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2013 International Conference on Human Health and Medical Engineering, HHME 2013

作者： Lin, Huibin Lin, Jianqun Lin, Jianqiang Shandong Institute of Traditional Chinese Medicine Jinan China State key Lab of Microbial Technology Shandong University Jinan China

ISBN: (纸本)9781845648923

Cuscuta chinensis Lam. is parasitic plant, and the seed of it is the kidney tonifying and yang-boosting Chinese herb. The herbal quality is affected by the wide variety of its host plants. In this research, HPLC, UV measurements methods were used to identify the chemical components and RAPD method was used to analyze the DNA of the C. chinensis grown on different host plants to investigate the effects of the host plants. The results showed that the total flavonoids of C. chinensis are higher than that of C. australis, and the total flavonoids of the above two plants being parasitic on Glycine max, Scutellaria baicalensis, and Phaseolus radiatus are higher. The RAPD analysis showed that the four kind species of Cuscuta can be identified, with the Subg. Grammica of C. chinensis and the C. australis having the same three bands of 1.3, 1.45, and 1.53 kb, and Subg. Monogyna of C. japonica and C. lupuliformis having a band of 1.48 kb. Plants of the same subgenus have similar band patterns in RAPD analyses, showing close genetic relationship. The RAPD analyses showed the polymorphism of the Cuscuta species DNA being parasitic on different host plants. In conclusion, the host plants affect the genomics and the chemical components and contents of Cuscuta species. © 2014 WIT Press.

关键词： Flavonoids

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Recombineering enables genome mining of novel siderophores in a non-model Burkholderiales strain

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Engineering Microbiology 2023年第3期3卷 30-36页

作者： Xingyan Wang Haibo Zhou Xiangmei Ren Hanna Chen Lin Zhong Xianping Bai Xiaoying Bian Helmholtz International Lab for Anti-Infectives State Key Laboratory of Microbial TechnologyShandong University-Helmholtz Institute of BiotechnologyShandong UniversityQingdao 266237China

Iron is essential for bacterial survival,and most bacteria capture iron by producing ***-riales bacteria produce various types of bioactive secondary metabolites,such as ornibactin and malleobactin *** this study,the genome analysis of Burkholderiales genomes showed a putative novel siderophore gene cluster crb,which is highly similar to the ornibactin and malleobactin gene clusters but does not have pvdF,a gene encoding a formyltransferase for N-δ-hydroxy-ornithine *** the bacteriophage recom-binase Redγ-Redδβ7029 mediated genome editing system in a non-model Burkholderiales strain Paraburkholderia caribensis CICC 10960 allowed the rapid identification of the products of crb gene cluster,caribactins A-F(1-6).Caribactins contain a special amino acid residue N-δ-hydroxy-N-δ-acetylornithine(haOrn),which differs from the counterpart N-δ-hydroxy-N-δ-formylornithine(hOrn)in ornibactin and malleobactin,owing to the absence of *** inactivation showed that the acetylation of hOrn is catalyzed by CrbK,whose homologs proba-bly not be involved in the biosynthesis of ornibactin and malleobactin,showing possible evolutionary clues of these siderophore biosynthetic pathways from different *** promote biofilm production and en-hance swarming and swimming abilities,suggesting that they may play crucial roles in biofilm *** study also revealed that recombineering has the capability to mine novel secondary metabolites from non-model Burkholderiales species.

关键词： Burkholderiales Recombineering Siderophore Genome mining Caribactins

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Study on Adsorption and Antirinsing Performances of Alcohol Ether Sulfate/Dodecyl Trimethylammonium Chloride Mixtures on Silica

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Langmuir 2025年 2025 May 8页

作者： Li, Mei He, Xiujuan Pu, Xue Gang, Hongze Chen, Xiaolu Su, Zhiqing Mu, Bozhong Li, Yingcheng State Key Laboratory of Bioreactor Engineering School of Chemistry and Molecular Engineering East China University of Science and Technology 130 Mei long Road Shanghai200237 China Sinopec Key Lab of Surfactants for EOR Sinopec Shanghai Research Institute of Petrochemical Technology Co. Ltd. 1658 Pudong Beilu Shanghai201208 China Engineering Research Center of Microbial Enhanced Oil Recovery East China University of Science and Technology Shanghai200237 China

This study investigated the adsorption and antirinsing performances of sodium alcohol ether sulfate (AEnS), dodecyl trimethylammonium chloride (DTAC), and mixtures of AEnS/DTAC with an equal molar ratio on silica. The adsorption process for individual surfactants was characterized by an initial slow stage, followed by a sharp increase with longer threshold times. In contrast, AEnS/DTAC exhibited a shorter threshold time. Molecular simulation results indicate that the AEnS/DTAC formed a structure wherein positively charged DTAC was close to the silica surface, while negatively charged AEnS resided close to the cation layer of DTAC. This assembly effectively reduced the electrostatic repulsion between AEnS and silica, as well as among DTAC molecules, thereby achieving the highest adsorption rate and adsorption amount. For antirinsing performances, AEnS was quickly washed off, whereas DTAC shows the lowest desorption rate due to their substantial electrostatic attraction toward silica. Notably, the AEnS/DTAC exhibits enhanced antirinsing, confirmed by atomic force microscopy (AFM) results. This research enhances our understanding of surfactant-silica interactions and offers valuable insights for practical applications in oil displacement, mineral flotation, and surface coatings. © 2025 American Chemical Society.

关键词： Cationic surfactants

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Erratum to “ In vitro characterization of a nitro-forming oxygenase involved in 3-( trans -2’-aminocyclopropyl)alanine biosynthesis” [Engineering Microbiology 2 (2022) 100007]

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Engineering Microbiology 2025年第1期5卷

作者： Linlin Pang Weijing Niu Yuwei Duan Liujie Huo Aiying Li Jiequn Wu Youming Zhang Xiaoying Bian Guannan Zhong Helmholtz International Lab for AntiInfectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao 266237 China Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals College of Pharmaceutical Sciences Zhejiang University of Technology Hangzhou 310014 China Suzhou Institute of Shandong University Suzhou 215123 China

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Novel Bacterial Proteases from Deep-Sea Sediments and Their Ecological Role in the Degradation of Sedimentary Organic Nitrogen

Novel Bacterial Proteases from Deep-Sea Sediments and Their ...

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21st IUBMB and 12th FAOBMB International Congress of Biochemistry and Molecular Biology

作者： Chen Xiulan Xie Binbin Blan Fel Zhao Guoyan Zhao Hullin Zhou Mingyang Zhang Yuzhong State Key Lab of Microbial Technology Shandong University

Nearly all high-molecular-wcight dissolved organic notrgen and particulate organic nitrogen in deep sea are hydrolysis-resistant amides,It is unclear how these organic nitrogen are degraded because little is known about the bacteria and their enzymes participating in this *** of proteaseproducing bacteria and proteases involved in deep-sea organic nitrogen was

关键词： Novel Bacterial Proteases from Deep-Sea Sediments and Their Ecological Role in the Degradation of Sedimentary Organic Nitrogen

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Peptalbols trigger apoptosis and autophagy Involved in calcium and Bcl-2-family proteins

Peptalbols trigger apoptosis and autophagy Involved in calci...

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21st IUBMB and 12th FAOBMB International Congress of Biochemistry and Molecular Biology

作者： Mei Shi Hong-Na Wang Shu-Tao Xie Yan Luo Cai-Yun Sun Xiu-Lan Chen Yu-Zhong Zhang State Key Lab of Microbial Technology Shandong University

Peptaibols,a family of peptides synthesized non-ribosomally by the Trichoderma species and other fungi,exhibit antibiotic activities against bacteria and ***,the mechanism involved in peptaibol-induced cell death remains poorly ***,we showed that Trichokonin VI（TK VI）,a peptaibol from Trichoderma pseudokoningii SMF,could trigger programmed cell death（PCD） in human hepatocellular carcinoma cells(HCC

关键词： apoptosis Peptalbols trigger apoptosis and autophagy Involved in calcium and Bcl-2-family proteins

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BIODESULFURIZATION OF DIBENZOTHIOPHENE BY A FACULTATIVE THERMOPHILIC BACTERIUM Mycobacterium goodii X7B

BIODESULFURIZATION OF DIBENZOTHIOPHENE BY A FACULTATIVE THER...

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第二届中日化工学术研讨会

作者：李福利许平马翠卿 State Key Lab of Microbial Technology Shandong University Jinan 250100 China State Key Lab of Microbial Technology Shandong University Jinan 250100 China State Key Lab of Microbial Technology Shandong University Jinan 250100 China

Dibenzothiophene (DBT) is the most excessive and refractory sulfur compound in fossil fuels. The methods for removing DBT, using bacteria, were twofold: the first one involved the destruction of the carobon skeleton;the second, the use of a sulfur-specific process of biodesulfurization, without cleaving the carbon ring. Because in the second method does not degrade the value of the fuel, it is considered by most researchers to be the method of choice. Bacteria used for this study, were obtained from soil collected from a field that contained waste water from a refinery. Using GC/MS, it was confirmed that the metabolic pathway used by this bacterium, involved a sulfur-specific process of biodesulfurization, named the "4S pathway" . The strain was designated X7B and has been identified as Mycobacterium goodii, using physiological and biochemical techniques. This strain appears to have the ability to remove the organic sulfur from thiophenic compounds over a wide temperature range from 25 to 45℃. And the half time of the resting cells desulfurization activity was 32 days, two times more than Rhodococcus erythropolis IGTS8. With the excellent stability, it may have industrial application for biodesulfurization.

关键词： Dibenzothiophene, Biodesulfurization, Hydrodesulfurization, Fuel Oil

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Deep Representation Learning for Electron Ionization Mass Spectra Retrieval

Deep Representation Learning for Electron Ionization Mass Sp...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Liu, Shibo Zhang, Xuan Jiao, Anlei Sun, Shiwei Dian, Longyang Cui, Xuefeng Shandong University School of Computer Science and Technology Qingdao China Chinese Academy of Sciences Key Lab of Intelligent Information Processing Institute of Computing Technology Beijing China Shandong University State Key Laboratory of Microbial Technology Qingdao China

ISBN: (纸本)9798350386226

The task of retrieving and analyzing mass spectra is indispensable for the identification of compounds in mass spectrometry (MS). This methodology is of critical importance as it enables researchers to correlate observed spectra with established databases, thereby precisely determining the chemical composition of samples. The primary challenges to its efficacy lie in optimizing the balance between retrieval accuracy and processing speed. Empirical studies have demonstrated that by converting mass spectra into embeddings via deep learning, it is possible to achieve both high accuracy and speed in retrieval. Nevertheless, there are complex challenges associated with employing deep learning for spectral embedding, particularly within the domain of electron ionization mass spectrometry (EI-MS). In this paper, we introduce a novel representation learning technique termed EI-MS2VEC for EI-MS retrieval. Our spectrum retrieval methodology surpasses current state-of-the-art techniques such as FastEI. For the in-silico library, we attain hit rate@1 and hit rate@10 of 43.6% and 84.5%, respectively, compared to FastEI's 36.7% and 80.4%. Moreover, our retrieval approach operates with an order of magnitude greater speed than FastEI. The source code is available on Github (https://***/xfcui/EI-MS2VEC). © 2024 IEEE.

关键词： Embeddings

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How to Train Your Neural Network for Molecular Structure Generation from Mass Spectra?

How to Train Your Neural Network for Molecular Structure Gen...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Zhao, Kai Liu, Yanmin Dian, Longyang Sun, Shiwei Cui, Xuefeng Shandong University School of Computer Science and Technology Qingdao China Shandong University State Key Laboratory of Microbial Technology Qingdao China Chinese Academy of Sciences Key Lab of Intelligent Information Processing Institute of Computing Technology Beijing China

ISBN: (纸本)9798350386226

Mass spectrometry serves as a pivotal tool for the analysis of small molecules through an examination of their mass-to-charge ratios. Recent advancements in deep learning have markedly enhanced the analysis of mass spectrometric data, facilitating the prediction of novel small molecule structures without the necessity of extensive databases. Nonetheless, the paucity of annotated datasets impedes the efficacious training of molecular generation models predicated on MS2 spectra. To mitigate this limitation, we introduce ctMSNovelist, an avant-garde method that amalgamates pre-training, fine-tuning, and co-training techniques to construct a more precise model for the generation of molecular structures from tandem mass spectrometry data. This novel approach augments both the training regimen and the predictive accuracy of the MSNovelist model, thereby surmounting the obstacle of limited data. The methodology commences with the pretraining of a Variational Autoencoder (VAE) to generate molecular fingerprints derived from SMILES strings. Subsequently, it undergoes fine-tuning to emulate noisy fingerprints originating from mass spectrometry (MS) data. Concurrently, MSNovelist is co-trained utilizing these simulated fingerprints, inclusive of the highly noisy variants produced in the early stages of VAE training. The incorporation of a substantial volume of noisy data serves to enhance model accuracy and avert overfitting. We evaluated ctMSNovelist using the GNPS dataset and attained a SMILES prediction accuracy of 48.8%, representing a 4.1% enhancement over MSNovelist. It is pertinent to note that the sole distinction between ctMSNovelist and MSNovelist in this experiment was the training process. The code and models are publicly available at https://***/xfcui/ctMSNovelist. © 2024 IEEE.

关键词： Neural networks

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bHLH-PAS Proteins as Potential Drug Targets for Various Diseases Including Psychiatric Disorders

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神经药理学报 2019年第Z1期 67-68页

作者： WU Da-lei Helmholtz International Lab State Key Laboratory of Microbial TechnologyShandong University

The mammalian basic helix-loop-helix-PER-ARNT-SIM(bHLH-PAS) transcription factors share common architectural features that include a bHLH DNA-binding domain and tandemly positioned PAS domains. The sixteen members of this family include the hypoxia-inducible factors(HIF-1/2α),neuronal PAS domain proteins(NPAS1/3),ARNT(also known as HIF-1β) and so on. Most bHLH-PAS proteins have been genetically linked to variety of diseases in humans,including cancers,inflammation,metabolic syndromes and psychiatric conditions. To function as transcription factors,the bHLH-PAS proteins must form heterodimeric complexes. We examined the crystal structures of multi-domain NPAS1-ARNT and NPAS3-ARNT complexes,discovering each to contain four putative ligand-binding pockets in the PAS domains. Through expanded architectural comparisons between these complexes and HIF-1α-ARNT,HIF-2α-ARNT and CLOCK-BMAL1,we show the wider mammalian bHLH-PAS family is capable of multi-ligand-binding and presents as an ideal class of transcription factors for direct targeting by small-molecule drugs.

关键词： transcription factor bHLH-PAS proteins drug targets psychiatric disorders crystal structure drug discovery ligand binding pockets

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