Endogenous Elements Research Articles

CNSC-59. EPIGENETIC POTENTIATION OF ANTI-TUMOR IMMUNE RESPONSES USING VIRAL MIMICRY IN GLIOMAS

Abstract Clinical trials using immune checkpoint inhibition(ICI) have traditionally failed in glioblastoma (GBM). Viral mimicry, which augments anti-tumor immune responses and sensitizes response to immunotherapy in other cancers, involves the epigenetic activation of endogenous retroelements (REs). REs are silenced via the HUSH complex and H3K9me3. This process is mediated by ZNF638. We aimed to elucidate the role of viral mimicry in enhancing ICI through epigenetic reprogramming of the HUSH complex. We demonstrated that RE expression among 48 superfamilies inversely correlated with ZNF638 expression in gliomas, based on data from 71 newly-diagnosed GBMs. Using transcriptional deconvolution, we showed ZNF638 negatively correlates with innate antiviral immune response signatures(TLR3)(RTLR3=-0.300,pTLR3=0.00006). We validated these in-silico results in pure glioma cell lines, patient-derived GBM neurospheres, and syngeneic murine models. ZNF638 knockdown induced intracellular RE-mediated dsRNA signaling cascades via RIG-I and TLR3. This knockdown significantly increased PD-L1 expression(p<0.001), reduced H3K9 trimethylation, and enhanced cytoplasmic dsRNA accumulation in glioma cell lines. In patient-derived GBM neurospheres, ZNF638 knockdown upregulated immune and antiviral programs. Additionally, knockdown resulted in upregulation of several endogenous repeat elements (Alu, LTR). Single-cell RNA sequencing showed ZNF638 clustering in neural progenitor-like and oligodendrocyte-like cells, with increased retroelement expression in low ZNF638 cells. Tumors with lower ZNF638 expression showed increased CD8+ populations. Bulk RNA sequencing deconvolution revealed that ZNF638 is linked to reduced CD8 and DC infiltration in gliomas (RCD8=-0.202,RDC=-0.198;pCD8=8.79E-06,pDC=1.34E-05). In immunocompetent mice, ZNF638 KO and PD-L1 inhibition significantly improved survival (mOS >50 days, p<0.0001) and reduced tumor volume (p<0.001). Analysis of cohorts from multiple cancer types treated with anti-PD1 therapy demonstrated that ZNF638 expression predicts therapeutic response and overall survival. Our findings suggest that epigenetic reprogramming through HUSH inhibition may potentiate immunotherapy for GBM.

Advancing elemental analysis by collision/reaction cell technology and micro-droplet calibration for bioimaging applications by LA-ICP-TOFMS

BackgroundBioimaging applications by laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOFMS) require comprehensive elemental analysis spanning the entire mass range. Within biological systems, endogenous elements are critical for maintaining metal homeostasis in cells, a fundamental aspect in disease progression when disrupted. Additionally, elements from the higher mass range may originate from various sources such as metal-tags for immuno-mass spectrometry, nanoparticles, or metal-based anticancer drugs. This study assesses the efficacy of collision/reacton cell (CCT) mode for simultaneously analysing elements across the complete mass spectrum. Furthermore, we demonstrate the accuracy of the LA-ICP-TOFMS methodology through the analysis of serum reference material. ResultsOur findings demonstrate that the CCT mode outperforms the standard/no gas mode for LA-ICP-TOFMS measurements, particularly in quantifying endogenous elements susceptible to interferences. Through the analysis of picolitre-volume micro-droplet standards and serum reference material (deposited as micro-droplets), we observed accurate quantification of elements such as iron and selenium, with isotope ratios closely resembling natural compositions. As key advantage, the utilization of the CCT mode eliminated the need for labor-intensive post-data processing, streamlining analytical procedures. Additionally, the CCT mode also provided enhanced sensitivity (factor of 1.5–2) for elements in the higher mass range compared to the standard mode, without compromising the sensitivity for endogenous elements. SignificanceWe successfully integrated Seronorm serum reference material-containing micro-droplets into LA-ICPMS bioimaging workflows for quality control, enabling validated measurements of key biological elements. The use of the CCT mode is highly recommended for bioimaging applications that address the analysis of elements across the entire mass range.

The NHR-23-regulated putative protease inhibitor mlt-11 gene is necessary for C. elegans cuticle structure and function.

C. elegans molting offers a powerful entry point to understanding developmentally programmed apical extracellular matrix remodeling. However, the gene regulatory network controlling this process remains poorly understood. Focusing on targets of NHR-23, a key transcription factor that drives molting, we confirmed the Kunitz family protease inhibitor gene mlt-11 as an NHR-23 target. Through reporter assays, we identified NHR-23-binding sites that are necessary and sufficient for epithelial expression. We generated a translational fusion and demonstrated that MLT-11 is localized to the cuticle and lined openings to the exterior (vulva, rectum, mouth). We created a set of strains expressing varied levels of MLT-11 by deleting endogenous cis-regulatory element sequences. Combined deletion of two cis-regulatory elements caused developmental delay, motility defects, and failure of the cuticle barrier. Inactivation of mlt-11 by RNAi produced even more pronounced defects. mlt-11 is necessary to pattern every layer of the adult cuticle, suggesting a broad patterning role prior to the formation of the mature cuticle. Together these studies provide an entry point into understanding how individual cis-regulatory elements function to coordinate expression of oscillating genes involved in molting and how MLT-11 ensures proper cuticle assembly.

Genome-Wide Analysis of the Phospholipase Ds in Perennial Ryegrass Highlights LpABFs-LpPLDδ3 Cascade Modulated Osmotic and Heat Stress Responses.

The phospholipase Ds (PLDs) are crucial for cellular signalling and play roles in plant abiotic stress response. In this study, we identified 12 PLD genes from the genome data of perennial ryegrass (Lolium perenne), which is widely used as forage and turfgrass. Among them, LpPLDδ3 was significantly repressed by ABA treatment, and induced by drought stress and heat stress treatments. The ectopic overexpression (OE) of LpPLDδ3 in Arabidopsis enhanced plant tolerance to osmotic and heat stress as demonstrated by an increased survival rate and reduced malondialdehyde (MDA) accumulation and electrolyte leakage (EL). Arabidopsis endogenous ABA RESPONSIVE ELEMENT BINDING FACTORs (ABFs) and heat stress responsive genes were elevated in LpPLDδ3 OE lines under osmotic and heat stress treatments. Additionally, overexpression of LpPLDδ3 in perennial ryegrass protoplasts could increase heat stress tolerance and elevate expression level of heat stress responsive genes. Moreover, LpABF2 and LpABF4 depressed the LpPLDδ3 expression by directly binding to its ABRE core-binding motif of promoter region. In summary, LpPLDδ3 was repressed by LpABF2 and LpABF4 and positively involved in perennial ryegrass osmotic and heat stress responses.

THE UTILIZATION OF STRUCTURAL EQUATION MODELLING TO DETERMINE CASUALITY ON CONSUMER DECISION OF E-WALLET

One of the technological innovations that exemplifies transactional innovation is the use of an E-Wallet as a means of carrying out financial transactions. This invention enhances transactional ease and quickness. The E-Wallet is the most popular means of financial transaction among the general population. The traditional marketing mix has developed into the product, price, place, promotion, personalization, privacy, customer service, community, site, security, and sales promotion (4Ps+P2C2S3). These criteria are used to evaluate their efficacy in persuading customers to adopt an E-Wallet. Structural Equation Modeling (SEM) is used to assess the causal link between e-marketing mix items and customer decisions to use E-Wallet. SEM provides the core capability of validating the validity and reliability of procedures such as Confirmatory Factor Analysis (CFA). by investigating the pattern of linkages between latent variables and showing them with route diagrams. This study employed 200 E-Wallet users in Palembang for modeling. with the criterion of having one of the E-Wallet programs on a smartphone and having used the application at least once. According to the results of the consumer response processing. all constructs have Cronbach's Alpha (CA) > 0.60, indicating that all constructs are valid for use in measurement. As do the Average Variance Extracted (AVE) and Composite Reliability (CR) values > 0.70, indicating that the construct explains more than half of the variance coming from the indicators. Furthermore, we show the results of evaluating the causal relationship between endogenous construct elements that influence customer decisions, such as location, security, and sales promotion.

Original Research Paper

Plants inhabiting adverse growth conditions compete against stresses by the endogenous regulatory elements viz., promoters and terminators at the ‘right time’ (time-of-stress-act), ‘right place’ (tissue-of-act), and ‘right expression’ (time-of-transcription). Heat stress at the reproductive stage impedes pollen viability and stigma receptiveness, affecting the seed set. Prosopis cineraria, the dominant desert-inhabiting legume tree, is heat- and drought-tolerant. The distribution of heat shock elements in a heat-inducible promoter determines the magnitudes of target gene expression in different tissues/organs. Relative expression of P. cineraria heat shock protein 18.2 (PcHsp18.2) in alternate months of 2021 displayed the highest expression in summer. The flowers collected in June, the hottest month (47oC) of 2021, exhibited a high expression of PcHsp18.2. The germination of the pollen collected was 80%, and the trees eventually set seeds. Comprehensive analysis of the promoter (pPcHSP18.2) and terminator (tPchsp18.2) of PcHsp18.2 by expressing the gusA in tobacco exhibited the highest expression under heat stress as similar to the expression of PcHsp18.2 in environmental samples. Ectopic expression of gusA under PcHsp18.2 promoter and terminator resulted in an increased seed set due to the viability of pollen and stigma under heat stress. The gusA expression under PcHsp18.2 promoter and terminator was high-fold in anther compared to the Lat52 and g10 (endogenous genes under its promoter and terminator) genes under heat stress. The expression of genes under strong and balanced endogenous inducible promoter and terminator combinations, as in the desert-growing P. cineraria in transgenic plants, enables the development of resilient crops.

Determination of proteins in hypoxic Müller glia cells by single-cell ICP-MS: The use of a Rh-DNA intercalator for enhanced cell detection

Single cell − inductively coupled plasma-mass spectrometry (sc-ICP-MS) enables the identification and quantification of elements and biomolecules within individual cells. Target proteins can be analyzed by sc-ICP-MS using metal nanoclusters (MNCs)-based immunoprobes, facilitating the detection of low amounts of proteins in each cell. However, for the full implementation of sc-ICP-MS, an effective strategy to enhance the detection of cellular events is required. In this work, the measurement of endogenous elements and two external tags (ruthenium red and Rh-DNA intercalator) was investigated for cell detection. As a proof of concept, the sequential determination of two proteins (hypoxia inducible factor-1α and vascular endothelial growth factor; HIF-1α and VEGF, respectively) in individual human Müller glia cells (MIO-M1) was pursued. Specific antibodies against HIF-1α and VEGF were labelled with AuNCs and IrNCs, respectively. The results demonstrated the advantages of using Rh-DNA intercalator for the detection and discrimination of cellular events by sc-ICP-MS for quadrupole (Q) mass spectrometers. Additionally, applying this analytical method to cultured MIO-M1 cells under hypoxic and to normoxic conditions showcased the ability of sc-ICP-QMS to study hypoxia-induced changes in the cell-to-cell distributions of HIF-1α and VEGF levels.

Multistep allelic conversion in mouse pre-implantation embryos by AAV vectors

Site-specific recombinases (SSRs) are critical for achieving precise spatiotemporal control of engineered alleles. These enzymes play a key role in facilitating the deletion or inversion of loci flanked by recombination sites, resulting in the activation or repression of endogenous genes, selection markers or reporter elements. However, multiple recombination in complex alleles can be laborious. To address this, a new and efficient method using AAV vectors has been developed to simplify the conversion of systems based on Cre, FLP, Dre and Vika recombinases. In this study, we present an effective method for ex vivo allele conversion using Cre, FLP (flippase), Dre, and Vika recombinases, employing adeno-associated viruses (AAV) as delivery vectors. AAVs enable efficient allele conversion with minimal toxicity in a reporter mouse line. Moreover, AAVs facilitate sequential allele conversion, essential for fully converting alleles with multiple recombination sites, typically found in conditional knockout mouse models. While simple allele conversions show a 100% efficiency rate, complex multiple conversions consistently achieve an 80% conversion rate. Overall, this strategy markedly reduces the need for animals and significantly speeds up the process of allele conversion, representing a significant improvement in genome engineering techniques.

Expressions of the satellite repeat HSAT5 and transposable elements are implicated in disease progression and survival in glioma.

The glioma genome encompasses a complex array of dysregulatory events, presenting a formidable challenge in managing this devastating disease. Despite the widespread distribution of repeat and transposable elements across the human genome, their involvement in glioma's molecular pathology and patient survival remains largely unexplored. In this study, we aimed to characterize the links between the expressions of repeat/transposable elements with disease progression and survival in glioma patients. Hence, we analyzed the expression levels of satellite repeats and transposons along with genes in low-grade glioma (LGG) and high-grade glioma (HGG). Endogenous transposable elements LTR5 and HERV_a-int exhibited higher expression in HGG patients, along with immune response-related genes. Altogether, 16 transposable elements were associated with slower progression of disease in LGG patients. Conversely, 22 transposons and the HSAT5 satellite repeat were linked to a shorter event-free survival in HGG patients. Intriguingly, our weighted gene coexpression network analysis (WGCNA) disclosed that the HSAT5 satellite repeat resided in the same module network with genes implicated in chromosome segregation and nuclear division; potentially hinting at its contribution to disease pathogenesis. Collectively, we report for the first time that repeat and/or transposon expression could be related to disease progression and survival in glioma. The expressions of these elements seem to exert a protective effect during LGG-to-HGG progression, whereas they could have a detrimental impact once HGG is established. The results presented herein could serve as a foundation for further experimental work aimed at elucidating the molecular regulation of glioma genome.

Establishment of an RNA-based transient expression system in the green alga Chlamydomonas reinhardtii

Chlamydomonas reinhardtii, a unicellular green alga, is a prominent model for green biotechnology and for studying organelles’ function and biogenesis, such as chloroplasts and cilia. However, the stable expression of foreign genes from the nuclear genome in C. reinhardtii faces several limitations, including low expression levels and significant differences between clones due to genome position effects, epigenetic silencing, and time-consuming procedures. We developed a robust transient expression system in C. reinhardtii to overcome these limitations. We demonstrated efficient entry of in vitro-transcribed mRNA into wall-less cells and enzymatically dewalled wild-type cells via electroporation. The endogenous or exogenous elements can facilitate efficient transient expression of mRNA in C. reinhardtii, including the 5’ UTR of PsaD and the well-characterized Kozak sequence derived from the Chromochloris zofingiensis. In the optimized system, mRNA expression was detectable in 120 h with a peak around 4 h after transformation. Fluorescently tagged proteins were successfully transiently expressed, enabling organelle labeling and real-time determination of protein sub-cellular localization. Remarkably, transiently expressed IFT46 compensated for the ift46–1 mutant phenotype, indicating the correct protein folding and function of IFT46 within the cells. Additionally, we demonstrated the feasibility of our system for studying protein-protein interactions in living cells using bimolecular fluorescence complementation. In summary, the established transient expression system provides a powerful tool for investigating protein localization, function, and interactions in C. reinhardtii within a relatively short timeframe, which will significantly facilitate the study of gene function, genome structure, and green biomanufacturing in C. reinhardtii and potentially in other algae.

P-based referencing for correcting tissue artifacts in laser ablation-inductively coupled plasma-mass spectrometry imaging of cancer samples.

A referencing strategy based on the element P is presented to compensate for cryosectioning tissue artifacts in laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) data. The study examines how the gadolinium-based contrast agent Gadofosveset is distributed in murine cancer tissue, and illustrates how referenced images can compensate for tissue artifacts like folds, overlaps, and density variations. Compared to non-referenced images that provide information on the absolute distribution of the analyte, referenced images allow for the representation of the analyte distribution relative to the amount of material introduced into the instrument, which in this case is correlated to the P signal. Tissue artifacts were corrected in referenced images for both Gadofosveset and endogenous elements, such as Fe and Zn. Additionally, the referencing approach provides valuable information on the Gd uptake relative to the tissue density in necrotic compared to vital tumor areas, which is not obtained from in vivo magnetic resonance imaging (MRI) data. However, validation of in vivo MRI and ex vivo LA-ICP-MS methods was possible by establishing a mean ratio of necrotic to vital tumor areas in the T1-weighted image post Gadofosveset injection and the non-referenced LA-ICP-MS image of Gd. In summary, P-based correction of LA-ICP-MS imaging data allows for a more accurate spatial representation of certain elements, including endogenous and exogenous elements such as injected contrast agents.

Dynamics of Replication-Associated Protein Levels through the Cell Cycle.

The measurement of dynamic changes in protein level and localization throughout the cell cycle is of major relevance to studies of cellular processes tightly coordinated with the cycle, such as replication, transcription, DNA repair, and checkpoint control. Currently available methods include biochemical assays of cells in bulk following synchronization, which determine protein levels with poor temporal and no spatial resolution. Taking advantage of genetic engineering and live-cell microscopy, we performed time-lapse imaging of cells expressing fluorescently tagged proteins under the control of their endogenous regulatory elements in order to follow their levels throughout the cell cycle. We effectively discern between cell cycle phases and S subphases based on fluorescence intensity and distribution of co-expressed proliferating cell nuclear antigen (PCNA)-mCherry. This allowed us to precisely determine and compare the levels and distribution of multiple replication-associated factors, including Rap1-interacting factor 1 (RIF1), minichromosome maintenance complex component 6 (MCM6), origin recognition complex subunit 1 (ORC1, and Claspin, with high spatiotemporal resolution in HeLa Kyoto cells. Combining these data with available mass spectrometry-based measurements of protein concentrations reveals the changes in the concentration of these proteins throughout the cell cycle. Our approach provides a practical basis for a detailed interrogation of protein dynamics in the context of the cell cycle.

Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in Myotis daubentonii.

Bats are ecologically diverse vertebrates characterized by their ability to host a wide range of viruses without apparent illness and the presence of numerous endogenous viral elements (EVEs). EVEs are well preserved, expressed, and may affect host biology and immunity, but their role in bat immune system evolution remains unclear. Among EVEs, endogenous bornavirus-like elements (EBLs) are bornavirus sequences integrated into animal genomes. Here, we identified a novel EBL in the microbat Myotis daubentonii, EBLL-Cultervirus.10-MyoDau (short name is CV.10-MyoDau) that shows protein-level conservation with the L-protein of a Cultervirus (Wuhan sharpbelly bornavirus). Surprisingly, we discovered a transcript on the antisense strand comprising three exons, which we named AMCR-MyoDau. The active transcription in Myotis daubentonii tissues of AMCR-MyoDau, confirmed by RNA-Seq analysis and RT-PCR, highlights its potential role during viral infections. Using comparative genomics comprising 63 bat genomes, we demonstrate nucleotide-level conservation of CV.10-MyoDau and AMCR-MyoDau across various bat species and its detection in 22 Yangochiropera and 12 Yinpterochiroptera species. To the best of our knowledge, this marks the first occurrence of a conserved EVE shared among diverse bat species, which is accompanied by a conserved antisense transcript. This highlights the need for future research to explore the role of EVEs in shaping the evolution of bat immunity.

Metabolic and tolerance engineering of Komagataella phaffii for 2-phenylethanol production through genome-wide scanning

Background2-Phenylethanol (2-PE) is one of the most widely used spices. Recently, 2-PE has also been considered a potential aviation fuel booster. However, the lack of scientific understanding of the 2-PE biosynthetic pathway and the cellular response to 2-PE cytotoxicity are the most important obstacles to the efficient biosynthesis of 2-PE.ResultsHere, metabolic engineering and tolerance engineering strategies were used to improve the production of 2-PE in Komagataella phaffii. First, the endogenous genes encoding the amino acid permease GAP1, aminotransferase AAT2, phenylpyruvate decarboxylase KDC2, and aldehyde dehydrogenase ALD4 involved in the Ehrlich pathway and the 2-PE stress response gene NIT1 in K. phaffii were screened and characterized via comparative transcriptome analysis. Subsequently, metabolic engineering was employed to gradually reconstruct the 2-PE biosynthetic pathway, and the engineered strain S43 was obtained, which produced 2.98 g/L 2-PE in shake flask. Furthermore, transcriptional profiling analyses were utilized to screen for novel potential tolerance elements. Our results demonstrated that cells with knockout of the PDR12 and C4R2I5 genes exhibited a significant increase in 2-PE tolerance. To confirm the practical applications of these results, deletion of the PDR12 and C4R2I5 genes in the hyper 2-PE producing strain S43 dramatically increased the production of 2-PE by 18.12%, and the production was 3.54 g/L.ConclusionThis is the highest production of 2-PE produced by K. phaffii via l-phenylalanine conversion. These identified K. phaffii endogenous elements are highly conserved in other yeast species, suggesting that manipulation of these homologues might be a useful strategy for improving aromatic alcohol production. These results also enrich the understanding of aromatic compound biosynthetic pathways and 2-PE tolerance, and provide new elements and strategies for the synthesis of aromatic compounds by microbial cell factories.

Characterization of Caulimovirid-like Sequences from Upland Cotton (Gossypium hirsutum L.) Exhibiting Terminal Abortion in Georgia, USA.

In this study, we investigated the potential involvement of endogenous viral elements (EVEs) in the development of apical tissue necrosis, resulting in the terminal abortion of upland cotton (Gossypium hirsutum L.) in Georgia. The high-throughput sequence analysis of symptomatic and asymptomatic plant tissue samples revealed near-complete EVE-Georgia (EVE-GA) sequences closely related to caulimoviruses. The analysis of EVE-GA's putative open reading frames (ORFs) compared to cotton virus A and endogenous cotton pararetroviral elements (eCPRVE) revealed their similarity in putative ORFs 1-4. However, in the ORF 5 and ORF 6 encoding putative coat protein and reverse transcriptase, respectively, the sequences from EVE-GA have stop codons similar to eCPRVE sequences from Mississippi. In silico mining of the cotton genome database using EVE-GA as a query uncovered near-complete viral sequence insertions in the genomes of G. hirsutum species (~7 kb) but partial in G. tomentosum (~5.3 kb) and G. mustelinum (~5.1 kb) species. Furthermore, cotton EVEs' episomal forms and messenger RNA (mRNA) transcripts were detected in both symptomatic and asymptomatic plants collected from cotton fields. No significant yield difference was observed between symptomatic and asymptomatic plants of the two varieties evaluated in the experimental plot. Additionally, EVEs were also detected in cotton seeds and seedlings. This study emphasizes the need for future research on EVE sequences, their coding capacity, and any potential role in host immunity or pathogenicity.

External Factors and Endogenous Elements Fostering Critical Thinking of Tertiary EFL Learners in China: A Grounded Theory Study

The cultivation of critical thinking (CT) skills is a fundamental aim within the realm of higher education. It assumes particular significance within the domain of Teaching English as a Foreign Language (TEFL). This study directs its focus on the Chinese tertiary TEFL context and endeavours to explicate what the external factors are, as well as endogenous elements and ways to foster students’ critical thinking. Methodologically, the study adopted grounded theory (GT) and drew upon qualitative data gathered through interviews with 36 participants, including both students and instructors recruited from prestigious universities, mid-tier colleges, and less developed college across China. The data analysis, utilizing NVivo12 software, encompasses a multilevel coding process, including open, axial, and selective coding, in accordance with the principles of GT. The outcome of this meticulous analysis results in the formulation of a comprehensive model revealing the interplay among external influences, endogenous elements, and ways to foster the development of CT skills among tertiary English as a Foreign Language (EFL) students. The implications of these findings extend pedagogically to multiple stakeholders within the tertiary TEFL context.

Genetic diversity of Flaviviridae and Rhabdoviridae EVEs in Aedes aegypti and Aedes albopictus on Hainan Island and the Leizhou Peninsula, China

BackgroundHainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where Aedes aegypti and Ae. albopictus are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that Aedes endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of Aedes mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies. MethodsIn this study, specific primers for endogenous Flaviviridae elements (EFVEs) and endogenous Rhabdoviridae elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two Aedes mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed. ResultsThe results showed that many EVEs associated with Zika virus infection were detected in both Aedes species, with the detection rates were 47.68% to 100% in Ae. aegypti and 36.15% to 92.31% in sympatric Ae. albopictus populations. EVEs detection rates in another 17 Ae. albopictus populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of Ae. aegypti showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene. ConclusionThe EFVEs and ERVEs tested were present at high frequencies in the field Aedes mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the Ae. aegypti population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to Aedes mosquitoes.

Endogenous retrotransposable elements as a novel predictive biomarker of response to immunotherapy.

Endogenous retrotransposable elements as a novel predictive biomarker of response to immunotherapy.

Molecular Characterization of the Actin Gene and 5′ Flanking Sequence from Brown Macroalga Saccharina japonica (Laminariales, Phaeophyta)

The brown macroalga Saccharina japonica (Laminariales, Phaeophyta) is the most productive cultured seaweed in the world. In order to improve the biosafety of transgenic kelp, it is necessary to develop endogenous constitutive promoters, replacing those of virus origin. In this study, the housekeeping actin gene from S. japonica (SjACT) was found to contain three exons and two introns, representing a unique actin gene structure pattern in brown algae. Additionally, the 5′ upstream region was obtained using genome walking, and fused to the reporter gene lacZ or EGFP to construct promoter-detective vectors. Using an established genetic transformation system, kelps in different life-cycle stages were transformed. The detection results showed that, in the diploid sporophyte stage, the transient expression from the lacZ gene could be observed in the frond, stipe, or holdfast of kelps, indicating a manner of being non-tissue-specific. And, in the haploid gametophyte stage of S. japonica, the fluorescence of the expressed EGFP were detected in vivo in gametophyte cells of both genders. These results indicate that the promoter of the SjACT gene (pSjACT) functions in a constitutive manner and is expected to be a key endogenous element in the genetic manipulation of kelps.

Epigenome editing revealed the role of DNA methylation of T-DMR/CpG island shore on Runx2 transcription

RUNX2 is a transcription factor crucial for bone formation. Mutant mice with varying levels of Runx2 expression display dosage-dependent skeletal abnormalities, underscoring the importance of Runx2 dosage control in skeletal formation. RUNX2 activity is regulated by several molecular mechanisms, including epigenetic modification such as DNA methylation. In this study, we investigated whether targeted repressive epigenome editing including hypermethylation to the Runx2-DMR/CpG island shore could influence Runx2 expression using Cas9-based epigenome-editing tools. Through the transient introduction of CRISPRoff-v2.1 and gRNAs targeting Runx2-DMR into MC3T3-E1 cells, we successfully induced hypermethylation of the region and concurrently reduced Runx2 expression during osteoblast differentiation. Although the epigenome editing of Runx2-DMR did not impact the expression of RUNX2 downstream target genes, these results indicate a causal relationship between the epigenetic status of the Runx2-DMR and Runx2 transcription. Additionally, we observed that hypermethylation of the Runx2-DMR persisted for at least 24 days under growth conditions but decreased during osteogenic differentiation, highlighting an endogenous DNA demethylation activity targeting the Runx2-DMR during the differentiation process. In summary, our study underscore the usefulness of the epigenome editing technology to evaluate the function of endogenous genetic elements and revealed that the Runx2-DMR methylation is actively regulated during osteoblast differentiation, subsequently could influence Runx2 expression.