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Single-cell Hi-C (scHi-C) sequencing technologies allow us to investigate three-dimensional chromatin organization at the single-cell level. However, we still need computational tools to deal with the sparsity of the contact maps from single cells and embed single cells in a lower-dimensional Euclidean space. This embedding helps us understand relationships between the cells in different dimensions, such as cell-cycle dynamics and cell differentiation. We present an open-source computational toolbox, scHiCTools, for analyzing single-cell Hi-C data comprehensively and efficiently. The toolbox provides two methods for screening single cells, three common methods for smoothing scHi-C data, three efficient methods for calculating the pairwise similarity of cells, three methods for embedding single cells, three methods for clustering cells, and a build-in function to visualize the cells embedding in a two-dimensional or three-dimensional plot. scHiCTools, written in Python3, is compatible with different platforms, including Linux, macOS, and Windows. 相似文献
94.
Jin-tian Li Jing-li Lu Hong-yu Wang Zhou Fang Xiao-juan Wang Shi-wei Feng Zhang Wang Ting Yuan Sheng-chang Zhang Shu-ning Ou Xiao-dan Yang Zhuo-hui Wu Xiang-deng Du Ling-yun Tang Bin Liao Wen-sheng Shu Pu Jia Jie-Liang Liang 《Biological reviews of the Cambridge Philosophical Society》2021,96(6):2771-2793
Phosphate-solubilizing microbes (PSMs) drive the biogeochemical cycling of phosphorus (P) and hold promise for sustainable agriculture. However, their global distribution, overall diversity and application potential remain unknown. Here, we present the first synthesis of their biogeography, diversity and utility, employing data from 399 papers published between 1981 and 2017, the results of a nationwide field survey in China consisting of 367 soil samples, and a genetic analysis of 12986 genome-sequenced prokaryotic strains. We show that at continental to global scales, the population density of PSMs in environmental samples is correlated with total P rather than pH. Remarkably, positive relationships exist between the population density of soil PSMs and available P, nitrate-nitrogen and dissolved organic carbon in soil, reflecting functional couplings between PSMs and microbes driving biogeochemical cycles of nitrogen and carbon. More than 2704 strains affiliated with at least nine archaeal, 88 fungal and 336 bacterial species were reported as PSMs. Only 2.59% of these strains have been tested for their efficiencies in improving crop growth or yield under field conditions, providing evidence that PSMs are more likely to exert positive effects on wheat growing in alkaline P-deficient soils. Our systematic genetic analysis reveals five promising PSM genera deserving much more attention. 相似文献
95.
Hong-Bin Liu Xiaoxu Li Jun Cai Ling-Li Jiang Xin Zhang Dousheng Wu Lifeng Wang Aiguo Yang Cun Guo Jia Chen Wenxuan Pu Feng Yu 《Plant biotechnology journal》2023,21(1):63-77
Receptor-like kinases (RLKs) constitute the largest receptor family involved in the regulation of plant immunity and growth, but small-molecule inhibitors that target RLKs to improve agronomic traits remain unexplored. The RLK member FERONIA (FER) negatively regulates plant resistance to certain soil-borne diseases that are difficult to control and cause huge losses in crop yields and economy. Here, we identified 33 highly effective FER kinase inhibitors from 1494 small molecules by monitoring FER autophosphorylation in vitro. Four representative inhibitors (reversine, cenisertib, staurosporine and lavendustin A) inhibited the kinase activity of FER and its homologues in several crops by targeting the conserved ATP pocket in the kinase structure. FER contributes to the physiological impact of representative inhibitors in plants. The treatment of roots with reversine, staurosporine and lavendustin A enhanced innate immunity in plant roots and thus alleviated soil-borne diseases in tobacco, tomato and rice without growth penalties. Consistently, RNA sequencing assays showed that lavendustin A and reversine exert profound impacts on immunity-related gene expression. Our results will set a new milestone in the development of the plant RLK kinase regulation theory and provide a novel strategy for the prevention and control of plant soil-borne diseases without growth penalties. 相似文献
96.
Jiahui Pu Nan Jiang Yulan Zhang Lingling Guo Wenjing Huang Lijun Chen 《Global Change Biology Bioenergy》2023,15(1):88-98
Returning straw to the field is an effective method for optimizing the soil phosphorus (P) availability, in which bacteria play an important role. However, the effects of various straw incorporation strategies on P transformation between different soil P pools remain unclear. In this study, variations in soil P fractions, phosphatase activities and the abundance of phosphatase genes (phoD, phoX and phoC) as well as a P-solubilizing gene (pqqC) at DNA (total) and cDNA (transcribed) levels were analysed in three straw incorporation treatments, including chopped straw (StrawD), straw compost (Compost) and straw-derived biochar (Biochar), and control (no straw, CK). Compared with the CK, the moderately labile inorganic P (NaOH I-Pi) content significantly decreased and the non-available P (Residual P) content significantly increased in the StrawD treatment. At the same time, phosphodiesterase (PD) activity and the transcribed phoC and phoX genes as well as total pqqC gene abundance significantly increased in the StrawD treatment, suggesting that the input of chopped straw stimulated P transformations from both organic and inorganic P pools. In addition, the stable Pi (NaOH II-Pi) content and total pqqC gene abundance in the Biochar treatment were significantly higher than that in the CK, indicating that the input of biochar increased the NaOH II-Pi that could release available P by Pi-solubilizing bacteria. In comparison to the CK, the Compost input significantly decreased one labile Pi (resin-Pi) only. However, its P fractions were significantly different from that of CK, Biochar and StrawD treatments, suggesting that the effects of compost input on P should not be ignored. In conclusion, chopped straw input increased soil P transformation but not available P, biochar input may promote inorganic P transformation, and compost input has a latent effect on P transformation. The study provided a comprehensive understanding of straw incorporation strategies for regulating soil P availability. 相似文献
97.
Kuang Cheng-Hao Zhao Xiao-Fang Yang Ke Zhang Zhi-Peng Ding Li Pu Zhi-En Ma Jian Jiang Qian-Tao Chen Guo-Yue Wang Ji-Rui Wei Yu-Ming Zheng You-Liang Li Wei 《Physiology and Molecular Biology of Plants》2020,26(6):1295-1307
Physiology and Molecular Biology of Plants - The spike traits of wheat can directly affect yield. F2 and F2:3 lines derived from the cross of the multi-spikelet female 10-A and the uni-spikelet... 相似文献
98.
Qian P Marklew CJ Viney J Davison PA Brindley AA Söderberg C Al-Karadaghi S Bullough PA Grossmann JG Hunter CN 《The Journal of biological chemistry》2012,287(7):4946-4956
The biosynthesis of chlorophyll, an essential cofactor for photosynthesis, requires the ATP-dependent insertion of Mg2+ into protoporphyrin IX catalyzed by the multisubunit enzyme magnesium chelatase. This enzyme complex consists of the I subunit, an ATPase that forms a complex with the D subunit, and an H subunit that binds both the protoporphyrin substrate and the magnesium protoporphyrin product. In this study we used electron microscopy and small-angle x-ray scattering to investigate the structure of the magnesium chelatase H subunit, ChlH, from the thermophilic cyanobacterium Thermosynechococcus elongatus. Single particle reconstruction of negatively stained apo-ChlH and Chl-porphyrin proteins was used to reconstitute three-dimensional structures to a resolution of ∼30 Å. ChlH is a large, 148-kDa protein of 1326 residues, forming a cage-like assembly comprising the majority of the structure, attached to a globular N-terminal domain of ∼16 kDa by a narrow linker region. This N-terminal domain is adjacent to a 5 nm-diameter opening in the structure that allows access to a cavity. Small-angle x-ray scattering analysis of ChlH, performed on soluble, catalytically active ChlH, verifies the presence of two domains and their relative sizes. Our results provide a basis for the multiple regulatory and catalytic functions of ChlH of oxygenic photosynthetic organisms and for a chaperoning function that sequesters the enzyme-bound magnesium protoporphyrin product prior to its delivery to the next enzyme in the chlorophyll biosynthetic pathway, magnesium protoporphyrin methyltransferase. 相似文献
99.
Bioprocess and Biosystems Engineering - A new applicability of wastewater of dextran fermentation (WWDF) for biological production of succinic acid with A. succinogenes CCTCC M2012036 was reported... 相似文献
100.