Beatriz Andujar's Blog

The end of this wonderful experience is almost here and I feel grateful for all the knowledge I have gained throughout these years. It seems like just yesterday when we all did our first bio-blog post. My participation in this excellent program has helped me overcome many fears and become a great young scientist. The past two years have helped me grow both emotionally and professionally. I feel very capable of making basic decisions in the laboratory and successfully preparing a well written report as well as an oral presentation. I will never forget this wonderful experience and I am forever grateful to the BioMinds Program and all the people in charge for all the times they have helped and supported me.

I would also like to thank Dr. Juan López Garriga and Dr. Juan Martinez Cruzado for allowing me to work in their laboratory and becoming my mentors. Their support, confidence and ability to guide my ideas have been an invaluable contribution not only in the development of my work, but also in my training as a researcher. It is therefore necessary for me to acknowledge their presence in my growth as a researcher.

There is no doubt that my participation in BioMINDS has enriched my life and also help me become stronger as research trainee. I will keep you informed of my progress.

The following photos show my BioMINDS journey. Enjoy!

Since last semester, I have been working under the guidance of Dr. Juan Martínez Cruzado. The research project that was assigned to me was a very challenging one: collect 100 duplicate samples from Las Marías, Puerto Rico in order to extract and quantify their DNA to later perform the polymerase chain reaction (PCR) technique and amplify the CCR5 gene. With the DNA amplification of each sample, I would then be able to analyze the genetic variation of the Puerto Rican population in order to find disease related mutations that convey risks or immunity. So far, I have collected more than the 100 samples that were assigned to me and have extracted the DNA of most of the samples I recollected. Since all the recollection of DNA is already done, and the extraction of it is mostly finished, the next step is to take all that extracted and purified DNA and perform the polymerase chain reaction (PCR) technique to amplify the CCR5 gene. This part should not take too long, since I have already done it in the past. The hard stuff comes next, which is to analyze all the results and use statistic knowledge to organize those results.

The achievements I have obtained during this period of time and obstacles that I have overcome are many but some examples are the following: I have presented my work in meetings and conferences; I have wrote a paper about my research work without any major problems; I now feel confident with the idea of talking about my project in front of a large group of people while using scientific language (which I actually understand quite well); and my people skills have developed significantly because of the fact that throughout my whole research I have been talking with hundreds of people in order to obtain their samples (saliva samples which contain DNA). Honestly, although I have gone through a lot, I would not change any of it because I have learned immensely and my growth has been noticeable. I really want to thank the BioMINDS program for this wonderful opportunity and for giving me the tools needed in order to be the junior scientist that I have become. See you all in the PRISM 2011 presentations!

We have come a long way. It seems like yesterday when most of us were starting our scientific careers and didn’t know much about abstracts or poster presentations. This is our last semester in this wonderful program and now we have to show all that we have learned. A lot of things have happened during this time. Although it was a long road, I feel that I have grown as a scientist and as a human being as well. We have overcome all the obstacles that life has put on our way and now it is time to show all that knowledge that we have gained during this experience. The 31st Puerto Rico Interdisciplinary Scientific Meeting (PRISM)
and 46th Junior Technical Meeting is coming soon and, as a requirement of the BioMINDS program, all of us have to participate in it. This is our last chance to, once again, do our best and prove that we have a genuine interest in science and that we are ready to fight for a better future. The following abstract is about the research that I am currently conducting under the guidance of Dr. Juan Martínez Cruzado. If you have any comments, please feel free to contacting me or stop by my oral presentation at the Interamerican University- Bayamon Campus on March 12, 2011. I hope you like it.

Frequency of the CCR5 32-bp deletion allele on Las Marías, Puerto Rico

The human immunodeficiency virus (HIV) is a lentivirus that causes acquired immunodeficiency syndrome (AIDS), which leads to failure in the immune system and life-threatening opportunistic infections. Due to the high rates of infected people around the world, multiple studies have been conducted over the years to determine the leading causes for the spread of this virus. Previous studies have demonstrated that a 32-bp deletion in the CCR5 gene has been shown to display reduced susceptibility to HIV infection. It is believed that because of the geographic distribution of this mutation, it can be found in Europeans, West Asian, and North African populations. Due to admixture, it is hypothesized that a low percent of Puerto Ricans posses this mutation and are immune to the HIV-1 infection. To study this mutation and other genetic variations among the Puerto Rican population, samples from all over the island were collected and analyzed in the laboratory. Sixty-eight samples from Las Marías, Puerto Rico were collected. DNA extraction was performed and DNA quantification to verify if the extraction was properly conducted. The overall goal of the study is to collect ninety-six to one hundred samples in order to then extract and quantify that DNA to later perform the polymerase chain reaction (PCR) technique and amplify the CCR5 gene. With the DNA amplification of each sample, we would be able to analyze the genetic variation of the Puerto Rican population in order to find disease related mutations that convey risks or immunity.

So far, the first semester of the academic year 2010-2011 has been full of exciting surprises. Although I have new projects and ambitions, my main goal remains the same which is to do good science, share the knowledge obtained by it with others and keep learning more each day.

I had the opportunity to present my summer research findings in the ABRCMS convention in Charlotte, North Carolina, USA. I was very excited when I received the acceptation letter by email informing me that I was selected to do an oral presentation. Although the letter was in front of me, I still couldn’t believe it because the ABRCMS committee only accepts a few for this type of presentation. But I left all the fears behind and I packed my bags and came to the conference confident that I was ready to do this presentation and that, as always, I would do my best. Before departing to Charlotte the rush was unbelievable. I had to take some of my classes earlier than the rest of the students in order for the instructors to not take any points off my final grade and I had to go from Mayagüez to San Juan early in the morning to prepare my luggage. However, after all, it was definitely worth the effort. The title of my oral presentation was The Response of the p53 Pathway Following Dose Dependent Irradiation in Mdm2 ^SNP309 Mice and it was based on all the results obtained from the research I performed at the University of Texas.

The overall experience was fantastic and I don’t regret anything. There were different forums and meetings directed so that the participants could have a better understanding of all the different graduate schools and the importance of research in the biomedical field. I had the opportunity to accomplish one of my many goals. I learned more about hundreds of graduate schools, more about myself and more about the next steps I have to take in order for me to keep growing as a scientist, as a student and as a human being. Basically, I overcame all my fears and insecurities and I proved that there is nothing impossible in this life.

I want to thank all the people that have contributed in one way or another to my research experiences and growth as a young scientist. Without them, I could not have achieved many of the goals that I proposed for this year. I want to thank my summer research mentor, Dr. Guillermina Lozano, my current research mentor, Dr. Juan Martínez Cruzado, and all of the lab members for their unconditional support with my research. Thanks to the Bio-Minds Program for providing me the funds and opportunity to keep developing my skills and fulfilling my dreams. I promise that I will keep working hard to make all of you and myself proud.

A look into each other’s blogs always means we will learn new concepts and techniques. This is a great opportunity for me to know more about some of the students that surround me. It is unbelievable how similar a group of people can be. Most of the BioMinds participants have similar goals and ambitions and if I get to know some of them more deeply, I will see I am not the only one with dreams bigger than the world renowned Empire State Building.  For this occasion, I was assigned to visit the blogs of Gladys Diaz and Tatiana Rodriguez. Gladys Diaz is a Biology student at the University of Puerto Rico, Río Piedras Campus. She is working under the guidance of Dr. Ayala at the School of Medical Sciences in Río Piedras and her goal is to have a Ph.D. in Genetics. The project that Gladys is working on is related to cancer and biochemistry. For this project, she is analyzing if apoptotic pathways of human lymphoblasts induced by 25-hydroxycholesterol (a derivative of cholesterol) involves oxidative stress. In other words, her main objective is to measure protein carbonylation as markers of oxidative stress using the CEM cells. In order to fulfill her project goals, she has used a method that includes protein isolation, quantification, electrophoresis and detection of carbonylations using antibodies.

As part of Gladys’s research work, she has been able to identify a positive control for analyzing the samples treated with 25-hydroxycholesterol. The positive control is the one where cells are treated with an oxidative agent and produce a great amount of protein carbonylations. She did several experiments and proved that hydrogen peroxide could be used as an oxidative agent. To get the samples needed for the experiments, she worked with tissue culture of CEM C7 lymphoid cells (sensitive to 25-OHC) and M10R5 cells (resistant to 25-OHC) which are a complementary cell clone to her study. Until now, she has not obtained clear results due to diverse factors such as the low viability of the cells before starting the treatment and the diminished viability of the control.

I truly believe that this is an excellent topic with a very promising future for a poster, an oral presentation or both. Although the student Gladys Diaz mentioned the methods she has used since the beginning of the project and explained the research status, my advice or positive critique to her is to give a brief summary (three to four sentences) in which she explains the importance of this project and the effect it could have on cancer patients or humans in general. This summary about the importance of the project will improve her blog and the reader will be more interested in the topic.

The other blog I was assigned to look up is Tatiana Rodriguez’s blog. The first thing that caught my attention is that her blog is well developed and full of interesting pictures. Tatiana Rodriguez is a Biological Sciences student of the University of Puerto Rico at Humacao with huge but focused dreams. After her bachelor’s degree completion, Tatiana wants to do her doctoral studies in the areas of Microbiology or Cell Biology. Currently, she is working under the guidance of Dr. Ariel Diaz of the University of Puerto Rico at Humacao in a project titled Collection and Identification of Unreported Mite Genera in Puerto Rico. The research project goal is to collect and identify genera that have not yet been recorded in Puerto Rico and place the slides in the Acarology Collection at UPRH. At the beginning of this jorney, Tatiana explained the reason or importance of this research and wrote that although there is a lot of information about a wide variety of genres of mites in other countries and continents, in Puerto Rico this tissue has not been well researched. The research analyzes five genera of mites and in order to do this, they need to collect dead animals to obtain the specimens. So far Tatiana has learned how to use different types of microscopes, mounting slides and how a specimen is prepared before mounting. Also, she has learned how to use dichotomous keysand and has already identified mites in the following bird species: T. dominicensis, E. holoceriseus and C. maugeus.

After visiting Tatiana Rodriguez’s blog, I totally love her idea of adding colorful and interesting pictures to the blog because they can catch the reader’s attention faster than words alone. Also, I admire the outstanding work she did with all the posts related to her usual visit to the assigned blogs. Her blog definitely shows that she is a very organized, hard working woman with good feelings and an immense future ahead of her. In regards to her research work I find it amazing because mites are not a common topic among the Puerto Rican community and although they are not usually the first thing that comes to most people’s mind, they can help us understand the flora and fauna of Puerto Rico.

During this summer I had the wonderful opportunity to participate in a Summer Research Program in the University of Texas. I learned techniques such as Immunohistochemistry, Real-time RT-PCR, and Western Blotting, different scientific terms, and practiced my English. I gained new knowledge about all that is currently happening within the scientific community and met new outstanding people.  This experience has impacted me enormously because I had the opportunity to grow as a professional and as a human being. Also, it was a great opportunity to do a little bit of networking because it will allow me to be able to do more research next summer and to be one step closer to be part of an excellent graduate school.

After the unbelievable experience of this summer, I am more than 100% sure that this is what I want to keep doing for the rest of my life. I’m full of hopes, dreams, and goals which I want to accomplish during this semester. To the end of this semester I definitely hope to have accomplished all of the following goals:

1)      An outstanding poster presentation and a marvelous oral presentation because if we make new discoveries but do not publish them, all our work would be for nothing.

2)       To spend every second I’m not in class doing research and trying to apply all the knowledge I gained during the summer into my research project.

3)      To learn new crystal growth techniques. Until now, I have been practicing the hanging drop technique but for the end of the semester I want to be able to realize the sandwich drop crystallization, the free interface diffusion, batch, MicroBatch under oil, or the microdialysis crystallization.

This semester research work is extremely related to the previous semester because it is the same topic. Although I will be working with the same topic, there are some factors that are different such as the fact that I have now gained more knowledge and will be learning new techniques or the fact that Darya Marchany, the graduate student that was working with me in the project, will no longer be with me in the laboratory. Because of this situation, during this semester I will be working with another BioMinds participant named Ulises Marrero. Things will definitely be different because we are both undergraduate students and do not have the knowledge that the graduate students have but we do have motivation, interest and faith in ourselves. I know I can do this and I’m more than ready for all the challenges that come my way.

The following is a picture taken during the Summer Research Program.  In this photo, one may observe me and the rest of the laboratory members.

Similarly to the third bio-blog of last semester, for this third blog entry I was assigned to visit three other blogs. After visiting the other blogs, I realized that I had forgotten how much fun and how much one can learn while reading someone’s blog.  It is amazing how different people are. Every person has his own way of describing what they see, hear or learn. We are all exceptional and there is something amazing inside each one of us.  Each research topic is interesting and the knowledge you gain during this process will definitely help you in the future. The first blog I visited was of Erika Martinez. What I first noticed about this blog is that I totally loved the colorful background that Erika selected for her blog. Then I read all her posts and learned a little more about her. Erika is a fourth year student from the University of Puerto Rico, Mayaguez Campus. She is working with Gustavo Lopez in the Chemistry Department in a bio-computational investigation. During her research, she has been working with a Course Grained Model program for the study of DPPC which is a lipid found in human lungs that helps stabilize the respiratory surface of lungs against collapsing. While visiting her blog, I learned that the Coarse Grained Model is a computer model for the representation of molecules and calculates the DPPC’s enthalpy and other values such as potential energy according to temperature. All this information helps us to know if the molecule will be stable or not within the created environment in that given temperature. Erika’s main goal is to perfect the Coarse Grained Model, study the data when there is water in between the two layers, and later on, replace the water with different kinds of proteins. Currently, Erika is working on a new project related to the original DPPC project. In this project, she is modeling a rhombus surface and studying its behavior as temperature rises with time.

After entering Erika’s bio-blog, I moved on to Diana Rosario’s blog. Diana is also a fourth year student but, instead of being from UPR – Mayaguez Campus, she is from the Cayey Campus. She is working under the guidance of Dr. Wilfredo Otaño. Erika’s research title is “Deposition of Hydroxyapatite Coatings by Magnetron Sputtering” and it is based in nanotechnology. Amongst the different techniques she has had to use, the first one she learned was the sputtering deposition technique which has a vacuum process in order to realize a deposition of coatings with excellent adhesion of coating. In one of her posts, Diana explains that the sputtering process begins when the atoms of argon impacts the commercial target of hydroxyapatite (HA) transferring their energy to the elemental components of the target. These collisions occur continuously and cause the occurrence of the plasma. Finally, the elements travel away from the target and are deposited on the substrate.  Also, I learned that the hydroxyapatite is the main constituent of bone and teeth and a bioactive material with important clinical applications.

And last but not least, I visited Angel Torres’s bio-blog. As soon as I entered Angel’s bio-blog, I couldn’t stop noticing that his background was very peaceful and that the information of each one of his post was very organized. After reading each one of Angel’s posts, I noticed he doesn’t give any information about his age or where he is studying but I could infer that he is a student from the University of Puerto Rico, Mayaguez Campus because his mentor is the professor Nilka Rios and she is from this Campus. Angel research topic is called “Surface-Enhanced Raman Spectroscopy (SERS)”. The Surface Enhanced Raman Spectroscopy, or Surface Enhanced Raman Scattering,  is a surface sensitive technique that results in the enhancement of Raman scattering by molecules adsorbed on rough metal surfaces. The enhancement factor can be as much as 10¹⁴-10¹⁵, which allows the technique to be sensitive enough to detect single molecules. In the laboratory that Angel is working, there are using silver nanospheres of different sizes to see the effect of the surface charge of silver nanoparticles on the DNA and RNA SERS signal by changing the pH and laser excitation. Also, they are determining the absorption constants and limit of detections at the optimum surface charges.

This semester has been a very productive one for many reasons. I used techniques that I haven’t had the opportunity to use before, such as centrifugation and chromatography. I have learned how to organize my results and knowledge in order to prepare a presentation and a 3.5 ft high by 6 ft wide poster board. Also, I have learned a lot more about the reactions that occur every time the Sulfhemoglobin complex is formed and the reactions that have to occur in order to stabilize it. In order for me to obtain the knowledge that I have gained during the past months, I have faced some barriers and challenges. Amongst the difficulties that I have had to face, there is the fact that I haven’t had the opportunity to make a poster board before so it was kind of difficult for me at first but I managed to do it and everything went amazing. Also, I faced problems with the chromatography column and with my presentation skills. The key to overcome all this barriers and challenges was a lot of patience, and trust in me.  Instead of been angry or frustrated every time something didn’t go as I planned it, I tried to find another way to do it. There is always more than one option for everything in this life. There are a lot of choices; we just have to take the ones that are going to help us reach our aspirations.

I have a lot of aspirations, or goals, for next semester. I would like to give as many oral presentations as I can because I know that I need to improve in that area and I’m not afraid of the challenge. Practice makes perfection. Also, I would like to follow the same methods used in the scientific paper titled Three-dimensional structure of cyanomet-sulfmyoglobin C to stabilize the Sulfhemoglobin complex because we tried to follow them on this semester but unfortunately the results weren’t the expected, maybe it is because of the fact that we did some changes to the methods the scientific paper presented. Additionally, I expect to do my best, as always, next semester and study as hard as I can to learn something new each day and live life at its fullest always following my values and keeping my focus very clear.

Since I have been working with BioMinds, I have learned different techniques but definitely the one that I have used the most, because of its importance in my research project, is the Hanging Drop technique. The hanging drop technique is one of several techniques for setting up crystallization experiments. This technique is also one of the most commonly used methods for protein crystallization and, among all the crystal growth techniques, it falls under the category of vapor diffusion. The hanging drop technique consists of placing a small droplet of the sample mixed with crystallization reagent on a siliconized glass cover slide inverted over the reservoir in vapor equilibration with the reagent. Initially, the reagent concentration in the droplet is less than that in the reservoir. Eventually, the reservoir will pull water from the droplet in a vapor phase such that an equilibrium will exist between the drop and the reservoir. During this equilibration process the sample is also concentrated, increasing the relative supersaturation of the sample in the drop (Hampton Research, 2001).  This technique is definitely very useful for my research project because my research is all about crystallization, especially the crystallization of the Sulhemoglobin complex.

If I have to evaluate the progress I have reached in relation to the goals that I have stated in my previous bio-blog posting using a scale from 1-5, I would have to say that my progress is a 3 which mean “intermediate progress. I have achieved at least 50% of the proposed objectives.” I think that my progress is a 3 because we have not really being able to crystallize the Sulhemoglobin complex yet or tried new forms of doing it. We haven’t tried new forms of doing it because we want to exhaust all our resources so that we can then start from the beginning and try new stuff. On the other hand, I’m sure that I have accomplished at least 50% of the proposed objectives because I already prepared the PowerPoint presentation that I will give in the 2010 Junior Technical Meeting (JTM) and the Puerto Rico Interdisciplinary Scientific Meeting (PRISM) and I have been reading more about my research topic.

Some of the difficulties that I have faced in achieving my goals are that we haven’t received some of the necessary equipment in order to follow with our research and that we are now in that time of the semester where most of the classes give tests. For example, this week I had three tests and some quizzes. In order for me to overcome these difficulties I’m studying harder and using the free time between each class to study for future tests so that way, when the professors give them all at once, I would be more prepared.

Note- The picture showed in this post was obtained from the following source:

“Protein Crystallization.”2003. Davidson College. Accessed: March 04, 2010. <http://www.bio.davidson.edu/courses/MolBio/MolStudents/spring2003/Kogoy/protein.html>

Welcome 2010! As soon as the new semester started, I went to the laboratory to discuss the goals for this second semester 2009-2010 with my co-worker, the graduate student, Darya Marchany Rivera. After talking about our much deserved vacations, we began our journey and decided that we will continue our main goal, which is to crystallize the Sulfhemoglobin Complex, but we will also follow some excellent ideas that emerged last semester. We think these ideas can help us in order to fulfill our expectations. Among the ideas that we think will help us accomplish our goals, there are some changes in the equipment we used last semester and new techniques we are going to put in practice. For example, this semester we will use a different type of column in order to do the column chromatography needed to purify our example of protein. After the protein is purified and it has the right buffer, we are then going to do the hanging drop technique and we will hope for the formation of crystals. In order to see the growth of the crystals we will use a very advanced microscope. Also, we are no longer using the H2S buffer with a pH count of 6.5. Instead, we are using a phosphate buffer with a pH count of 6.

I have many objectives for this semester. Among my objectives, there is definitely to be able to crystallize the unsteady Sulfhemoglobin Complex so we can know more about it; be able to give an excellent presentation about my research in the 2010 Junior Technical Meeting (JTM) and the Puerto Rico Interdisciplinary Scientific Meeting (PRISM); to keep learning new techniques and improving the skills I already know; and to keep myself updated with the information related to my research topic. I’m sure these objectives are going to be very useful not only for this semester but for the rest of my life. If I have a good understanding of my research topic, I will be able to contribute even more in the laboratory. Also, with the experience that I would get from the presentation I would be more prepared for the real life that is waiting for us outside the campus. I’m very excited for this semester, and I’m 100% sure that I can do this. I will give my best everyday to fulfill my goals and to be more than satisfied with my job inside the laboratory as a researcher and outside of it as an Industrial Biotechnology student.

For this entry I was assigned three other blogs to visit. I enjoyed visiting other student’s bio-blogs because I was able to learn from each one of them. The first blog I visited was Amanda Flores. Amanda is a fourth year industrial biotechnology student in the Mayaguez Campus who is interested in continuing her studies in order to gain a Ph. D in another university outside of Puerto Rico. Amanda has obtained an excellent opportunity to work with Dr. Lorenzo Saliceti at the Industrial Biotechnology Learning Center(IBLC). Together with Dr. Saliceti, Amanda is working on a project titled Monitoring of Mammalian Suspended Cells Cultures Using Spectroscopy Techniques. After entering Amanda’s bio-blog, I moved on to Aurian Garcia’s blog. Aurian is a student who is working on a Bioinformatics program under the advice of Dr. Steven Massey. Aurian is working on a very interesting investigation because she is looking at DNA repair genes in 699 species of eubacteria. Even though it appears to be a lot of work, Aurian says that it isn’t that difficult because of the fact that she has access to sequence databases such as NCBI and these make it simpler. At last but not least, I visited Carlos Pasiche’s bio-blog. Carlos is a student in the Mayaguez campus who is working with the Dr. Ines Sastre. When I entered his page I could rapidly observe that he was very responsible, organized and very interested with his project. Carlos was working on bryophyte ecology, more specifically, with neotropical species.

This semester has been very productive and very fun for me. Thanks to the BioMinds Program I have learned to work as a team, be more organized, work in a lab, and even do a blog online. I have also learned a lot about hemoglobin, myoglobin and sulfhemoglobin. I have learned about the different processes of crystallization, preparation of the hanging drop, and also how to make the calculations necessary in order to prepare the sulfhemoglobin complex. Recently, I had the opportunity to mix the materials needed to make the sulfhemoglobin complex and had the marvelous opportunity to observed how the solution changes colors when the ingredients react with each other (from reddish brown to intesnse green). I was also able to use UV rays in order to see if I could find a 620 band and confirm that the sulfhemoglobin was formed. Effectively, the band I had obtained indicated that there was the presence of sulf and we rapidly prepared the hanging drop technique in order to see if we had cristalization but, to our dismay, we did not.

Amongst the barriers that I have faced since I began this Project, I can mention the different manifestations or student protests that have blocked our access to the university. This has caused some serious problems because I was not able to enter the lab at all. Besides this barrier I have also had to face the challenge of working in a group because of the fact that we do not all have the same times off during the day.In order to defeat the obstacles that I have had to face I have worked harder and during extra hours in order to complete all the work I was not able to do during the strike. On the positive side, I have established more efficient communication with my lab partners in order to find time when we are all available.

My goals for next semester are to continue learning something new every day and do my best in order to be useful in the laboratory. I would like to learn more techniques that are used in the laboratory and be able to create sulf on my own and be able to identify it with my eyes closed. I would also like to know everything there is to know about my investigative project and finally achieve the crystallization of the sulfhemoglobin in order to truly contribute to the scientific field that deals with my investigation and also in order to amplify my knowledge.

Here are some pictures taken in the laboratory the day I prepared my first sulfhemoglobin complex.