Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp.

ABSTRACT: Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.

SUBMITTER: Satti SM

PROVIDER: S-EPMC8305213 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of PE-degrading Pseudomonas aeruginosa

Project description:Four purified RNA extracts (2 from cells grown in glucose supplemented medium and another 2 from cells grown in PE supplemented medium) were subjected to sequencing. Following cDNA library preparations, the final sequencing libraries were quantified using the KAPA kit (KAPA Biosystem, USA) on a Stratagene Mx-3005P qPCR system (Agilent Technologies, USA) and the respective library sizes were confirmed using Agilent Bioanalyzer High Sensitivity DNA Chip (Agilent Technologies, USA). The resulting libraries were subjected to cluster generation and sequenced using an Illumina flow cell, 202 cycles (101 bp paired-end reads) on the Illumina HiSeq 2000 system (Illumina, USA).

2017-12-19 | E-MTAB-4182 | biostudies-arrayexpress

Isothermal Crystallization Process of Poly(l-lactic acid)/Poly(d-lactic acid) Blends after Rapid Cooling from the Melt.

Project description:We observed the crystallization process in poly(l-lactic acid) (PLLA) and poly(d-lactic acid) (PDLA) blends using in situ simultaneous small- and wide-angle X-ray scattering measurements with a high-speed temperature control cell. In situ X-ray scattering measurements revealed that density fluctuations larger than the long spacing periods grew during crystallization above 130 °C. In particular, the time evolution of the density fluctuations has a strong dependence on the crystallization temperature. The density fluctuations will promote the crystal nucleation and growth processes of the stereocomplex and increase with increasing crystallization temperature, which is strongly correlated with the complexation of PLLA and PDLA chains. On the other hand, below 120 °C, the kinetics of stereocomplex formation might be hindered by the decreased mobility, and no density fluctuations were observed in the case of homo crystal growth of PLLA or PDLA.

| S-EPMC6640745 | biostudies-literature

Complete Genome Sequence and Biodegradation Characteristics of Benzoic Acid-Degrading Bacterium <i>Pseudomonas</i> sp. SCB32.

Project description:Allelochemicals are metabolites produced by living organisms that have a detrimental effect on other species when released into the environment. These chemicals play critical roles in the problems associated with crop replanting. Benzoic acid is a representative allelochemical found in root exudates and rhizosphere soil of crops and inhibits crop growth. The bioremediation of allelochemicals by microorganisms is an efficient decontamination process. In this research, a bacterial strain capable of degrading benzoic acid as the sole carbon source was isolated. The genome of the strain was sequenced, and biodegradation characteristics and metabolic mechanisms were examined. Strain SCB32 was identified as Pseudomonas sp. based on 16S rRNA gene analysis coupled with physiological and biochemical analyses. The degradation rate of 800 mg L-1 benzoic acid by strain SCB32 was greater than 97.0% in 24 h. The complete genome of strain SCB32 was 6.3 Mbp with a GC content of 64.6% and 5960 coding genes. Potential benzoic acid degradation genes were found by comparison to the KEGG database. Some key intermediate metabolites of benzoic acid, such as catechol, were detected by gas chromatography-mass spectrometry. The biodegradation pathway of benzoic acid, the ortho pathway, is proposed for strain SCB32 based on combined data from genome annotation and mass spectrometry. Moreover, the benzoic acid degradation products from strain SCB32 were essentially nontoxic to lettuce seedlings, while seeds in the benzoic acid-treated group showed significant inhibition of germination. This indicates a possible application of strain SCB32 in the bioremediation of benzoic acid contamination in agricultural environments.

| S-EPMC7354641 | biostudies-literature

Uniformly Dispersed Poly(lactic acid)-Grafted Lignin Nanoparticles Enhance Antioxidant Activity and UV-Barrier Properties of Poly(lactic acid) Packaging Films.

Project description:Poly(lactic acid) (PLA) represents one of the most widely used biodegradable polymers for food packaging applications. While this material provides many advantages, it is characterized by limited antioxidant and UV-barrier properties. Blending PLA with lignin is an attractive strategy to address these limitations. Lignin possesses antioxidant properties and absorbs UV-light and is a widely available low value byproduct of the paper and pulp industry. This study has explored the use of lignin nanoparticles to augment the properties of PLA-based films. A central challenge in the preparation of PLA-lignin nanoparticle blend films is to avoid nanoparticle aggregation, which could compromise optical properties as well as antioxidant activity, among others. To avoid nanoparticle aggregation in the PLA matrix, PLA-grafted lignin nanoparticles were prepared via organocatalyzed lactide ring-opening polymerization. In contrast to lignin and unmodified lignin nanoparticles, these PLA-grafted lignin nanoparticles could be uniformly dispersed in PLA for lignin contents up to 10 wt %. The addition of as little as the equivalent of 1 wt % of lignin of these nanoparticles effectively blocked transmission of 280 nm UV-light. At the same time, these blend films retained reasonable visible light transmittance. The optical properties of the PLA lignin blend films also benefited from the well-dispersed nature of the PLA-grafted nanoparticles, as evidenced by significantly higher visible light transmittance of blends of PLA and PLA-grafted nanoparticles, as compared to blends prepared from PLA with lignin or unmodified lignin nanoparticles. Finally, blending PLA with PLA-grafted lignin nanoparticles greatly augments the antioxidant activity of these films.

| S-EPMC9274615 | biostudies-literature

Poly(lactic acid) Matrix Reinforced with Diatomaceous Earth.

Project description:The poly(lactic acid) (PLA) biodegradable polymer, as well as natural, siliceous reinforcement in the form of diatomaceous earth, fit perfectly into the circular economy trend. In this study, various kinds of commercial PLA have been reinforced with diatomaceous earth (DE) to prepare biodegradable composites via the extrusion process. The structure of the manufactured composites as well as adhesion between the matrix and the filler were investigated using scanning electron microscopy (SEM). Differential scanning calorimetry (DSC) analyses were carried out to determine crystallinity of PLA matrix as function of DE additions. Additionally, the effect of the ceramic-based reinforcement on the mechanical properties (Young's modulus, elongation to failure, ultimate tensile strength) of PLA has been investigated. The results are discussed in terms of possible applications of PLA + DE composites.

| S-EPMC9501419 | biostudies-literature

Encapsulation of Amikacin into Microparticles Based on Low-Molecular-Weight Poly(lactic acid) and Poly(lactic acid-<i>co</i>-polyethylene glycol).

Project description:The aim of this study was to fabricate novel microparticles (MPs) for efficient and long-term delivery of amikacin (AMI). The emulsification method proposed for encapsulating AMI employed low-molecular-weight poly(lactic acid) (PLA) and poly(lactic acid-co-polyethylene glycol) (PLA-PEG), both supplemented with poly(vinyl alcohol) (PVA). The diameters of the particles obtained were determined as less than 30 μm. Based on an in-vitro release study, it was proven that the MPs (both PLA/PVA- and PLA-PEG/PVA-based) demonstrated long-term AMI release (2 months), the kinetics of which adhered to the Korsmeyer-Peppas model. The loading efficiencies of AMI in the study were determined at the followings levels: 36.5 ± 1.5 μg/mg for the PLA-based MPs and 106 ± 32 μg/mg for the PLA-PEG-based MPs. These values were relatively high and draw parallels with studies published on the encapsulation of aminoglycosides. The MPs provided antimicrobial action against the Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae bacterial strains. The materials were also comprehensively characterized by the following methods: differential scanning calorimetry; gel permeation chromatography; scanning electron microscopy; Fourier transform infrared spectroscopy-attenuated total reflectance; energy-dispersive X-ray fluorescence; and Brunauer-Emmett-Teller surface area analysis. The findings of this study contribute toward discerning new means for conducting targeted therapy with polar, broad spectrum antibiotics.

| S-EPMC8397404 | biostudies-literature

Biobased Poly(ethylene terephthalate)/Poly(lactic acid) Blends Tailored with Epoxide Compatibilizers.

Project description:To increase the biobased content of poly(ethylene terephthalate) (PET), up to 30 wt % poly(lactic acid) (PLA) was blended with PET using twin-screw compounding and injection molding processes. Multifunctional epoxide compatibilizers including a chain extender and an impact toughening agent were used as blend modifiers to improve the poor mechanical properties of PET/PLA blends. The mechanical and thermodynamic performances were investigated along with the morphological features through scanning electron microscopy, atomic force microscopy, and interfacial tension determination. From rheological and differential scanning calorimetry results, it was observed that the molecular weight of both PET and PLA increased with compatibilizers because of epoxide reactions. The toughening agent, poly(ethylene-n-butylene-acrylate-co-glycidyl methacrylate) (EBA-GMA), provided a 292% increase in impact strength over the blend but reduced modulus by 25%. In contrast, 0.7 phr addition of the chain extender, poly(styrene-acrylic-co-glycidyl methacrylate) (SA-GMA), yielded comparable performance to that of neat PET without sacrificing the tensile and flexural properties. When both compatibilizers were present in the blend, the mechanical properties remained relatively unaltered or decreased with increasing EBA-GMA content. The differences in mechanical performance observed were considered in relation to the strengthening mechanism of the two differing compatibilizers and their effects on the miscibility of the blend.

| S-EPMC6645286 | biostudies-literature

Well-defined Poly(lactic acid)s Containing Poly(ethylene glycol) Side-chains.

Project description:Poly(ethylene glycol) (PEG) side-chain functionalized lactide analogues have been synthesized in four steps from commercially available L-lactide. The key step in the synthesis is the 1,3-dipolar cycloaddition between PEG-azides and a highly strained spirolactide-heptene monomer, which proceeds in high conversions. The PEG-grafted lactides analogues were polymerized via ring-opening polymerization using triazacyclodecene as organocatalyst to give well-defined tri- and hepta-(ethylene glycol)-poly(lactide)s (PLA) with molecular weights above 10 kDa and polydispersity indices between 1.6 and 2.1. PEG-poly(lactide) (PLA) with PEG chain M(n) 2000 was also prepared but GPC analysis showed a bimodal profile indicating the presence of starting macromonomer. Cell adhesion assays were performed using MC3T3 E-1 osteoblast-like cells demonstrating that PEG-containing PLA reduces cell adhesion significantly when compared to unfunctionalized PLA.

| S-EPMC3263433 | biostudies-literature

Bio-Based Poly(lactic acid)/Poly(butylene sebacate) Blends with Improved Toughness.

Project description:A series of poly(butylene sebacate) (PBSe) aliphatic polyesters were successfully synthesized by the melt polycondensation of sebacic acid (Se) and 1,4-butanediol (BDO), two monomers manufactured on an industrial scale from biomass. The number average molecular weight (Mn) in the range from 6116 to 10,779 g/mol and the glass transition temperature (Tg) of the PBSe polyesters were tuned by adjusting the feed ratio between the two monomers. Polylactic acid (PLA)/PBSe blends with PBSe concentrations between 2.5 to 20 wt% were obtained by melt compounding. For the first time, PBSe's effect on the flexibility and toughness of PLA was studied. As shown by the torque and melt flow index (MFI) values, the addition of PBSe endowed PLA with both enhanced melt processability and flexibility. The tensile tests and thermogravimetric analysis showed that PLA/PBSe blends containing 20 wt% PBSe obtained using a BDO molar excess of 50% reached an increase in elongation at break from 2.9 to 108%, with a negligible decrease in Young's modulus from 2186 MPa to 1843 MPa, and a slight decrease in thermal performances. These results demonstrated the plasticizing efficiency of the synthesized bio-derived polyesters in overcoming PLA's brittleness. Moreover, the tunable properties of the resulting PBSe can be of great industrial interest in the context of circular bioeconomy.

| S-EPMC9572606 | biostudies-literature

Poly(lactic acid)/Poly(3-hydroxybutyrate) Biocomposites with Differently Treated Cellulose Fibers.

Project description:The growing concern about environmental pollution has generated an increased demand for biobased and biodegradable materials intended particularly for the packaging sector. Thus, this study focuses on the effect of two different cellulosic reinforcements and plasticized poly(3-hydroxybutyrate) (PHB) on the properties of poly(lactic acid) (PLA). The cellulose fibers containing lignin (CFw) were isolated from wood waste by mechanical treatment, while the ones without lignin (CF) were obtained from pure cellulose by acid hydrolysis. The biocomposites were prepared by means of a melt compounding-masterbatch technique for the better dispersion of additives. The effect of the presence or absence of lignin and of the size of the cellulosic fibers on the properties of PLA and PLA/PHB was emphasized by using in situ X-ray diffraction, polarized optical microscopy, atomic force microscopy, and mechanical and thermal analyses. An improvement of the mechanical properties of PLA and PLA/PHB was achieved in the presence of CF fibers due to their smaller size, while CFw fibers promoted an increased thermal stability of PLA/PHB, owing to the presence of lignin. The overall thermal and mechanical results show the great potential of using cheap cellulose fibers from wood waste to obtain PLA/PHB-based materials for packaging applications as an alternative to using fossil based materials. In addition, in situ X-ray diffraction analysis over a large temperature range has proven to be a useful technique to better understand changes in the crystal structure of complex biomaterials.

| S-EPMC9032581 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data