The study of circadian cycles is TIMELESS

Circadian rhythmicity is an essential biological process that regulates the sleep-wake cycle through both internal processes located primarily within the suprachiasmatic nucleus, as well as external environmental cues like light. Many circadian proteins work to maintain this rhythmicity, with one being TIMELESS which is within a feedback loop with other proteins such as BMAL1/CLOCK to promote or repress clock-dependent genes. TIMELESS has a clear role in maintaining our “biological clock” but its role in other processes such as synaptic plasticity is less apparent. In order to examine the role TIMELESS plays in memory and learning, Barrio-Alonso et al. utilized a combination of conditional region specific knockouts of TIMELESS done using CRE-Lox and subsequent behavioral and quantification experiments.

To obtain behavioral data, the mice were placed in a Y-maze and underwent a contextual fear conditioning (CFC) test. In the Y-maze the mice were given 10 min to interact with two arms of the maze while a third arm was blocked off. After 1 hr, the mice would be reintroduced to the maze with the third arm “novel arm” now available. The preference for the novel arm served as an index of short-term working memory. The conditional knockout (CKO) mice had a substantially lower preference for the novel arm compared to wild type mice (Figure 1A). The decreased preference indicated the CKO mice had impaired working memory. However, the mice explored the maze at similar distances, indicating no changes in exploration between the CTRL and CKO mice (Figure 1B).  In the CFC test the mice were subjected to paired stimuli, they were played a neutral tone while simultaneously they received a mild foot shock. This would result in the mice instinctively freezing due to fear. The neutral tone was the conditioned stimuli (CS) and the foot shock was the unconditioned stimulus (US). Over the course of three days the mice were subjected to different stimuli.  

Day 1: CS+US 

Day 2: CS only with the same context. 

Day 3: CS only with different context.   

On each day the freezing behavior was scored but had different implications for each day. On Day 2 freezing served as a measure of contextual fear while Day 3 freezing served as a measure of cued fear memory. On the first day, the CKO and control group had similar results indicating memory acquisition was intact as mice in both groups associated the neutral tone with the foot shock (Figure 1C). However, on day 2, the CKO group had reduced freezing behavior when in the contextual setting without the CS, indicating impaired memory (Figure 1D). On Day 3, the CKO group exhibited reduced freezing behavior in the presence of the conditioned stimulus, as well (Figure 1E). They repeated the setup of days 1-3 but instead tested after 60 min post training. With this, no difference between the CKO and control groups were observed. With these results, they concluded Timeless must contribute to long term memory. They repeated this experiment with mice at ZT10 and found no long term fear memory deficits as seen with the ZT12 mice. This implied the effects of TIMELESS ablation in a circadian context were most prominent at ZT12. 

Kathryn Casey and Brianna Tsakh

Figure 1: TIMELESS deletion impairs short-term spatial memory and retrieval of long-term memory. (A) Quantification of the preference for the “novel” arm compared to the “familiar arm” between CTRL and CKO mice. (B) Distance explored by CTRL mice vs. CKO mice in the Y-Maze. (C) Measurement of the ability of the CTRL vs. CKO mice to learn and associate a conditioned stimulus (neutral tone) with an unconditioned stimulus (toe shock). (D) Measurement of the ability of the CTRL vs. CKO mice to freeze in response to being in the same context without adding the conditioned stimulus. (E)  Measurement of the ability of the CTRL vs. CKO mice to freeze in response to the addition of the conditioned stimulus.

Reference: Barrio-Alonso E, Lituma PJ, Notaras MJ, Albero R, Bouchekioua Y, Wayland N, Stankovic IN, Jain T, Gao S, Calderon DP, Castillo PE, Colak D. Circadian protein TIMELESS regulates synaptic function and memory by modulating cAMP signaling. Cell Rep. 2023 Apr 25;42(4):112375. doi: 10.1016/j.celrep.2023.112375. Epub 2023 Apr 11. PMID: 37043347; PMCID: PMC10564971.

TDP-43 depletion disrupts blood brain barrier in neurodegeneration

Capillary epithelial cells within the blood brain barrier (BBB) breakdown in neurodegenerative disorders. A loss of a DNA binding protein called TDP-43 is thought to be the reason for blood-brain barrier breakdown. ECs and microglia are usually underrepresented in single nuclei analysis of the brain, so ERG transcription factor was stained to enrich them and sort them based on ERG subtype. Three clusters of ECs were identified: aging, degenerative and healthy. The degenerative group showed downregulation of β-catenin and upregulation of TNF/NF-kB with a loss of TDP-43. Capillary ECs were further separated into five clusters based on the top genes expressed within a cluster. Reactive clusters (REV1) were enriched degenerative ECs and homeostatic clusters (HC) were enriched normal ECs. REV1 had increased TNF/NF-kB signaling and decreased Wnt/ β-catenin compared to the HCs.Researchers also saw capillary ECs switching to a proinflammatory subtype during disease, which is thought to contribute to the breakdown of the BBB seen in neurodegenerative diseases. They used Uniform Manifold Approximation and Projection (UMAP) visualization which showed a clear increase in nuclear β-catenin in the HC cluster. Additionally, β-catenin transcriptional targets, such as TCF/LEF1, ABCG2, and APCDD1, were significantly upregulated in the HC cluster compared to REV1. These findings suggest that the REV1 population exhibits reduced nuclear β-catenin, lower TDP-43 levels, and diminished expression of Wnt signaling genes. NF-kB and Wnt function to maintain the BBB in the presence of TDP-43 and so it is theorized that a loss of TDP-43 shifts NF-kB to its proinflammatory functions causing the BBB to breakdown.

 

 

Reference:

Omar, O.M.F., Kimble, A.L., Cheemala, A. et al. Endothelial TDP-43 depletion disrupts core blood–brain barrier pathways in neurodegeneration. Nat Neurosci (2025). 

A PCR approach to disease diagnosis

 

Hello Readers! 

We are part of the PCR team in the Scimemi Lab at SUNY UAlbany: Catherine Lienemann, Alaina Jeeson, and Dr. Phillip Albrecht, our lab manager.

The polymerase chain reaction (PCR) is a laboratory technique that is used to amplify DNA fragments. Amplifying DNA fragments is useful as it allows us to create large amounts or copies of a DNA sample that is required for analysis, using only one copy of DNA doesn’t give us enough information for any molecular or genetic analyses (Nhgri, 2019). In the lab, we use PCR to confirm the genotypes of mice in our mouse colony. We extract DNA from mice tail snips and make digestions as well as 1:1 dilutions of the DNA. We then set up reaction samples that include DNA polymerase, DNA primers, and DNA dilutions, which go into the thermocyclers. Lastly, we conduct gel electrophoresis which separates the contents of the samples and image them to analyze further. Components needed for PCR include double-stranded template DNA, DNA primer, and DNA polymerase. DNA primers are short DNA fragments that bind to specific complementary sequences in the template DNA strand, this prepares the DNA strand for amplification. DNA polymerase is an enzyme that connects nucleotides, makes DNA molecules that form PCR products, and initiates replication. The PCR process consists of three consecutive steps including: (i) denaturation; (ii) annealing; (iii) elongation. DNA denaturation happens at high temperatures (95°C in our case). During denaturation, the DNA double-strands are separated from each other. The annealing process allows primers to bind to the single-stranded DNA. Lastly, elongation takes place where the DNA polymerase initiates DNA replication and new DNA strands are synthesized in the 5’-3’ direction, making multiple copies of DNA. All of the previously mentioned steps are accomplished in a thermocycler which can control temperatures and incubation times, allowing for many PCR cycles to amplify DNA (Khehra et al., 2023).  

PCR is a tool not limited to the world of genotyping and research labs, it found itself center stage in labs around the globe as diagnostic technology during the COVID-19 Pandemic. A paper by Velavan, T. P et al. (2021) dives into the use of “real-time reverse transcriptase Polymerase-Chain Reactions (RT-PCR)” which detects SARS CoV-2 easily by converting the viral RNA into complementary DNA (cDNA) through reverse transcription, and then amplifying specific segments of the cDNA. The genetic sample is obtained using swab tests of the upper respiratory system such as the nose or mouth. There can be some hiccups in this process such as improper swabbing technique or False-negatives. These false-negatives can occur through the mutation of the reverse transcriptase-PCR primer and the probe target segments of the virus’s genome. The RNA is then extracted and diluted with the standard elements of a PCR  such as “forward and reverse primers, nuclease-free water, a fluorophore-quencher probe and a reaction mix (magnesium, transcriptase, nucleotides, polymerase, and additives)” (Velavan, T. P et al., 2021). 

A paper by Fallon et al. (2022), discusses the use of PCR in the diagnosis of uveitis, a disease that is identified by inflammation of the eye. The aqueous or vitreous fluid of the eye was used to run PCR to detect Herpes Simplex Virus, Varicella Zoster Virus, Cytomegalovirus, Toxoplasmosis gondii, Mycobacterium tuberculosis and Epstein-Barr Virus. In this study, data that was used included the pre-PCR test diagnosis and treatment and the post-PCR test diagnosis and treatment from 116 patients. Using this data Fallon et al. (2022) wanted to see the significance of PCR in diagnosing and treating uveitis. 49% of patients had a diagnosis change and 27% of patients had a treatment change based on the results of PCR testing.

The results of the study by Fallon et al. (2022) showed that PCR testing in patients allows for treatment changes and improved diagnosis of infectious uveitis. It was also noted that the PCR testing results had a higher impact on uveitis diagnosis in patients who didn’t have a pre-test diagnosis or had an unknown diagnosis. The CDC also performed a study using the Fulgent COVID-19 RT-PCR test to examine the testing’s specificity and accuracy. The results out of a total 2039 subjects was a testing sensitivity of 94.7% and a specificity of 100% making it one of the most accurate tests on the market for the diagnosis of COVID-19 (Velavan, T. P et al. (2021). These results show us that PCR testing is confirmatory in nature, and can greatly impact patient care treatments, diagnosis, and management even in cases where patients have been previously diagnosed using other laboratory methods. 

References

• Fallon, J., Narayan, S., Lin, J., Sassoon, J., & Llop, S. (2022). The impact of polymerase chain reaction (PCR) on diagnosis and management of infectious uveitis at a tertiary care facility. Journal of Ophthalmic Inflammation and Infection, 12(1).  
• Khehra, N., Padda, I. S., & Swift, C. J. (2023). Polymerase chain Reaction (PCR). StatPearls - NCBI Bookshelf.  
• Nhgri. (2019, March 9). Polymerase Chain Reaction (PCR) fact sheet. Genome.gov. 
• Velavan, T. P., & Meyer, C. G. (2021). COVID-19: A PCR-defined pandemic. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 103, 278–279. 

Brianna and Umair: partners with no crimes!

 

Umair, here. I’m a senior here at SUNY ALBANY with a bachelor’s in biology. I have always found the physiology of the brain to be interesting and that is what drove me to join the Scimemi Lab in Fall 2020 semester. It truly been an amazing experience from the beginning. I came in the lab with no prior research experience and spent most of my time with Gabrielle on the Polymerase Chain Reaction to genotype the mouse colony. Later, I was given a wonderful opportunity to lead the PCR team and manage the mouse colony. I really enjoyed the process of navigating between different project and communicating with everyone in the lab. I feel extremely grateful that I was able to mentor so many amazing people in this lab. Something I realized was the more I shared my knowledge, the more I expanded my own level of understanding. The first project that I worked on was the Circadian rhythm project to study the changes in the memory consolidation and learning during the light and dark phase. I gained expertise in circadian modulation of hippocampal glutamate receptors and the chemical pathways that contributes to synaptic plasticity. I also worked on the Alzheimer Disease project, which involved looking at the role of astrocytes and Glutamate transporters in the Alzheimer's disease pathogenesis using whole cell patch patching and dot blot. I have to say, electrophysiological technique like patch clamping is truly a thrilling experience. 

I cannot say this enough that I wouldn’t be where I am today, without the help of everyone in this lab. Maurice and Nurat were always there to support me in every little step. Especially, Dr. Scimemi who encouraged me throughout the whole journey. 

Last but not least, I hope my partner in crime as well all my friends in the lab go above and beyond their potential and rock the world…

Hi everyone, my name is Bri, I am a second year Biology major at UAlbany and I’ve been working in the lab since Spring 2023. I first started on the PCR team where I learned how to manage the mouse colony and properly genotype and identify the mice. From there, I gained my footing in the lab and was able to progress onto the ABeta project, where we investigated the influence of ABeta accumulation on glutamate transporters in astrocytes. Here, I was responsible for executing dot blot procedures and analyzing our results and applying them to the context of the experiment, and I was able to become much more independent in my research. I have also been able to work on our western blot team which focuses on circadian modulation of glutamate transporters, where I was responsible for executing not only the western blot procedure, but also the analysis that accompanied it. Through my time in this lab, I’ve been able to build my wet lab skills, learn how to read and write research papers, create posters and present them effectively and have made connections and friendships I value greatly. There has never been a moment where I haven’t felt challenged, and that has been something that has kept me on my toes and always learning. I am specifically thankful for Umair’s mentorship and guidance throughout my time working with him, and I will miss him and his presence in the lab immensely. I am very thankful for the opportunities I’ve gotten through this lab and look forward to my future time here!

Adam

Hello everyone!

My name is Adam and I’m currently a junior at this university. This is my third semester in the lab and I’ve learned so much more than I expected coming into this program! When I first started, I began training in immunohistochemistry to help work on the circadian rhythm project. Within this project, I initially helped obtain data on layer-specific circadian changes in the expression and cytoskeletal organization of astrocytes. These past two semesters, I shifted gears to focus on glutamate receptor expression in two layers of the hippocampus. I really enjoy the training and procedures I’ve been taught while in this lab. Aside from learning immunostaining, brain slicing, confocal imaging, and data analysis, my favorite procedure has got to be trans-cardial perfusions, which are essentially mice brain extractions. I feel like a mini surgeon every time I perform them! Another major experience I never thought I’d be able to have was being able to create and present a poster on my project. I presented in both the Undergraduate Symposium and the UAlbany Showcase events which have been amazing experiences! Aside from this lab, I’m a part-time student on the pre-med track majoring in biochemistry and molecular biology. I’m also a part-time medical assistant at the Bone & Joint Center right across UAlbany’s campus. One thing the hands-on work in this lab has shown me is how much I would love to do surgery in the future! I’m also the current and upcoming treasurer for the Muslim Student’s Association (MSA) on this campus. When I can finally get some free time, I enjoy weightlifting, watching UFC, and playing videogames with friends. Thanks to this lab, I also recently discovered how enjoyable hiking can be!

Zaden

Hey there!

My name is Zaden and I am a Psychology major with a minor in Italian and English. I have worked with this lab since Spring 2023, and I’m currently planning to attend graduate school for clinical therapy once I obtain all my credits here at UAlbany. I work with the behavior team, where we study and observe differences between wildtype and EAAC1 knockout mice with reward seeking behavior, how well they perform these tasks, how fast they learn the new tasks, and so on. Initially most of my time was spent training these mice, however with the help of my labmates I’ve been able to dedicate more time to data analysis using the Igor and SPSS software applications. It has certainly been challenging being in a new environment (and becoming more tech savvy with computers), oftentimes it feels that I am drinking from a fire hose when it comes to learning, but overcoming these obstacles is immensely gratifying. Not only has this experience taught me more about neuroscience, but also about being a more competent, responsible, and efficient worker. The people here are very cooperative, making the workload more manageable and enjoyable. It's been a genuine pleasure working here, and I’m eager to witness further progression of this lab. In times of leisure I typically read, play video games, go hiking with friends and spend time with family. When finances and spare time align, I love to travel and attend music festivals.

Massa

Hi everyone!

My name is Massa and I’m majoring in biology on the pre-med track with a business minor.  I would love to pursue a career in medicine as a doctor where I can learn about the human body and take care of patients. This was my first year at UAlbany after I had transferred from FMCC and my first semester at the lab. I was interested in joining so I can learn more about neurodegenerative disease, lab techniques, and just understanding how research is actually conducted beyond looking at a scientific paper. I’ve learned so much already with the help of my teammates and Annalisa, and am looking forward to learning more and working with everyone! My favorite thing about the lab is… mice! I used to be very scared of them, and after training them for a while I got used to them and now I enjoy it! I spend most of the time in LAR training the mice with the lever press training where they have to press the lever to get a reward. In my free time,  I like to discover new coffee shops and I LOVE to color.

Jessica

Hello everyone!

My name is Jessica and I’m a second semester freshman. I have been working in Annalisa’s lab since January 2024. I am a Biochemistry major with a Spanish minor on a pre-med track. Even though I am still fairly new to the lab, I can already say I’ve learned so much. As a part of the behavior team I’ve gained a lot of new skills including: handling lab animals, data analysis, and I am in the process of learning procedures using immunohistochemistry and further proficiency with analysis software with the help of my fellow lab members, Zaden, Abby, and Massa. Being in this lab has not only helped foster my interest in neuroscience but also given me hands-on experience while working in tandem with other lab members. In my free time you can find me sleeping, studying, or spending time with friends. I am grateful for this experience and for such an understanding PI for answering all of my questions when I was first starting out. I am excited to see what else I will learn here!

Abby

Hello everyone! 

My name is Abby, a second semester sophomore. I’ve been working in Annalisa’s lab since spring 2023. I’m pursuing a career in medicine and can say working in lab has given me lots of valuable skills I can carry into the future. I’ve been working on the behavioral EAAC1 project where I’ve learned skills in data analysis, immunohistochemistry, handling lab animals and performing stereotaxic surgery. Working hands on in the lab has given me experience past any class along with being able to work effectively on a team. I’m a chemistry major with a biological emphasis on the pre-med track. In my free time I love hanging out with my friends, working out and of course, studying.  

Mya

Hey everyone!

My name is Mya, and I’m a second semester freshman! I have been working with Annalisa since fall semester ’23, and have learned a lot. I always wanted to go into medicine and learning different techniques and methods to solving different problems and since being in this lab I have learned a bunch of new things I wouldn’t have learned in my classes. I am a biology major with a minor in medical anthropology and neuroscience, with a goal to learn more about the different regions of the brain and apply that to medicine. In my downtime I enjoy hanging out with friends, taking a nap or I’ll be in the library “studying”. But I can’t wait to continue next with the lab next year and see what happens along the way!

Aiden

Hello everyone!

My name is Aiden Cho, and I’ve been working with Annalisa throughout the course of my second-semester as a freshman student. I am a Biochemistry and Psychology Major at University at Albany, and there is still so much for me to learn. At first glance at the lab, all this neuronal terminology was a bit provoking, however through great lab-mates and a great PI, I was able to further understand the fundamentals of what I was actually learning. I realized I was not alone and was able to rely on my fellow mentors, Umair Hassan and Brianna Tsakh. This lab has given me so much experience, as well as knowledge on the human brain, and only piqued my interest in it further. From dot-blot to western-blot, I learned a variety of skills such as focusing on the measurement of expression levels of glutamate receptors in the hippocampus, communication, PCR, and brain slicing. Just by getting hands on experience, I could feel myself learning more information than I had learned in actual classes. Outside the lab, I am often actively participating in a wide variety of sports, or caught taking a nap in my dorm. Although I am relatively new, I see myself enjoying my time at the lab further throughout the course of my college years, and I am so excited to see what obstacles I will have to overcome. I can’t wait to see what next year has for me!

Working as a team

We are the PCR Team at the Scimemi Lab at UAlbany. We manage all the identification, genotyping, and breeding of the mouse colony. We mastered all these skills over the course of the Spring 2024 semester. Most importantly, we developed teamwork. Our Team consists of Victoria Fiorelli, Kathryn Casey, and Alaina Jeeson as well as our day-to-day mentor, Dr. Phillip Albrecht. 

Victoria: I feel honored to be working in Dr. Scimemi’s lab as a second-semester transfer student. I am currently a Biology Major at UAlbany. When I joined the lab, I thought I would witness research in action and contemplate the implications that follow, such as passing on learned information in the context of basic science with long-term implications on human health. My expectations were far exceeded: almost instantly I caught the neuroscience bug. Everyone within Dr. Scimemi’s lab is not only intelligent but also talented in the way they describe and orchestrate their methods within the mouse brain. I am always delighted with the buzz of activity and knowledge that fills her lab, and it has been such an inspiring atmosphere. Needless to say, I will be reading some neuroscience texts over the summer. When I am not wondering about how in the world Dr. Scimemi let me be a part of her work, I am usually found reading, training my dogs, volunteering, or out in the wilderness. 

Kathryn: Hi everyone, I’m a junior at UAlbany working in the Scimemi lab as of January 2024. I transferred to the school this past fall from Siena College and gained interest in Dr. Scimemi’s lab after taking an introductory neuroscience class. I have been able to meet like-minded peers and gain access to mentors who have really helped me develop my critical thinking, and practical skills and have provided guidance on how to tackle my journey in the world of research. Outside of the lab, you can find me at the gym, at Afrim’s playing for my Co-ed soccer league, or in line at Starbucks in the campus center for a matcha latte. 

Alaina: Hello everyone! I am a Freshman at UAlbany, the youngest member of the team. I also joined the Scimemi Lab in January 2024. Joining the lab was a completely new experience for me as I didn’t have prior familiarity with a bio laboratory, it was also a huge step out of my comfort zone. People in my team, my mentors as well as other lab members contributed greatly to my learning experience here. From knowing only theory about PCR, working in the lab has taught me about the hands-on aspect of it, greatly increasing my understanding of the process and its use in research. I developed skills like teamwork, communication, and problem-solving.

What do we do? Our main goal in the lab is to ensure that all the mice of interest in our colonies are properly genotyped. First, our team runs cage checks to ensure our mice are healthy. Second, we monitor potentially pregnant females and wean litters who are ready to be separated. To ensure we can identify pups within our litters we also use this time to give them an identification code consisting of their birth date, and unique tattoo markings on their hind and front paws. We take tissue samples from their tails and extract DNA from them. Third, we run PCR for the samples and gel electrophoresis for the analysis of specific genes. Fourth, We enter the information into a litter record to share the genotyping results with the rest of the lab.

 

Niitiggya

Hello everyone!

My name is Niitiggya and I am a junior in the honors college majoring in human biology. I am part of the Upstate Accelerated Scholars program and I will be matriculating to SUNY Upstate for medical school after graduating from UAlbany. In my free time, I enjoy working out and going on scenic drives.

I joined the Scimemi lab in spring 2022 to learn more about Alzheimer’s. To my surprise, I learned more than I thought imaginable in such a short period of time. Over the last four months, I performed stereotaxic surgeries, PCR, and perfusions. To be able to see a project through all the way from the characterization of a young mouse’s genotypes to an analysis of its cortical tissue has been a rewarding experience. The first project I worked on was understanding the role of amyloid-beta plaques in synaptic transmission in the CA1 region of the hippocampus. I injected a viral vector bilaterally into the hippocampus and performed a perfusion of the brain to analyze hippocampal slices after 3 weeks. While I read about this procedure multiple times in textbooks, to see perform it in person expanded my knowledge of the subject tenfold. Aside from lab skills, I learned a great deal about data collection and analysis. I learned how to not only interpret data, but to also convey my findings to an audience. I am so grateful for my time in the Scimemi lab thus far and I cannot wait for all that I will learn over the upcoming semesters!

Niitiggya Taneja

And then came graduation time!

Hello everyone,

My name is Saad Ahmad, and I am a graduating senior at SUNY Albany. I have been an undergraduate researcher in the Scimemi Lab since freshman year in 2018. I have recently completed my honors thesis on the Circadian Modulation of Astrocyte Morphology and Synaptic Transmission. I would like to extend my gratitude to everyone in the Scimemi Lab for supporting me through my undergraduate research career, as without their help I would never have been able to complete an honors thesis. Furthermore, the Scimemi Lab has been instrumental in helping me develop skills that I would not have been proficient in with just classwork. From learning PCR in my freshman year to performing image analysis with Imaris, they have been consistently patient and encouraging despite my many mistakes. One of the most valuable lessons I have learned through my undergraduate career is to own up to my mistakes and understand why they happened. By doing this, I gained a better understanding of procedures and troubleshooting steps. The lab also frequently hosted speakers and attended seminars together so I knew if I didn’t understand something there would be others to lean on for help.

My future career goals are to attend medical school and eventually become a physician. While I prepare my application, I will be working with Dr. Jaqueline Burre and Dr. Manu Sharma at the Appel Alzheimer’s Disease Research Institute. I hope to continue to expand my interest in neuroscience and research during my gap year and hopefully carry the skills I learn over into my career as a physician.

Saad

Corey

Hi!

I am Corey Nilon and I am about to finish my third year here at SUNY Albany. I am pursuing a Bachelor’s in biology and have minors in sociology and neuroscience. I originally joined the Scimemi lab in Fall 2020 and have happily been here for two years now! In my free time, I like to be outdoors, play sports, and travel.

In Fall 2020, I started learning polymerase chain reaction and the process of genotyping. Now, for over the last year, I have been focusing on the behavioral aspect of the EAAC1 project. With the help of others in the lab, I was able to truly organize and design my own experiment. I was  knee-deep in each part of the project- it’s planning, data collection, analysis, and conclusions. While there have certainly been many bumps in the road, I am thankful for them, as they’ve directly contributed to my learning. Overall, I would say this experience so far has been incredible. My knowledge of scientific theory, experimental design, general motor behaviors, and neuroscience have all expanded significantly. I presented my research on behavior twice this semester, first at the 19th Annual Student Conference and then at the Biology Undergraduate Symposium. This were my first experiences creating a scientific poster and presenting my research- it was awesome. Of all I’ve learnt in college, these have definitely been among the most rewarding experiences I’ve had.

Going forward, I am excited to build upon my studies by trying something new- computational neuroscience. This summer, I will be interning at the lab and I’ll be taking my first dive into astrocyte imaging/modeling and analysis through programs like Imaris. I look forward to trying something new!

Sarah

  

   Hello everyone!

    I am Sarah Anderson, I am just about to finish my junior year here at SUNY Albany. I am currently working towards a Bachelor’s in Science with a double major in biology and psychology! I joined the team as an undergraduate research assistant in September of 2021 and it has been an incredible experience thus far! I will continue to gain experience in the Scimemi lab throughout the rest of 2022 and into 2023. This research has expanded my knowledge of neuroscience tenfold and continues to be a learning experience.

    Being a member of the Scimemi lab has been such a great experience. From the moment I joined this lab, everyone has been incredibly welcoming and always willing to help one another out. This was very reassuring, as I had done all of my previous biology labs virtually, I was nervous that the hands-on work would present a tough learning curve. However, with the support of everyone within the Scimemi lab, the transition from virtual to in-person was made relatively easy.

    Throughout the fall 2021 semester, I was learning PCR and the proper way to maintain the mouse colony by backcrossing the mice to prevent genetic drift. Towards the end of the fall semester, I began to focus on other projects that were being done by Gabrielle Todd. During the spring 2022 semester, I had transitioned to helping Gabrielle perform a dot blot that compares the glutamate transporter concentrations in wild type and Aß mice at different age cohorts. By learning each step of the complex process from Gabrielle, I was eventually able to perform protein purifications, Bradford assays and dot blots almost entirely independently. I was fortunate enough to get to present my research in the 39th Annual Biological Sciences Research Symposium. This event broadened my horizons to the range of research that is being conducted here at SUNY Albany, and it was overall a really fun event!

    The opportunity that Dr. Scimemi gave me by letting me become one of the undergraduate researchers in her lab is priceless, I have learned so much and will continue to actively learn until I graduate! I can’t wait to be a part of the Scimemi lab for another year!

Sarah Anderson

Mustafa

Hello everyone!

My name is Mustafa Muhi, a Junior Biology major at SUNY Albany. I joined the Scimemi lab in January 2022 and have been working since then. I enjoy reading, traveling, playing video games, and playing soccer. Since I joined the Scimemi I have learned a wide variety of skills ranging from learning to do literature reviews, write papers, PCR, and the ability to scientifically approach challenges that I may face. At the start of my time in the lab, I learned how to handle the mice colonies and genotype the mice through PCR. Although at that time I was very inefficient at those tasks and often needed help, with the help of everyone in the lab I became very efficient and comfortable with my roles. As the lab received the new mouse strains mice, I began with optimization of their PCR protocol. This required me to combine everything I have learned throughout the semester. Although I am still working on some protocol optimization, I hope I could eventually create an efficient protocol for people to use in the future. I have learned so much in the time I have been in this lab, I plan to continue to be a part of the lab this semester and next year. I hope to be able to learn how to do stereotaxic brain surgeries and to be more involved in the lab. I cannot wait to learn more from all the kind people in the Scimemi lab!

Mustafa

Garrett

 

Hi everyone!

   My name is Garrett Wagner, and I am about to graduate here at SUNY Albany with a Bachelor’s in Science in Biology and a minor in Neuroscience. I joined the Scimemi lab in July of 2021 hoping to further my knowledge on how certain mechanisms work within the brain.

   From my interview with Dr. Scimemi, before I even began, I knew that her current work would be quite fascinating to learn.  I began my time in the lab learning PCR as well as how to take care of the mouse colony. In the fall of 2021, I began working with Nurat Affinih and Monica Rodriguez to analyze mouse brain images to determine the effects that the loss of the glutamate transporter, EAAC1, has on dopaminergic cell survival within the mouse midbrain.  My role involved using programs such as Fiji to count the dopaminergic cells and determine regions of interest such as the VTA and SNc.  I also began to familiarize myself with Igor which was used for analysis of our cell count totals and create figures to present our data in a more reasonable format.  Those figures were then included in my presentation at the 39th Annual Biological Sciences Undergraduate Research Symposium.  I valued this opportunity greatly as I gained more experience in presenting to others. 

   From my time in the lab, I have learned so much in just a short period of time.  I’ve gained a much better understanding of how research is performed and the time and effort it takes from everyone in the lab.  As I continue my journey following undergrad, I plan to take a gap year and apply for medical school.  I look forward to continuing my time in the Scimemi Lab this summer as well as other opportunities that may come about. 

Garrett

Jaci

Hello! 

My name is Jaci Yong and I am a sophomore at the University at Albany majoring in Psychology and minoring in Neuroscience. I joined Dr. Scimemi’s neuroscience research lab as a volunteer from Fall 2021 to Spring 2022. After attending one of Dr. Scimemi’s virtual seminars in the Honor’s College during my freshman year about glutamate transporters and the mechanisms that control neurotransmitter release and information transfer among neurons, I became very interested in her research and wanted to get involved with it. Later that summer, the Center for Undergraduate Research and Creative Engagement sent out an email saying that Dr. Scimemi was looking to recruit 2 undergraduate students to join her lab in Fall 2021, so I filled out an application, was interviewed, and then accepted into the lab.

As a student who was spending my first year in college learning remotely from home, I felt a bit isolated from the campus community and from research opportunities, which is a big reason why I wanted to get involved in research as soon as I was able to go to campus in-person. I had never worked in a research lab previously, so my first day touring the lab felt a bit intimidating, but I met a lot of great people in the lab who were eager to share their work with me and explain things that I was unsure about. 

In Dr. Scimemi’s research lab, I shadowed PhD student Ben Bennink for my first semester and was trained in mouse colony management and behavior analysis. I worked with the other new undergraduate student, Stephanie Fischer in running behavioral experiments with different groups of mice. Having never worked with animals in a research setting, working with mice (especially newborn mice) took some getting used to, but eventually as I worked with them more frequently and they got older, I became a lot more comfortable. Another challenge I faced was learning how to run software such as MATLAB and Igor Pro for data collection and analysis. I had very little knowledge about technology and coding before this lab, but after becoming more familiar with these programs, I have definitely learned a lot more and I am still learning more new things every day! I have applied to continue conducting behavior research in the 2022-2023 academic year under the Honors Psychology Department and I am excited to explore more aspects of neuroscience research in this lab as well!

Hasan

Hello reader!

My name is Hasan Mehdi and I am an upcoming senior at the University at Albany, pursuing a BS in Biology. I joined the Scimemi lab in the summer of my junior year and have been here ever since!
In my free time, I love playing videogames, ping pong, and basketball. I also love hiking.
Doing research at the lab has taught me a wide range of skills that I never would have imagined. Over the summer, I was taught how to care for a mice colony by Gabrielle Todd as well as genotype them using the polymerase chain reaction. I watched and performed stereotaxic brain surgeries with Patrick Wehrle and learned how to read and present research papers to the rest of the lab. During the school year, I worked with Saad Ahmad and learned the software side of neuroscience, using programs like Imaris to reconstruct confocal images of astrocytes and dendrites, and Igor to conduct density analyses and compile our raw data into figures to present in papers and posters. I also learned how to use Fiji to perform a simple neurite tracer analysis to create figures of all the neurons we analyzed and observed and conducted mouse perfusions with Saad.
Being at the lab has kept me busy. Just in the last couple weeks I presented our poster Dendritic spine morphology changes following stereotaxic injections of A𝛽42-AAV for the 39th Annual Biological Sciences Undergraduate Research Symposium and the CURCE 19th Annual Student Conference. In the future, I want to combine my love of Biology with the world of coding, in the Bioinformatics field. This summer I have been accepted to do a Bioinformatics fellowship at the RNA Institute to get some direct experience with the field.

Hasan