scholarly journals Separation and Detection of Escherichia coli and Saccharomyces cerevisiae Using a Microfluidic Device Integrated with an Optical Fibre

Biosensors ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 40
Author(s):  
Mohd Kamuri ◽  
Zurina Zainal Abidin ◽  
Mohd Yaacob ◽  
Mohd Hamidon ◽  
Nurul Md Yunus ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Optical Fibre ◽  
Flow Rate ◽  
Incident Light ◽  
Microfluidic Channel ◽  
Integrated System ◽  
Time Range ◽  
Constant Frequency ◽  
E Coli

This paper describes the development of an integrated system using a dry film resistant (DFR) microfluidic channel consisting of pulsed field dielectrophoretic field-flow-fractionation (DEP-FFF) separation and optical detection. The prototype chip employs the pulse DEP-FFF concept to separate the cells (Escherichia coli and Saccharomyces cerevisiae) from a continuous flow, and the rate of release of the cells was measured. The separation experiments were conducted by changing the pulsing time over a pulsing time range of 2–24 s and a flow rate range of 1.2–9.6 μ L min − 1 . The frequency and voltage were set to a constant value of 1 M Hz and 14 V pk-pk, respectively. After cell sorting, the particles pass the optical fibre, and the incident light is scattered (or absorbed), thus, reducing the intensity of the transmitted light. The change in light level is measured by a spectrophotometer and recorded as an absorbance spectrum. The results revealed that, generally, the flow rate and pulsing time influenced the separation of E. coli and S. cerevisiae. It was found that E. coli had the highest rate of release, followed by S. cerevisiae. In this investigation, the developed integrated chip-in-a lab has enabled two microorganisms of different cell dielectric properties and particle size to be separated and subsequently detected using unique optical properties. Optimum separation between these two microorganisms could be obtained using a longer pulsing time of 12 s and a faster flow rate of 9.6 μ L min − 1 at a constant frequency, voltage, and a low conductivity.

scholarly journals Efficient Escherichia coli (E. coli) Trapping and Retrieval from Bodily Fluids via a Three-Dimensional (3D) Microbeads Stacked Nano-Device

2019 ◽  
Author(s):  
Xinye Chen ◽  
Abbi miller ◽  
Shengting Cao ◽  
Yu Gan ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Flow Rate ◽  
Magnetic Beads ◽  
Three Dimensional ◽  
E Coli ◽  
Bodily Fluids ◽  
3D Space ◽  
Fluidic Device ◽  
Computational Fluid Dynamics Cfd ◽  
On Chip

<div>A micro- and nano-fluidic device stacked with magnetic beads is developed to efficiently trap, concentrate, and retrieve Escherichia coli (E. coli) from bacteria suspension</div><div>and pig plasma. The small voids between the magnetic beads are used to physically isolate the bacteria in the device. We use computational fluid dynamics (CFD), 3D</div><div>tomography technology, and machine learning to probe and explain the bead stacking in a small 3D space with various flow rates. A combination of beads with different sizes is utilized to achieve a high capture efficiency of ~86% with a flow rate of 50 μL/min. Leveraging the high deformability of this device, the E. coli sample is retrieved from the designated bacteria suspension by applying a higher flow rate, followed by rapid magnetic separation. This unique function is also utilized to concentrate E. coli from the original bacteria suspension. An on-chip concentration</div><div>factor of ~11× is achieved by inputting 1,300 μL of the E. coli sample and then concentrating it in 100 μL buffer.</div><div>Importantly, this multiplexed, miniaturized, inexpensive, and transparent device is easy to fabricate and operate, making it ideal for pathogen separation in both laboratory and pointof- care (POC) settings.</div>

scholarly journals Efficient Escherichia coli (E. coli) Trapping and Retrieval from Bodily Fluids via a Three-Dimensional (3D) Microbeads Stacked Nano-Device

2019 ◽  
Author(s):  
Xinye Chen ◽  
Abbi miller ◽  
Shengting Cao ◽  
Yu Gan ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Flow Rate ◽  
Magnetic Beads ◽  
Three Dimensional ◽  
E Coli ◽  
Bodily Fluids ◽  
3D Space ◽  
Fluidic Device ◽  
Computational Fluid Dynamics Cfd ◽  
On Chip

<div>A micro- and nano-fluidic device stacked with magnetic beads is developed to efficiently trap, concentrate, and retrieve Escherichia coli (E. coli) from bacteria suspension</div><div>and pig plasma. The small voids between the magnetic beads are used to physically isolate the bacteria in the device. We use computational fluid dynamics (CFD), 3D</div><div>tomography technology, and machine learning to probe and explain the bead stacking in a small 3D space with various flow rates. A combination of beads with different sizes is utilized to achieve a high capture efficiency of ~86% with a flow rate of 50 μL/min. Leveraging the high deformability of this device, the E. coli sample is retrieved from the designated bacteria suspension by applying a higher flow rate, followed by rapid magnetic separation. This unique function is also utilized to concentrate E. coli from the original bacteria suspension. An on-chip concentration</div><div>factor of ~11× is achieved by inputting 1,300 μL of the E. coli sample and then concentrating it in 100 μL buffer.</div><div>Importantly, this multiplexed, miniaturized, inexpensive, and transparent device is easy to fabricate and operate, making it ideal for pathogen separation in both laboratory and pointof- care (POC) settings.</div>

scholarly journals RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase

1997 ◽  
Vol 327 (3) ◽  
pp. 847-851 ◽  
Author(s):  
Zengji LI ◽  
Yue SUN ◽  
L. David THURLOW
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Single Base ◽  
Three Dimensional Structure ◽  
E Coli ◽  
Base Identity

Twenty-one RNA minihelices, resembling the coaxially stacked acceptor- /T-stems and T-loop found along the top of a tRNA's three-dimensional structure, were synthesized and used as substrates for ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae. The sequence of nucleotides in the loop varied at positions corresponding to residues 56, 57 and 58 in the T-loop of a tRNA. All minihelices were substrates for both enzymes, and the identity of bases in the loop affected the interaction. In general, RNAs with purines in the loop were better substrates than those with pyrimidines, although no single base identity absolutely determined the effectiveness of the RNA as substrate. RNAs lacking bases near the 5ʹ-end were good substrates for the E. coli enzyme, but were poor substrates for that from yeast. The apparent Km values for selected minihelices were 2-3 times that for natural tRNA, and values for apparent Vmax were lowered 5-10-fold.

scholarly journals Microbial diversity beyond E. coli: new microbial worlds, new concepts in biology

2011 ◽  
Vol 32 (2) ◽  
pp. 73
Author(s):  
John A Fuerst
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Influenza Virus ◽  
Microbial Diversity ◽  
Microbial Evolution ◽  
E Coli ◽  
New Concepts ◽  
Wide Range ◽  
Classical Models ◽  
The Universe

Microbial diversity explores the universe of microorganisms beyond classical models such as Escherichia coli, influenza virus, or Saccharomyces cerevisiae. Exploring such new microbial worlds is essential for a microbiology which needs to learn about all the scientific and practical possibilities offered by billions of years of microbial evolution. Here we illustrate some examples of how studying a wide range of microbial diversity can assist microbiology as a fundamental and a practical science.

scholarly journals Effects of antibacterial compound of Saccharomyces cerevisiae from koumiss on immune function and caecal microflora of mice challenged with pathogenic Escherichia coli O8

2019 ◽  
Vol 88 (2) ◽  
pp. 233-241
Author(s):  
Yujie Chen ◽  
Chen Aorigele ◽  
Chunjie Wang ◽  
Wenqian Hou ◽  
Yunsheng Zheng ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Immune Function ◽  
T Lymphocyte ◽  
Lymphocyte Subsets ◽  
Clinical Symptoms ◽  
Pathological Changes ◽  
T Lymphocyte Subsets ◽  
E Coli ◽  
Antibacterial Compound

The yeast Saccharomyces cerevisiae from koumiss has been shown to have antibacterial effects on Escherichia coli, possibly by producing antibacterial compound in metabolism; however, there is limited knowledge about its application in animal production. We therefore investigated the effects of an antibacterial compound of S. cerevisiae from koumiss on the immune function and caecal microflora of mice challenged with pathogenic Escherichia coli O8. Three groups were formed: negative control (NC), positive control (PC), and the antibacterial compound of S. cerevisiae at pH 2.0 (S2). Mice in the NC and PC groups were orally administered phosphate buffer solution (PBS) for 7 d. At 4 d, E. coli O8 was administered intraperitoneally in group PC. Mice in group S2 were first administered orally as mice in group NC, and subsequently intraperitoneally administered E. coli O8 as mice in group PC. Compared with the NC group, mice in the PC group displayed clinical symptoms and pathological changes in the small intestine. Small intestine villi in the S2 group also developed some histologically pathological changes but not as severe as in the PC group. Moreover, there was less mortality in the S2 group than in the PC group. In PC group, thymus indexes, immunoglobulin A (IgA) in serum and Bifidobacterium in caecum were decreased and E. coli in the caecum was increased. In the S2 group, CD8+ of T lymphocyte subsets in blood and Bifidobacterium in caecum were decreased, while spleen indexes, IgG, IgM in serum, and CD3+ of T lymphocyte subsets in blood were increased. This suggests that S2 can relieve clinical symptoms of mice challenged with pathogenic E. coli O8, enhance their immune function, and influence their caecal microflora. The study will provide a theoretical foundation for utilizing antibacterial compound of S. cerevisiae from koumiss for curative purposes.

scholarly journals Cloning of Phanerochaete chrysosporium leu2 by Complementation of Bacterial Auxotrophs and Transformation of Fungal Auxotrophs

1998 ◽  
Vol 64 (7) ◽  
pp. 2624-2629 ◽  
Author(s):  
Laura Schick Zapanta ◽  
Takefumi Hattori ◽  
Magarita Rzetskaya ◽  
Ming Tien
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Phanerochaete Chrysosporium ◽  
Expression Vector ◽  
Selectable Marker ◽  
Genomic Clone ◽  
Selectable Markers ◽  
E Coli ◽  
Number Of Genes ◽  
Isopropylmalate Dehydrogenase

ABSTRACT A Phanerochaete chrysosporium cDNA library was constructed in an expression vector that allows expression in bothEscherichia coli and Saccharomyces cerevisiae. This expression vector, λYES, contains the lacZ promoter for expression in E. coli and the GAL1 promoter for expression in yeast. A number of genes were cloned by complementation of bacterial amino acid auxotrophs. The cDNA encoding the β-isopropylmalate dehydrogenase from P. chrysosporiumwas characterized further. The genomic clone (gleu2) was subsequently isolated and was used successfully as a selectable marker to transform P. chrysosporium auxotrophs for LEU2. Protoplasts for transformation were prepared with readily obtained conidiospores rather than with basidiospores, which were used in previous P. chrysosporium transformation procedures. The method described here allows other genes to be isolated from P. chrysosporium for use as selectable markers.

scholarly journals Cloning of Thalassiosira pseudonana’s Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli

Biology ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 358
Author(s):  
Ryan R. Cochrane ◽  
Stephanie L. Brumwell ◽  
Arina Shrestha ◽  
Daniel J. Giguere ◽  
Samir Hamadache ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Mitochondrial Genome ◽  
Phaeodactylum Tricornutum ◽  
Genome Engineering ◽  
Genome Instability ◽  
Thalassiosira Pseudonana ◽  
Genome Integrity ◽  
Mitochondrial Genomes ◽  
E Coli

Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae Phaeodactylum tricornutum can be cloned and engineered in Saccharomyces cerevisiae and Escherichia coli. Here, we show that the same approach can be used to clone mitochondrial genomes of another microalga, Thalassiosira pseudonana. We have demonstrated that these genomes can be cloned in S. cerevisiae as easily as those of P. tricornutum, but they are less stable when propagated in E. coli. Specifically, after approximately 60 generations of propagation in E. coli, 17% of cloned T. pseudonana mitochondrial genomes contained deletions compared to 0% of previously cloned P. tricornutum mitochondrial genomes. This genome instability is potentially due to the lower G+C DNA content of T. pseudonana (30%) compared to P. tricornutum (35%). Consequently, the previously established method can be applied to clone T. pseudonana’s mitochondrial genome, however, more frequent analyses of genome integrity will be required following propagation in E. coli prior to use in downstream applications.

scholarly journals Excision repair functions in Saccharomyces cerevisiae recognize and repair methylation of adenine by the Escherichia coli dam gene.

1986 ◽  
Vol 6 (10) ◽  
pp. 3555-3558 ◽  
Author(s):  
M F Hoekstra ◽  
R E Malone
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Excision Repair ◽  
Yeast Cells ◽  
Pyrimidine Dimer ◽  
Repair System ◽  
E Coli

Unlike the DNA of higher eucaryotes, the DNA of Saccharomyces cerevisiae (bakers' yeast) is not methylated. Introduction of the Escherichia coli dam gene into yeast cells results in methylation of the N-6 position of adenine. The UV excision repair system of yeast cells specifically responds to the methylation, suggesting that it is capable of recognizing modifications which do not lead to major helix distortion. The UV repair functions examined in this report are involved in the incision step of pyrimidine dimer repair. These observations may have relevance to the rearrangements and recombination events observed when yeast or higher eucaryotic cells are transformed or transfected with DNA grown in E. coli.

Isolation of the ARO1 cluster gene of Saccharomyces cerevisiae

1983 ◽  
Vol 3 (9) ◽  
pp. 1609-1614
Author(s):  
F W Larimer ◽  
C C Morse ◽  
A K Beck ◽  
K W Cole ◽  
F H Gaertner
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Shuttle Vector ◽  
Autonomously Replicating Sequence ◽  
Bamhi Fragment ◽  
Restriction Fragments ◽  
E Coli ◽  
Dna Library ◽  
Partial Digestion ◽  
Cluster Gene

The AROl cluster gene was isolated by complementation in Saccharomyces cerevisiae after transformation with a comprehensive yeast DNA library of BamHI restriction fragments inserted into the shuttle vector YEp13. Most of the transformants exhibited the expected episomal inheritance of the ARO+ phenotype; however, one stable transformant has been shown to be an integration of the AROl fragment and the vector YEp13 at the arol locus. The insert containing AROl is a 17.2-kilobase pair (kbp) BamHI fragment which complements both nonsense and missense alleles of arol. Subcloning by Sau3AI partial digestion further locates the AROl segment to a 6.2-kbp region. An autonomously replicating sequence (ars) was found on the 17.2-kbp fragment. Yeast arol mutants transformed with the AROl episome express 5 to 12 times the normal level of the five AROl enzyme activities and possess elevated amounts of the AROl protein. The yeast AROl fragment also complemented aroA, aroB, aroD, and aroE mutants of Escherichia coli. The expression of AROl in both S. cerevisiae and E. coli was independent of the orientation of the fragment with respect to the vector.

Excision repair functions in Saccharomyces cerevisiae recognize and repair methylation of adenine by the Escherichia coli dam gene

1986 ◽  
Vol 6 (10) ◽  
pp. 3555-3558
Author(s):  
M F Hoekstra ◽  
R E Malone
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Excision Repair ◽  
Yeast Cells ◽  
Pyrimidine Dimer ◽  
Repair System ◽  
E Coli

Unlike the DNA of higher eucaryotes, the DNA of Saccharomyces cerevisiae (bakers' yeast) is not methylated. Introduction of the Escherichia coli dam gene into yeast cells results in methylation of the N-6 position of adenine. The UV excision repair system of yeast cells specifically responds to the methylation, suggesting that it is capable of recognizing modifications which do not lead to major helix distortion. The UV repair functions examined in this report are involved in the incision step of pyrimidine dimer repair. These observations may have relevance to the rearrangements and recombination events observed when yeast or higher eucaryotic cells are transformed or transfected with DNA grown in E. coli.

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