Rutgers Cognitive dev lab final round

My final blog post. The summer was great, but first let’s cover the time since my last post. I went to the preschool I had been working on all summer, called seedlings. It was an old church converted to a preschool, which was beautiful, but bad for my lab manager, Alex, who was trying to test kids on their ability to cheat. He told me that he could not run the experiment in the church because other studies had proved that when in the presence of an authority figure (even a representation of one) lower instances of cheating drastically. Michelle ran her study (TFB) with mixed results, some of the kids were very willing, but not very able, and some were neither. Anyway, this was probably my favorite preschool of the three, simply because it was rural and beautiful. I forgot to mention this in my previous blog posts, but all summer kids we recruited came into the lab to run studies. Most of my part was recording the experiment on the video recorder and coding, but it was fun anyway. Before each experiment, we played with the kids to get them comfortable, and so my puppet skills have increased beautifully throughout the summer. This lab was great. Although some of my work was making phone calls and sending emails, I would not trade this lab for any other. By the end of the summer, my lab manager and I were friends due to the fact that we spent long stretches of time alone together on the computers, trying to get people to come into the lab. I learned a great deal about child development and psychology, but I also learned that this is a field I don’t think I want to go into when I get older, children are simply too difficult as test subjects. I will say goodbye to my lab tomorrow, and will see you all in September.

Rutgers Cognitive Dev lab round 4

  Hi, I just remembered something that should’ve been in my last blog post, I fell off by bike while leaving the lab, which sucked, and has encouraged me to wear a helmet while biking on the busy roads of Busch Campus. Since my last post, Talia request to go to Peru and study John Mikhail’s Universal Moral Grammar by handing out surveys at a bus stop has been struck down by the IRB. On the brighter side, I preschool that we(I) have been in contact with all summer, trying to get their O.K. to do a study at their school, has finally agreed and established a date next week. This week however, I went to the Douglas Campus Daycare, a daycare for the staff of Douglas Campus. It was interesting. I went with Michelle, Lu (who both ran the same experiments as last time) and Sydney, who was running an experiment called Good Intention Default. Essentially, she was trying to show that when people evaluate a trolley problem, they assume that the character acting has the best possible intentions for all characters. DCD was interesting, as it is used by a lot of child labs as a place to get subjects. Most of the kids were familiar with taking part in studies, and were far more enthusiastic than the last preschool I went to. Most were very smart, passing all control questions and providing promising results for the grad students. Anyway, this was a much better preschool for both me and the grad students.

Rutger Cognitive Lab round 3

  This week, I presented a paper to my lab in one of our weekly lab meeting. As our lab takes lots of RAs, they try to teach them as much as possible, one of the ways being through these weekly meetings in which every RA reads the same paper and one presents it. The article I presented was “Universal Moral Grammar” (John Mikhail.) It was not a research paper, rather, it is meant to do to Moral Grammar that which Chomsky did to language. Mikhail proposes that we are all born with an innate ability to develop similar moral decisions. However, abnormal development (abuse, psychopathy, ect.) can hinder this development. He cites as evidence the fact that most cultures, however different, have bans on battery of all forms. Also, he claims that the intuition for a set of trolley problems is similar across cultures. Trolley problems are hypothetical situations in which a trolley is headed down a track to 5 people, and a separate character presses a button to divert the train onto another track where only one person is standing. The purpose is to see what people’s intuition on the morality of the characters actions are. There have been dozens of variations on the trolley problem which attempt to explain why some situations are acceptable and others are not. From asking people about their intuitions, the “Doctrine of double effect” has been established. The doctrine attempts to set parameters to predict if people will think if something is morally acceptable. There are several stipulations, but the most important are these; if the harm outdoes the good of an action, or if harm is a direct means of achieving good, people find it morally objectable. Anyway, presenting to a group of grad and college students was a nerve racking experience, but I think I did well.

Rutgers Cog Dev Lab round 2

        This week in the Rutgers Cognitive Development lab, I got to visit a preschool to test children. I went with the two grad students, Lu and Michelle. The kids in the preschool were aged three to five and we tested about fifteen. Most of what I did was filling out coding sheets (the sheets with the kid’s responses) and brining the kids in and out of the room where we were testing. Michelle ran Triple False Belief by telling a story and Lu ran Double False Belief on an eye tracker TV monitor. Both studies test how many false belief states children can keep track of, where a false belief is a when a character has an incorrect belief about the thoughts or actions of another character. TFB was done through a story, and DFB was done through video. Unfortunately, most of the kids failed the control questions for TFB (questions to make sure they understand the facts of the story.) However, it was a good experience to go to my first preschool. 

Last Week - Finally got rid of dimers

Hi this is Harry Zhang, and I just finished my 5-week lab work with Dr. Ballatore at UPenn. I participated in Dr. Ballatore's current project of making and categorizing carboxylic acid isosteres.

Methylation and LDA alkylation both failed to get rid of the CPD dimer, so Dr. Ballatore suggested another possible factor: the concentration of the starting material. If the starting CPD is too concentrated, it would be easier for it to attach to itself and form dimers. Using the rest of the new batch of CPD, I ran the same alkylation, again with LDA, but this time added more solvent so the starting CPD was ten times more dilute. Since this was the last week, I really hoped that this would work because we have been tackling this problem for almost the full duration of my stay and I would not have really contributed to the making of model compounds if this method did not work. Thankfully, after a work up and column, the LC-MS graph showed only our desired product's mass, and no dimers. That basically concluded my work with Dr. Ballatore and he said that he would send me more data once he finishes the whole project.

Although I have really only made one new model compound (the unmethylated CPD isostere was already made before and I only did it as a practice), I got a taste of what it is like to work with a scientific problem in real labs. By working at the issue in different angles, accompanied with constant testing, we were able to solve the persistent dimerization problem.

Overall, I think the 5 weeks at UPenn showed me what it is like to work in the field of scientific research. It consists of both logical and creative thinking, a lot of cool technology, but also a lot of repetitive work that sometimes even drives Dr. Ballatore crazy.

Week 4 - In the process of solving the dimerization issue

Hi this is Harry Zhang, I'm working at the Ballatore lab at UPenn and this is the 4th week that I've been working with Dr.Ballatore on making carboxylic isosteres (model compounds).

Towards the end of last week, I made another batch of protected CPD for the new LDA alkylation. Making the LDA was also a tedious process, and that was why Dr. Ballatore preferred using KHMDS. The making of LDA was mostly done by him and I was responsible for the alkylation. Since I've already done at least three alkylations, the process was familiar and I didn't make any mistakes so the color of the product was more "right", according to Dr. Ballatore. After working up the product and doing an HPLC, we still found the existence of the dimer. Dr. Ballatore collected samples for NMR to further analyze it while I made more methylated CPD.

I think after three weeks of practice, this week's lab work felt a lot more manageable and I actually had confidence that I wouldn't make a mistake like spilling dichloryl methane or making a cloud of silica powder. I felt that I was able to get a lot more done without the help of either Dr. Ballatore or the post-doc Bryant.

This was also the last week of the stay at Peddie. Over the weekend I moved to a hotel 2 blocks away from the lab to make life a lot easier (no more 3 hour commutes every day).

Adam Levine and Kelly Clarkson come to celebrate my last week at CHOP!! (kinda)

Overall my time at the Falk lab at CHOP this summer was really enjoyable. Though my stay was longer than expected, I got exposure to a number of techniques and had the opportunity to give a presentation to the entire genetics department at CHOP. It was definitely nerve racking at first, once got into my presentation it was very easy for me to talk about my project. Because I was going to present to  all the other PI's and lab members in the department I gave a few practice presentations to Dr. Falk. After spending a lot of effort of my powerpoint and doing a couple run throughs, I built my confidence. Rebecca and Fred, undergrads in my lab, also gave presentations on their projects. I really enjoyed my time at CHOP and also the commute through Philly since I feel much more comfortable with the city than before. Walking through CHOP everyday was also a humbling and eye-opening experience because I got to frequently see ill children and it reminded me of the difference CHOP makes in so many family's lives. On one of my last days at CHOP, Maroon 5's Adam Levine and Kelly Clarkson came to visit and I got to see them give an interview in the Ryan Seacrest Media Center. I managed to snap a picture too!!

Computer Networking Lab Week 9

Hi this is Sohan checking in for the last time. I finished working in a computer networking lab this summer at Columbia University.

I finished on August 1st after Varun left for India for the rest of summer. I did more of the same kind of work: ran tests on the orbit lab, processed the .pcap files using the Python scripts, and then graphed the data using the MATLAB scripts. This week, however, I spent most of my time debugging parts of the MATLAB script. Some of the nodes in the Orbit-lab create .pcap files and .txt files that are different that those of the other nodes. They include extraneous information that the MATLAB script cannot process. My job was to create a code where the script could automatically detect the defective file, delete it, and then move on to the next in tact file. 

On August 1st, Josiah, the visiting undergraduate student from North Arizona University presented his end project. He did a very good job and even after working with him and performing the same tasks as him, I got the chance to clarify some aspects of the work we did, and gained some insight into the changes he made to the scripts as well. 

Lastly, I held off writing this post since Varun had wanted to come back and present my work and research to the lab group. Unfortunately, the curcumstances did not work out and he had to stay in India for a little while longer and thus I was unable to return. Nonetheless, I greatly enjoyed my time working under Varun and alongside the other members of Dr. Zussman's group. 

The End of Summer

Last week, I finished my work at Princeton. Although it is not the ending of our project, the progress we made this summer is really important for the whole project.

The main part of our improvement includes two parts: thylakoid extraction and photosynthesis efficiency testing.

For the first part, the main procedures include: 1. using a lab blender to blend the mixture of alginate leaf pieces with grinding buffer; 2. putting the solution into the centrifuge for the pellet; 3. putting the pellet into the washing buffer and do the resuspension; 4. go through few more times of centrifuge to get the concentrated thylakoid.

For the testing, the main procedures include: 1. adding 0.10 mL of the suspension to 10 mL of 80% acetone in a test tube; 2. inverting the solution several times and then filtered through a Whatman filter paper into a large cuvette using a 50 mL glass funnel; 3. measuring the absorbance of the green solution using 80% acetone to zero the spectrophotometer. The concentration of chlorophyll in the original sample is calculated using the relative equation. 

We tried multiple methods to see which works the best. There was failure sometimes, but we got through it and kept on moving forward. This project includes a lot of brainstorming and testing. Different from my last project, I have experienced more about the beginning part of a science project, including proposal writing, idea design and other preparation.

Since the project is still in progress, I will go back to Princeton to continue my lab experience during the school year. It is the consistency that makes a difference. 

Week 7 Mendelsohn Lab

This was my last week at the Mendelsohn lab. As I approached my last week, I felt it went by very quickly. I briefly learned how to use a digital microscope to take pictures of the slides that I have stained. Other than that, I did much of the same paraffin sectioning and staining, which felt interestingly comfortable.

One of the digital microscopes

On the last day, I bought doughnuts to share and thanked everyone for giving me the opportunity to work at the lab. I really enjoyed my seven week lab experience at the Mendelsohn lab and would highly recommend it to anyone who would be interested in working with cellular biology and genetics. Hopefully, I will be able to come back next summer.

This is the building where I worked

Tissue Morphodynamics Lab: Weeks 9-10

Hello, this Danny from Dr. Nelson's Lab in Princeton, and its been quite a while since my last post. I been done for about a week now and I've just finished up organizing my data and images. The last two weeks at the lab were exciting and busy, as many of the graduate students and post-docs were preparing posters and presentations. Although Amira and Sriram seemed busy with experiments throughout the week, they still both made time to continue helping me with my research. 

During the ninth week, I was mainly focused on dissecting day 4, day 5, day 6, day 7 chicken lungs in order to create a morphology chart for my upcoming poster presentation. Ideally, I wanted to get the dissection done in the late morning, but if the microscopes were taken, I usually resorted to tracking cells on Imaris. On Imaris, I needed to track squares with higher densities and more cellular divisions per 12 hours, because Sriram and Dr. Gleghorn wanted to see if the cells illustrated similar rotational patterns to previous research done on rotational axes. There were on average 20 to 30 more divisions per data set in the higher density than the normal density data sets. After I finished cell tracking, the data was then analyzed through MatLab and saved. We also tracked cells in a worm structure, rather than in a square structure to see how different structural shape would affect the division of cells. The results were similar to the square, as the cells divided parallel to the edges of the structure.

The last week at the lab, there was a research symposium similar to the one EXP went in the Fall, that highlighted Physics in Living Systems. Although I only listened in on one day out of the four day conference, the research other universities were doing were astonishing. During the last week I continued culturing lungs in tissue culture, and observed the mechanical effects of Hepatocyte growth factor (HGF) and Transforming Growth Factor Beta 1 (TGFβ1) over the course of three days. I also learned 2D patterning from Sriram, who was really helpful throughout the process. I stamped 2 gels onto coverslips, and luckily one of the two came out alright. It was a great experience but it was definitely a lot harder than I could of imagined. The last week was essentially dedicated to compiling all my images and finalizing my research. I had a great time at the laboratory and really thank everyone at the lab for making me feel welcome. 

NLP week 7: finishing up pipeline wrapper and web interface

Hi again, my name is Jiehan Zheng.  I worked on NLP and some machine learning at Columbia University.

I skipped writing about week 6 because we were working on something secret!  We will publish our work on that during the upcoming fall term if things go smoothly.  So I am writing about my work during my 7th week.  I was too busy working on the project so I didn't have time to post updates to this blog...

Since week 7 is the last week I physically work at CCLS at Columbia University this summer, we chose to finish up things that require face-to-face collaboration first, so we don't have to wait on each other to finish our tasks.  My work on the web interface and pipeline wrapper would be the thing that we have to finish together before I go--so the last week I mainly worked on pipeline wrapper and web interface.

Apoorv's work is on the pipeline that takes in sentences, gold dependency parse trees, semantic parse trees, and entity annotations.  It spits out a file in graph modeling language containing the interactions between entities.  In order to make the pipeline work for any unprocessed text and returns a social network, it has to be wrapped around by some wrapper code--I named that part of the code as "pipeline wrapper," and I feel like that's a smart name, isn't it?

So the pipeline wrapper has to take in raw text, split it into sentences and call various parsers and process the result from the parsers into a format that the pipeline expects.  There was code on that but it no longer worked, and when it was working, it was poorly written and inefficient.  I rewrote the wrapper in a more organized way.  For instance, the old wrapper had to call NYU Jet's main method twice to get named entities and split sentences separately--I read Jet's source code and managed to call Jet once and get both information, making it faster.  I also prevented Jet from performing useless operations that takes time, like relation extraction.

Then the pipeline gets dependency parses from Stanford parser.  My refactoring effort also enables us to run multiple tasks in parallel.  For instance, we are going to run CMU's SEMAFOR semantic parser as well in the future, and running SEMAFOR takes a long time.  Had we added SEMAFOR to the old wrapper, it has to wait until Stanford parser finishes its job.  With the new structure, SEMAFOR and Stanford parser runs in different processes, can take advantage of multiple CPU cores and run at the same time, cutting the running time by at least 50%.  SEMAFOR integration is a bit harder than other parsers, so I decided to work on that after I go back to China.

After we have all the parses and other files, the wrapper calls the pipeline with the files, and waits for pipeline to finish processing the files.  Once it gets the interactions in text, the wrapper calls the postprocessor that I made during week 2 which merges duplicate entities, finds out the best name for each entity, analyzes interactions and finally organizes these information and outputs a social network file.

The web interface is just some pure programming effort and is nowhere as interesting as working on the pipeline wrapper and other machine learning aspects.  My work on the pipeline wrapper, postprocessor and web interface had been included in a demo paper that is going to be presented in IJCNLP 2013 this October in Japan, and I've been made an co-author on that paper--I am very excited for that!

Apoorv and I have made that arrangement with Mr. Corica that I will be continuing our work on that "secret project" as an independent project at Peddie during my fall term.  This is indeed a very precious opportunity for me to learn more machine learning--from implementing tools, extracting features, run experiments and tune SVM parameters and our features, to finally evaluating the result.

As for the rest of my summer, I did figure out a way to integrate SEMAFOR so I will spend some time to make enhancements to the web interface and pipeline wrapper by adding in SEMAFOR integration.  I will describe more in my next blog post!

Week 8 - 10

Hello, this is Jacky Jiang from McAlpine group in Princeton. It has been a long time from last post. In the past three weeks, we keep on testing the efficiency of our methods to make thylakoid and the concentration of our chlorophyll.

To get better concentration, I need to come up with different methods of producing the thylakoid. As I have tried the classic procedures, the basic steps would be similar. First of all, I need to use a lab blender to blend the mixture of alginate leaf pieces with grinding buffer. After we get the solution, we will put it into the centrifuge for the pellet. The pellet we get need to go through another step, which is called resuspension. In this step, we put the pellet into the washing buffer and do the resuspension procedure. Then, we need to go through few more times of centrifuge to get the concentrated thylakoid. To make modification, I tried different kinds of centrifuge rate, which made the composition of the pellet different. This change could be very critical. Since the nuclei and other fragments of plant cells have different density, the centrifuge rate determines which component would be at the bottom of the pellet. What’s more, I also change the grinding buffer I used for blending the mixture. The different concentration of tricine would make the grinding level different, so that the size of membrane fragments would be different, too.

After I tried different methods, the results comes out that the classic steps with appropriate concentration of grinding buffer and high centrifuge rate worked the best. I also tried to change the sequence of centrifuging and buffer mixing, which didn’t turn out well in the end.

 To determine if our thylakoid is efficient enough, we still need to determine it by the concentration of chlorophyll. The experiment methods are the same as we did last time. The chlorophyll concentration in the thylakoid suspension is determined by adding 0.10 mL of the suspension to 10 mL of 80% acetone in a test tube. This solution is mixed by inverting several times and then filtered through a Whatman filter paper into a large cuvette using a 50 mL glass funnel. The absorbance of the green solution is measured at 663 nm and at 645 nm using 80% acetone to zero the spectrophotometer. The concentration of chlorophyll in the original sample is calculated using the relative equation.  

Our thylakoid concentration has improved a lot after we modify the methods. In the rest of the summer, we will move on to the electrical part of our project. 

Week 4 at Chandran Laboratory

My name is Anna, and I'm working at Dr. Kartik Chandran's Laboratory at Columbia University in Earth & Environmental Engineering.

So this week was mostly defined by transitions. Our batch reactor's finally reached their stable population so we took them and put the reactor into chemostat. Where batch reactor's have nothing going in or out (technically) and are used to watch change over time, chemostat reactors have influent and effluent moving at the same rate. This means that nothing changes: the population is constant, as is the amount of ammonia, nitrite, etc. The reactor is going to spend two weeks stabilizing in chemostat and then the real interesting stuff will begin. Even though I won't be there for it, the next step will be disturbance, or increased feed chemostat. In this phase, the bacteria will be subject to one hour of ammonia loading. Our strain, Nitrosomonas eutropha, is known to prefer larger quantities of ammonia as compared to its N. europa cousins, and hopefully this means that it produces NO and N20 gases differently (i.e. less of them.) However, this ammonia loading will require hourly testing for 12-15 hours every day, so I'm not completely heartbroken to be missing it. After those two weeks, tests will be done to see if the bacteria retained any of the previous traits.

We will be testing for the next few days to get baselines for ammonia, nitrite, hydroxalimine, and some mRNA stuff as well. We will also be creating our own standard curves for the aforementioned chemicals because we are finally getting into work that could be publish-able. Next week I will also be working on some poster drafts to present to Medini and Dr. Chandran.

In the past week, there has been an influx of people coming to the lab, including high school students, and new grad students. (Very thankful that I've had my own desk this whole time.)  

Although I can't stick around any longer, I look forward to periodically seeing how this project develops and maybe working with Medini again.

Week 6 Mendelsohn lab

Hi again. This is a summary of what I did during my sixth week at the Mendelsohn lab.

I briefly worked on Sol's silk bladder augmentation project by paraffin sectioning some of his blocks. I found these paraffin blocks much more difficult to cut because the silk embedded into the bladder tissue made it harder to fully slice without it ripping apart. 

Throughout my stay at the lab, I have been paraffin sectioning many mouse embryos, not fully understanding where and how these embryos have been embedded into the paraffin wax. During the week, Katya brought an E17 pregnant mouse into the lab to remove its embryos. She removed all 13 embryos from the mouse and placed them in 1x PBS, while I prepared 13 tubes of diluted formaldehyde fixing agent. Katya showed me the following steps to dissect a mouse embryo and told me to dissect the rest of the twelve embryos. First, I removed the amniotic sac and cut a small piece of its tail to be further genotyped through PCR. Then I bisected the embryo, under the arms, removing the upper half of the embryo (because we are only looking at the lower half). After bisecting, I moved under the microscope to clean out the rest of the embryo removing everything but the bladder and kidneys. After removing the existing limbs and tail, I placed the embryos into each of the 13 formaldehyde tubes to be fixed and eventually paraffin blocked at the histology department for future sectioning. 

Mouse embryo E17

                          

                                  Dissecting microscope

Under the microscope

The next day we ran a PCR on the small pieces of embryo tail (that I previously mentioned) and the following day we ran a gel to confirm the Cre genotyping of the embryos to see which had the gene and which didn't because eventually we want to cross mouses that have Cre with mouses that have Apaf mutations. 

Gel

If you have been reading, I haven't explained what this project has been really about. Basically, the Apaf project (the one involving mouse embryos) is about the connections between the ureter and the bladder. In embryos, the ureters are joined in the nephric duct through the common nephric duct. Normally, the ureters would detach from the nephric duct and fuse with the bladder epithelium. This project is trying to analyze Apaf (Apoptotic protease activating factor, one of the major proteins that form the apoptotic regulatory network) mutants to determine whether apoptosis is required for ureter insertion.

Week 5 Mendelsohn Lab

This is Jason again from the Mendelsohn Lab at Columbia. I have been behind writing my blogs and will update you all as soon as possible. I am writing this not actually in my fifth week, but here is what I did anyway.

Throughout the week, I have again been practicing and understanding how to stain slides using immunohistochemistry (briefly mentioned in my previous post). After paraffin sectioning and a day to let the tissue dry and settle on to the slide, these slides were ready for immunostaining. First these slides were deparaffinized in xylene solution and hydrated with ethanol so that the paraffin wax was fully dissolved, leaving only the desired tissue on the slides. After the deparaffinization process, the slides underwent heated antigen retrieval, which means the slides are placed back to back in a pH 9 buffer at 100˚C and steamed for 30 minutes. We did this because when the tissue is processed into paraffin blocks for sectioning, the tissue is added with fixatives that masks and cross-links its proteins, making successful antibody binding almost impossible. This way in the buffer and hot temperature, these fixed proteins were unfolded allowing our specific antibodies to successfully bind. After the 30 minute steam, the slides went straight into PBS .1% triton (a very common buffer solution) for 15 minutes to wash. Then horse serum blocking solution was applied to the slides for 90 minutes to reduce background or unspecific staining. After the blocking solution, the slides were ready for the specific antibody application. Lastly, I applied DAPI (a fluorescent DNA stain), washed in PBS .1% triton, and put on the cover slips. 

Staining hood (Deparaffinization on the right)

Slides deparaffinized and hydrated

Heated antigen retrieval

It might seem like a lot to remember at first, but after a couple times of practice you get the hang of it. 

My bench

On Wednesday, we had a formal lab meeting where everyone in the lab presented there work. I listened and learned as the other five lab members explained their projects. Katya, Kerry, Tammer, Hanbin, and Sol all amazed me with the work they were doing. The Mendelsohn lab focus spanned far beyond just bladder cancer and touched upon several different areas within the field of urology. For example Sol's project involves bladder augmentation using silk fibers as a scaffold to increase the size of the bladder and lower its pressure for impaired bladders.

I have continued my work on the BBN and Apaf projects and will explain them later in my next post. 

Murphy Lab- Last Week

Richard again, continuing on from my last post.

My last week was a week with more experiments than usual.  On Monday, I did an STAM with the unc-73 mutant and wild type worms, and then tested chemotaxis up to two hours after training.  I analyzed the images I took of the chemotaxis plates on Tuesday, and bleached my egl-4::GFP worms with the hope of doing one last adaptation assay on Friday.  From what I observed, the unc-73 mutant did not make the food-odorant association as effectively as wild type, but it retained its memory better than wild type did, which is consistent with what Geneva found.

On Wednesday, I did the egl-4 and wild type STAM again, since there were various things that went wrong with my egl-4 strain in the past, and after analyzing my results, it seems that I have good data that confirms what is expected.  I did the goa-1 and wild type STAM on Thursday, and like the unc-73 mutant, the goa-1 worms didn't learn as effectively, but retained a longer lasting association between food and butanone.  Today I was hoping to do one last adaptation assay, but the worms that I had bleached were overgrown, and thus many had died, leaving only the young ones with very few eggs as the worms I had to bleach.  As a result, the worms grew very poorly, and I had to spend much of the day analyzing my data from Wednesday.

Overall, reflecting on these past nine weeks, I felt I've learned a lot.  Doing chemotaxis assays can get a bit routine, but it is nevertheless exciting to test new mutants and see what their learning and memory is compared to wild type.  I was really hoping I could test the egl-4 crh-1 double mutant, since no one else has done that so far, but sometimes matings don't work out.  Still, a lot of the STAMs I performed in the last few weeks were useful replicates for Geneva, and she is in the process of publishing her paper, which she said will most likely have me as one of the authors, since I produced some data that is of use.  And that's really cool, because not many high schoolers can say that they've been published.

Anyway I'd just like to thank Dr. Murphy for giving me the opportunity to work in her lab, Geneva for mentoring me all while she is dealing with her pregnancy, Dr. Peretz for helping me throughout the year, and everyone else involved.  Time to enjoy the last couple of hours I have left in lab.

Murphy Lab- Weeks 7-8

Hi, this is Richard, and I'm studying learning and memory at Princeton.  I will break up the last three weeks I spent at the Murphy Lab into two posts, and this is the first of the two.

I spent the majority of my seventh week repeating the egl-4::GFP nuclear localization assays that I had started earlier.  Since we don't really know what is supposed to happen in regards to the GFP-tagged EGL-4 protein entering the nucleus, I wasn't able to make too much sense of my results for my naive and trained worms.  In some cases, the GFP localized into the nucleus of the AWC neuron, thus causing the nucleus to flash a bright green, and in other cases, it was mostly the surrounding cytoplasm that was lit up.  Such ambiguity held true in both the naive and trained worms.  We did however, know what to expect with my adaptation assay, so we tried to confirm this result in which for adapted worms, EGL-4 enters the nucleus and for mock adapted worms, it doesn't.  However, while in some of the worms the EGL-4 protein had clearly localized into the nucleus, in other cases it seemed that it was present throughout the entire cell, not just the nucleus, as evidenced by the entire neuron being bright.  Unfortunately, I didn't have enough time to repeat this again and get a definitive result.

I tried my egl-4 and crh-1 cross again, and got to the point where I had candidates who had a 1/16 chance of being double mutants, but I did not have the time to run a PCR and isolate the successful candidates that I could use for my double mutant chemotaxis assay.  I did a PCR earlier, but none of the 30 candidates I picked out were identified as double mutants, and within a 9 week timeframe, it's pretty difficult to start from scratch and set up the same cross again.  I was really looking forward to this, because, as of know, according to wormbase.org, pretty much the bible of C. elegans research, no one has tested egl-4 crh-1 double mutants.  I could've been the first.  But not anymore.

Anyway, I spent the rest of the two weeks on a couple of STAMs and an LTAM as well, to help with Geneva's project.  The difference between an STAM and an LTAM (long term associative memory) is that rather than training the worms once (starve, food w/butanone, test), I must train them seven times in 30 minute intervals (starve, train, starve, train...).  I didn't test chemotaxis, but Geneva used the worms I trained to observe fluorescence.

These two weeks were definitely more eventful than some I've had in the past.

Glowing Worms -Last Week

Hi everyone, this is Rhea researching mitochondrial disease at CHOP.

Because last week, my life span results found that the gas-1 mutant worm had lost its main phenotype, a short lifespan, my PI asked my to perform florescence tests on it to see if it still had chemical differences  from the wild type. Since Fred, an undergrad, has been working with fluoresce for the past few months and perfecting the assay, he taught me what information fluorescence can uncover about the worms being studied. There are three different dyes that the worms are fed, Mito Sox, Mito Tracker Green (MTG), and TMRE. Mito Sox measures the oxidant burden in the animal's mitochondrion which should be higher in gas-1 mutant worms because the sicker animal experiences more oxidative stress in its cells. MTG measures the mito content in the animals cells and should be less in gas-1 worms because the mutant strain is born with less functioning mitochondria. TMRE measures the membrane potential in the animal's mitochondrial complex which should be less in gas-1 worms because their mitochondria are less capable of creating a concentration gradient with H+ ions.

To perform the fluorescence experiment, I first had to prepare enough plates. I had to spread them with OP50 e.coli and then with each dye. After placing about 60 young adults by hand on each plate, I incubated them for 24 hours so that they have time to ingest the e.coli with dye and the dye had time to adhere to the fatty cells in the animal. Then after 24 hours, I handpicked them again and transferred them onto a plate of fresh bacteria. This is done so that the worms can eat the e.coli without dye and clear their gut of the dye. We want only the dye that had penetrated into the cells to fluoresce not the food in the gut itself. After letting them clear their gut for 3-4 hours, I put levamisole (a drug that temporarily paralyzes them) on each plate making sure every worm is submerged in the drug. After giving the worms 30 minutes to fully paralyze, I took the plates to the microscope with a camera. I used different filters on the microscope for each dye, and zoomed into each individual worm and took pictures of each worm's pharyngal bulb.


Here's a good one:

About 2 hours of picture taking later I have to manually circle the pharyngal bulb using a software. This software then counts the pixels and measures the amount of light per pixel and calculates the necessary information. According to the fluorescence experiment, everything seems normal with the gas-1 strain. Nevertheless, my PI has ordered a fresh batch of worms for the lab to work with.  

Week 2 and 3: Reactors and Reacting

My name is Anna Piwowar, and I am currently working at Dr. Kartik Chandran's lab at Columbia University, working with ammonia oxidzing bacteria in batch reactors and studying their kinetics.

This week began with Medini and I cleaning out the reactors and setting them up for a new cycle. Between rinsing and autoclaving, it was a lengthy process. We had to overcome many problems (pieces that didn't fit, screws that had to be unscrewed, and everything in between). Finally, we thought we would be ready to inoculate our sparkling clean reactors and begin looking at cell growth. However, problems kept cropping up, and Murphy's Law held true: everything that could go wrong did. *(Not everything did go wrong, yet. So I don't want to jinx anything but we are still able to move forward with the process.) The DO (Dissolved Oxygen) probe on one of the reactors was found to be defunct, so now we are in the process of ordering a new one (and they do not come cheap). We do have the one reactor working properly enough for the time being, and hopefully we'll start collecting data on cell growth and nitrite formation.

While the process goes, I have a lot of time to read. Medini has many textbooks to offer me, and on Tuesday it was all about studying reactors, all the types and the equations. Sadly, I lack the Calculas to understand some of the things, but after an arduous tutoring session with Medini, I understand what the kinetics are and what we need and why.

By the end of the week we decided to go forward with the second reactor without the DO probe, and instead opting to manually find the dissolved oxygen. Even though we can't have simultaneous growth, we will at least have two sets of data.

The third week was all about data collection. We went forward with the second reactor, and now we're just working on maintaining the reactors and improving my laboratory skills. My PI is out a lot, but I will be meeting with him soon to talk about other things I might pursue for my last few weeks here.

Other than that, Columbia is beautiful, especially with the cooler weather, and having the chance to travel around Manhatten is wonderful.

Rutgers WAre Lab - Week 5 (Last week!)

Hi everyone, this is Michael and I've been working in Ware Lab at Rutgers. We focus on studying the body and shape of dragonflies and damselflies.

Coming back from the weekend, I started off with creating draft phylogenetic trees for my Orthetrum leg sample. This time, however, instead of a single cycle, I adjusted the program to create a draft tree for 100 cycles and pick the best tree. This would prove that I had not related my sample with Orthetrum by chance. This took a long time, since I was comparing my sample with about 20 other Odonata. Creating a tree for one cycle itself took about 15 minutes. Gettign a best tree, with 100 cycles, would took a couple hour; basically it was lots of waiting for the tree.

On Tuesday, I got to go on a field trip to catch some dragonflies for the lab. I was lucky since the day before had been raining the whole time, and now it was quite wet outside. Will taught me two basic ways of catching dragonflies: when they were resting on something, you can sneak up to them and and catch them with a net in a burst of action; the other way, when they are flying around, is to simply chase and swing your net around, hoping that you will catch one. (This way is especially exhausting - there was one dragonfly that totally drove my crazy; I was exhausted at the point when I decide to give it up). When you manage to catch one, there will be buzzing noise coming from the dragonfly trying to escape, so you can tell if you catch one. One thing to keep in mind is that be sure to fold your net and seal its opening; dragonflies can escape if you don't.

Anyway, at the end of the day, I caught about 9 dragonflies, including a lot of blue dashers (since they were literally everywhere for some reason), a couple other species, and a metal hawk, which people from my lab had never caught one before.

For the rest of the week, I made more draft trees for my other samples. My professor said that she will probably publish a paper on my discovery with the Orthetrum, and we were all excited about this news.

Overall, this has been a really nice experience for me. I got to experience the environment in college labs, and got some idea about what do people do in lab, how do they get money for research (for this, there was a grad students in the lab,Melissa , who was recruited by National Geographic by writing a proposal to them), how do they find topics to work with, etc. I'm really glad that my professor offered me this opportunity, and along with the lab members for guiding me through my works.