Characterization of Pseudomonas putida genes responsive to nutrient limitation

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1661-1669 ◽  
Author(s):  
Chris K. C. Syn ◽  
Jon K. Magnuson ◽  
Mark T. Kingsley ◽  
Sanjay Swarup
Keyword(s):  
Pseudomonas Putida ◽  
Expression Profiles ◽  
The Novel ◽  
Low Carbon ◽  
Soil Environment ◽  
Quinone Oxidoreductase ◽  
Highly Active ◽  
Phosphate Nitrate ◽  
Absolute Expression ◽  
Nutrient Conditions

The low bioavailability of nutrients and oxygen in the soil environment has hampered successful expression of biodegradation and biocontrol genes that are driven by promoters highly active during routine laboratory conditions of high availability of nutrients and oxygen. Hence, in the present study, expression of the gus-tagged genes in 12 Tn5-gus mutants of the soil microbe Pseudomonas putida PNL-MK25 were examined under various conditions chosen to mimic the soil environment: low carbon, phosphate, nitrate or oxygen, and in the rhizosphere. Based on their expression profiles, three nutrient-responsive mutant (NRM) strains, NRM5, NRM7 and NRM17, were selected for identification of the tagged genes. In strain NRM5, expression of the glutamate dehydrogenase (gdhA) gene was increased 4·9–26·4-fold under various low-nutrient conditions. In NRM7, expression of the novel NADPH : quinone oxidoreductase-like (nql) gene was consistently amongst the highest and was synergistically upregulated by low-nutrient and anoxic conditions. The cyoD gene in NRM17, which encodes the fourth subunit of the cytochrome o ubiquinol oxidase complex, had decreased expression in low-nutrient conditions but its absolute expression level was still amongst the highest. Additionally, it was independent of oxygen availability, in contrast to that in Escherichia coli.

scholarly journals The characteristics of circRNA as competing endogenous RNA in pathogenesis of acute myeloid leukemia

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Siyuan Zhang
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
The Novel ◽  
Competing Endogenous Rna ◽  
Regulatory Modules ◽  
Cerna Network ◽  
Regulatory Module ◽  
Acute Myeloid

Abstract Background As one of the novel molecules, circRNA has been identified closely involved in the pathogenesis of many diseases. However, the function of circRNA in acute myeloid leukemia (AML) still remains unknown. Methods In the current study, the RNA expression profiles were obtained from Gene Expression Omnibus (GEO) datasets. The differentially expressed RNAs were identified using R software and the competing endogenous RNA (ceRNA) network was constructed using Cytoscape. Functional and pathway enrichment analyses were performed to identify the candidate circRNA-mediated aberrant signaling pathways. The hub genes were identified by MCODE and CytoHubba plugins of Cytoscape, and then a subnetwork regulatory module was established. Results A total of 27 circRNA-miRNA pairs and 208 miRNA-mRNA pairs, including 12 circRNAs, 24 miRNAs and 112 mRNAs were included in the ceRNA network. Subsequently, a subnetwork, including 4 circRNAs, 5 miRNAs and 6 mRNAs, was established based on related circRNA-miRNA-mRNA regulatory modules. Conclusions In summary, this work analyzes the characteristics of circRNA as competing endogenous RNA in AML pathogenesis, which would provide hints for developing novel prognostic, diagnostic and therapeutic strategy for AML.

scholarly journals Transcriptome Dynamics of Pseudomonas putida KT2440 under Water Stress

2011 ◽  
Vol 78 (3) ◽  
pp. 676-683 ◽  
Author(s):  
Gamze Gülez ◽  
Arnaud Dechesne ◽  
Christopher T. Workman ◽  
Barth F. Smets
Keyword(s):  
Gene Expression ◽  
Pseudomonas Putida ◽  
Unsaturated Soils ◽  
Water Deprivation ◽  
Expression Profiles ◽  
Liquid Films ◽  
Thin Liquid Films ◽  
Surface Model ◽  
Matric Potential ◽  
Peg 8000

ABSTRACTWater deprivation can be a major stressor to microbial life in surface and subsurface soil. In unsaturated soils, the matric potential (Ψm) is often the main component of the water potential, which measures the thermodynamic availability of water. A low matric potential usually translates into water forming thin liquid films in the soil pores. Little is known of how bacteria respond to such conditions, where, in addition to facing water deprivation that might impair their metabolism, they have to adapt their dispersal strategy as swimming motility may be compromised. Using the pressurized porous surface model (PPSM), which allows creation of thin liquid films by controlling Ψm, we examined the transcriptome dynamics ofPseudomonas putidaKT2440. We identified the differentially expressed genes in cells exposed to a mild matric stress (−0.4 MPa) for 4, 24, or 72 h. The major response was detected at 4 h before gradually disappearing. Upregulation of alginate genes was notable in this early response. Flagellar genes were not downregulated, and the microarray data even suggested increasing expression as the stress prolonged. Moreover, we tested the effect of polyethylene glycol 8000 (PEG 8000), a nonpermeating solute often used to simulate Ψm, on the gene expression profile and detected a different profile than that observed by directly imposing Ψm. This study is the first transcriptome profiling of KT2440 under directly controlled Ψmand also the first to show the difference in gene expression profiles between a PEG 8000-simulated and a directly controlled Ψm.

scholarly journals Activity of the Novel Extended-spectrum β-Lactamase Inhibitor AAI101 in Combination with Cefepime Towards a Challenge Panel of Acinetobacter baumannii

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S366-S367 ◽  
Author(s):  
Ian Morrissey ◽  
Sophie Magnet ◽  
Stephen Hawser ◽  
Stuart Shapiro ◽  
Harald Seifert ◽  
...  
Keyword(s):  
Combination Therapy ◽  
Clinical Isolates ◽  
The Novel ◽  
Phase 2 ◽  
Broth Microdilution ◽  
Highly Active ◽  
Southern Us ◽  
Extended Spectrum ◽  
Broad Array ◽  
Lactamase Inhibitor

Abstract Background AAI101 is a novel extended-spectrum β-lactamase inhibitor (BLI), active against ESBLs and a broad array of other BLs. AAI101 in combination with cefepime (FEP) is in Phase 2 development. Infections caused by A. baumannii, a pathogen endemic to the southern US and other global regions, are very challenging to treat, and often require combination therapy. This study examined the activity of FEP/AAI101 against a challenge set of A. baumannii clinical isolates enriched with OXA carbapenemase producers. Methods BLs in A. baumannii were identified by genotyping. Broth microdilution MICs and susceptibilities were obtained following CLSI methods and breakpoints (BPs), except for ceftazidime-avibactam (CAZ/AVI) where FDA P. aeruginosa BPs were used. CLSI FEP BPs were used for FEP/AAI101. Results All OXA-51 producers had the ISAba1 promoter. MIC90 data and % susceptibilities (%S) for FEP/AAI101 and comparators are shown in the Table: FEP/AAI101 was highly active against meropenem-susceptible (MPMs) isolates. FEP/AAI101 (AAI101 fixed at 8 µg/ml) covered 67% of OXA-51 and 53% of OXA-58 strains. Lower susceptibilities were obtained for OXA-23 and OXA-24/40 producers. FEP/AAI101 was the most active β-lactam product. Colistin (COL) was the only agent with consistently high activity against all A. baumannii isolates. Conclusion FEP/AAI101 was the most potent β-lactam product tested against clinical isolates of A. baumannii producing OXA-51 and OXA-58 β-lactamases. Infections by this difficult pathogen often require combination therapy, of which FEP-AAI101 may be a component. Disclosures S. Shapiro, Allecra: Employee, Salary

scholarly journals Effect of the Novel Antifungal Drug F901318 (Olorofim) on Growth and Viability ofAspergillus fumigatus

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Saskia du Pré ◽  
Nicola Beckmann ◽  
Mariana Cruz Almeida ◽  
Graham E. M. Sibley ◽  
Derek Law ◽  
...  
Keyword(s):  
Prolonged Exposure ◽  
De Novo ◽  
Hyphal Growth ◽  
Cell Lysis ◽  
Antifungal Drug ◽  
The Novel ◽  
Content Type ◽  
New Class ◽  
Highly Active ◽  
Germination And Growth

ABSTRACTF901318 (olorofim) is a novel antifungal drug that is highly active againstAspergillusspecies. Belonging to a new class of antifungals called the orotomides, F901318 targets dihydroorotate dehydrogenase (DHODH) in thede novopyrimidine biosynthesis pathway. In this study, the antifungal effects of F901318 againstAspergillus fumigatuswere investigated. Live cell imaging revealed that, at a concentration of 0.1 μg/ml, F901318 completely inhibited germination, but conidia continued to expand by isotropic growth for >120 h. When this low F901318 concentration was applied to germlings or vegetative hyphae, their elongation was completely inhibited within 10 h. Staining with the fluorescent viability dye bis-(1,3-dibutylbarbituric acid) trimethine oxonol (DiBAC) showed that prolonged exposure to F901318 (>24 h) led to vegetative hyphal swelling and a decrease in hyphal viability through cell lysis. The time-dependent killing of F901318 was further confirmed by measuring the fungal biomass and growth rate in liquid culture. The ability of hyphal growth to recover in drug-free medium after 24 h of exposure to F901318 was strongly impaired compared to that of the untreated control. A longer treatment of 48 h further improved the antifungal effect of F901318. Together, the results of this study indicate that F901318 initially has a fungistatic effect onAspergillusisolates by inhibiting germination and growth, but prolonged exposure is fungicidal through hyphal swelling followed by cell lysis.

scholarly journals Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L.

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lian Chee Foong ◽  
Jian Yi Chai ◽  
Anthony Siong Hock Ho ◽  
Brandon Pei Hui Yeo ◽  
Yang Mooi Lim ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Early Stage ◽  
Expression Profiles ◽  
Bioactive Compound ◽  
Anticancer Activities ◽  
Quinone Oxidoreductase ◽  
Impatiens Balsamina ◽  
Genes Expression ◽  
Pcr Method

Abstract Impatiens balsamina L. is a tropical ornamental and traditional medicinal herb rich in natural compounds, especially 2-methoxy-1,4-naphthoquinone (MNQ) which is a bioactive compound with tested anticancer activities. Characterization of key genes involved in the shikimate and 1,4-dihydroxy-2-naphthoate (DHNA) pathways responsible for MNQ biosynthesis and their expression profiles in I. balsamina will facilitate adoption of genetic/metabolic engineering or synthetic biology approaches to further increase production for pre-commercialization. In this study, HPLC analysis showed that MNQ was present in significantly higher quantities in the capsule pericarps throughout three developmental stages (early-, mature- and postbreaker stages) whilst its immediate precursor, 2-hydroxy-1,4-naphthoquinone (lawsone) was mainly detected in mature leaves. Transcriptomes of I. balsamina derived from leaf, flower, and three capsule developmental stages were generated, totalling 59.643 Gb of raw reads that were assembled into 94,659 unigenes (595,828 transcripts). A total of 73.96% of unigenes were functionally annotated against seven public databases and 50,786 differentially expressed genes (DEGs) were identified. Expression profiles of 20 selected genes from four major secondary metabolism pathways were studied and validated using qRT-PCR method. Majority of the DHNA pathway genes were found to be significantly upregulated in early stage capsule compared to flower and leaf, suggesting tissue-specific synthesis of MNQ. Correlation analysis identified 11 candidate unigenes related to three enzymes (NADH-quinone oxidoreductase, UDP-glycosyltransferases and S-adenosylmethionine-dependent O-methyltransferase) important in the final steps of MNQ biosynthesis based on genes expression profiles consistent with MNQ content. This study provides the first molecular insight into the dynamics of MNQ biosynthesis and accumulation across different tissues of I. balsamina and serves as a valuable resource to facilitate further manipulation to increase production of MNQ.

scholarly journals Effects of Temperature and Nutrient Conditions on Biofilm Formation of Pseudomonas putida

2012 ◽  
Vol 18 (6) ◽  
pp. 879-883 ◽  
Author(s):  
Kazuya MORIMATSU ◽  
Kodai EGUCHI ◽  
Daisuke HAMANAKA ◽  
Fumihiko TANAKA ◽  
Toshitaka UCHINO
Keyword(s):  
Pseudomonas Putida ◽  
Biofilm Formation ◽  
Effects Of Temperature ◽  
Nutrient Conditions

Magnetic NiO nanoparticles confined within open ends MWCNTs: a novel and highly active catalyst for hydrogenation and synthesis of imines

RSC Advances ◽  
2016 ◽  
Vol 6 (63) ◽  
pp. 58805-58812 ◽  
Author(s):  
Gangquan Chen ◽  
Wenbin Gao ◽  
Xuejun Wang ◽  
Hongfei Huo ◽  
Wenzhu Li ◽  
...  
Keyword(s):  
Active Catalyst ◽  
The Novel ◽  
Nio Nanoparticles ◽  
Highly Active ◽  
Novel Catalyst

The novel catalyst is highly active for hydrogenation and synthesis of imines.

Entrainment of the master circadian clock by scheduled feeding

2004 ◽  
Vol 287 (3) ◽  
pp. R551-R555 ◽  
Author(s):  
Marina R. Castillo ◽  
Kelly J. Hochstetler ◽  
Ronald J. Tavernier ◽  
Dana M. Greene ◽  
Abel Bult-Ito
Keyword(s):  
Circadian Clock ◽  
Wheel Running ◽  
Expression Profiles ◽  
The Novel ◽  
Suprachiasmatic Nuclei ◽  
Behavioral Rhythms ◽  
Entrainment Process ◽  
Protein Expression Profiles ◽  
Access To Food ◽  
Constant Dark

The master circadian clock, located in the mammalian suprachiasmatic nuclei (SCN), generates and coordinates circadian rhythmicity, i.e., internal organization of physiological and behavioral rhythms that cycle with a near 24-h period. Light is the most powerful synchronizer of the SCN. Although other nonphotic cues also have the potential to influence the circadian clock, their effects can be masked by photic cues. The purpose of this study was to investigate the ability of scheduled feeding to entrain the SCN in the absence of photic cues in four lines of house mouse ( Mus domesticus). Mice were initially housed in 12:12-h light/dark cycle with ad libitum access to food for 6 h during the light period followed by 4–6 mo of constant dark under the same feeding schedule. Wheel running behavior suggested and circadian PER2 protein expression profiles in the SCN confirmed entrainment of the master circadian clock to the onset of food availability in 100% (49/49) of the line 2 mice in contrast to only 4% (1/24) in line 3 mice. Mice from line 1 and line 4 showed intermediate levels of entrainment, 57% (8/14) and 39% (7/18), respectively. The predictability of entrainment vs. nonentrainment in line 2 and line 3 and the novel entrainment process provide a powerful tool with which to further elucidate mechanisms involved in entrainment of the SCN by scheduled feeding.

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