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181.
Fang Wang Dunmei Lin Wei Li Pengpeng Dou Le Han Mingfen Huang Shenhua Qian Jingmei Yao 《Ecology and evolution》2020,10(17):9257-9270
Litter decomposition, a fundamental process of nutrient cycling and energy flow in freshwater ecosystems, is driven by a diverse array of decomposers. As an important component of the heterotrophic food web, meiofauna can provide a trophic link between leaf‐associated microbes (i.e., bacteria and fungi)/plant detritus and macroinvertebrates, though their contribution to litter decomposition is not well understood. To investigate the role of different decomposer communities in litter decomposition, especially meiofauna, we compared the litter decomposition of three leaf species with different lignin to nitrogen ratios in litter bags with different mesh sizes (0.05, 0.25, and 2 mm) in a forested stream, in China for 78 days. The meiofauna significantly enhanced the decomposition of leaves of high‐and medium‐ quality, while decreasing (negative effect) or increasing (positive effect) the fungal biomass and diversity. Macrofauna and meiofauna together contributed to the decomposition of low‐quality leaf species. The presence of meiofauna and macrofauna triggered different aspects of the microbial community, with their effects on litter decomposition varying as a function of leaf quality. This study reveals that the meiofauna increased the trophic complexity and modulated their interactions with microbes, highlighting the important yet underestimated role of meiofauna in detritus‐based ecosystems. 相似文献
182.
Fajuan Cheng Bin Zheng Jianwei Wang Guiting Zhao Zhongshun Yao Zhihong Niu Wei He 《Bioscience reports》2021,41(6)
Histone deacetylase (HDAC) 10, a class II family, has been implicated in various tumors and non-tumor diseases, which makes the discovery of biological functions and novel inhibitors a fundamental endeavor. In cancers, HDAC10 plays crucial roles in regulating various cellular processes through its epigenetic functions or targeting some decisive molecular or signaling pathways. It also has potential clinical utility for targeting tumors and non-tumor diseases, such as renal cell carcinoma, prostate cancer, immunoglobulin A nephropathy (IgAN), intracerebral hemorrhage, human immunodeficiency virus (HIV) infection and schizophrenia. To date, relatively few studies have investigated HDAC10-specific inhibitors. Therefore, it is important to study the biological functions of HDAC10 for the future development of specific HDAC10 inhibitors. In this review, we analyzed the biological functions, mechanisms and inhibitors of HDAC10, which makes HDAC10 an appealing therapeutic target. 相似文献
183.
Acute leukemia is a hematological malignant tumor. Long non-coding RNA urothelial cancer-associated 1 (UCA1) is involved in the chemo-resistance of diverse cancers, but it is unclear whether UCA1 is associated with the sensitivity of acute leukemia cells to daunorubicin (DNR). DNR (100 nM) was selected for functional analysis. The viability, cell cycle progression, apoptosis, and invasion of treated acute leukemia cells (HL-60 and U-937) were evaluated by cell counting kit-8 (CCK-8) assay, flow cytometry assay, or transwell assay. Protein levels were detected with Western blot analysis. Expression patterns of UCA1 and miR-613 were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). The relationship between UCA1 and microRNA-613 (miR-613) was verified by dual-luciferase reporter assay. We observed that UCA1 expression was elevated in HL-60 and U-937cells. DNR constrained viability, cell cycle progression, invasion, and facilitated apoptosis of HL-60 and U-937 cells in a dose-dependent manner, but these impacts mediated by DNR were reverted after UCA1 overexpression. MiR-613 was down-regulated in HL-60 and U-937 cells, and UCA1 was verified as a miR-613 sponge. MiR-613 inhibitor reversed DNR treatment-mediated effects on viability, cell cycle progression, apoptosis, and invasion of HL-60 and U-937 cells, but these impacts mediated by miR-613 inhibitor were counteracted after UCA1 inhibition. Notably, the inactivation of the PI3K/AKT pathway caused by DNR treatment was reversed after miR-613 inhibitor introduction, but this influence mediated by miR-613 inhibitor was offset after UCA1 knockdown. In conclusion, UCA1 up-regulation facilitated the resistance of acute leukemia cells to DNR via the PI3K/AKT pathway by sponging miR-613. 相似文献
184.
185.
Min Peng Weilin Zhu Chunling Yang Jiuxiang Yao Huifang Chen Weiming Jiang Zhenhan He Qiangyong Li Qingyun Liu Yongzhen Zhao Yong Lin Xiaohan Chen Digang Zeng Xiuli Chen 《Zeitschrift fur angewandte Ichthyologie》2021,37(1):73-82
The genetic diversity of 289 spotted scat (Scatophagus argus) from seven populations along the northern coast of the South China Sea was studied by analyzing the full-length sequences of the mitochondrial control region (D-LOOP). The S. argus D-LOOP sequence was 1,004–1,010 bp long and contained 156 variant sites. The seven studied S. argus populations had a high degree of genetic diversity (haplotype diversity [Hd] = 0.99135; nucleotide diversity (π) = 0.01313). There was no obvious genetic differentiation among the seven geographical populations and gene exchange was frequent (Fst = −0.01867–0.01117, p > .05). Four distinct mitochondrial lineages were identified in the phylogenetic tree and the haplotype network. The between-lineage Fst was 0.71690–0.84940 (p < .001), but these lineages showed no obvious phylogeographic pattern. Based on D-LOOP mutation rates, we estimated that the four lineages diverged approximately 513,800–93,600 years ago, during the Eocene ice age, at which time falling sea levels may have led to population segregation. We estimated that S. argus population expansion occurred approximately 2.29–0.68 million years ago, during the late Pleistocene. During this period, sea levels rose again, allowing previously separated lineages to come into sympatry, which eventually gave rise to a highly genetically diverse population without pyhlogeographic structure. Here, we characterized the genetic structure and differentiation of seven S. argus populations from the northern coast of the South China Sea. Our results suggested that the seven S. argus populations from the northern coast of the South China Sea have a relatively low level of genetic variation and can be considered a single unit for the purposes of fishery development, utilization, and management. 相似文献
186.
Jia Song Yao Liu Xuebing Zhang Qiuyue Wu Juan Gao Wei Wang Jin Li Yanling Song Chaoyong Yang 《Nucleic acids research》2021,49(3):e18
Single-cell RNA sequencing enables us to characterize the cellular heterogeneity in single cell resolution with the help of cell type identification algorithms. However, the noise inherent in single-cell RNA-sequencing data severely disturbs the accuracy of cell clustering, marker identification and visualization. We propose that clustering based on feature density profiles can distinguish informative features from noise. We named such strategy as ‘entropy subspace’ separation and designed a cell clustering algorithm called ENtropy subspace separation-based Clustering for nOise REduction (ENCORE) by integrating the ‘entropy subspace’ separation strategy with a consensus clustering method. We demonstrate that ENCORE performs superiorly on cell clustering and generates high-resolution visualization across 12 standard datasets. More importantly, ENCORE enables identification of group markers with biological significance from a hard-to-separate dataset. With the advantages of effective feature selection, improved clustering, accurate marker identification and high-resolution visualization, we present ENCORE to the community as an important tool for scRNA-seq data analysis to study cellular heterogeneity and discover group markers. 相似文献
187.
Zhanhuai Wang Lindsay M. Hopson Stephanie S. Singleton Xiaochun Yang Wilma Jogunoori Raja Mazumder Vincent Obias Paul Lin Bao-Ngoc Nguyen Michael Yao Larry Miller Jon White Shuyun Rao Lopa Mishra 《生物化学与生物物理学报:疾病的分子基础》2021,1867(10):166179
Emerging data show a rise in colorectal cancer (CRC) incidence in young men and women that is often chemoresistant. One potential risk factor is an alteration in the microbiome. Here, we investigated the role of TGF-β signaling on the intestinal microbiome and the efficacy of chemotherapy for CRC induced by azoxymethane and dextran sodium sulfate in mice. We used two genotypes of TGF-β-signaling-deficient mice (Smad4+/? and Smad4+/?Sptbn1+/?), which developed CRC with similar phenotypes and had similar alterations in the intestinal microbiome. Using these mice, we evaluated the intestinal microbiome and determined the effect of dysfunctional TGF-β signaling on the response to the chemotherapeutic agent 5-Fluoro-uracil (5FU) after induction of CRC. Using shotgun metagenomic sequencing, we determined gut microbiota composition in mice with CRC and found reduced amounts of beneficial species of Bacteroides and Parabacteroides in the mutants compared to the wild-type (WT) mice. Furthermore, the mutant mice with CRC were resistant to 5FU. Whereas the abundances of E. boltae, B.dorei, Lachnoclostridium sp., and Mordavella sp. were significantly reduced in mice with CRC, these species only recovered to basal amounts after 5FU treatment in WT mice, suggesting that the alterations in the intestinal microbiome resulting from compromised TGF-β signaling impaired the response to 5FU. These findings could have implications for inhibiting the TGF-β pathway in the treatment of CRC or other cancers. 相似文献
188.
189.
Barry J. Grant Lars Skjrven Xin‐Qiu Yao 《Protein science : a publication of the Protein Society》2021,30(1):20-30
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ . 相似文献
190.
生物反应工程作为一门理论性与应用性都很强的专业课程,在生物工程等相关专业的课程设置中处于桥梁和纽带地位,对新型应用型工科人才的培养发挥着重要的作用。但由于该课程中公式等抽象理论知识过多,导致学生学习效率十分低下。因此,为了适应新工科教育背景下对创新型人才培养的需求,提高学生的学习兴趣和积极性,并培养学生的自主学习等创新能力,教学团队在课程教学中通过引入虚拟仿真技术、开展微课教学、采用案例式教学模式、利用科研平台等多元化方式,对该课程的教学模式、方法和手段尝试改革和探索,取得了一定的教学效果,并就此进行了一些探讨,以期能为相关课程的教学改革提供一些思路和启示。 相似文献