Search Results (66)

RNA-seq analysis of the highly differentiated human retinal pigment epithelial (RPE) cell-line ARPE-19, cultured on transwells for ≥4 months, yielded 44,909 genes showing 83.35% alignment with the human reference genome. These included mRNA transcripts of RPE-specific genes and those involved in retinopathies. Monolayers were fed photoreceptor outer segments (POS), designed to be synchronously internalised, mimicking homeostatic RPE activity. Cells were subsequently fixed at 4, 6, 24 and 48 h when POS were previously shown to maximally co-localise with Rab5, Rab7, LAMP/lysosomes and LC3b/autophagic compartments. A comprehensive analysis of differentially expressed genes involved in proteolysis revealed a pattern of gene orchestration consistent with POS breakdown in the autophagy-lysosomal pathway. At 4 h, these included elevated upstream signalling events promoting early stages of cargo transport and endosome maturation compared to RPE without POS exposure. This transcriptional landscape altered from 6 h, transitioning to promoting cargo degradation in autolysosomes by 24–48 h. Longitudinal scrutiny of mRNA transcripts revealed nuanced differences even within linked gene networks. POS exposure also initiated transcriptional upregulation in ubiquitin proteasome and chaperone-mediated systems within 4–6 h, providing evidence of cross-talk with other proteolytic processes. These findings show detailed evidence of transcriptome-level responses to cargo trafficking and processing in RPE cells. Full article

In vitro maturation (IVM) of oocytes retrieved from ovum pick-up (OPU) or ovarian tissue (OT) is a standard approach for patients with specific conditions where prior hormonal stimulation is contraindicated. However, the developmental competence of oocytes matured in vitro is still inferior to that of oocytes matured in vivo. Capacitation IVM (CAPA-IVM) includes an extra step of pre-maturation culture (PMC) with c-type natriuretic peptide (CNP) as a meiotic arrestor to better synchronize cytoplasmic and nuclear maturity in oocytes by allowing the cytoplasm additional time to acquire essential components critical for optimal competency. This study aims to evaluate the effect of CAPA-IVM on equine oocyte quality and developmental competence. Immature cumulus–oocyte complexes (COCs) were retrieved from slaughterhouse ovaries and matured in vitro either in CAPA-IVM (short 6 h, long 24 h pre-maturation) or standard IVM. Mature oocytes from each group were analyzed for calcium-releasing potential (n = 52) and single-oocyte proteomics (n = 44), and embryo development (n = 229) was assessed after fertilization with piezo-drilled intracytoplasmic sperm injection (ICSI). Genetic analysis of developed blastocysts (n = 41) was performed to detect chromosomal aberrations. Our findings demonstrate that CAPA-IVM of equine COCs yields significantly higher maturation rates than controls. Moreover, short CAPA-IVM with six hours pre-maturation culture showed substantially higher embryo development potential than the control group (20/69 vs. 9/63, respectively). Genetic analysis revealed a high euploidy rate in equine blastocysts regardless of the maturation conditions. Live calcium imaging of the fertilized oocytes demonstrated that the majority of oocytes displayed non-continuous calcium oscillation patterns, irrespective of maturation conditions. Single-oocyte proteomics reveals a comparable proteomic landscape between mature oocytes subjected to short CAPA-IVM and standard IVM. However, we identified four enriched gene sets with positive enrichment scores after short CAPA-IVM, related to cytoskeleton regulation, ribosomal function, and cytosolic components. Our findings indicate that CAPA-IVM holds the potential to improve oocyte quality and competence in horses. However, further fine-tuning of culture conditions would benefit the effective use of these IVM systems. Moreover, given that the mare serves as an excellent model for human reproduction, the molecular trends identified in this study could provide valuable insights for advancing human artificial reproductive technologies. Full article

The widespread practice of deliberate human displacement for biodiversity conservation remains a contentious issue in the Anthropocene era. This study explores the ecological impacts of conservation-led resettlement (ER) in Nepal’s Terai Arc Landscape (TAL), a biodiverse region under significant conservation and development pressures. Although ER aims to enhance ecological integrity, the role of displacement in conservation has been understudied. Using case studies from the TAL, we examined ecological indicators in vacated settlement areas within parks and newly resettled sites outside protected zones. Data were collected through a review of secondary literature, 240 household interviews, 5 focus group discussions, 25 key informant interviews, and multiple field visits across resettlement sites. Between 1973 and 2019, TAL gained 922.52 sq. km of core protected areas (displacing over 4800 households) and dispossessed communities from 2120.12 sq. km of buffer zones, significantly expanding protected areas and upgrading conservation standards from IUCN category IV to II. This contributed to the recovery of key species such as tigers, rhinos, and elephants. However, resettlements, often located along critical biological corridors and buffer zones, led to habitat fragmentation, endangering the gene pool flow and creating isolated habitats. Results show that, in general, most ecosystem and environmental variables were perceived significantly different (p < 0.05) among resettled communities in the study area. The cultural and land-based attachments of displaced communities were overlooked. These findings highlight the risks of short-term resettlement planning, which can exacerbate pressures on critical corridors, escalate human–wildlife conflicts, and provide a clear indication of the trade-off between conservation benefits and social costs. Full article

In the context of global urbanization and the concomitant tension between heritage conservation and urban development, there is an urgent need to explore effective strategies for addressing the challenges posed by fragmented conservation, static cognition, and homogeneous renewal in conservation practice. Utilizing the theoretical framework of urban historic landscape, this study integrates urban morphology, architectural typology, urban imagery, and catalyst theory to formulate a progressive study on the evolution of historic districts through the layers of “historic areas, spatial forms, material carriers, value characteristics”. The research path is a progressive one that analyses the regularity of historic districts. The present study focuses on Shenyang as the object of empirical research, employing a multifaceted research method that integrates multiple scenarios and sub-cases within a single case. This method utilizes a combination of the literature and field research to obtain diversified data. The study then undertakes a systematic analysis of the accumulation of Shenyang’s historic districts through the application of kernel density analysis and geometric graphical methods. The study found that the dimension of the historical area of the Shenyang historic district presents the layering law of “single-core dominant–dual-core juxtaposition–fusion collage–extension–multi-point radiation”, and that the spatial form is summarized as seven types of the layering law, such as radiation type, ring type, triangular type, and grid type. The spatial form is summarized into seven types of laminar laws, such as radial, ring, triangular, grid, etc. The material carriers exhibit the conventional law of anchoring point-like elements, employing line-like elements as the skeletal structure and surface-like elements as the matrix. The value laminations are diversified, centralized, and self-adaptive. The study proposes the concept of “layer accumulation law” to elucidate the carrier transformation mechanism of cultural genes, and it provides a methodological tool for addressing the dilemma of “layer accumulation fracture”. The findings of this study not only deepen the localized application of HUL theory but also provide an innovative path for the practice of heritage conservation in urban renewal. Full article

Hemerocallis middendorffii is widely used in the landscaping of Northern China for its exceptional ornamental and ecological attributes. It is also the focus of a substantial body of germplasm development and stress tolerance research. However, the absence of an efficient regeneration and genetic transformation system has been a critical barrier to conducting gene function studies on this species. In this research, the aerial parts of seed-derived H. middendorffii plantlets were used as explants, and the callus induction, proliferation, subculture, differentiation, and rooting conditions in the in vitro regeneration process were optimized. A callus induction rate of 95.6% was achieved, with a regeneration rate of 84.4%. Based on this procedure, a simple and effective Agrobacterium-mediated genetic transformation system was preliminarily developed using a hygromycin-based selection system. The system comprised an Agrobacterium tumefaciens culture solution optical density at 600 nm (OD₆₀₀) of 0.6, an acetosyringone concentration of 100 μmol·L⁻¹ in both the A. tumefaciens infection solution and the co-cultivation medium, a sterilization culture with Timentin at 300 mg·L⁻¹, and a selection culture with hygromycin at 9 mg·L⁻¹. Transgenic H. middendorffii T0 rooted plants were produced within a 5-month period, with a transformation rate of 11.9% and positive rate of 32.8%. The regeneration and genetic transformation system established in this study should help advance functional gene research and genetic improvement in H. middendorffii. However, the genetic transformation was only validated in the T0 plants. To confirm stable integration and long-term transgene stability, future research on the phenotypic and molecular characterization of T1 progeny, including segregation analysis and Southern blot verification, will be conducted. Full article

Loropetalum chinense is a significant small tree and ornamental shrub known for its colorful foliage and is widely used in landscaping in tropical and subtropical regions. This study aimed to establish an efficient, tissue culture-independent genetic transformation system for L. chinense. Cuttings from two varieties, ‘Xiangnong Xiangyun’ and ‘Hei Zhenzhu’, were infected with different strains of Agrobacterium rhizogenes. The results showed that the K599 strain significantly induced hairy roots in both varieties, with ‘Xiangnong Xiangyun’ demonstrating a higher survival rate (60%), rooting rate (51.66%), and hairy root induction efficiency (45%) compared to ‘Hei Zhenzhu’. Based on these findings, ‘Xiangnong Xiangyun’ and the K599 strain were selected for further optimization through an orthogonal L9 (3³) experiment, which focused on optimizing the infection solution composition, bacterial concentration, and infection duration, Finally, the genetic transformation system established at the beginning of the experiment was validated on ‘Xiangnong Xiangyun’ plants using the pre-screening LcDREB-43 gene of our group. Among these factors, infection duration was identified as the most influential for improving transformation efficiency. The optimal conditions were determined as an infection solution containing MES solution, a bacterial concentration of OD₆₀₀ = 0.8, and a 15 min infection duration. Under these optimized conditions, the survival rate, rooting rate, induction efficiency, and transformation efficiency reached 86.67%, 70%, 61.67%, and 43.33%, respectively. Furthermore, the transgenic plants with LcDREB-43 overexpression and pCAMBIA1305-GFP were obtained through the established transformation system, the authenticity of the system was proved, and the production application was carried out through phenotypic observation, molecular identification, and auxiliary verification of physiological indicators. Full article

Since ancient times, the community of Xochimilco in the south of Mexico City has provided vegetables for the entire city. Today, Lake Xochimilco is listed as a UNESCO World Heritage Site because it is the last remaining bastion of Aztec culture and preserves the extraordinary ecological landscape of chinampas, a system of arable islands that has endured for over 1000 years. Here, we report on the microbiological communities currently existing in the lake. This is relevant since the water irrigates crops on the islands, known as chinampas. To achieve this, samples from the lake were collected at two different sites, and metagenomics analysis of the 16S gene was conducted. The results indicate the presence of five dominant bacterial phyla: Actinobacteria (44.5%), Proteobacteria (22.5%), Firmicutes (13%), Bacteroidota (6%), and Chloroflexi (4.6%). The most abundant families were Micrococcaceae, Intrasporangiaceae, and Rhodobacteraceae. The results correlate with current anthropogenic activity, indicating a moderate problem associated with contamination. Our findings suggest that immediate actions and increased awareness are necessary to preserve this cultural and natural heritage site and to take steps to comply with Sustainable Development Goal 11 (Sustainable Cities and Communities). Furthermore, this is the first report to characterize microbial communities in the water of Lake Xochimilco using 16S rRNA gene sequencing. Full article

The accelerating processes of globalization and modernization have imposed unprecedented anthropogenic pressures on the cultural diversity of historic districts, leading to the physical degradation of historical heritage and the fragmentation of cultural transmission chains. To address this challenge, this study establishes an innovative spatial-gene theoretical framework that seeks to balance heritage protection with urban development by integrating landscape characteristics and cultural connotations, thereby enhancing the conservation of cultural diversity in historic districts. Focusing on the historic Small Wild Goose Pagoda district as a case study, we developed a comprehensive methodology integrating field research, historical induction, spatial analysis, and place-making. Through this operational framework, we systematically identified four constitutive spatial genes: the mountain–water pattern, the urban-axis, the li-fang, and the architectural courtyard. These genetic elements inform a dual-regeneration strategy that promotes synergy and dialogue between old and new: (1) place-making guided by historical morphological grammar rules and (2) activity organization that reconfigures the value system of “openness and inclusiveness”. This research not only advances spatial-gene theory but also provides a replicable model for regenerating historic districts oriented toward cultural diversity, effectively combining historical authenticity with contemporary functionality to promote sustainable urban development. Full article

The highly contagious FMDV is the agent responsible for foot-and-mouth disease, significantly impacting animals with cloven hooves and incurring substantial economic losses globally. The FMDV genome, composed of single-stranded RNA, consists of approximately 8500 nucleotides and harbors a single open reading frame (ORF) encoding both structural and non-structural proteins vital for the virus’s pathogenicity and replication. BHK-21 (baby hamster kidney) cells are the optimal cell line for FMDV culture due to their robust viral replication ability and high infection susceptibility. The insufficient elucidation of the host response to FMDV hampers progress towards the establishment of precise therapeutic interventions. To fill this void in understanding, samples from FMDV-challenged and control BHK-21 cells were systematically procured, with comprehensive transcriptome sequencing subsequently undertaken to delineate the gene expression landscapes of each group. A total of 4018 differentially expressed genes were identified, of which 2044 were downregulated and 1974 were upregulated. The data indicate that FMDV infection significantly enhances transcription initiation in BHK-21. According to GO and KEGG enrichment analysis, FMDV affects a number of immune-related processes as well as the movement of chemicals within cells. In the analysis of the protein–protein interaction network, Fos, Flt3lg, Rpl22l1, Ifi35, Ep300, and Rps16 emerged as pivotal hub proteins, underscoring their significant roles within the cellular interactome. The RT-qPCR experiment of Lgfb5, Ler2, Vgll3, and Ahr verified that the DEGs’ expression profiles matched the results of the RNA-seq investigation. The study’s findings have enhanced our understanding of the molecular pathways underlying FMDV pathogenesis and host interactions. Furthermore, the identification of key genes could serve as potential targets for therapeutic strategies and diagnostic tools, thereby enhancing control measures for livestock foot-and-mouth disease and mitigating its economic impact. Full article

Abelmoschus manihot L. (Jinhuakui, JHK) is widely cultivated for its pharmacological properties owing to its high flavonoid content and is commonly used as a garden landscape plant. However, the absence of an efficient genetic transformation system poses significant challenges for functional gene studies in this species. Virus-induced gene silencing (VIGS) is a well-established technique for exploring plant gene functions; however, this technique has not been applied to JHK. Here, a tobacco rattle virus (TRV)–VIGS system was successfully developed for the first time in JHK using the gene encoding phytoene desaturase (AmPDS) as a marker gene. This study investigated the impact of various Agrobacterium infection methods on the efficiency of AmPDS silencing. The results demonstrated that administering two injections—the first on the day of complete cotyledon expansion and the second 14 days later—using pTRV1 and pTRV2–AmPDS cultures resuspended to an OD₆₀₀ of 1.0 and via the backside of the blade—led to significant photobleaching in the cotyledons 2 days after the second injection. Subsequent analyses revealed a marked reduction in both chlorophyll content and AmPDS expression. These findings suggest that a VIGS system was successfully developed in JHK, thus providing a rapid and effective method for studying gene function in this species and facilitating future research in JHK genetics. Full article

The intensifying urbanization has led to the increasing risk of urban landscape character fading away. How to inherit and control the “genes” of urban landscape features is a crucial issue that needs urgent resolution. To address this issue, this study draws on the theory of biological genes, employing methods such as historical information translation, deconstruction and extraction of landscape features, and genetic analysis to establish a research paradigm of “holistic composition interpretation—dynamic evolution interpretation” for historic urban landscape genes. The study applies this paradigm in practice using Harbin, China, as an example. The results indicate that: (1) The historic urban landscape genes are comprised of explicit landscape pattern genes; street and alley texture genes; architectural appearance genes; and implicit human settlement culture genes, industrial culture genes, historical culture genes, and spiritual culture genes. (2) The evolutionary traits of Harbin’s historic urban landscape genes manifest in several ways: the evolution of its landscape pattern genes, featuring “three-tiered terraces, balanced spatial arrangement, surrounded by mountains and rivers, and fan-shaped radial layout”; the evolution of its street and alley texture genes, exhibited through “a blend of Chinese and Western styles, sprawling and interconnected, unit linkage, and multi-dimensional intersections”; the evolution of its architectural style genes, marked by “diverse styles, a harmonious fusion of Chinese and Western elements, grouped interdependence, and adaptation to the times”; the evolution of its human settlement culture genes, highlighted by “a secluded lifestyle, diverse customs, and the coexistence of Chinese and Western cultures”; the evolution of its historical culture genes, distinguished by “unity in diversity and multicultural differentiation”; and the evolution of its spiritual culture genes, characterized by “pluralistic beliefs and inclusiveness”. (3) The essential difference between historic urban landscape genes and other genes lies in their adaptive evolution in response to environmental changes over generations and their ability to reveal the influence mechanisms among genes, between genes and landscape features, and between genes and the environment. The distinction between historic urban landscape genes and other types of genes lies in the adaptive changes that historic urban landscape gene types undergo in response to changes in time and environment. The historic urban landscape gene system itself undergoes adaptive evolution with the urban environment of various historical periods, leading to the emergence and differentiation of new levels. This study can provide new insights into urban heritage conservation, urban landscape management, and rational allocation of urban land use. Full article

To better understand host–phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host rpoC gene, which encodes the RNA polymerase β’ subunit. To examine the hypothesis that mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and rpoC_G17D mutant cultures infected with phage K, at different timepoints after infection. Infection of the WT host led to a steady increase of phage transcription relative to the host. Our analysis allowed us to define 53 transcriptional units and to categorize genes based on their temporal expression patterns. Predicted promoter sequences defined by conserved −35, −10, and, in some cases, extended −10 elements, were found upstream of early and middle genes. However, in many cases, sequences upstream of late genes did not contain clear, complete, canonical promoter sequences, suggesting that factors in addition to host RNA polymerase are required for their expression. Infection of the rpoC_G17D mutant host led to a transcriptional pattern that was similar to that of the WT at early timepoints. However, beginning at 20 min after infection, transcription of late genes (such as phage structural genes and host lysis genes) was severely reduced. Our data indicate that the rpoC_G17D mutation prevents the expression of phage late genes, resulting in a failed infection cycle for phage K. In addition to illuminating the global transcriptional landscape of phage K throughout the infection cycle, this study will inform our investigations into the basis of phage K’s control of its transcriptional program as well as mechanisms of phage resistance. Full article

The Yuan River Basin in Hunan Province, known for its rich history and cultural heritage, is home to traditional village landscapes characterized by distinct cultural genes and regional features. This study focuses on 21 traditional villages in Xupu County, Huaihua, and develops four types of traditional village landscape cultural genome atlases at three hierarchical levels: individual villages, multiple villages, and a specific research area. These atlases include genetic linkage maps, spatial sequence maps, distribution pattern maps, and geographical pattern maps. Using Yangquepo in Zhumucun Village as a case study, we constructed a genetic linkage map for the landscape cultural genome of a single traditional village, based on the arrangement structure of courtyard layouts. Spatial sequence maps were derived from the overall spatial configuration, while distribution pattern maps and geographical pattern maps for the 21 villages were developed using kernel density analysis in ArcGIS 10.8 software. The results reveal that traditional village landscapes in the region possess a diverse cultural genome, marked by distinct regional characteristics and spatial organization patterns. Full article

Hepatocellular carcinomas (HCCs) are highly heterogeneous malignancies. They are characterized by a peculiar tumor microenvironment and dense vascularization. The importance of signaling between immune cells, endothelial cells, and tumor cells leads to the difficult recapitulation of a reliable in vitro HCC model using the conventional two-dimensional cell cultures. The advent of three-dimensional organoid tumor technology has revolutionized our understanding of the pathogenesis and progression of several malignancies by faithfully replicating the original cancer genomic, epigenomic, and microenvironmental landscape. Organoids more closely mimic the in vivo environment and cell interactions, replicating factors such as the spatial organization of cell surface receptors and gene expression, and will probably become an important tool in the choice of therapies and the evaluation of tumor response to treatments. This review aimed to describe the ongoing and potential applications of organoids as an in vitro model for the study of HCC development, its interaction with the host’s immunity, the analysis of drug sensitivity tests, and the current limits in this field. Full article

Traditional villages along the Jinzhong section of the Wanli Tea Road possess unique geographical locations and cultural heritage, showcasing a rich variety of cultural landscapes. Among these, village temple buildings play a crucial role as the core of spiritual and belief life in traditional villages. In the context of rapid urbanization and modernization, a new perspective is needed to thoroughly explore the deeper connotations of cultural landscape characteristics in traditional villages along the Wanli Tea Road, particularly by examining the composition and inherent features of their landscape genes. This study employs landscape gene theory, using the village temple system as a lens to identify and analyze the landscape genes of traditional villages along the Jinzhong section of the Wanli Tea Road. Based on the results, a genealogy and a map of landscape genes are constructed to clearly and effectively present the typical characteristics and expressions of these genes in a logical and visual manner. The findings indicate the following: (1) The village temple system in traditional villages along the Jinzhong section of the Wanli Tea Road is closely related to the formation and expression of their landscape genes and can play a critical role in the protection and transmission of cultural landscapes. (2) As important nodes along the historical trade route, the landscape gene characteristics of these villages reflect their unique natural environments and historical development trajectories, illustrating the deep intertwining of commercial activities and local cultural landscapes. (3) This study establishes a replicable research framework that is not only applicable to local studies but also provides valuable references for broader cultural landscape research. Full article