Field of Science

Is there DNA in oreos?

I have to weigh in on this.

I spend a lot of time discussing the idea that bacteria can use DNA as a source of nutrients, and audiences are always surprised when I show this graphic and point out that DNA is ubiquitous in our foods.  And these are scientifically sophisticated molecular biologists and microbiologists.

So it's not at all surprising to me that 80% of the general public would check 'Yes' when asked, in a set of survey questions about food labelling and regulation, whether foods containing DNA should be labelled as such.  Instead of laughing at their ignorance we should think about how much expert knowledge is needed to evaluate this issue.

Many people, if guided by a series of prompting questions, could figure out that there's probably some DNA in at least some natural foods. But would you expect someone who hadn't taken high-school biology, or took it a long time ago, to know the answers to any of these questions?
  • Is there DNA in meat?
  • Is there DNA in leaves?
  • Is there DNA in potatoes?  In rice?  In noodles?
  • Is there DNA in fruit?  What if you don't eat the seeds?  In fruit juice?
  • Is there DNA in beer?  In wine?  In scotch? 
  • Is there DNA in flour?  In butter?  In olive oil?  In oreos?
  • Is DNA destroyed by being cooked?
  • Does DNA break down (like some vitamins) when food is stored?
  • Does DNA dissolve in water?

RNAseq success!

The sequences are back for our big RNAseq project, and the big good news is that the RNA preps were of good enough quality to give useful sequences for all the samples!  Thos was very much in doubt, because the Bioanalyzer characterization of the RNA samples showed almost no detectable mRNA-sized molecules in the samples we tested.

Now we have all this data, we need to decide how to analyze it.  It's not just a big dataset but a very rich one since the samples differed in what can be considered to be three independent directions, all of which are underlain by rich sets of biological information about phenotypes and molecular events.

  1. Each sample was in one of two different culture media, either rich growth medium (supplemented brain-heart infusion, sBHI) or the competence-inducing starvation medium M-IV.
  2. Each sample is part of a time course, either three different cell densities in sBHI or four time points of a culture transferred to M-IV.
  3. Each sample has a specific genotype: wildtype, knockout mutations in well characterized competence-regulating genes (sxy or crp or cya), mutations that cause hypercompetence (sxy-1, murE747 or rpoD753), and other mutations that affect competence by unknown mechanisms (knockouts of hfq and of one or both members of the mysterious toxin/antitoxin system
  4. Most samples have one or two replicates, from independent cultures usually on different days.
Ideally we would first characterize the data quality of each sample, and decide if we need to apply any constraints to its use.  Then we'd do a very meticulous analysis of the wildtype cultures to identify the genes that change when cells become competent, followed by analysis of the sxy and crp/cya knockouts to identify the genes that are specifically responding to these regulators.  This would let us identify all the genes we know we should pay attention to when looking at the effects of the other mutations.

But I don't have a regimented team of minions to do exactly what I tell them.  There will be several of us working on this data set, with different skill levels and research goals.  So here's my tentative plan to keep us at least informed about what each other is doing.

Group blog: I've set up a group blog on Blogger, called The Sense Strand (great name, right?).  Each of us needs to post there to tell the others what we've done and what we've learned.  These posts should be in plain English, this is not a place for data files or code.

Gene-info: We have a big table of information about the known competence genes, and I'm going to convert this into a Google Docs spreadsheet that we all can edit, adding new genes and new information as we develop it.

Shared data files: We've created a shared folder on Google Drive, where we all will post copies of the useful data files we generate.

Code repository:  Finally, I've just learned how to create a shared code repository on GitHub (I'm doing the short Coursera course A Data Scientist's Toolbox, in preparation for their short R Programming course.)  We'll all use this to archive copies of the code we use to do our analyses.

Transformations with dirty DNA

The previous post considers ways to test the effects on transformation of chromosomal proteins bound to donor DNA, by gently lysing donor cells and transforming recipient cells with the crude lysate.  We've now done one experiment trying out some methods.

We used donor cells resistant to novobiocin.  We tried freezing the cells without adding the usual 16% glycerol as cryoprotectant, vortexing them with a drop of chloroform or in 0.0001% SDS to disrupt the membranes, with or without pretreatment with EDTA and lysozyme (0.1 mg/ml, 1/10 the normal concentration) to break down the cell walls.

One question was how efficiently different methods would kill all the donor cells.  If some donor cells remain alive they will form colonies on the selective plates used to isolate transformants, confounding measurements of transformation.  Freezing was surprisingly effective.  Many aliquots of a single 'late-log' culture (OD600 = 1.0) were originally frozen at -80 °C in their normal growth medium.  After thawing, 20-40% of the cells were still viable.  All the treatments (listed below) decreased viability, but most left 10,000 or more viable cells per ml.  But after the various treatments we froze the cells again, this time at -20 °C, and when these were thawed there were no viable cells.  This is good, because freezing/thawing is very easy and we don't expect it to disrupt the associations of chromosomal proteins with DNA.

We had 5 treatments:

  1. just chloroform
  2. just SDS
  3. lysozyme then chloroform
  4. lysozyme then SDS
  5. just lysozyme

After the various treatments we pelletted the remaining cells and/or debris, and used 10 µl and 100 µl of each sample as 'donor DNA' in transformations of sensitive wildtype cells.  We got LOTS of transformants from all the treated samples, sometimes as many or more than from an equivalent amount of purified DNA.  There were differences between samples but the causes are unclear.

Next steps:

Freezing/thawing:  try just -20 °C with no other treatment.  Does this kill all the cells?  Does it liberate transforming DNA?

Try less SDS plus lysozyme, and try a milder detergent.

To characterize the DNA, try running the treated samples in an agarose gel, say 0.5% agarose so that large DNA enters the gel.  Run samples ± lots of SDS, to see what difference bound proteins might be making.

Do chromosomal proteins on 'donor' DNA affect transformation?

I've started polishing my not-quite-good-enough CIHR proposal for what's called the 'Transitional Open Operating Grant Program' competition.  This is the last-chance-under-the-old-system competition; any future proposals will be evaluated under the new system, which doesn't have much use for pure science or small labs. Proposals are due March 2 2015.

Before then I'd like to do some preliminary experimental work on one of the studies I'm proposing. I expect that the H. influenzae DNA available to H. influenzae cells in the host environment will still have bound to it many of the normal chromosomal proteins (HU, H-NS. Fis), and might even retain aspects of the normal nucleiod structure.  I want to find out how this affects the ability of the DNA to be taken up by competent cells, particularly whether specific sequences or segments are affected more than others.

My poorly thought-out plan is to lyse donor cells carrying one or more antibiotic resistance alleles in a way that doesn't disrupt bindings of proteins to DNA (so not with 1% SDS), and then mix this lysate with competent sensitive cells.

Big problems I forsee:

1.  How to lyse the donor cells without disrupting the nucleoid proteins?

My original plan was to use the H. influenzae phage HP1.

I could probably instead lyse the cells with lysozyme and a small amount of a surfactant that disrupts membranes but not proteins.

2.  How to lyse the donor cells without killing the recipient cells?

If the recipient cells are lysogenic for this phage (I have such a strain in the freezer), then they will be resistant to the free phage in the lysate.  An undiluted lysate has an enormous number of phage (>10^10 per ml), but I'll dilute the lysate to a chromosomal DNA concentration of about 1 µg/ml, which would be saturating for uptake if the DNA had been purified.
(Hmm, what will be the chromosomal DNA concentration of a lysate?  Say 3x10^9 cells/ml, most of them lyse, 1,830 kb of DNA/cell, 10^-12 µg of DNA/kb...  That's only about 4 µg of chromosomal DNA per ml.)
I can dilute the DNA way more than this, because transformation has such a wide sensitivity range.  I could also make it difficult for the phage to infect by eliminating Mg, but that might also hinder DNA uptake (the normal competence medium is 10 mM Mg).  If I had antibodies to the phage I could block infection that way (we used to do this with lambda), but I don't.

If I lysed the cells with surfactant, I could then easily dilute the lysate to reduce the concentration of the surfactant to a concentration that wouldn't harm the recipient cells (10-fold or 100-fold wouldn't be a problem).

3.  How to kill off or remove all the donor cells that aren't lysed, without disrupting the nucleoid proteins?

I don't know if it would be possible to pellet the cells without pelleting the nucleoids, especially since the nucleoids and DNA may be still attached to the cell wall.  Or to filter out the cells without removing or disrupting the nucleoids.

I don't really need intact nucleoids, but I'd like to still have the proteins bound to much of the DNA.

How can I check the state of the DNA?  I hope I wouldn't need to use electron microscopy.  Maybe I could use a simple very-low concentration agarose gel? Like an Eckhart gel, but interested in the DNA+gunk, not the megaplasmid?

4.  How to kill off or remove all the donor cells that aren't lysed, without killing the recipient cells?

If the recipient cells are already resistant to an antibiotic that the donor cells are sensitive to, I can include this antibiotic in my selective plates.

Or maybe I could kill them by adding a bit of chloroform to the lysate, and then diluting or evaporating the chloroform before I add the lysate to the cells.  Chloroform is normally used to sterilize phage lysates, but I don't know if it would affect the nucleoid proteins.

Interaction of a ∆hfq mutation with the rpoD mutation

Here's the last part of the summary of what our senior co-op technician has been doing.  The last set of experiments tested the interaction between a new ∆hfq mutation we've been studying, which reduces competence) and the rpoD mutation (which increases competence).

The Hfq protein binds small regulatory RNAs, helping them to form base-pairs with the mRNAs that they regulate.  In other bacteria we know that this base pairing can either reduce the mRNA expression (usually mediated by RNase E degradation) or increase it (by reducing the effect of otherwise-inhibitory mRNA secondary structure).  Our ∆hfq mutation reduces competence in MIV-induced cells by about 10-fold, suggesting that it increases the translatability of sxy mRNA.

The technician tested whether this effect is still seen in cells with the rpoD mutation.  She first had to construct the double-mutant strain.  This was relatively easy because the ∆hfq mutation is 'marked' with a SpcR cassette, and the honours student who's studying this mutation had already made chromosomal DNA.  So she used his chromosomal DNA to transform strain RR753 (rpoD mutant) to spectinomycin resistance.

She then did a competence time course, following development of competence in rich medium in four strains.  In the graph below we see that the ∆hfq mutant (green line) develops competence later than the wildtype cells (KW20, blue line) and to a lower final level.  This mutation also reduces the competence of the rpoD mutant (compare red and purple lines), although not as severely.

So we conclude that, whatever Hfq is doing to promote competence, it's still at least partly needed by the rpoD mutant.

The honours student has been analyzing the interactions of the ∆hfq mutant with other factors and other hypercompetence mutations.  I'll do a separate post pulling this together, unless he does it on his blog first.

Effects of cAMP and AMP on competence development by the rpoD mutant

This is a continuation of yesterday's post on the phenotype of our hypercompetent rpoD mutant strain RR753.  Yesterday we wrote about its behaviour under 'normal  growth conditions, and now we're going to consider two new factors, cyclic AMP (cAMP), which induces competence under what are otherwise non-inducing conditions, and AMP, which inhibits competence development under what are normally inducing conditions.

First the effect of adding cAMP: We tested this by adding 1 mM cAMP to cells growing exponentially at an OD600 of 0.1, and measuring transformation 60 min. later.  At this growth stage, normal cells do not transform detectably, but addition of cAMP turns on sxy transcription.  Some of the resulting sxy mRNA is translated and the Sxy protein acts with CRP to stimulate transcription of genes encoding the DNA uptake machinery.  In the tech's experiment, cAMP addition raised the transformation frequency about 500-fold, from 1-3 x 10^-8 (just at the detection limit) to 6.5-8 x 10^-6.  The rpoD mutant is somewhat transformable even with out cAMP (01-3 x 10^-6), and cAMP addition raised this about 100-fold, to ~2 x 10^-4.

So we conclude that the rpoD mutant does not bypass the need for cAMP in competence induction. This rules out the boring hypothesis that changing Sigma 70 activity perturbs cellular metabolism, causing an elevation of baseline cAMP levels that in turn causes the mutant's increased competence. Instead it's consistent with our interesting hypothesis that the rpoD mutation likely changes one or more events after the sxy transcription is stimulated by cAMP and CRP.

Next, the effect of adding AMP:  Maximal competence is normally induced by transferring exponentially growing cells from rich medium to a 'starvation' medium called 'MIV' and incubating them for 100 min.   Previous work has shown that adding purine nucleotides or nucleosides (usually 1 mM AMP) to the MIV prevents normal competence development by reducing the translation of sxy mRNA (Sinha et al. 2013).  The next experiments tested whether AMP has the same effect in the rpoD mutant.

Both wildtype and rpoD mutant cells have high transformation frequencies after incubation in MIV. In these experiments the rpoD cells had slightly higher transformation frequencies (about 4 x 10^-3) than the wildtype cells (about 1 x 10^-3).  Adding AMP to the MIV used to induce competence reduced the transformation of wildtype cells more severely than seen in previous work, about 5000-fold (from 1.7 x 10^-3 to 3.4 x 10^-7) and at least 10,000-fold (from 3 x 10^-4 to 3 x 10^-8).  The AMP also reduced the viability of the cells by several fold. (Both replicates gave no transformants at all with added AMP, so these estimates are upper limits.)

Added AMP also reduced the transformability of the rpoD mutant.  The first replicate gave no transformants (the plated cells were too dilute) indicating that transformability as reduced at least 1000-fold, and the second replicate showed a ~6700-fold reduction.

These numbers are all lower than previous results, but the conclusion is clear that adding AMP to the MIV medium strongly inhibits the development of competence in the rpoD mutant.  We don't know how the added AMP caused the reduction in competence, but, based on other evidence from analysis of purine-biosynthesis mutants, I've hypothesized that the key factor is a decrease in the concentration of another metabolite (PPRPP), which maybe interacts with sxy mRNA.  Production of Sxy by the rpoD mutant is still sensitive to this effect, so... (I don't know what).

Phenotype of the rpoD mutant

This mutation causes H. influenzae cells to become competent prematurely, and to reach levels of competence in rich medium that are about 100 times higher than normal cells.  The mutation causes a single amino acid substitution in domain 3 of the 'housekeeping' transcription factor called 'sigma 70'.  rpoD is an essential genes, needed for transcription of most housekeeping genes.  Since the mutant strain (named RR753) shows only a very slight decrease in exponential growth rate we think the mutation causes only a very minor change in the protein's function

My earlier post this morning said I had never explained my hypothesis about how this mutation causes increased competence, but actually I did, briefly here.  Here's the key sentences from that post:
My hypothesis is that the mutation's effect on transcription of sxy mRNA increases competence by increasing sxy translation.   I've long hypothesized that slowing elongation or increasing pausing in the 100 nt segment of sxy mRNA that forms its regulatory secondary structure will promote sxy translation by increasing the ribosome's access to the sxy ribosome-binding site and start codon. 
Then I listed some low-tech phenotypic analyses that the senior of our two co-op technicians could do:
  • Is RR753 sensitive to the inhibition of competence by added purines?
  • What's the effect of an hfq deletion in this background?
  • How does this strain respond to added cAMP?
  • How does it respond to the standard competence-inducing MIV treatment?
  • Does the mutation increase competence of a sxy mutant (sxy6) that has an extra-stable secondary structure?
  • Does it further increase log-phase competence of the sxy hypercompetence mutants, which have weakened sxy mRNA secondary structures?
She's now done all but the last of these, and we're considering what she should do next.  So here we're going to summarize what she's found and what we think it means.

Her first experiments gave a better characterization of RR753's growth rate.  She's done both Bioscreen growth curves (high-precision analysis of exponential growth) and manual ones (lower precision but better for cultures at low and high densities).

First the Bioscreen results:  Here growth of RR753 (red line) is compared to wildtype cells (KW20) and two other hypercompetence mutants, RR563 (sxy-1) and RR749 (murE).  This clearly shows the slightly slower exponential growth of the rpoD mutant.

The Bioscreen analysis measures OD600, so it doesn't tell us about the actual numbers of viable cells. The tech has also done a number of manual growth curves, mostly as control parts of experiments examining other variables.  These agree with the Bioscreen results in showing usually a slightly slower exponential growth rate, and no obvious differences in later survival.  

Her next time courses replicated my earlier measures of transformation frequency.  It looks like the rpoD mutant differs from the other hypercompetence mutants (in sxy and murE) in having very low competence at very low cell density, perhaps as low as that of wildtype cells.  The other mutants at 100-1000-fold more competent than wildtype cells at very low cell density. The rpoD mutant may also become highly competent at lower cell densities than wildtype cells, but may not be any different than the other hypercompetent mutants - these data are hard to interpret.

What could be the significance of having very low competence at very low cell densities?  I'd been assuming that the moderate competence of the sxy-1 hypercompetent mutants at low cell density reflected a baseline level of sxy transcription and an increased efficiency of translation.  If the rpoD mutation acts as I've hypothesized, it should have the same effect.  Provided the cells are in real exponential growth, the cell density shouldn't matter.  Might the rpoD mutant have two different 'exponential' growth phases, one at very low cell density and another at moderately low cell density?

Is this an important issue?  It would be quite a bit of work to investigate carefully, so let's set it aside for now.

The next experiments analyzed the effects of adding cAMP (known to stimulate transcription of sxy) and AMP (known to reduce translation of sxy mRNA).  I'll leave these for the next post.

What should our 'senior' co-op tech do next?

We have two co-op (undergraduate) technicians at present (paid from the last of our leftover CIHR funds).  Each is with us for 8 months; one started in May and the other in September, so there's a 4 month overlap.

The senior one has done almost all of the work preparing the samples for the RNA-seq project, and lately she's also been doing competence time courses to characterize the phenotype of our hypercompetent rpoD mutant.  She's looked at growth conditions, at the effects of added cAMP (competence up) and added AMP (competence down), and the effects of knocking out the small-RNA regulator Hfq (down).  Writing this post makes me realize that we haven't summarized her results anywhere, so I'll sit down with her and pull it all together this morning (I think that will be another post).

Now we need to decide whether there are still more rpoD phenotype assays she should do, or whether she should move on to another project for her last two months.  Since I hypothesize that the rpoD mutation causes competence by slowing sxy transcription and increasing its mRNA translatability, she could assay the effects of of the rpoD mutation in combination with our various sxy mutations that affect its mRNA translatability.  But this would be very much a fishing expedition, lots of work but probably no new insights (because it's not testing any specific hypotheses).

Hmmm, looking back, I discover that I've never written a blog post clearly explaining the general hypothesis about how the rpoD mutation causes hypercompetence.  I think it's time I did that.

So long since I've posted...

But here's an update on the RNA-seq saga.

We've been struggling to get evidence that our RNA preps are of good enough quality for library preparation and sequencing.  Because the Ribo-zero kits that we use to remove the rRNA from the samples are so expensive, we wanted to be sure the final mRNA concentrations and integrity would be good enough to make the equally expensive sequencing worthwhile.

Unfortunately my attempts at using a Bioanalyzer have been very frustrating (and it's not cheap - several $ per sample), with odd smeary/spiky patterns and poor recognition of the size standards. This is partly because the concentrations are so low and the 'pico-RNA kits are very fussy, and partly because it's just a fussy procedure and easy (for me) to make mistakes.

We sought advice from the person who will be preparing the sequencing libraries for us.  She said that samples that appeared bad on Bioanalyzer results often gave excellent sequencing results, and suggested that we have her prep an initial 8 libraries.  She would then pass these on to the person who does the sequencing, who could just run her initial quality checks on the libraries and tell us whether there were suitable for sequencing.  So that's what we did, and the news was good - these initial libraries look OK.

Now it's time to do the Ribo-zero and final clean-up on the rest of the samples, so they can be handed over for eventual library prep and sequencing.  There's a two-month backlog so we likely will get the results as a Christmas present.

Our sample processing had been a bit scattershot, so now I needed to go through the sample information and make sure we have the right samples, and that the numbers add up.  They do, so I think we're all set to quickly complete the remaining Ribo-zero treatments and use RNeasy-Min-elute columns to clean up each RNA sample after Ribo-zero.  Then the remaining 64 samples can be handed over.  (The 'we' here is our excellent UBC-Co-op program technician.)

We have accidentally wasted two of our Ribo-zero treatments on duplicate samples, and I was thinking that this meant that we'd have to buy another 6-sample kit ($650).  But now I think we can get by without this, either by not treating two samples (the G6 samples in the table above) or by using slightly less of the reagent for a subset of samples.

We had been using only 1 µg of total RNA for Ribo-zero treatment, but for these samples we'll sue all the DNase-treated RNA we have (typically several µg).  In some cases the volume of sample will be too high (max 28 µl for Ribo-zero), but singe the samples are in H2O we can just evaporate them a bit to decrease the volume.

Possible work with the new rpoD mutation

I'm up to my ears preparing materials for the new version of Useful Genetics, but we have a great new technician through UBC's Science Co-op program.  She's nearly finished the work preparing the RNA samples for our big RNA-seq project, so it's time to consider what she should work on next.

One possibility is characterizing the newly identified rpoD mutant strain.  This strain (RR753) has a point mutation in HI0533, which encodes the sigma factor that regulates initiation and early elongation of transcription of 'housekeeping' genes, especially during exponential growth.

One analysis we need is BioScreen growth curves of the mutant and a wildtype control, to confirm the preliminary growth curve data suggesting that this mutation causes slightly slower cell growth (lower graph).  I think this slower growth results from a general slowing or minor disruption to normal transcription of many genes, and is not specific to its effects on competence. 

My hypothesis is that the mutation's effect on transcription of sxy mRNA increases competence by increasing sxy translation.   I've long hypothesized that slowing elongation or increasing pausing in the 100 nt segment of sxy mRNA that forms its regulatory secondary structure will promote sxy translation by increasing the ribosome's access to the sxy ribosome-binding site and start codon.  We're not in a position to dive into the molecular analyses of RNA and protein that will probably be needed, but I wonder if there are some genetic or culture-conditions approaches that will shed light on the situation.
  • Is RR753 sensitive to the inhibition of competence by added purines?
  • What's the effect of an hfq deletion in this background?
  • How does this strain respond to added cAMP?
  • How does it respond to the standard competence-inducing MIV treatment?
  • Does the mutation increase competence of a sxy mutant (sxy6) that has an extra-stable secondary structure?
  • Does it further increase log-phase competence of the sxy hypercompetence mutants, which have weakened sxy mRNA secondary structures?
I think the technician is going to be doing a lot of competence time-courses...

CIHR depressing

The results have been released for the latest competition for operating grants from the Canadian Institutes for Health Research (Canada's equivalent of NIH).  Our proposal was ranked 13/72 by its assessment committee (Microbiology and Infectious Disease), but they only funded 11.

This is our 7th failed CIHR proposal in a row.  They all had good scores, and several, like this one, were very close to being funded.  The scores show that our proposals do keep getting better (this time 4.5/5), but the funding cutoffs also keep rising and we're never quite good enough.

Will I try again?  Perhaps not.  This was the last round under the old funding system, and the new system is even less favourable to the small-lab fundamental research that we do. 

I'm not quitting research.  For this year we have funds left from a previous CIHR grant (must be all spent by the end of March), and after that we'll potter along on our very small NSERC grant.  Luckily most of what we do isn't very expensive, but I can now only support one grad student, supplemented with several excellent undergrads who'll work mostly for free.

More cell preps for RNA-seq analyses

Unfortunately we have to repeat most of the cell preps I made for the big planned RNA-seq analysis , because our RNA preps used up all the cells without producing any RNA.

The main problem was that we were using a Qiagen RNeasy Plus kit (designed to remove contaminating DNA) instead of the usual plain RNeasy kit.  I had bought the Plus kit because of a cheap introductory price, planning to just leave out the final 'on-column DNase digestion step, since this hadn't been very effective in the past.  However Qiagen had changed the kit without changing its name, replacing the final 'on-column' digestion with an initial pass through a 'G-DNA eliminator column' (before the usual RNeasy column steps).

The kit instructions didn't say anything about its suitability for bacterial cells, so I contacted Qiagen technical support.  They assured me that, although the kit would not remove DNA from bacterial cells, it would give a normal recovery of RNA.  What they didn't tell me was that the initial detergent treatment would not lyse bacterial cells - at least I think this must be the reason we didn't find any RNA when we ran all our RNA samples in a gel and a Nanodrop spec.  We had also processed some samples with the normal RNeasy kit, but most of these can't be used because we need complete sets of samples from replicate cultures.

Qiagen responded bvery well to my complaint about our results, providing us with two new RNeasy kits and 500 ml of the RNA Protect solution.  But we still have to do the work of regenerating the samples.  Luckily we have a very competent new technician, hired through UBC's Biology CO-op program, and she's doing most of the work.  In particular she's regenerating the samples of cells during induction of competence by our MIV starvation medium.  But tomorrow I'm going to (finally) spend a day in the lab generating all the samples from cells growing in rich medium.  This is 9 cultures, with 3 samples from each.

I think I can do them all in one day, if I plan carefully.  So here's some planning:

I'm collecting cells at three different densities:  OD600 = 0.02, 0.6 and 1.0.  I freeze pellets from 2 ml of cells for RNA prep (3 tubes with 0.67 ml cells and 1.3 ml RNA-Protect) and 1 ml of cells with 0.25 ml 80% glycerol, for later testing of transformation frequency if needed.  The OD 0.02 cells need to be concentrated 10-fold before freezing so we'll get enough RNA from them, so I need to start with a larger-than-usual volume of cells - last time I used 75 ml.

I'll be starting with the OD=0.02 cells frozen in glycerol in the last preps, rather than from fresh cultures.  These cells are already in log phase; I'll just pellet them to remove the glycerol and resuspend them in the 75 ml sBHI.  The initial density will be about OD=0.003, but previous experiments suggest that not all these cells will be viable, so the cultures may take several hr to grow back to OD=0.02. Then I'll concentrate 40 ml by filtration, resuspend the cells in 4 ml, and freeze 2 ml for RNA and 1 ml for competence assay.  The remaining culture (~ 20 ml after OD sampling) will continue shaking to OD=0.6 and OD=1.

I'll need to have the filters ready, and all the tubes to put the samples into, each labelled and preloaded with RNA-Protect or glycerol.

What are the cultures?

  • 3 replicates of KW20 (names on tubes: FK, GK, HK)
  • 2 replicates of murE749 (names: G7, H7)
  • 2 replicates of sxy1 (RR563; names: G5, H5)
  • 1 replicate of ∆crp (RR668; name: FC)
  • 1 replicate of ∆sxy (RR648; name: G6)

Why isn't competence regulated by the availability of DNA?

Most bacteria tightly regulate the genes that enable them to take up DNA from their surroundings.  This makes sense, since the uptake machinery is complicated, probably expensive to produce, and may interfere with other membrane functions, and since the benefits of DNA uptake may arise only under particular circumstances.

The regulatory signals include diverse physiological and environmental cues. In other posts I've discussed the signals that regulate H. influenzae competence, and here's a couple of recent reviews for Gram-negative and Gram-positive bacteria (;  (Unfortunately neither is open access, sorry.)

But none of these bacteria are known to regulate competence by what should be the most important information - whether or not there's any DNA in their environment to take up.  I say 'known to' because in fact there is almost no published information addressing this point, and the researchers I've contacted don't know of any relevant data. 

It's possible that bacteria don't need this information because DNA is always within reach in their environments, but we don't really have data addressing this point either.

My lab has a new undergrad who doesn't yet have a project to work on.  I wonder if he'd like to test this point, first in H. influenzae and then maybe in other competent species?  Given the lack of positive evidence I'd expect negative results (external DNA doesn't affect competence), but I think this might be a case where negative results would be publishable.

The tests are tricky because addition of external DNA is also how we sensitively measure competence, so we might need a way to get rid of the 'inducing' DNA before measuring competence with the 'assaying' DNA. And good controls...

UBC's new website

Here's the email UBC sent everyone the day before they launched their new web presence:
"To the UBC Community,

We are pleased to announce that a significantly redesigned website will launch on April 25th, 2014.

Consultation and research showed that the current site could do a better job reflecting the true nature and scope of our university. The navigation, content
and functionality of the current site makes it difficult for our visitors to find the information they are looking for and the overall look is considered conservative and dated. The redesign addresses these challenges; it is bold and experiential, offering improved design, navigation and content. A few highlights of these changes are:

1. Moving from a solely internally-focused navigation structure to one that is also audience-based

2. Expanding the opportunity for faculties and units to share their content through a new homepage section called “UBC Now”

3. Creating innovative and in-depth stories on the homepage that illustrate the impact UBC is making in the world

4. Implementing secondary pages that provide a stronger introduction to internal UBC partner sites to improve site navigation and hand-off

We are encouraged by the positive feedback we have received from those who have seen the site while in development and will continue to monitor its performance and fine-tune as required following launch.

We wish to thank the large number of contributors from across our campuses for bringing their energy and ideas to the project.

We invite you to explore the site in the days ahead:

Kari Grist
Managing Director
Communications & Marketing

UBC a place of mind"

 And here's the home page:

Actually there are several other versions with different photos, all of people evidently thrilled by what they're discovering at UBC.  The little dots in the ring around his head are links to pages about specific aspects of UBC's wonderfulness.

And here's the obligatory xkcd cartoon.  Rich FitzJohn found this and points out how obedient UC remains to its precepts.

A new mutation causing hypercompetence

I described last month how we were revisiting on old hypercompetent mutant whose causative gene was unknown.  I rechecked its phenotype and prepped DNA to sequence, from both the original EMS-induced mutant strain (strain RR735) and from a 'backcross' strain where the unknown mutation had been transferred to an unmutagenized genetic background by transformation (strain R753). 

Here's the phenotype again.  The lower graph shows that it grows slightly slower than wildtype, and the upper graph that it has a 10-200 times higher transformation frequency in the rich medium sBHI.

The postdoc just emailed me the sequencing results.  Both the original and backcross strains have the same single mutation, an amino acid substitution in the rpoD gene, which encodes the sigma-70 transcription factor.

This is a surprisingly clear result.  We had expected to find many EMS-induced mutations in the original strain, and probably several mutations in the segments of DNA transferred in the backcross transformation, and were planning another series of analyses to sort out which mutation causes the phenotype.  But both strains have only the one rpoD mutation, suggesting that our EMS mutagenesis wasn't nearly as heavy as we had thought.  As controls we had sequenced the original and backcross strains of another hypercompetence mutant (RR749, known to have a mutation in I, and both these strains also had only the single known mutation.

A hypercompetence mutation in rpoD fits very nicely into my thinking about how competence is regulated.  I'll write a separate post about this.

Cell preps for RNAseq are all done

I'm pretty sure that I've now done all of the cell preps for our big planned RNAseq analysis, more or less as diagrammed in the previous post. 

Instead of a cya knockout mutant as a negative control (pink in the diagram I used a crp knockout.  cya encodes the enzyme that synthesizes cyclic AMP (cAMP), and crp encodes the transcriptional activator CRP, whose ability to induce transcription is entirely dependent on cAMP, so the two mutants have the same phenotype - inability to induce both the competence genes and the energy-balance genes in the CRP regulon.  I decided to use the crp mutant partly because that strain grew up first and partly just in case there are traces of cAMP in our sBHI medium.  I did one MIV-competence time course with this mutant (4 samples) and one sBHI time course (3 samples rather than the 2 in the diagram).

I also did 3 sBHI-timecourse samples of the sxy knockout as another negative control (also pink in the diagram).  I think I now have two more samples than will fit in 3 lanes of sequencing (24 samples multiplexed per lane), so I'll probably omit the OD=0.6 samples of the negative control sBHI timecourses.  But I'll process the RNA from them just in case something goes wrong with another sample.

I found my missing DNase.  I hadn't lost it, just ordered the wrong kind.  So now I have $250 worth of a high-quality DNase I don't really need, and will need to order the right kind.

I'll get to the RNA preps once I get some teaching responsibilities under control - partly the grading for my face-to-face Human Ecology course but mainly the need to rerecord ~150 lecture videos for Useful Genetics/Genetics for Life.

RNA-seq progress, problems and plans

I've been growing the cell preps for the RNA-seq analysis, as shown in the planning figure below.

I did Day C's cultures, freezing 1 ml of cells for later transformation testing if needed, and 2 ml of cells for RNA purification.  The first snag was the invisibility of the cells!  Following instructions from the former RA, I mixed 2 ml cells from each of the first samples with 4 ml of the magic 'RNAprotect' reagent, let the mixture sit for 5 min at room temperature, and spun down the cells (2 ml of mixture in each of three 2 ml tubes) in our mini-spin microcentrifuge.  The plan was to discard the liquid and freeze the cell pellets at -80 °C, for later RNA preps.  But there was no visible cell pellet!  This amount of cells typically forms a small but easily visible pellet when centrifuged, but the bottoms of the plastic tubes looked perfectly clean.

I spun the tubes again - still no pellet.  So I pretended a pellet was present, discarded the liquid, and froze the apparently empty tubes anyway.  I checked the RNAprotect instruction booklet which reassuringly said that sometimes the pellet might be invisible, but I also contacted the RA, who said that her preps had given clearly visible pellets.  Later I thawed out one tube and did a wilful-suspension-of-disbelief RNA prep using the RNeasy kit, which produced the same concentration of (high-quality) RNA as the RA's original preps.  So I'm now assuming that there are invisible cell pellets in all the tubes, and I've done Day D's preps.

The RNAeasy kit also had some surprises, a solution that was supposed to be clear (or with a bit of particulates that could be removed by centrifugation), instead was very cloudy, and centrifuging it raised the cloudy material to the top (as a diffuse scum) rather than pelletting it.  I couldn't get rid of the scum (it just redispersed when I tried to pipette it), so I went on to the next step (adding 100% ethanol), which eliminated the cloudiness completely.  (Maybe this cloudiness came from the presence of too much residual RNAprotect in my tubes - because I couldn't see any pellet I didn't thoroughly drain the tubes before freezing them.)

I would have also tested the DNA-elimination step, which uses Turbo Dnase and a DNase-inactivator chemical.  But my brand new box of TurboDNase ($250) has gone missing.  I've searched the freezer a couple of times, and racked my brain in case I put it somewhere special for 'safekeeping', with no success. My next step is to go down to Stores and have them show me exactly what the TurboDNase box looks like, so I know I have the right search image.

I've also revised my plans for the cells I'll test.  As I wrote earlier, I'm only going to do one replicate of the ∆hfq mutant in MIV, since we really should use special precautions to avoid losing small RNAs from the prep (and maybe to do strand-specific sequencing).  Since we planned on three full lanes of Illumina sequencing, each 24-fold multiplexed, this change opens up space for 8 additional samples. Four of these will come from a MIV time-course using a crp or cya knockout strain (in Day E, which will be tomorrow).  This is an excellent control since it lets us identify all of transcripts dependent on the transcription factor CRP.  I'll also include both crp (or cya) and sxy knockout strains in the rich medium cultures on Day H; taking two time points for each will give the four additional cultures to complete the first two lanes of sequencing. 

Big prep of MAP7 DNA

We're almost out of the standard DNA that we use in our transformation assays.  It's chromosomal DNA of a strain called MAP7 (because it contains point mutations conferring resistance to seven different antibiotics).

So I grew up a liter of cells and prepped DNS from them.  Now I have 25 ml of nicely viscous DNA solution.  It's transparent and colourless but I suspect it's not really pure yet, so I'm doing a second purification on 0.5 ml just to check if the apparent concentration or purity changes when examined with the Nanodrop spectrophotometer.  I'll also do test transformations, with the last of the old DNA preps as a control.

Later:  The Nanodrop spec found that the repurified DNA had half the concentration of the big stock. So I ran a gel and found that the big stock still contains a lot of RNA.  My original RNase step must not have worked very well, probably because of the high concentration of SDS and of proteinase K.  So I';ve now incubated the prep with more RNase overnight.