The research program has expanded since the last blog post we made back in December; we have conducted more research and refined our Qualtrics survey to reflect the most accurate results possible. In addition to displaying biometric facial scanners to the elderly, we have also introduced USB fingerprint scanners to them. Although it is a different kind of technology, it essentially does the same thing; it incorporates a unique feature of each person’s body to authenticate a machine. Fingerprint scans and facial scans can extremely rarely lead to false positives; this is why development is currently leaning towards vein-scanning technology, as it would render less false acceptances into another person’s system (no false positives have been witnessed in the research).
It is actually interesting and exciting to see the elderly actually engaged in using a newer technology; in past cases, older family members often turn away technology but we are seeing an embrace of it at a rapid weight. Some of the elderly people we survey have new iPhone/Android phones that incorporate fingerprint scanners into their hardware; they say they enjoy it because they do not have to remember a password (the less clicks to do something for an elderly person, the better). According to our survey at this point, 76% of elderly people use technology often; with that information, it can be inferred that 100% of that group of people are vulnerable to cyber attacks and need security measures to protect their data and personal information.
We have encountered a challenge; an original goal of this research project was to create an app/software that would improve upon the current biometric softwares provided by Intel and the companies that actually make the hardware, but making one would be almost like reinventing the wheel and would take years of algorithm research and intense development. Rather than create our own version of our vision of these applications, we will forward our research to these companies in hopes that they can make improvements on what we have found to be troublesome aspects. Maneuvering around patents would also make for a huge hassle; it is best if we let the original creators refine their application.
Ever since December, I have been able to make progress with my research. Every single week, I was able to come in and run my four fluoroquinolone drugs. I have been testing them constantly with the same power at 50 and multiplier factor at 50. I’ve tested the samples at 3 different times: 1,3, and 5. Using the scans, I was able to produce spectras for each drug using Igor software. Igor allows me to open up excel files and label the graphs with its peaks accordingly. Since I was able to do run my samples every single week, I took the average of my runs at the different times. This helps to improve the signal to noise ratio and produce accurate results. Seeing all the progress I have made so far makes me feel a lot better about my research because I was struggling a bit in the beginning. I was able to however overcome my issues with the laser Raman and produce results.
From my research so far, I was able to print out a poster of my work and present at the annual Dyson Society of Fellows this past March. It felt good to see my hard work on display for others to understand. I was able to tell those who came up to my poster all of the accomplishments I have achieved thus far. I also was able to answer questions and take in advice that I could use for future work with my fluoroquinolone drugs.
Looking back at the results produced so far, I have been able to obtain accurate spectras for the four fluoroquinolone drugs. Sarafloxacin, norfloxacin, and ciprofloxacin produced peaks using the laser Raman that were similar to its Raman spectras from before. However, enrofloxacin’s spectra produced no peaks that can be used to identify the drug. I find this interesting because the laser Raman was able to produce spectras for the other three types, just not this one. For the rest of my time doing this research, I want to continue running my samples to see if taking the average for all of my trials help my results. I also want to investigate why in particular enrofloxacin only produces peaks with the original Raman, not the laser Raman used.
The two tasks that have been developing are the literature review and data collecting information on Police Shootings with the mentally ill. Paper writing is not my forte. After struggling to write a literature review, something I’ve never done before, I was able to complete it. There still need to be edits and additions but I think I did a good job considering the circumstances.
After that was submitted, I worked on some of the information for the database and researched missing parts of information on a data sheet. Through an excel spread sheet I enter different aspects about many officer involved shootings. The hardest cell to fill was the one that determined mental illness. Many articles made no mention of mental illness or had conflicting views. Some would say mentally ill, and others would say intoxicated or sometimes both. I completed as much of the data sheet as I could in the short amount of time and enjoyed that more than writing the literature review. I want to continue working on it and look more extensively without the time crunch.
Through collecting data I was able to see obvious patterns within geographical areas that struggle the most with police involved shootings. Although I recognized that I was not working on the complete data, just 100 cells, many of the incidents occurred in California. This could be simply because the state is so large, but it could also speak to their policing abilities. The victims were also almost entirely male. Determining the race of a victim was not always easy but there was a high volume of minority victims on my sheet, but again I am aware that it is such a small section of the present data so not to make and final judgments based on that alone.
The progress of this research has been slow and steady. I am currently adding more sources to the literature review. My schedule this semester has been harder than I anticipated, but I will still work on the things Professor Arslan has given me to contribute to the research. The experience of data collecting was so far the best part of this research for me. I hope I do more of it.
So far only a little more research has happened since the last time a blog post was written. The only field research that has been able to be conducted since the Winter break has been on how the elderly use the mobile application Apple News. This is due to the fact that the researchers had to get seniors to do research with at senior centers. The most common observation of seniors using Apple News is that this application is too difficult for the elderly to use. This is due to how it represents itself, the app opens up to a screen exploding with many different news articles. Which is not bad design by the app, though other functions of the app make this not as wonderful. The seniors were able to click on each article they wanted to read in order to learn more information about an event. The problem occurred when they realized they did not know how to get back to the original screen. This trapped some seniors to only be able to read one article. On a side note other seniors also explored the applications tabs on the bottom of the screens and got lost and were not able to get back to the main page with the news articles.
A simple solution to a problem like this would be to just make the application much simpler. All that would be required of you would be to remove all of the extra functions which may seem important. Perhaps this new version of the app’s only purpose was to provide the news with no special features. This would mean that you could just simply have an article on the page and the user could swipe left or right to the next article and scroll up or down to read the rest of the article. This would follow the golden rule of being simple which allows for a more optimized user interface for senior citizens.
When conducting this research the hardest challenge that has been experienced with doing this research is finding a senior citizen to do research with. This requires the cooperation of a senior center as well as the senior citizen. Then setting up meeting with a senior can take time as well, but once that is all completed conducting the research itself is rather simple. All that is required is for the researcher to observe how the senior citizen reacts to the mobile application, as well as how they use the application. A researcher is able to determine rather quickly if the application is properly optimized for the senior citizen. If it is not then the researcher is able to observe more details of how the senior citizen is using the application and ask them questions to find the reasons for their dissatisfaction with the application. Though this is also done even if the senior citizen likes the application because it will tell the researcher what the mobile application did right.
After doing this research my biggest take away from what I have done would be that more research is always better. The more data that I collect means that I will be able to come to conclusions and to formulate a hypothesis that I am able to back up with research. For example, one of the things that I have realized from all this research that I have been doing is that simplicity is the key for designing mobile applications. It’s also the number one solution to designing a mobile application for the elderly and I have a lot of research that I can use to back this up. Without learning how to collect large amounts of observations I would not know how to go about defending an argument. Therefore I have learned a lot from conducting this research.
The beginning of this semester we continued our work on the C. elegans’ gene T20B12.7 and it was a little shaky due to the snowstorm and school closure. The first RNAi experiment we performed was unsuccessful because we could not get into the lab to record the results. We then performed another RNAi experiment, which show similar results as the previous semester. The RNAi T20B12.7 worms had only a small difference from the L440 worms in unhatched embryos. Another RNAi experiment was performed with rff-3 worms in the hope a more significant difference would be seen. The rff-3 worms are more sensitive to the RNAi treatment. However, the results from the RNAi experiments with rff-3 worms still had an insignificant difference. These results could have been for two different reasons. The first reason was that the RNAi was effecting the worms in another way besides embryo lethality. This was possible, but previous studies showed that this gene influences embryo development so not as likely as the second reason. The second reason for the insignificant difference could have been that something in our RNAi experiment was contaminated or defective. We decided since we were getting deterred by the RNAi experiments for T20B12.7, that we would hold on further experiments for this gene and complete experimentation on another gene, F55A3.3, that had had successful RNAi results.
F55A3.3 is a gene in C. elegans that is involved in embryo development, molting cycle, nucleus organization and reproduction. F55A3.3 is a human ortholog, spt16, that facilitates chromatin remodeling in the FACT complex. Previously performed RNAi experiments in our lab to knockdown F55A3.3 resulted in a sterile phenotype. We hypothesize that the loss of F55A3.3 may be necessary for normal embryo development. Our current experiments will analyze this hypothesis and help further understand the role this gene has in C. elegans. The next step was to use fluorescent microscopy to identify cause of sterility. We have performed two RNAi experiments and used microscopy to image the worms after they were treated. The first experiment we saw several abnormalities in the RNAi treated worms compared to the L44o worms. The abnormalities consisted of changed in the germline shape and irregular dividing in the embryos. The second RNAi experiment was not as successful. The imaging could not be performed properly. We are now in the process of troubleshooting the imaging process to see if the microscope is not working properly or if the worms that are tagged with GFP are contaminated.
Since my last update I have hit a few snags. My samples did not keep as well as I had hoped they would over winter break and I lost the half of the samples that I had not yet identified. I also had some problems getting all of the necessary supplies together, accidentally getting the wrong size pipettes. The good news is that I still have all of the water samples I collected, so it will not be a problem to simply restart that process for those half. This won’t waste much time either, so it isn’t a disaster. I have also gotten the correct pipettes since.
I am currently getting all of my identified samples ready to make frozen stock out of them. Remarkably, all of my already identified bacteria survived the break and are growing wonderfully. (I will attach a picture I took today) This way I will have the samples ready and in the lab to grow whenever I need them. I am about halfway done with identifying the bacteria that I will be using in my experiment. Now that I have all my supplies ready and in the lab, this process should begin moving so much faster.
What I have learned from my project so far is less of a scientific discovery and more of a personal one. I have learned to become adaptive and patient. Working with bacteria, especially those isolated from nature, can be incredibly tiring. It becomes even more complicated when you add work, school, illness, and breaks into the mix. I have had some issues getting my bacteria to grow under lab conditions as they are used to the Hudson supplying their nutrients and growth conditions. The Hudson varies greatly in temperature from season to season, so the bacterial diversity is probably much greater than I am able to see on my simple petri dishes grown in lukewarm conditions. It can be incredibly frustrating when something decides it no longer wants to grow for me, but often times stepping back and giving the organism time or a new growth condition will fix everything.
I have never been a very patient person, but I am slowly getting there with this work. I see things running much more smoothly after from here on out. Hopefully next post I will have much more to tell you!
In the time since our last blog post we have tried several attempts to perform a successful conjugation with multiple strains of Pseudoalteromonas and Planococcus associated with the accessory nidamental gland of the squid. We follow the conjugation protocol for the conjugation. Conjugation is how bacteria exchange genetic information. In this case our E. coli conjugates contain a transposon, which basically randomly inserts into DNA and we are hoping for this transposon to insert in the codon that codes for biofilms for our bacterial samples. Here are the basic steps from this protocol: first overnight cultures of or samples are grown. The next day we combine our intended recipient bacteria with the E. coli conjugant that has the transposon and pellet them using a centrifuge. We then resuspend the pellet and then spot the mixture of the two on a plate. We then let the bacteria grow over night at room temperature where the two should conjugate. The next day we scrape the spot off the plate, resuspend in Luria broth and pipette 10-50 microliters onto fresh plates and spread it evenly using sterile glass beads. These plates are then grown at room temperature overnight.
There is a selective antibiotic marker for erythromycin that is combine into the recipient bacterium during the transposition. This selective agent allows for us to grow up our transformed bacterial colonies. What we are hoping to get for results include interruption of the genes for biofilm and pigment formation. We will be screening for colonies with no biofilms and impaired pigment formation. However we have had difficulties with the bacterial conjugation and we have not had high numbers of bacterial transformants. Which means for some reason our bacteria isn’t conjugating with E. coli and we are trouble shooting this process.
We have recently ordered fresh antibiotic to add to the plates which should limit the growth of the donor E. coli but allow for our transformed bacteria to grow. One other factor that can be optimized to increase transformation is increasing the moisture content of the media. If this next round is not successful we may need to reorder our conjugate strains.
Over this semester we have made a lot of progress on our research. We started by finalizing the literature review and methodology portions of our paper and right now we are at the stage of gathering all the data. Right after getting the research approved by IRB two weeks ago I started interviewing students on the Pleasantville campus. It has been a great experience full of learning. Since this is the first time I conduct interviews at the beginning knowing how to remain neutral throughout the interview was a big challenge. However, by sticking to the questions that we have drafted and some practice, I have been able to learn some strategies to make sure the question I am asking are as neutral as possible.
Over the last few weeks, I have learned more than I thought. A very valuable lesson has been understanding how to get people to discuss topics that are usually avoided in social settings. Since our research is focused on identifying behaviors and perceptions towards community service and civic engagement, the role of politics and government plays is significant and usually avoided by people. For my surprise, all the students that I have interviewed have reacted in a very positive way and have been willing to share all their opinions very openly despite how strong they are.
It is now a critical time in my research process. After working on developing a thorough literature review and seeing what similar research has shown, it is time for me to analyze the results from my survey. I have never done research quite as extensive as this so I am both excited to see the results and what they will dictate, as well as nervous. I know I have full support from my advisor but it is still an intimidating concept to analyze research like this when you have never been in this sort of situation. I am ready to dive in though, and I know that this will be a learning and growing experience for me.
As the deadlines for my research are growing closer, I know the critical nature of this time in my research process is so important. This is the time where I will truly discover if all of the time I have spent wondering what my results will yield will finally come to light. I downloaded the results from my survey today and will begin analyzing them over the course of the next few weeks. I look forward to this extensive process and cannot wait to put my final results into my report. I am ready to share with my community what I have discovered.
Since my last blog post, I have made promising progress with my research project. My main goal of this semester was to focus on microscopy. Now that I have established that my gene of interest, F10C2.4, clearly shows some kind of reproduction problem when not present using RNA interference, I wanted to utilize the unique feature of my model organism, Caenorhabditis elegans, to determine what is going wrong in the organisms without this gene. One of the drawbacks from using technology such as a microscope hooked up to a computer is that sometimes things can go wrong; however, I feel that I have learned so much from the mistakes, which has helped me get a better understanding of the research I do.
Caenorhabditis elegans have many benefits for genetic manipulation and research. One of the most beneficial features is that it is transparent. This is great for microscopy because it makes it easier for us to see what is different with the worm’s reproductive system when comparing it to the normal, not treated worm. For the experiments I perform for the microscopy element, we repeat the RNAi interference experiments with strains with fluorescent markers. GFPs are green fluorescent proteins that can stain a particular part of a cell; like a cell wall and RFP are red fluorescent protein can stain the chromosomes within the nucleus of the cell. With the strain I am working with, AJ740, I can utilize the GFP and RFP to see what is happening to the shape and overall placement of the eggs within the affect mother worm treated through RNA interference along with what is going on with the chromosomes. I have several questions. General questions like: are the eggs going to the right place and are there too many or too little eggs in the mom’s body? In regards to the chromosomes, are they separating at the right time? Is there an issue that is causing the incorrect amount of chromosomes in the cell which is not allowing them to hatch once they are laid? Does the egg go through the correct amount of cell divisions before being laid? All these questions can be answered using microscopy thanks to the organism, C. elegans.
A challenge that I have been facing, along with other members in my research group, is in regards to getting the microscopy aspect to work. This has opened my eyes to the many components involved in a task like this where things can go all good for one week but the next week, multiple things can go wrong. That being said, it is important to troubleshoot what went wrong and come up with ways to fix the problem at hand. An example of this is when the GFP and RFP do not show up bright enough to identify anything going on in the C. elegans. This could be due to the organisms not growing properly due to a lack of food or temperature sensitivity. Whichever the case, it was important for us to work together as a team to come up with a way to avoid this issue for the next week. For the future, I hope I can take more images from microscopy to look further into what is going on internally to determine what the function is of my gene of interest, F10C2.4.