ORCID Profile
0000-0001-9627-3393
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Publisher: Frontiers Media SA
Date: 03-07-2023
Publisher: Research Square Platform LLC
Date: 11-05-2022
DOI: 10.21203/RS.3.RS-1633326/V1
Abstract: A Gram-stain-negative, non-motile, aerobic, red colony, mesophilic, and slightly halotolerant bacteria, designated strain D16 T , was separated from intertidal surface sediments from Xiaoshi Island, Weihai, China. The strain was able to grow at 10-43°C, pH 5.5-9.5 and in 0-5 % (w/v) NaCl. Optimum growth conditions of the strain were at pH 7.0, 30-33 °C and 1 % (w/v) NaCl. The predominant respiratory quinone, major fatty acids and polar lipids of the strain were (MK-6), (C 15:0 iso, 32.0 %, C 16:0 , 10.5 %) and (DPG、PE、AGL、 GL、 AL、PGS), respectively. Phylogenetic analysis based on 16S rRNA gene sequences and genomes indicated that strain D16 T was the closest to genera Eudoraea , Poritiphilus, Muriicola , Robiginitalea and Zeaxanthinibacter , sharing 92-93 % 16S rRNA gene sequence similarity with the representative of these genera. The draft genome of strain D16 T composed 3,225,638 bp, and the G+C content was 42.8 mol %. The ANI, dDDH, AAI values of strain D16 T compared to similar genera ranged from 67.3 to 70.2 %, 16.2 to 19.1 % and 68.3 to 70.1 %, respectively, below the threshold for recommended species ision of ANI 95–96%, dDDH 70% and AAI 95%. Furthermore, POCP values between strain D16 T and similar genera were less than 50.0%, consistent with the description of a new genus. Based on the results of phylogenetic, phenotypic, genotypic, chemotaxonomic analyses and comparative analysis of metabolic pathway, environmental distribution and characterization between in strain D16 T and other relative genera of family Flavobacteriaceae, it is concluded that strain D16 T represents a novel species of a noval genus of the family Flavobacteriaceae , for which the name Actobacterium tashihtau gen.nov., sp. is proposed. The type strain is D16 T (=MCCC 1H00463 T = KCTC 82746 T ).
Publisher: Cold Spring Harbor Laboratory
Date: 27-06-2023
DOI: 10.1101/2023.06.27.546232
Abstract: Genome sequencing has revolutionized the study of biological systems, enabling exploration of species origins, evolution, and identification. However, traditional methods for constructing phylogenetic trees based on raw sequence data require substantial computational resources and may be challenging for biologists with limited computer knowledge. To address this, a lightweight tree-building tool was developed, Metabolic-Pathway-Presence-Heatmap (MPPH), leveraging Python programming and the KEGG metabolomics database to construct phylogenetic trees based on metabolic pathway information. This approach reduces computational and time requirements while focusing the analysis on metabolic pathways. The tool provides a rapid and reliable option for biologists to investigate the evolutionary and taxonomic aspects of species. Additionally, the tool incorporates a heatmap feature, allowing users to visualize the presence or absence of metabolic pathways across multiple species. The code is available at github.com/DeweyYihengDu/Metabolic-Pathway-Presence-Heatmap .
Publisher: Cold Spring Harbor Laboratory
Date: 26-06-2023
DOI: 10.1101/2023.06.25.546472
Abstract: Liver cancer is a prevalent and deadly malignancy worldwide, with a rising incidence rate. In this study, we focused on the role of NAD + metabolism-related genes in liver cancer prognosis prediction. We identified key genes among NAD + metabolism-related genes and explored their relationship with cancer staging and prognosis using gene expression data. A risk score model was constructed to assess cancer risk and survival status. The model demonstrated significant predictive potential for survival outcomes. Furthermore, we analyzed the risk scores in different populations and performed functional enrichment analyses to gain insights into the biological processes involved. Our study highlights the clinical value and significance of NAD + metabolism-related genes in liver cancer. The findings provide a foundation for personalized treatment strategies and open new avenues for further research in liver cancer management.
Publisher: Elsevier BV
Date: 12-2022
DOI: 10.1016/J.IJPHARM.2022.122385
Abstract: Wound dressings can be applied over the wound sites to provide long-lasting wound management and improve wound healing. Biological wound dressings are superior to synthetic materials due to biodegradability and biocompatibility. These biomaterials have demonstrated huge potential in the field of wound dressings. Applying bibliometric analysis combined with results-based descriptions to characterize the research status, hotspots, and cutting-edge topics, this study is the first in-depth qualitative, quantitative, data-driven overview of biological wound dressings research in recent decades. Filtered data were used to construct co-citation, heatmaps, bi-clustering, strategy maps, and other analyses and visualization. The results show that research on biological wound dressings has progressed considerably in the last 5 years with extensive global collaboration. A clear knowledge base has been developed. Chitosan hydrogels, bacterial cellulose, active agents (silver nanoparticles, growth factors, curcumin, etc.), and electrospinning fibers stand out as research hotspots. The research frontiers include novel starting materials, precise and controlled release systems, and clinical and regenerative medicine applications. We interpreted an overview of the excavated topics and expected the findings here to provide a guide and inspire innovations for developing the next generation wound dressings.
Publisher: Research Square Platform LLC
Date: 09-05-2023
DOI: 10.21203/RS.3.RS-2898458/V1
Abstract: Known for its species abundance and evolutionary status complexity, family Roseobacteraceae is an important subject of many studies on the discovery, identification, taxonomic status, and ecological properties of marine bacteria. In this study, six species from three genera ( Psychromarinibacter , Lutimaribacter , and Maritimibacter ) of family Roseobacteraceae were analyzed and compared , many intergeneric differences and intra-generic ersity were found in phylogenetic, genomic, biochemical, and chemo taxonomical properties. Moreover, a novel strain, named C21-152 T was isolated from solar saltern sediment in Weihai, China. The values of 16S rRNA gene sequence similarity, the average nucleotide identity (ANI), and the digital DNA–DNA hybridization (dDDH) between genomes of the novel strain and P. halotolerans MCCC 1K03203 T were 97.19%, 78.49%, and 21.90%, respectively. Genome sequencing revealed a complete Sox enzyme system related to thiosulfate oxidization as well as a complete pathway for the final conversion of hydroxyproline to α-ketoglutarate. In addition, strain C21-152 T was resistant to many antibiotics and had the ability to survive under salt tolerance. This strain had versatile survival strategies in saline environments. Some of its physiological features enriched and complemented the knowledge of the characteristics of genus Psychromarinibacter . Optimum growth of strain C21-152 T occurred at 37℃, with 5-6% (w/v) NaCl and at pH 7.5. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain C21-152 T should represent a novel specie of the genus Psychromarinibacter , for which the name Psychromarinibacter sediminicola sp. nov. is proposed. The type strain is C21-152 T (=MCCC 1H00808 T =KCTC 92746 T =SDUM1063002 T ).
Location: Australia
Location: No location found
No related grants have been discovered for Yiheng Du.