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.

Rutgers Ware Lab - Week 4

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.

Throughout the week, I worked on Will's wing scan project, and managed to finish scanning all of the wings he had given me earlier. Aside from that, most gene alignments were also completed. I also re-ran many PCR for the samples with poor quality.

At the end of the week, after numerous processes on organizing and comparing my dna sequences with the database online, I made an interesting discovery. The larva leg sample from Florida, which I got for a collector about 3 weeks ago, had thought to belong to the Libellula family. Now with my data, it showed that the sample was more closely related to the Orthetrum genus, a group that was not supposed to be found in the new world. On the next week, I would continue to work with this discovery.

Week four: FlyVac Machine

Hi everyone. This is Sandra again. I am writing my forth week in  the Evolution and Behavior Lab in Harvard University.This week is quite exciting for me. I've finally got the chance to use the FlyVac machine to measure the flies' photo-tactic behavior!!

FlyVac machine and the computer

The data in the computer

The process was doing it was actually not as difficult as I thought. As you see in the picture, the FlyVac machine is connected to a computer that is used to collect the data. Lighter blue means a light choice and the darker blue means the dark choice. The white column is used for labeling the specific type of each fly. (Enriched or controlled, Canton.S or DGRP, Female or male). After doing the labeling and set up the computer, I have to load the flies that were in the second-staging tubes (Since they already been tested in Y-maze) into the choice tubes. There are 32 choice tubes in the FlyVac.Once the flies finished 40 choices (complete line in the computer), I would use a tube to suck the fly out(which is still alive inside the choice tube), and put another fly into the choice tube.

The tube I used to load the flies in and suck them out

The place where the flies end their life.....

In this coming week I will start analyzing the data in both Y-maze and FlyVac machine. I can't wait!! Hope everyone is doing fine in their labs too!

Computer Networking Lab Week 8

Hi again, this is Sohan and I am working in a computer networking lab this summer at Columbia University.

Once again, my routine this past week was essentially the same as the weeks prior; try to run the test on the Orbit-lab, process the .pcap files, and graph the results. This last time, however, after several attempts, I was finally able to obtain some data as the test bed did not give too many insurmountable issues. With this new data, I am currently trying to run the Python scripts and MATLAB script to complete the post-processing of this new data set. instead of processing and graphing previous data sets. Given that this is a new data set, the post-processing also poses issues as some of the nodes from the test bed cannot properly create .pcap files and thus the Python script cannot process them. My new challenges include trying to figure out which .pcap files are causing the issues and to further develop the script and make adjustments to it so that it can process the .pcap files smoothly without any errors arising.

Also, this past week, we had a lab meeting where all the Ph.D students had to present their recent work, and a few had to practice their presentations for their posters in some upcoming gatherings. The most intriguing, and the one I could probably understand the most, was one on cascade power failures and how to predict which power lines will go out depending on which line fails. Since Varun was at Bell Labs that day (since our project is in conjunction with Bell Labs), me and Josiah had to present in his place. All the other Ph.D provided very constructive criticism and offered other solution to more efficiently process the .pcap files such as eliminating certain steps, like storing the values in an excel file, that can be avoided entirely and save some time without altering anything whatsoever.

Lastly, since our lab is under rennovation, we are currently working in another work area. However, this past Friday, some workers came to put in some cable trays, can be used to pass wires through and create a mini network of sorts. Instead of it taking them one hour to finish as they said it would, it took them five. Instead, the five of us working in this area went into the kitchen area and watched a few episodes of Breaking Bad to pass the time - one of my favorite days on the job!

Rutgers Ware Lab - Week 3

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.

This week started off me completing everything needed to be done for sequencing. The samples were submitted on Tuesday, and I got the sequence files (files used for analyzing dna on computer) back on Wednesday. While I was waiting, I scanned more wings for Will, and aligned more dna files.

On Wednesday, my professor guided me what to do with the raw sequence files, which involves playing with a handful of programs such as sequencher, clustal, mesquite, etc. Afterwards, I transformed those files into nexus files, ready to be analyzed and compared with gene database. At the end, I combined the genes coding for the same type of dna (such as 16s, 28s), and used the programs garli and figtree to produce a phylogenetic tree.

This is how the final image of a
wing scan looks like; the letters at the
bottom are the code for this sample.

On Thursday, a friend of my professor had an emergency at her lab in NJIT, and they picked me to assist her. She received more bee samples than she had expected, and she had to organize them into an excel file before Saturday. This involvd putting the code and information of each sample into rolls in excel.

The process of scanning wings. The pair of
wings are placed at the top left corner of a printer

Rutgers Ware Lab - Week 2

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.

After a week of presentations in Germany, my professor and some lab members assigned me to run PCRs for about 50 samples. Since I had to pipette chemicals into vials for PCR one by one prior to running the PCR, the process took almost the whole day. After PCR was done, however, I used a pipette with 8 slots for gel electrophoresis, which probably saved me about an hour of work.

On Wednesday, Dominic, the third member of the lab, returned from Guiana with a lot of samples. One of them is a complete massive beetle he found in his house (see image below). Along with them were bees, ants, all sorts of interesting insects.

On thursday, Will introduced me to his project: he is designing a program that can identify Odonata species just by matching images of wings from those in a large database. I decided to take part in his project. The work basically involves scanning wings in a way much like how you scan papers, except they fly away extremely easily, so I had to perform every action gently to avoid messing up the scanning process.

Dominic's beetle
This is about the size of my palm. Dominic even
says that "it's like a toy", since you can move
its wings and claws freely.

Pipette with eight slots: without this, those samples would
take hours of work jsut to run a gel electrophoresis.

Tissue Morphdynamics Lab: Week 7-8

Hi, it's Danny again from Dr. Nelson's Tissue Morphodynamics Lab and its been about a week or so since my last update. Most of my time has largely been devoted to working on lung morphogenesis or essentially lung development, but also I got introduced to a new and exciting topic regarding divisional axes in tissue. Although the two topics don't necessary overlap in terms of research, the work I did the previous year at a UCLA Head and Neck Cancer Lab is very similar in terms of techniques but very different in terms of direction.

Sriram's project focuses on the effects of endogenous stress and motility in cell division. In previous experiments, it was shown that when two cells are attaches at opposite poles of another cell, they tend to create a polarity and divide along a parallel axis. Additionally, it is known that if there is no endogenous stress on the walls of a cell, the cell divides in an unpredictable manner. The objective of Sriram's graduate work is to determine how endogenous stress and cell motility affect cells' divisional pattern on 250 to 500 micron squares.

The process in create a small micron square and treat it with the necessary drugs and cells is a rather long but straightforward. Using soft lithography one can etch patterns into a film that can be used as a base for future experiments. Lithography is useful because it can create any pattern or shape but the pattern that is desired for this particular experiment is 250 micron to 500 micron squares. An essential material of the experiment is Polydimethylsiloxane (PDMS) masters, which is made by mixing cross-linkers to PDMS in a 1:10 ratio and vacuuming out an air bubbles. PDMS masters can then be applied to the lithography film which will result in a negative copy of the film. Then the negative PDMS masters stamp is coated with silane, a substance that prevents PDMS from sticking to itself. After the silane has dried, the PDMS masters negative can be used as a stamp and reused multiple times, until the quality of the stamps produced is subpar. PDMS masters is applied to a negative base and cultured in a thermo-regulator at about 60°C for 3 to 4 hours. As the PDMS masters is being cultured, one can spin down cover slips with PDMS masters on it. Once fours hours has passed, the positive copy is removed from the stamp, which is then cut into little squares using a razor. The PDMS masters squares are then treated with fibronectin protein and then stamped onto the PDMS cover slips. These cover slips are then treated with mammalian cells with a variety of drugs and analyzed using a con-focal microscope over 12 hours.

The machine used to spin down PDMS on cover slips
in order to create an even layer.

PDMS and cross-linkers (right)
Vacuum used to remove air bubbles (left)

I was supposed to attempt to make a cover slip treated with cells this week, but the fume hoods in the culture room were replaced due to ventilation issues. Sriram told me that the insides of new fume hoods are usually quite dirty and suggested that we wait some time before culturing and analyzing new cells. The past two weeks have been a mixture of chicken embryo dissections and imaging lungs as well as a lot of Imaris and image analysis.

PDMS masters stamps that will eventually be covered with fibronectin proteins.  

The next week is going to consist of micro-dissecting about 4 lungs in the morning and 4 lungs in the afternoon for day 4, day 5, day 6, and day 7 chicken lungs in order to start preparing for my poster and presentation. I will also hopefully attempt to go through the aforementioned process with the help of Sriram, if the fume hoods are restocked with equipment by then.

In terms of life outside of the lab, I've been working on my senior thesis paper over the summer and started on the dreaded summer homework. Josh has just left his lab, so if he reads this, hopefully he got back home safely. It's been a great 8 weeks so far at the lab and I've learned so much and met so many great people.

On a side note, today is Friday and I just got a new assignment to start going back through a set of data and count the number of cells in the data that has over 110 cells at around 11 hours. I've been counting cells for the past two hours because I would really dislike doing this on a Monday morning, so if you need anyone to count up to 150 in 2's as quickly as possible; I'm your guy. 

Week two and three--The staging process and the Y-maze experiment

Hello Everyone. My name is Sandra Ho and I am writing about my second and third week in the Evolution and Behavior Lab at Harvard University.

My second week was quite easy and simple. On the first two days I created more enriched and standard tubes for all types of flies for trials, which included: Canton.S and DGRP( include 45,105, 796 and 535). The flies in DGRP are not genetically identical as some of them exhibits higher variability and some of them exhibits lower variability. During the middle of the week, I noticed a lot of the flies in the trial tubes started to hatch. Ben suggested me to put them in the staging tubes for five days and then they would be available to test for behavior. I put 10 male and 10 female in each of the enriched tubes and 20 males or 20 females in each of the control tubes for staging. He also gave me a suggestion for my project: collect flies in outdoor by using traps. He thought it was a good idea to test them because those flies are wild types and the environment they used to live is a lot different from the flies in our lab, hence the results might be different. Therefore, I made five traps( put a paper funnel in the opening of the test tube which contains fly food) and put them behind a bush near my dorm.

The third week I finally got the chance to do the Y-maze experiment! Basically, the Y-maze experiment is to quantify left and right turning of the flies. An individual fly is placed in a Y-shaped maze on top of a light box, allowed to walk freely for two hours, and the X-Y position of the fly’s centroid  is tracked by a camera. The first thing I had to do was to make the flies asleep by using CO2 gas and use a brush to put them into a tray that consist of 120 individual Y-mazes. One fly in each maze and each maze is covered by a lid.This set up allows 120 flies to be run in parallel, and each of which makes hundreds of turns during the two-hour experiment Then I had to put the tray inside the light box and put all the information of the flies in the computer that is connected to the light box. And finally, when I clicked the button "Start Data Collection", the computer would then start collecting data!

This is the light box used for the Y-maze experiment.

This is the computer that is used for data collection.

And those are my trials and stocks of flies.

For the coming week, I will start analyze the data with Ben because there are soon enough flies that have been tested for behavior. I am really excited about it and I hope everyone is doing well in their lab too!

Week 5 to 7

Hi, this is Jacky and I am working in McAlpine Lab at Princeton. 

These three weeks have been very busy. Our projects have been moving to the first critical point, which is about measuring the quality of the thylakoids we make.

                The first test we perform is chlorophyll concentration measurement. The chlorophyll concentration in the thylakoid suspension is determined by adding 0.10 mL of the suspension to 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 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. Once the chlorophyll concentration is determined, the total chlorophyll yield should be determined by multiply the chlorophyll concentration in mg /mL times the volume (mL). Once the chlorophyll concentration and the total chlorophyll yield is known, the chlorophyll concentration should be adjusted by adding the appropriate amount of Washing Buffer or by centrifuging again the thylakoids and resuspending in the appropriate amount of Washing Buffer.

                By determining the concentration of chlorophyll we make, we can decide if the procedures we use is appropriate since there are a lot of different methods that we are able to choose from literature. It is always important in science research to try as much methods as possible.

                                          

                What’s more, we need to test the efficiency of the thylakoids we extract. In this case, we need to use a chemical method called Hill Reaction. As we learned in Biology class, during light reaction photosynthesis, electrons will end up in NADPH. In Hill reaction, we need to separate thylakoid with stroma so that NADP won’t be available. Instead, we will put DCPIP, a blue oxidant, into the solution. DCPIP is blue in its oxidized form, and becomes colorless when it is reduced during the Hill reaction. Thus, the rate at which electron transport occurs in the Hill reaction can be measured spectrophotometrically (at 620 nm) by following the change in absorbance of DCPIP as it accepts electrons from the electron transport chain. To perform the Hill reaction, a sample of a chloroplast suspension will be mixed with the Hill reaction buffer (containing DCPIP) and exposed to light for a series of 30 second intervals. After each exposure period, the absorbance of the DCPIP will be measured. The absorbance values can then be plotted versus time to determine the rate of DCPIP reduction as a measure of PET.

It turns out that the thylakoids we make are pretty efficient. We will keep on testing and trying for next couple days and shift our focus to other aspects. 

Problems and Solutions (Week 6-7)

Hey guys! This is Rhea at CHOP, working on Mitochondrial Disease research.

Because I discovered that the mutated worms we're working with are showing less signs of well..being mutated, Julian asked me to preform a lifespan experiment without using FUDR to figure out if that was the cause of the strange results. FUDR is a chemical used to stop cell growth and this prevents the worms being observed to reproduce and infest our plates with hundreds of worm larvae. Julian has been using FUDR for many years now and it has never shown affects on the lifespan of worms but there has been a paper published which reads that FUDR may affect worms. I set up a lifespan experiment without FUDR to check if it was the source of lifespan longevity and when I checked on it the following day it looked like this.

The big clumps on the plate are colonies of contamination (bacteria). 

All of my lifespan plates looked like this and so I had to discard them all (about 25 plates of 20 individually picked and placed worms).

Because now I won't have time to restart my lifespan, I've decided to take on a fluoresce project which I've watched Fred do a few times. He grows worms in plates with different dyes which illuminate the pharyngeal bulb and he takes pictures of them under a special microscope. I'll be analyzing pictures to see if the mutated gas-1 strain compares to previous results to make sure the gas-1 are truly gas-1... addressing what I had found with my lifespan. 

Computer Networking Lab weeks 6&7

Hi again, this is Sohan and I am working in a computer networking lab this summer at Columbia University.

These past 2 weeks have been more of the same. I have continued to run tests on the Orbit-lab, process the .pcap files using the Python scripts, and graph the results using the MATLAB scripts. Though it may seem monotonous and redundant, each time accessing the Orbit-lab presents its own adventure with its own unique challenges.

More recently, the nodes in the network are successfully uploading the requisite version of Ubuntu which solved one of my major problems before. However, other problems have occurred such as the nodes failing to communicate effectively with one another and sometimes the drivers not being installed properly (drivers are the device which helps the software communicate with the hardware and vice versa ex: the trackball on the older mouses interpreted the motion of the mouse and sent that information to the mouse driver which interpreted the signal and made the pointer on the screen move in the designated direction). In our case, the driver helps interpret the commands we are inputting and makes the hardware act accordingly ex. if we want the wlan card in the AP to release a signal of 18mbps, we input a command, the driver interprets the commands, and send a signal to the wlan device to release a signal of 18mbps. When the drivers are not installed properly, our commands may be ineffective and futile at points making the process of running the experiment very difficult. Nonetheless, there have been times where the Orbit-lab does in fact cooperate and work adequately and I have obtained data sets to analyze.

Also, over the past few weeks, Varun has had me debug/clean-up/develop the Python and MATLAB scripts. Some of the information previously had to be manually inputted such as the time/date and now, I have made them so that they can obtain the information directly from some of the files in our data sets. Similarly, since we use 2 Python scripts to process the .pcap files and one script is based off of the outputs of the previous script, I have made them more automated where the last script can retrieve the data from the text files outputted from the first script to make the process less complicated and help it run more smoothly.

Lastly, one of the members of the lab is leaving for Korea tomorrow. He will be starting graduate school in the fall at Michigan and will spend the rest of his summer at home in Korea. We had a nice little going away party for him this past week and at the same time welcomed a new member to our lab who will essentially take his place from China.

So far, work has been going well and hopefully, we have some more productive weeks ahead!

Chandran Laboratory Week 1: Dawn in Morningside Hights

So unlike my peers, who are mostly finishing up their lab work, I have only just begun my work at the Chandran Laboratory at Columbia University, working with a graduate student studying ammonia oxidizing bacteria and nitrous oxide and nitric oxide emissions.

 My new role as a commuter began when I was dropped off at the PATH station, gearing up for what I assumed to be a 2 hour commute to upper Manhattan. To my delight, everything went much faster than expected. I arrived and with only minimal trouble, found the correct building, and met my mentor, Medini, who is a first year graduate student and whose research I'm helping with. My PI, Dr. Chandran, was doing "field research" with another graduate student, and I would soon learn that he is often out of the office and very busy (although we did get a chance to meet to talk about the lab goals).

The first few days I passed the time observing Medini and her pure-culture batch reactor. Thus far all that she had been doing is observing the cell growth and troubleshooting reactor problems. The machinery is pretty cool, with the tub full of the media and cells connected via all these tubs to a fancy machine that regulates everything and shows all the things happening for you, except cell growth and product formation, which would be our job to track. Basically, her work involves Nitrosonomas eutropha, which is an ammonia oxidizing bacteria vital in nitrification, which is the change of ammonia into nitrate (via a few intermediate steps). Because the batch is a pure culture, meaning that no other bacteria are growing in it, this means that every piece of equipment and everything around it has to be extremely sterilized. Right off the bat, in order to retrieve a sample from the reactor, Medini had to use a Bunsen burner to switch out the tubing. Until my safety training, I could only observe, take notes, and hopefully absorb some skills.

Friday came quickly, and just in time for a new cycle of cell growth to begin. We had to make new media and autoclave many things and will soon be inoculating the reactor. While the cells grow in the reactor, we will be first observing their batch growth curve, which will involve lots of cell counting. Then we will be looking at product formation, in this case nitrite, using a spectrophotometer. Once the cell population stabilizes, then the real experimentation can begin.

 Fortunately, the heat wave is subsiding and I am particularly grateful seeing as I'd have to walk through the heat in my lab-appropriate long pants and cardigans. Today I met another high school student who is beginning a two year stint in the lab for INTEL and other lab research work, so it's good to see a familiar unsure face. The rest of the lab is graduate students and post-doc's from all over the world. According to Medini, it's one of the most diverse group of people around. From China to Brazil to New Jersey, the lab guarantees a lot of learning experience.

Week 5 at the Donohue Lab

Hi this is Meg and I’ll be talking about my fifth week working at the Donohue Lab at Duke. This week has been far less busy than the 2 weeks before. We still have to census every day. However, many of the plate have begun to plateau, meaning that nothing new is germinating. As a result, there are less and less plates to census every day.

In addition to censusing, Lien had to hand in a rough draft for her poster on Wednesday, and her proposal on Friday. As a result, Bri, Tarek, and Lien have been working hard analyzing Lien’s data and attempting to clean it up.

On Tuesday and Wednesday, I helped clean some of Lien’s data. Often after the data is compiled, there is a problem with the order, meaning that an earlier day has a higher number of germinants than a later day, which is impossible since we don’t remove seeds that have germinated. Therefore each successive day should have the same amount or a greater amount of germinated seeds than the previous day. In order to fix this, we attempted to modify the least amount of data as possible. This meant trying to only change one day’s data. However, a couple of times the data was just too out of order to fix. As a result, it couldn’t be used and we had to throw that data away.

Data that needs to be cleaned. Each column represents the day the data is from. The highlighted row is an example of data that needs to be cleaned since on day 3, there were 14 germinated seeds and on day 4, there were 10. Similarly later in the same data, on day 6 there were 14, and on day 7 there were 11. 

Although this week has been a lot slower than I’m used to, it’s been nice to have a bit of a break, especially since my lab manager has been letting me leave earlier than usual. However, hopefully it picks up a little bit so that I’m still fairly active in the lab.

On to the Next Phase-- Weeks 4-6 at the Murphy Lab

Hi everyone, I'm Richard and I'll be talking about my past 3 weeks spent at the Murphy Lab, which examines various aspects of the aging process in C. elegans.

Week 3 was a definite struggle.  I ran 3 STAMs with my egl-4 mutants and wild type worms, all of which produced results opposite from what I expected, and since the entire lab was in California at the International C. elegans meeting, I was pretty much on my own when trying to figure out what exactly went wrong.  Geneva hypothesized that the worms were too young, so I made sure to bleach the egl-4 mutants a few hours earlier than I had previously done, and luckily, I was able to confirm my expected result in another STAM.  The rest of the week was spent primarily on preparation for future experiments and analyzing my data.

Week 5 was, for the most part, uneventful.  Originally I had planned to do PCR and run a gel to confirm that my egl-4 crh-1 mating worked to produce double mutants, but since a previous PCR and gel showed that I had no double mutants, I decided it would be best to re-do the original cross. So, once again, the week was spent mostly preparing for the next phase of my project, examining EGL-4::GFP nuclear localization.

For the nuclear localization assay, I first starved my egl-4::GFP worms (these are not the same as egl-4 mutants; rather, they are wild type worms with the EGL-4 protein tagged with GFP so that fluorescence can be observed).  I waited an hour, as I usually do for my chemotaxis assays, and then put the worms on conditioning plates spotted with butanone.  After another hour, I transfered these worms onto a hold plate and prepared microscope slides as quickly as possible to ensure the worms didn't lose their food-odorant association, and then examined fluorescence under a microscope.  To do this, I first locate the head of the worm, at about 60x magnification, and then switch to the option that allows me to view the RFP tagged (red color) AWC neuron.  At this point, the entire neuron, except for the nucleus in the center, flashes a bright red.  I then switch to the option that allows me to view GFP (green color), and depending on whether the nucleus is a bright green or still dark, as observed under RFP, I can tell whether or not the EGL-4 protein has entered the nucleus. I repeated this procedure with naive (untrained) worms, and also with adapted worms (adaptation is when a long, repeated exposure to a certain odor actually diminishes the worms' response to that same odor).  Today I will be analyzing the images I took during these nuclear localization assays.

Overall, I've enjoyed my experience in lab.  However, my days are not always as busy as one would expect, and I've had a couple of setbacks with various aspects of my project, which have consequently resulted in less eventful days.  I guess failure is something every scientist has to deal with sooner or later.

Linksvayer Lab week 6- Gels and why I don't like them

Hi my name is Ben Wagner and I've been working in the Linksvayer Lab at Penn. We work on evolutionary biology and collective decision making in ants.

Although I still have 2 weeks left in the lab, I feel like I've already learned what will be my most important lesson from this summer. This lesson is simple: Science takes forever. I'm not saying this is a negative way (necessarily) but more of an important lesson all future exp-ers and scientists should know. I have had multiple hour long incubation and waiting periods, ant feeding periods that took up most of my day, and my project expand until it is 10 times the original size, with 20 times as much work.

But regardless, week 6 was an excellent week, although it started off very badly. The week was a week of PCR and Gel electrophoresis, which shouldn't be bad. PCR is easy, gels are fine, just a lot of waiting time, but that's okay! PCR appeared to be running correctly We had already run a number of gels, and the creation of these gels lead to spills, leaks, and a small TAE buffer explosion in the microwave. But that's okay, nothing serious and its all in the name of science! Probably half our samples had been tested in at least one marker in the gel (so 1/8th what the final sample amount will be). 
Then, A talk with an old lab Post-Doc, Luigi, resulted in my learning that all the PCR i had run so far, and tested on the gels, was completely wrong. It pretty much came down to my strands had been coming out at somewhere around 50 bp, which Riley and I thought was correct. Nope!   They should be around 250-300. So we decided to find the issue. We started single-plexing (one marker instead of multiple), fiddled with the marker amount, changed temperatures in the thermocycler. Then, Dr. Linksvayer gave us the advice to use use 4uL DNA, instead of the 1uL that multiple protocols told us to use. Now we have have successful results on the gel!!! The next step is to see if this will work with multiplexing, because otherwise this project will not be finished anytime soon.

With only 2 weeks left, I'm not so sure this project will be finished, especially because Dr. Linksvayer wants me to help with behavioral things in those weeks. And because we haven't actually submitted anything to sequencing yet, which normally takes about a month, and then after that statistical tests need to be run to make a photogenic tree.... So it won't be done by the time I am. But maybe data collection will be. We'll just have to see. Hope all my fellow exp-ers have had a good summer in their labs, I'll keep you guys posted.

NLP week 4, 5: a crazy (but lazy) workaround and some machine learning

Hi!  My name is Jiehan Zheng and I work at CCLS at Columbia University on natural language processing and machine learning.  I've been doing some training data collection, evaluation and postprocessing work in previous weeks, and finally in week 4 and 5 I get to do some real machine learning!  It's been busy but interesting two weeks.  I did too many things and I am not sure if I can recall all of them...but let me try--

After building the model comparison framework in HTML and JavaScript, Apoorv asked for a new feature--calculating p-values from Χ^2 from McNemar's test for models to indicate how differently any two models perform on the dataset.  I had no clue how to do this, even after looking at Wikipedia and several papers, so I asked Apoorv how he used to calculate the p-value before having my framework.  He sent me a MATLAB function file that he used to use at IBM.

I tried the MATLAB on Columbia server and verified that this function file works.  Then another software, Octave, immediately came up to my mind.  Octave is open-source and although it doesn't advertise as so, it is known to be an open-source "implementation" of MATLAB's features, so that everyone can use it freely.  So I ran the function in Octave as well and it works too.

I then looked into the source code of that MATLAB function (although I've never used MATLAB before...), and found out that although most of the calculation steps are fairly simple and straightforward, it calls a function called chi2cdf() from MATLAB.  By looking at MATLAB documentation I found that the chi2cdf() function, as expected, contained a definite integral in it.  So I basically ran into the same problem of not being able to calculate definite integral in JavaScript.

Then, I don't know why, a crazy (but lazy) idea came to my mind...  If it is hard to calculate definite integral in JavaScript, then why bother doing it in JavaScript?!?!  I can simply install Octave on my server and set up an API on the server to pass the X^2 to Octave and ask Octave to calculate p-value for us!  I quickly installed Octave and wrote up a short Node.js program that listens for requests, and spawns a new Octave process whenever it receives a request, pass the X^2 value to Octave's chi2cdf() function and collects its output then returns it to the browser.  So whenever Apoorv enters the command to calculate p-value in the browser, my code is going to send a request to my server and wait for the server's response and display that answer.  And very luckily I proved this idea actually works and was eventually able to implement this in a few hours.

Well, that's all I can say for now...which is the work I did in the afternoon on July 4.  For the rest of the time I wrote code to extract features and making training examples (without any annotation from human!) in preparation for a machine learning task (sequence labeling), and got some training data from several websites and stored them to a MongoDB database.  I also posted an answer on Stack Overflow for the first time while looking for solutions to a PyMongo error and after reading some MongoDB's documentation!  Unfortunately I can't share more details on the machine learning task for now but I will in the future!

Oh, and on July 4th Apoorv asked me if I'd like to see fireworks at Dr. Rambow's apartment building.  I went and it was very amazing!  I also changed my plane tickets so that I can extend my internship by a few days.  So now officially I will work at CCLS with Apoorv for almost 7 weeks!

Thanks for reading!  See you next week!