| 1. |
- Cai, Yanling, et al.
(författare)
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Bacteria viability assessment after photocatalytic treatment
- 2014
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Ingår i: 3 Biotech. - : Springer. - 2190-5738 .- 2190-572X. ; 4:2, s. 149-157
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Tidskriftsartikel (refereegranskat)abstract
- The aim of the present work was to evaluate several methods for analyzing the viability of bacteria after antibacterial photocatalytic treatment. Colony-forming unit (CFU) counting, metabolic activity assays based on resazurin and phenol red and the Live/Dead® BacLight™ bacterial viability assay (Live/Dead staining) were employed to assess photocatalytically treated Staphylococcus epidermidis and Streptococcus mutans. The results showed conformity between CFU counting and the metabolic activity assays, while Live/Dead staining showed a significantly higher viability post-treatment. This indicates that the Live/Dead staining test may not be suitable for assessing bacterial viability after photocatalytic treatment and that, in general, care should be taken when selecting a method for determining the viability of bacteria subjected to photocatalysis. The present findings are expected to become valuable for the development and evaluation of photocatalytically based disinfection applications
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| 2. |
- Li, Yuanzi, et al.
(författare)
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Optimization of the l-tyrosine metabolic pathway in Saccharomyces cerevisiae by analyzing p-coumaric acid production
- 2020
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Ingår i: 3 Biotech. - : Springer Science and Business Media LLC. - 2190-572X .- 2190-5738. ; 10:6
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we applied a series of genetic modifications to wild-type S. cerevisiae strain BY4741 to address the bottlenecks in the l-tyrosine pathway. A tyrosine ammonia-lyase (TAL) gene from Rhodobacter capsulatus, which can catalyze conversion of l-tyrosine into p-coumaric acid, was overexpressed to facilitate the analysis of l-tyrosine and test the strain's capability to synthesize heterologous derivatives. First, we enhanced the supply of precursors by overexpressing transaldolase gene TAL1, enolase II gene ENO2, and pentafunctional enzyme gene ARO1 resulting in a 1.55-fold increase in p-coumaric acid production. Second, feedback inhibition of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase and chorismate mutase was relieved by overexpressing the mutated feedback-resistant ARO4(K229L) and ARO7(G141S), and a 3.61-fold improvement of p-coumaric acid production was obtained. Finally, formation of byproducts was decreased by deleting pyruvate decarboxylase gene PDC5 and phenylpyruvate decarboxylase gene ARO10, and p-coumaric acid production was increased 2.52-fold. The best producer-when TAL1, ENO2, ARO1, ARO4(K229L), ARO7(G141S), and TAL were overexpressed, and PDC5 and ARO10 were deleted-increased p-coumaric acid production by 14.08-fold (from 1.4 to 19.71 mg L-1). Our study provided a valuable insight into the optimization of l-tyrosine metabolic pathway.
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| 3. |
- Linder, Tomas
(författare)
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Development of a yeast heterologous expression cassette based on the promoter and terminator elements of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene
- 2018
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Ingår i: 3 BIOTECH. - : Springer Science and Business Media LLC. - 2190-572X .- 2190-5738. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- A new expression cassette (EC0) consisting of the fused 5′ and 3′ intergenic regions (IGRs) of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene was evaluated through expression of the bacterial hygromycin B phosphotransferase (hph) resistance gene in the common baker’s yeast Saccharomyces cerevisiae. Progressively shorter versions of the hph-containing EC cassette (hphEC1 though hphEC6) with trimmed 5′ and 3′ EcTEF1 IGRs were tested for their ability to confer resistance to hygromycin B in S. cerevisiae. Hygromycin B resistance was retained in all six generated hphEC variants up to a concentration of 400 mg/L. The hphEC6 cassette was the shortest cassette to be assayed in this study with 366 and 155 bp of the EcTEF1 5′ and 3′ IGRs, respectively. When tested for deletion of the S. cerevisiae proline oxidase gene PUT1, the hphEC6 cassette was shown to successfully act as a selection marker on hygromycin B-containing medium. The hphEC6 cassette could be placed immediately adjacent to a kanMX4 G418 disulfate resistance marker without any discernable efect on the ability of the yeast to grow in the presence of both hygromycin B and G418 disulfate. Co-cultivation experiments under non-selective conditions demonstrated that a PUT1 deletion strain carrying the hphEC6 cassette displayed equivalent ftness to an otherwise isogenic PUT1 deletion strain carrying the kanMX4 cassette.
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| 4. |
- Mun, Bong-Gyu, et al.
(författare)
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Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana
- 2017
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Ingår i: 3 Biotech. - : Springer. - 2190-5738 .- 2190-572X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.
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| 5. |
- Singh, Rajesh
(författare)
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Tocopherol levels in different mango varieties correlate with MiHPPD expression and its over-expression elevates tocopherols in transgenic Arabidopsis and tomato
- 2017
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Ingår i: 3 BIOTECH. - : Springer Science and Business Media LLC. - 2190-572X .- 2190-5738. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Mango fruit tocopherol levels vary in different varieties during ripening. This study shows that tocopherol accumulation is highly correlated with its p-hydroxyphenyl pyruvate dioxygenase (MiHPPD) gene expression during ripening. MiHPPD transcript is ethylene induced and differentially expressed in four mango varieties used in this study. Higher/lower accumulation of tocopherol (mainly alpha-tocopherol) was achieved by heterologous expression of MiHPPD in Arabidopsis and tomato. The results suggest that tocopherol accumulation in mango fruit is correlated to MiHPPD gene expression. Over-expression of MiHPPD gene channelizes the flux towards tocophreol biosynthesis and could be used as a potential tool for metabolic engineering.
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| 6. |
- Vélëz, Heriberto, et al.
(författare)
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Annulohypoxylon sp. strain MUS1, an endophytic fungus isolated from Taxus wallichiana Zucc., produces taxol and other bioactive metabolites
- 2021
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Ingår i: 3 BIOTECH. - : Springer Science and Business Media LLC. - 2190-572X .- 2190-5738. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- The current study focuses on the isolation and in vitro characterization of bioactive metabolites produced by endophytic fungi isolated from the Himalayan yew (Taxus wallichiana Zucc.). The endophytic fungi were isolated on artificial media from inner tissues of bark and needles. Antimicrobial and antioxidant activity, along with total phenolic- and flavonoid-content assays were used in the evaluation of bioactivity of the fermented crude extracts. The ability of the endophytes to produce the anticancer compound Taxol was also analyzed using thin-layer chromatography (TLC) and reverse-phase high-performance liquid chromatography (RP-HPLC). A total of 16 fungal morphotypes were obtained from asymptomatic inner tissues of the bark and needles of T. wallichiana. Among the 16 isolates, the ethyl acetate (EA) fraction of isolate MUS1, showed antibacterial and antifungal activity against all test-pathogens used (Streptococcus faecalis ATCC 19433, Staphylococcus aureus ATCC 12600, Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25922, Salmonella enterica ATCC 13076, Pseudomonas aeruginosa ATCC 27853, and Candida albicans). MUS1 showed significant inhibition against Pseudomonas aeruginosa ATCC 27853 (minimum inhibitory concentration (MIC): 250 mu g/ml) and the pathogenic yeast, Candida albicans (MIC: 125 mu g/ml). Antioxidant activity, total phenolic, and total flavonoid content as well as in vitro Taxol production were evaluated for EA fraction of isolate MUS1. Antioxidant activity was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. At a concentration of 100 mu g/ml, the % DPPH radical scavenging activity was 83.15 +/- 0.40, 81.62 +/- 0.11, and 62.36 +/- 0.29, for ascorbic acid, butylated hydroxytoluene (BHT), and the EA fraction of MUS1, respectively. The DPPH-Half maximal inhibitory concentration (DPPH-IC50) value for the EA fraction was 81.52 +/- 0.23 mu g/ml, compared to BHT (62.87 +/- 0.08 mu g/ml) and ascorbic acid (56.15 +/- 0.19 mu g/ml). The total phenolic and flavonoid content in the EA fraction were 16.90 +/- 0.075 mu g gallic acid equivalent (GAE) and 11.59 +/- 0.148 mu g rutin equivalent (RE), per mg of dry crude extract, respectively. TLC and RP-HPLC analysis showed that the isolate MUS1 also produces Taxol (282.05 mu g/l of fermentation broth). Isolate MUS1 was identified as Annulohypoxylon sp. by internal transcribed spacer (ITS) sequencing. Having the ability to produce antimicrobial and antioxidant metabolites, as well as the anticancer compound Taxol, makes Annulohypoxylon sp. strain MUS1, a promising candidate for further study of naturally occurring bioactive metabolites.
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| 7. |
- Verma, Swati, et al.
(författare)
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Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences
- 2019
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Ingår i: 3 Biotech. - : Springer Berlin/Heidelberg. - 2190-5738 .- 2190-572X. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.
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