Research progress on ecology and sustainable development of Guilin Lijiang River Basin, China, based on bibliometric analysis.

Guilin is a typical representative of karst landform in South China. Because of its unique geographical landform and hydrological environment, Lijiang River Basin has received a certain degree of attention in field of ecology and sustainable development. Explore and visualize the hotspots and frontiers of Guilin Lijiang River Basin Ecology and Sustainable Development (GLRBESD) by using bibliometrics, CiteSpace, and VOSviewer. Results showed that number of published papers was in a fluctuating upward trend from 1992 to 2022 and from 2011 to 2022, respectively. Work of scholars in this field has been continuously strengthened and deepened, and overall scientific research results show an increasing trend. Research objects and topics are mainly aimed at the water resources, climate, and environment of GLRB Landscape ecology and SDG index construction. Research of GLRBESD-published documents has the characteristics of multi-disciplinary and interdisciplinary integration. High-frequency keywords in research field focus on ecotourism, ecological restoration, and sustainable development, mainly based on the research of ecotourism development. Impact of environmental factor changes and human activities on land use change in different periods is an important research topic. Core research field of GLRBESD on macro-scale can be divided into ESV and function, ecological compensation and ecotourism, ecological environment and ecological restoration, ecological network and ecological risk assessment, and sustainable development. This research provides systematic scientific research basis for enhancing sustainable development ability and ecosystem functions and services of World Natural Heritage Site.

CRISPR-based targeted haplotype-resolved assembly of a megabase region.

Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

Altered DNA methylation pattern reveals epigenetic regulation of Hox genes in thoracic aortic dissection and serves as a biomarker in disease diagnosis.

BACKGROUND: Thoracic aortic dissection (TAD) is a severe disease with limited understandings in its pathogenesis. Altered DNA methylation has been revealed to be involved in many diseases etiology. Few studies have examined the role of DNA methylation in the development of TAD. This study explored alterations of the DNA methylation landscape in TAD and examined the potential role of cell-free DNA (cfDNA) methylation as a biomarker in TAD diagnosis. RESULTS: Ascending aortic tissues from TAD patients (Stanford type A; n = 6) and healthy controls (n = 6) were first examined via whole-genome bisulfite sequencing (WGBS). While no obvious global methylation shift was observed, numerous differentially methylated regions (DMRs) were identified, with associated genes enriched in the areas of vasculature and heart development. We further confirmed the methylation and expression changes in homeobox (Hox) clusters with 10 independent samples using bisulfite pyrosequencing and quantitative real-time PCR (qPCR). Among these, HOXA5, HOXB6 and HOXC6 were significantly down-regulated in TAD samples relative to controls. To evaluate cfDNA methylation pattern as a biomarker in TAD diagnosis, cfDNA from TAD patients (Stanford type A; n = 7) and healthy controls (n = 4) were examined by WGBS. A prediction model was built using DMRs identified previously from aortic tissues on methylation data from cfDNA. Both high sensitivity (86%) and specificity (75%) were achieved in patient classification (AUC = 0.96). CONCLUSIONS: These findings showed an altered epigenetic regulation in TAD patients. This altered epigenetic regulation and subsequent altered expression of genes associated with vasculature and heart development, such as Hox family genes, may contribute to the loss of aortic integrity and TAD pathogenesis. Additionally, the cfDNA methylation in TAD was highly disease specific, which can be used as a non-invasive biomarker for disease prediction.