So this story comes to an end… Or has it? One and a half years ago, 100 students ventured into the world of scientific research sponsored by BioMINDS. Some students had already developed a degree of lab skills, while others were just beginning to acquire them. I belonged to the latter of these two groups. 

Yet after all this time, I have seen how we have surpassed many obstacles, endured numerous hardships, and most of all: acquired valuable knowledge that classes alone cannot provide. We have learned to make better use of our time, we have seen how significant some seemingly irrelevant findings can be, and we have begun to develop a set of analytical skills to interpret real-life data that may someday lead to scientific breakthroughs!

In order to asses our analytical skills and our experience in the BioMINDS program, we attended at the BioMINDS Annual Poster Day, just about a month ago. During this day, we heard and participated in a series of conferences given by leaders in the pharmaceutical-biotechnological  industry, such as Mr. Emilio Rivera, Vice President of Operations at Amgen and Mr. Pablo Vila, Training Manager at Abbott ABL. Also, we shared our experience in this program and got hear what some mentors thought about the program in general and how this initiative has lead to positive outcomes at all the different campuses from the University of Puerto Rico. 

Near the end of the program, all of us, students from BioMINDS, got to present our posters, as well as evaluate three other randomly selected ones. The students I got to evaluate were: Josué Millán, from the laboratory that I worked at last year, Rey Yamil Pagán, also from my college, and Charles Fermaintt from UPR at Humacao. All three made excellent posters. Their presentations were clear and well informed. Here is learned:

Josué’s project focuses on the isolation and characterization of bioprospects from the Pitcher plant Nepenthes sp. Indeed, he had already isolated and characterized a variety of organisms that were capable of surviving highly acidic environments, that are natural to the gooey substance inside Pitcher plants. He also characterized the bioprospects biochemically and was waiting for the results of the sequencing laboratory.

Rey worked on the biological analysis of a biomedical material – Titanium Alloy. He investigated how different fusions of the metal along with other inorganic substances affected osteoblast adhesion to the material. He determined that two of the Ti-fusions were not biocompatible and therefore, not suited for osteoblast growth.

Charles, on the other hand, worked on a project involving gene expression. He intended to identify certain genes expressed by Saccharomyces cerevisiae via the use of repressor genes. His work plays a very significant role in processes such as embryonic development and tumor progression.

Visit the blog at:  http://magcan.wordpress.com/

I think my previous post merits more explanation. In this research project, as you may have read from my very first post, we intend to complete two objectives: genetic screening for uncultivable antimicrobial production and whole-cell screening for cultivable antimicrobial production from soil samples. Both start by randomly taking soils samples out of areas such as a rainforest, salt lands, and parking lots (incredible!) in Puerto Rico. 

Genetic screening is rather simple in comparison to troublesome incubators and take-too-long-to-grow microbes. In this phase, soil samples are subjected to commercially available soil DNA isolation kits. This DNA extract is then put into a thermocycler  where it undergoes polymerase chain reaction using selective primers that amplify genes encoding for enzymes strongly associated to antibiotic production called PKS and NRPS. In the previous post, I explained that even tough amplification occurred, the primers for PKS were not being used at conditions that optimized their specificity. Hence, we obtained positive results, all samples had PKS amplifications, but further optimization will give us a better idea of the concentration of amplicons and variability within them. 

In another level, we want to search for novel antimicrobial activity from cultivable soil microorganisms. After obtaining soil samples, we suspend them in water, dilute them, plate them on solid media, and incubate them under different conditions. Once the microbial populations start to flourish, we isolate those microorganisms that present antimicrobial activity – ergo, inhibition zones – and test them against our target bacteria. From the results that I posted the other day you can observe that we focused this aspect of our experiment on two actinomycetes isolated by the grad student Vanessa Cardona. The first one, AR, did not present any antagonistic activity over Staphylococcus aureus or Pseudomonas aeruginosa. However, in a very intense week at the lab, every single culture plate belonging to my experiment with AR got contaminated. Guess who? Well Fungi of course! Not only does every microbiology laboratory has to fight against fungal contamination, but  when you live in a sunny, beautiful and immensely humid tropical island such as Puerto Rico, you are forced to take extreme caution with the purity and sterility of the incubators, tools, etc. Well, during Mr. Fungi’s visit to my AR cultures, we were surprised to see that AR was able to inhibit microbial growth after all, just that it was not bacteria. It was all the fungus in the plate. We decided to isolate both funguses present in the plate and run further tests on AR and the other actinomycete AV against them. We dubbed the funguses H1 and H2. As we can see from the image in the previous post, AR was able to inhibit growth in both funguses, as opposed to AV and our control of course. That means that AR produces an antifungal substance. Now we look forward in doing further experiments to characterize H1 and H2 and to see if we can isolate the antifungal. 

Now it was a whole different story with AV. On the first test of antimicrobial activity of AV against our microbial targets, we observed something that looked like an inhibition zone in the S. aureus culture. Upon repetition of this assay we confirmed that indeed there was a 0.5 – 0.7 cm inhibition zone between S. aureus and the yellow pigment secreted by the actinomycete. Nothing against P. aeruginosa though. Therefore, it is safe to say that AV is secreting an antimicrobial agent against S. aureus, yet we would like to test the antimicrobial potential of AV against other gram positive-bacteria to verify its specificity.

This month’s Bio-Blog Entry contains: A comment regarding my experience visiting three blogs from other BioMINDS participants and an account of two                   techniques that I have learned so far in biotechnological research.

                     In order to complete the blog entry requirements, I was assigned to visit the blogs of Yanira Marrero Rodríguez, Sheila M. González, and Laura Almodóvar. Visiting the blogs of these three students reminds me that biotechnological research is as interdisciplinary and diverse as science itself. Yanira, for example, is working in bioprocess engineering and her research goal is to develop an efficient method of converting biomass into ethanol, as means to fuel our everyday machinery. Contrary to Yanira’s alternative fuel development goal, Sheila is working in the ecological and molecular characterization of Cryptococcus neoformans in Puerto Rico, particularly focused in understanding the pathogenic routes of C. neoformans. At a difference from both Yanira’s and Sheila’s research, Laura is working in developing methods to remove heavy metals from plants in Adjuntas and Mayagüez, Puerto Rico. I also learned that although Sheila’s research appears to be rather local, the applications of her discoveries can affect crop growth and irrigation methods worldwide.

                 Almost three months have passed since I began working in B-266 Research Laboratory of Biotechnology and Bioprospecting. So far, I have learned a variety of molecular techniques that range from DNA electrophoresis, to preparation of Polymerase Chain Reaction (PCR) cocktails. Electrophoresis is a commonly employed molecular protocol that focuses in separating different macromolecules such as proteins and DNA. This separation technique is achieved thanks to the mobility of ions in an electric field (Physics!). Similarly, PCR is a commonly employed molecular technique, but instead of separating DNA or proteins, it amplifies nucleic acid fragments. Typical PCR uses specific cocktails composed of enzymes, nuclease-free water, primers, and a DNA sample.

            The scarcity of novel antibiotics has turned into a global health hazard. Every day, more drug resistant diseases are discovered yet no new treatments have been developed. Methicillin-resistant Staphylococcus aureus (MRSA) is an example of a drug-resistant microbe that has taken the lives of a considerable amount of people all around the world since its discovery in 1947. In the midst of this alarming situation researchers have strived to come up with new antibiotics, but the race for life continues and only combined efforts will ensure the development of an effective solution. This is the reason why I fully accepted the research project proposed by my mentor, Dr. Carlos Ríos.

            Although I did not know my mentor until after being selected in the BioMINDS program, I have to say that I could not have chosen any better. Dr. Carlos Ríos is a humble and extremely dedicated professor, researcher, leader, and friend. He has put a lot of effort into the individual scientific growth of all of his graduate and undergraduate students alike. Furthermore, I appreciate the initiative BioMINDS has had and I also thank Amgen for funding the active participation of 200 students in total, along this journey for the progress and joy of life.