Bio Minds Research Day

In March 21, 2009 we celebrated the Bio Minds Research Day. I along with many other students have the opportunity of present and share the product of three Semesters full of hard work in the lab. The activity was carried out in the Bioprocess Development & Training Complex. In this day I had the privilege of learn and evaluate three amazing projects.

The fist poster that I visited had the title of: “Lysozyme Crystallization with Neutral Hydrogels Providing Conditions for Counter-Diffusion.” Basically the project consisted on modifying the Counter-Diffusion technique by the usage of hydrogels instead of other commonly used gels such as agarose. I find this work to be very relevant given that through the implementations of efficient protein crystallization techniques this may facilitate the structural of proteins study and therefore their respective function.

The second project that I evaluated had the title of: “Microalgae Derived C10-C14 Biofuels.” I was amazed with this particular project, because I never though that oils that are contained in microalgae may serve as starting products for Biofuels. What is even more amazing is how efficiency of the process, since it doesn’t require too many steps to obtain the biodiesel. The microalgaes are exposed to and ultrasound procedure and in approximately 15 minutes one can obtain 90% of the final product. I strongly consider that this project is of great importance to us because in a world which is in constant demand of energy it is convenient to find alternate ways of producing sources of renewable energy.

The final project which I evaluated had the title of: “Functional Genomics and Culture Independent Approaches to Search for Protease Activity in Forests Soils in Puerto Rico”. Through this project I became aware of the important role that protease have due to their numerous applications. They are used in detergents, leather industry, food industry, pharmaceutical industry and bioremediation process. Therefore, given that they are so versatile it is desirable to find new sources of this protein.

In Our Way to Progress

Unfortunately, we haven’t been able to proceed with the investigation, given that all the cultures of the fungus we intend to study got severely contaminated. Nevertheless, this doesn’t mean that we have done nothing in the past month. Our focus has been on literature revision and experimental design. So far we have conducted three journal clubs; all of them specifically related to our project. I had the opportunity to conduct one of the journal clubs, and even though  I didn’t performed as I would like, at least I had the experience. I will focus on learning from my mistakes in order to have a better performance when the next opportunity shows up. It is for this reason that will attribute our progress with a 3 (scale of 5).

Thankfully a few days ago we received the good news from one of our lab partners that a person that works in the Darlington provided us with a fresh culture of the desired fungus. This means that the month of March is going to be very intense and hopefully I will be sharing some of the findings on the next post.

Here is a summary of our project:

Our project is focused on the design and characterization of engineered materials with intrinsic antifungal activity. We have chosen beta-peptides as a platform for the synthesis of target-specific antifungal agents. The already studied molecular interactions of antimicrobial synthetic peptides with cell membranes of pathogenic fungi and bacteria provide an excellent start point from which to optimize our designs. We propose the utilization of chitin-binding domains (CBDs) as models to create target-specific beta-peptides. CBDs are short amino acid sequences that bind specifically to the N-acetyl glucosamine subunits of the structural biopolymer chitin. We hypothesize that since chitin is a specific structural component of fungal cell walls, a CBD-based beta-peptide will exhibit an enhanced antifungal activity and decrease cytotoxicity particularly in mammalian cells, which lack chitin as a structural component. We will synthesize and characterize CBD-based beta-peptides and assess their activity against fungal cells in vitro using the fungus Cryptococcus neoformans, an important human pathogen. Furthermore, we will characterize the in vivo activity of CBD-based beta peptides using the murine pathogenesis model for cryptococcosis.

The Beggining of a New Journey

This Semester will be very different at from the others given that I’m on a new research project in the Department of Chemical Engineering under the custody Dr. Patricia Ortiz Bermudez. The project involves the field of nanobiology and primarily consists of developing ant-microbial particles; specifically anti-fungal. This will be done by synthesizing a special peptide functionalized to attack fungal cells. At the present moment we don’t have available this peptide. For this reason we are using and studying a particle composed of magnetite that may have a similar effect of the peptide.

Right now our main goal is to observe the interaction between non functionalized magnetite particles and the fungal cells. If the interactions turn favorable for the research’s objectives, then we can proceed to the fictionalizations of the particles and the peptides eventually.

Final Entry: End of a Sad Journey

Results for the double encapsulations experiments revealed that the seeds did not germinate on the sphagnum moss. Nevertheless the dehydration and contamination of the seeds was successfully overcome. This indicates that the antifungal agent that was used worked efficiently. As for the liquid culture on the rotating drums previous results showed that large volumes of medium do not promote an optimal environment for the development of the protocorms. This led us to perform a duplicate of this experiment but reducing the mediums volume. Even though this was employed last results indicated that most of the protocorms began to die. This suggests that there is a possibility that liquid culture is not a viable method for the propagation of this orchid specie. Based on this it was conjectured that this may be related with the epiphyte (they grow on tree cortex) property that characterizes such species.

Unfortunately, due to some unexpected events the laboratory suffered a permanent damage which turned it into a nonfunctional one. Hence the project had to be put of hold and therefore remaining unconcluded. For this reason that next semester I will begin a new investigation with Dr. Patricia in the Chemical Engineering Department. Further one I will post brief explanation of what is my new project about.

October 25 – Third Entry

This has definitely been a hard month due to literally a “series of unfortunate events”. Apparently some students from the laboratory above us left for the weekend and forgot to close their lab sink. Hence, their lab got flooded and subsequently ours along with other major consequences. Unfortunately, the damage our lab suffered was greater than we thought. I am not going to focus on the details, but I would like to make clear that our lab isn’t functional. As one would have expected most of the experiments got ruined, including ours.

Naturally, our research progress has been ZERO thanks to this little incident. At the present moment, our mentor is doing every thing humanly possible to get us a new lab so we can continue with our work. On the meantime he told us to start working on the written final paper due on November. As matter of fact, I took the initiative of searching and analyzing scientific literature, before all this occurred. Aside from this all I am do is trust on my mentor’s success on finding us a new lab soon so we can start all over again (as much as I hate saying it).

Second Entry

Sadly our current situation in our lab is very critical. In fact, if I had to be honest I’ll say that in a scale to one to five our research’s progress will be a two; we have achieved at least 10% of our goals. This may seem not so good, but it’s better than having nothing, I guess.

The humidity in our lab has a lot to do with this limiting us significantly for not letting us use certain components (including sugars), since it will surely result in contamination. While working with plants it is of great important not to exclude certain components such as sugars, because after all sugar is essential to plant’s growth. It is for this reason that we have tried remake all our experiments using sugar, especially when our aseptic methods seemed to improve greatly (our main goal from last semester). Basically we haven’t incorporated any new techniques. The results showed a few survivors (this is the part which I owe the 2 in progress), but still most of them ended up severely contaminated. Sometimes I feel (and my partner Sully agrees with me) that we should rather investigate the orchids’ parasites (fungus) given that is the only thing that seems to grow efficiently in our medium. To make things even more frustrating, the few that survived are dying for other causes.

Right now what we are doing is pointing out the possible variables that are not letting us proceed with the project. We have managed to indicate one, which is probably the main reason to our work’s failure so far. I’m counting on this, because if this doesn’t work we might have to start all over again and this kind of stresses me. On the other hand, I’m also aware that this is all part of a process that all scientists have to go through.

Goals For The Second Semester

Sadly I didn’t have the opportunity to participate on a of summer research program; I had other priorities. Hopefully, I’m planning on do it so next summer. Basically what we have done so far this first month is establishing the goals for the semester. From what I can tell this semester is going to be tougher than last, due to the many goals our mentor want us (Sully an me) to accomplish.

Unfortunately, most of the plantlets on the clinostat died, with a very few remaining alive, which is not that bad at all. At least we manage to overcome almost at perfection our main adversary, CONTAMINATION. The few plantlets that survive showed something peculiar, which was that they all had very little contact with the matrix solution. It is for this reason that we are going to perform once again but this time incorporating new ingredients such as sugars and other vitamins, and using less volume of the matrix solution.

On of the projects we had last semester was to design an air bioreactor, whose purpose I’m not allowed to tell yet (rules are the rules). This semester our mentor wants us to focus more on putting the bioreactor to work. Another project we have in mind is work on the acclimatization (root formation) of the plantlets, and compare in vivo observations with the in vitro ones. Our mentor also told us that this semester he’s going to be a little stricter on the written paper, so I need to improve my writing skills in order not disappoint him. Aside from this he wants us to start preparing (separately of course) a poster.

For what has been said, it is clearly seen that our goals for this semester relates in a great manner with our work done last semester. There’s no doubt that this semester is going to be challenging, but fortunately my perspective remains positive.

Third Month

I must admit that I am very grateful to this program, sue to all the knowledge that I was able to gain. My mentor has exposed my partner and myself to all the basic techniques involving micropropagation and tissue culture. Something really amazing that has occur in this month is that thanks to a little mistake we are about to discover something (which of course I can not tell you). We are still making adjustments in our procedure, but I think we are very close at finally determine the optimum one.

To tell the truth not everything was like this, especially at the beginning. I consider myself a person of little patience and you can say that this semester has tested me a lot. As I stated earlier in the other blog post, I believe that my greatest challenge was to get used to the investigation itself, especially in the part of research. First, I was really hard for me to adapt myself in my mentor’s methodology. It contrasted greatly with my idea of it. It reached to the point that just thinking of my research provoked me stress. Before let things get any worse, I fill myself in courage and decided to tell the mentor how I felt. Thankfully, we were able to clear things up and everything turned out great. So communication is very important factor when doing an investigation along with other people. Concerning the research, our repeated failures thanks to contamination did not wake up feelings of joy in me. Believe me, it is very frustrating you keep something several times and no matter how careful you are things end up contaminated. It feels like you’re stuck and there’s no on moving on. One of the most important things that I was able to comprehend was that one can not expect to have perfect results always. Our mentor once told us that part of doing research is to be wrong; to commit mistakes. Otherwise it wouldn’t be research. He also indicated that many times mistakes have lead many scientists to make the greatest discoveries. His words were very comforting and made us wonder that our mistakes could lead us also to important discoveries and as matter of fact, we are about to make one. We only need to do some test before making any conclusions.      

My primordial expectation for the next semester is to improve my skills in doing research. I believe that this could help me find or determine other procedures that could be incorporated in our project and hopefully they will give better results compared to the ones we are having now.

The Second Month

This has been a very difficult month, due to the many adversities that we have facing that are keeping us apart from success. Several adjustments have been done concerning the aseptic aspects and the concentrations of our matrix components, but unfortunately the seed are still getting contaminated by the fungus. Not knowing what else to do, we went to the basis once again, search in the literature. We found another procedure for the preparation encapsulating matrix and we decided to implement it in our own. Everything seemed perfect until we noticed that the encapsulating solution seemed less viscose as it used to be. The consequence was that the resulting seeds were too a fragile. That means that we are still making adjustments to our procedure. In spite of it all, not everything has been that bad, given that I have been able to nurture myself in knowledge during this month. The mentor has exposed my partner and me in the different plant propagation techniques. Among them is the production of protocorm-like bodies (PLBs), which consist in taking out seeds from the orchid’s seed pod and transfer them into a black medium (charcoal). The utility of this medium is that absorbs the toxins and promotes the production of the PLBs. Another technique that I have learned is the tissue culture technique, which consists in transferring the PLBs from charcoal to a sugar free medium to promote a better growth environment and acclimatization. 

I had the opportunity of visiting the blogs of others students also from the BioMinds Program. It is remarkable the variety of fields with applications to Biotechnology. I found fascinating all their works and they all seem to be exited with their respective investigations which are the most important thing. The one that I liked most was the Angel’s Casanova, a student from the UPR of Humacao, and whose investigation is in the field of Geomicrobiology. 

General Information About Synthetic Seeds and My Experience So Far

The following information is based on the web article: “Artificial Seeds and Their Applications”. Plant propagation using artificial or synthetic seeds opens up new vistas in the fields of agriculture and plant biotechnology. This technology provides a promising system for the propagation of non-seeds producing plants, polyploids with elite traits, plant lines with problems in seed propagation, and transgenic plants. The micropropagation techniques ensure abundant supply of the desired plant species. However seed propagation has not been successful in some species. Possible reasons for this may be the seed’s heterozygosity, size of the seed, insufficient endosperm and the necessity of an association with mycorrhizal fungi for the seed to germinate (which is our case with orchids). Synthetic seed production technology is currently considered as an effective alternate process for seed propagation and it has been recommended as a very powerful device for mass propagation of plant species that are commercially valuable, such as the orchids.                  

Personally, I am very satisfied with the all work my partner and I have done so far. We have already decided which are going to be the main components of the encapsulating matrix (which of course I can not tell you) and we have done several tests varying their concentrations. After this we selected by our judgment, which were the best concentrations. Using the proper techniques we manage to encapsulate some orchid’s embryos with our created matrix. Then the seeds were submerged into the nutrient medium and were stored. We did this on a Friday. Sadly our seeds did not survive the weekend given that when we came on the next Monday we observed that they all got severely contaminated. This was of course very frustrating, but one can not expect to have excellent results all the time. After all that is what research is all about, learning from the mistakes, determining the possible sources of error and making the proper adjustments in order to not repeat those mistakes again. We believe that out failure had to do with aseptic manners and so we decided to give it a second try but this time doing the process in a more aseptic condition. Let’s hope that this time works. I really can not say that my experience on this research was always this wonderful. I must admit that it took me some time on getting used my research, but thank God I was able to overcome that. Concerning my lab partner, I love working with her. We definitely make the perfect team and the mentor is very pleased with our work. I believe that our success as a team has a lot to do with our commitment with the investigation. Another fact that is needed to be considered is that when we used to be lab partners in back in first year when we studied General Chemistry. One of the reasons why I like working with her is that we have somehow managed to make the perfect balance of having fun while working responsibly. I consider that I have learned a lot during this first month, and not only in the academic, but in how to be tolerating towards others opinion that differs from mine. I really can not complain on anything.