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Identification of Bio-oil Compound Utilizing Yeasts Through phenotypic microarray Screening

WASTE AND BIOMASS VALORIZATION 2020年第6期11卷 2507-2519页

作者： Kostas, Emily T. Cooper, Mick Shepherd, Benjamin J. Robinson, John P. Univ Nottingham Fac Engn Microwave Proc Engn Res Grp Nottingham NG7 5RD England UCL Adv Ctr Biochem Engn Dept Biochem Engn Bernard Katz BldgGower St London WC1H 6BT England Univ Nottingham Sch Chem Nottingham NG7 SRD England

Biomass pyrolysis bio-oil contains a plethora of carbon sources with the potential to be utilized by microorganisms and converted into high value products. However, the majority of these compounds are either highly toxic to microorganisms or are not directly utilizable. Hence research is required to develop methods of separating microbe friendly compounds from inhibitory ones, and to also identify novel microorganisms that can utilise the principal carbon sources in pyrolysis bio-oil. This study employed a phenotypic microarray (PM) technique that measured yeast metabolic output to screen for and shortlist yeast strains able to metabolize various bio-oil carbon sources, with a focus on the anhydrosugar levoglucosan. Four strains of yeast (two Pichia spp. and two Kluyveromyces spp.) were shortlisted due to their high metabolic output (between 79.7 and 113.7 redox signal intensity) on levoglucosan from the PM assay. Under anaerobic fermentation conditions the strains were able to uptake levoglucosan (between 79 and 100% uptake efficiency) but not produce bioethanol;yet trace amounts of acetic acid were generated. This study demonstrated the application of applying the PM technique to screen for novel yeast strains with abilities to metabolize compounds present in pyrolysis bio-oil that could lead to the identification of novel levoglucosan utilization pathways. [GRAPHICS] .

关键词： phenotypic microarray Yeast Pyrolysis Bio-oil compound Fermentation

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UTILIZATION OF A phenotypic microarray FOR SCREENING OF CLOSTRIDIUM BOTULINUM GROWTH-ENHANCING SUBSTRATES

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TOXICON 2021年第Sup1期190卷 S68-S68页

作者： Selby, Katja Douillard, Francois P. Lindstrom, Miia Univ Helsinki Dept Food Hyg & Environm Hlth Fac Vet Med POB 66 Helsinki 00014 Finland

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Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere

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CURRENT RESEARCH IN MICROBIAL SCIENCES 2021年 2卷 100025页

作者： Kumar, Ashwani Dubey, Anamika Malla, Muneer Ahmad Dames, Joanna Rhodes Univ Dept Biochem & Microbiol Mycorrhizal Res Lab Grahamstown South Africa Dr Harisingh Gour Univ Cent Univ Dept Bot Metagen & Secret Res Lab Sagar 470003 MP India Dr Harisingh Gour Univ Cent Univ Dept Zool Sagar 470003 MP India

Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1);Mpumalanga-West - (ASHSOIL2);and Free State-North West -(ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.

关键词： Sorghum rhizosphere 16S rRNA sequencing phenotypic microarray Community profiling

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The application of phenotypic microarray analysis to anti-fungal drug development

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JOURNAL OF MICROBIOLOGICAL METHODS 2017年 134卷 35-37页

作者： Greetham, Darren Lappin, David F. Rajendran, Ranjith O'Donnell, Lindsay Sherry, Leighann Ramage, Gordon Nile, Christopher Univ Nottingham Sch Biosci Bonington Campus Sutton Surrey England Univ Glasgow Glasgow Dent Sch Sch Med Coll MedVet & Lifen SciOral Sci Res Grp 378 Sauchiehall St Glasgow G2 3JZ Lanark Scotland

Candida albicans metabolic activity in the presence and absence of acetylcholine was measured using phenotypic microarray analysis. Acetylcholine inhibited C. albicans biofilm formation by slowing metabolism independent of biofilm forming capabilities. phenotypic microarray analysis can therefore be used for screening compound libraries for novel anti-fungal drugs and measuring antifungal resistance.(C) 2017 Elsevier B.V. All rights reserved.

关键词： phenotypic microarray Acetylcholine Candida albicans Metabolism Anti-fungal Resistance

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Evaluation of different lignocellulosic biomass pretreatments by phenotypic microarray-based metabolic analysis of fermenting yeast

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BIOFUEL RESEARCH JOURNAL-BRJ 2016年第1期3卷 357-365页

作者： Wilkinson, Stuart Greetham, Darren Tucker, Gregory A. Univ Nottingham Div Food Sci Brewing Sci Sect Sutton Bonington Campus Loughborough LE12 5RD Leics England

Advanced generation biofuel production from lignocellulosic material (LCM) was investigated. A range of different thermochemical pre-treatments were evaluated with different LCM. The pre-treatments included;alkaline (5% NaOH at 50 degrees C), acid (1% H2SO4 at 121 degrees C) and autohydrolytical methods (200 degrees C aqueous based hydrothermal) and were evaluated using samples of miscanthus, wheat-straw and willow. The liberation of sugars, presence of inhibitory compounds, and the degree of enhancement of enzymatic saccharification was accessed. The suitability of the pre-treatment generated hydrolysates (as bioethanol feedstocks for Saccharomyces cerevisiae) was also accessed using a phenotypic microarray that measured yeast metabolic output. The use of the alkaline pre-treatment liberated more glucose and arabinose into both the pre-treatment generated hydrolysate and also the hydrolysate produced after enzymatic hydrolysis (when compared with other pretreatments). However, hydrolysates derived from use of alkaline pre-treatments were shown to be unsuitable as a fermentation medium due to issues with colloidal stability (high viscosity). Use of acid or autohydrolytical pre-treatments liberated high concentrations of monosaccharides regardless of the LCM used and the hydrolysates had good fermentation performance with measurable yeast metabolic output. Acid pre-treated wheat straw hydrolysates were then used as a model system for larger scale fermentations to confirm both the results of the phenotypic microarray and its validity as an effective high-throughput screening tool. (C) 2016 BRTeam. All rights reserved.

关键词： Lignocellulosic ethanol Pre-treatment Yeast Metabolic output phenotypic microarray

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Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine

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G3-GENES GENOMES GENETICS 2024年第4期14卷 jkae002页

作者： Remines, Mckayla Schoonover, Makailyn G. Knox, Zoey Kenwright, Kailee Hoffert, Kellyn M. Coric, Amila Mead, James Ampfer, Joseph Seye, Serigne Strome, Erin D. Northern Kentucky Univ Dept Biol Sci Highland Hts KY 41099 USA

The SAM1 and SAM2 genes encode for S-Adenosylmethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1 Delta/sam1 Delta, and sam2 Delta/sam2 Delta strains in 15 different phenotypic microarray plates with different components and measured growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. We explored how the phenotypic growth differences are linked to the altered gene expression, and hypothesize mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact pathways and processes. We present 6 stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role in production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.

关键词： S-Adenosylmethionine SAM1 SAM2 methyl cycle phenotypic microarray dNTPs glutathione arginine metabolism tamoxifen fluconazole ergosterol biosynthesis cisplatin

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Elucidating the role of c-di-AMP in Mycobacterium smegmatis: phenotypic characterization and functional analysis

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HELIYON 2023年第5期9卷

作者： Chaudhary, Vikas Pal, Aditya Kumar Singla, Mamta Ghosh, Anirban Indian Inst Sci Mol Biophys Unit Bangalore 560012 India

Cyclic-di-AMP (c-di-AMP) is an important secondary messenger molecule that plays a critical role in monitoring several important cellular processes, especially in several Gram-positive bacteria. In this study, we seek to unravel the physiological significance of the molecule c-di-AMP in Mycobacterium smegmatis under different conditions, using strains with altered c-di-AMP levels: cdi-AMP null mutant (& UDelta;disA) and a c-di-AMP over-expression mutant (& UDelta;pde). Our thorough analysis of the mutants revealed that the intracellular concentration of c-di-AMP could determine many basic phenotypes such as colony architecture, cell shape, cell size, membrane permeability etc. Additionally, it was shown to play a significant role in multiple stress adaptation pathways in the case of different DNA and membrane stresses. Our study also revealed how the biofilm phenotypes of M. smegmatis cells are altered with high intracellular c-di-AMP concentration. Next, we checked how c-di-AMP contributes to antibiotic resistance or susceptibility characteristics of M. smegmatis, which was followed by a detailed transcriptome profile analysis to reveal key genes and pathways such as translation, arginine biosynthesis, cell wall and plasma membrane are regulated by c-di-AMP in mycobacteria.

关键词： Mycobacterium smegmatis Second messenger c-di-AMP Stress response Antibiotics phenotypic microarray RNA-Seq

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Analysis of glycogen metabolic pathway utilization by dendritic cells and T cells using custom phenotype metabolic assays

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JOURNAL OF IMMUNOLOGICAL METHODS 2018年 458卷 53-57页

作者： Thwe, Phyu M. Amiel, Eyal Univ Vermont Dept Med Lab & Radiat Sci Burlington VT 05405 USA

In the field of immunology, there is an increasing interest in cellular energy metabolism and its outcome on immune cell effector function. Activation of immune cells leads to rapid metabolic changes that are central to cellular biology in order to support the effector responses. Therefore, the need for user-friendly and dependable assay technologies to address metabolic regulation and nutrient utilization in immune cells is an important need in this field. Redox-dye reduction-based Phenotype microarray (PM) assays, which measure NADH reduction as a readout, developed by Biolog Inc., provide a wide screening of metabolites both in bacteria and mammalian cells. In this study, we delineate a detailed protocol of a customized Biolog assay for investigation of a specific metabolic pathway of interest. The option to be able to easily customize this technology offers researchers with a convenient assay platform to methodically examine specific nutrient substrates or metabolic pathways of interest in a rapid and cost effective manner.

关键词： Metabolism Dendritic cells Biolog phenotypic microarray Glucose Glycogen

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Multi-level evaluation of Escherichia coli polyphosphate related mutants using global transcriptomic, proteomic and phenomic analyses

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BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 2017年第4期1861卷 871-883页

作者： Varas, Macarena Valdivieso, Camilo Mauriaca, Cecilia Ortiz-Severin, Javiera Paradela, Alberto Poblete-Castro, Ignacio Cabrera, Ricardo Chavez, Francisco P. Univ Chile Fac Sci Dept Biol Syst Microbiol Lab Santiago Chile Univ Chile Fac Sci Dept Ecol Santiago Chile CNB CSIC Prote Serv Madrid Spain Univ Andres Bello Biosyst Engn Lab Ctr Bioinformat & Integrat Biol Fac Ciencias Biol Santiago Chile Univ Chile Fac Sci Dept Biol Santiago Chile

Background: Polyphosphate (polyP) is a linear biopolymer found in all living cells. In bacteria, mutants lacking polyphosphate kinase 1 (PPK1), the enzyme responsible for synthesis of most polyP, have many structural and functional defects. However, little is known about the causes of these pleiotropic alterations. The link between ppkl deletion and those numerous phenotypes observed can be the result of complex molecular interactions that can be elucidated via a systems biology approach. Methods: By integrating different omics levels (transcriptome, proteome and phenome), we described the functioning of various metabolic pathways among Escherichia coli polyphosphate mutant strains (Delta ppk1, Delta ppx, and Delta polyP). Bioinformatic analyses reveal the complex metabolic and regulatory bases of the phenotypes unique to polyp mutants. Results: Our results suggest that during polyP deficiency (Delta ppk1 mutant), metabolic pathways needed for energy supply are up-regulated, including fermentation, aerobic and anaerobic respiration. Transcriptomic and q-proteomic contrasting changes between Delta ppk1 and Delta ppx mutant strains were observed in those central metabolic pathways and confirmed by using phenotypic microarrays. In addition, our results suggest a regulatory connection between polyp, second messenger metabolism, alternative Sigma/Anti-Sigma factors and type-II toxin-antitoxin (TA) systems. Conclusions: We suggest a broader role for polyp via regulation of ATP-dependent proteolysis of type II toxin-antitoxin system and alternative Sigma/Anti-Sigma factors, that could explain the multiple structural and functional deficiencies described due to alteration of polyp metabolism. General significance: Understanding the interplay of polyp in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Systems Biology Q-proteomics phenotypic microarray Polyphosphate Omics Polyp-dependent proteolysis

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Light-Phyllosphere Interactions in Greenhouse Grown Ornamentals

Light-Phyllosphere Interactions in Greenhouse Grown Ornament...

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作者： Samareh Gharaie

学位级别：博士

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