome profiling identified thousands of DEGs across JK, C8 and CJ transgenic plants. Functional annotation analysis revealed enrichment in metabolic pathways such as flavonoid biosynthesis, MAPK signaling, and hormone signaling transduction among these DEGs. Specifically, the expression of DEGs involved in the anthocyanin pathway, such as PAL, CHS, CHI, F3H, DFR, and ANR, was upregulated in JK lines, suggesting their regulatory role in pigmentation. Additionally, DEGs related to MAPK cascade, ethylene, auxin, and abscisic acid were preferentially expressed in JK lines, indicating their potential involvement in abiotic stress responses. The co-expression complex of MYB, bHLH, and WD40 also revealed the transcriptional activation model of anthocyanin biosynthesis in JK lines. In conclusion, these findings provide crucial molecular insights into MYB-induced regulation of anthocyanin biosynthesis and abiotic stress tolerance in tobacco, offering potential strategies for enhancing anthocyanin content and improving resistance.

Abstract 1712: Identifying a novel alternative promoter usage in HDAC9: Implications for LUAD prognosis and therapy

Abstract Promoters are key elements in gene regulation. It has been estimated that more than half of protein-coding genes in the human genome possess multiple promoters. Aberrant expression and dysregulated activity of alternative promoters have been correlated with numerous diseases, especially cancer. In this study, we utilized RNA-seq data from 608 lung adenocarcinoma (LUAD) patients and systematically analyzed promoter activities using the proActiv algorithm. Of the expressed genes in LUAD, approximately 57% have at least two distinct promoters. In addition, we identified 1852 tumor-specific alternative promoters that showed a significant shift (2-fold changes) in promoter activity without any notable changes in the expression of corresponding 1603 genes between tumor and adjacent non-tumor tissues. Functional enrichment analysis showed that these genes were associated with key cellular functions such as signaling pathways, cell cycle, and cell junctions. Unsupervised clustering of patients based on altered promoters revealed a significant prognostic value. Among them, we observed a major promoter switch in HDAC9, which mainly utilizes three promoters: prmt3280, prmt3283, and prmt3287 in our LUAD dataset. Notably, prmt3287 was exclusively active in tumor samples and functioned as the dominant promoter, while prmt3283 served as the main promoter in adjacent non-tumor samples. Intriguingly, even though the overall expression of HDAC9 mRNA lacked prognostic relevance both in our dataset and in the TCGA dataset, higher expression of the alternative promoter prmt3287 (using ≥50% activity level as a cutoff) was associated with adverse outcomes in LUAD patients. We further compared the DNA methylation level around the HDAC9 domain between paired tumor and non-tumor samples and found that positions with the most significant differences (p<0.001) overlapped with the prmt3287 region. Moreover, DNA methylation levels around prmt3287 significantly decreased in prmt3287 high-activity patient groups. Next, we investigated the ChIP-seq levels over the HDAC9 region, and ChIPseeker successfully annotated the alternative promoters of HDAC9. In addition, the alternative promoter prmt3287 exhibited the highest active enhancer signals. Furthermore, we performed PCR to determine the expression of six distinct transcript isoforms from alternative promoters in four different LUAD cell lines, and we observed high expression of isoform 10, which is possibly generated by prmt3287 in all cell lines. The impact of prmt3287 on cell proliferation, cell cycle, and cell migration will be further addressed. Our results indicate that alternative promoter usage can capture insights that might be missed at the overall gene expression level, and alternative promoter usage in HDAC9 could be a novel biomarker and a promising therapy target. Citation Format: Amina Bolatkan, Ken Asada, Syuzo Kaneko, Masaaki Komatsu, Ryuji Hamamoto. Identifying a novel alternative promoter usage in HDAC9: Implications for LUAD prognosis and therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1712.

Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host–microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

Resting-state functional connectivity and structural differences between smokers and healthy non-smokers

Previous studies have shown an association between cigarette use and altered resting-state functional connectivity (rsFC) in many large-scale networks, sometimes complemented by measures of cortical atrophy. In this study, we aimed to further explore the neural differences between smokers and healthy non-smokers through the integration of functional and structural analyses. Imaging data of fifty-two smokers and forty-five non-smokers were analyzed through an independent component analysis for group differences in rsFC. Smokers showed lower rsFC within the dorsal attention network (DAN) in the left superior and middle frontal gyrus and left superior division of the lateral occipital cortex compared to non-smokers; moreover, cigarette use was found to be associated with reduced grey matter volume in the left superior and middle frontal gyrus and right orbitofrontal cortex, partly overlapping with functional findings. Within smokers, daily cigarette consumption was positively associated with increased rsFC within the cerebellar network and the default mode network and decreased rsFC within the visual network and the salience network, while carbon monoxide level showed a positive association with increased rsFC within the sensorimotor network. Our results suggest that smoking negatively impacts rsFC within the DAN and that changes within this network might serve as a circuit-based biomarker for structural deficits.

Abstract 3550: PerturbDB: A resource for revealing gene functions and cancer-associated phenotypes

Abstract Perturb-seq is a high-throughput technique that combines clustered regularly interspaced short palindromic repeats (CRISPR)-based screens with single-cell RNA sequencing (scRNA-seq) readouts for high-content phenotypic screens to comprehensively map the transcriptional effects of genetic perturbations, showing great advantages in revealing disease-associated gene functions and mechanisms in high volumes. Despite the rapid accumulation of Perturb-seq datasets, no dedicated database exists for reusing these valuable information. In this study, we developed a platform called PerturbDB (http://research.gzsys.org.cn/perturbdb) to facilitate users to unveil genotype-phenotype relations, especially gene functions and regulatory networks involved in several classical cancer associated phenotypes using 37 Perturb-seq datasets from 15 studies. By reanalyzing 3,429,829 single-cell transcriptomes from the knockdown of 3214 genes across 10 different cell lines, we identified 749 classical cancer phenotype-related genes and 373 functional gene clusters annotating potential novel functions. Utilizing Marker genes scoring and the InferCNV algorithm, we identified genes involved in 9 malignant phenotypes, which consists of sustaining proliferative signaling (362 genes), resisting cell death (120 genes), inducing angiogenesis (145 genes), tissue invasion and metastasis (321 genes), enabling replicative immortality (160 genes), deregulating cellular metabolism (247 genes), avoiding immune destruction (95 genes), unlocking phenotypic plasticity (231 genes), and chromosome instability (231 genes). Additionally, functional clusters were calculated utilizing Principal Component Analysis (PCAs) and the HDBSCAN package to introduce unknown gene functions related to the cancer associated phenotypes. Perturbation clusters (PCs) were identified by comparing similarities in the transcriptomes of perturbed cells, suggesting individual genes in the same functional cluster perform similar gene functions, and therefore novel functions of 735 genes can be inferred from the known functions of neighboring genes. The PGSEA tool was developed to facilitate functional analysis of genes not yet included, which helps users to predict gene functions through a combination of PerturbDB datasets and personalized RNA-seq datasets. This study will greatly expand our understanding of genes involved in emblematic cancer associated phenotypes and their coordinated functions and regulatory networks. Citation Format: Bing Yang, Man Zhang, Yanmei Shi, Yi-Ming Dong, Xingyu Ma, Jingyuan Zhang, Daning Lu, Jian-You Liao, Dong Yin. PerturbDB: A resource for revealing gene functions and cancer-associated phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3550.

Research on design requirements for passive residual heat removal system of lead cooled fast reactor via model-based system engineering

Traditional text-based system engineering, which has been used in the design and application of passive residual heat removal system (PRHRS) for lead-cooled fast reactors, is prone to several problems such as low development efficiency, long iteration cycles, and model ambiguity. This study aims to effectively address the above-mentioned problems by adopting a model-based system engineering (MBSE) method, which has been preliminarily applied to meet the design requirements of a PRHRS. The design process has been implemented based on the preliminary design of the system architecture and consists of three stages: top-level requirement analysis, functional requirements analysis, and design requirements synthesis. The results of the top-level requirements analysis and the corresponding use case diagram can determine the requirements, top-level use cases, and scenario flow of the system. During the functional requirements analysis, the sequence, activity, and state machine diagrams are used to develop the system function model and provide early confirmation. By comparing these sequence diagrams, the requirements for omissions and inconsistencies can be effectively checked. In the design requirements synthesis stage, the Analytic Hierarchy Process is used to conduct preliminary trade-off calculations on the system architecture, after which a white box model is established during the system architecture design. Through these two steps, the analysis and design of the system architecture are ultimately achieved. The resulting system architecture ensures the consistency of the design requirements. Ultimately, a functional hazard analysis was conducted for a specific incident to validate case requirements and further refine the system architecture. Future research can further reduce the design risk, improve the design efficiency, and provide a practical reference for the design and optimization of PRHRS in digital lead-cooled fast reactors.

Sensitive electrochemical flow injection analysis of H2O2 released from cells with a pass-through mode

Conventional plate electrodes were commonly used in electrochemical flow injection analysis and only part of molecules diffused to the plane of electrodes could be detected, which would limit the performance of electrochemical detection. In this study, a low-cost native stainless steel wire mesh (SSWM) electrode was integrated into a 3D-printed device for electrochemical flow injection analysis with a pass-through mode, which is different compared with previous flow-through mode. This strategy was applied for sensitive analysis of hydrogen peroxide (H2O2) released from cells. Under the optimal conditions (the applied potentials, the flow rate and the sample volume), the device exhibits high sensitivity toward H2O2. Linear relationships could be achieved between electrochemical responses and the concentration of H2O2 ranging from 1 nM to 1 mM. The excellent analytical performance of the SSWM-based device could be attributed to the pass-through mode based on the mesh microstructure and intrinsic catalytic properties for H2O2 by stainless steel. This approach could be further successfully extended for screening of H2O2 released from HeLa cells with electrochemical responses linear to the number of cells in a range of 3 - 1.35 × 104 cells with an injection volume of 30 μL. This study revealed the potential of mesh electrodes in electrochemical flow injection analysis for cellular function and pathology and its possible extension in cell counting and on-line analysis.

Faktor-Faktor Yang Memengaruhi Risiko Produksi Bawang Putih Di Indonesia

Garlic productivity in Indonesia is still low and fluctuates every year. The productivity fluctuations indicate production risks. This research aims to analyze the factors that influence the productivity and risks of garlic production in Indonesia. The data used in this study is secondary data from BPS 2014 in the three largest production centers, namely Central Java, West Nusa Tenggara, and East Nusa Tenggara, with a total sample of 305 farmer respondents from 333 farmer respondents. The method used in this study is a multiple linear regression model with the Just and Pope model approach. Multiple linear regression analysis for the productivity function is estimated through the Ordinary Least Squares (OLS) method, whereas for the production risk function, estimation is conducted using the Maximum Likelihood Estimation (MLE) method. The results showed that the risk level of garlic production in Indonesia was high. Factors significantly increased productivity, including seeds, labor, the dry season, and climate change. Meanwhile, factors that significantly reduced productivity are organic fertilizers and SP36 fertilizers. The risk-inducing production factor is climate change, while the risk-reducing factors are pest attacks and liquid pesticides. To boost productivity, farmers can cultivate garlic during the dry season, increase the use of high-quality seedlings and labor, and reduce the application of organic and SP36 fertilizers. To mitigate production risks, farmers can enhance the use of liquid pesticides following recommended usage standards.

Prognostic value of inflammation and immune-related gene NOD2 in clear cell renal cell carcinoma.

Inflammation and immune responses play important roles in cancer development and prognosis. We identified 59 upregulated inflammation- and immune-related genes (IIRGs) in clear cell renal cell carcinoma (ccRCC) from The Cancer Genome Atlas database. Among the upregulated IIRGs, nucleotide binding oligomerization domain 2 (NOD2), PYD and CARD domain (PYCARD) were also confirmed to be upregulated in the Oncomine database and in three independent GEO data sets. Tumor immune infiltration resource database analysis revealed that NOD2 and PYCARD levels were significantly positively correlated with infiltration levels of B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages and dendritic cells. Multivariate Cox hazards regression analysis indicated that based on clinical variables (age, gender, tumor grade, pathological TNM stage), NOD2, but not PYCARD, was an independent, unfavorable ccRCC prognostic biomarker. Functional enrichment analyses (GSEA) showed that NOD2 was involved in innate immune responses, inflammatory responses, and regulation of cytokine secretion. Meanwhile, mRNA and protein levels of NOD2 were elevated in four ccRCC cell lines (786-O, ACHN, A498 and Caki-1), and its knockdown significantly inhibited IL-8 secretion, thereby inhibiting ccRCC cell proliferation and invasion. Furthermore, results showed that miR-20b-5p targeted NOD2 to alleviate NOD2-mediated IL-8 secretion. In conclusion, NOD2 is a potential prognostic biomarker for ccRCC and the miR-20b-5p/NOD2/IL-8 axis may regulate inflammation- and immune-mediated tumorigenesis in ccRCC.

HIF1A-dependent overexpression of MTFP1 promotes lung squamous cell carcinoma development by activating the glycolysis pathway

IntroductionMitochondrial fission process 1 (MTFP1) is an inner mitochondrial membrane (IMM) protein implicated in the development and progression of various tumors, particularly lung squamous cell carcinoma (LUSC). This study aims to provide a more theoretical basis for the treatment of LUSC. MethodsThrough bioinformatics analysis, MTFP1 was identified as a novel target gene of HIF1A. MTFP1 expression in LUSC was examined using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Proteomics Data Commons (PDC) databases. The Kaplan-Meier plotter (KM plotter) database was utilized to evaluate its correlation with patient survival. Western blot and chromatin immunoprecipitation (ChIP) assays were employed to confirm the regulatory relationship between MTFP1 and HIF1A. Additionally, cell proliferation, colony formation, and migration assays were conducted to investigate the mechanism by which MTFP1 enhances LUSC cell proliferation and metastasis. ResultsOur findings revealed that MTFP1 overexpression correlated with poor prognosis in LUSC patients(P < 0.05). Moreover, MTFP1 was closely associated with hypoxia and glycolysis in LUSC (R = 0.203; P < 0.001, R = 0.391; P < 0.001). HIF1A was identified as a positive regulator of MTFP1. Functional enrichment analysis demonstrated that MTFP1 played a role in controlling LUSC cell proliferation. Cell proliferation, colony formation, and migration assays indicated that MTFP1 promoted LUSC cell proliferation and metastasis by activating the glycolytic pathway (P < 0.05). ConclusionsThis study establishes MTFP1 as a novel HIF1A target gene that promotes LUSC growth by activating the glycolytic pathway. Investigating MTFP1 may contribute to the development of effective therapies for LUSC patients, particularly those lacking targeted oncogene therapies.

Stable reconstruction of anisotropic scattering objects from electromagnetic Cauchy data

ABSTRACT This paper addresses the electromagnetic inverse scattering problem of determining the location and shape of anisotropic objects from near-field Cauchy data. We investigate both cases involving the Helmholtz equation and Maxwell's equations for this inverse problem. Our study focuses on developing efficient imaging functionals that enable a fast and stable recovery of the anisotropic object. The implementation of the imaging functionals is simple and avoids the need to solve an ill-posed problem. The resolution analysis of the imaging functionals is conducted using the Green representation formula. Furthermore, we establish stability estimates for these imaging functionals when noise is present in the data. To illustrate the effectiveness of the methods, we present numerical examples showcasing their performance.

Crystal structure of the ATPase domain of porcine circovirus type 2 Rep protein.

PCV2 belongs to the genus Circovirus in the family Circoviridae, whose genome is replicated by rolling circle replication (RCR). PCV2 Rep is a multifunctional enzyme that performs essential functions at multiple stages of viral replication. Rep is responsible for nicking and ligating single-stranded DNA and unwinding double-stranded DNA (dsDNA). However, the structure and function of the Rep are still poorly understood, which significantly impedes viral replication research. This study successfully resolved the structure of the PCV2 Rep ATPase domain (PRAD) using X-ray crystallography. Homologous structure search revealed that Rep belonged to the superfamily 3 (SF3) helicase, and multiple conserved residues were identified during sequence alignment with SF3 family members. Simultaneously, a hexameric PRAD model was generated for analysing characteristic structures and sites. Mutation of the conserved site and measurement of its activity showed that the hallmark motifs of the SF3 family influenced helicase activity by affecting ATPase activity and β-hairpin just caused the loss of helicase activity. The structural and functional analyses of the PRAD provide valuable insights for future research on PCV2 replication and antiviral strategies.

Mechanistic insight into the degradation of sulfadiazine by electro-Fenton system: Role of different reactive species

Sulfadiazine (SDZ), a widely used effective antibiotic, is resistant to conventional biological treatment, which is concerning since untreated SDZ discharge can pose a significant environmental risk. Electro-Fenton (EF) technology is a promising advanced oxidation technology for efficiently removing SDZ. However, due to the limitations of traditional experimental methods, there is a lack of in-depth study on the mechanism of ·OH-dominated SDZ degradation in EF process. In this study, an EF system was established for SDZ degradation and the transformation products (TPs) were detected by mass spectrometry. Dynamic thermodynamic, kinetic and wave function analysis of reactants, transition states and intermediates were proposed by density functional theory calculations, which was applied to elucidate the underlying mechanism of SDZ degradation. Experimental results showed that amino, benzene, and pyrimidine sites in SDZ were oxidized by ·OH, producing TPs through hydrogen abstraction and addition reactions. ·OH was kinetically more likely to attack SDZ- than SDZ. Fe(IV) dominated the single-electron transfer oxidation reaction of SDZ, and the formed organic radicals can spontaneously generate the de-SO2 product via Smiles rearrangement. Toxicity experiments showed the toxicity of SDZ and TPs can be greatly reduced. The results of this study promote the understanding of SDZ degradation mechanism in-depth. Environmental ImplicationSulfadiazine (SDZ) is one of the antibiotics widely used around the world. However, it has posed a significant environmental risk due to its overuse and cannot be efficiently removed by traditional treatment methods. The lack of in-depth study on SDZ degradation mechanism under reactive species limits the improvement of SDZ degradation efficiency. Therefore, this work focused on SDZ degradation mechanism in-depth under electro-Fenton system through reactive species investigation, mass spectrometry analysis, and theoretical calculation. The results in this study can provide a theoretical basis for improving the SDZ degradation efficiency which will contribute to solving SDZ pollution problems.

Analysis of Structure and Function of Ladybird Leg and Subsequent Design and Fabrication of a Simplified Leg Structure for Robotic Applications.

Many insects are able to walk vertically or upside down on both hard and soft surfaces. In beetles such as the ladybird (Coccinella septempunctata), intermolecular forces between tarsal setae on the footpads of the insects make this movement possible. In prior work, adhesion structures made from polydimethylsiloxane (PDMS) that mimic the action of the tarsal setae have been developed. It is proposed that these adhesion structures could be attached to a simplified version of the leg of a ladybird and used in practical applications. For example, the leg structures could potentially be employed in small surveillance drones to enable attachment to surfaces during flights, in order to preserve battery power. Alternatively, the structures could be used in small robotic devices to enable walking on steeply inclined surfaces. In this program of work, the morphology and movement of the leg of a ladybird were closely studied using a 3D X-ray microscope and a high-speed microscope. The positions of the tendons that facilitated movement were identified. From this knowledge, a simplified leg structure using pin-joints was designed and then fabricated using 3-D printing. The PDMS adhesion structures were then attached to the leg structure. The tendons in the actual insect leg were replicated using thread. Typical detachment forces of about 4 N indicated that the simplified leg structure was, in principle, more than capable of supporting the weight of a small device and then detach successfully. Attachment/detachment movement operations were performed using a linear actuator and controlled remotely. Therefore, proof of concept has been demonstrated for the use of such a simplified ladybird leg structure for the attachment/detachment of small robotic devices to horizontal, inclined, or vertical surfaces.

Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean.

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

Beyond the dominant narratives: Identifying Indigenous and African individuals in Quebec St-Lawrence Valley colonial cemeteries by three-dimensional morphometrical analysis of the temporal bone

In Quebec, written accounts of free or enslaved Indigenous and African individuals during colonial times are few and limited. Three-dimensional geometric morphometric methods applied on 214 temporal bones individuals are used to explore intra-cemetery population variation throughout three centuries (1683–1878), to identify plausible non-European or admixed individuals. First, Principal Component Analysis (PCA) was generated from populations originated from Africa, North-America (Indigenous) and Europe where colonial cemeteries are projected to assess their degree of overlap with the reference groups. Second, Discriminant Function Analysis (DFA) based on typicality probabilities also allowed to assign unknown individuals to the three reference groups. Our results highlighted discrepancy between PCA and DFA. With the PCA, Quebec colonial groups overlap with the Europeans except for three individuals. For the DFA, 64 % (n = 136) were classified as typical to one group and 36 % as atypical (n = 77). Most were European, (82 %; n = 112), followed by those as Indigenous (7 %; n = 10), intermediate between Africans and Indigenous (6 %; n = 8) and Africans (5 %; n = 7). Compared with previous research, one individual from the first Protestant cemeteries of St-Matthew in Quebec could be assessed as plausible African or admixed origin. Two others need further analysis: one from St-Matthew and one from the first Catholic cemetery of Notre-Dame in Montreal. Finally, in response to dominant narratives that focused mainly on Euro-colonists, this research provided for the first time a new snapshot of several colonial population diversity in Quebec, underlining the presence of marginalized groups -especially those of African origin, who are absent from the archaeological reports under study.

Bioengineered Hydrogels Recapitulate Fibroblast Heterogeneity in Cancer.

Recently mapped transcriptomic landscapes reveal the extent of heterogeneity in cancer-associated fibroblasts (CAFs) beyond previously established single-gene markers. Functional analyses of individual CAF subsets within the tumor microenvironment are critical to develop more accurate CAF-targeting therapeutic strategies. However, there is a lack of robust preclinical models that reflect this heterogeneity in vitro. In this study, single-cell RNA sequencing datasets acquired from head and neck squamous cell carcinoma tissues to predict microenvironmental and cellular features governing individual CAF subsets are leveraged. Some of these features are then incorporated into a tunable hyaluronan-based hydrogel system to culture patient-derived CAFs. Control over hydrogel degradability and integrin adhesiveness enabled derivation of the predominant myofibroblastic and inflammatory CAF subsets, as shown through changes in cell morphology and transcriptomic profiles. Last, using these hydrogel-cultured CAFs, microtubule dynamics are identified, but not actomyosin contractility, as a key mediator of CAF plasticity. The recapitulation of CAF heterogeneity in vitro using defined hydrogels presents unique opportunities for advancing the understanding of CAF biology and evaluation of CAF-targeting therapeutics.

Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses.

Photoperiod employs complicated networks to regulate various developmental processes in plants, including flowering transition. However, the specific mechanisms by which photoperiod affects epigenetic modifications and gene expression variations in plants remain elusive. In this study, we conducted a comprehensive analysis of DNA methylation, small RNA (sRNA) accumulation, and gene expressions under different daylengths in facultative long-day (LD) grass Brachypodium distachyon and short-day (SD) grass rice. Our results showed that while overall DNA methylation levels were minimally affected by different photoperiods, CHH methylation levels were repressed under their favorable light conditions, particularly in rice. We identified numerous differentially methylated regions (DMRs) that were influenced by photoperiod in both plant species. Apart from differential sRNA clusters, we observed alterations in the expression of key components of the RNA-directed DNA methylation pathway, DNA methyltransferases, and demethylases, which may contribute to the identified photoperiod-influenced CHH DMRs. Furthermore, we identified many differentially expressed genes in response to different daylengths, some of which were associated with the DMRs. Notably, we discovered a photoperiod-responsive gene MYB11 in the transcriptome of B.distachyon, and further demonstrated its role as a flowering inhibitor by repressing FT1 transcription. Together, our comparative and functional analysis sheds light on the effects of daylength on DNA methylation, sRNA accumulation, and gene expression variations in LD and SD plants, thereby facilitating better designing breeding programs aimed at developing high-yield crops that can adapt to local growing seasons.

Stylistic and syntactic functions of parceling (on the material of B.L. Vasilyev’s novella "The Dawns Here Are Quiet")

The article describes one of expressive syntax techniques, namely parcelled constructions, identified in B.L. Vasilyev’s novella "The Dawns Here Are Quiet". The stylistic and syntactic functions of parcelling are determined and analysed using structural-semantic and functional stylistic analysis. The article concludes that parcelling as a stylistic device is a universal phenomenon of a multifunctional nature. It facilitates the implementation of the author’s various pragmatic ideas. Besides the main stylistic function, i. e. the function of expressively highlighting a certain part of the utterance, parcelled sentences perform several additional functions in a literary text: figurative, characterological, emotional-emphatic, expressive-grammatical. It is revealed that the syntactic functions of parcels in the novella are diverse. In simple sentences, they can be both their main and secondary parts. In composite sentences, they function as the predicative part which is attached to the main utterance using a subordinating, coordinating, or asyndetic connection. The variety of stylistic and syntactic functions of parcelled constructions enabled B. Vasilyev to realistically convey the atmosphere of the pre-war and war periods. He managed to describe the protagonists’ characters and their actions in a true to life way, making the narrative sound natural.