BioMinds Program

Third Bio-Blog Post [3rd semester BioMinds]

During this semester I stopped focusing on my previous work with Geobacter (bacteria which can generate electricity). Instead, my professor assigned me to work with his graduate student Odalys Alvarez. With her project, Odalys was building an Escherichia Coli genotec. A genotec is a collection of clones each of which contains a vector to which has been inserted a DNA fragment derived from DNA or total RNA of a cell (or tissue). This means that Odalys was recording all the genes of Escherichia Coli (their locus, length, etc.). Up to this point in the project the only part left is the genes’ sequence. The samples were prepared and sent for sequencing. Actually we’re waiting for the results to finish the project. Nevertheless, next semester I will be working with another graduate student named Glenda. Her project focuses on analyzing bacteria in samples of human impacted areas to check for antibiotic resistance genes. The problem is that up to now we think that these genes are only present in hospitals, but early results suggest that humans already have bacteria with these genes in them. As for this semester’s project, I will post the results as soon as I have them.

Peer Review Bio-Blog Post (3rd semester)

Hello! I visited two blogs of my BioMinds partners. I resume their research topics in the following two paragraphs:

Lorena Rios is a senior at the University of Puerto Rico at Mayagüez in the Industrial Biotechnology Program. She spent her first year in BioMinds working with Dr. Gill looking for an optimized method of somatic embryogenesis of sugarcane. They developed an optimized growth medium for the first part of the somatic embryogenesis and observed until the third part (of four), which is the root formation. Lorena plans to continue her studies in plant biotechnology because she believes that agriculture is essential for life. Nevertheless, she’s now going to be working with Dr. Dimuth Siritunga in an experiment which goal is to compare the relationship within different varieties of sweet potato using DNA. This semester Lorena plans to establish tissue culture of different sweet potato varieties by the micropropagation method and develop an effective method of DNA extraction on sweet potato; which is somewhat different than what she did last year but new experiences are always beneficial.

Nicole Del Valle is a junior Biology student in the University of Puerto Rico at Cayey. She’s working with Dr. Chiesa who’s interested in observing the pathway of Neuropeptide-Y in C. elegans. They have proposed a pathway and will use different knockouts to prove it; she will be working with the knockout for the neuropeptide-Y receptor 1. Throughout last year they used different cells form different organisms to validate their pathway. Inmunoblot is a procedure Nicole uses very frequently to determine if her protein of interest (Neuropeptide-Y) is present in the samples and at which ratio with other proteins in the same sample. She had a lot of problems with the protocol for this procedure, so she spent the majority of last year optimizing it. Nevertheless, this semester Nicole and her professor have found ways to optimize and have decided to use other techniques for the expression of certain proteins. For this she seems very enthusiastic, so I hope she can wrap the next year with revealing results.

I think both research are very interesting and have different types of long-term goals. Lorena’s blog is easier to read because she explains her investigation like she was writing to a 13-year-old student. This is particularly good for a blog who is open for public access. On the other hand Nicole wrote like she was writing directly to her peers; which is good, but not in this case. Nevertheless I understood them and congratulate them on having well established goals. I think this is very important when conducting a scientific investigation and in the personal-life decisions.

First Bio-Blog Post [3rd Semester BioMinds]

This semester I will focus on helping Odalys, a graduate student who is working with my mentor, Dr. Carlos Rodriguez. She needs lots of help on this phase of her work which involves the construction of an E. coli clone’s library. These clones have a recombinant plasmid with inserts of PCR products resulting from gene amplification of antibiotic resistance and integrases (they capture these resistance genes and incorporate them into a factory of operons known as the integrons). These PCR products were amplified from DNA samples taken from different coastal habitats exposed to different levels human influence. The idea is to evaluate if there’s a relationship between the level impact or contamination by human activity and the abundance and distribution of these genes.

Goals you plan to achieve by the end of this semester.

“By the end of this semester I plan to …

1) finish building the clones of E. coli necessary for the graduate student project Odalys.

2) continue my initial research.

3) get a rewarding experience this semester in the laboratory.

Last semester I was working with another project with Dr. Carlos Rodriguez called “Enrichment of microbes producing electricity using graphite electrodes.” However, for now (the beginning of this semester), I’ll be helping a graduate student, Odalys, in her project that has little to do with what I was doing so far. Nevertheless, I’ll put into practice the basic techniques of microbiology, which will be very useful when continuing with the initial project.

I hope later in the course of the semester to continue the initial project assigned by my mentor in this way I’ll develop new techniques (since I had never worked with biofilms). By far I’ll only review basic techniques of microbiology by helping Odalys graduate student, who can guide me to make these techniques in a less theoretical and more practically effective way.

Third Bio-Blog Post [2nd Semester BioMinds]

Like the last semester, I visited blogs of three of my BioMinds’ partners. I will talk a little bit of this experience and later update what’s happening with the investigation I’m being part of.

First I visited Wilmer Rodrigo’s Blog. His assisting Dr. Carlos Rios’ investigation about Hyper Saline Microbial Mats that we can found in Cabo Rojo, PR. He’s studying microorganism that grow at high concentrations of salt. Their goal is to identify at which concentration do this organisms produce antibiotics. He doesn’t explicitly informs which is the benefit of this investigation, but we can assume that it has to do with searching for higher production rates of antibiotics. I liked reading this blog because his language is simple and he goes to the point.

Second I visited Gabriela Rivera’s Blog. She’s assisting Dr. Jose Garcia Arrraras’ and Dr. Francisco Javier Ramirez Gomez’s investigation with Holothuria glaberrima, which is an invertebrate. They’re specifically analyzing genes that are involved in the inmune system. Gabriela’s mentors propose that the inmune system of invertebrates serves as an early model of the innate immune system of vertebrates. This study can contribute to the understanding of our own inmune system at the molecular level, which can later in the future yield new medical treatments.

Third I visited Tatiana Rodriguez’s Blog. She’s assiting Dr. Ariel Diaz from the University of Puerto Rico at Humacao. They’re investigation is about feather mites, they wan to identify unknown species of this organisms in Puerto Rico. The’ve already identified two new species and one is giving them some difficulties (which are not specified). They’re goal is to publish their findings to help in the undestanding of the fauna, which this organisms are a part of.

About the progress of my research this semester, I’m very excited. We’ve assembled the sediment battery (or MFC: microbe fuel cell) and have already some preliminary results which show that electricity production rate is augmenting. I’ve learnt how to assemble MFC and how to measure voltage with a voltimeter. Some obstacles have been to find a place where to leave the MFC because it produces an unfriendly odor, but the biology department at UPRM resolved this problem. Other than that this semester has been running really well. For next semester my mentor, Dr. Carlos Rodriguez, and I plan to assemble more MFC to produce enough data to overcome statistical error and identify the time at maximum electricity production. When we reach this goals next semester we’re going to get samples of the microbes growing in the anode and identify them with PCR (Polymerase Chain Reaction). I think this are realistic goals for next semester.

Second Bio-Blog Post [BioMind’s 2nd Semester]

One of the most often used laboratory techniques, in the investigation I am participating, is PCR (Polymerase Chain Reaction). This procedure is used to replicate DNA, which is very important in the biological sciences. Commonly there is not enough DNA sample available for study, so with PCR we can replicate our DNA sample of interest in the amount we consider necessary. This way we can collect more information about an organism without extracting a lot of DNA. Regarding the investigation I am working on, I will use this technique to replicate DNA extracted from the biofilm that will form in the anode. That way I will have more sample to examine and identify the organism growing in that biofilm. Identification of these organisms is key in this investigation; it will provide information on which organisms enhance electron flow from anode to cathode producing electricity, which is the purpose.

This semester I have had the problem of “not enough time”, which influences greatly in achieving my goals. Since I am convinced that I will reach my goals, I make time every Sunday to sit down and organize my week with a specific hour for everything, including relaxation time. This helps in fulfilling my duties without being under stress.

Using a scale from 1-5 indicate the progress you have reached in relation to the goals that you stated in your previous bio-blog posting:

• 1 – no progress at all, I have not achieved any of the proposed objectives.
• 2 – some progress, I have achieved at least 10% of the proposed objectives.
3 – intermediate progress, I have achieved at least 50% of the proposed objectives.
• 4 – a lot of progress, I have achieved at least 80% of the proposed objectives.
• 5 – excellent progress, I have achieved all of the proposed objectives.

First Bio-Blog Post [BioMind’s 2nd Semester]

• Three (3) objectives to achieve in this semester are:

(a) investigate deeper about the electrochemical processes of Geobacterarchae’s metabolism,
(b) revise my knowledge of electrochemistry and acquire more through my Prof. Carmen Vega from the Chemistry Department which will be working with us in this investigation, and
(c) get involved and more familiar with the process of sediment battery assembly. I can only go further on this by practicing because this first month I’ve been reading the scientific literature on this procedure.

• These objectives give continuity to the project by:

(a) helping me understand what’s happening between Geobacterarchae and the other organisms that perhaps will be present in the biofilm,
(b) making more likely for me to contribute new and improving ideas to the experiment.
(c) helping me make less systematic errors, thus enhancing more accurate results.

• Some of the skills I will strengthen this semester are:

(a) independent work,
(b) scientific literature search,
(c) handling of new electrochemical equipment, and
(d) my initiative.

NOTE: I will provide the experimental procedure on a post next week.

Third Bio-Blog Post

I was assigned to visit three bio-blog mates: Jonathan Marín from UPRM, Nashicel Rodríguez from UPRC and Yohaselly Santiago from UPRM. Reading their posts helped me visualize the program’s scope in terms of scientific advances and student’s development as scientists.

Jonathan’s research is investigating the hemoglobin HbI found in certain clams which live in environments rich in H2S. I will keep in touch with him because I would like to know the importance of that type of hemoglobin.

On the other hand, Nashicel is working with a plant, Agave Americana, which is used in Puerto Rico to make tea for people with diabetes. If this investigation discovers new ways to enhance the plant’s medicinal properties, then hopefully a large group of people with diabetes will be able to consider a new medicine with fewer side effects.

Yohaselly’s research is very important nowadays because it deals with issues that concern our generation. She’s working on the production of biodiesel from microalgae. She explains how she uses Ultrasonic Waves to isolate the microalgae and break its membrane to extract oil and produce biodiesel. I will also keep in touch with her because I would like to understand exactly how biodiesel is produced from oil extracted from the microalgae.

As for my research experience, this first semester I’ve learned the basic techniques in molecular biology and genetics, as well as the basic rules of an investigation laboratory, which are stricter than a class laboratory. I’ve also reinforced abilities in teamwork and self-discipline.

The challenges I faced were necessary and not difficult to overcome, like learning all the steps of the procedures (which have to be done accurately) and develop logical thinking to do things on my own in the laboratory. As for the barriers, they were not in our hands, like the time lost with the strikes and therefore significant lost of coordination.

Nevertheless all these barriers and challenges, we overcame them with dedication, effort and discipline. This was not a normal semester, but we made everything in our hands to complete this semester’s goals. Even though we didn’t achieve all those goals, we spent the time we had completing the majority of them.

For next semester, my goal is to get the investigation on the bacteria, Geobacteraceae, running. At the end, I would like to have indentified the bacteria that live on the surface of the electrode (specifically the anode) and their function in the biofilm.

Second Bio-Blog Post

At the time I posted “First Bio-Blog Post” my mentor, Dr. Carlos Rodríguez, was teaching me basic techniques of molecular biology through his research “Probing for integron-encoded antibiotic resistant genes in clinical bacterial isolates”. Now I’ve been reassigned to work on the chemistry field with microorganisms capable of extracellular electron transfer to an electrode in order to produce electricity.

The theory of microbial electricity has been around for nearly a hundred years. This source of power consists of complete complex oxidation of organic compounds and efficient electron transfer to an electrode via direct contact. But it was in this decade that scientists found Geobacteraceae, microorganisms capable of making this kind of respiration. Then the question was to understand the microbe-electrode interaction in order to increase the electrical power output of these microbial fuel cells. The bigger the electrical output, the greater the applications of this new technology will be. The problem is that there is a wide phylogenetic diversity of microorganisms capable of performing this respiration as well as microorganisms capable of interacting with electrodes. It’s necessary to isolate these organisms with the appropriate strategies to understand their role in this system and to identify the microbes with the highest rates of electron transfer between them and electrodes. Once these microorganisms are identified genetics techniques could be used to enhance this ability on future microbial generations making the electrical power output stronger than what has actually been found.

As for the research experience, I can say that it has been very enriching so far. I’ve established new professional and personal relationships with my laboratory partners. I’m working on a laboratory that is shared between three professors, so I have a lot of company. This has made me a more organized and careful person as I care for the few materials we have. I’m aware that I’m not the only person in this project, so my actions will have consequences not only for me, but for the rest of the team. I’m also interacting with more experienced students that help me through some complex procedures; in the future I will help other students less experienced than me.

An obstacle that I will face, from the experimental point of view, is the DNA extraction part. DNA extraction of biofilms associated with an electrode is more difficult than DNA extraction from a culture of cells because it’s difficult to get enough material for the procedure. PCR is another technique I have to be careful in, because its success depends on how well I can manage micropipettes. But these are all obstacles that I will overcome with enough practice.

Bibliography:

Lovley, Derek R. “The microbe electric: conversion of organic matter to electricity” Current Opinion in Biotechnology 19(2008): 564–571.

First Bio-Blog Post

My topic to investigate is Probing for integron-encoded antibiotic resistant genes in clinical bacterial isolates. In this research, molecular methods will be applied for the detection of antibiotic resistant mechanisms encoded by a bacterial genetic system known as the integron platform.

My research mentor is Dr. Carlos Rodríguez. He’s a professor of microbiology in the University of Mayaguez. I chose microbiology as my research area because it’s a quickly advancing science. Pathogens and antibiotic resistant genes are especially of my concern because society is now facing these issues. Researches like the one I’m involved in help in the understanding of these problems, thus improving our ability to find the solution.

So far my laboratory experience has been very enriching. My mentor is helping me and another undergraduate student of BioMinds through the basic techniques of molecular biology. This has helped the confidence I have in my abilities as a scientist. I have learned some techniques like Electrophoresis and PCR. For this semester my mentor and I expect to find antibiotic resistance genes in bacteria from food, soil, and other places other than hospitals. We are also expecting to help in an investigation on chemistry involving bacteria and other sources of energy.

See the Blogroll section on your right for related material on the web.

WELCOME

Good day! I’m Priscila M. Rodríguez García, student of the Industrial Biotechnology Program at the UPR Mayaguez and member of the BioMinds Program starting August 2009.

My BioMinds’ mentor is Dr. Carlos Rodríguez ,who’s a professor of microbiology at UPR Mayaguez. My goal is to earn a PhD in Molecular Biology so I can  contribute to society by improving the quality of human life.