Statistical Optimization of Medium Components for Milk-Clotting Enzyme Production by Bacillus amyloliquefaciens D4 Using Wheat Bran-an Agro-Industry Waste

( Wei Bing Zhang ),( Xiao Ling He ),( Hong Na Liu ),( Hui Yuan Guo ),( Fa Zheng Ren ),( Wei Dong Gao ),( Peng Cheng Wen ) 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.8

In this paper, two statistical methods were applied to optimize medium components to improve the production of the milk-clotting enzyme by Bacillus amyloliquefaciens D4. First, wheat bran juice, skim milk powder, and Na2HPO4 were shown to have significant effects on D4 enzyme production using the Plackett?Burman experimental design. Subsequently, an optimal medium was obtained using the Box?Behnken method, which consisted of 3.31 g/l of skim milk powder, 5.0 g/l of sucrose, 0.1 g/l of FeSO4?7H2O, 0.1 g/l of MgSO4?7H2O, 0.1 g/l of MnSO4?2H2O, 0.1 g/l of ZnSO4?7H2O, 1.52 g/l of Na2HPO4, and 172.45 g/l of wheat bran juice. With this optimal medium, the milk-clotting enzyme production was remarkably enhanced. The milk-clotting enzyme activity reached 3,326.7 SU/ml after incubation of 48 h, which was 1.76-fold higher than that of the basic medium, showing that the Plackett?Burman design and Box?Behnken response surface method are effective to optimize medium components, and B. amyloliquefaciens D4 possessed a high rennet-producing capacity in the optimal medium.

An Improved LDV-Hop Localization Algorithm in Wireless Sensor Networks

Xiaoan Bao,Zhongtao Ren,Na Zhang,Xing Hu,Tongshu Wu,Yangqiu Liu 보안공학연구지원센터 2014 International Journal of Control and Automation Vol.7 No.10

Localization of sensor nodes is a fundamental and a key technology in wireless sensor networks, it has been widely studied by many universities and research institutions in recent years and many localization algorithms have been put forward by scholars from diverse aspects. A new localization algorithm, which is based on the LDV-Hop algorithm, is proposed in this paper. Firstly, to reduce the localization error we modify the average one-hop distance between anchor nodes, and the average one-hop distance used for each unknown node's location is also modified through weighting the received average one-hop distance from anchor nodes. Then, to solve the problem of low localization coverage which is the main disadvantage of LDV-Hop localization algorithm, we regard regular node with newly estimated location as anchor node and utilize believable factor threshold to restrain the error accumulation brought by this method.

Optimization of chemico-physical transformation methods for various bacterial species using diverse chemical compounds and nanomaterials

Ren, Jun,Na, Dokyun,Yoo, Seung Min Elsevier 2018 Journal of biotechnology Vol.288 No.-

<P><B>Abstract</B></P> <P>Bacterial transformation is a fundamental technology to deliver engineered plasmids into bacterial cells, which is essential in industrial protein production, chemical production, <I>etc</I>. Previously, we developed a simple chemico-physical transformation method that can be applied to various bacterial species. Here, to accelerate the advance of bacteria biotechnology we optimize our method by combinatorially evaluating chemical compounds (rubidium chloride, lithium acetate, cesium chloride, dimethyl sulfoxide, and magnesium chloride) for increasing membrane permeability and nanomaterials (sepiolite, gold(III) chloride, multiwalled carbon nanotube, and chitosan) for piercing the membranes. The best transformation efficiencies were achieved as follows; 2.84 × 10<SUP>4</SUP> CFU/μg DNA in <I>Lactococcus lactis</I> subsp. <I>lactics</I> (0.1 M CsCl and gold(III) chloride), 3.60 × 10<SUP>4</SUP> CFU/μg DNA in <I>Enterococcus faecalis</I> (1 M Li-acetate and MWCNT), 2.41 × 10<SUP>4</SUP> CFU/μg DNA in <I>Bacillus</I> sp. (0.01 M RbCl and sepiolite), 3.49 × 10<SUP>4</SUP> CFU/μg DNA (0.1 M RbCl and gold(III) chloride) in <I>Ralstonia eutropha</I> (also known as <I>Cupriavidus necator</I>) and 8.78 × 10<SUP>4</SUP> CFU/μg DNA (1 M RbCl and chitosan) in <I>Methylomonas</I> sp. DH-1. The efficiencies are up to 100-fold higher than those without optimization. Accordingly, our fast and simple chemico-physical transformation with chemical–nanomaterial optimization allows for the efficient DNA entry into various bacterial cells with high efficiency.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A chemico-physical transformation method with high efficiency was developed. </LI> <LI> RbCl, LiAc, CsCl, DMSO, and MgCl2 were used for increasing membrane permeability. </LI> <LI> Sepiolite, gold(III) chloride, MWCNT, and chitosan were used for piercing the membranes. </LI> <LI> High efficiency was achieved by optimizing chemical–nanomaterial combinations. </LI> <LI> The efficiencies are up to 100-fold higher than those without optimization. </LI> </UL> </P>

Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide

Ren Jun,Hwang Suhee,Shen Junhao,Kim Hyeongwoo,Kim Hyunjoo,Kim Jieun,Ahn Soyoung,Kim Min-gyun,Lee Seung Ho,Na Dokyun 한국미생물학회 2022 The journal of microbiology Vol.60 No.9

In protein biotechnology, large soluble fusion partners are widely utilized for increased yield and solubility of recombinant proteins. However, the production of additional large fusion partners poses an additional burden to the host, leading to a decreased protein yield. In this study, we identified two highly disordered short peptides that were able to increase the solubility of an artificially engineered aggregationprone protein, GFP-GFIL4, from 0.6% to 61% (D3-DP00592) and 46% (D4-DP01038) selected from DisProt database. For further confirmation, the peptides were applied to two insoluble E. coli proteins (YagA and YdiU). The peptides also enhanced solubility from 52% to 90% (YagA) and from 27% to 93% (YdiU). Their ability to solubilize recombinant proteins was comparable with strong solubilizing tags, maltosebinding protein (40 kDa) and TrxA (12 kDa), but much smaller (< 7 kDa) in size. For practical application, the two peptides were fused with a restriction enzyme, I-SceI, and they increased I-SceI solubility from 24% up to 75%. The highly disordered peptides did not affect the activity of I-SceI while I-SceI fused with MBP or TrxA displayed no restriction activity. Despite the small size, the highly disordered peptides were able to solubilize recombinant proteins as efficiently as conventional fusion tags and did not interfere with the function of recombinant proteins. Consequently, the identified two highly disordered peptides would have practical utility in protein biotechnology and industry.

Improving Test Efficiency through Prioritization Based On Testing Dependency

Na Zhang,Yangqiu Liu,Xiaoan Bao,Xiaoming Xie,Zhongtao Ren,Hui Lin 보안공학연구지원센터 2015 International Journal of u- and e- Service, Scienc Vol.8 No.6

During the various iterations of software development, test case prioritization generally schedules test cases in order to increase test efficiency as soon as possible without reducing the scale of the test. It is noted that currently, many prioritization techniques are usually based on the assumption that the test cases are independent so as to reduce testing effort. However in the actual test, the dependencies and relations exist between the test cases. In this paper, we propose a new type of prioritization technique based on the relationship of dependencies between test cases. We gather the dependency information of a test suite and then put forward a weighted depth-first search algorithm to determine the most effective order. To assess our approach, an academic feasibility study and three industrial experiments are conducted. Evaluation results indicate that our proposed method can be used to improve the fault detection effectiveness when compared with random ordering and some existed prioritization techniques which are based on function coverage.

Anti-Inflamatory Activity of Compounds from the Whole Plant of Patrinia saniculaefolia

( Ren Bo An ),( Min Kyun Na ),( Byung Sun Min ),( Hyeun Wook Chang ),( Ki Hwan Bae ) 영남대학교 약품개발연구소 2011 영남대학교 약품개발연구소 연구업적집 Vol.21 No.-

Medicinal Chemistry : Anti-complement Activity of Triterpenoids from the Whole Plant of Patrinia saniculaefolia

( Ren Bo An ),( Min Kyun Na ),( Byung Sun Min ),( Hyeong Kyu Lee ),( Ki Hwan Bae ) 영남대학교 약품개발연구소 2009 영남대학교 약품개발연구소 연구업적집 Vol.19 No.-

Evidence for the Presence of Long-Lived Plasma Cells in Nasal Polyps

Ya-Na Zhang,Jia Song,Guan-Ting Zhai,Hai Wang,Ren-Zhong Luo,Jing-Xian Li,Bo Liao,Jin Ma,Heng Wang,Xiang Lu,Da-Bo Liu,Zheng Liu 대한천식알레르기학회 2020 Allergy, Asthma & Immunology Research Vol.12 No.2

Purpose: Plasma cells and immunoglobulins (Igs) play a pivotal role in the induction and maintenance of chronic inflammation in nasal polyps. During secondary immune responses, plasma cell survival and Ig production are regulated by the local environment. The purpose of the present study was to investigate the presence of long-lived plasma cells (LLPCs) and specific survival niches for LLPCs in human nasal polyps. Methods: Nasal mucosal samples were cultured with an air-liquid interface system and the Ig levels in culture supernatants were analyzed by enzyme-linked immunosorbent assay. The characteristics of LLPCs in nasal polyps were determined by immunohistochemistry and immunofluorescence. The expression of neurotrophins as well as their receptors was detected by quantitative real-time polymerase chain reaction, immunohistochemistry, immunofluorescence, and Western blotting. Results: The numbers of CD138+ total plasma cells and BCL2+ plasma cells were increased in both eosinophilic and non-eosinophilic nasal polyps compared with those in normal tissues. The production of IgG, IgA, and IgE was detected in culture supernatants even after a 32-day culture of nasal polyps. Although the total numbers of plasma cells were decreased in nasal polyps after culture, the numbers of BCL2+ plasma cells remained stable. The expression of nerve growth factor (NGF) as well as tropomyosin receptor kinase (Trk) A, a high-affinity receptor for NGF, was upregulated in both eosinophilic and non-eosinophilic nasal polyps. In addition, BCL2+ plasma cell numbers were positively correlated with NGF and TrkA mRNA expression in nasal mucosal tissues. Polyp plasma cells had the expression of TrkA. Conclusions: Human nasal polyps harbor a population of LLPCs and NGF may be involved in their prolonged survival. LLPCs may be a novel therapeutic target for suppressing the local Ig production in nasal polyps.

Recent advances in genetic engineering tools based on synthetic biology

Jun Ren,Jingyu Lee,Dokyun Na 한국미생물학회 2020 The journal of microbiology Vol.58 No.1

Genome-scale engineering is a crucial methodology to rationally regulate microbiological system operations, leading to expected biological behaviors or enhanced bioproduct yields. Over the past decade, innovative genome modification technologies have been developed for effectively regulating and manipulating genes at the genome level. Here, we discuss the current genome-scale engineering technologies used for microbial engineering. Recently developed strategies, such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, multiplex automated genome engineering (MAGE), promoter engineering, CRISPR-based regulations, and synthetic small regulatory RNA (sRNA)-based knockdown, are considered as powerful tools for genome-scale engineering in microbiological systems. MAGE, which modifies specific nucleotides of the genome sequence, is utilized as a genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi, and CRISPRa are mainly used to regulate gene expression without modifying the genome sequence. This review introduces the recent genome-scale editing and regulating technologies and their applications in metabolic engineering.

Association of the intercellular adhesion molecule-1 gene polymorphisms with type 2 diabetes and diabetic peripheral neuropathy in a Chinese Han population

Zhanjie Ren,Na Ji,Kebao Jia,Li Wang,Harvest F. Gu,Jun Ma 한국유전학회 2015 Genes & Genomics Vol.37 No.1

Intercellular adhesion molecule-1 (ICAM-1) isan inflammation cytokine. Previous studies have demonstratedthat genetic polymorphisms in the ICAM-1 gene areassociated with chronic inflammation and diabeticnephropathy. The present study aimed to investigate theassociation of ICAM-1 gene polymorphisms with type 2diabetes (T2D) and diabetic peripheral neuropathy (DPN)in a Chinese Han population. Four valid single nucleotidepolymorphisms (SNPs) in the ICAM-1 gene were genotypedin 672 control subjects, 787 T2D patients with andwithout DPN with TaqMan allelic discrimination. Singlemarker association analyses indicated that A allele of SNPrs5498 was associated with DPN (P = 0.037, OR 1.715,95 % CI 1.027–2.865). Further analyses of clinicalparameters according to the genotypes of this polymorphismdemonstrated that T2D patients with DPN carryingAA and AG genotypes had higher risk of coronary heartdisease compared with those carrying GG genotype(30.6 % vs. 11.5 %, P = 0.040). In SNP rs1799969, thedifference of minor allele frequencies between the patientswithout and with DPN was found (0.02 vs 0.01, P = 0.014,OR 3.695, 95 % CI 1.211–11.277). SNP rs281432 hadhigher frequency of G allele in all T2D patients comparedwith control subjects (0.35 vs. 0.31, P = 0.041, OR 1.200,95 % CI 1.008–1.428). The present study provides evidencethat rs5498 (A/G E469K) polymorphism is associatedwith DPN in T2D, and also implicates that theassociation of ICAM-1 with DPN may be related to othervascular complications.