Saludos a todos! El mes pasado los estudiantes de Bio Minds tuvieron la oportunidad de presentar sus trabajos de investigación a través de afiches. Personalmente, esto fue una gran experiencia ya que te informas sobre lo que los compañeros están investigando y su aportación científica. Pude visitar a 3 de personas microbiología y me hablaron sobre sus proyectos y los 3 son bien interesantes.

Uno de ellos se titula “Search for Antibiotic Resistance Gene from Metagenomic Libraries Derived from Microbial Mats at the Cabo Rojo Salterns”. Como el título indica, en las Salinas de Cabo Rojo se buscan bacterias resistentes a antibióticos. Se escoge este lugar ya que se considera un ambiente extremo y hay una gran variedad de microorganismos con potencial biotecnológico que no han sido identificados todavía. Por esta razón están haciendo una biblioteca metagenómica. El procedimiento que llevan a cabo es aislar microorganismo, extraer su ADN e insertarlo a una bacteria que se pueda cultivar en el laboratorio como Escherichia coli. Encontraron 33,000 clones capaces de resistir Carbenicilina y Gentamicina.

Otro de los proyecto se titulaba “Characterization of Culivable Bacteria in Activated Sludge from the Adjuntas Waste Water Treatment Plant in Puerto Rico”. Nuevamente se quiere identificar microorganismos pero en distintos puntos de una misma área. Para determinar qué organismos son, se cultiva el mismo y se realizan pruebas bioquímicas. Se ha encontrado que la mayoría de los organismos presentes son gran positivos y capaces de utilizar distintas azúcares como fuentes de carbono.

El último afiche que puede visitar, fue el más complicado para mí debido a la terminología usada. Este proyecto titulado “Screening and Analysis of Error Prone PCR Generated Green Fluorescent Protein (GFP) Variants” involucra mucho la genética y mutaciones. El propósito y aportación a la comunidad científica es determinar las propiedades de los mutantes de la proteína GFP. Como el plásmido pGLO contiene la proteína GFP, se amplificó la misma, y luego se llevó a cabo Error Prone PCR, donde se inducen errores al azar y ocurren mutaciones. Estos fragmentos mutados se transferirán a microorganismo extremófilos como Halobacterium.

En general, los 3 experimentos me gustaron ya que cada uno se enfocaba en un área distinta y los estudiantes tenían un amplio conocimiento del tema. El privilegio de estar en el programa Bio-Minds me ayudó a desarrollarme más como estudiante, profesional y científica. También me ayudó a establecer prioridades en mi vida y a tener un balance en la misma. Quiero agradecer al estudiante graduado Josué Malavé Orengo, al profesor Carlos Ríos Velázquez y a todo el equipo de Bio-Minds que estaba en el laboratorio B-266 de Biología en Mayagüez. El que haya acabado este programa, no significa que nos quedamos aquí; seguiremos luchando por lo que queremos y llegar a alcanzar nuestras metas. Mucho éxito a todos!!

This semester, I have many objectives of my research project. The first one is to determine i f the bioluminescent bacteria can decompose the hydrocarbon naphthalene based on turbidity of the medium. The second one, is to determine if these bacteria can decompose naphthalene and phenanthrene analyzing the results of the medium based on nuclear magnetic resonance spectroscopy. With this technique I wil know if the phenanthrene and naphthalene have any structural change caused by the degradation of the bacteria. Also, another objective is to see if the morpholoy of the bacteria change using the electronic microscopy and comparing with photos of the bacteria before they are exposed in the hydrocarbon medium.

The first objective of this project, mentioned above, has been reached. By this week the other two objectives will be done.  After doing this and confirm the results, we will look for molecular techniques to finally know what is the gen responsible of the hydrocarbon degradation. Because of this, I have completed 50% of the objectives, but by this week, I will complete 80% of my research project. I am excited of what would be the results for this week, because I will really know that the biluminescent bacteria are capable of tolerate and/or decompose the hydrocarbon. Depending on the results using spectroscopy and microcopy techniques, the remaining objective of the research project may change.  I will notice you next month the results!

The expecting of this new year had created in me an anxiety to begin to work in the scientific research. Last semester I obtained positive results for the experiments and I want to proof them again. The objective of this semester is still the same: Characterize bioluminescent bacteria capable of tolerate and/or decompose any hydrocarbon, but last semester the hydrocarbon used for this experiment was phenanthrene. This year we will be working with different organisms and different hydrocarbons, like anthracene and khrysene. The methods will be same with some modifications.

By the end of the semester I expect to have results from bioluminescent bacteria that can decompose any of these hydrocarbons. Then we will begin to identify these organisms. I know that this semester is full of challenges and I will give all my efforts.

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Este semestre ha sido uno de muchos retos y logros. Durante la investigación tuve la oportunidad de desarrollarme como científico, ya que tuve que inferir sobre lo que estaba haciendo. Seguí buscando en la literatura sobre la investigación y relaciones con la misma. Acerca de los últimos resultados con las bacterias bioluminescentes, encontramos una mejor lectura de densidad óptica después del crecimiento de las cepas a una concentración de .125 microgramos/mililitro del hidrocarburo fenantreno. Luego de esto inoculamos las cepas con esta misma concentración de fenantreno, pero en un medio mínimo para saber si lo puede degradar o usar como fuente de carbono. Hasta ahora hemos tenido unos resultados negativos, excepto por el organismo utilizado como control. Esta parte del experimento se deja incubando por una semana por lo que todavía no se tienen los resultados finales.

Durante el próximo semestre estaré trabajando con las mismas bacterias bioluminescentes pero con otro hidrucarburo diferente. El posible hidrocarburo será para-nitrofenol, con el cual se tomarán las mismas precauciones que con fenantreno. Seguiremos buscando una bacteria que pueda resitir o degradar estos hisdrocarburos. Estoy muy motivada con esta investigación, ya posiblemente encontremos una que sea capaz de ello. Esto es de mucho interés para el equipo de laboratorio ya que en un futuro se podría crear un biosensor con las bacterias bioluminescentes.

These last months I had been busy with the class works and tests, but I, always, spend time in what defines me: science investigation. Last time, I wrote that we found at what concentration of the hydrocarbon phenathrene the bioluminescent bacteria may grow doing the test of Minimum Inhibitory Concentration (MIC). Knowing this, we inoculated 6 different organisms in a medium with phenanthrene and incubated them for a week. Then we found that all the organisms grew but when we obtained the optical density in a spectophotomter, this one was too little. The experiment was repeated and the same results were obtained. We can infere many things about this, like the phenanthrene are breaking the membrane of the cells. If this is happening we have to design another experiment with other interesting purpose. For now, we will repeat the experiment with a lower concentration of phenanthrene to see if we obtain different results related with the optical density. I think that I had completed 50%-80% of the experiment objectives. In future plans we will repeat this experiment with the hydrocarbon para-nitrophenol.

These months I had worked with the hydrocarbon phenantrene. A  technique that I learned and realized in the laboratory is how to know the Minimum Inhibitory Concentration (MIC) of the bioluminescent bacteria in this hydrocarbon.  First of all, we did many dilutions of phenantrene calculating the concentration of the medium. By this way, we found at what concentration the different bacteria may grow.  Then, we inoculated the bacteria in the medium with phenantrene at a specific concentration beginning with an optical density of .025 measured with a spectrophotometer.  After 3 hours in the shaker at 37°C, we inoculated 100 micro liters of bacteria in the medium and incubated them for 24 hours. The results shows grow of the bacteria in the medium, but now we have to analyze the absorbencies  given in the spectrophotometer after the experiment.

This experiment will be repeated to confirm the results and will be repeated with other organisms. The next step is to see if they can degrade the hydrocarbon. For this reason I think that I had completed 50% of the research objectives.  The expectative is positive to me and all the lab team.

Here we are again!! After a wonderful summer vacation I am back to the science and investigation world.  This semester is one of the most important to me because I hope to obtain some results about the experiments.  This time we are focused to obtain the Minimum Inhibitory Concentration (MIC) of bioluminescent bacteria from different hydrocarbons. To know this we want a control which is Escherichia coli. We are starting this experiment with the polycyclic aromatic hydrocarbon (PAH) Phenantrene, which is found in cigarette smoke. Once we have the minimum inhibitory concentration (MIC) of Escherichia coli, we have an idea of at what concentration the bioluminescent bacteria can grow with the presence of the hydrocarbons.

After the results (MIC), different bioluminescent bacteria will be inoculated in a medium with the hydrocarbons with a known concentration,n and they will be studied with more emphasis. The objective of this semester stills the same of the past one: to identify bioluminescent bacteria that can tolerate or degrade different hydrocarbons. If we reach this goal, one future objective will have relation with BIOSENSORS!!

Hola!!! Se acerca el fin del semestre y estoy muy contenta de formar parte del programa Bio-Minds. El mismo ha sido de grandes retos y desarrollo academico y personal. Lo primero que aprendi fue a relacionarme con todos mis compa~eros de laboratorio con mucho respeto. Me di cuenta que todos tienen el deseo de ayudar a los demas y esa conducta positiva, aunque ya estaba en mi, tuvo un impacto mayor a seguir haciendolo. Las tecnicas aprendidas o discutidas en el laboratorio todos los jueves con el Profesor Carlos Rios Velazquez son varias. Ejemplos de ellas son hacer amplificacion o duplicacion del DNA a traves del Polymerize Chain Reaction (PCR), como se hace el metodo de clonaje, como correr un fragmento de DNA en una gel a traves de la tecnica de electroforesis para  saber su concentracion, enre otras mas. Debido al proposito de mi investigacion, mis tecnicas se concentran en preparacion de medios de cultivos para las bacterias e inoculacion de las mismas teniendo en cuenta las tecnicas ascepticas. 

Al comienzo del semestre me tomo un poco de tiempo a acostumbrarme a estar tanto tiempo dentro de un laboratorio. Esto afectaba el horario que tenia establecido para mis estudios, pero con esto aprendi a hacer un balance entre la investigacion y mis estudios en la Universidad. Gracias a mis compa~eros entendi que lo que deseo hacer en un futuro como profesional no es facil pero se logra con mucho esfuerzo y voluntad.  Para el proximo semestre mis expectativas son bien parecidas a las de este semestre. Seguire trabajando con mucho mas esfuerzo para seguir haciendo pruebas a las bacterias y poder encontrar alguna resistente a hidrocarburas y estudiar la misma en especifico. Espero seguir buscando mas en la literatura sobre mi investigacion para poder tomar otras opciones o puntos de vistas al obtener unos resultados. Se que el proximo semestre va a ser uno de grande retos y estoy dispuesta a enfrentarlos.

Hi!!! The last month and during this semester I had learned some laboratory techniques. One of them is how to inoculate bacteria in petri plates and to diffeent tubes. The most importatn part is to do it in a hood with the necessary aseptic methods. By this way, different particles in the environment can not interfer in the medium.  Other technique is how to do an electrophoresis with DNA samples and we can know their concentration. For this tecnique we need restriction enzymes and the enzyme depends on the sequence of DNA.  Our Professor, also, was interested to teach how to clone. For this, we need a plasmid with a multiple clonning site, replication origin, a selection gene , and a gene that is resistant to an antibiotic. This technique is very important in my investigation because if I have the sequence that makes possible the hydrocarbon degradation I can replicate it.

Before doing this post I visited other students’ blogs and their investigations are very different to mine but all of us have the same purpose. We want to collaborate to make different biotechnological advance. Some students are investigation medicinal plants and others are concentrated in how to reduce the environmental contamination. It is good to know about other investigations because we would have different points of view. At the same time, we are knowing each other and making friendship with students that mey work with us in the future.

Hello:

I am Eva Nelly Rubio, student of Industrial Biotechnology in the University of Puerto Rico, Mayaguez Campus. There had been passed a month in the program Bio-Minds, and, for me, this is a unique experience. In the lab B-266 with Dr. Carlos Rios Velazquez and Josue Malave, I had learned that the most important thing when we want to do an investigation is to look the literature. To begin working with bio-luminescent bacteria we have to know their main characteristics.  These bacteria are present in all the coasts of Puerto Rico, but we can not see its luminescence because it depends on cell density. This is related to a small auto-regulator, the lux auto-inducer, that provides communication between the cells and allows them to sense their population density. This reaction is catalyzed by luciferase and involves the oxidation and reduction of a long chain liberating free energy in the form of a blue green light.

The relationship in the laboratory had been excellent. I feel the support from the graduated students, and also, from my own lab partners of Industrial  Biotechnology that work in the same laboratory. I had learned that working in a lab is not easy. It takes much more time that I expected, but I know that this is a great experience and it will help me to develop different skills. I want to thank Dr. Carlos Rios, Josue Malave, and all the lab partners of B-266 for the supporting.