The risk of disturbing a balance-Non-specific DNA attack

Although the result is good and probablely the result can tell me many things. Still several questions are unresolved. Firstly, even without antibiotic transformants can be detected. Secondly, cat gene can also be transformed in the similar way.

I observed another important phenomenon that transformants prefer grow near low antibiotic concentration region to the high region. This might be not surprise since all of us prefer some cozy places and bacteria as well. However, rec-2 mutant transformants does not like low antibiotic regions. Instead, most transformants appear at middle concentration and even a little high concentration place. What does it tell us? For application, it means that if we design a drug targeting on Rec-2/ComEC protein we will activate another transformation pathway and make things worse. I believe this type of transformation did not confine to plasmid. But indeed, it is hard to prove that this type of transformation also occur in genome. Because if it is true, then the type of recombination should not be homologous transformation. Since non-specific DNA has no homologous regions for recombination. Also, the host cell will employ diverse ways to protect the attack of exogenous DNA. Otherwise, this species will be 'eaten' by another species whoes DNA is highly infectious. Nontheless, non-specific DNA still have special skills to penetrate barriers because we can see their trace through genome comparison.

I have another interesting phenomenon as well. But I have to time to write because I have to do my experiments now.

Antibiotic also induces another transformation pathway

My experiment shows that antibiotic can induce the cryptic transformation. Importantly, transformation was not completely dependent on antibiotic because even antibiotic was abscent, still a few transformants were observed. This indicate the the ability of transformation is inherent and antibiotic just induce (not trigger) transformation. The addition of antibiotic can induce transformation in the rec-2 mutant about 20-fold. I was shocked. A paper published in Science reported that antibiotic can induce natural transformation in S. pneumonia. My data indicate that antibiotic can also induce the non-traditional transformation as well. Still, I do not know how antibiotic induce this cryptic transformation since we know little about it. This is a completely new area waiting for further investigation and the implication of this study is immense (read my post yesterday).

Butterfly effect in HGT

Although many people know the butterfly effect, the wave of butterfly wing at one corner of earth can cause tsunami in another place, many scientific researchers forget this story in their actual study unconsciously. Afraid of inexorable critique, only events with high possibility were concerned and events with low possibility and not easily detectable were neglected or were considered to be ignorable 'background'. Take recent research in genetic transformation for example. Admittedly, transformation with homologous DNA was much easier than that with heterologous DNA. As one can get more obvious phenotype in homologous transformation and the evidence with large magnitude difference in their data presented make the arguer standing on a better ground for defencing their theory. However, nature is not just arguing for theory. Like fatal diseases appear out of our conciousless but develop irreversible, many events take place unappreciable but with immense impact in the later phase. Although we get much information about the later events of tranfsormation, our recent transformation mechanism study is just confined to the tsunami and the butterfly was almost completely forgotten.

From the evolution perspective, homologous tranformation makes significant contribution to a special species, but make little impact to the whole ecosystem. The genetic communication between the same species is common to all over the eukaryotic and prokaryotic kindom. So, it is not surprise to discover natural transformation among bacteria of the same species with their own chromosomal DNA. However, this can not explain high frequency event of HGT among different bacterial species providing the information from comparing known genomes. Neitheir conjugation can explain this because gene communication in this form occurs only in conjugative plasmid, another special form of DNA with non-comprehensive impact. Butterfly event might edify us to find the right way to this important issue. The first step of explaning high HGT among different species is to prove that heterogenous DNA is able to be taken up and sucessfully transformed. For self-protecting, the frequency of heterogenous DNA transformation (butterfly wave) should be considerably low but the accumulation impact is high enough to change the whole bacterial world regarding information of genome comparing among species (tsunami).

The significance of the low frequency of heterogenous DNA transformation should not be negligible in our study since this might be the main channel through which different species communicate with one other. This communication would cause a long inevaluable impetus to the whole ecosystem in the background of the whole life history.

Pense plus et fait moin

To assay hofQ mutant from another lab, I used hofQ OUT and hofQ IN primers. Using hofQ OUT primers, no obvious difference can be found in hofQ mutant and WT because PCR product from the mutant is less than 200 bp smaller than that from the wild type. This is comprehensible. However, the appearance of stripe which is the same as that of wild type when using primer IN demonstrated that hofQ still exist in the genome. Strangely, I also PCR amplified out the corresponding stripe which indicating the existance of cat gene. This might imply that there are not only one hofQ gene in the genome and the lab who donates me the mutant might not completely eliminate all hofQ genes in genome. Nevertheless, I will reconstruct hofQ mutant after I finish my experiments in hand.

P1 transduction est OK. Il toujour comme ca. Quand le theorie est tres complex, la experimentation est tres simple. Au contraire, quand le experimentation est tres complex, on dois réfléchir. Parce que la nature aime bien simple en action. J'ai une l'autre idée qui peut simplier la experimentation mais peut me montre la chose tres importante. Je la pense ce soir. Si il marche bien, je vais ravir. Il faut qu'on recherche comme la nature. On pense plus et fait moin.

Today's expermient --Bad Luck!

I used ampicillin which was not prepared for a long time. However, lawn grow on selective plates. This must be resulted from the ineffectivity of ampicillin. I have experienced similar cases several times. I have to reprepare ampicillin tomorrow and try my experiments again.

My recent result is exiting. Because it suggested me that the rusty transformation machine works in a bacterium with different background. Does this means that the two transformation machines compete for translocation DNA IN different bacterial backgroundS?? If so, how do they compete? Which kind of mechanism controls the two? Before I know this, I have to characterize each of them. This a long long aim. Firstly, I have to recheck all my previous data firstly. The blamed ampicillin!

Leading from the past to the future

Continue the work done decades ago.