BioMINDS Poster Presentation

Yay!! I got data for my poster. I did all I proposed to do this semester in two weeks in the lab. I had to work night and day but it was worth it because I found some pretty interesting facts.

I was supossed to evaluate 3 of my fellow scholars. Overall their poster were very goodand their presentations were excellent. I was surprised that their research is really good. I mean it’s really good science and interesting topics.

However, the poster session and the conference overall, wasn’t well planned. There was no room at all between posters, and while looking for those you had to evaluate, you interrupted fellows that were presenting.  In addition, the time for presentations just wasn’t enough. I would recommend for next time to limit the speaches and trivial talks, so we can have time and space for our presentations.

Here is the abstract of my poster.

 

Characterization of Bacterial Communities Associated to the Phyllosphere of Coffea arabica by 16S rDNA Profiling

 Fransheska J. Rivera Vega1 and Arturo Massol-Deyá2

1Industrial biotechnology Program, University of Puerto Rico, Mayagüez, PR

2Department of Biology, University of Puerto Rico, Mayagüez, PR

Category: Microbial Ecology and Microbiology

Phyllosphere is the term utilized to describe the habitat of the aerial part of a plant. This habitat can be colonized by microbes and in comparison to other microbial habitats non exhaustive examination of it has been done. Bacteria are by far the most abundant inhabitants of leaves and contribute greatly in many processes of global importance. They contribute to the behavior of the individual plant to which they are associated, as well. The diversity of bacterial profile of a plant can differ among the same specie and different species. This can be caused by large fluctuation in the physical and nutritional conditions characteristic of a particular phyllosphere. In our study we explored the bacterial communities associated to the phyllosphere of Coffea arabica individuals through culture dependent methods. Collected samples were washed in 10X PBS Tween 20 and an aliquot of this solution was spread on R2A + Nistatine + Ciclohexamide media. Plates were incubated for 48 hours at 30°C. DNA from grown bacterial colonies was isolated and 16S rDNA amplified with a fluorescent primmer for terminal restriction fragment length polymorphism (tRFLP) analysis. Results suggested genetic diversity among different individuals of the same species. A similar genetic pattern was observed on different leaves of the same individual. This study will set base of the expected bacterial communities associated to the leaves of coffee trees for future culture independent studies.

 

Research Update!

It has been a little bit difficult to work in the lab since this is my last semester and I’ve been doing interviews for grad school. However, I would say that, according to the scale, I’ve had a progress of 2. I know I should have at least 3 by now, but I haven’t had the time. I’ll work hard to have some data for the poster presentation, I promise.

 

Back to School, Back to the Lab!

Hi!

This semmester I’m back to school for one last semmester and back to Dr. Arturo Massol’s lab. After my last summer experience, we have decided to give our project a little twist.

Since it has been so difficult to isolate the DNA utilizing culture independent methods and we do not have a genomic filing of the microbial comunnities, we decided to do both, culture dependent and culture independent. This approach is virtually opposite of the previous one but will provide more quantities of DNA that can allow us a more effective screening of the cultivable microbial communities. 

I hope to achieve my previous goals with this new approach. I know this experience will be different from other beacuse of the techniques I will use and so I’m looking forward to it. This project has a  great potential for a master’s student, so I’ll try to make it work so someone else can keep on with it.

I’ll keep you posted!!

 

Industrial Internship Finale

The semmester has come to an end and stil I have not recieved propper training on the ProteomeLab PA800. Because of this, all my research and my proposed goals have been delayed. So I had to figure out myself how the system works. Right now I’m waiting for the upstream research done on our target protein to finish the purification so I can verify the samples and characterize the protein. I can’t wait to run a real sample. Technically I won’t leve without the training because the equipment’s vendor will come during the first two weeks of December to give the training. By then it would be just to late. 

I must admit that this experience is not what I expected. This experience has only made me more hessitant to working in any industry ever in my life. Not just because of the barriers that I have encounter to do my job here, but of the whole industrial environment. I don’t like it even a little bit.

During the rest of my internship, I’ll try to design a protocol with the knowledge that I have acquired on my own. 

I hope next semmester is more exciting than this one. I’m still not sure on what project I wll be working on.

 

Mid-term Assesment on Industrial Internship

Hello World!

I have to say that working in industry is not as easy as I thought. It is a lot more complicated system than just going to the lab and doing your things at your own time. In industry you have weekly schedule to follow and you cannot alterate much of it. I would have to asses my progress with a number 3. I have recieved all trainings on the high tech equipments that I mentioned I was going to, but because of circumstances I cannot control, I haven’t recieved much training on the capillary electrophoresis system. Once again, the system is complicated; and I do not mean the equipment. At least I know basic procedure like system maintenance and I have self studied most of the applications of the equipments. 

To be honest, I’m getting desperate. I can’t wait to do real science. I have prospect samples already to analyze but I can’t do it. On the other hand, I have also learned some procedures and protocols that will help me later when I’m a principal investigator and I need to set up my laboratory. 

I has been a good experience but it could have been better and greater.

Good luck to all my fellows on their respective research.

 

Industrial Internship – A whole different world

As part of my curriculum as an Industrial Biotechnology student, I have to do an internship this semmester in a biotech company. I’m doing my internship at the Bioprocess Development and Training Complex, also known as BDTC. The mission of the BDTC is to promote the growth of the biotechnology industry in Puerto Rico and the Americas by: 

• Providing biotechnology education and training
• Offering bioprocess development and technical support, and
• fostering innovation through research and development

By working at BDTC, I will be trained in the technique of capillary electrophoresis (CE) and this will provide me the opportunity to enhance my previous knowledge in protein characterization. CE technology has been valuable for the comprehensive characterization of macromolecules used both as biologics and in proteomic study. The analysis of proteins at a proteome level involves not only the characterization and quantification of proteins, but also the study of interactions between proteins with other proteins, nucleic acids and small molecules.  At the end of the internship I will be able to generate SOP’s for the different applications such as SDS-Gel Molecular Weight Analysis, Isoelectric Focusing Analysis, and Carbohydrate Analysis Peptide Mapping applying my experience in experimental procedure development.

This is a completely different and exciting new kind of science for me just for the fact of being in an industrial atmosphere. I’m looking forward to learn as much as I can on developing SOPs and validating pocedures, and most importantly learning to collaborate and work with my colleagues in Industry. I’m also looking forward learning to use high tech equipment to perform scietific research on a larger scale. I’m going to be trainined not only on CE, but on TFF, bacterial cultures in bioreactors and high throughput protein characterization and isolation.

 

Summer Research Experience at UC Berkeley!

During this past summer I had the opportunity to participate of the Amgen Scholars Program hosted by the University of California in Berkeley. I worked for 10 weeks on a research project with Dr. John D. Coates from the Department of Plant & Microbial Biology. His lab is focused on Applied Environmental Microbiology and most of his research is focused to understanding anaerobic microbes and their metabolisms in order to provide an understanding to develop biotechnological applications such as harvesting energy and bioremediation of contaminated soils and waters. My particular project intended to develop a novel rapid screening method to study a library of mutants. The main goal was to understand the underlying genetic mechanisms of iron biooxidation in Diaphorobacter sp. strain TPSY. This project required a lot of hard work, dedication and patience, since method development for any research project is the hardest and most tedious part.

Berkeley is a great place to do science. Throughout the years, Berkeley has been recognized as one of the places where most scientific discoveries occur. UC Berkeley provides students a great and solid training, helping the student develop its ability to think critically as a scientist and as a human being. It is very diverse and promotes a free spirit feeling. Berkeley and UC Berkeley motivate their citizens and students to be actively involved on environmentally related issues, on politics and all socially related issues. Scientists do science but are as well concerned of everything that it is happening on the society that surrounds them and they as well contribute to the community’s collective survival.

I had a great learning experience in Berkeley. It helped me develop my abilities as a scientist to think independently and critically. It also led me the opportunity to collaborate with top notch scientists and researchers. I can definitively see myself studying in Berkeley for grad school. In fact, the professor I collaborated with wants me to join his lab by next fall for graduate school because he was very pleased by my passion and dedication on my project.

And for those who are still wondering about the outcomes of my project, we succeeded on the development of the assay and we have already identified some mutants that will be further rescreen. Once and iron biooxidadizing mutant is identified, the genetic mechanisms involved will be known. This project was only the first step on understanding the unknown mechanism of anaerobic nitrate dependent iron biooxidation.

 

A semester is comming to an end

We only got two more weeks to be done with classes and then finals. I’ve had so many difficulties to get my project done. But once I had all the materials available, I started to have problems getting my samples analyzed. The DNA I’m studying is isolated from the surfaces of leaves and along with it a lot of inhibitors and phenolic compounds. This is the first time it happens, because a year ago it all worked well. However science is unpredictable and that’s something I’ve learned through out all these years doing research. You can never have a one definite plan, because things not always work the way you want. I’ve done DNA extractions twice and the quality of it it’s so poor that everyone in the lab thought that the amplification of 16s rDNA wouldn’t work. Guess what! It did! Now I’m in the process to prepare the samples for the tRFLP experiment.

Sometimes when you are not getting everything done because your experiments aren’t succeeding you get depressed and you just wanna give up. In my case I take it as a challenge  and I just keep repeating everything over and over again until it works. It’s all about perseverance. Next semester I hope to have these results analyzed and apply these findings in more specific studies of specific crops or plants.

 

Get to know who invented the most used technique on Biotechnology

You gotta follow these links:

http://www.nytimes.com/books/98/10/11/reviews/981011.11teresit.html

http://www.thegooddrugsguide.com/articles/famous_users/lsd.htm

And maybe read this:

And about other Nobel Prize winners … you’ll be in shock trust me but then it’ll all make sense.

http://www.hallucinogens.com/lsd/francis-crick.html

 

New techniques and bioblogs review

Basically I’ve used before almost all the techniques I’m currently doing in the lab. I’m using molecular techniques such as DNA Extraction, PCR and 16s rRNA tRFLP. This last one, Terminal Restriction Fragment Length Polymorphism, is the most important to carry out the research. Since what we are pursuing is to identify bacterial communities in the phyllosphere, the surface of the leaves, this is the most employed technique to do so.

“Terminal restriction fragment length polymorphism is a recent molecular approach that can assess subtle genetic differences between strains as well as provide insight into the structure and function of microbial communities. The technique has both high sensitivity and throughput making it ideal for comparative analyses.”

Source: Terence L Marsh. Terminal restriction fragment length polymorphism (T-RFLP): An emerging method for characterizing diversity among homologous populations of amplification products.

About other bio blogs I’ve visited…

I liked most of them but however I think that what is missing is the identity of the researcher. It’s your blog, express yourself however you want. Give the blog the sense of who you are and what your passions are. However it is very inspiring that other young people just like us, instead of wasting our life, we are building our future even since freshmen in college.

And PCR is … My new best friend!!

Step1

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*** It seems very easy… but don’t you just hate it when it doesn’t works!