| 1. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition
- 2019
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Ingår i: Biotechnology Reports. - : Elsevier. - 2215-017X. ; 22, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases. Methods: The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles. Results: A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts. Conclusions: Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods. © 2019 The Author
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| 2. |
- Danesh, Abolghasem, et al.
(författare)
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Synergistic effect of haloduracin and chloramphenicol against clinically important Gram-positive bacteria
- 2017
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 13, s. 37-41
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of drug-resistant pathogens has triggered the search for more efficient antimicrobial agents and formulations for treatment of infections. In recent years, combination therapy has become one of the effective clinical practices in treating infections. The present study deals with the effect of haloduracin, a lantibiotic bateriocin and chloramphenicol against clinically important bacteria. The combined use of haloduracin and chloramphenicol resulted in remarkable synergy against a spectrum of microorganisms including strains of Staphylococcus aureus, Enterococcus faecium, Enterococcus faecalis and different groups of Streptococcus. The synergy allowed using these antimicrobial agents at substantially reduced concentrations without compromising their efficiency. Use of lower doses of chloramphenicol can avoid the severity of its side effects. In addition to minimizing undesirable side effects of some drugs, this approach brings the possibility of using antibiotics that are no longer effective due to drug resistance. Furthermore, the observed synergy between haloduracin and chloramphenicol opens a new window of using bacteriocins and antibiotics in combination therapy of infections.
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| 3. |
- Ertürk, Gizem, et al.
(författare)
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Microcontact-BSA imprinted capacitive biosensor for real-time, sensitive and selective detection of BSA
- 2014
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 3, s. 65-72
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Tidskriftsartikel (refereegranskat)abstract
- An analytical method is presented, combining novel microcontact imprinting technique and capacitive biosensor technology for the detection of BSA. Glass cover slips were used for preparation of protein stamps. The microcontact-BSA imprinted gold electrodes were prepared in the presence of methacrylic acid (MAA) and poly-ethylene glycol dimethacrylate (PEGDMA) as the cross-linker by bringing the protein stamp and the gold electrode into contact under UV-polymerization. Real-time BSA detection studies were performed in the concentration range of 1.0 × 10-20-1.0 × 10-8 M with a limit of detection (LOD) of 1.0 × 10-19 M. Cross-reactivity towards HSA and IgG were 5 and 3%, respectively. The electrodes were used for >70 assays during 2 months and retained their binding properties during all that time. The NIP (non-imprinted) electrode was used as a reference. The microcontact imprinting technology combined with the biosensor applications is a promising technology for future applications.
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| 4. |
- Gerlach, Inga, et al.
(författare)
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Operator training simulation for integrating cultivation and homogenisation in protein production
- 2015
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Ingår i: Biotechnology Reports. - : Elsevier. - 2215-017X. ; 6, s. 91-99
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Tidskriftsartikel (refereegranskat)abstract
- Operating training simulators (OTS) are virtual simulation tools used for training of process operators in industry in performing procedures and running processes. Based on structured mathematical models of the unit operations of a bioprocess an OTS can train a process operator by visualising changing conditions during the process, allow testing operator actions, testing controller settings, experience unexpected technical problems and getting practice in using prescribed standard procedures for a plant. This work shows the design of an OTS where two sequential steps of a recombinant protein production process, a fed-batch cultivation and a high-pressure homogenisation, are integrated. The OTS was evaluated on a user test group and showed that the OTS promoted and developed their understanding of the process, their capability to identify parameters influencing process efficiency and the skills of operating it.
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| 5. |
- Gutierrez, Alvaro V R, et al.
(författare)
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Bioimprinting as a tool for the detection of aflatoxin B1 using a capacitive biosensor
- 2016
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 11, s. 12-17
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Tidskriftsartikel (refereegranskat)abstract
- A strategy for the detection of aflatoxin B1 using a capacitive biosensor has been studied. The use of proteins for the generation of sites with high specificity against aflatoxin B1 are produced via bioimprinting. This technique has become a tool for the detection of aflatoxin B1 using a capacitive biosensor. The results demonstrate the ability to generate specific interactions with aflatoxin B1 with a linear relation between signals registered and log concentration of the target aflatoxin in the concentration range of 3.2 × 10-6 to 3.2 × 10-9 M when using ovalbumin as framework for the bioimprinting.
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| 6. |
- Hapeta, Piotr, et al.
(författare)
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Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica
- 2020
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 27
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Tidskriftsartikel (refereegranskat)abstract
- Yarrowia lipolytica is an important industrial microorganism used for the production of oleochemicals. The design of effective biotechnological processes with this cell factory requires an in-depth knowledge of its metabolism. Here we present a transcriptomic study of Y. lipolytica grown in the presence of glycerol and glucose, and mixture of both at different carbon to nitrogen ratios. It emerged that the transcriptomic landscape of Y. lipolytica is more sensitive to the nitrogen availability than to the utilized carbon source, as evidenced by more genes being differentially expressed in lower carbon to nitrogen ratio. Specifically, expression of hexokinase (HXK1) is significantly susceptible to changes in nitrogen concentrations. High HXK1 expression in low nitrogen seems to impact other genes which are implicated in tricarboxylic acid cycle and erythritol biosynthesis. We further show that expression of HXK1 and two genes belonging to the sugar porter family might be controlled by GATA-like zinc-finger proteins.
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| 7. |
- Hüttner, Silvia, 1984, et al.
(författare)
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Genome sequence of Rhizomucor pusillus FCH 5.7, a thermophilic zygomycete involved in plant biomass degradation harbouring putative GH9 endoglucanases
- 2018
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- We report here the annotated draft genome sequence of the thermophilic zygomycete Rhizomucor pusillus strain FCH 5.7, isolated from compost soil in Vietnam. The genome assembly contains 25.59 Mb with an overall GC content of 44.95%, and comprises 10,898 protein coding genes. Genes encoding putative cellulose-, xylan- and chitin-degrading proteins were identified, including two putative endoglucanases (EC 3.2.1.4) from glycoside hydrolase family 9, which have so far been mostly assigned to bacteria and plants.
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| 8. |
- Jansson, Linda, et al.
(författare)
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Blending DNA binding dyes to improve detection in real-time PCR
- 2017
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 14, s. 34-37
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Tidskriftsartikel (refereegranskat)abstract
- The success of real-time PCR (qPCR) analysis is partly limited by the presence of inhibitory compounds in the nucleic acid samples. For example, humic acid (HA) from soil and aqueous sediment interferes with amplification and also quenches the fluorescence of double-stranded (ds) DNA binding dyes, thus hindering amplicon detection. We aimed to counteract the HA fluorescence quenching effect by blending complementary dsDNA binding dyes, thereby elevating the dye saturation levels and increasing the fluorescence signals. A blend of the four dyes EvaGreen, ResoLight, SYBR Green and SYTO9 gave significantly higher fluorescence intensities in the presence and absence of HA, compared with the dyes applied separately and two-dye blends. We propose blending of dyes as a generally applicable means for elevating qPCR fluorescence signals and thus enabling detection in the presence of quenching substances.
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| 9. |
- Jansson, Linda, et al.
(författare)
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Evaluation and modification of lanthanum-based flocculation for isolation of bacteria from water samples
- 2018
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Molecular detection of pathogenic microorganisms in drinking and natural water is often challenged by low concentrations of the sought-after agents. Convenient methods to concentrate bacteria from water samples ranging from 1-10 L are highly warranted. Here we account for the evaluation of a lanthanum-based flocculation method to concentrate bacteria from water samples, applying four different bacterial species in tap water as well as river water. Our results show that the success of lanthanum-based flocculation is determined by both the bacterial species and the nature of the water sample. For tap water, satisfying flocculation efficiencies (above 60 %) were only reached for autoclaved water samples. However, the performance of the lanthanum-based flocculation method for non-autoclaved water was markedly improved by the addition of 20 mM bicarbonate to increase alkalinity. Our modified flocculation protocol may be applied as an alternative concentration method for bacteria in water samples of one liter or more.
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| 10. |
- Knudsen, Jan Dines, et al.
(författare)
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Exploring the potential of the glycerol-3-phosphate dehydrogenase 2 (GPD2) promoter for recombinant gene expression in Saccharomyces cerevisiae
- 2015
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 7, s. 107-119
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Tidskriftsartikel (refereegranskat)abstract
- A control point for keeping redox homeostasis in Saccharomyces cerevisiae during fermentative growth is the dynamic regulation of transcription for the glycerol-3-phosphate dehydrogenase 2 (GPD2) gene. In this study, the possibility to steer the activity of the GPD2 promoter was investigated by placing it in strains with different ability to reoxidise NADH, and applying different environmental conditions. Flow cytometric analysis of reporter strains expressing green fluorescent protein (GFP) under the control of the GPD2 promoter was used to determine the promoter activity at the single-cell level. When placed in a gpd1Δgpd2Δ strain background, the GPD2 promoter displayed a 2-fold higher activity as compared to the strong constitutive glyceraldehyde-3-phosphate dehydrogenase (TDH3). In contrast, the GPD2 promoter was found to be inactive when cells were cultivated in continuous mode at a growth rate of 0.3 h-1 and in conditions with excess oxygen (i.e. with an aeration of 2.5 vvm, and a stirring of 800 rpm). In addition, a clear window of operation where the gpd1Δgpd2Δ strain can be grown with the same efficiency as wild type yeast was identified. In conclusion, the flow cytometry mapping revealed conditions where the GPD2 promoter was either completely inactive or hyperactive, which has implications for its implementation in future biotechnological applications such as for process control of heterologous gene expression.
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| 11. |
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| 12. |
- Le, Kim-Cuong, et al.
(författare)
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Temporary immersion bioreactor system for propagation by somatic embryogenesis of hybrid larch (Larix × eurolepis Henry)
- 2021
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 32
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Tidskriftsartikel (refereegranskat)abstract
- Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).
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| 13. |
- Mahadhy, Ally, et al.
(författare)
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Rapid detection of mecA gene of methicillin-resistant Staphylococcus aureus by a novel, label-free real-time capacitive biosensor
- 2020
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 28
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Tidskriftsartikel (refereegranskat)abstract
- This work presents a rapid, selective and sensitive automated sequential injection flow system with a capacitive biosensor for detection of the mecA gene (the model chosen for this study), which emerges from methicillin-resistant Staphylococcus aureus. A DNA-based 25-mer capture probe was immobilized on the surface of a gold electrode which was integrated in the capacitive sensor system. A constant current pulse was applied and the resulting capacitance was measured. Injection of the target DNA sample to the sensor surface induced hybridization to occur between the target and the complementary sequence, which resulted in a shift in the measured capacitance (ΔC). The ΔC was directly proportional to the concentrations of the applied target probe with linearity ranging from 10−12 to 10−7 M. The biosensor had a detection limit of 6.0 × 10−13 M and a recovery of 95 % of the mecA gene when spiked in human saliva. The biosensor showed a promising selectivity. It could clearly discriminate single-base, two-base and twelve-base mismatch probes with a decrease in the signal strength by 13 %, 26 %, and 89 %, respectively relative to the signal strength of the complementary target probe. There was no significant signal observed for the non-complementary probe. The biosensor-chip could be re-used for more than 12 cycles with residual capacity of 94.5 ± 4.3 % and a RSD of 4.6 % by regenerating the biosensor-chip with a solution of 50 mM NaOH.
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| 14. |
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| 15. |
- Perruca-Foncillas, Raquel, et al.
(författare)
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Assessment of fluorescent protein candidates for multi-color flow cytometry analysis of Saccharomyces cerevisiae
- 2022
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 34
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Tidskriftsartikel (refereegranskat)abstract
- Transcription factor-based biosensors represent promising tools in the construction and evaluation of efficient cell factories for the sustainable production of fuels, chemicals and pharmaceuticals. They can notably be designed to follow the production of a target compound or to monitor key cellular properties, such as stress or starvation. In most cases, the biosensors are built with fluorescent protein (FP) genes as reporter genes because of the direct correlation between promoter activity and fluorescence level that can be measured using, for instance, flow cytometry or fluorometry. The expansion of available FPs offers the possibility of using several FPs - and biosensors – in parallel in one host, with simultaneous detection using multicolor flow cytometry. However, the technique is currently limited by the unavailability of combinations of FP whose genes can be successfully expressed in the host and whose fluorescence can be efficiently distinguished from each other.In the present study, the broad collection of available FPs was explored and four different FPs were successfully expressed in the yeast Saccharomyces cerevisiae: yEGFP, mEGFP, CyOFP1opt and mBeRFPopt. After studying their fluorescence signals, population heterogeneity and possible interactions, we recommend two original combinations of FPs for bi-color flow cytometry: mEGFP together with either CyOFP1opt or mBeRFPopt, as well as the combination of all three FPs mEGFP, CyOFP1opt and mBeRFPopt for tri-color flow cytometry. These combinations will allow to perform different types of bi-color or possibly tri-color flow cytometry and FACS experiments with yeast, such as phenotype evaluation, screening or sorting, by single-laser excitation with a standard 488 nm blue laser.
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| 16. |
- Schmitz, Eva, et al.
(författare)
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Chemical and biochemical bleaching of oat hulls : The effect of hydrogen peroxide, laccase, xylanase and sonication on optical properties and chemical composition
- 2021
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Ingår i: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 30
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Tidskriftsartikel (refereegranskat)abstract
- Oat hulls are an excellent dietary fibre source for food supplements due to their rich lignocellulose composition as well as their great abundance as low-value agricultural side stream. For the production of white fibre supplements, a mild, but effective bleaching of the hulls is required. Chemical bleaching with hydrogen peroxide and sodium hydroxide was here found to be a suitable method increasing the CIE L* value (corresponds to a lightness value) above 85. The developed method is mild, retaining the hull's chemical composition. Only a minor decrease in coniferaldehyde structures upon bleaching was detected. Colour and chemical variabilities of oat hulls from different growth seasons did not influence the required bleaching conditions to achieve the desired optical properties. The inclusion of biochemical bleaching steps utilizing the xylanase Pentopan Mono BG, the laccase NS51003 and sonication was industrially not feasible as they could not reduce the required amount of subsequently applied bleaching chemicals significantly.
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