The first blog I visited was from Aurian Garcia, she is from the University of Puerto Rico at Rio Piedras. She is working on a very interesting field, bioinformatics. Her specific goal is to study the reason that when bacteria changes lifestyles it loses important information on its genome regarding DNA repair mechanisms. I look forward to see the published research paper of Aurian’s!

On the other hand, Diana Rosario’s research deals with the main constituent of our bones & teeth, crystalline hydroxyapatite. It uses the amazing field of nanotechnology.  Important applications could be discovered from this young girl such as the fabrication of hydroxyapatite nanocoating deposited on silicon used to overcome the existing barriers of biomedical coatings commercially used with metallic implants. I am impressed with the research that she is doing!

German Velez research deals with the Human Papiloma Virus and its correlation with cancerous tumors. It is also an important research because its findings will help a lot of people. I am happy for him, because he will present his work at the American Association of Cancer Research. Look forward to see the conclusion of his research!

I still can’t believe that the semester is going to end in a couple of weeks. This semester it has been a great experience for me. It was the introduction to a new laboratory which I feel very proud to belong to Dr. Carlos Rios lab. My lab partners are very smart, kind and have a lot of knowledge. I know that I am a Chemical Engineering Student and everyone around me is from Biology related majors, but I love it, science is an interdisciplinary field. I really appreciate the help that my mentor has given me; he is always available to help you, no matter in what circumstances.

On the other hand, I had one of my short term goals completed. My goal was to present my undergraduate research to the academic community. Although I have presented my project on important activities before it was at high school level. Now, I am a college sophomore and the feeling it is different.

XV Sigma XI Student Poster Day

I would say that the biggest challenge for me, it is to be on Chemical Engineering major (that does not have classes of Biology), when all my lab partners are from Biology related majors. It is sometimes difficult when everybody around you knows things and terms that you do not know. To overcome it, I have to read more research papers to could understand them. I would also want to enroll in Biology classes that will help me a lot to understand such themes in the lab. It has been a tough semester. Because I had to take difficult classes such as Physical Chemistry & Differential Equations among others that require a lot of time and dedication. And I have to add the time that being in a laboratory leads. But I just love it, I hate being in the comfort zone, just outside of it we can grow and let the potential inside of us exit. I have to say that I have learned a lot from themes that I do not even know that they existed, such as metagenomics! And once you know from them, it is amazing! My goals for the next semester are to keep searching for a positive DNAse clone; and to look for another bioactive molecule with biomedical applications. I would love to hear suggestions. Thanks for reading; I really appreciate your dedication! I wish the very best for you. Feel free to contact me for any questions you may have.

SCREENING FOR DNASES AND OTHER BIOACTIVES MOLECULES WITH BIOMEDICAL IMPORTANCE FROM METAGENOMIC LIBRARIES AT TROPICAL AND DRY FORESTS IN PUERTO RICO.

      Metagenomics, is a new discipline in biosciences capable of having access and studying microorganisms that are unable to grow in laboratory conditions; 99% of the species belong to this category. Functional metagenomics allows us to test for activities in cultivable hosts which have environmental DNA cloned. This is a powerful research tool for the discovery of bioactive molecules with medical & industrial applications. Antimicrobial agents, proteases & lipases are some of the activities that can be monitored using metagenomics. The forests are excellent environments and resources for the discovery of new microorganisms with bioactive capacities due to their degree diversity.

     The main purpose of the research is to monitor a tropical and a dry forest in Puerto Rico, for DNase activity. DNase is an enzyme that breaks down molecules of DNA, and a powerful tool for scientists in Genetic Engineering, and Molecular Genetics. The selection tool being used is the DNase Test Agar with Toluidine Blue (TBA). A positive clone will turn pink the media creating a pink halo around the colony. By using serial dilutions, approx. 1000 clones from the forests metagenomic libraries sub-pools were spreaded on TBA, and incubated at 37°C. Serratia marcescens was used as a positive control. The metagenomic libraries have an a approximate of 800,000 clones contained on 40 different sub-pools. A total of five sub-pools (approx. 40,000 have been already screened under standard conditions without finding a positive clone yet. There are ongoing experiments to complete the rest of sub-pools. I really appreciate the unconditional support that my mentor, Dr. Ríos, has provided me. I want to thank the Bio-Minds Program, which have been an essential part for my development as a young researcher.

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I would love to answer questions that you may have; also to hear comments. Feel free to contact me or to visit me  the day of the activity! Look forward to talk to you.

In the previous laboratory meeting, we had training on how to use a digital multichannel pipette. This is a powerful laboratory technique that will reduce systematic errors during the pippeting process and that will save a lot of time. I have always believed that there is only one technique for pippeting. But in the training, I learned that there is another type of technique called reverse pippeting that I can use for more viscous liquids and/or low volume discharge.

                Actually, I am working actively on the laboratory. However, I have been on the laboratory for about only four weeks, in which I have attended several laboratory meetings and I am constantly learning new techniques in addition to information. I have to tell that I am not been able to achieve the proposed semester goals, which indicate a 1 on the provided scale. It is important to note that I am actively working and learning for the completion of the specified goals.

In the laboratory, there are many sub-pools (samples) that were taken from the Yunque & Guanica forests and contain metagenomic DNA. Answering the question, about the difficulties that I am having; is that there are many samples to look for Dnase activity. But this is very positive, because there are greater chances for finding a colony with Dnase activity.

Thanks for your interest!

This is my first post on the 2010 Year. I have to tell you that there have been some changes since the last semester. Unfortunately, the graduate student that I was working on the Microbial and Biochemical Laboratory is not able to supervise undergraduate students. After several meetings with Dr. Ortiz, she told me that I have done and excellent job in her lab but for situations beyond her control, I will not work anymore in the MBT.

Great news!!!! Dr. Carlos Rios from the Biology Department accepted me on his research laboratory. On the several laboratory meetings attended, students have been talking about their research and a very important security workshop has been performed.

I have always been passionate for biosciences, although I am a Chemical Engineering major. This is the reason why I propose Dr. Rios to be my research mentor and to work on his prestigious laboratory: Microbial Biotechnology and Bioprospecting Laboratory. During these weeks, I have been on what it is called a “shadowing experience” in which I see the lab mates working in their respective areas. The purpose of this is to know which research topics I like most and off course that I will love to work on!

I have seen many wonderful projects and I have asked several questions about them. In addition, in the lab there are weekly meetings in which students present their status of the proyects. Also our lab realizes monthly journal clubs open to the public. On the last one, two professors from the Biology Department presented their research that will be published soon!

In one of the laboratory meetings, I was able to tell Jose Cruz that I was interested on his research and he told me, because of the large size of his research project, that he had several areas that need someone to continue expanding them. I agreed immediately. His research deals directly with looking for antibiotics using metagenomics. Currently I am investigating for Dnase activity on the metagenomic sub-pool from the Yunque & Guanica forests.  This is a totally new area for me, and I found it very interesting. I am learning a lot in the laboratory and the literature search. My laboratory experience has been very positive; all of my lab mates are good persons and also top students (one of them was accepted on MIT Graduate School, I hope I will be accepted too!!!).

My mentor and I have established some objectives for this semester. The first objective is to isolate the responsible gene and protein for expressing Dnase activity. Another is to characterize the gene and its product. Last but not least, to sequence the gene, and to characterize the protein structurally and kinetically.

During the past months, I was able to experience how the life of a researcher was like. I learnt a lot of things: like how caffeine is degraded, the benefits of its application, different laboratory techniques, organizing the data and to make technical reports, among others.

What barriers and challenges I have faced on the start of the project? How have you overcome those barriers and challenges? What are your goals for next semester?

First of all, when I started on the Microbial and Biochemical Laboratory I was an amateur with the research on progress. So I did not know what type of experiments I have to realize. My reaction was to soak myself onto all the topics related to understand more-in-depth. I even asked for previous presentations, I participate on meetings in which I asked a lot! Another thing was to get use to the location of the instruments in the lab, at first I was always searching for the instruments. But as I spent more time in the lab I was able to resolve that problem.

Using research papers, I was able to use other experiment data to my research saving a lot of time. But recently, I have had some problems with the microorganism used. Basically, I schedule or run an experiment in which I wanted to test the degradation of caffeine with different fungi. I wanted to run the experiment as much as close to the literature, in which they counted 10⁶ spores per mL. The problem is that the fungi cells are not creating any spore at all. As part of the goals for next semester I want to resolve the spore’s problem. My hypothesis is that the organism is under very comfortable conditions for its growth, so it does not need to produce spores. I want to submit it onto more extreme conditions, like low nutrients and colder temperatures. So, one of my objectives for next semester is to look for the conditions in which the fungi cells develop sufficient amount of spores.

After visiting all of the blogs assigned, I have seem that they contain researches with important applications for today’s society. Laura del Valle, is making research trying to resolve a very interesting and important topic: what if the probiotics that we consume are causing an antibiotic resistant with different pathogens?  However, Xyomara Castillo is conducting research to try came up with correlations between growth factors in front of colorectal cancer, which is a big problem for our society. On the other hand, Nerymar Ortiz has a research based on the transformation of hemoglobin into another type called myoglobin, that it is very inefficient carrying oxygen. I can tell that a healthy population needs to have a lot of research and development, and all of the Bio-minds are making the difference. I feel very proud to be part of it.

Personally, it was easy to enter to the group of talented students working on the MBT Lab. I was able to make good interpersonal relationships with my group. But there are certain parts of the experiments that I have done, that a graduate student assists me with them. However, I had a little issue. There are times when I am available, but the other person cannot. So, I come up with an approach to resolve the problem. This is to specify the available times of every research member in a table. In that manner, each member can coordinate and separate their respectful time to work in the lab efficiently. What are the characteristic are important for a successful team? Organization, dedication, good interpersonal skills, to keep informed, etc.

As an introduction, I will be working in the Biochemical and Microbial Technology Laboratory in the Chemical Engineering Department at the University of Puerto Rico at Mayaguez. My research mentor is Dr. Patricia Ortiz, a Chemical Engineer with innovative research projects involving different areas that I am very interested like: glycol-nanotechnology, bio-sensors, biotechnology & microbiology, among others. I love these research areas because they have made a huge impact on today’s human health & quality of life. Why I choose this area? Well, because I want to be part of a team that is working to make and improve useful and beneficial applications for all of us.

In the past weeks, I was able to meet with my mentor discussing about my past research experiences, classes taken and possible areas of research. Basically, in our lab there are different main groups of students that are making research on: biosensors, nanotechnology, improving antibiotics & degradation of biomass using biotechnology.  My mentor and I agree that the group that I fit more due to my classes taken & the past research experiences is the biomass group. In this group, we will be working with several microorganisms to identify methods that will degrade efficiently different complex compounds like: lignocelluloses and caffeine. The group has a big interest working with the coffee plant, which their residues are big problems for today’s global agriculture.

The main objectives for this semester are to: perform a literature review on caffeine detoxification of coffee pulp and its biotransformation; to establish and standardize a solid-state fermentation of filamentous fungi on coffee pulp; and to carry out a Chemical Analysis of the solid with the fungus to study the removal of lignocellulose and caffeine, in addition to proteins, sugars, etc. Also there are other objectives: to maintain a good communication between all the peers, to work in an organized manner, to be secure at all times, to stay informed about new research and techniques, among others. Also, I meet with the entire research group. I was able to know each student and to talk about their research. The truth is that I feel very privileged to be a new member of an impressive group and program in my sophomore year.  All of them are very focused on their goals. I haven’t had any laboratory experience, yet. But I will publish my experience on the next post. I will keep my blog updated monthly to present the progress of this research. Here is a link of a similar research: http://www.fpl.fs.fed.us/documnts/pdf1992/culle92a.pdf.

If you have any suggestions or questions, feel free to contact me through my blog or e-mail: rhyanv@gmail.com

There is more information in the “About Me” Page.

My name is Rhyan Villanueva-Gonzalez. I am a sophomore majoring Chemical Engineering at the University of Puerto Rico at Mayaguez. The purpose of this blog is to present the status of my research research. I will be updating it with new information every month. Thanks for your interest!