Journal: Journal of Biological Inorganic Chemistry

Article Title: Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions

doi: 10.1007/s00775-020-01759-2

Figure Lengend Snippet: THB11 length variants form different oligomeric states. a Anion exchange chromatography (AEC) profiles of the indicated protein variants, which had been purified from E. coli cell lysates by Strep -tag affinity chromatography before. The brackets above the peaks indicate the elution fractions that were combined for subsequent analyses [black, blue: peak (P) 1, 2]. The molecular mass of each protein calculated from the primary sequence are indicated to the left. b Denaturing (SDS) and native gel electrophoreses of the protein solutions collected from the AEC peaks P1 and P2. The numbered bands observed in the native gels were cut out and subsequently subjected to denaturing gel electrophoresis. c Size exclusion chromatography (SEC) profiles of the proteins present in the two AEC peaks. kDa labels within the SEC graphs indicate the molecular masses calculated from the elution volumes according to the column’s calibration curve, colors indicate the original AEC P1 (black) or P2 (blue). d UV–Vis spectra of the protein solutions collected from the two AEC peaks, P1 and P2. The spectra were normalized with regard to the Soret maxima (set to 1)

Article Snippet: Cloning was done using E. coli strain DH5α MCR grown in LB Broth (Lennox) or on LB Agar (Lennox) from Carl Roth GmbH ( https://www.carlroth.com ) supplied with 100 μg × ml −1 ampicillin at 37 °C.

Techniques: Chromatography, Purification, Strep-tag, Affinity Chromatography, Sequencing, Nucleic Acid Electrophoresis, Size-exclusion Chromatography

Journal: bioRxiv

Article Title: Mechanical strain modulates Min patterning and division in E. coli filaments

doi: 10.1101/2025.02.21.638242

Figure Lengend Snippet: A . Phase contrast images of a representative E. coli filament growing on 10 µ g/ml aztreonam agarose pads. Following cell segmentation and tracking (Methods), the curvature of the filaments is computed along the midline. At a given location (e.g. yellow point) the curvature, | κ |, is computed as the inverse of the radius of the circumference that is tangent to that point (green circle): | κ | = 1 /R . As time progresses and the filament grows, the snapshots reveal a buckling instability where large values of | κ | are reached by the central region of the filament (see E ). B . Cartoon of the mechanical toy model. Forces are exerted by a chain of connected springs (black). Nodes (grey circles) are subjected to elastic and bending forces. Due to cellular growth, the elastic energy relies on the time-dependent distance, L ( t ), between consecutive nodes (Methods). Bending energy depends on the angle θ as determined by neighboring segments. C . Snapshots of a simulated growing filament (initial length: 50 µ m; doubling time: 50 min). Color scales for each time point indicate the elastic (top) and bending (bottom) energies using pair-wise moving average coordinates (Methods). As time progresses elastic energy accumulates by the central region. Buckling leads to a relaxation of the elastic energy at the expense of an increase of the bending energy (black triangles). D . Ratio of the total energy between soft and stiff filaments (soft: ; stiff: sample size: n = 100 simulations). As time progresses the panel shows that stiff filaments that are not able to buckle increase their energy. E . Density histograms of the curvature of filaments as a function of the relative position as obtained in experiments (left) and simulations (pair-wise moving average coordinates; right). Sample size: n = 22 (experiments) and n = 100 (simulations). The color scale represents probability. Larger curvatures (buckling) accumulate by the central region of the filament.

Article Snippet: Experiments were conducted using the Escherichia coli strain DH5 α (NZYTech), transformed with the plasmid pYLS68 (P lac -YFP::minD minE::CFP), generously provided by Dr. Shih [ ].

Techniques:

Journal: bioRxiv

Article Title: Mechanical strain modulates Min patterning and division in E. coli filaments

doi: 10.1101/2025.02.21.638242

Figure Lengend Snippet: A . Fluorescence channel (YFP, false color scale) of the illustrative filament shown in ( t = 30 min). The zoomed region (circle) highlights the increase of MinD in buckled regions. In addition, the white arrows indicate the anti-correlation effect between MinD and locations with a high curvature. B . Top: Kymographs of the filament shown in panel A representing curvature (top) and MinD intensity (middle) profiles along the filament middle axis as a function of time. Color scales account for the curvature ( µ m −1 ) and for MinD concentration (arbitrary units). The zoomed region in the MinD kymograph indicates the period, T , and the wavelength, λ , of the MinD standing-wave pattern. Bottom: Overlay of the time average of MinD and curvature profiles. Black arrows highlight the locations pinpointed in panel A by means of white arrows. Averages are computed within the region delimited by the white dashed lines. C . Violin plots showing the distribution of values of the Pearson’s correlation coefficient between MinD and curvature (sample size: n = 19 filaments where high and low curvature regions were analyzed separately, , Methods). Black solid lines represent the mean (Low: 0.22; High: −0.14). D . Normalized MinD intensity (mean and standard deviation) as a function of the curvature in non-patterned agarose pads (same dataset as in C ) and in micro-patterned growth substrates ( n = 20 filaments). Solid lines are, in both cases, a logarithmic fit: , Methods. Inset: Illustrative phase contrast image of an E. coli filament growing in a micro-patterned agarose pad (scale bar: 10 µ m).

Article Snippet: Experiments were conducted using the Escherichia coli strain DH5 α (NZYTech), transformed with the plasmid pYLS68 (P lac -YFP::minD minE::CFP), generously provided by Dr. Shih [ ].

Techniques: Fluorescence, Concentration Assay, Standard Deviation

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Growth curve for E. coli DH5α-pCMV-lacZ . The growth curve based on OD 600 measurements is marked by small black circles and the appropriate best-fit curve is indicated in blue. The harvesting time points T 1 , T 2 , and T 3 are presented as bold big points. The minimum–maximum area, within which the measurement values have to reside, is bordered by the red curve (minimal measured OD 600 value) and the green curve (maximal measured OD 600 value).

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques:

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Growth curve for E. coli DH5α-pSUP 201-3 . The growth curve based on OD 600 measurements are marked by black circles and the appropriate best-fit curve is indicated in blue. The harvesting time points T 1 , T 2 , and T 3 are presented as bold big points. The minimum–maximum area, within which the measurement values have to reside, is bordered by the red curve (minimal measured OD 600 values) and the green curve (maximal measured OD 600 values).

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques:

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Measured RNAI-, RNAII-, and plasmid concentrations for DH5α-pSUP at the three harvesting time points, depicted in Figure 1 .

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques: Plasmid Preparation

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Measured RNAI-, RNAII-, and plasmid concentrations for DH5α-pCMV-lacZ at the three harvesting time points, depicted in Figure 2 .

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques: Plasmid Preparation

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Results of the in vitro and in silico determined PCNs for DH5α-pSUP .

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques: In Vitro, In Silico

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Results of the in vitro and in silico determined PCNs for DH5α-pCMV-lacZ .

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques: In Vitro, In Silico

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: ColE1-Plasmid Production in Escherichia coli : Mathematical Simulation and Experimental Validation

doi: 10.3389/fbioe.2015.00127

Figure Lengend Snippet: Simulation of the plasmid replication control for E . coli DH5α-placZ, beginning at time point T 3 , for the following three different growth conditions: blue, growth with normal nutrient conditions; green, growth with amino acid starvation conditions, red, growth with modified tRNA gene without amino acid starvation conditions .

Article Snippet: The Escherichia coli strain DH5α (F–Φ80 lac ZΔM15 Δ( lac ZYA- arg F) U169 rec A1 end A1 hsd R17 (rK−, mK+) pho A sup E44 λ− thi -1 gyr A96 rel A1) (Source: Plasmid Factory, Bielefeld, Germany) was used as a host strain for transformation of the high copy plasmid pCMV-lacZ (Source: Plasmid Factory, Bielefeld, Germany) as well as the low copy plasmid pSUP 201-3 (Simon et al., ). pCMV-lacZ is a ColE1-derived high copy plasmid for therapeutic pDNA production with a size of 7164 bp.

Techniques: Plasmid Preparation, Modification