Friday, April 26, 2019

Venturing from informatics to neuroscience

Greetings, listeners of the Neurovoice! 

My name is Jesse Parent and I’m a graduating Informatics senior in Dr. Scimemi’s Neuroscience lab. I am actually a non-traditional 'transfer' student who went back to school for a STEM career change. I originally came to UAlbany because it was an online-only degree and I had to work during the day. Fortunately, I had a flexible enough to work and slowly gain more research experience over time, and upon recommendation I found my way into this lab. I started last semester in the Fall.

My first outreach at the Brain Awareness Day 2018 at Bethlehem High School (Delmar, NY)
What an experience it has been! I would encourage anyone interested in cross-disciplinary research or applying computer science or informatics to biology to try it out. A lab like Dr. Scimemi's is open and welcoming and there are a lot of different ways to contribute - even if you have little background in Neuroscience. I wasn't sure how much real biology I would touch upon during my time in the lab; when I showed up, there was strange looking grey box and some parts to assemble and I spent several months setting up that hardware and related software. But the neuroscience was there: my first project involved using custom telemetry for electroencephalograms (EEG) to interpret brain activity in mice.

Our lab at the 2018 Society for Neuroscience Hudson-Berkshire Chapter Meeting (Scotia, NY)

One of my favorite things about undergraduate research is that the learning is much more raw, and real. It's a challenge, and sometimes (or a lot of times) you are dealing with questions that nobody knows the answer to - unlike your typical classroom lecture. But you have to stay humble and persistent. I was humbled often by thinking I had solutions that weren't solutions, and I had no way of knowing they weren't solutions until I asked the right question. Sometimes you won’t know which question is helpful - but it's OK! That's part of the process; just keep communicating where you are along the way - this was one of my first Big Lessons. 

Not being a natural science major, I gained a lot of respect with real life challenges of "doing science", and having to know the "full stack" of science. That is, having to know the ‘why’ at all of the different levels, from where to put electrodes, to how the signal is transmitted and converted into what the software reads out, how to process that data to illustrate what we're looking at, why we're looking at this subject specifically, and how all of this relates to a particular issue within the field. A formative experience was my first lab report, an in-house presentation of what had done so far in the lab. During your first life science presentation, you make mistakes and learn a lot. There's a precision and familiarity that comes with each specific field of study, and I've only touched upon what that is in neuroscience. It has been like painting: setting a primer coat on for the first time - a bit messy, but I feel confident about building upon it in the future. Experiences like this really make undergraduate research worth it, in my opinion. 

I have been a part of research teams in four different departments on campus (which actually my secondary agenda for coming to UAlbany; previous institutions I attended did not have this diversity in undergraduate research opportunities). If you are at all considering doing research, I must encourage you to do so. The Center for Undergraduate Research and Creative Engagement (CURCE) has really developed nicely and its staff are exceedingly helpful. I actually received two grants from CURCE for some of my other independent research projects! If you are interested in biology and neuroscience, definitely check out Scimemi Lab. When your PI gives you room to try and fail, explore, and is willing to invest in you as a student and cares about your career future, it makes a big difference in your lab experience and how you feel about the subject matter.

The best mentors and PIs will help you capture enthusiasm while helping you get a lay of the land, and I really wish everyone can experience that in their undergraduate studies. It changes how you view understanding, how you see yourself in the process of education, and gives you a glimpse of how hard it is to build knowledge. Maybe, like me, you discover you like this process and want to work at contributing to the what knowledge we have. Having great labmates around you help, too - which was a part of this lab experience for me. Previously, I worked one-on-one or in isolated pairings, but this open lab atmosphere and ability to communicate and be next to others “in the trenches” - it was really my favorite environment so far. There are overlapping, interesting projects, and some of the best moments are the side conversations that offer perspective and insight into other’s situations - or at least commiserating about The Struggle of science!

My secondary project involves setting up an open-sourced MySQL-based database to automate some of the downstream computations involved in processing large batches of data. Being able to work with new software, hardware, databases, documentation, talking with creators/inventors of devices, and trying to relate all of this understanding functionally to the lab has absolutely been challenging, but it has also been great training and exposure to lab life. Of course, it is a lot of fun, too; it lets you feel like you are voyaging out on the great sea of understanding, and you have your role, your mission and you have to play your part. You have good days and bad days in the lab, but that's all part of the journey.

I wish I started sooner so I'd have more time in the lab and get more experience in a biology environment. It has helped me solidify that I want to take my informatics training towards biology, rather than leaning purely towards computer science. Particularly, the area of computational cognitive neuroscience or the computation that underpins cognition and information processing. I hope to pursue graduate research on that topic, and will be involved in summer research on representational brains and phenotype, modeling neural development.

Outside of the lab, I’ve worked on research projects in Informatics (Autonomous Systems and Machine Learning), Cybersecurity, and Electrical & Computer Engineering (Human-Robot Interaction); I’ve been involved in student tech groups such as IEEE, ACM & ACM-W, ASIS&T; UAlbany Students Stopping Trafficking & Exploitation of People (SSTEP); and e-NABLE (simple prosthetic hands for those in need). I also frequently bothered folks via departmental list servs about cool events such as Princeton Envision Conference, Machine Intelligence Conference, Ethics of AI, or New York Celebration of Women in Computing. There’s are many quality opportunities locally (and Dr. Scimemi is a great facilitator of opportunities for you to develop your skills and provide outreach for the community). Get involved! 

Feel free to connect on Twitter @JesParent, and good luck on your journey of understanding!

Jesse Parent

Wednesday, April 24, 2019

Microetching neurons with Gabrielle!

Greetings! My name is Gabrielle and I am the Scimemi Lab Manager. I have a BA in Biology from Cornell University, a PhD in Chemical Biology from the University of Michigan and several years of post doc experience. My expertise lies in molecular biology, although I have dabbled in NMR, mass spectrometry, biochemistry and microscopy. I have worked in a wide range of organisms from plants to bacteria to viruses, but the Scimemi lab marks my inauguration into mammalian research. Managing a mouse colony can be challenging as there are a lot of moving parts, but it is a fun organization/optimization problem. While I have no formal training in neurobiology, it is exciting to be able to apply my molecular biology skills to a new field.

I recently came across a ScienceFriday interview with the artist Greg Dunn. He uses a technique called photolithography to make detailed artwork of neurons. He draws neurons with ink, scans the image and prints microetching data at ultrahigh resolution onto a transparency to generate a mask. He places these masks onto a photoresist surface and shines UV light over it. Wherever UV light penetrates the mask, it polymerizes the photoresist material, which hardens it; regions shielded by the mask do not polymerize and can be washed away with a basic solution. The remaining features are subsequently plated in gold leaf. This microetching process generates features with single micron resolution (or about 1/100 of the width of human hair!).

Intriguingly, in addition to creating beautiful two dimensional images, Dunn has also incorporated animations into his microetched patterns such that as a light source is moved over the image (or when your perspective changes) the reflection of light from the gold leaf fluctuates to portray electrical signals travelling across the neurons. He has used this technique to generate an image of a slice of the entire brain, incorporating real scientific data about the size of ~500,000 neurons and their features, the connectivity between different parts of the brain, and information about the coordination among firing neurons during 500 microseconds of “brain time”. These exquisite images serve to highlight the complexity and the stunning beauty of our brains. More artwork can be found here. Enjoy!

Gabrielle Todd



Wednesday, April 17, 2019

If you cannot 3D print it, it's not fun!

Hello!

My name is Desirée and I am a senior at SUNY Albany majoring in Physics. I have been a member of the lab since Fall 2017. I have taken on the role of the lab’s Computer Aided Design (CAD) designer and 3D printing enthusiast. From PCR combs to behavioral apparatus, 3D printing has allowed us to develop tools that are useful for our specific research needs. The possibilities are endless! I have also been practicing my coding skills and learning methods of statistical analysis.

Aside from working in the lab, I was a board member for Volunteers Around the World, where I, along with 22 other aspiring health care professionals, traveled to the Dominican Republic to shadow doctors, distribute pharmaceuticals to residents of impoverished areas, and teach a hygiene class to an orphanage. I also attended Hackathons, including HackRU, HackRPI, and MedHacks at John’s Hopkins (you can find me on the MedHacks Instagram page demonstrating my prototype of a glove-donning device!). I love designing, and I have developed quite the portfolio of CAD designs, scientific illustrations, and 3D printed tools and toys (playing Overcooked and Mario Kart on the Nintendo Switch has never been more addicting since I made controller adapters).

Upon hearing about Dr. Scimemi’s lab and how its members come from many different backgrounds, I realized that neuroscience is truly multidisciplinary. It combines biology, chemistry, physics and even engineering and math in order to fully understand the most important, and puzzling, organ: the brain.

In the lab, we are expected to be independent and work autonomously, but have the amazing support from Dr. Scimemi and the other lab members. We are also given amazing opportunities to network with people in the field through the Society for Neuroscience and events not only at SUNY Albany, but other universities as well. The main takeaway is that Dr. Scimemi’s lab environment encourages risk taking and delving further into your interests for a unique development of passion and curiosity.

If you are thinking about joining the lab, remember to embrace your talents and interest and know that there is always room for you in the quest for scientific exploration!

Desirée D’Moore

Desirée is the recipient of the following award:
2018            Situation Interactive Prize for Experience Research




Thursday, April 11, 2019

What do we work on in the lab? Shergil explains...

Hello to all the lovely readers of Neurovoice!

My name is Shergi Zahid and I am an undergraduate senior here in the lab, majoring in Biochemistry/Molecular Biology. This is my second semester working in the lab and it has been a blast! My latest assignments in the lab include reconstructing medium spiny neurons (MSNs) and rendering them into realistic computational models, which we can use to develop biophysical model and analyse their fine morphology. It’s actually pretty interesting. But you know what is even more interesting? Some of the publications our lab has produced! I would like to present to everyone a paper published in the Journal of Neuroscience on January 24, 2018, titled “Neuronal glutamate transporters control dopaminergic signaling and compulsive behaviors”. This paper is still very relevant to our current work in the lab so it should be good for anyone who’s interested in joining us to not only read the paper but also read this blog post to help you better understand the research we’re conducting here. I’m going to try to keep this as simple as possible to not scare anyone away. So to get started, what is the premise of this whole study? To start, the focus of the study is on the neuronal glutamate transporter EAAC1 and its impact on signaling and stereotyped behaviors associated with obsessive compulsive disorder (OCD). The region of the brain that our study focuses on is the striatum. It is the part of the brain that controls execution of stereotyped movements. This region of the brain is hyperactive when examining the brains of OCD patients. In normal brains, EAAC1 is largely expressed in the striatum. Its loss is associated with increased execution of ritual and anxiety-like behaviors in mice. But what are molecular the mechanisms behind these behaviors? The paper addresses this exact question.  Through electrophysiological, viral and molecular techniques as well as behavioral studies that were done on mice, we found the explanation to this question. When explaining the molecular mechanism of these behaviors we must look at two receptors found in the brain that we had described to be associated with EAAC1, group I metabotropic glutamate receptors (mGluRI) and D1 dopamine receptors (D1R). Here’s the basic idea, when EAAC1 is expressed, it reduces the activation of mGluRI receptors which results in increased D1R expression, this ultimately leads to long term potentiation (LTP) leading to normal signaling activity in the striatum. When observing mice with the EAAC1-/- you wouldn’t see this type of result. However, if you blocked mGluRI, D1R expression would be restored. Interestingly enough, when we have an EAAC1 expressing mouse in which we can activate signal cascades coupled to GluRI we are able to trigger a decrease in D1R expression and increased stereotyped movement.  Below is a quick and easy summary of everything.

With EAAC1 = mGluRI Activation ↓ & D1R Expression ↑   Leading to LTP
No EAAC1 = blocked mGIuRI,  Activation ↓ & D1R Expression ↑ Leading to LTP
With EAAC1= coupled mGluRI Activation ↑ & D1R Expression ↓ Leading to stereotyped movement
No EAAC1 = mGIuRI Activation ↑ & D1R Expression ↓ Leading to stereotyped movement                                                                 
Now onto the behavioral part. We subjected mice of two different genotypes (WT and EAAC1-/-) to a SHIRPA screening, which tests for general behavioral abnormalities. We only found subtle motor deficiencies in EAAC1-/- mice. Although both mouse strains had similar levels of motor activity, EAAC1‑/- mice showed increased anxiety like behaviors. These differences could be detected over a broad age range (P14- P35), in male and female mice alike. When analyzing more specifically striatal controlled behaviors (e.g. grooming), we found that EAAC1-/- groomed more frequently than WT mice. Together, these data identify EAAC1 as a key regulator of striatal activity, movement execution and anxiety, which are all disrupted in OCD.

So…if you want to know more about how the brain works, at a very deep and detailed level, this is the place to be!

Shergil Zahid

Shergil is the recipient of the following award:
2019            Presidential Award for Undergraduate Research



Friday, April 5, 2019

DJ Saad @ The Honors College

Hi everyone,

My name is Saad and I’m currently an undergraduate freshman majoring in Biology and minoring in French. I have been in the lab since the Fall 2018 semester and my duties in the lab have included PCR, behavioral studies, and some 3D printing design.

On campus I am a DJ and internal events director for WCBD radio, you can catch my show from 12-2 am on Thursdays. Most of the music I play is either hip hop or electronic, also a lot of Frank Ocean. I am also the secretary for UAlbany Peace Action which organizes campaigns for social justice issues. Most recently, we held a movie screening of Hotel Rwanda to raise awareness for genocidal actions happening throughout the world. We’d love to have new members so if your interested feel free to send me an email at sahmad2@albany.edu.

I am also a part of the Honors College at UAlbany which is an amazing program. The honors program gives you the ability to take courses at an honors level and make great connections with professors that come in to visit the Honors College as part of the weekly speaker series. I am also a part of the Honors Event Planning Committee which organizes a wide range of events from parties to faculty book panels.

After undergrad, I hope to attend medical school and go on to become a psychiatrist. I’ve always been interested in the psychology of and neuroscience behind mental illness and I hope to continue learning about it.

Saad Ahmad

Saad is the recipient of the following awards:
2020            Selected for ICAN Paris Forum


Tuesday, April 2, 2019

Fresh as a Freshman

Hello everyone!

My name is Ian Tschang and I am a Freshman at SUNY Albany majoring in Biology. I have been in the lab since October of 2018 and have thoroughly enjoyed it. I have done PCR and immunolabeling and am now working on using in situ hybridization to detect the expression of different genes in brain slices. Some of my hobbies include playing the piano (especially Chopin, Rachmaninoff, and Liszt) and watching YouTube. I am currently in the Pre-Med Club, Albany Student Television, and Presidential Honors Society. I also volunteer at Albany Medical Center on Sundays. I hope to graduate and attend medical school or go into research in order to help those who are suffering from diseases and contribute to an ever widening body of scientific knowledge. I can’t wait to see what advancements and developments the future has in store for us! Thanks for reading!

Ian Tschang




Monday, April 1, 2019

Learn your acronyms: Nurat introduces us to CURCE, CSTEP, UASRP and running!

Hi everyone!

My name is Nurat Affinnih and I am a junior at SUNY Albany. I have a minor in Neuroscience and will be majoring in Biochemistry and Molecular Biology. I have been in Dr. Scimemi’s lab for about two years now. I am extremely interested in the topics that we study in the lab, specifically neuropsychiatric disorders. This was my main reason for joining the lab. I am fascinated by mental disorders and my goals involve learning about the procedures through which these disorders occur.

I am currently working on a research project that investigates how striatal hyperactivity contributes to obsessive compulsive disorder (OCD). We address this question using chemo and optogenetics approaches, which require delivering viral constructs to the striatum using stereotaxic surgeries. Being in the lab has allowed me to become a skilled micro-surgeon, which I think will be invaluable for my future career.

Research aside, I am an ambassador for the Center for Undergraduate Research and Creative Engage (CURCE) and a member of the Collegiate Science and Technology Entry Program (CSTEP). CURCE works to help undergraduate students find and participate in research, scholarship, and creative activities by providing them with information, resources, and events related to their goals. If you are interested in getting involved in research, you can find out more about CURCE here! CSTEP works to increase the number of historically underrepresented and economically disadvantaged students in Science, Technology, Engineering, and Mathematics (STEM) professions by providing students with opportunities for academic enrichment and research experience. Through CSTEP, I was able to conduct research during the summer of 2018 by participating in one of their programs, the University at Albany Summer Research Program (UASRP). If you would like to be part of CSTEP, you can find more information here!

Outside of these activities, I love to run! I am part of the UAlbany Running Exchange, a running club on campus. We are currently looking for new members. If you enjoy running, consider joining the club!

My plan after graduating is to attend medical school. Doing research in Neuroscience has become an important part of my college career, so much so that I have been motivated to pursue an MD-PhD in medical school. One day, I hope to be able to treat patients and conduct research in the Neuroscience of mental illness.

Thank you very much for your attention!

Nurat Affinnih

Nurat is the recipient of the following awards:


2020            President's Award for Leadership – Great Dane Award 
2020            Accepted to NCRC 2020 at Harvard University 
2020            Accepted to NCUR 2020 at Montana State University 
2020            CURCE Travel Award
2019            CURCE Award
2019            Initiative for Women Award
2019            Spellman Academic Achievement Award  
2019            Presidential Award for Undergraduate Research
2018            Spellman Academic Achievement Award  
2018            CSTEP Summer Research Program - SUNY Albany  
2017            Spellman Academic Achievement Award