Accomplished Work with Integron Integrases pressence in Organic Yogurts

Until now I have had interesting and favorable results within the research.  The first goal was to do a DNA extraction from the organic yogurt and I did various DNA extractions.  After the DNA’s extractions, our goal was to find if or if not there were integron integrases (Universal, class I,II, and III).  Before doing so, I did a PCR for the amplification of the 16S region, which was succesful.  Last week I ran a PCR to find the pressence of Universal Integrases from the yogurts DNA, it came out to be positive.  Having this good results we are looking forward to find integron integrases class I, class II or class III. 

My progress with the research can be classified as (3).  It has open my interest in not just the lactose products but also the organic ones.  Most people put their trust without question in organic products and this research has made me realize the importance in the different perpectives.

In Process to Obtain DNA from Lactose Products

     Since I started this novel facet of my investigation it has all been an accurate opportunity knowing that I was expected to stay working with the sequences analysis.  I have been introduced to the laboratory a month ago and I am in the phase of being educated on how to do the processes by my own.  During this month I have learned to use the autoclave and I did my first PCR of Intl1.  To extract the DNA from the yogurt, I had to prepare solutions of NaCl, in one of two of those solutions is where I poured the yogurt.  From there I learned how to do a filtration.  Also, I obtained DNA from an extraction protocol established by Dr. Rodriguez.  After having the DNA from the yogurt I ran an electrophoresis.   All of these processes are the ones I have been trained to do.

      Right now I found myself in the initial course of the investigation.  I have accomplished an intermediate process since I have to deal with getting to know how to use the laboratory equipment.  One of my difficulties is that I have to learn everything really fast and I have to pay attention to every detail.  Sometimes it is hard but I know that as time passes by I will acquire the experience needed to do a great work and become practically better.

2nd Semester in BioMinds

In this semester I’m in transition from an entirely theoretical work to a more practical stage of the research.  I’ll be extracting DNA and doing PCR to find out if integron integrases from class 1, 2, and class 3 are present in some daily use products.

@ the END…

My objectives during this first semester with the BioMinds program was to be capable to analyze DNA and protein sequences using as a model integron integrases sequences extracted from marine environments.  I used GeneBank to get sequences from the database bank.  Also, I worked with MEGA 4 to do alignments, to recover sequences, and to construct phylogenetic trees and do analysis.  While I analyzed the alignment and the phylogenetic tree I looked for additional domains, the conservative sites, and the catalytic residues that made integron integrases functional.

After all, while analyzing the alingment I found how the integron integrases have a additional domain compare to XerC and XerD.   These two are enzymes that belong to the tyrosine site-specific recombinase family.  I also found that the integron integrases acquired from marine environments conserve different sites that the integrases from other environments do not, but still are functional.  I would like to recall that in the alingment I found a sequence that its functional activity is due to question.  That sequence does not conserve many catalytic residues that are needed to express the integron integrase activity.  Because of that I found alignments and literary work so important.

For the next semester I’m looking forward to keep sequencing and to do PCR of the specific regions found to be conserved by integron integrases.  Also I want to prove that integron integrases exist in every environment and at broad conditions. 

I’d like to thank BioMinds for this opportunity! and Dr. Carlos Rodriguez for all his help and time.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

My experience visitng blogs and the new techniques I have acquired

After visitng three blogs, I realized how BioMinds prepares us not only in our research but also expanding our knowledge in a diversity of fields linked to science. 

 I visited the blogs of Pamela Silens, Abby Joyce, and Jessica Torres. The three of them were really diverse, but that’s how science is.  Pamela is working in the genetics field.  In her blog, she discusses that the way medicines react is due to genetic polymorphisms of the enzymes that metabolize them.  She is focused in the study of variants clinically relevant, so then she could determine if the results she gets are accepted from the one Hardy-Weinberg gives.  On the other blog I visited, Abby’s, I could not understand very well what the research main goal was.  From what I read, I know she is working in molecular biology and that she works controlling gene expression at the post transcriptional level in eukaryotic cells. She used a very technical language, may be that is why I could not understand most of the things that were written on the blog.  The last blog I visited was Jessica’s; I loved her theme.  She is isolating organic compounds from medical plants and crude extracts to treat diabetes type II.  I am very interested with her work because many members of my family suffer from diabetes type II and also because it gives them another way to treat the illness.

Sincerely, I would have never read another blog unless I knew the person.  I have to admit that I am glad I did it; I have learned so much… and by reading other blogs I have the will to improve the way I write mine.  I have realized how helpful these blogs can be for everyone. After all this time that I have been working with bioinformatics I have almost mastered the art of sequencing, making phylogenetic trees, and analyzing the information.  Even though it sounds really trivial, sequencing requires a lot of patience, especially when you have plenty of sequences that come from diverse environments.

Ciao!

Integron Integrases Conservative Sites

 Integron integrases (IntIs) are site-specific recombinases that form a subclass within the tyrosine recombinase family owing to the presence of a unique insertion that is required for activity, among other that from the data collected I conclude that they are important due to their conservation or alikeness in most of the integron integrases I have.

During the past weeks I have worked analyzing multiple sequences of a variety of integrons integrase.  Some of the sequences were obtained from the paper “Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents” –Enviromental Microbiology (2007), and others from sequences Dr. Carlos Rodriguez got when he extracted DNA from deep-sea samples that he collected form the Artic.  To compare if these integrons integrase were functional I used the sequence of  Vibrio cholerae integrase   (VchIntI4) as a rule, being this integrase one of the class 4, the longest and most antique.  As an integrase class 1 I used one from E. coli and as a class 2 one from Shiguella.

The main focus is for me to find the integrases that are functional by comparing their sequences in the alignment.  The sequences come from extremely cold or from extremely hot environments and yet I could find conservative sites.  Then I could do PCR of those…

Integron Integrases

Integrons are found in nucleic acid; plasmids, chromosomes, and transposons. They work as a system that leads to gene capturing; by wich they can incorporate, express, and disseminate pieces of DNA. This pieces of DNA could encode genes for antibiotic resistance, but not all.   Also, integrons cotain integrases; that are enzymes that enable its genetic material to be integrated into the DNA of the infected cell. 

                                                          

BioMinds =)

My name is Agnes and I’m part of the BioMinds program @ UPR.  I am a Biotech student from UPR Mayaguez, going through my second year of College.  Interested in completing my BA to study a Md.PhD  linked to molecular science.

 By now, in BioMinds, I work with Dr. Carlos Rodríguez-Minguela doing theorical research; reading papers and doing bioinformatics.  I might be one of the few working with theorical research, and because of that, if any of you need help with nucleotide sequences, proteins or phylogenetic trees; don’t hesitate in asking me.  I might be helpful!!!

  For those working with bioinformatics, I’m using the MEGA 4 program to do my work and as a guide I recommend a book from Barry G. Hall—  Phylogenetic Trees Made Easy.

                                     

Ciao!!!!!!  Good luck to all of the members of BioMinds!!!