Brainbrow Imaging of the Zebrafish Lateral Line: Retrospective

As the summer winds down, I have been reflecting on the project Dr. Steiner and I began working on in June. Dr. Steiner and I have been utilizing multi-transgenic zebrafish to deeply explore the regeneratory process of zebrafish sensory hair cells. The current body of zebrafish research suggests supporting mantle cells divide to produce hair cells during regeneration of neuromast sensory organs along the lateral line, although evidence of such is lacking. Together, we created a plan to manipulate three transgenic lines to image the regeneration of these neuromast cells, with the end-goal of better understanding this regeneratory process and the factors that control it.

With these research goals in mind, I’ve been learning about the complexities of conducting biological research with living specimens. Many times during the semester, my colleagues and I have sacrificed time to come in on weekends to feed the fish; there have been several weeks the fish didn’t cooperate with breeding, and we had to quickly work on a new plan for the week. Truthfully, though, working with live zebrafish brings an element of physicality and life to my research. It’s a pleasure starting my day seeing our entire population of zebrafish greet me with frantic swimming.

Also challenging, but extremely rewarding, is developing the Zebrabow process I’ve been using to visualize cells of zebrafish. At its best, this method makes the cells of zebrafish fluoresce a beautiful mosaic of colors, allowing a researcher to better understand the cell divisions that potentially lead to new hair cells. No single procedure will work for every lab; Dr. Steiner has greatly helped me in creating a Zebrabow process that works for our fish in particular. At the start of the summer, we had very little mosaic fluorescence amongst the cells. This provided me several opportunities to review the process we had used, and modify it for better performance in the future. Such modifications make this research project feel like it is truly our own; over the next few semesters, I hope to refine this procedure to obtain consistent and repeatable results.

This summer project has not only taught me about valuable lab techniques, such as confocal & fluorescent microscopy and taking care of living specimens; working with Dr. Steiner this summer made me increasingly comfortable with the research process and environment, which I hope to be a part of for years to come. Being able to pave my own way through a new set of procedures is fantastic experience for my future endeavors. Most of all, I’m excited to continue my research with Dr. Steiner over the upcoming year, building upon everything I’ve learned over the past months.

Included in this blog post is an image of one of the Zebrabow treatments I’ve done, in order for readers to better understand the process. This image was taken as numerous ‘slices’ of images from the confocal microscope, then compressed into a single image. On the bottom right is the neuromast, the organ containing hair cells that Dr. Steiner & I study. One can see numerous flourescent cells, as well as some macrophages (depicted by amorphous green-flourescent projections).

Blog 2

Over the course of the past couple of weeks, collaboration has continued with a number of different senior citizens. In each of the sessions students sit down with at least one senior (sometimes in a small group) and guide them through different aspects of technology. Based on the research so far, four “critical areas” have been established and will serve as the foundation for the technology program that is being developed. These findings are based upon personal surveys and interactions, previous research, and social needs. The four critical areas are: Mobile Banking, Tele-Health Services, Digital Communication, and Basic Computer Literacy. “Mobile Banking” includes viewing online bank accounts, paying bills online, and using ATMs. “Tele-Health Services” encompasses online patient registration portals, at-home medical tests, and virtual doctor visits. “Digital Communication” is a combination of traditional social media platforms (Facebook, Twitter) and other online communication tools (Skype, email). Finally, “Basic Computer Literacy” is providing the seniors with the basic skills to interact with their computers on a daily basis. This includes teaching them how to interact with computer hardware, basic keyboard tricks, and how to work their operating system. The research thus far has suggested that if older adults are provided with the skills listed above, then they will be better equipped to interact with current and future technologies. In establishing a better understanding of these topics, older adults will be able to properly interact with today’s society, other adults, and younger generations, thus lessening their feelings of social isolation. It is interesting to note that three of the four critical areas that have been identified were ones that were hypothesized at the beginning of the project. In speaking with the older adults and their families, and aids, these were areas that they hoped to learn more about. Additionally, these are areas that many younger individuals utilize on a daily basis.

 

The research has raised a number of questions, and provided subsequent challenges in developing a proper technology program at Carter Burden. First and foremost, how can the success of the technology program be accurately measured in a meaningful way? It is hard to quantify the success rate because so much of the work that is being done is subjective to the individual. The understanding of the findings is limited because a proper survey (or tool) that is able to adequately measure the success rate has not yet been established. Furthermore, another challenge/question that has come up is how to teach and interact with older adults with physical/mental handicaps. Many of the challenges that are associated with teaching older adults such as memory loss, and decreased mobility, are magnified with those with a mental/physical disability (dementia, etc.). Research is still being done in understanding how the program will overcome these challenges in helping the adults learn.

 

One of the main successes and lessons of the research is that the needs and abilities of this community are now better understood, which provides a solid foundation as the research continues. There is an entire community of individuals who were not privy to growing up with today’s technology, but who nonetheless, are wanting to better understand and connect with these devices. Not only are older adults able to learn about technology with the proper teacher and resources, but they are eager to jump into the digital age! It has been very interesting to see how these adults approach new technology and ideas with a sense of ambition and determination. There are so many aspects of the digital age that many take for granted, but it has been wonderful to see these adults grow as they learn more about the technology that surrounds them.

 

This research and project have greatly impacted me and my future studies in this field. I now have a better understanding of an underrepresented community within our society. It has been a pleasure to meet and interact with so many diverse and welcoming individuals. Furthermore, I have firsthand knowledge of what it takes to teach older adults, and how although it can be a timely process, it is equally if not, more fulfilling and enjoyable.

 

Second post for my summer research project

Recently I have been reviewing the interactions between Dr. Fink and former college journalists who were members of their student newspapers. I have been listening to the recorded interviews done by Dr. Fink and then I have been highlighting key components that was said by the former college journalists so it could be used in our findings.

My biggest question that I have from my research is that nine out of the ten interview subjects were at private schools, so I was curious to know that if public colleges ran into the same issues when it came to FOI. I wondered if it would be easier to request information at a public school because it is  government funded.

The biggest challenge I had in this project was finding people that met our requirements. Our requirements were that they had to have held a editor position for their college newspaper in the 2016-2017 academic year, and they have to have filled a FOI request. So finding people that fit that criteria was a bit difficult.

I learned how valuable it is to file FOI requests. Doing that can be a very valuable tool to journalists because it gives you access to information pertaining to your school or government. This upcoming semester when I am editor- in-chief of the Pace Chronicle  I will use FOI laws to my advantage.

Blog #2

We have come to the final tweaks of the project and I believe we did an amazing job. It is something that will be useful to so many different teachers and students for years to come. Throughout the project, I have learned so many different things that I can carry with me through life. The process was difficult at times with sometimes very little information to go off of, but the more I learned the better I felt about the outcome of the project.

Since our project was not a data based project we did not have any results to experiments or any studies to have findings for. We did our research based on what these four helpers experienced back in the 1940s and how their actions helped stretch the Frank’s lives for just a few years longer. With this project, we had our main subjects to find information on, but the deeper we searched we found different people that were involved that hardly anyone knew about. It was great to be able to not only bring awareness to the amazing people who helped the Frank’s and the others in the Secret Annex but to also shine a light on others who survived and rebelled against the Nazi regime.

With this project, I have learned what bravery can do to help save lives. The bravery to stand up for what you know is right and to not let fear deter you. This project has helped me in numerous academic ways such as with research, but the more important lesson is one I can carry with me for the rest of my life. These four helpers risked their lives to help those innocent families and others and stood up for what they knew was right. They knew the risks of what they were doing, but they did not back down. Even when they were caught they did not let fear overtake them. With what is happening now in this country and around the world this lesson is one that is necessary for everyone to know. This study guide is not only a way for students to learn about what these helpers did, but to help them take the courage the helpers used and use it in their day-to-day lives.

Electron Transfer via Quantum Systems

My understanding of the processes involved in heat transfer has been expanding greatly in the past few weeks of research with Dr. Walczak. We are exploring quantum heat flux with the Landauer formula, which allows us to calculate thermal conductance. The Landauer formula along with the Fermi-Dirac distribution factors, for left and right heat reservoirs, follows.


We have employed a Taylor expansion with respect to temperature difference for this formula; allowing for a non-linear correction to heat flux in the quantum systems.

We are applying these and other functions so as to define the probability for electrons to be transferred via systems of coupled quantum dots. In such, we have employed different interference conditions which will affect electron transport. The particular couplings can be controlled by applied voltages by external gate terminals.

There are 8 differing configurations which we are analyzing currently. We are analyzing them with the aid of Mathematica and MATLAB, in which Dr. Walczak has created codes that allow for computation.

As our reasearch continues, we are working to create another code in MATLAB to integrate the convolutions of our transmission functions which will allow us to obtain the thermal conductance of samples. We aim to analyze all 8 configurations in depth and provide computation results and graphs within the final weeks of the summer.

Blog Post #2: Update

Following up from the prior blog post, this research project requires a lot of trial and error, which has proven to be very tedious and requires a lot of patience. Since the last blog post, we have yet to successfully extract the RNA required to perform the gene insertion into. This could be due to the fact that the primers that have been designed are not binding to the specified binding sites and cutting the RNA enough for it to be visible in the gel.

As previously mentioned, there have been a lot of PCR conditions that were previously tested and manipulated but we have yet to find the right one for the experiment that will give us the results we need. Other changes we have made to the experiment were creating dilutions of the RNA because it actually found in a capsid – or shell, that may be hard to break if using too much concentration of RNA. When using the dilution of the RNA, there is less to work with, therefore may be easier to break the capsid. Once the dilutions were made – 5x,10x, 20x; a gel was run but the results we hoped to obtain did not work.

The two main research goals for the rest of the summer and the rest of the research project is to extract RNA by creating the right primers and conditions, and successfully inserting the GFP gene into the RNA of the parasite.

From this research, I have found that the patience is definitely key because we aren’t just tweaking one part of the research for the results we require, but are actually tweaking multiple aspects of it at the same time and seeing what works and where. Also, this research helped me to be a lot more focused on minor details because it could be the smallest thing that needs to be adjusted or changed to create a very major difference.

Thankfully, I believe that my professor and this research project has prepared me for the steps I will be taking once I graduate in the spring. This research has helped to perfect my skills in various techniques such as PCR and proper pipetting that will be useful when I work in a lab as a forensic scientist. Hopefully, the results in this research will positively impact the science community and further studies and research will be conducted to expand on this topic.

Inelastic Heat Conduction in Molecular Quantum Systems

After several weeks I have challenged and learned many things about physics. This subject may be hated by many people which is understandable but there is still many things to be discovered which makes me more impatient.                                                                               The quantum heat transporters for lattice vibration, phonons, electrons and electromagnetic fluctuations which distance is very short compared with our macroscopic world. The purpose of my research is to study electron-phonon coupling effects on electronic heat transfer at molecular levels. How electron interaction work and how does it lead to phonon-mediated changes the characteristics in transport. A brief definition of thermal conductivity is defined as a ratio of energy flux and temperature gradient. Once the phonons move freely, arbitrary energy flux will be there without temperature gradient so the finite phonon velocity will not make the thermal conductivity final. So basically, the conductivity increases with temperature because the phonons carry more energy.              In this work, we used non-perturbative functions and well known formulas  in order to present atomic preciseness combining microscopic Maxwell equations and atomic Green’s function to grasp the physical picture of the transition from photon-mediated thermal radiation to phonon-mediated heat conduction at connection. That is why with the help of these formulas we have formed a scheme described as the“Ladder Model” to help understand and generate definite results.

After couple of trials the scheme above used to conclude that there is dynamics which the electron-phonon interaction on the molecule connected by  two different thermal reservoirs. This effect is thermal rectification proving that the thermal properties of molecular systems are conducted as finite temperatures and this action of molecular transport is in the presence of molecular vibrations- phonons. Appropriate graph  model of thermal conductance and temperatures easily presents that at low temperatures there is a stronger electron-phonon coupling interaction where at higher temperatures there is more dynamic phonons in the inelastic conduction process.                                                                    As for our future studies we will be contemplating high intensity heat fluxes and their disruptions, expanding used energy-domain transport preciseness onto  time-dependent development to analyze the relaxation processes in the presence of strong electron-phonon interaction effects. An important factor for future studies will be a detailed analysis of phonon sidebands onto heat conduction along with realistic biological systems due to their molecular complexities.

 

 

The need for more research

While continuing my research the further in depth more questions began to arise. Moving closer to more recent years, allowed for more sources overall however still presented many limits. Many of the cases are currently still be reviewed or are going through the legal process currently.  This was one of the challenges I faced while completing this research.

I began to contemplate what factors play a role in the shootings that perhaps aren’t as obvious or as apparent as race or gender. One factor that I began considering is mental health. I became curious as to what the mental state of both the officer who committed the shooting and the victim of the shooting was on the date of the shooting.

I was curious to how many of these victims had diagnosed or undiagnosed illnesses that led to their victimization at the hands of police? Perhaps if these illnesses were diagnosed or treated the victim would have never been in the situation to get shot or injured in the first place. On the other hand, how many police officers had diagnosed or undiagnosed illnesses that made them more prone to the discharging of their weapon? As a psychology minor having basic knowledge that mental health impairs decision making. I came to the realization that there is a need for research in this topic. Mental health is stigmatized in social media. It is a very delicate topic, therefore leaving a hole in research on this aspect. The mental health of the officer, who was involved in the shooting might present certain symptoms of this social issue. Associating mental health with law enforcement might further cause tensions between law enforcement and citizens.

One take away from this project, which I really enjoyed was being able to use my knowledge from Criminal Justice and Psychology to look at aspects a certain way with certain perspectives. It provided different types of insights and complimented my work.

Moving forward these questions and thoughts are ones that I will keep in mind when drawing overall conclusions of the research. I plan on continuing my work in this research because it is imperative to my field and also current to this time period.

Characterization of the Microbial Community of the Accessory Nidamental Gland of the Longfin inshore squid, Loligo pealei

The 16srRNA gene from cultured isolates from the squid accessory nidamental gland was amplified using PCR and sent out for sequencing. Results from the 8 initial isolates came back, allowing us to identify the different genera of bacteria associated with the squid. The amplified 16srRNA gene that was amplified was almost the entire length of the gene allowing for a reliable identification of each bacterial isolate. The two different primers (8F, 1514R) utilized caused replication from different sides of the DNA strand. From the two independent sequencing reactions, a contiguous DNA sequence was aligned with CodonCode Aligner. We performed a Standard Nucleotide BLAST (NCBI) in attempt to find closely related bacteria and other invertebrates that might be associated.

These basic molecular and microbiological techniques were applied to an unsuspected discovery of invasive Clinging Jellyfish, Gonionemus vertens,  that were discovered in July during research in the Long Island Sound. I have isolated 31 different bacterial colonies derived from a single cling jellyfish specimen. We have gone through the process of isolating several samples, amplifying the 16srRNA  gene as well as characterizing the basic bacterial morphology. The process of isolating these Clinging Jellyfish bacterial isolates revealed a number of colonies that had a green or orange iridescence. We are interested in identifying these novel bacteria and would like to discover the role of this iridescent bacteria with this jellyfish. After the 16srRNA gene is amplified, cleaned up and sequenced, they will be sent out for sequencing. From there, we will once again be able to further classify and explore the different type of bacteria that are associated with the Clinging jellyfish.

Blog #2

Since the last blog, our research project has developed and we have made many strides and have crossed many tasks off of our research checklist. Some of those tasks include reviewing in depth the current research on our topic and beginning a literature review, registering with IRB, creating an informed consent document for the human research subjects, and creating a flyer to attract nursing majors to participate in our study, and compiling a list of questions for our student interviews.

Some of our successes include frequent and open communication between Dr. Northrup and I and swiftly completing tasks to get our research to where we want it to be. Some difficulties include needing to wait for the school year to conduct our nursing student interviews and not having many current articles or research about our specific topic to use as a guide.

I have learned that the research process is always changing. I have learned to let the process guide the project instead of letting my original idea of the project control the process. The ending product may be very different from the original idea, but that is the beauty of research.

This research project has made a lasting impression on me. As someone who has always found research very intimidating, I have learned that by taking it step by step, it can be an enjoyable journey. For this upcoming year, Dr. Northrup and I will be conducting interviews on junior nursing students, compiling the data, and obtaining conclusions based on the interviews.