Gerrich

@gerrich

Non-conventional microbes, metabolic engineering and microbial genetics. Bacteria go brrr Finally, finished with my thesis, now off to new frontiers!

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Gerrich@gerrich· 27d

The ATPase seems to be quite important for pH homeostasis. Z. mobilis produces lots of CO2 and HCO3-. This should be somehow related to the strong need to pump protons. Here we used a pHluorin sensor to estimate cytosolic pH over time of cultivation with different starting pH. 12/13

Growth behavior and PHP signals in ZM4, ZM4 ΔFO and ZM4 ΔF1 growing in ZM medium with different starting pHe values. Cells from an actively growing preculture were harvested and resuspended in ZM medium with different pHe values. The cultures were inoculated in a microplate reader at 30 °C with vigorous shaking and the OD600 was monitored throughout the experiment. All strains carry pZP1573 expressing PHP. Columns are showing data from ZM4 (left), the ΔFO mutant (middle) and the ΔF1 mutant (right). The top row shows growth over time via confidence interval (95%). The middle row shows the R 405/485. The bottom row shows the R 405/485 of each replicate (difference in shape indicates different replicates) plotted against the biomass. Shown is either the confidence interval (95%) or the direct measurements, each variation is based on three replicates.

Gerrich@gerrich· 27d

Weirdly, the ΔFo mutant seem to retain some ATPase activity. This can be seen subliminally over all the experiments. We still don't have a good explanation for this. 11/13

Analysis of ATP synthesis in starved cell suspensions of ZM4 and the mutant strains. A) Fold change of intracellular ATP levels of starved cells after acid pulse. B) Fold change of intracellular ATP levels of ZM4, ΔFO and ΔF1 strains after glucose addition. ATP levels are normalized against the ATP concentration measured at the initiation of the pulse at t = 0.

Gerrich@gerrich· 27d

Also, the mutants seem to have a higher biomass yield than the wild-type. Though we couldn't detect it under all conditions. Our collaborators in Riga saw it in shake flasks, while we only saw it in chemostat. 10/13

Gerrich@gerrich· 27d

Now comes the interesting part: Non-growing cultures of the mutants (ΔFo, ΔF1) had much lower specific glucose consumption rates! Strongly suggesting that the high glycolytic flux of Z. mobilis depends on ATP usage of FoF1. 9/13

Glucose uptake rates in non-growing Z. mobilis ZM4 and ΔFO and ΔF1 mutant suspension cultures

Gerrich@gerrich· 27d

We also characterized the strains in a bioreactor. Unsurprisingly, the mutant strains consumed more O2 per glucose than the wild-type. 8/13

Y EtOH is the yield of ethanol produced per mole of glucose. qGlc, qEtOH, OTR, and CTR are the consumption or production rates of the respective substances, calculated per gram of dry cell weight per hour.

Gerrich@gerrich· 27d

If you add KCN the mutants' growth is disrupted , while the wild-type grows fine. 7/13

Growth of ZM4, ZM4 ΔFO and ZM4 ΔF1 in ZMG in shake flasks A) without and B) with addition of 100µM KCN. KCN was added after about 2 h incubation when all cultures showed exponential growth. Shown are three independent biological repeats.

Gerrich@gerrich· 27d

But now let's come to our findings! The knockouts both grow better with more oxygen supplied (higher shaking speed). No big surprise here. 6/13

Shown are the maximal growth rates [h− 1] observed in the growth experiments. The values represent the mean and standard deviations of at least three independent repeats.

Gerrich@gerrich· 27d

I got partial knockouts (Z. mobilis being polyploid, but when I selected under oxygen rich conditions, I got proper clean knockouts. 3/13

Graphical overview of the gene clusters encoding the A) FO and B) F1 ATPase subcomplexes on the chromosome of Z. mobilis ZM4. The region between the homology arms (black) is deleted in the mutants. Below each gene cluster is a map showing the altered chromosomal region in the ΔFO or ΔF1 mutant, respectively. Genes are shown with their ZM4 numerical identifiers and coding sequence orientation is indicated with arrows. Intergenic regions surrounding both subcomplex clusters were left intact.

Gerrich@gerrich· Jul 2

Die Variante mit Kirschgeschmack ist mit Abstand mein Favorit!

Gerrich@gerrich· Jun 25

They also have the inverted gel photo! 🧪

Similar (or the same?) photo of an agarose gel but inverted and as a long tank top for 491 USD. Worn by a different model.

Gerrich@gerrich· Jun 25

Who is going to give me the funding to get the DNA agarose gel electrophoresis sustainable designer t-shirt for 441 USD?

Maison Blanche web shop screenshot. Showing a model wearing a white t-shirt with a DNA agarose gel electrophoresis print.

Gerrich@gerrich· May 23

When the scale is doing heavy lifting for production optimization... 🧪🦠

Two bar charts comparing unstable vs stable terminators. Panel E (green bars): GFP/CH fluorescence ratio, with unstable averaging ~4.43 and stable ~4.59. Panel F (blue bars): 2,3-butanediol/ethanol carbon conversion ratio in percent, with unstable ~21.6% and stable ~22.4%. Both panels show individual data points overlaid on bars with error bars; stable terminators yield modestly higher values in both readouts, though the spread overlaps substantially.

Importantly, the GFP scale start at 4.4 and goes up to 4.8, the 2,3-BDO scale goes from 20 to 24. Bullshit data viz.

Gerrich@gerrich· May 19

Four of them work well in Z. mobilis. The known LacI-Plac and TetR-Ptet and the novel (not yet adapted by the community) VanR-Pvan and CinR-Pcin. The novel ones are quite tight. VanR reacts to vanillic acid, which is a cheap inducer. OHC14 (CinR) is more expensive, but has a great range. 3/4

Figure 3 from the paper: dose–response titration curves for all seven inducible systems in Zymomonas mobilis, measured 10 hours into cultivation. Three panels share a common y-axis showing mCherry fluorescence normalised to OD₆₀₀ on a log scale, ranging from about 10⁰ to 10⁵ arbitrary units.
The left panel shows basal expression at zero inducer for all seven systems, with individual replicate dots and coloured horizontal bars marking the means. CinR^AM-P_cin and VanR^AM-P_vanCC sit lowest (around 10–20 AU), TetR-P_tet and LacI-P_lacT7A1_O3O4 in the middle, and XylS-P_m, NahR-P_salTTC and LuxR-P_luxB at the top of the basal range (around 200 AU), confirming their leakiness.
The central panel plots mCherry/OD₆₀₀ against inducer concentration on a log x-axis spanning 10⁻³ to 10⁴ µM, with Hill-fit curves through each replicate cloud. TetR-P_tet (yellow) saturates earliest, with EC₅₀ near 0.06 µM and a maximum around 10⁴ AU. CinR^AM-P_cin (green) follows, with EC₅₀ near 1 µM and a similar maximum. LuxR-P_luxB (teal) and NahR-P_salTTC (orange) plateau in the mid-10³ range with shallow slopes. LacI-P_lacT7A1_O3O4 (blue) and VanR^AM-P_vanCC (pink) require ~10²–10³ µM inducer for half-maximal response but reach high maxima, LacI being the highest overall (>2×10⁴ AU). XylS-P_m (tan) has the smallest dynamic range, rising only marginally above its already-high basal level.
The right panel shows reference constitutive promoters previously characterised in Z. mobilis: P_gap, P_pdc334, P_tuf, P_strong1k, P_strong100k*, and the plasmid-free wild type, plotted as replicate clouds in grey. P_strong100k* sits highest (~1–2×10⁴ AU), P_gap, P_pdc334 and P_tuf cluster around 5×10³ AU, P_strong1k sits near 10² AU, and the wild-type autofluorescence sits lowest (~20 AU). Several induced systems (LacI, CinR, TetR) reach or exceed the strong native promoters at full induction.

Gerrich@gerrich· May 19

I tested seven chemically inducible regulator-promoter pairs for their functionality in Z. mobilis. 2/4

Figure 1 from the paper: schematic overview of the seven inducible transcription regulators tested in Zymomonas mobilis, drawn in SBOL notation. Each of the seven panels (A–G) shows a separate construct with the same genetic background — regulator gene, constitutive P_lacI (or equivalent) driving the regulator, the inducible promoter, mCherry, and a terminator — differing only in the regulator-promoter pair. Each panel also shows the small-molecule inducer binding the regulator above the DNA.
Panel A (tan): m-toluate activates XylS, which binds upstream of P_m. Panel B (orange): salicylic acid activates NahR^AM, binding upstream of P_salTTC. Panel C (teal): N-(3-oxohexanoyl)-homoserine lactone (OC6) activates LuxR, binding upstream of P_luxB. Panel D (pink): vanillic acid binds VanR^AM, which binds regions flanking P_vanCC (repression released). Panel E (yellow): anhydrotetracycline binds TetR, which sits inside the bidirectional P_tet. Panel F (blue): IPTG binds LacI, which binds operators within and downstream of P_lacT7A1_O3O4. Panel G (green): hydroxytetradecanoyl-homoserine lactone (OHC14) binds CinR^AM, binding upstream of P_cin.
Arrows from inducer to regulator indicate activation of an activator; blunt-ended (red) lines indicate inhibition of a repressor. Colour coding is carried through the rest of the manuscript.

Gerrich@gerrich· May 11

Is there a good colony counting tool for images as this one out there? I tried OpenCFU here and it didn't work at all. 🧪

Gerrich@gerrich· Apr 23

My first manuscript submitted as corresponding author got accepted! It took about a month from submission, reviews, revision to accept. I am so happy about this! I really hope this step up as corresponding author will help my soo-to-be proposal submission. 🥹🧪

The submission history for "Seven inducible promoters for Zymomonas mobilis" at Microbial Cell Factories. The timeline shows: submission received 20 Mar 2026, passed technical check 24 Mar 2026, editor assigned 24 Mar 2026, first reviewers invited 25 Mar 2026, reviewer reports received 01 Apr 2026, revision requested 08 Apr 2026, revision received 13 Apr 2026, second round of review completed 22 Apr 2026, and submission accepted 22 Apr 2026. The manuscript is now in publishing and rights as of 22 Apr 2026.

Gerrich@gerrich· Apr 20

Screenshot of a Facebook report dialog asking "What's going on?" with four radio button options: "It's annoying or not interesting," "I'm in this photo and I don't like it" (selected), "I think it shouldn't be on Facebook," and "It's spam."

Gerrich@gerrich· Apr 14

This project started back in the days of science twitter. @hsalis.bsky.social reposted my first first-author paper, so @matick.bsky.social noticed it and saw potential. It is amazing how projects can start, I love the online science community and hope that it will thrive here. 9/10

Screenshot of a tweet by Howard Salis (@hsalis) from 2022. Text reads: "Great paper! Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. It's the first time someone has used the Promoter Calculator to design synthetic promoters for another organism. P100k* is 💪💪💪". Below the tweet text, a figure from the Zymo-Parts paper shows a schematic of the Golden Gate cloning system: a library of regulatory elements (promoter, RBS, GOI, terminator) in individual entry plasmids with ColE1 ori and AmpR, assembled via Golden Gate cloning into an acceptor plasmid containing a Zymomonas mobilis replication origin and KanR, yielding a final expression plasmid depicted next to a Z. mobilis cell. A link preview to the Zymo-Parts paper on pubs.acs.org is shown at the bottom.

Gerrich@gerrich· Apr 14

Finally, this is where standardized parts pay off. 5 promoters × 6 RBSs × 4 terminators assembled combinatorially on an Opentrons OT2. 38 plasmids in 5 days, hands-on time cut from ~4h to ~2h. 961-fold dynamic range across the full combinatorial space. This is were collaborations shine! 7/10

Three-panel figure showing combinatorial part characterization using a semiautomated cloning workflow. Panel A: top left, network diagram showing combinatorial assembly of 5 promoters (red squares, varying shades) with 6 RBSs (green squares, varying shades) driving eGFP, connected to 4 terminators (blue squares); top right, photograph of a fluorescent colony plate showing green-yellow fluorescent colonies of varying intensity on amber-colored agar; bottom, timeline of the semiautomated workflow using an Opentrons OT2 liquid handling robot: Day 1 — Golden Gate assembly and chemical transformation; Day 2 — conjugation into R. sphaeroides; Days 3-4-5 — strain recovery. 38 strains built in 5 days. Panel B: heatmap of combinatorial promoter-RBS expression strengths; promoters (PJ23100, PJ95025, PcrtE, PrpmI, PJ95027) on y-axis, RBSs (B0034, B0030, J95018, J95016, J95019, J95015) on x-axis; color scale from 10³ (dark purple) to 10⁵ (yellow); crosses indicate failed assemblies. Panel C: bar chart comparing four terminator performances (T0, B0010, B0015, J95029) across four promoter-RBS combinations; J95029 consistently lowest.

Gerrich@gerrich· Apr 14

11 RBSs characterized, with 49-fold range. Interestingly, again E. coli-based elements (B0034, J61100, B0030) outperform the strongest R. sphaeroides-native designs. Source your RBSs from iGEM registry! 6/10

Two-panel figure characterizing ribosome binding site (RBS) strength in R. sphaeroides. Panel A: horizontal bar chart ranking 11 RBSs by biomass-normalized eGFP fluorescence (a.u./OD, log scale from 10² to 10⁵), all assessed with promoter PrpmI. Strongest RBSs (dark green): B0034, J61100, B0030. Medium strength (medium green): J95028, J95018, J95017, J95019, B0032, J95016. Weakest (light green): B0031, J95015. Overall 49-fold dynamic range. E. coli-based RBSs B0034, J61100 and B0030 outperform the strongest R. sphaeroides-native designs. Panel B: scatter plot correlating RBS strengths when coupled with promoter PrpmI (y-axis) versus promoter PcrtE (x-axis), both on log scale from 10² to 10⁶. Points colored by RBS strength group. Linear regression line shown. Pearson r = 0.97, p < 0.0001, indicating highly predictable RBS behavior across two different promoter contexts.

Gerrich@gerrich· Apr 14

A proper selection of inducible promoters had been mostly missing for R. sphaeroides #synbio, but no longer: NahR-PsalTTC (salicylic acid), 136-fold range LacI-PlacT7A1 (IPTG), 27-fold range VanR-PvanCC (vanillic acid), 432-fold range Their characterization inspired me, more to follow soon! 5/10

Three-panel figure characterizing inducible expression systems in R. sphaeroides. Panel A: schematics of three transcriptional unit constructs, each with a constitutive promoter driving a regulatory gene (NahR, LacI, or VanR) and an inducible promoter (PsalTTC, PlacT7A1_O3O4, or PvanCC) driving eGFP with RBS J61100 and T0 terminator, all in a pBBR1-based vector with kanamycin resistance. Panel B: dose-response curves for three inducible systems on log-log scale; inducer concentration (mM) on x-axis, biomass-normalized fluorescence (a.u./OD) on y-axis. NahR-PsalTTC (dark orange circles): 136-fold range. LacI-PlacT7A1 (medium orange diamonds): 27-fold range. VanR-PvanCC (light orange squares): 432-fold range with near-zero basal expression. Fitted Hill equation curves shown. Panel C: bar chart comparing maximum expression levels of the three systems relative to reference promoter PrpmI-J61100; NahR-PsalTTC highest (~7.2×), followed by LacI-PlacT7A1 (~5×) and VanR-PvanCC (~2×).

Gerrich@gerrich· Apr 14

13 constitutive promoters characterized, 270-fold range Synthetic σ70-based elements designed for E. coli (Anderson) are among the strongest in R. sphaeroides, despite the different RNAP architecture of Alphaproteobacteria. Worth trying your E. coli parts in your non-model host! 4/10

Two-panel figure assessing promoter strength in R. sphaeroides. Panel A: horizontal bar chart ranking 13 promoters by biomass-normalized eGFP fluorescence (a.u./OD, log scale from 10² to 10⁶), assessed with RBS J61100. Strongest promoters (dark red): PJ23100, Pstrong100K, PJ23104, PJ95025. Medium strength (medium red): PJ23116, PJ95027, PcrtE, PJ23105, PrpmI. Weakest (light red/pink): PJ23114, Pstrong1K, Pstrong10K, PJ95023. Overall 270-fold dynamic range. Panel B: scatter plot correlating promoter strengths when combined with either RBS J61100 (y-axis) or RBS J95017 (x-axis), both on log scale from 10² to 10⁶. Points colored by promoter strength group. Linear regression line shown. Pearson r = 0.94, p < 0.0001, indicating high correlation of promoter ranking across the two RBS contexts.

Gerrich@gerrich· Apr 14

As they are interested in R. sphaeroides and other Proteobacteria they added new broad-host-range vectors to the framework. pBBR1, RK2, RSF1010 Each combined with 4 antibiotic markers as lvl 1 or lvl 2 entry vectors, all conjugateable. 3/10

Four-panel figure characterizing origins of replication (ORIs) in R. sphaeroides. Panel A: schematic of assessed constructs showing a transcriptional unit with promoter PrpmI, RBS J95017, eGFP and T0 terminator, cloned into plasmid backbones carrying either pBBR1, RK2, or RSF1010 ORI with kanamycin resistance marker. Panel B: schematic of the extended Level 1 and 2 broad-host entry plasmid collection, showing three ORIs (pBBR1, RK2, RSF1010) combined with four antibiotic resistance markers (kanamycin, spectinomycin, chloramphenicol, gentamicin) and a dropout cassette. Panel C: bar chart of biomass-normalized eGFP fluorescence (a.u./OD) for the three ORI-containing plasmids; RSF1010 highest (~700), followed by RK2 (~575) and pBBR1 (~510). Panel D: bar chart of relative plasmid copy number determined by qPCR; RSF1010 highest (~17), followed by pBBR1 (~13) and RK2 (~10). Error bars represent standard deviation.

Gerrich@gerrich· Apr 14

The team in Wageningen @w-u-r.bsky.social outdid me with their overview of the assembly framework. They were interested in it for the high-fidelity overhangs, loop assembly structure, but most of all the option to assemble polycistronic expression units natively inside the system. 2/10

Diagram of the Zymo-Parts Golden Gate MoClo assembly system showing four hierarchical levels. Level −1: individual RBS-GOI operon fragments in entry plasmids, assembled using BbsI. Level 0: basic parts (Promoter, RBS, Operon, GOI, Terminator) in E. coli-based entry plasmids, assembled using BsaI. Level 1: complete transcriptional units (Promoter-RBS-Gene-Terminator) in R. sphaeroides-compatible plasmids with antibiotic resistance marker, assembled using BsaI. Level 2: multi-transcriptional unit plasmids in R. sphaeroides-compatible backbone, assembled using BbsI. Arrows indicate double-loop architecture allowing recursive reassembly between Level 1 and Level 2.

Gerrich@gerrich· Apr 1

Ahhh , this can't be good! 🧪 I am not prepared for rejection. 🥲

Screenshot of a journal manuscript tracking timeline showing five completed steps (bottom to top): Submission checks complete (24 Mar 2026), Editor assigned (24 Mar 2026), Reviewers invited (25 Mar 2026), Reviewers agreed (1 Apr 2026), Reviews received (1 Apr 2026).

Gerrich@gerrich· Dec 25

Doing some tricky organic chemistry with "Feuerzangenbowle".

Gerrich@gerrich· Dec 15

Love it when a Golde Gate cloning result looks like this. 🦠

Blue white screening of colonies in front of a black screen. One can see lots of white colonies.

White and blue screening in front of a pink screen. It's the same plate , but a few blue colonies are visible in front of the pink screen.

Gerrich@gerrich· Dec 15

I am obsessing waaay too much about getting cited for my research this year.

A fake screenshot of a skeet from me. It shows a photo of 'me' holding my baby , which is my google scholar citation count. The left panel shows the citation count until last year , where it reached 18 citations per year. The right panel shows it until this year where 36 citations per year have been reached.

The text accompanying the photos says 'my yearly citation count is now twice as high as it was last year. It's on track to about 7.5 trillion citations per year in 38 years.'

This is a reference to a meme where a dad ironically assumes exponential growth of his child.

Gerrich@gerrich· Dec 10

My contamination made it into the @contamclub.bsky.social calendar for 2026! 🦠 I just got my copy. Also will send out some calendars as x-mas presents to friends and collaborators. 🎅🏻🌲

Me dressed up for christmas , with a red x-mas hat and next to a lit x-mas tree. I am holding the contamination club calendar for 2026 with April turned up. It displays a mount Fuji like colony growth of a contaminant.

Gerrich@gerrich· Nov 13

Me reading this thread on rebuilding lichen in vitro. I previously didn't question the claims of 'in lab lichen formation'.