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Benchmarking two Saccharomyces cerevisiae laboratory strains for growth and transcriptional response to methanol

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Synthetic and Systems Biotechnology 2019年第4期4卷 180-188页

作者： Monica I.Espinosa Thomas C.Williams Isak S.Pretorius Ian T.Paulsen ARC Centre of Excellence in Synthetic biology Department of Molecular SciencesMacquarie UniversityNSWAustralia CSIRO Synthetic biology Future Science platform CanberraACT2601Australia

One-carbon compounds,such as methanol,are becoming potential alternatives to sugars as feedstocks for the biological production of chemicals,fuels,foods,and *** biological production often requires extensive genetic manipulation of a microbial host strain,making well-characterised and geneticallytractable model organisms like the yeast Saccharomyces cerevisiae attractive targets for the engineering of methylotrophic *** strains S288C and *** are the two best-characterised and most widely used hosts for yeast synthetic biology and metabolic engineering,yet they have unpredictable metabolic phenotypes related to their many genomic *** therefore sought to benchmark these two strains as potential hosts for engineered methylotrophic metabolism by comparing their growth and transcriptomic responses to *** had improved growth in the presence of methanol relative to the S288C derivative *** *** transcriptome also had a specific and relevant response to methanol that was either absent or less pronounced in the BY4741 *** response included up-regulation of genes associated with mitochondrial and peroxisomal metabolism,alcohol and formate dehydrogenation,glutathione metabolism,and the global transcriptional regulator of metabolism ***-expression of MIG3 enabled improved growth in the presence of methanol,suggesting that MIG3 is a mediator of the superior *** strain *** was therefore identified as a superior strain for the future development of synthetic methylotrophy in ***.

关键词： Yeast Methylotrophy Synthetic biology Metabolic engineering MIG3 Methanol

Heme oxygenase-1 and gut ischemia/reperfusion injury: A short review

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World Journal of Gastroenterology 2013年第23期19卷 3555-3561页

作者： Yu-Feng Liao Wei Zhu Dong-Pei Li Xiao Zhu Department of Laboratory Medicine Ningbo No.2 Hospital molecular Pathology platform Key Laboratory of Molecular Diagnosis Guangdong Medical College Institute of molecular Medicine and Genetics Georgia Health Sciences University

Ischemia/reperfusion (I/R) injury of the gut is a significant problem in a variety of clinical settings and is associated with a high morbidity and mortality. Although the mechanisms involved in the pathogenesis of gut I/R injury have not been fully elucidated, it is generally believed that oxidative stress with subsequent inflammatory injury plays an important role. Heme oxygenase (HO) is the rate-limiting enzyme in the catabolism of heme, followed by production of CO, biliverdin, and free iron. The HO system is believed to confer cytoprotection by inhibiting inflammation, oxidation, and apoptosis, and maintaining microcirculation. HO-1, an inducible form of HO, serves a vital metabolic function as the rate-limiting step in the heme degradation pathway, and affords protection in models of intestinal I/R injury. HO-1 system is an important player in intestinal I/R injury condition, and may offer new targets for the management of this condition.

关键词： Heme oxygenase Ischemia/reperfusion injury Oxidative stress Cytoprotection Gut

Structural Flexibility Enables Alternative Maturation, ARGONAUTE Sorting and Activities of miR168, a Global Gene Silencing Regulator in Plants

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molecular Plant 2018年第8期11卷 1008-1023页

作者： Taichiro Iki Antoine Cléry Nicolas G. Bologna Alexis Sarazin Christopher A. Brosnan Nathan Pumplin Frédéric H.T. Allain Olivier Voinnet Department of biology Swiss Federal Institute of Technology (ETH) Universit&tstrasse 2 ZUrich 8092 Switzerland Institute of molecular biology and Biophysics Department of Biology Swiss Federal Institute of Technology (ETH) Zürich Switzerland Biomolecular NMR spectroscopy platform ETH Zürich Switzerland Present address: Laboratory of Germline biology Graduate School of Frontier Biosciences Osaka University 1-3 Yamadaoka Suita Osaka Japan

In eukaryotes, the RNase-Ⅲ Dicer often produces length/sequence microRNA （miRNA） variants, called ＂isomiRs＂, owing to intrinsic structural/sequence determinants of the miRNA precursors （pre-miRNAs）. In this study, we combined biophysics, genetics and biochemistry approaches to study Arabidopsis miR168, the key feedback regulator of central plant silencing effector protein ARGONAUTE1 （AGO1）. We identified a motif conserved among plant premiR168 orthologs, which enables flexible internal basepairing underlying at least three metastable structural configurations. These configurations promote alternative, accurate Dicer cleavage events generating length and structural isomiR168 variants with distinctive AGO sorting properties and modes of action. Among these isomiR168s, a duplex with a 22-nt guide strand exhibits strikingly preferential affinity for AGO10, the closest AGO1 paralog. The 22-nt miR168-AGO10 complex antagonizes AGO1 accumulation in part via ＂transitive RNAi＂, a silencing-amplification process, to maintain appropriate AGO1 cellular homeostasis. Furthermore, we found that the tombusviral P19 silencing-suppressor protein displays markedly weaker affinity for the 22-nt form among its isomiR168 cargoes, thereby promoting AGO10-directed suppression of AGOl-mediated antiviral silencing. Taken together, these findings indicate that structural flexibility, a previously overlooked property of premiRNAs, considerably increases the versatility and regulatory potential of individual MIRNA genes, and that some pathogens might have evolved the capacity or mechanisms to usurp this property.

关键词： microRNA miR168 Dicer ARGONAUTE tombusvirus P19

Characterization and analysis of petrochemical wastewater through particle size distribution, biodegradability, and chemical composition

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Chinese Journal of Chemical Engineering 2019年第2期27卷 444-451页

作者： Xiaoqiang Jia Dayao Jin Chen Li Wenyu Lu Department of Biochemical Engineering School of Chemical Engineering and Technology Tianjin University Key Laboratory of Systems Bioengineering Tianjin University Synthetic biology platform Collaborative Innovation Center of Chemical Science and Engineering(Tianjin)

The centralized treatment method is a widely used form of wastewater treatment that tends to be less effective at removing toxic substances. Therefore, a detailed analysis of the composition of wastewater can provide important information for the design of an effective wastewater treatment process. The objective of this paper was to investigate particle size distribution(PSD), biodegradability, and the chemical composition of the petrochemical wastewater discharges. For this purpose, this project selected the petrochemical wastewater and treated wastewater of China National Offshore Oil Corporation Zhongjie Petrochemical Co, Ltd. as the analysis *** step-by-step filtration method, along with a molecular weight classification method, was selected to build the chemical oxygen demand(COD) and biochemical oxygen demand(BOD) fingerprints of petrochemical wastewater and treated wastewater. The results showed that the main pollutants were settleable particles in petrochemical wastewater, which contributed to over 54.85% of the total COD. The colloidal particles with particle sizes in the range of 450–1000 nm had the highest COD value in the treated wastewater, which contributed34.17% of the total COD of treated wastewater. The results of the BOD analysis showed that the soluble fractions were the main reason that treated wastewaters did not meet the treatment standards. Tests on the organic compounds in petrochemical wastewater found that there were mainly linear paraffins, branched paraffins, benzene series compounds, and some plasticizers in the influent of the petrochemical wastewater. The most abundant pollutants in treated petrochemical wastewater were the adjacent diisobutyl phthalate and the linear *** transform infrared(FTIR) transmission spectroscopy analysis showed that the settleable particles of petrochemical wastewater and membrane bioreactor(MBR)-treated wastewater contained multiple types of organic substances. The results also indicated

关键词： Petrochemical wastewater Gradient membrane separation Chemical oxygen demand Biochemical oxygen demand

Rational design and biomedical applications of DNA-functionalized upconversion nanoparticles

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Chinese Chemical Letters 2018年第9期29卷 1321-1332页

作者： Xinwen Liu Meng Liu Jiajia Chen Zhihao Li Quan Yuan Key laboratory of Analytical Chemistry for biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University

Lanthanide-doped upconversion nanoparticles （UCNPs） offer unique advantages in term of low autofluorescence, high signal-to-noise ratio and deep tissue penetration, and have attracted considerable attention in biomedical applications. DNA, beyond the properties of self-assembly, also exhibits multiple functions such as molecular recognition, drug loading capacity and therapeutic effect. In this regard, the combination of UCNPs and DNA offers a promising and powerful platform for potential applications in biosensing, bioimaging and disease therapy. In this review, we mainly introduce recent progresses of DNA-functionalized upconversion materials, providing an overview of the design and applications in biosensing, bioimaging and therapy. The challenges and future perspectives are also discussed, aiming to promote their applications in material science and biomedicine.

关键词： Lanthanide-doped upconversion nanoparticles DNA Biosensor Bioimaging Disease therapy

Alpha-fetoprotein-targeted reporter gene expression imaging in hepatocellular carcinoma

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World Journal of Gastroenterology 2016年第27期22卷 6127-6134页

作者： Kwang Il Kim Hye Kyung Chung Ju Hui Park Yong Jin Lee Joo Hyun Kang molecular Imaging Research Center Korea Institute of Radiological and Medical Sciences Korea Drug Development platform using Radio-Isotope Korea Institute of Radiological and Medical Sciences

Hepatocellular carcinoma (HCC) is one of the most common cancers in Eastern Asia, and its incidence is increasing globally. Numerous experimental models have been developed to better our understanding of the pathogenic mechanism of HCC and to evaluate novel therapeutic approaches. molecular imaging is a convenient and up-to-date biomedical tool that enables the visualization, characterization and quantification of biologic processes in a living subject. molecular imaging based on reporter gene expression, in particular, can elucidate tumor-specific events or processes by acquiring images of a reporter gene’s expression driven by tumor-specific enhancers/promoters. In this review, we discuss the advantages and disadvantages of various experimental HCC mouse models and we present in vivo images of tumor-specific reporter gene expression driven by an alpha-fetoprotein (AFP) enhancer/promoter system in a mouse model of HCC. The current mouse models of HCC development are established by xenograft, carcinogen induction and genetic engineering, representing the spectrum of tumor-inducing factors and tumor locations. The imaging analysis approach of reporter genes driven by AFP enhancer/promoter is presented for these different HCC mouse models. Such molecular imaging can provide longitudinal information about carcinogenesis and tumor progression. We expect that clinical application of AFP-targeted reporter gene expression imaging systems will be useful for the detection of AFP-expressing HCC tumors and screening of increased/decreased AFP levels due to disease or drug treatment.

关键词： Alpha-fetoprotein Hepatocellular carcinoma molecular imaging Reporter gene Tumor-specific enhancer/promoter

The updated weeping forsythia genome reveals the genomic basis for the evolution and the forsythin and forsythoside A biosynthesis

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Horticultural Plant Journal 2023年第6期9卷 1149-1161页

作者： Yong Li Fan Wang Nancai Pei Qian Li Hongli Liu Wangjun Yuan Hechen Zhang Innovation platform of molecular biology College of Landscape and ArtHenan Agricultural UniversityZhengzhou 450002China Research Institute of Tropical Forestry Chinese Academy of ForestryGuangzhou 510520China School of Pharmacy Henan UniversityKaifengHenan 475000China Horticultural Research Institute Henan Academy of Agricultural SciencesZhengzhou 450002China

Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of ***,the species still lacks a chromosome-level *** this study,the former draft genome (Accession ***00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome *** forsythia underwent a and b whole-genome duplication *** the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant *** enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and *** contracted genes suggested that the resistance of weeping forsythia to cold and drought was *** last glacial period led to a significant decline in the effective population size of weeping ***-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic *** this study,we improved the previous draft genome of weeping *** genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.

关键词： Forsythia suspensa Chromosome-level genome Comparative genomics Forsythoside A Forsythin Whole-genome duplication

n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil

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Chinese Journal of Chemical Engineering 2019年第2期27卷 411-417页

作者： Xiaoqiang Jia Yun He Lei Huang Dawei Jiang Wenyu Lu Department of Biochemical Engineering School of Chemical Engineering and Technology Tianjin University Key Laboratory of Systems Bioengineering (Tianjin University) Ministry of Education Synthetic biology platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)

The high-molecular weight polycyclic aromatic hydrocarbons(PAHs) pyrene and typical long chain alkane nhexadecane are both difficult to degrade. In this study, n-hexadecane and pyrene degrading strain Rhodococcus sp. T1 was isolated from oil contaminated soil. Strain T1 could remove 90.81% n-hexadecane(2 vol%) and 42.79% pyrene(200 mg·L^(-1)) as a single carbon within 5 days, respectively. Comparatively, the degradation of pyrene increased to 60.63%, but the degradation of n-hexadecane decreased to 87.55% when these compounds were mixed. Additionally, identification and analysis of degradation metabolites of Rhodococcus sp. T1 in the above experiments showed that there were significant changes in alanine, methylamine, citric acid and heptadecanoic acid between sole and dual substrate degradation. The optimal conditions for degradation were then determined based on analysis of the pH, salinity, additional nutrient sources and liquid surface *** the optimal conditions of pH 7.0, 35 °C, 0.5% NaCl, 5 mg·L^(-1) of yeast extract and 90 mg·L^(-1) of surfactant,the degradation increased in single or dual carbon sources. To our knowledge, this is the first study to discuss metabolite changes in Rhodococcus sp. T1 using sole substrate and dual substrate to enhance the long-chain alkanes and PAHs degradation potential.

关键词： Biodegradation Metabolite n-Hexadecane Pyrene Rhodococcus sp. T1

Ultra-highly diluted plant extracts of Hydrastis canadensis and Marsdenia condurango induce epigenetic modifications and alter gene expression profiles in HeLa cells in vitro

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Journal of Integrative Medicine 2015年第6期13卷 400-411页

作者： Santu Kumar Saha Sourav Roy Anisur Rahman Khud a-Bukhsh Cytogenetics and molecular biology Laboratory Department of ZoologyUniversity of Kalyani Department of Entomology and Institute for Integrative Genome biology University of California Riverside

OBJECTIVE： Methylation-specific epigenetic process and gene expression profiles of HeLa cells treated with ultra-high dilutions （HDs） of two plant extracts, Hydrastis canadensis （HC-30） and Marsdenia condurango （Condu-30）, diluted 106o times, were analyzed against placebo 30C （PI-30） for alterations in gene profiles linked to epigenetic modifications. METHODS： Separate groups of cells were subjected to treatment of Condu-30, HC-30, and PI- 30 prepared by serial dilutions and succussions. Global microarray data recorded on Affymetrix platform, using 25-mer probes were provided by iLifeDiscoveries, India. Slides were scanned with 3000 7G microarray scanner and raw data sets were extracted from Cel （raw intensity） files. Analyses of global microarray data profile, differential gene expression, fold change and clusters were made using GeneSpring GX12.5 software and standard normalization procedure. Before microarray study, concentration of RNA （ng/IJL）, RIN value and rRNA ratio for all the samples were analysed by Agilant Bioanalyzer 2100. Reverse transcriptase polymerase chain reaction （RT-PCR） and quantitative RT- PCR were done for analyzing SMAD-4 expression. Fluorescence-activated cell sorting study was further made to elucidate fate of cells at divisional stages. Methylation-specific restriction enzyme assay was conducted for ascertaining methylation status of DNA at specific sites. RESULTS： HDs of HC-30 and Condu-30 differentially altered methylation in specific regions of DNA and expression profiles of certain genes linked to carcinogenesis, as compared to PI-30. Two separate cut sites were found in genomic DNA of untreated and placebo-treated HeLa cells when digested with McrBC, compared to a single cut observed in Condu-30-treated genomic DNA. SMAD-4 gene expression validated the expression pattern observed in microarray profile. Methylation-specific restriction enzyme assay elucidated differential epigenetic modifications in drug-treated and control cells. CON

关键词： plant extracts homeopathy reactive oxygen species apoptosis gene expression epigenesis,genetic Smad4 protein