Results for Fall 2008 semester Biopost

This semester our team finally developed a metagenomic library from a tropical and dry forest of Puerto Rico. From that library I with the help of some screened for antibiotic resistance for three antibiotics. I found antibiotic resistance activity in clones from each metagenomic library and for all three antibiotics respectively. These clones were inducted and a restiction analysis was done. From this study e obtained that there were different size fragments coferring resistance to the clones. That conferred resistance was confirmed by retransforming the cloned fragments to an isogenic strain of the bacteria we used to clone. From these studies we could measure the quantity of clones that had resistance to an antibiotic; study the different fragments obtained through the clones plated in each antibiotic; and finally to see if the gene conferring resitance was indeed in the cloned fragment and not a mutation in the strain’s genome the fragemnts were retransformed. We concluded that the gene coferring resistance was in the fosmid and not a mutation. The fragments that contain the gene conferring resistance will be sequenced. That sequence would be used to make an in silico analysis and frther study the mechanisms of the resistance in eac fragment.

ABRCMS was a conference were I exposed myself to a new experience in which I learned to communicate science to people doing things alike or have no experience at all in my field of study. I also exposed myself to different institutions were I would like to continue graduate of M.D. studies after I graduate. I met students like me making science. Learned a lot of things that are being researched on and heard and discussed new ideas that could lead to new research developments. I took conferences about graduate schools and how to fill applications. Took a workshop on how to study for the GRE exams, etc.

Bioblog Jan 09

On this semester I plan to sequence the fragments cloned that contain the antibiotic resistance and study new mechanisms that may appear or search for existing mechanisms but had not been studied using bioinformatics.  Based on my past work this is the mos important and detailed. It takes many procedures and readings to understand each of the components to be studied here. Plan to master the use of bioinformatics.

Biopost 25/10/08

I’m currently at a 70% aproximately of completition of my objectives for this semester.

Looking for antibiotic resistance is very important to be able to understand how mechanisms for resistance in bacteria work and for discovering new genes that could not be unravelled using cultivable techniques. The use of uncultivable techniques to find genes for resistance is a far more complete way than the cultivable ones. It reaches the 99% of the microbial environment that cannot be cultivated.

Biopost 25/09/2008

This semester I’m applying a restriction analysis technique on the antibiotic resistant clones obtained in the antibiotic resistance experiment out of three antibiotics that were chosen (ARA clones).  This technique enables me to compare between the ARA clones in each antibiotic to give an idea if those fosmids are related between them or not.

Concerning to the progress of the objectives of this semester I would say that we’re at a 60% of progress. 

Along the progress of the experiments we’ve been dealing with some difficulties still on developing the low molecular weight libraries from soils of forest in Puerto Rico. We’ve tried changing the vector and also doing the genomic DNA extraction more carefuly but none of these measures have been able to get us past that. We’ll work harder to get those libraries during the rest of the semester and also continue to screen for aantibiotic resistance.

Biopost 25/08/2008

On summer I spent a week or so at the University of Wisconsin at Madison taking a workshop at the Jo Handelsman’s Laboratory. There I learned many new techniques that will be used during the semester on the proposal. These techniques include genomic DNA extraction from soils using a freeze/thaw method to obtain gDNA of medium molecular weight. This technique is a direct DNA extraction method. Also we learned to use some equipment to which we were not used to see in Puerto Rico. From the workshop we were able to build an approximately 52,000 clone’s metagenomic library.
This semester my objective is to continue building metagenomic libraries from soils from different size gDNA (low, medium, and high molecular weight) and search for specific bioprospects in these libraries. Hopefully at the end of the semester we will be able to publish some work.
In respect to the past semester the methodology in general will be the same but with certain modifications to the protocols and development of some new ones from literature.
New techniques I’m planning to learn are the development of high molecular weight metagenomic libraries and selecting and screening methods (to apply to those libraries).

Biopost #3

During this semester I have been mastering techniques I learned last semester and of which some I mentioned in last entry. Whatsoever in general I’ve learned that in a laboratory one has to develop toughness and resistance to failures. Not always things in a laboratory go well. Better said is rare the occasion that something goes right. So, when something does go right CELEBRATE! because it doesn’t happen often. I got the opportunity to have a different perspective of observing biological processes and how to manipulate them to make the process more effective to our purpose.

Our team is struggling in a critical step of the project. That is, we haven’t been able to clone the competent cells effectively with the insert. We do have been successful in transforming the cells with the vector but no clone has been obtained that had an insert. Trying to solve this we are in a scientific paper’s search to see if we can find a different and/or better process to do this. Meanwhile we are trying to develop protocols to see if we find the solutions along with the professor.

For next semester, if all goes right, we are planning to screen the meta-genomic libraries we are working on to see if we can find bio-prospects in them.

Biopost#2

Ultimately in my lab I have been working on new techniques and machinery that gave the team a benefit of effectiveness in our research. Among these new techniques are electroporation, the chef mapper machinery, “worm cell extration” and some new vector extraction techniques. We have been working on these low molecular weight meta-genomic libraries since August 2007 but no library has been done, we are trying, still, to find the problem. The “worm cell extraction” technique is to extract high molecular weight genomic DNA from soils. Cell electroporation has many uses but we are using it to transform electrocompetent cells, which, as I said before, is more effective that the traditional way. The chef mapper is used to by electrophoresis separate better the DNA so we can take from the sample the molecular weight we need more effectively. The new vectors we are extracting are to find a better vector so we may transform the cells, because the one we used before apparently didn’t work but that is why we are extracting new ones so we may know if that is the problem. It is very difficult to find the solution to why the results we need do not appear but we are on our way to it.

I’ve visited some of my colleagues blogs and found them really interesting even though they are way far from my theme of research. Rey Yamil’s research is awesome because those alloys that he is studying could be used in time to replace bone structures, Irisbel’s research is interesting because it is possible that in this research she may find a new drug that cures neuro-degenerative deceases and Erick’s research is great because those cells he is working on are of great importance to bio-remediation, for example these cells could be used to identify contaminants in water or sources of a mineral in an environment. It has an infinite number of uses so rock on!!!!

Intro

Well, this is my first blog entry. The purpose of this blog is simple; I will let people know what is going on in my lab experience and diseminate useful information that anyone could need and/or would like to know.