Publications by authors named "Junhui Li"

206 Publications

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures.

J Hazard Mater 2021 Jun 10;418:126384. Epub 2021 Jun 10.

Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR 999078, China. Electronic address:

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.
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http://dx.doi.org/10.1016/j.jhazmat.2021.126384DOI Listing
June 2021

Metabolic Engineering of Aspartic Acid Supply Modules for Enhanced Production of Bacitracin in .

ACS Synth Biol 2021 Jul 29. Epub 2021 Jul 29.

State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.

Bacitracin, a type of cyclic dodecapeptide antibiotic mainly produced by , is widely used in fields of veterinary drug and feed additive. Modularization of metabolic pathways based on the concept of synthetic biology has been widely used in the efficient synthesis of target products. Here, we want to improve bacitracin production through strengthening aspartic acid (Asp) supply in DW2. First, exogenous Asp addition assays implied that strengthening Asp supply benefited bacitracin production. Second, Asp synthetic pathways were strengthened via overexpressing aspartate dehydrogenase AspD and asparaginase AnsB, attaining recombinant strain DW2-ASP2, and bacitracin yield produced by DW2-ASP2 was 862.81 U/mL, increased by 14.05% compared with that of DW2 (756.49 U/mL). Then, to improve precursor oxaloacetate (OAA) accumulation for Asp synthesis, pyruvate carboxylase PycA and carbonic anhydrase EcaA were co-overexpressed in DW2-ASP2, and malic enzyme gene was deleted to weak overflow metabolism of tricarboxylic acid, and the attained strain DW2-ASP7 showed further increased bacitracin production from 862.81 to 989.23 U/mL. Subsequently, transporter YveA was identified as an Asp exporter, and bacitracin yield was increased to 1025.26 U/mL via deleting , attaining strain DW2-ASP9. Finally, Asp ammonia-lyase gene was disrupted to weaken Asp degradation, and bacitracin yield of attained strain DW2-ASP10 reached 1059.86 U/mL, increased by 40.10% compared to DW2. Taken together, this research demonstrated that metabolic engineering of Asp metabolic modules is an efficient strategy for enhancing bacitracin production, and these strategies could also be applied in the production of other peptide-related metabolites.
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http://dx.doi.org/10.1021/acssynbio.1c00154DOI Listing
July 2021

Combined foliar and soil selenium fertilizer improves selenium transport and the diversity of rhizosphere bacterial community in oats.

Environ Sci Pollut Res Int 2021 Jul 26. Epub 2021 Jul 26.

Shanxi Institute of Geological Survey, Taiyuan, 030000, China.

Agronomic selenium (Se) biofortification of grain crops is considered the best method for increasing human Se intake, which may help people alleviate Se-deficiency. To investigate the efficiency of agronomic Se biofortification of oat, four Se fertilizer application treatments were tested: topsoil (T), foliar (S), the combination of T and S (TS), and control without Se application (CK). Compared with CK, TS significantly increased the 1000-grain weight, grain yield, Se contents in all parts of oats, contents of soil available N, K, and organic matter by 18%, 8.70%, 19.7-60.2%, 6.00%, 8.02%, and 17.95%, respectively. Leaves, roots, and ears had the highest conversion rate of exogenous Se in S (644.63%), T (416.00%), and TS (273.20%), respectively. TS also increased the activities of soil urease, alkaline phosphatase, and sucrose and the diversity of soil bacterial communities. TS and T increased the relative abundance of bacteria involved in the decomposition of organic matter, such as Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes positively correlated with soil nutrients and enzyme activities, and reduced Proteobacteria and Firmicutes negatively correlated with them, Granulicella, Bacillus, Raoultella, Lactococcus, Klebsiella, and Pseudomonas. Furthermore, TS significantly increased the relative abundance of Planctomycetes, Chlorobi, Nitrospinae, Nitrospirae, Aciditeromonas, Gemmatimonas, Geobacter, and Thiobacter. T significantly increased the abundance of Lysobacter, Holophaga, Candidatus-Koribacter, Povalibacter, and Pyrinomonas. S did not significantly change the bacterial communities. Thus, a combined foliar and soil Se fertilizer proved conducive for achieving higher yield, grain Se content, and improving Se transport, the diversity of rhizosphere bacterial community, and bacterial functions in oats.
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http://dx.doi.org/10.1007/s11356-021-15439-4DOI Listing
July 2021

Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community.

Nat Commun 2021 06 7;12(1):3381. Epub 2021 Jun 7.

Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.

Nutrient amendment diminished bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Here, we show strong differences in the bacterial taxa responsible for respiration from four ecosystems, indicating the potential for taxon-specific control over soil carbon cycling. Trends in functional diversity, defined as the richness of bacteria contributing to carbon flux and their equitability of carbon use, paralleled trends in taxonomic diversity although functional diversity was lower overall. Among genera common to all ecosystems, Bradyrhizobium, the Acidobacteria genus RB41, and Streptomyces together composed 45-57% of carbon flow through bacterial productivity and respiration. Bacteria that utilized the most carbon amendment (glucose) were also those that utilized the most native soil carbon, suggesting that the behavior of key soil taxa may influence carbon balance. Mapping carbon flow through different microbial taxa as demonstrated here is crucial in developing taxon-sensitive soil carbon models that may reduce the uncertainty in climate change projections.
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http://dx.doi.org/10.1038/s41467-021-23676-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8184982PMC
June 2021

Establishment of a nomogram prediction model for long diameter 10-15 mm gallbladder polyps with malignant tendency.

Surgery 2021 Jun 2. Epub 2021 Jun 2.

Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China. Electronic address:

Background: Surgical indications for the treatment of gallbladder polyps are controversial. Evaluation of gallbladder polyps with malignant tendency and indications for cholecystectomy in patients with long diameter polyps of 10 to 15 mm require further analysis and discussion. In this study, our objective was to re-evaluate indications for the surgical resection of gallbladder polyps and construct a nomogram model for the prediction of gallbladder polyps with malignant tendency.

Methods: Clinicopathologic data of 2,272 patients who had undergone cholecystectomy for gallbladder polyps were collected from 11 medical centers in China. Risk factor analyses and nomogram prediction model for gallbladder polyps with malignant tendency were conducted.

Results: Excluding 311 patients with cholelithiasis and 488 patients with long diameter polyps ≤5 and >15 mm, factors that differed significantly among patients with gallbladder polyps having a long diameter of 6 to 9 mm (885 cases) and 10 to 15 mm (588 cases) were polyp detection time, CEA and CA19-9 levels, number of polyps, fundus, echogenicity, gallbladder wall thickness and postoperative pathologic features (P < .05). Among 588 patients with gallbladder polyps with a long diameter of 10 of 15 mm, multivariate analysis indicated the following independent risk factors of gallbladder polyps with malignant tendency: single polyps (OR = 0.286/P < .001), polyps with broad base (OR = 2.644/P = .001), polyps with medium/low echogenicity (OR = 2.387/P = .003), and polyps with short diameter of 7 to 9 or 10 to 15 mm (OR = 3.820/P = .005; OR = 2.220/P = .048, respectively). The C-index of the nomogram model and internal validation were .778 and .768, respectively. In addition, a sample online calculator for the nomogram prediction model had been created (https://docliqi.shinyapps.io/dynnom/).

Conclusion: Indications for cholecystectomy in patients with gallbladder polyps with a long diameter of 10 to 15 mm should be assessed by combining the information on short diameter, number of polyps, fundus, and echogenicity. The nomogram model can be used to predict the risk for the development of gallbladder polyps with malignant tendency.
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http://dx.doi.org/10.1016/j.surg.2021.04.035DOI Listing
June 2021

A functional motif of long noncoding RNA Nron against osteoporosis.

Nat Commun 2021 06 3;12(1):3319. Epub 2021 Jun 3.

Clinical Research Platform for Interdiscipline of Stomatology, The First Affiliated Hospital of Jinan University & Department of Stomatology, College of stomatology, Jinan University, Guangzhou, China.

Long noncoding RNAs are widely implicated in diverse disease processes. Nonetheless, their regulatory roles in bone resorption are undefined. Here, we identify lncRNA Nron as a critical suppressor of bone resorption. We demonstrate that osteoclastic Nron knockout mice exhibit an osteopenia phenotype with elevated bone resorption activity. Conversely, osteoclastic Nron transgenic mice exhibit lower bone resorption and higher bone mass. Furthermore, the pharmacological overexpression of Nron inhibits bone resorption, while caused apparent side effects in mice. To minimize the side effects, we further identify a functional motif of Nron. The delivery of Nron functional motif to osteoclasts effectively reverses bone loss without obvious side effects. Mechanistically, the functional motif of Nron interacts with E3 ubiquitin ligase CUL4B to regulate ERα stability. These results indicate that Nron is a key bone resorption suppressor, and the lncRNA functional motif could potentially be utilized to treat diseases with less risk of side effects.
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http://dx.doi.org/10.1038/s41467-021-23642-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8175706PMC
June 2021

Primary restriction of S-RNase cytotoxicity by a stepwise ubiquitination and degradation pathway in Petunia hybrida.

New Phytol 2021 08 30;231(3):1249-1264. Epub 2021 May 30.

State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.

In self-incompatible Petunia species, the pistil S-RNase acts as cytotoxin to inhibit self-pollination but is polyubiquitinated by the pollen-specific nonself S-locus F-box (SLF) proteins and subsequently degraded by the ubiquitin-proteasome system (UPS), allowing cross-pollination. However, it remains unclear how S-RNase is restricted by the UPS. Using biochemical analyses, we first show that Petunia hybrida S -RNase is largely ubiquitinated by K48-linked polyubiquitin chains at three regions, R I, R II and R III. R I is ubiquitinated in unpollinated, self-pollinated and cross-pollinated pistils, indicating its occurrence before PhS -RNase uptake into pollen tubes, whereas R II and R III are exclusively ubiquitinated in cross-pollinated pistils. Transgenic analyses showed that removal of R II ubiquitination resulted in significantly reduced seed sets from cross-pollination and that of R I and R III to a lesser extent, indicating their increased cytotoxicity. Consistent with this, the mutated R II of PhS -RNase resulted in a marked reduction of its degradation, whereas that of R I and R III resulted in less reduction. Taken together, we demonstrate that PhS -RNase R II functions as a major ubiquitination region for its destruction and R I and R III as minor ones, revealing that its cytotoxicity is primarily restricted by a stepwise UPS mechanism for cross-pollination in P. hybrida.
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http://dx.doi.org/10.1111/nph.17438DOI Listing
August 2021

Full-color micro-LED displays with cadmium-free quantum dots patterned by photolithography technology: retraction.

Appl Opt 2021 Mar;60(8):2281

The referenced article [Appl. Opt.59, 11112 (2020)APOPAI0003-693510.1364/AO.412267] has been retracted by the author.
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http://dx.doi.org/10.1364/AO.423154DOI Listing
March 2021

Mining Unknown Porcine Protein Isoforms by Tissue-Based Map of Proteome Enhances the Pig Genome Annotation.

Genomics Proteomics Bioinformatics 2021 Feb 22. Epub 2021 Feb 22.

National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address:

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. We developed the tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellular components and potential function for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.75% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.
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http://dx.doi.org/10.1016/j.gpb.2021.02.002DOI Listing
February 2021

Coupling of biostimulation and bioaugmentation for enhanced bioremoval of chloroethylenes and BTEX from clayey soil.

Ecotoxicology 2021 Jan 7. Epub 2021 Jan 7.

Faculty of Science and Technology, Department of Civil and Environmental Engineering, University of Macau, Macau SAR, 999078, China.

The bioremoval potential of Pseudomonas plecoglossicida toward mixed contaminants was explored through the coupled biostimulation and bioaugmentation in soil microcosm. Response surface methodology was employed to optimize nutrients and innoculum size for the cometabolic removal of two representative chloroethylenes, trichloroethylene (TCE) and cis-1,2-dichloroethylene (cis-DCE), mixed with benzene, toluene, ethylbenzene, and xylenes (BTEX). The interactive effects of nutrients [nitrogen (N) and phosphorus (P)] and inoculum size toward the bioremoval of mixture of BTEX (600 mg kg), cis-DCE (10 mg kg), and TCE (10 mg kg) were estimated using principal component analysis and two-dimensional hierarchical cluster analysis. The optimal condition was confirmed with C:N:P ratio of 100:26.7:1.8-4.8 and higher inoculum size (≥25%), where 97.7% of benzene, 98.3% of toluene, 91.2% of ethylbenzene, 45.6% of m,p-xylene, 31.2% of o-xylene, 26.9% of cis-DCE, and 33.5% of TCE were bioremoved.
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http://dx.doi.org/10.1007/s10646-020-02323-zDOI Listing
January 2021

A role for intestinal alkaline phosphatase in preventing liver fibrosis.

Theranostics 2021 1;11(1):14-26. Epub 2021 Jan 1.

Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, US.

Liver fibrosis is frequently associated with gut barrier dysfunction, and the lipopolysaccharides (LPS) -TLR4 pathway is common to the development of both. Intestinal alkaline phosphatase (IAP) has the ability to detoxify LPS, as well as maintain intestinal tight junction proteins and gut barrier integrity. Therefore, we hypothesized that IAP may function as a novel therapy to prevent liver fibrosis. Stool IAP activity from cirrhotic patients were determined. Common bile duct ligation (CBDL) and Carbon Tetrachloride-4 (CCl4)-induced liver fibrosis models were used in WT, IAP knockout (KO), and TLR4 KO mice supplemented with or without exogenous IAP in their drinking water. The gut barrier function and liver fibrosis markers were tested. Human stool IAP activity was decreased in the setting of liver cirrhosis. In mice, IAP activity and genes expression decreased after CBDL and CCl4 exposure. Intestinal tight junction related genes and gut barrier function were impaired in both models of liver fibrosis. Oral IAP supplementation attenuated the decrease in small intestine tight junction protein gene expression and gut barrier function. Liver fibrosis markers were significantly higher in IAP KO compared to WT mice in both models, while oral IAP rescued liver fibrosis in both WT and IAP KO mice. In contrast, IAP supplementation did not attenuate fibrosis in TLR4 KO mice in either model. Endogenous IAP is decreased during liver fibrosis, perhaps contributing to the gut barrier dysfunction and worsening fibrosis. Oral IAP protects the gut barrier and further prevents the development of liver fibrosis via a TLR4-mediated mechanism.
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http://dx.doi.org/10.7150/thno.48468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7681079PMC
January 2021

161  W middle infrared ZnGeP MOPA system pumped by 300  W-class Ho:YAG MOPA system.

Opt Lett 2021 Jan;46(1):82-85

We demonstrated a high-power -switched two-stage Ho:YAG master-oscillator power-amplifier (MOPA) system dual-end pumped by Tm:YLF lasers. A new method was introduced by rotating and swapping spatial axial directions of pump beams to improve the beam quality of the Ho:YAG oscillator and first-stage amplifier. Two parallel second-stage Ho:YAG amplifiers were employed to output high power. A total maximum average output power of 332 W at 2091 nm with pulse repetition frequency of 20 kHz was achieved. Then a MOPA system was demonstrated using the Ho:YAG MOPA as the pump source. A maximum average output power of 161 W at 3-5 µm was obtained with 290 W incident Ho pump power, corresponding to beam quality factors of 3.42 and 3.83 for horizontal and vertical directions, respectively.
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http://dx.doi.org/10.1364/OL.413755DOI Listing
January 2021

Full-color micro-LED displays with cadmium-free quantum dots patterned by photolithography technology.

Appl Opt 2020 Dec;59(35):11112-11122

A full-color display consisting of red and green photoluminescence cadmium-free quantum dots (QDs) as the color conversion material and excited by a 68×68 blue micro-LED flip chip array mounted on an active-matrix driving board was completed in this study. The QD photoresist (QDPR) lithography technology was reported in detail, and it has been proven to be a stable process route. The suitable thickness of 12±1µ of the QDPR and black matrix was proposed to reduce the light cross talk between different sub-pixels. The thickness of the common color filter of 1-2 µm was made successfully between the quantum dot film and the cover glass, which can greatly reduce the leakage of blue backlight and decrease the quantum dots excitation by the ambient light, as well as improve the color gamut and color purity of the display panel. In addition, the high red and green light conversion efficiency reaches up to 78.1% and 296.5%, respectively, and the screen display can reach 98.8% NTSC on the CIE 1931 chromaticity. Representative RGB monochromatic pictures were displayed successfully and ≤0.04 viewing angle deviation of the display was measured precisely.
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http://dx.doi.org/10.1364/AO.412267DOI Listing
December 2020

Magnolol Suppresses Pancreatic Cancer Development and Negatively Regulating TGF-β/Smad Signaling.

Front Oncol 2020 2;10:597672. Epub 2020 Dec 2.

Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China.

Magnolol, a hydroxylated biphenyl extracted from , has recently drawn attention due to its anticancer potential. The present study was aimed to explore the effects of Magnolol on restraining the proliferation, migration and invasion of pancreatic cancer and . Magnolol showed significant anti-growth effect in an orthotopic xenograft nude mouse model, and immunohistochemical staining of the xenografts revealed that Magnolol suppressed vimentin expression and facilitated E-cadherin expression. The cytoactive detection using CCK-8 assay showed Magnolol inhibited PANC-1 and AsPC-1 concentration-dependently. Scratch healing assay and the Transwell invasion assay proved the inhibiting effects of Magnolol on cellular migration and invasion at a non-cytotoxic concentration. Western blot and rt-PCR showed that Magnolol suppressed epithelial-mesenchymal-transition by increasing the expression level of E-cadherin and decreasing those of N-cadherin and vimentin. Magnolol suppressed the TGF-β/Smad pathway by negatively regulating phosphorylation of Smad2/3. Moreover, TGF-β1 impaired the antitumor effects of Magnolol . These results demonstrated that Magnolol can inhibit proliferation, migration and invasion and by suppressing the TGF-β signal pathway and EMT. Magnolol could be a hopeful therapeutic drug for pancreatic malignancy.
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http://dx.doi.org/10.3389/fonc.2020.597672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7738609PMC
December 2020

Transcriptional Profiling Reveals the Regulatory Role of DNER in Promoting Pancreatic Neuroendocrine Neoplasms.

Front Genet 2020 27;11:587402. Epub 2020 Nov 27.

Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.

Wnt/β-catenin and NOTCH signaling contribute to the pathogenesis and growth of (PanNENs). The wnt and Notch signaling pathways form an integrated signaling device termed "wntch" and regulate stochastic cell fate decisions, suggesting the essentiality of Wnt/Notch interactions in disease progression. However, the function of Wnt/Notch interactions in PanNENs is unclear. We analyzed RNA sequencing (RNA-seq) data to identify differentially expressed lncRNAs, mRNAs and pathways according to enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with PanNENs. RNA-seq analysis revealed that the levels of the lncRNA XLOC_221242 and the mRNA encoding Delta/Notch-like epidermal growth factor (EGF)-related receptor (DNER) were significantly increased in tumor tissues compared with normal tissues ( = 3). Protein-protein interaction (PPI) prediction combined with transcriptional profiling data analysis revealed that DNER expression levels were positively correlated with those of DNA-binding factor (RBPJ), S phase kinase-associated protein 1 (Skp1), CTNNB1 and Cadherin-2 (CDH2), which promote PanNEN tumorigenesis and progression. These results were consistent with those of immunohistochemical analysis of DNER, RBPJ, SKP1, CTNNB1, and CDH2 expression ( = 15). These findings provide compelling clinical and molecular evidence supporting the conclusion that DNER and the related RBPJ, SKP1, CTNNB1, and CDH2 signaling contribute to PanNEN tumorigenesis and progression by activating wnt/Notch interactions.
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http://dx.doi.org/10.3389/fgene.2020.587402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728999PMC
November 2020

Association Between Sarcopenia and Its Components and Dependency in Activities of Daily Living in Patients on Hemodialysis.

J Ren Nutr 2021 Jul 10;31(4):397-402. Epub 2020 Dec 10.

Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China. Electronic address:

Objectives: To investigate the association of sarcopenia and its components (muscle mass, muscle strength, and physical performance) with dependency in activities of daily living (ADLs) in maintaining patients on hemodialysis.

Design And Methods: This is a cross-sectional study. Sarcopenia was identified according to the Asian Working Group for Sarcopenia 2019 criteria. Basic ADLs (BADLs) and instrumental ADLs (IADLs) were assessed. Logistic regression was used to estimate the association of sarcopenia and its components with dependency. Area under the receiver-operating characteristic curve of gait speed corresponding with dependency was calculated.

Results: A total of 238 patients on hemodialysis were included. The proportion of enrolled male candidates was 67.6%, and the average age was 60.9 years. In all, 49.2% (n = 117) and 30.7% (n = 73) of patients on dialysis were diagnosed with sarcopenia and severe sarcopenia, respectively. Dependency in BADLs was 21.0% (n = 50), and dependency in IADLs was 41.2% (n = 98). Severe sarcopenia was significantly associated with dependency in BADLs and IADLs after adjustment of clinical covariables (odds ratio [OR], 4.68 [95% confidence interval (CI): 2.11-10.40]; OR, 3.24 [95% CI: 1.61-6.53], respectively), whereas those effects for sarcopenia were not significant. With all three sarcopenia components in the analysis model, high gait speed remained strongly associated with low function dependency in BADLs and IADLs (per 0.1 m/s increase of gait speed: OR, 0.52 [95% CI: 0.41-0.66]; and 0.46 [95% CI: 0.35-0.59], respectively). Area under the receiver-operating characteristic curve of gait speed corresponding with dependency in BADLs and IADLs was 0.827 (0.759, 0.896) and 0.878 (0.832, 0.925), respectively.

Conclusions: Severe sarcopenia was closely related to dependency in ADL in patients on hemodialysis. Gait speed was the most important factor affecting dependency in sarcopenia and had good diagnostic accuracy for screening dependency in ADL.
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http://dx.doi.org/10.1053/j.jrn.2020.08.016DOI Listing
July 2021

Genome-wide association analysis of stripe rust resistance in modern Chinese wheat.

BMC Plant Biol 2020 Oct 27;20(1):491. Epub 2020 Oct 27.

Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, China.

Background: Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm.

Results: Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015-2016 cropping season, and in Wuhan in Hubei province in the 2013-2014, 2016-2017 and 2018-2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation.

Conclusion: The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.
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http://dx.doi.org/10.1186/s12870-020-02693-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590722PMC
October 2020

Size-dependent optical-electrical characteristics of blue GaN/InGaN micro-light-emitting diodes.

Appl Opt 2020 Oct;59(29):9225-9232

To derive the impact of chip size reduction on optical efficiency in micro-LED array panels, blue InGaN/GaN LEDs, which consist of 21×7 arrays (60 ppi display) with different mesa sizes on sapphire substrates, are designed and fabricated in this study. Changing the mesa area of the chip is first proposed to investigate the luminous efficiency (cd/A) of the screen. The current efficiency with a peak wavelength of 450 nm reaches up to 14.29 cd/A for the biggest pixel 50µ×60µ and to 12.25 cd/A for the 15µ×25µ chip, delivering high-level efficiencies to the current LED research field. The mechanisms of size-dependent efficiency variation trends and efficiency droops of blue LEDs are investigated experimentally, confirming that the current efficiency is more efficient at high injection current density while exhibiting poorer performance at the low current density region for smaller chips. The peak efficiency corresponds to higher current density with a decrease in chip size according to the carrier recombination ABC model. Moreover, the characteristic curve of the spectrum and the changes in the yellow light band under different incident light conditions (i.e., 355 nm and 375 nm) are analyzed by photoluminescence.
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http://dx.doi.org/10.1364/AO.405572DOI Listing
October 2020

Image recovery of ghost imaging with sparse spatial frequencies.

Opt Lett 2020 Oct;45(19):5356-5359

When the spatial frequencies of the object are insufficiently sampled, the reconstruction of ghost imaging will suffer from repetitive visual artifacts, which cannot be effectively tackled by existing ghost imaging reconstruction techniques. In this Letter, extensions of the CLEAN algorithm applied in ghost imaging are explored to eliminate those artifacts. Combined with the point spread function estimation using the second-order coherence measurement in ghost imaging, our modified CLEAN algorithm is demonstrated to have a fast and noteworthy improvement against the spatial-frequency insufficiency, even for the extreme sparse sampling cases. A brief explanation of the algorithm and performance analysis are given.
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http://dx.doi.org/10.1364/OL.403288DOI Listing
October 2020

The study of the association between immune monitoring and pneumonia in kidney transplant recipients through machine learning models.

J Transl Med 2020 09 29;18(1):370. Epub 2020 Sep 29.

Transplantation Center, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Changsha, Hunan, 410013, P. R. China.

Background: Kidney transplantation is the optimal treatment to cure the patients with end-stage renal disease (ESRD). However, the infectious complication, especially pneumonia, is the main cause of mortality in the early stage. Immune monitoring by relevant biomarkers provides direct evidence of immune status. We aimed to study the association between immune monitoring and pneumonia in kidney transplant patients through machine learning models.

Methods: A total of 146 patients receiving the immune monitoring panel in our center, including 46 pneumonia recipients and 100 stable recipients, were retrospectively reviewed to develop the models. All the models were validated by external data containing 10 pneumonia recipients and 32 stable recipients. The immune monitoring panel consisted of the percentages and absolute cell counts of CD3CD4 T cells, CD3CD8 T cells, CD19 B cells and natural killer (NK) cells, and median fluorescence intensity (MFI) of human leukocyte antigen (HLA)-DR on monocytes and CD64 on neutrophils. The machine learning models including support vector machine (SVM), logistic regression (LR), multi-layer perceptron (MLP) and random forest (RF) were applied for analysis.

Results: The pneumonia and stable groups showed significant difference in cell counts of each subpopulation and MFI of monocyte HLA-DR and neutrophil CD64. The SVM model by monocyte HLA-DR (MFI), neutrophil CD64 (MFI), CD8 T cells (cells/μl), NK cells (cell/μl) and TBNK (T cells, B cells and NK cells, cells/μl) had the best performance with the average area under the curve (AUC) of 0.940. The RF model best predicted the patients who would progress into severe pneumonia, with the average AUC of 0.760. All the models had good performance validated by external data.

Conclusions: The immune monitoring panel was tightly associated with pneumonia in kidney transplant recipients. The models developed by machine learning techniques identified patients at risk and predicted the prognosis. Based on the results of immune monitoring, better individualized therapy might be achieved.
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http://dx.doi.org/10.1186/s12967-020-02542-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526199PMC
September 2020

Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge.

Appl Environ Microbiol 2020 11 10;86(23). Epub 2020 Nov 10.

Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China

Pretreatment of waste-activated sludge (WAS) is an effective way to destabilize sludge floc structure and release organic matter for improving sludge digestion efficiency. Nonetheless, information on the impact of WAS pretreatment on digestion sludge microbiomes, as well as mechanistic insights into how sludge pretreatment improves digestion performance, remains elusive. In this study, a genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different types of feeding sludge: WAS pretreated with 0.25 mol/liter alkaline/acid (APAD), WAS pretreated with 0.8 mol/liter alkaline/acid (HS-APAD), thermally pretreated WAS (thermal-AD), and fresh WAS (control-AD). We retrieved 254 metagenome-assembled genomes (MAGs) to identify the key functional populations involved in the methanogenic digestion process. These MAGs span 28 phyla, including 69 yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were enriched in APAD and HS-APAD, while lineages related to protein and lipid fermentation were enriched in thermal-AD, corroborating the idea that different substrates are released from alkaline/acid and thermal pretreatments. Among the major functional populations (i.e., fermenters, syntrophic acetogens, and methanogens), significant correlations between genome sizes and abundance of the fermenters were observed, particularly in APAD and HS-APAD, which had improved digestion performance. Wastewater treatment generates large amounts of waste-activated sludge (WAS), which consists mainly of recalcitrant microbial cells and particulate organic matter. Though WAS pretreatment is an effective way to release sludge organic matter for subsequent digestion, detailed information on the impact of the sludge pretreatment on the digestion sludge microbiome remains scarce. Our study provides unprecedented genome-centric metagenomic insights into how WAS pretreatments change the digestion sludge microbiomes, as well as their metabolic networks. Moreover, digestion sludge microbiomes could be a unique source for exploring microbial dark matter. These results may inform future optimization of methanogenic sludge digestion and resource recovery.
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http://dx.doi.org/10.1128/AEM.01920-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657636PMC
November 2020

Resolution enhancement of overlapping peaks of ion mobility spectrometry based on improved particle swarm optimization algorithm.

Rapid Commun Mass Spectrom 2021 Jan;35(1):e8935

Institute of Mass Spectrometry, Ningbo University, Ningbo, 315211, China.

Rationale: Ion mobility spectrometry (IMS) is a powerful analytical tool that has been widely applied in many fields. However, the limited structural resolution of IMS results in peak overlapping in the analysis of samples with similar structures. We propose a novel method, improved particle swarm optimization (IPSO), for the separation of IMS overlapping peaks.

Methods: This method, which prevents local optimization, is used to identify the peak model coefficients of IMS. Moreover, we use the half-peak width characteristics of IMS to determine the particle position range, which eliminates impossible combinations of single peaks and reduces the difficulty of identification of coefficients.

Results: During a comparison in performance between IPSO and the genetic algorithm (GA), the results show that the maximum separation error of IPSO is only 1.45%, while the error of the GA is up to 17.43%. Moreover, the time consumed by IPSO is 95% less than that of the GA, and IPSO has a greater robustness under the same separation error conditions.

Conclusions: The method proposed provides accurate analytical results in separating overlapping IMS peaks even in cases of severe overlaps, which greatly enhances the structural resolution of IMS.
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http://dx.doi.org/10.1002/rcm.8935DOI Listing
January 2021

Inoculation Reduces the Incidence of Clubroot Disease in Chinese Cabbage by Regulating the Rhizosphere Microbial Community.

Microorganisms 2020 Aug 31;8(9). Epub 2020 Aug 31.

School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.

Clubroot is a disease of cruciferous crops that causes significant economic losses to vegetable production worldwide. We applied high-throughput amplicon sequencing technology to quantify the effect of LTR-2 inoculation on the rhizosphere community of Chinese cabbage ( subsp. cv. Jiaozhou) in a commercial production area. inoculation of cabbage reduced the incidence of clubroot disease by 45.4% ( < 0.05). The disease control efficacy (PDIDS) was 63%. This reduction in disease incidence and severity coincided with a drastic reduction in both the relative abundance of , the causative pathogen of cabbage clubroot disease, and its copy number in rhizosphere soil. Pathogenic fungi and were also negatively associated with inoculation according to co-occurrence network analysis. Inoculation drastically reduced the relative abundance of the dominant bacterial genera and , whilst increasing others including . Our results demonstrate that LTR-2 is an effective biological control agent for cabbage clubroot, which acts through modulation of the soil and rhizosphere microbial community.
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http://dx.doi.org/10.3390/microorganisms8091325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563613PMC
August 2020

Interferon Inducing Porcine Reproductive and Respiratory Syndrome Virus Vaccine Candidate Protected Piglets from HP-PRRSV Challenge and Evoke a Higher Level of Neutralizing Antibodies Response.

Vaccines (Basel) 2020 Aug 31;8(3). Epub 2020 Aug 31.

Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.

Although widespread administration of attenuated porcine reproductive and respiratory syndrome virus (PRRSV) vaccines has been implemented since they first became commercially available two decades ago, PRRSV infection prevalence in swine herds remains high. The limited success of PRRSV vaccines is partly due to the well-established fact that a given vaccine strain confers only partial or no protection against heterologous strains. In our past work, A2MC2-P90, a novel PRRSV vaccine candidate that induced a type I IFNs response in vitro, conferred complete protection against challenge with genetically heterologous PRRSV strains. Here we assessed the ability of the PRRSV vaccine candidate A2MC2-P90 to protect piglets against the HP-PRRSV challenge and compared its efficacy to that of a licensed HP-PRRSV-specific vaccine (TJM-F92) assessed in parallel. A2MC2-P90 provided vaccinated piglets with 100% protection from a lethal challenge with extremely virulent HP-PRRSV-XJA1, while 100% mortality was observed for unvaccinated piglets by day 21 post-challenge. Notably, comparison of partial sequence (GP5) of XJA1 to A2MC2-P90 suggested there was only 88.7% homology. When comparing post-HP-PRRSV challenge responses between piglets administered A2AMC2-P90 versus those immunized with licensed vaccine TJM-F92, A2MC2-P90-vaccinated piglets rapidly developed a stronger protective humoral immune response, as evidenced by much higher titers of neutralizing antibodies, more rapid clearance of viremia and less nasal virus shedding. In conclusion, our data suggest that this novel vaccine candidate A2MC2-P90 has improved protection spectrum against heterologous HP-PRRSV strains.
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http://dx.doi.org/10.3390/vaccines8030490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565719PMC
August 2020

Peptidoglycan derived from MLGA up-regulates the expression of chicken -defensin 9 without triggering an inflammatory response.

Innate Immun 2020 11 26;26(8):733-745. Epub 2020 Aug 26.

Jiangxi Province Key Laboratory of Animal Nutrition, 91595Jiangxi Agricultural University, China.

Defensins are critical components of the innate immune system and play an important role in the integration of innate and adaptive immune responses. Although information on the immunomodulatory properties of peptidoglycan from bacteria is abundant, little is known about the β-defensin induction effect of peptidoglycan from the probiotic . This study investigated the effect of intact peptidoglycan from MLGA on the induction of avian β-defensin 9 in chicken immune cells and intestinal explants. Peptidoglycan from MLGA dose dependently promoted avian β-defensin 9 mRNA expression in chicken PBMCs, splenocytes, thymocytes, hepatocytes, and chicken embryo jejunum, ileum, and cecum explants and increased the capacity of PBMC or splenocyte lysates to inhibit the growth of Enteritidis. In contrast to the effect of MLGA-derived peptidoglycan, peptidoglycan derived from pathogenic reduced avian β-defensin 9 mRNA expression in chicken PBMCs and splenocytes. The inducible effect of peptidoglycan from MLGA on avian β-defensin 9 expression in PBMCs and splenocytes was observed without activation of the expression of associated pro-inflammatory cytokines IL-1β, IL-8, and IL-12p40, whereas these cytokine expressions were suppressed by peptidoglycan hydrolysate obtained by lysozyme digestion. The results of the present study show the capability of peptidoglycan derived from MLGA to induce the antimicrobial peptide defensin while simultaneously avoiding the deleterious risks of an inflammatory response.
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http://dx.doi.org/10.1177/1753425920949917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787553PMC
November 2020

Thin-film lithium niobate electro-optic modulator on a D-shaped fiber.

Opt Express 2020 Jul;28(15):21464-21473

We propose a low-insertion-loss electro-optic modulator formed with LNOI bonded on a D-shaped SMF. The proposed modulator employs high-performance Mach-Zehnder interferometer (MZI) formed with ridge LNOI waveguides and driven by travelling-wave electrodes. The light from the fiber core is coupled into a thin strip LNOI waveguide and then launched into the MZI via a ridge LNOI waveguide with tapered slab height and vice versa. Such all-fiber configuration exempts the need of the butt-coupling with an SMF. The calculated results show that our proposed modulator is capable of achieving a low insertion loss of less than 1.5 dB, an EO modulation efficiency (Vπ·L) of 2.05 V·cm, and a 3-dB modulation bandwidth of larger than 80 GHz. Our all-fiber LNOI modulator is feasible in practice and opens a new door to realize high-speed fiber devices by the integration of an optical fiber and thin film LN.
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http://dx.doi.org/10.1364/OE.396613DOI Listing
July 2020

Multi-shelled cobalt-nickel oxide/phosphide hollow spheres for an efficient oxygen evolution reaction.

Dalton Trans 2020 Aug 28;49(31):10918-10927. Epub 2020 Jul 28.

School of Materials Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China.

Because of their low cost and Earth-abundant characteristics, materials based on 3d transition metals have attracted great research interest and are considered as promising electrocatalysts for the oxygen evolution reaction (OER), besides the commercial noble metal-based materials, in recent years. In order to improve electrocatalytic activity, it is necessary to design the structures and compositions of electrocatalysts. In this study, a series of multi-shelled CoNi oxide/phosphide hollow spheres with tunable element ratios were prepared. The electrocatalytic activity of the multi-shelled CoNi oxide/phosphide is strongly dependent on the molar ratio of Co and Ni. Based on the combined advantages of complex structures and compositions, the multi-shelled CoNi oxide/phosphide displays outstanding electrocatalytic performance in terms of high activity and stable durability for the OER, surpassing those of RuO and multi-shelled CoNi oxide/phosphide with other element ratios of Co and Ni. This result suggests a great possibility of rationally designing the composition for highly efficient electrocatalysts.
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http://dx.doi.org/10.1039/d0dt01523gDOI Listing
August 2020

Inhibition of miR-93 promotes interferon effector signaling to suppress influenza A infection by upregulating JAK1.

Int Immunopharmacol 2020 Sep 8;86:106754. Epub 2020 Jul 8.

Institute of Organ Transplantation, Changzhen Hospital, Navy Medical University, Shanghai, China. Electronic address:

Type I interferons play a critical role in host defense against influenza virus infection. Interferon cascade induces the expression of interferon-stimulated genes then subsequently promotes antiviral immune responses. The microRNAs are important regulators of innate immunity, but microRNAs-mediated regulation of interferon cascade during influenza infection remains to be fully identified. Here we found influenza A virus (IAV) infection significantly inhibited miR-93 expression in alveolar epithelial type II cells through RIG-I/JNK pathway. IAV-induced downregulation of miR-93 was found to upregulate JAK1, the target of miR-93, and then feedback promote antiviral innate response by facilitating IFN effector signaling. Importantly, in vivo administration of miR-93 antagomiR markedly suppressed IAV infection, protecting mice form IAVs -associated death. Hence, the inducible downregulation of miR-93 feedback suppress IAV infection by strengthening IFN-JAK-STAT pathway via JAK1 upregulation, and in vivo inhibition of miR-93 bears considerable therapeutic potential for suppressing IAV infection.
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http://dx.doi.org/10.1016/j.intimp.2020.106754DOI Listing
September 2020

Systematic engineering of branch chain amino acid supply modules for the enhanced production of bacitracin from .

Metab Eng Commun 2020 Dec 11;11:e00136. Epub 2020 Jun 11.

State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.

Bacitracin is a broad-spectrum cyclic peptide antibiotic mainly produced by , precursor amino acid supply served as the critical role during its synthesis. In this study, we systematically engineered branch-chain amino acid (BCAA) supply modules for bacitracin production. Firstly, we demonstrated that Ile and Leu acted as limiting precursors for bacitracin synthesis, and that BCAA synthetic pathways were strengthened via simultaneous overexpression of, feedback-resistance acetolactate synthase IlvBN, 2-isopropylmalate synthetase LeuA and BCAA aminotransferase YbgE. Using this approach, bacitracin yield from strain DW-BCAA2 was 892.54 U/mL, an increase of 18.32% compared with that DW2 (754.32 U/mL). Secondly, the BCAA permeases, YvbW and BraB, which have higher affinities for Leu and Ile transportation, respectively, were both identified as BCAA importers, with their overexpression improving intracellular BCAA accumulations and bacitracin yields. Finally, the leucine-responsive family regulator, was deleted to generate the final strain DW-BCAA6, with intracellular concentrations of Ile, Leu and Val increased by 2.26-, 1.90- and 0.72-fold, respectively. The bacitracin yield from DW-BCAA6 was 1029.83 U/mL, an increase of 36.52%, and is the highest bacitracin yield reported. Equally, concentrations of other byproducts including acetic acid, acetoin and 2,3-butanediol were all reduced. Taken together, we devised an efficient strategy for the enhanced production of bacitracin, and a promising DW-BCAA6 strain was constructed for industrial production of bacitracin.
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http://dx.doi.org/10.1016/j.mec.2020.e00136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7326738PMC
December 2020
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