Publications by authors named "Xiao Dong"

705 Publications

Environmental filtering drives the establishment of the distinctive rhizosphere, bulk, and root nodule bacterial communities of in hilly and gully regions of the Loess Plateau of China.

Front Microbiol 2022 22;13:945127. Epub 2022 Jul 22.

College of Life Sciences, Yan'an University, Yan'an, China.

In addition to the rhizobia, other non-rhizobial endophytes (NREs) have been simultaneously isolated from the root nodules. The existence of NREs in leguminous root nodules is a universal phenomenon, and they have the potential to enhance legume survival, especially under conditions of environmental stress. However, the diversity and biogeographic patterns of microbial communities inhabiting root nodules are not well studied or understood. Here, we explored and characterized the diversity of NRE bacteria by using 16S rRNA gene high-throughput amplicon sequencing. Additionally, we compared the biogeography and co-occurrence patterns in review of the bacterial microbiota inhabiting the rhizosphere, the bulk soil and the root nodule bacterial communities associated with , a native N-fixing wild leguminous shrub in hilly and gully regions of the Loess Plateau of China. The results showed the presence of a large diversity of bacteria belonging to 81 phyla, 154 classes, 333 orders, 463 families, and 732 genera inside the nodules. Proteobacteria were dominant in the nodule and rhizosphere soil samples, and Actinomycetes were dominant in the bulk soil samples. was the dominant genus in the nodules, accounting for between 60.15 and 83.74% of the bacteria. The microbial community composition of the NRE in the root nodules differed from that in the rhizosphere soil and the bulk soil of . . Moreover, we found that the biogeographic patterns and assembly process of the rhizobia and non-rhizobia communities differed in the root nodule, the rhizosphere soil and the bulk soil. Furthermore, the correlation analysis between the soil's physical and chemical properties and the bacteria showed that available phosphorus was the predominant factor affecting the bacterial diversity within the rhizosphere soil. Finally, our results revealed that the microbial network diagram of co-occurrence patterns showed more complexes in the soil than in the root nodules. This indicates that only specific microorganisms could colonize and thrive in the rhizosphere through the selection and filtering effects of roots. In conclusion, there are significant differences in bacterial community composition in the nodules, rhizosphere and bulk soil in the hilly and gully region of the Loess Plateau, which is the result of environmental filtration. Our study improves the understanding of the biogeographic patterns and diversity of bacterial microbiota inhabiting root nodules and can help quantify and define the root nodule assemblage process of . .
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http://dx.doi.org/10.3389/fmicb.2022.945127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355530PMC
July 2022

Empagliflozin inhibits macrophage inflammation through AMPK signaling pathway and plays an anti-atherosclerosis role.

Int J Cardiol 2022 Aug 2. Epub 2022 Aug 2.

Hubei University of Medicine, Shiyan 442000, Hubei, China; Taihe Hospital, Shiyan 442000, Hubei, China. Electronic address:

Objective: In recent years, some authoritative clinical studies have found that SGLT2 inhibitor can reduce cardiovascular risk in patients with diabetes, which may imply that SGLT2 inhibitor can play a role beyond lowering blood glucose. In this study, we explored the effect of empagliflozin on vascular atherosclerosis after removing the effect of diabetes.

Methods: The interaction between SGLT2 inhibitor and the AMPK(Adenosine 5'-monophosphate-activated protein kinase) signal pathway to attenuate atherosclerosis was studied in both spontaneously atherosclerotic mice in vivo and oxidized low-density lipoprotein(ox-LDL) induced macrophage inflammation model in vitro. In vivo experiment the aorta tree and aortic valve area were stained with oil red, and the level of inflammatory factors in the diseased tissue was evaluated by immunohistochemistry. Meanwhile, serum was collected to detect the levels of inflammatory factors. In vitro experiment, the RAW264.7 cell line was selected and ox-LDL was used to induce the release of proinflammatory factors, and different doses of empagliflozin were added. The phagocytosis of macrophages to ox-LDL density lipoprotein, and the expression of inflammatory factors at the protein and RNA levels were measured.

Results: Empagliflozin reduced the area of atherosclerotic plaque and macrophage infiltration in atherosclerotic plaques, decreased the expression of inflammatory factors in local plaque tissues and serum of APOE mice fed with high-fat diet. Empagliflozin can improve the protein expression level of p-AMPK affected by ox-LDL in cell and reduce the gene expression level of inflammatory factors and protein expression level of NF-κB, thus playing an anti-atherosclerosis role.

Conclusions: Empagliflozin improves energy metabolism and reduces the expression of inflammatory factors by activating AMPK. As empagliflozin inhibits atherosclerosis progression, it may be of use in prevention of cardiovascular diseases.
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http://dx.doi.org/10.1016/j.ijcard.2022.07.048DOI Listing
August 2022

BcWRKY33A Enhances Resistance to via Activating in Non-Heading Chinese Cabbage.

Int J Mol Sci 2022 Jul 26;23(15). Epub 2022 Jul 26.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China.

The transcription factor WRKY33 is a vital regulator of the biological process of the necrotrophic fungus (). However, its specific regulatory mechanism remains to be further investigated. In non-heading Chinese cabbage (NHCC, (syn. ) ssp. ), our previous study showed that BcWRKY33A is induced not only by salt stress, but also by infection. Here, we noticed that BcWRKY33A is expressed in trichomes and confer plant defense resistance. Disease symptoms and qRT-PCR analyses revealed that -overexpressing and -silencing lines were less and more severely impaired, respectively, than wild type upon treatment. Meanwhile, the transcripts' abundance of indolic glucosinolates' (IGSs) biosynthetic genes is consistent with plants' tolerance. Identification and expression pattern analysis of BcMYB51s showed that BcMYB51-3 has a similar trend to BcWRKY33A upon infection. Moreover, BcWRKY33A directly binds to the promoter, which was jointly confirmed by Y1H, dual-LUC, and EMSA assays. The importance of MYB51, the homolog of BcMYB51-3, in the BcWRKY33A-mediated resistance was also verified using the TRV-based VIGS system. Overall, our data concludes that BcWRKY33A directly activates the expression of and downstream IGSs' biosynthetic genes, thereby improving the tolerance of NHCC plants.
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http://dx.doi.org/10.3390/ijms23158222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9331318PMC
July 2022

Quantitative Analysis of Structure Color of Photonic Crystal Sensors Based on HSB Color Space.

ACS Appl Mater Interfaces 2022 Aug 20;14(30):35010-35019. Epub 2022 Jul 20.

School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China.

The photonic crystals (PhCs) have a bright structural color, but their angular dependence and naked-eye observation subjectivity only apply for qualitative analysis. The HSB color space is a three-channel color analysis technology based on hue (H)-saturation (S)-brightness (B). We use the HSB color space to analyze the structural color of the AM/NIPAM PhCs hydrogel sensor in response to temperature and organic solvents. We proved that the structural color analysis based on the hue value (H) could achieve an analysis accuracy close to the spectrum analysis. In addition, we have obtained stimulus-responsive PhCs structure color images from references and quantitatively analyzed them through the HSB color space. The results show that the H of the structural color can establish a high correlation with the specified target. In some cases, its best fitness exceeds traditional spectroscopy methods. This analysis method will provide a general and quantitative analysis technology for the structural color of PhCs by consumer-grade computers and smartphones.
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http://dx.doi.org/10.1021/acsami.2c08431DOI Listing
August 2022

BcOPR3 mediates defense responses to biotrophic and necrotrophic pathogens in Arabidopsis and non-heading Chinese cabbage.

Phytopathology 2022 Jul 19. Epub 2022 Jul 19.

Nanjing Agricultural University State Key Laboratory of Crop Genetics and Germplasm Enhancement, 200645, Department of Horticulture, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, 210095, Nanjing, China;

In plants, the salicylic acid (SA) and jasmonic acid (JA) signaling pathways usually mediate the defense response to biotrophic and necrotrophic pathogens, respectively. Our previous work showed that after non-heading Chinese cabbage (NHCC) was infected with the biotrophic pathogen Hyaloperonospora parasitica, expression of the JA biosynthetic gene BcOPR3 is induced; yet its molecular mechanism remains unclear. Here, we overexpressed BcOPR3 in Arabidopsis and silenced BcOPR3 in NHCC001 plants to study the defensive role of BcOPR3 in plants against pathogen invasion. The results showed that overexpression of BcOPR3 increased the susceptibility of Arabidopsis to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), but enhanced its resistance to Botrytis cinerea. BcOPR3-silenced NHCC001 plants with a 50% reduction in BcOPR3 expression increased their resistance to downy mildew by reducing the hyphal density and spores of H. parasitica. In addition, BcOPR3-partly silenced NHCC001 plants were also resistant to B. cinerea, which may be the result of a synergistic effect of JA and SA. These findings indicated a complicated role of BcOPR3 in the mediating defense responses to biotrophic and necrotrophic pathogens.
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http://dx.doi.org/10.1094/PHYTO-02-22-0049-RDOI Listing
July 2022

Coal Identification Based on Reflection Spectroscopy and Deep Learning: Paving the Way for Efficient Coal Combustion and Pyrolysis.

ACS Omega 2022 Jul 29;7(27):23919-23928. Epub 2022 Jun 29.

School of Information Science and Engineering, Northeastern University, Shenyang 110819, China.

Coal plays an indispensable role in the world's energy structure. Coal converts chemical energy into energy such as electricity, heat, and internal energy through combustion. To realize the energy conversion of coal more efficiently, coal needs to be identified during the stages of mining, combustion, and pyrolysis. On this basis, different categories of coal are used according to industrial needs, or different pyrolysis processes are selected according to the category of coal. This paper proposes an approach combining deep learning with reflection spectroscopy for rapid coal identification in mining, combustion, and pyrolysis scenarios. First, spectral data of different coal samples were collected in the field and these spectral data were preprocessed. Then, an identification model combining a multiscale convolutional neural network (CNN) and an extreme learning machine (ELM), named RS_PSOTELM, is proposed. The effective features in the spectral data are extracted by the CNN, and the feature classification is realized utilizing the ELM. To enhance the identification performance of the model, we utilize a particle swarm optimization algorithm to optimize the parameters of the ELM. Experimental results show that RS_PSOTELM achieves 98.3% accuracy on the coal identification task and is able to identify coal quickly and accurately, providing a low-cost, efficient, and reliable approach for coal identification during the mining and application phases, as well as paving the way for efficient combustion and pyrolysis of coal.
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http://dx.doi.org/10.1021/acsomega.2c02665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9280928PMC
July 2022

A 16-miRNA Prognostic Model to Predict Overall Survival in Neuroblastoma.

Front Genet 2022 29;13:827842. Epub 2022 Jun 29.

Shenzhen Children's Hospital, Shenzhen, China.

Neuroblastoma is the most malignant childhood tumor. The outcome of neuroblastoma is hard to predict due to the limitation of prognostic markers. In our study, we constructed a 16-miRNA prognostic model to predict the overall survival of neuroblastoma patients for early diagnosis. A total of 205 DE miRNAs were screened using RNA sequencing data from GSE121513. Lasso Cox regression analysis generated a 16-miRNA signature consisting of hsa-let-7c, hsa-miR-135a, hsa-miR-137, hsa-miR-146a, hsa-miR-149, hsa-miR-15a, hsa-miR-195, hsa-miR-197, hsa-miR-200c, hsa-miR-204, hsa-miR-302a, hsa-miR-331, hsa-miR-345, hsa-miR-383, hsa-miR-93, and hsa-miR-9star. The concordance index of multivariate Cox regression analysis was 0.9, and the area under the curve (AUC) values of 3-year and 5-year survival were 0.92 and 0.943, respectively. The mechanism was further investigated using the TCGA and GSE90689 datasets. Two miRNA-gene interaction networks were constructed among DEGs from two datasets. Functional analysis revealed that immune-related processes were involved in the initiation and metastasis of neuroblastoma. CIBERSORT and survival analysis suggested that lower CD8 T-cell proportion and higher SPTA1 expressions were related to a better prognosis. Our study demonstrated that the miRNA signature may be useful in prognosis prediction and management improvement.
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http://dx.doi.org/10.3389/fgene.2022.827842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9278893PMC
June 2022

Regulatory interaction of BcWRKY33A and BcHSFA4A promotes salt tolerance in non-heading Chinese cabbage [ (syn. ) ssp. ].

Hortic Res 2022 17;9:uhac113. Epub 2022 May 17.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China.

Salinity is a universal environmental stress that causes yield reduction in plants. WRKY33, which has been extensively studied in plant defense against necrotrophic pathogens, has recently been found to be important in salt-responsive pathways. However, the underlying molecular mechanisms controlling the involvement of in salt tolerance have not been fully characterized. Here, we explored the function of BcWRKY33A in non-heading Chinese cabbage (NHCC). Under salt stress, expression is significantly induced in roots. As a nuclear protein, BcWRKY33A has strong transcriptional activation activity. Overexpression of confers salt tolerance in , whereas silencing of causes salt sensitivity in NHCC. Furthermore, BcHSFA4A, a protein that interacts with BcWRKY33A, could directly bind to the HSE motif within the promoters of and , which are involved in the plant response to salt stress. Finally, we found that BcWRKY33A could enhance the transcriptional activity of BcHSFA4A and affect its downstream genes (e.g. and ), and co-overexpression of and could promote the expression of salt-related genes, suggesting that the regulatory interaction between BcWRKY33A and BcHSFA4A improves salt tolerance in plants. Overall, our results provide insight into the molecular framework of the BcWRKY33A-BcHSFA4A signaling pathway, which also aids in our understanding of the molecular mechanism of salt tolerance in plants.
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http://dx.doi.org/10.1093/hr/uhac113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9273956PMC
May 2022

Coherent interfaces govern direct transformation from graphite to diamond.

Nature 2022 07 6;607(7919):486-491. Epub 2022 Jul 6.

Center for High Pressure Science (CHiPS), State Key Laboratory of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao, China.

Understanding the direct transformation from graphite to diamond has been a long-standing challenge with great scientific and practical importance. Previously proposed transformation mechanisms, based on traditional experimental observations that lacked atomistic resolution, cannot account for the complex nanostructures occurring at graphite-diamond interfaces during the transformation. Here we report the identification of coherent graphite-diamond interfaces, which consist of four basic structural motifs, in partially transformed graphite samples recovered from static compression, using high-angle annular dark-field scanning transmission electron microscopy. These observations provide insight into possible pathways of the transformation. Theoretical calculations confirm that transformation through these coherent interfaces is energetically favoured compared with those through other paths previously proposed. The graphite-to-diamond transformation is governed by the formation of nanoscale coherent interfaces (diamond nucleation), which, under static compression, advance to consume the remaining graphite (diamond growth). These results may also shed light on transformation mechanisms of other carbon materials and boron nitride under different synthetic conditions.
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http://dx.doi.org/10.1038/s41586-022-04863-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9300464PMC
July 2022

[Characteristics and Assembly Process of Reclaimed Soil Microbial Communities in Eastern Plain Mining Areas].

Huan Jing Ke Xue 2022 Jul;43(7):3844-3853

School of Public Administration, Hohai University, Nanjing 211100, China.

Understanding how soil microorganisms respond to land reclamation is essential to evaluating the success of ecological restoration actions in disturbed mine soil. However, the microbiological mechanism referred to as productivity reconstruction of the reclaimed soil is still unclear. To shed light on this mechanism, a total of 75 soil samples were collected for 16S rRNA amplicon high-throughput sequencing. The five sampling sites contained four reclamation plots (reclaimed 8 a, 11 a, 14 a, and 17 a) and 1 non-reclaimed plot, which served as the control sampling site. The microbial community composition, potential functions, and assembly mechanisms were also analyzed. The results showed that:①the richness of the microbial community increased with the reclamation time and was higher than that of the control site. However, the community diversity and evenness decreased with the increasing reclamation year (<0.05). ②Acidobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes dominated in the reclaimed soil, and the relative abundances of the first two phyla were significantly higher than that of the control (<0.05), whereas the latter two presented the opposite trends (<0.05). ③ Eight functions, including coenzyme transport and metabolism, translation, ribosomal structure, and biogenesis, showed a positive succession in the reclamation sites and enhanced with increasing reclamation years. ④ The molecular ecological networks of the microbial community in the plain mining area were well modular, whereas the key microbial groups belonged to the Acidobacteria and Bacteroidetes. The microbial communities were dominantly assembled with the deterministic process, and the homogeneous selection contributed the most, which might have been mainly controlled by the local special environment. The results presented herein will undoubtedly aid in the establishment of success indicators of ecological restoration activities in disturbed mining soil. These findings also provide the theoretical basis for improving the productivity and ecological services of reclaimed soil.
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http://dx.doi.org/10.13227/j.hjkx.202110018DOI Listing
July 2022

Dataset of response characteristics of H-producing bacteria consortium to β-lactams, aminoglycosides, macrolides, quinolones antibiotics.

Data Brief 2022 Aug 6;43:108354. Epub 2022 Jun 6.

Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China.

Antibiotics on H producing bacteria shall be considered as being one of the critical elements in biological H production utilizing livestock manure as raw resources. Despite the fact that the manure stands a significance role in bio-fermentation, the possibility of antibiotics being contained in excreta shall not be eliminated. Findings of whether the above saying might threaten the safety of bio-H production needs to be further studied. The experiment subjects include: six single and three combined antibiotics were tested and analyzed by the application of the gradient experiment method. Along with the H production rate, CHO content, pH and OD were used to analyze the effects of various antibiotics introduction on the hydrolysis, fermentation and H production. To a further extent, four typical representative samples were selected for biodiversity analysis from the single antibiotic experiment groups. Amounting more than 6000 pieces of data were obtained in a series of experiments. Data suggested that remarkable measure of antibiotics have various degrees of H production inhibition, while some antibiotics, Penicillin G, Streptomycin Sulfate, and their compound antibiotics, could promote the growth of sp. and improve H yield in the contrary. Correspondent to the transition of key metabolic intermediates and end products, the mechanism of each antibiotic type and dose on H production were summarized as follows: the main inhibitory mechanisms were: (1) board-spectrum inhibition, (2) partial inhibition, (3) H consumption enhancement; and the enhancement mechanisms were: (1) enhance the growth of H-producing bacteria, (2) enhanced starch hydrolysis, (3) inhibitory H consumption or release of acid inhibition. Meanwhile, data analysis found that the effect of antibiotics on H producing was not only related to type, but also to dosage. Even one kind of antibiotic may have completely opposite effects on H-producing bacteria under different dosage conditions. Inhibition of H yield was highest with Levofloxacin at 6.15 mg/L, gas production was reduced by 88.77%; and enhancement of H yield was highest with Penicillin G at 7.20 mg/L, the gas production increased by 72.90%.
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http://dx.doi.org/10.1016/j.dib.2022.108354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9234353PMC
August 2022

Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development.

BMC Genomics 2022 Jun 27;23(1):473. Epub 2022 Jun 27.

National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.

Background: Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is unclear.

Results: In this study, the transcriptome of fibrous roots (R0) and tuberous roots in three developmental stages (Rl, R2, R3) were analyzed in two sweet potato varieties, GJS-8 and XGH. A total of 22,914 and 24,446 differentially expressed genes (DEGs) were identified in GJS-8 and XGH respectively, 15,920 differential genes were shared by GJS-8 and XGH. KEGG pathway enrichment analysis showed that the DEGs shared by GJS-8 and XGH were mainly involved in "plant hormone signal transduction" "starch and sucrose metabolism" and "MAPK signal transduction". Trihelix transcription factor (Tai6.25300) was found to be closely related to tuberous root enlargement by the comprehensive analysis of these DEGs and weighted gene co-expression network analysis (WGCNA).

Conclusion: A hypothetical model of genetic regulatory network for tuberous root development of sweet potato is proposed, which emphasizes that some specific signal transduction pathways like "plant hormone signal transduction" "Casignal" "MAPK signal transduction" and metabolic processes including "starch and sucrose metabolism" and "cell cycle and cell wall metabolism" are related to tuberous root development in sweet potato. These results provide new insights into the molecular mechanism of tuberous root development in sweet potato.
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http://dx.doi.org/10.1186/s12864-022-08670-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235109PMC
June 2022

Nature of Five-Coordinated Al in γ-AlO Revealed by Ultra-High-Field Solid-State NMR.

ACS Cent Sci 2022 Jun 23;8(6):795-803. Epub 2022 May 23.

State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.

Five-coordinated Als (Al(V)) on the surface of aluminas play important roles when they are used as catalysts or catalyst supports. However, the comprehensive characterization and understanding of the intrinsic structural properties of the Al(V) remain a challenge, due to the very small amount in commonly used aluminas. Herein, the surface structures of γ-AlO and Al(V)-rich AlO nanosheets (AlO-NS) have been investigated and compared in detail by multinuclear high-field solid-state NMR. Thanks to the high resolution and sensitivity of ultra-high-field (up to 35.2 T) NMR, the arrangements of surface Als were clearly demonstrated, which are substantially different from the bulk phase in γ-AlO due to the structure reconstruction. It reveals for the first time that most of the commonly observed Al(V)s tend to exist as aggregated states on the surface of γ-AlO, like those in amorphous AlO-NS liable to structure reconstruction. Our new insights into surface Al(V) species may help in understanding the structure-function relationship of alumina.
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http://dx.doi.org/10.1021/acscentsci.1c01497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9228550PMC
June 2022

Comparative Transcriptome Analysis of Purple and Green Non-Heading Chinese Cabbage and Function Analyses of Gene.

Genes (Basel) 2022 May 31;13(6). Epub 2022 May 31.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of the P. R. China, Nanjing Agricultural University, Nanjing 210095, China.

Non-heading Chinese cabbage ( ssp. ) is an important vegetative crop in the south of China. As an antioxidant, anthocyanin is the major quality trait for vegetables with purple leaves or petioles. However, the molecular biosynthetic mechanism of anthocyanin in non-heading Chinese cabbage has not been explained exclusively. In this study, two non-heading Chinese cabbage with contrasting colors in the leaves were used as the materials for RNA-seq. A total of 906 DEGs were detected, and we found that the anthocyanin and flavonoid biosynthetic pathways are significantly enriched in the purple NHCC. The transcriptome result was verified by RT-qPCR. Though bioinformatics analysis, was selected as the candidate gene for the regulation of anthocyanin synthesis, and the characterization of was elucidated by the functional analyses. The results proved that BcTT8 is a nucleus protein and phylogenetically close to the TT8 protein from . After silencing , the total anthocyanin content of pTY- plants decreased by 42.5%, and the relative expression levels of anthocyanin pathway genes , and were significantly downregulated, while the transcription level of was significantly upregulated. Compared with the wild type, the transgenic showed obvious violet in the cotyledons part, and the anthocyanin biosynthetic genes such as and were significantly upregulated. In conclusion, is critical in the anthocyanin synthesis process of non-heading Chinese cabbage. Our findings illustrated the molecular mechanism of anthocyanin biosynthesis in non-heading Chinese cabbage.
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http://dx.doi.org/10.3390/genes13060988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9222865PMC
May 2022

Dataset of coal bio-gasification and coalbed methane stimulation by single well nutrition injection in Qinshui anthracite coalbed methane wells.

Data Brief 2022 Aug 4;43:108353. Epub 2022 Jun 4.

CUMT-UCASAL Joint Research Center for Biomining and Soil Ecological Restoration, State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Xuzhou, Jiangsu 221116 China.

In-situ coal bio-gasification can be defined as one of the coal bio-mining methodology that fully utilizes the methanogenic bacteria in coal to review the current findings, namely anaerobic digestion of organic components. The following experiment has been done in regards, one vertical well and one multi-branch horizontal well were used as experiment wells and two vertical wells were used as control wells, the pilot test was carried out with single well nutrition injection method. By applying the above mentioned method, the concentration of Cl ion and number altered in spp. were used to trace nutrition diffusion. Furthermore, technical implementation results analysis has been made with the observation of CH production changes and coal bed biome evolution. Gas production rates in each well were monitored by using the FLLQ gas roots flow mete. The concentration of CH and CO were evaluated by using the Agilent 7890A gas chromatograph, on the other hand, concentrations of Cl were determined by the application of ICS-1100 ion chromatography system. The F fluorescence method was adopted to test for the presence of methanogenic bacteria. In the interim of the completion stage, the study stated that the bacterial diversity of underground water of Z-7H well has a high pass sequence with the experimental period of 814 days. Gas production data in Z-159 and Z-7H wells showed the gasification of coal lasted 635 and 799 days, yielded 74817 m and 251754 m coalbed methane, respectively. Furthermore, experimental data presented that one time nutrition injection in anthracite coalbed methane wells achieved an average of 717 days of continuous gas production among all experimental wells. The above fore-said study dedicated the significance of native bacterial fermentation, as it proven the fact that anthracite can be applied to accomplish coal bio-gasification and coalbed methane production stimulation in-situ.
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http://dx.doi.org/10.1016/j.dib.2022.108353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9190020PMC
August 2022

Incidence and Risk Factors Associated with Technique Failure in the First Year of Peritoneal Dialysis: A Single Center Retrospective Cohort Study in Southern China.

BMC Nephrol 2022 06 11;23(1):207. Epub 2022 Jun 11.

Department of Nephrology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.

Background: Technique failure is more likely to occur during the first 12 months after peritoneal dialysis (PD) initiation, which is a great challenge encountered in PD patients. The aim of this study was to investigate the incidence and risk factors associated with technique failure within the first year of PD patients in Southern China.

Methods: Incident PD patients who were followed up for at least one year at The First Affiliated Hospital of Sun Yat-sen University from January 1, 2006 to December 31, 2015 were included. Technique failure was defined as transferring to hemodialysis (HD) for more than 30 days or death within the first year after start of PD. A competitive risk regression analysis was used to explore the incidence and risk factors of the technique failure.

Results: Overall, 2,290 incident PD patients were included in this study, with a mean age of 48.2 ± 15.7 years, 40.9% female and 25.2% with diabetes. A total of 173 patients (7.5%) had technique failure during the first year of PD. Among them, the patient death account for 62.4% (n = 108) and transferring to HD account for 37.6% (n = 65). The main reasons for death were cardiovascular diseases (n = 32, 29.6%), infection (n = 15, 13.8%) and for conversion to HD were mechanical cause (n = 28, 43.1%), infection cause (n = 22, 33.8%). The risk factors for the technique failure included advanced age (HR 2.78, 95%CI 1.82-4.30), low body mass index (BMI < 18.5 kg/m: HR 1.77, 95%CI 1.17-2.67), history of congestive heart failure (HR 2.81, 95%CI 1.58-4.98), or time on HD before PD ≤ 3 months (HR 1.49, 95%CI 1.05-2.10), peritonitis (HR 2.02, 95%CI 1.36-3.01);while higher serum albumin (HR 0.93, 95%CI 0.89-0.96) and using employee medical insurance to pay expenses (HR 0.47, 95%CI 0.32-0.69) were associated with reduced risk.

Conclusions: Advanced age, poor nutritional status, history of HD or congestive heart failure, and peritonitis are related factors that increase the risk of technique failure in the first year of PD, while patients' type of medical insurance may also have an influence on early technique failure.
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http://dx.doi.org/10.1186/s12882-022-02833-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9188716PMC
June 2022

Hierarchical micro/nanostructured silver hollow fiber boosts electroreduction of carbon dioxide.

Nat Commun 2022 Jun 2;13(1):3080. Epub 2022 Jun 2.

Low-Carbon Conversion Science and Engineering Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, PR China.

Efficient conversion of CO to commodity chemicals by sustainable way is of great significance for achieving carbon neutrality. Although considerable progress has been made in CO utilization, highly efficient CO conversion with high space velocity under mild conditions remains a challenge. Here, we report a hierarchical micro/nanostructured silver hollow fiber electrode that reduces CO to CO with a faradaic efficiency of 93% and a current density of 1.26 A · cm at a potential of -0.83 V vs. RHE. Exceeding 50% conversions of as high as 31,000 mL · g · h CO are achieved at ambient temperature and pressure. Electrochemical results and time-resolved operando Raman spectra demonstrate that enhanced three-phase interface reactions and oriented mass transfers synergistically boost CO production.
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http://dx.doi.org/10.1038/s41467-022-30733-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9163090PMC
June 2022

Prefiltered Single-Carrier Frequency-Domain Equalization for Binary CPM over Shallow Water Acoustic Channel.

Sensors (Basel) 2022 May 18;22(10). Epub 2022 May 18.

Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190, China.

The continuous phase modulation (CPM) technique is an excellent solution for underwater acoustic (UWA) channels with limited bandwidth and high propagation attenuation. However, the severe intersymbol interference is a big problem for the algorithm applying in shallow water. To solve this problem, an algorithm for prefiltered single-carrier frequency-domain equalization (PF-SCFDE) is presented in this paper. The regular whitening filter is replaced by a prefilter in the proposed algorithm. The output information sequence of this prefilter contains the forward information. To improve the performance, the output of the equalizer, combined with the forward information, is used to make the maximum likelihood estimation. The simulation results with minimum-shift keying and Gaussian-filtered minimum-shift keying signals over shallow water acoustic channels with low root mean square delay spread demonstrate that PF-SCFDE outperformed the traditional single-carrier frequency-domain equalization (SCFDE) by approximately 1 dB under a bit error rate (BER) of 10. A shallow sea trial has demonstrated the effectiveness of PF-SCFDE; PF-SCFDE had a reduction in BER of 18.35% as compared to the traditional SCFDE.
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http://dx.doi.org/10.3390/s22103821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9144432PMC
May 2022

Fast Analysis of Time-Domain Fluorescence Lifetime Imaging via Extreme Learning Machine.

Sensors (Basel) 2022 May 15;22(10). Epub 2022 May 15.

Department of Biomedical Engineering, University of Strathclyde, Glasgow G4 0RE, UK.

We present a fast and accurate analytical method for fluorescence lifetime imaging microscopy (FLIM), using the extreme learning machine (ELM). We used extensive metrics to evaluate ELM and existing algorithms. First, we compared these algorithms using synthetic datasets. The results indicate that ELM can obtain higher fidelity, even in low-photon conditions. Afterwards, we used ELM to retrieve lifetime components from human prostate cancer cells loaded with gold nanosensors, showing that ELM also outperforms the iterative fitting and non-fitting algorithms. By comparing ELM with a computational efficient neural network, ELM achieves comparable accuracy with less training and inference time. As there is no back-propagation process for ELM during the training phase, the training speed is much higher than existing neural network approaches. The proposed strategy is promising for edge computing with online training.
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http://dx.doi.org/10.3390/s22103758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9146214PMC
May 2022

A real-time pluripotency reporter for the long-term and real-time monitoring of pluripotency changes in induced pluripotent stem cells.

Aging (Albany NY) 2022 05 15;14(10):4445-4458. Epub 2022 May 15.

Cancer Research Institute, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China.

To master the technology of reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs), which will lay a good foundation for setting up a technology platform on reprogramming human cancer cells into iPSCs. Mouse iPSCs (i.e., Oct4-GFP miPSCs) was successfully generated from mouse embryonic fibroblasts (MEFs) harboring Oct4-EGFP transgene by introducing four factors, Oct4, Sox2, c-Myc and Klf4, under mESC (Murine embryonic stem cells) culture conditions. Oct4-GFP miPSCs were similar to mESCs in morphology, proliferation, mESC-specific surface antigens and gene expression. Additionally, Oct4-GFP miPSCs could be cultured in suspension to form embryoid bodies (EBs) and differentiate into cell types of the three germ layers . Moreover, Oct4-GFP miPSCs could develop to teratoma and chimera . Unlike cell cycle distribution of MEFs, Oct4-GFP miPSCs are similar to mESCs in the cell cycle structure which consists of higher S phase and lower G1 phase. More importantly, our data demonstrated that MEFs harboring Oct4-EGFP transgene did not express GFP, until they were reprogrammed to the pluripotent stage (iPSCs), while the GFP expression was progressively lost when these pluripotent Oct4-GFP miPSCs exposed to EB-mediated differentiation conditions, suggesting the pluripotency of Oct4-GFP miPSCs can be real-time monitored over long periods of time via GFP assay. Altogether, our findings demonstrate that Oct4-GFP miPSC line is successfully established, which will lay a solid foundation for setting up a technology platform on reprogramming cancer cells into iPSCs. Furthermore, this pluripotency reporter system permits the long-term real-time monitoring of pluripotency changes in a live single-cell, and its progeny.
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http://dx.doi.org/10.18632/aging.204083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9186763PMC
May 2022

[Effect of admission mode of septic patients in intensive care unit on acute kidney injury and prognosis].

Zhonghua Wei Zhong Bing Ji Jiu Yi Xue 2022 Mar;34(3):250-254

Department of Critical Care Medicine, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi 830000, Xinjiang Uygur Autonomous Region, China. Corresponding author: Xiao Dong, Email:

Objective: To investigate the effect of intensive care unit (ICU) admission model on acute kidney injury (AKI) development and the prognosis in patients with sepsis.

Methods: Patients with sepsis admitted to the ICU of Xinjiang Uygur Autonomous Region People's Hospital from January 2019 to July 2020 were retrospectively analyzed. According to the ICU admission model, the patients were divided into emergency group (first admission or emergency transfer from relevant surgical departments) and delayed group (transferred from the general ward due to disease evolution). Patients were divided into AKI group and non-AKI group according to whether AKI was accompanied. The gender, age, underlying diseases, surgical history, heart rate, laboratory test indicators, acute physiology and chronic health evaluation II (APACHE II), sequential organ failure assessment (SOFA), organ failure and acute complications were collected. The incidence of AKI, 28-day mortality and length of ICU stay were recorded. Univariate and multivariate Logistic regression was used to analyze the risk factors of AKI in patients with sepsis.

Results: A total of 185 patients with sepsis were enrolled, including 96 cases in the emergency group and 89 cases in the delayed group. 119 cases of AKI occurred while 66 cases without AKI development. The incidence of AKI within 7 days and the 28-day mortality of patients in the delayed group were significantly higher than those in the emergency group [AKI incidence rate: 77.53% (69/89) vs. 52.08% (50/96), 28-day mortality: 24.72% (22/89) vs. 10.42% (10/96), both P < 0.05], and the length of ICU stay was significantly longer than that of the emergency group (days: 18.70±7.29 vs. 14.56±4.75, P < 0.05). Univariate Logistic analysis showed that there were significant differences in age, diabetes, hypertension, organ failure, heart failure, APACHE II score, SOFA score, white blood cell count (WBC), absolute neutrophil value, platelet count (PLT), blood lactate, total bilirubin, and ICU transferred from general wards between AKI group and non-AKI group. Multivariate Logistic regression analysis showed that transfer from general ward to ICU due to disease evolution was an independent risk factor for AKI in ICU sepsis patients [odds ratio (OR) = 5.165, 95% confidence interval (95%CI) was 3.911-6.823, P < 0.001].

Conclusions: Septic patients transferred from general ward to ICU due to disease evolution are more likely to develop AKI, and also had a higher mortality and longer ICU stay. It may be an independent risk factor for AKI complicated by patients with sepsis in ICU.
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http://dx.doi.org/10.3760/cma.j.cn121430-20211110-01675DOI Listing
March 2022

Comparative Transcriptome Analysis Provides Insights into the Resistance in Pueraria [] in Response to Pseudo-Rust Disease.

Int J Mol Sci 2022 May 7;23(9). Epub 2022 May 7.

Academy of Agricultural Science, Guangxi University, Nanning 530004, China.

is an important medicinal and edible homologous plant that is widely cultivated in Asian countries. However, its production and quality are seriously threatened by its susceptibility to pseudo-rust disease. The underlying molecular mechanisms are poorly known, particularly from a transcriptional perspective. Pseudo-rust disease is a major disease in pueraria, primarily caused by (SpM). In this study, transcriptomic profiles were analyzed and compared between two pueraria varieties: the disease-resistant variety (GUIGE18) and the susceptible variety (GUIGE8). The results suggest that the number of DEGs in GUIGE18 is always more than in GUIGE8 at each of the three time points after SpM infection, indicating that their responses to SpM infection may be different, and that the active response of GUIGE18 to SpM infection may occur earlier than that of GUIGE8. A total of 7044 differentially expressed genes (DEGs) were identified, and 406 co-expressed DEGs were screened out. Transcription factor analysis among the DEGs revealed that the bHLH, WRKY, ERF, and MYB families may play an important role in the interaction between pueraria and pathogens. A GO and KEGG enrichment analysis of these DEGs showed that they were mainly involved in the following pathways: metabolic, defense response, plant hormone signal transduction, MAPK signaling pathway-plant, plant pathogen interaction, flavonoid biosynthesis, phenylpropanoid biosynthesis, and secondary metabolite biosynthesis. The CPK, CESA, PME, and CYP gene families may play important roles in the early stages after SpM infection. The DEGs that encode antioxidase (CAT, XDH, and SOD) were much more up-regulated. Defense enzyme activity, endogenous hormones, and flavonoid content changed significantly in the two varieties at the three infection stages. Finally, we speculated on the regulatory pathways of pueraria pseudo-rust and found that an oxidation-reduction process, flavonoid biosynthesis, and ABA signaling genes may be associated with the response to SpM infection in pueraria. These results expand the understanding of pueraria resistance and physiological regulations by multiple pathways.
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http://dx.doi.org/10.3390/ijms23095223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9101505PMC
May 2022

Cathelicidin-related antimicrobial peptide protects against enteric pathogen-accelerated type 1 diabetes in mice.

Theranostics 2022 24;12(7):3438-3455. Epub 2022 Apr 24.

Wuxi School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China.

Gut barrier disruption caused by enteric pathogen infection results in activated diabetogenic T cells and accelerated type 1 diabetes (T1D). Cathelicidin-related antimicrobial peptide (CRAMP) maintains intestinal barrier integrity, regulates the microbiome, and exerts positive immune-modulatory effects on pancreatic diseases. The model enteric pathogen was adopted to represent clinical colonic infection with gut barrier disruption. The protective role and gut-pancreas pathophysiological mechanism of CRAMP in enteric pathogen-accelerated T1D were investigated in spontaneous non-obese diabetic (NOD) mice and streptozotocin-induced diabetic mice. Colonic CRAMP production was defective in infection-accelerated T1D. infection triggered the recruitment of interferon-gamma (IFN-γ) T cells and accelerated T1D. In the -accelerated T1D mice, CRAMP deficiency further aggravated gut barrier disruption, gut dysbiosis, and diabetic phenotype, which could be reversed by CRAMP treatment. The protective effect of CRAMP may be due to CRAMP inhibiting -aggravated gut immune dysregulation, gut dysbiosis, and migration of gut-primed IFN-γ T cells to the pancreas, thus contributing to gut barrier protection and pancreatic-intestinal immune homeostasis. CRAMP plays a pivotal role in pancreatic-gut crosstalk during -accelerated T1D by gut barrier-protective, immune- and microbial-modulatory mechanisms. Cathelicidin supplementation to restore a healthy gut barrier may represent a novel therapeutic strategy for T1D.
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http://dx.doi.org/10.7150/thno.61433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9065195PMC
April 2022

Stimulus-responsive self-assembled prodrugs in cancer therapy.

Chem Sci 2022 Apr 18;13(15):4239-4269. Epub 2022 Mar 18.

Department of Chemistry, National University of Singapore Singapore 117543 Singapore

Small-molecule prodrugs have become the main toolbox to improve the unfavorable physicochemical properties of potential therapeutic compounds in contemporary anti-cancer drug development. Many approved small-molecule prodrugs, however, still face key challenges in their pharmacokinetic (PK) and pharmacodynamic (PD) properties, thus severely restricting their further clinical applications. Self-assembled prodrugs thus emerged as they could take advantage of key benefits in both prodrug design and nanomedicine, so as to maximize drug loading, reduce premature leakage, and improve PK/PD parameters and targeting ability. Notably, temporally and spatially controlled release of drugs at cancerous sites could be achieved by encoding various activable linkers that are sensitive to chemical or biological stimuli in the tumor microenvironment (TME). In this review, we have comprehensively summarized the recent progress made in the development of single/multiple-stimulus-responsive self-assembled prodrugs for mono- and combinatorial therapy. A special focus was placed on various prodrug conjugation strategies (polymer-drug conjugates, drug-drug conjugates, .) that facilitated the engineering of self-assembled prodrugs, and various linker chemistries that enabled selective controlled release of active drugs at tumor sites. Furthermore, some polymeric nano-prodrugs that entered clinical trials have also been elaborated here. Finally, we have discussed the bottlenecks in the field of prodrug nanoassembly and offered potential solutions to overcome them. We believe that this review will provide a comprehensive reference for the rational design of effective prodrug nanoassemblies that have clinic translation potential.
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http://dx.doi.org/10.1039/d2sc01003hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9006903PMC
April 2022

Pressure-Induced Hydrogen Transfer in 2-Butyne via a Double CH···π Aromatic Transition State.

J Phys Chem Lett 2022 May 4;13(18):4170-4175. Epub 2022 May 4.

Center for High Pressure Science and Technology Advanced Research, Beijing 100094, P. R. China.

Hydrogen transfer (H-transfer) is an important elementary reaction in chemistry and bioscience. It is often facilitated by the hydrogen bonds between the H-donor and acceptor. Here, at room temperature and high pressure, we found that solid 2-butyne experienced a concerted two-in-two-out intermolecular CH···π H-transfer, which initiated the subsequent polymerization. Such double H-transfer goes through an aromatic Hückel six-membered ring intermediate state via intermolecular CH···π interactions enhanced by external pressure. Our work shows that H-transfer can occur via the CH···π route in appropriate conformations under high pressure, which gives important insights into the H-transfer in solid-state hydrocarbons.
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http://dx.doi.org/10.1021/acs.jpclett.2c00877DOI Listing
May 2022

The response regularity of biohydrogen production by anthracite H-producing bacteria consortium to six conventional veterinary antibiotics.

J Environ Manage 2022 Aug 25;315:115088. Epub 2022 Apr 25.

School of Life Science, Central South University, Changsha, Hunan, 410083, China. Electronic address:

The impact of antibiotics on H-producing bacteria must be considered in the industrialization of biological H production using livestock manure as raw resources. However, whether antibiotics that may be contained in excreta will threaten the safety of biohydrogen production needs to be researched. This study explored the impact characteristics and mechanism of six single antibiotics and three groups of compound antibiotics on H production. Experiments confirmed that most antibiotics have different degrees of H production inhibition, while some antibiotics, which like Penicillin G, Streptomycin Sulfate, and their compound antibiotics, could promote the growth of Ethanoligenens sp. and improve H yield on the contrary. Comprehensive analysis shows that the main inhibitory mechanisms were: (1) board-spectrum inhibition, (2) partial inhibition, (3) H consumption enhancement; and the enhancement mechanisms were: (1) enhance the growth of H-producing bacteria, (2) enhanced starch hydrolysis, (3) inhibitory H consumption or release of acid inhibition. Meanwhile, experiment found that the effect of antibiotics on H producing was not only related to type, but also to dosage. Even one kind of antibiotic may have completely opposite effects on H-producing bacteria under different dosage conditions. Inhibition of H yield was highest with Levofloxacin at 6.15 mg/L, gas production was reduced by 88.77%; and enhancement of H yield was highest with Penicillin G at 7.20 mg/L, the gas production increased by 72.90%. In the selection of raw material, the type and content of antibiotics demand a detailed investigation and analysis to ensure that the sustainability of H yield.
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http://dx.doi.org/10.1016/j.jenvman.2022.115088DOI Listing
August 2022

Spatial resolution improved fluorescence lifetime imaging via deep learning.

Opt Express 2022 Mar;30(7):11479-11494

We present a deep learning approach to obtain high-resolution (HR) fluorescence lifetime images from low-resolution (LR) images acquired from fluorescence lifetime imaging (FLIM) systems. We first proposed a theoretical method for training neural networks to generate massive semi-synthetic FLIM data with various cellular morphologies, a sizeable dynamic lifetime range, and complex decay components. We then developed a degrading model to obtain LR-HR pairs and created a hybrid neural network, the spatial resolution improved FLIM net (SRI-FLIMnet) to simultaneously estimate fluorescence lifetimes and realize the nonlinear transformation from LR to HR images. The evaluative results demonstrate SRI-FLIMnet's superior performance in reconstructing spatial information from limited pixel resolution. We also verified SRI-FLIMnet using experimental images of bacterial infected mouse raw macrophage cells. Results show that the proposed data generation method and SRI-FLIMnet efficiently achieve superior spatial resolution for FLIM applications. Our study provides a solution for fast obtaining HR FLIM images.
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http://dx.doi.org/10.1364/OE.451215DOI Listing
March 2022

Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of (syn. ) ssp. .

Plants (Basel) 2022 Apr 7;11(8). Epub 2022 Apr 7.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, China.

The availability of a high-quality genome sequence of ssp. NHCC001 has paved the way for deep mining of genome data. We used the NHCC001 draft genome to develop a comprehensive database, known as the non-heading Chinese cabbage database, which provides access to the NHCC001 genome data. The database provides 127,347 SSR, from which 382,041 pairs of primers were designed. NHCCDB contains information on 105,360 genes, which were further classified into 63 transcription factor families. Furthermore, NHCCDB provides eight kinds of tools for biological or sequencing data analyses, including sequence alignment tools, functional genomics tools, comparative genomics tools, motif analysis tools, genome browser, primer design, and SSR analysis tools. In addition, eight kinds of graphs, including a box plot, Venn diagram, corrplot, Q-Q plot, Manhattan plot, seqLogo, volcano plot, and a heatmap, can be generated rapidly using NHCCDB. We have incorporated a search system for efficient mining of transcription factors and genes, along with an embedded data submit function in NHCCDB. We believe that the NHCCDB database will be a useful platform for non-heading Chinese cabbage research and breeding.
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http://dx.doi.org/10.3390/plants11081005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9029197PMC
April 2022

Crystalline CNH tube (3,0) nanothreads.

Proc Natl Acad Sci U S A 2022 04 19;119(17):e2201165119. Epub 2022 Apr 19.

Center for High Pressure Science and Technology Advanced Research, Beijing 100094, People's Republic of China.

Carbon nanothread (CNTh) is a “one-dimensional diamond polymer” that combines high tensile strength and flexibility, but it severely suffers from intrathread disorder. Here, by modifying the reactivity and the stacking ordering of the aromatic precursor, crystalline C3N3H3 CNTh with perfect hexagonal orientation and stacking was synthesized at 10.2 GPa and 573 K from s-triazine. By Rietveld refinement of X-ray diffraction data, gas chromatography mass spectrometry investigation, and theoretical calculation, we found that synthesized CNTh has a tube (3,0) structure, with the repeating s-triazine residue connected solely by C–N bonds along the thread. A “peri-cage” reaction, the concerted bonding between six C and N atoms, instead of [4 + 2] or [1,4] addition reactions, was concluded for the formation of CNThs, and the critical bonding distance between the nearest intermolecular C and N was ∼2.9 Å. The formation of a “structure-specific” crystalline CNTh with C and N orderly distributed highlighted the importance of reaction selectivity and stacking order of reactant molecules, which have great significance for understanding the polymerization of aromatic molecules under high pressure and developing new crystalline CNThs.
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http://dx.doi.org/10.1073/pnas.2201165119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9170061PMC
April 2022

Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking.

Nat Genet 2022 04 11;54(4):492-498. Epub 2022 Apr 11.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

Although lung cancer risk among smokers is dependent on smoking dose, it remains unknown if this increased risk reflects an increased rate of somatic mutation accumulation in normal lung cells. Here, we applied single-cell whole-genome sequencing of proximal bronchial basal cells from 33 participants aged between 11 and 86 years with smoking histories varying from never-smoking to 116 pack-years. We found an increase in the frequency of single-nucleotide variants and small insertions and deletions with chronological age in never-smokers, with mutation frequencies significantly elevated among smokers. When plotted against smoking pack-years, mutations followed the linear increase in cancer risk until about 23 pack-years, after which no further increase in mutation frequency was observed, pointing toward individual selection for mutation avoidance. Known lung cancer-defined mutation signatures tracked with both age and smoking. No significant enrichment for somatic mutations in lung cancer driver genes was observed.
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http://dx.doi.org/10.1038/s41588-022-01035-wDOI Listing
April 2022
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