What we don't know about dreams

I had the good luck to attend a class where Dr. Gabriela Torres spoke about her research on dreaming and what happens in the human brain during dreams. Due to my interest in this subject, I have made the decision to learn more about it and present my findings today. Because dreams could only be researched after awakening, which I believe is fantastic, dream science was unreliable and incomplete for most of history. Dr. Torre's research and other studies, however, are changing this by showing that dreams are not closed off experiences but rather measurable and, more significantly, interactive brain states. 

Before speaking in my Neuro 300 seminar class, Dr. Torres presented a study that shows how REM sleepers can use eye movements or facial muscle signals to receive questions and answers in real time. This implies that while completely asleep, the dream brain is capable of understanding speech, carrying out mental tasks, and purposefully responding. Their research demonstrates that dream cognition is more complex as well as well-organized and connected to reality than previously thought. 

I became interested in this because, when doing my own research, I found that a supplementary study by Horikawa, Tamaki, Miyawaki, and Kamitani (2013) further supports this. They used fMRI and machine-learning models to directly translate the visual content of dreams from brain activity. Because the same visual regions that are active during waking perception also become active during dream imagery, researchers were able to predict what patients were dreaming before they woke up. This shows that the brain's neuronal architecture for dream imagery is the same as that of real perception. 

When taken as a whole, these investigations offer a convincing conclusion, which is that dreams are not personal hallucinations but rather readable and interactive in cognitive states. While Konkoly (in the study, Dr. Torres presented) showed that dreamers can communicate openly, Horikawa, Tamaki, Miyawaki, and Kamitani (2013) (in the study I found) showed that researchers can analyze dream material inwardly. These findings support the idea that consciousness is not an "on and off" switch but rather a fluid spectrum, with elements of waking perception, memory, and reasoning staying partially active even during REM sleep. This new science may be used to treat PTSD and nightmares, as well as to enhance creativity, memory, and emotional processing while you sleep. Together, these investigations reveal a link between neurological interpretation and discourse, transforming dreams from a mysterious internal experience into a measurable and reachable part of human thought. 

 

APA Citations  

Horikawa, T., Tamaki, M., Miyawaki, Y., & Kamitani, Y. (2013). Neural decoding of visual imagery during sleep. Science, 340(6132), 639–642..https://pubmed.ncbi.nlm.nih.gov/23558170/ 

Konkoly, K. R., Appel, K., Chabani, E., Mangiaruga, A., Gott, J., Mallett, R., Caughran, B., Witkowski, S., Whitmore, N. W., Mazurek, C. Y., Berent, J. B., Weber, F. D., Türker, B., Leu-Semenescu, S., Maranci, J.-B., Pipa, G., Arnulf, I., Oudiette, D., Dresler, M., & Paller, K. A. (2021). Real-time dialogue between experimenters and dreamers during REM sleep. Current Biology, 31(7), 1417–1427.e6. 

Temperature as a Universal Regulator of Sleep

    Humans spend around one-third of their life sleeping. Sleep plays a huge role in memory consolidation, waste removal, cellular repair, and much more. Poor quality sleep is associated with problems such as dementia and CVD. Even with sleep playing such a big role in our lives, most of us neglect sleep, getting about 3 and a half ultradian sleep cycles or even less. Sleep is heavily regulated by many factors, with temperature being one of the biggest factors. In order for humans to fall asleep, their core temperature must drop by 1–3 °F. The timing of sleep is controlled by a circadian clock, the suprachiasmatic nucleus (SCN) in humans, and lateral posterior clock neurons (LPNs) in Drosophila. These structures are strongly influenced by temperature, and as they receive temperature information, they release signals that regulate sleep.

    Daniel J. Cavanaugh’s paper, “The cell-intrinsic circadian clock is dispensable for lateral posterior clock neuron regulation of Drosophila rest-activity rhythms,” written by Charlene Y.P. Guerrero et al., examines the role of LPNs in Drosophila circadian and sleep regulation. LPNs receive input from thermosensory pathways, which is essential for circadian rhythm regulation. Guerrero reports that reduced LPN excitability causes a slight reduction in sleep. However, when LPNs are silenced using CRISPR, total sleep is reduced, sleep becomes fragmented, and sleep bouts become shorter. Researchers then used CRISPR to delete clock genes (per and tim) inside LPNs, which normally create a 24-hour cycle acting as an internal clock. The flies with their LPN clock genes deleted still received timing information from other clock neurons with functional per and tim cycles, maintaining a normal 24-hour rhythm. This shows that LPNs do not set their own time but instead receive timing from other structures, functioning as driven oscillators. Guerrero’s article demonstrates that LPNs are important for regulating sleep but do not require their own internal clocks. This knowledge may lead to therapeutic strategies for circadian rhythm disorders.

    In a study by Roy J. E. M. Raymann et al. titled “Skin deep: enhanced sleep depth by cutaneous temperature manipulation,” Raymann discusses how skin temperature controls sleep quality in humans. Small increases in skin temperature have significant effects on sleep. Raymann et al. argue that adjusting the thermostat in a room has limited impact on sleep, while manipulating skin temperature has powerful effects. Previous experiments show that even a 0.4–1.0°C increase in skin temperature affects sleep. Researchers used slight skin warming and adjustments to the bedding microclimate to observe how it influenced sleep. They recorded sleep onset time, deep sleep duration, interruptions, and comfort. Participants also slept in cool and hot rooms to test whether air temperature made a difference. Results showed that in hot rooms, deep sleep decreased, wakefulness increased, and overall sleep quality worsened. When skin temperature was raised independently of room temperature, results changed dramatically: participants fell asleep faster, experienced more deep sleep, and had overall more restorative sleep. The study concludes that skin temperature plays a larger role in sleep quality than room temperature.

    Together, these findings show that temperature plays a major role in regulating sleep. In Drosophila, LPNs integrate thermosensory information to regulate sleep even without their own internal clocks. In humans, manipulation of skin temperature affects sleep more strongly than room temperature. Both articles highlight that sleep systems depend heavily on how the brain interprets thermal information. As research in this field continues, new strategies and treatments for sleep and circadian rhythm disorders may emerge.

References

1.) Guerrero, C. Y. P., Lam, V. H., Cusumano, P., Van Doren, M., & Cavanaugh, D. J. (2025). The cell-intrinsic circadian clock is dispensable for lateral posterior clock neuron regulation of Drosophila rest–activity rhythms. Neurobiology of Sleep and Circadian Rhythms. https://doi.org/10.1016/j.nbscr.2025.100198

2.) Raymann, R. J. E. M., Swaab, D. F., & Van Someren, E. J. W. (2008). Skin deep: Enhanced sleep depth by cutaneous temperature manipulation. Brain, 131(2), 500–513. https://doi.org/10.1093/brain/awm315

Network-based Timekeeping in Humans and Flies

    The circadian rhythm is responsible for organizing countless physiological and behavioral processes across many species. During his talk Dan Cavanaugh emphasized that circadian rhythms are not controlled by just one singular cell, but instead, it comes from the activity of many coordinated neurons working together. In his paper “The cell-intrinsic circadian clock is dispensable for lateral posterior clock neuron regulation of Drosophila rest-activity rhythms” (Cavanaugh et al., 2025), demonstrated this network-based idea in what I found a really surprising way: some neurons that participate in circadian timing don’t actually need their individual molecular clocks to regulate daily behavior. This challenged the common assumption that every clock neuron must keep track of time within themselves. 

In  Drosophila (flies), about 240 clock neurons form a network that coordinates daily patterns of activity. Cavanaugh focused on a subset called the lateral posterior neurons (LPNs). These neurons were thought to rely on their own intrinsic molecular clocks to support circadian behavior. However, by genetically disrupting the molecular clock only within LPNs, Cavanaugh et al. found that transitions, and rest-activity structure remained despite the absence of an intrinsic clock in these cells. The reason is that the LPNs receive timing cues from other clock  neurons, they don’t just function alone. But when Cavanaugh silenced the LPN completely using neuronal inhibition, the flies’ circadian rhythms weakened significantly. This shows that communication within the network is more essential than each neuron having its own cycle (Cavanaugh et al., 2025). 

This network-based view of circadian timing is similar in human neuroscience. In his article from 2025, “Brain circadian clocks timing the 24 hour rhythm of behavior,” Mendoza reviews recent research showing that human circadian rhythms also comes from suprachiasmatic nucleus (SCN) which is traditionally described as the “master peacemaker,” Mendoza explains that many other brain regions, including the hypothalamus, brainstem, and cortex, contain their own molecular clocks that interact with one another. These regions communicate through hormonal, metabolic, and neural pathways to generate a stable 24 hour rhythm (Mendoza, 2025). Just like the flies, coordination among nodes is seen to be more important than perfecting timing within every individual node.

What makes the two papers connect so well is their combined message that circadian rhythms are at their core network phenomena. Cavanaugh’s LPN study illustrates this idea on a cellular level that shows some neurons can lose their intrinsic clock without disrupting behavior because the rest of the network carries them. Mendoza’s review expands on this concept just on a larger scale–the human brain. This highlighted that the circadian stability depends on synchrony and communication, not isolated oscillators. When that communication fails in these systems, and rhythms break down, whether that is in a small fly or across the human brain.

The broader message of these findings are the most important. Understanding the circadian system as a distributed network helps explain why sleep and activity rhythms usually hold up to cellular-level distributions, but are still extremely sensitive to metabolic disorders. Both papers emphasize that future research should look into going beyond singular cells or singular genes and rather look into how circadian information is transmitted, integrated and lined up across the system. 

Together, Cavanaugh’s seminar and the research papers discussed in this post reinforce and back up the idea that biological timing isn’t focused on having perfect clocks in all individual neurons but it's more so about how those neurons can communicate with one another. Whether it's in flies or humans the brain is able to keep timing via the collaborative activity of the neurons. 

References

Cavanaugh, D. J., Guerrero, C. Y. P., Cusick, M. R., Samaras, A. J., & Shamon, N. S. (2025). The cell-intrinsic circadian clock is dispensable for lateral posterior clock neuron regulation of Drosophila rest-activity rhythms. Neurobiology of Sleep and Circadian Rhythms, 18, 100124. https://doi.org/10.1016/j.nbscr.2025.100124 

Mendoza, J. (2025). Brain circadian clocks timing the 24 h rhythms of behavior. NPJ Biological Timing & Sleep, 2(1). https://www.nature.com/articles/s44323-025-00030-8 

How Oxyphor 2P Is Transforming Deep-Tissue Oxygen Imaging

Understanding how oxygen is delivered and used in the brain is essential for uncovering the mechanisms behind stroke, dementia, traumatic brain injury, and many other neurological conditions. Yet measuring oxygen levels deep within living tissue has historically been extremely challenging. Traditional imaging tools either can’t reach deep enough, damage tissue during delivery, or are too slow to capture rapid physiological changes.

A new research breakthrough, Oxyphor 2P, a high-performance oxygen-sensing probe, may finally change that. Developed by Esipova, Barrett, Erlebach, Masunov, Weber, and Vinogradov, this innovative phosphorescent probe represents a major step forward in neuroscience and biomedical imaging. Their findings demonstrate that Oxyphor 2P makes oxygen imaging deeper, faster, and more stable than previously possible, opening the door to new insights into brain function and disease.

The authors introduce Oxyphor 2P as a high-performance phosphorescent probe designed specifically for measuring oxygen in biological systems. Unlike earlier probes, Oxyphor 2P is optimized for two-photon phosphorescence lifetime microscopy, a technique that allows scientists to visualize oxygen levels deep inside tissue using minimally invasive infrared light.

The researchers report several major advancements including two-photon imaging up to 600 micrometers deep, imaging speeds nearly 60 times faster than previous methods, delivery method that avoids local tissue damage, and reliable multi-day longitudinal oxygen measurements. These innovations make Oxyphor 2P one of the most promising tools for studying oxygen dynamics in living brains.

Oxygen is the primary fuel of the brain. Even slight disruptions can influence cognition and behavior and may contribute to conditions such as stroke, Alzheimer’s disease, Parkinson’s disease, and age-related cognitive decline. Historically, limited imaging tools have prevented scientists from monitoring oxygen levels at depth or over extended periods.

With Oxyphor 2P, researchers can achieve a multitude of things, including, observing oxygen levels across deeper cortical layers, tracking how oxygen changes during neural activity, studying chronic vascular and metabolic changes after injury, monitoring oxygen dynamics over days instead of minutes, and investigating early biomarkers of neurological disorders. The ability to perform multi-day, deep-tissue imaging without damaging the brain allows for more accurate and biologically realistic studies.

At a recent Loyola Neuroscience seminar, Dr. Tatiana V. Esipova, one of the lead authors of the Oxyphor 2P study, shared her experiences and scientific goals behind developing this probe. Dr. Esipova is a faculty member in the Department of Chemistry and Biochemistry at Loyola University Chicago, where she is now an Associate Professor. Her career has included research positions at the University of Pennsylvania and EPFL in Switzerland, building deep expertise in chemical probe design and biophysics.

During the seminar, Dr. Esipova emphasized the importance of designing oxygen probes that can reach deep brain layers without disrupting normal tissue architecture. She also highlighted how long-term tracking of oxygen levels can help researchers understand how the brain adjusts during learning, recovery, injury, and disease progression. Her work demonstrates how chemistry and neuroscience can intersect to create transformative tools.

The development of Oxyphor 2P shows how advancements in chemical probe design can reshape what neuroscientists are capable of studying. Just as multi-ancestry genetics has expanded our understanding of Parkinson’s disease, advanced oxygen imaging tools have the potential to unlock new insights into brain health.

Oxyphor 2P represents a major leap forward in deep-tissue oxygen imaging. With deeper penetration, faster imaging speeds, and multi-day stability, this probe allows researchers to view the brain’s oxygen landscape with an unprecedented level of detail. The work of Dr. Esipova and her collaborators highlights how innovation at the intersection of chemistry and neuroscience can drive meaningful progress in understanding human health and disease.

References

Esipova, T. V., Barrett, M. J. P., Erlebach, E., Masunov, A. E., Weber, B., & Vinogradov, S. A. (2024). Oxyphor 2P: A high-performance probe for deep-tissue longitudinal oxygen imaging. Cell Reports Methods.

Vinogradov, S. A., Wilson, D. F., & Lebedev, A. Y. (2020). Phosphorescent probes for oxygen imaging in vivo: Principles and applications. Progress in Molecular Biology and Translational Science.

Weber, B., & Helmchen, F. (2019). Imaging oxygen in the brain: Methods and applications. Annual Review of Neuroscience.

The language that goes unnoticed. Gestures: the way we learn

Just like before, in our Neuro Seminar at Loyola University, we welcome guest speakers to talk about their research/ findings that can inform us on the current area of study in the neuroscience field and that may inspire us to investigate in our future work/career. One of the guest speakers’ works I found intriguing was Sarah Delmar’s research on the ability to learn from just the gestures of hands. The title of the experiment is, “How our hands help us learn” by two researchers who evaluated this study at the University of Chicago, Chicago, Il.

Many questions begin to drive the purpose of this experiment, and it begins with, whether gestures, the way we move our hands reflect our thinking process?  And this experiment explains that instead of reflecting what we think, it is how we think. Gestures are the hidden language that our body shows, when we are ready to learn, it is also the most reciprocated language. It is a form of gesture mismatch and gesture match, that explains the capability of one’s ability to learn. In this experiment it reveals that the way we move our hands when we speak is to help our brain in the memory and learning process. This body language helps us form a recall or interleaving way that makes room in our brain that helps us take in more information all at once. It is an easier tool to teach with than words can. This experiment shows this example through teachers, teaching math problems, and through this experiment they found that when teachers focused on how the students picked up the topic with the gesture of their hand, the way the teacher went about in relaying the topic again so the student understood was based on those gestures. This experiment can improve the ways of teaching in future schools and through books. It is a possibility that students with learning disabilities aren’t struggling because they don’t understand, it is probably the wrong language.

Furthermore, to relate this to similar research that focus on learning abilities that are shown through gestures, it is called “Do Toddlers Learning to Spoon-Feed Seek Different Information From Caregivers’ Hands & Faces?” by 2 researchers at Kobe University. This experiment doesn’t explicitly speak on the importance of gestures but instead explains it through an experiment between a toddler and its provider during feeding time. During this session the experimenters took the time to evaluate how does a toddler learns to feed themselves, is it through speech or how the provider feeds herself through movement. And what they realized is that the toddler's focus was on the hands of the provider instead of instructions that she was stating. The provider wasn’t aware of it herself, but since she may have possibly learned to feed herself in a sort of step it is now being passed down into the toddler and so on. This experiment embarks on the difference of communication, and that every language is heard, explicitly or implicitly. Gestures aren’t the focus when teaching, but are the main focus, and famously reciprocated. 

To relate both experiments is the importance of gestures and that with each movement shows an action of learning and translation. The first experiment takes the time to evaluate the importance of it, and how gestures are usually ignored when teaching or talking, but aren’t ignored by visual learning. The 2 experiments are an example of how gestures go unnoticed by the teacher but are the prime source of learning for the student. These two experiments further helps us realize that the brain picks up on every detail of the environment, and that it explains the process of learning and the status of knowledge the student has. The brain continues to teach itself in many ways to guide the host in life, through perception and sensation, which continues to question the conscious being.

 

 

References

 

Nonaka, T. and Stoffregen, T.A. (2021) Do toddlers learning to spoon-feed seek different information from caregivers’ hands & faces?, Neuroscience News. Available at: https://neurosciencenews.com/toddler-feeding-hand-face-17519/.

Susan, G.-M. and Susan, W.M. (2005) How our hands help us learn | ScienceDirect , Trends in cognitive sciences. Available at: https://pubmed.ncbi.nlm.nih.gov/15866150/.

REM Sleep: Opening The Doors To Our Minds

REM Sleep: Opening The Doors To Our Minds 

Within my neuroscience seminar week 12, we had a guest speaker, Dr. Grabriela Torres-Platas, who gave a wonderful presentation on their research that they have done involving how one can benefit from something called dream yoga. Basically, they gathered a group of 20 participants who specialize and are vastly knowledgeable about how when in REM sleep  (is a state where you are asleep but still conscious, visibly seen with rapid eye movement)  to activate lucid dreaming (when you're able to control your dreams, defying natural law) and had them partake in different sleep experiments. When training for this previously, the participants learned different cues that indicated when they were lucid dreaming and when they were done and have completed the task that was set for them. These challenges were ones that involved walking through solid objects and flying in their dreams. In doing this it helped increase cognitive flexibility. There was also test and data that was collected form this that showed that sleep yoga improved memory and other health outcomes, such as a decrease in anxiety. Since sleep yoga holds so many benefits, Dr. Gabriela Torres-Platas and her team are trying to conduct more research on how to make the process of dream yoga learnable for everyone so they can obtain better health both physically and mentally. This all would not have happened if we had not analyse lucid dreaming which only takes place during REM sleep. This left me wondering what other amazing advances neuroscience has made analyzing more that can happen in this dreaming state. 

In an article that I had found,”Memory deficits link trait-like EEG spectral profiles during REM and slow-wave sleep with shared symptoms of depression and anxiety, published November 2025, they conducted an experiment to see if certain memories not being processed in a healthy way can lead to depression and anxiety. To test and see if this is in fact linked to one another they conducted a rest with 149 participants who did not have a history of sleep disorders and mental health disorders and had them partake in memory learning before sleeping. In the memory learning step the participants looked at images of 32 negative scenes (images that were upsetting)  and 32 natural scenes (images that had neutral emotion) in a random slideshow and tracked the thumb positioning of the participants that told the researchers what emotion they felt when shown each image. Participants then slept in the lab wearing EEG caps that recorded what is happening during REM sleep (when the brain is very active) and slow wave sleep (when the brain is in a deep state of sleep and memories are restored). In doing so they collected data that correlated in both of these sleep stages.  Then after they slept and it was 12 hours they conducted a recognition test that tested whether the images they were shown again were new, similar, or the same.  This allowed researchers to see if depending on what was shown, they had correct recognition or created false memories of seeing different images. Then after this participants partook in a survey that asked about if they had anxiety, stress/ negative emotions, and depression symptoms to allow this to be linked to the overall data, In the end when all of this was put together they discovered that with an increase of activity of the brain during REM sleep resulted in the participants to create false memories in regards to the negative images that were shown.  For those who had an increase of brain activity in slow wave sleep, memory recall was decreased for both negative and neutral images that were shown. To further this those whose memory was decreased for recall or created false memories did in fact score higher in terms of anxiety and depression.  In the researchers were able to show that brain activity during sleep state affects memory and mental health a lot and even more when you have experienced something negative. 

Both of these discuss two different things but in the end they both found important information on the effect that sleep has on our overall health. And something that correlates in both is the fact that they exported different sleep states, especially REM sleep. I feel like if we explore this sleep stage even more we will discover many new things and learn how that links to important functions that we never knew they could as in articles and presentations, lucid dreaming and memory processing. 

References:  

Niu, Xinran, Kristin E. G. Sanders, Dan Denis, Tony J. Cunningham, Guangjian Zhang, Elizabeth A. Kensinger, and Jessica D. Payne. 2026. “Memory Deficits Link Trait-Like EEG Spectral Profiles during REM and Slow-Wave Sleep with Shared “

https://www.sciencedirect.com/science/article/pii/S0166432825005194?ref=pdf_download&fr=RR-2&rr=9ac284126f17e811

Climate Change and Ecological Effects on Circadian Rhythm

Sleep is one of the most fundamental aspects of being alive. Despite its prevalence, the neurological underpinnings of the process behind sleep are very complex. Dr. Dan Cavanaugh gave a talk at the neuroscience seminar at Loyola University Chicago describing this process in detail, and what factors can affect it. Animals have adapted to the 24-hour rotation of the Earth to appropriately time their wake/sleep cycles. Clock cells found in the brain seem to be what are responsible for this internal clock. By recording activity levels in the fruit fly (Drosophila melanogaster), different peaks of activity were observed (Guerrero et al., 2025). When testing in light and dark (LD) vs. fully dark (DD) conditions, similar activity levels were observed, confirming the existence of this internal clock. 

One factor that is correlated with this internal clock is temperature. It is found that temperature is highly regulatory for the main clock neuron discussed by Cavanaugh, the Lateral Posterior Neuron (LPNs). They receive inputs from sensory afferent neurons and are thus activated by heat stimuli (Guerrero et al., 2025). At the end of his talk, Cavanaugh mentioned the relationship between temperature and the circadian rhythm, specifically in the Drosophila, and how this could potentially have ecological consequences. This immediately struck me, and my mind went to climate change and how that could now have potential neurological impacts on organisms. At the end of the paper provided by Cavanaugh, a majority of the future directions involved studying the effect of temperature further.

To investigate the specific issue of climate change and its potential impact on circadian rhythm further, I looked into the evolution of the circadian rhythm and thus how it could react to the increasing temperatures on Earth. It was found that there is an increasing temporal mismatch between the internal clock and environmental cues such as temperature (Jabbur & Johnson, 2022). While selective forces would cause a natural evolutionary process to take place to adapt to these unnatural temperatures, the rate at which the temperature increase is occurring makes it nearly impossible to keep up. Regardless, it will complicate the circadian cycle as specific clock genes related to photoperiods, or the length of day over the seasons, could be selected for. These changes nonetheless will not occur fast enough, leading to a mismatch between organic cycles in animals and on the Earth. The effects of this are yet to be seen, but will likely not be great. If we needed more reasons to combat climate change, look no further!

            Guerrero, C. Y. P., Cusick, M. R., Samaras, A. J., Shamon, N. S., & Cavanaugh, D. J. (2025). The cell-intrinsic circadian clock is dispensable for lateral posterior clock neuron regulation of Drosophila rest-activity rhythms. Neurobiology of Sleep and Circadian Rhythms, 18, 100124. https://doi.org/10.1016/j.nbscr.2025.100124

            Jabbur, M. L., & Johnson, C. H. (2022). Spectres of Clock Evolution: Past, Present, and Yet to Come. Frontiers in Physiology, 12. https://doi.org/10.3389/fphys.2021.815847