Much Ado About Sleep: the Importance of Getting Adequate Sleep

How was your sleep last night? Were you able to go to bed early and clock in a solid 7 to 9 hours of sleep, or were you tied up with work and had to postpone your bedtime till the draft was written and the email sent?

On average, we human beings spend 8 hours per day sleeping, which amounts to a total of one-third of our lifetime. That is, for a person who spends 75 years on earth, 25 years is spent sleeping. With such a significant amount of time spent in bed, one couldn’t help but wonder, what would happen if we just shift the bedtime later by an hour and a half, while keeping the wake-up time fixed? Surely it will not have much of an impact?

Well, turns out it will.

In a recent study published in Scientific Reports, Columbia postdoc Vikas Malik and colleagues found that for healthy females, after cutting sleep short by an hour and a half for a mere six weeks, cells that protect our blood vessels become negatively impacted. Evidence has shown that sleep restriction introduces a more pronounced risk for females than males, leading the researchers to focus solely on females for this study. With this reduction in sleep, the amount of harmful molecules (oxidants) starts to overpower that of the good molecules (antioxidants) in the cells. Since oxidants are harmful molecules which are responsible for producing the notorious “free radicals” and causing toxic effects in the body, and antioxidants good molecules responsible for detoxifying the body and repairing damages made by oxidants – this imbalance between the amount of oxidants and antioxidants will lead to impaired cell function and detrimental consequences in the form of cardiovascular diseases.

While the significance of sleep is well known, the mechanisms of how lack of sleep could impact human health has remained largely unclear. In fact, this study provides some of the first evidence demonstrating how mild chronic sleep deprivation could impact the health of our heart. In addition, contrary to previous studies that mainly examine sleep deprivation conditions in a compact time frame (e.g., acute sleep deprivation in flies for 10 days), the authors investigated how mild sleep restriction influences vascular cell health in females (i.e., pushing the bedtime 1.5 hours later than what the participants used to, while keeping the wake-up time fixed over the span of 6 weeks). Owing to a more “modern” work/life balance, the results from the authors’ experimental design carry higher relevance to our sleep patterns.

Specifically, the researchers found that after adequate sleep, the imbalance between oxidant (harmful) and antioxidant (good) molecules in the vascular cells can be cleared by a functional antioxidant response. This response is facilitated by a protein called serum response factor (SRF) – when sleep is adequate, the expression level of SRF increases to bring up the expression level of DCUN1D3, another protein which mediates antioxidant response of the cell. After sleep restriction, however, the antioxidant response cannot be turned on because the expression level of SRF is not adequate enough to activate a sequence of transcription of antioxidant genes, therefore hindering the restoration of balance between oxidant and antioxidant molecules in the cells (see illustration below).

Functional vs. impaired antioxidant response under adequate and inadequate sleep. Adequate sleep increases the expression level of SRF, which in turn increases the expression of DCUN1D3, freeing Nrf2 into the nucleus of the cell to activate the transcription of antioxidant genes, which then restores balance between oxidant and antioxidant molecules in the cells. Inadequate sleep, however, perturbs this process and interferes with the activation of antioxidant response. Figure is from the original publication.

These findings carry significant implications on how we should schedule our sleep. While deadlines will always be looming and stress will always be present, maybe we should still make the effort to defend our bedtime. After all, as Shakespeare puts it, sleep is the “balm of hurt minds, great nature’s second course, chief nourisher in life’s feast”. Perhaps, unlike Macbeth, we should all strive to sleep more.

Written by: Linbi Hong

Reviewed by: Vikas Malik, Trang Nguyen, Martina Proietti Onori, Giulia Mezzadri, and Patricia Cooney


When mitochondria get stressed, our brain suffers: Linking mitochondrial dysfunction to neurodegeneration.

Imagine It’s a Saturday morning and you decide to drive upstate for a nice hike. While on the trail, you have a too-close encounter with a too-curious bear, leaving you panting, perplexed. This acute stress response (the famous fight-or-flight response) is extremely useful for us to better react to danger. The main hormones released during a stress response, glucocorticoids (GC), help prepare our body for the adverse situation we may encounter, giving us a better chance of survival.

Chronic stress it’s not so beneficial for us. In fact, it has profound detrimental effects on our bodies, and especially in our brain. There is increasing evidence that it can make our mitochondria (the powerhouse of the cell) function poorly, which can lead to damage in our neurons. Another way chronic stress can damage the brain is by inducing accumulation of the protein Tau, which can lead to neurodegenerative diseases such as Alzheimer’s disease. Tau itself poses an interesting biological conundrum: While it is normally found in the neuron’s microtubules (the cell’s scaffolding) in a healthy setting, it can start to form clumps (i.e, oligomerize) when a neuron becomes stressed or damaged, interfering with the neuron’s basic functions such as synaptic transmission and protein transport.

Scientists are still unsure how exactly GC cause Tau to oligomerize. Furthermore, while the impact of GC in mitochondria’s fitness is pretty well studied, the mechanisms driving such dysfunction, and its downstream consequences, are still poorly understood. Overall, to the scientific community, the molecular mechanisms linking GC exposure, mitochondrial dysfunction, and Tau pathology, are still unclear.

 In a recent study published in Brain, Columbia postdocs Dr. Fang Du and Dr. Qing Yu and colleagues investigated the causal relationship between these three important components of brain health, and found that GC directly precipitate mitochondrial dysfunction and drive Tau oligomerization. In a series of elegant experiments in both mouse models (in vivo) and neurons grown in petri dishes ( in vitro),experiments, the group led by Dr. Clarissa Waites demonstrated that found the mechanism by which GC exposure drives mitochondrial dysfunction and Tau oligomerization, and even discovered a potential treatment.

Figure 1- Graphical representation of the findings by Dr Du, Dr Yu, and colleagues. During Chronic stress, Glucocorticoids induce mitochondria dysfunction by increasing its permeability, which turn promotes Tau oligomerization and neurodegeneration. Figure created with Biorender.


 First, Dr. Waites’ group established the role of chronic GC exposure in mitochondrial fitness and pathogenic Tau accumulation in vivo. Using the widely used synthetic glucocorticoid dexamethasone (DEX), they demonstrated that GC induce mitochondrial dysfunction (increased permeability and lower respiratory capacity) and oligomeric Tau accumulation. Next, Drs. Du and Yu very cleverly employed in vitro experiments to demonstrate that DEX triggered mitochondrial dysfunction by increasing mitochondrial permeability: their research showed that GC exposure stimulates the opening of the mitochondrial permeability transition pore, a big, non-discriminant, pathological hole in the mitochondrial membrane that when open, greatly compromises its function. Most importantly, they found that GC triggers opening of the pore by activating its key component, the protein cyclophilin D. This key finding led Dr. Waites’ group to block cyclophilin D activation, either genetically (i.e. changing the DNA of the protein) or using drugs, with great success: cells where cyclophilin D activation was prevented were remarkably resilient to GC stress, and showed much lower levels of mitochondrial dysfunction and pathological Tau accumulation.

 Although this was an extremely exciting result by itself, it posed a problem moving forward: neither genetical nor pharmacological inhibition of cyclophilin D are currently viable therapeutic approaches, due to their poor bio-availability or invasive methods required to deliver the treatments. So what other approach could they use to also prevent mitochondrial pore opening, while still being clinically tractable? After some digging, Drs. Du and Yu found apo-cyanin, an orally-available inhibitor of mitochondrial respiration that could tackle GC-driven brain pathology while not directly targeting cyclophilin D. In line with their predictions, this drug was able to restore mitochondrial function and prevent Tau pathology in DEX-treated cells. Most importantly, they were also able to restore neuronal health, neuronal connectivity, and prevent anxious and depressive behavior associated with GC treatment.

 All of these experiments clearly demonstrated that GC-exposure triggers mitochondrial dysfunction and Tau accumulation, which could in turn promote the development of brain pathologies. How could they demonstrate, however, that targeting mitochondrial permeability is a feasible approach to treat common brain pathologies such as Alzheimer’s disease? To tackle this question, Dr Waites’ group made use of an ingenious technique, where they replaced all mitochondria in a test cell with those coming from an Alzheimer’s disease patient. Excitingly, in this model, treatment with mito-apocynin was sufficient to partially reverse mitochondrial dysfunction and Tau oligomerization found in the cells containing mitochondria from Alzheimer’s patients.

 Dr Waites’ group story is a hallmark out-of-the-box thinking, and clinical relevance. While their research clearly highlights mitochondrial damage induced by GC and cyclophilin D activation as a key trigger of Tau accumulation, the implications of this finding could be much broader:  How generalizable is this mechanism to other forms of brain disease such as ischemia, inflammation, or aging? As a matter of fact, cyclophilin D levels are elevated in Alzheimer’s patients, and its inhibition is protective in mouse models of sclerosis, Parkinson’s, and Alzheimer’s disease.

While this story provided incredible insight into the role of mitochondria in controlling brain pathology, many other questions remain unanswered.  For example, What is the exact mechanism by which mitochondrial dysfunction promotes pathogenic Tau accumulation? It is highly likely that these two events are intertwined, and that oligomeric Tau can also drive mitochondrial dysfunction.

 Despite the still-unknowns, it is clear that after this publication from Dr Waite’s lab, we should re-contextualize our middle-school textbooks: The mitochondria is the powerhouse of the cell, and during stress, the gate-keeper of our brain’s health.

Reviewed by: Trang Nguyen, Erin Cullen 

When Numbers Play Tricks: Unraveling The Brain’s Biases

Imagine living in a dark cave, with your entire understanding of the world based on shadows on the wall. Sounds unrealistic and terrifying, right? However, this allegory presented by Plato is an apt metaphor for our brain’s perception of the real world. While we might believe we perceive reality in its entirety, our brain can only provide a shadowy representation of the variables in our environment, and our decisions are based on these shadowy representations.

A comforting thought might be that numbers are a universal language for Western countries and, specifically, for those who use Arabic numerals. For instance, when the price of a good is marked as $14, it conveys an unambiguous and specific value, meaning that one would unequivocally expect to pay exactly that amount. However, experiments show that people make mistakes when dealing with Arabic numerals. For instance, under time constraints, the closer two numbers are in value, the more challenging it becomes for us to rapidly and accurately pinpoint the larger one. These mistakes are very similar to those made in psychophysics tasks involving physical stimuli, such as comparing the length of segments or averaging the orientation of tilted lines. These results, together with neurobiological studies, suggest the existence of a representation system for numbers that is similar to how we interpret physical stimuli.

A popular idea in theoretical neuroscience is that while the brain’s computational abilities have inherent limits, leading to imprecise representations, these representations are optimal within those constraints. This theory, called “efficient coding”, suggests that our brain’s perceptions are influenced by how often these magnitudes are encountered (i.e., the prior). For example, vertical and horizontal orientations are perceived with more clarity than oblique ones, likely because they’re more common in our environment.

A recent study (, led by Columbia postdoc Arthur Prat-Carrabin and published in Nature Human Behaviour, delves into whether our brain treats numbers the same way it treats physical stimuli. In their experiment, participants were asked to determine which series of numbers, red or green, had a higher average value. For instance, as shown in Figure 1, the number 79.60 would flash in red on the computer screen, followed by 44.92 in green, and so forth. Participants were tasked with rapidly and intuitively calculating the average of the red and green numbers to determine which sequence had the greater average. To investigate how the frequency at which numbers were encountered impacts their representation, numbers were drawn from different distributions: one, in which smaller numbers were more frequent (Downward prior); another, in which all numbers had equal chances (Uniform prior); and a third, in which larger numbers were more frequent (Upward prior).

Figure 1: Example trial of the task. Participants were presented with 5 red and 5 green numbers and had to choose the color with the higher average.

To analyze the participants’ decisions, the researchers compared their answers with multiple computational models characterized by two components: first, whether or not the numbers are encoded with a bias that depends on the value of the number, and second, whether or not the imprecision (the noise) with which numbers are represented varies with the number. Their results showed that the model that best aligned with the participants’ answers had to include both components. Notably, less common numbers are fuzzier in their perception. So, when using the Downward prior, bigger numbers are encoded with more noise, while with the Upward prior, the smaller numbers are the noisiest ones.

This discovery not only supports the “efficient coding” theory, which posits that the brain encodes and represents information in the most efficient way possible, but also showcases its applicability beyond just physical perceptions. Whether we’re assessing the speed of a car, the talent of a dancer, or the sweetness of a cake, our brain might use a universal mechanism to represent these variables. This mechanism dynamically adjusts to the statistical distribution of numbers that are expected or experienced, which implies that our understanding of numbers and magnitudes isn’t static but can be influenced by our prior experiences and expectations. In the near future, we might be able to design environments that help people refine their perceptions (such as by crafting digital games to enhance the consumer’s responsiveness to certain prices), allowing them to better discern specific value ranges and improve their decision-making.

Reviewed by: Emily Hokett, Trang Nguyen, Martina Proietti Onori


What will capture your attention?

Ever wonder how your brain directs your attention to certain stimuli or events? For example, if you are walking into a crowded restaurant you will likely direct your attention to finding an empty seat or finding your friends rather than the color of the tablecloths or the number of tables and chairs in the restaurant. Our brains have to navigate and distinguish what is important in complex environments. The term “salience” is defined as a noticeable or important object that stands out from the surroundings or background. Salience processing has been studied in neuroscience and psychology in order to understand how our brains distinguish important stimuli. This phenomenon involves two general mechanisms: bottom-up processing in which sensory information can be amplified or filtered, or top-down processing which focuses on goal-directed behaviors and cognitive control. Prior research has identified areas of the brain that are involved in salience processing using functional magnetic resonance imaging (fMRI) studies. FMRI is a technique that measures brain activity by measuring minute changes in blood flow. The regions identified include the regions in the cortex: dorsal attention network (DAN), salience network (SN), sensory cortex, primary somatosensory cortex (S1), and subcortex (Figure 1). However, understanding how these regions communicate with one another in salience processing is still unknown. In addition to these cortical networks, the locus coeruleus (LC), which is the primary source of the neurotransmitter norepinephrine (NE) and located in the brain stem (Figure 1), is also associated with salience processing. 

Figure 1. Cortical and non-cortical regions of the brain involved in salience processing.

Researchers commonly use MRI or FMRI (functional magnetic resonance imaging) as a technique to detect active areas of the brain while performing an activity. This is complemented with EEG (electroencephalogram) scans to measure electrical activity in the brain while performing different tasks.  One of the widely used experimental designs to evaluate salience processing includes the oddball task. For these experiments, subjects are instructed to detect infrequent target stimuli (a sound of a laser gun)  in a stream of standard stimuli (standard tones). FMRI and EEG measurements were obtained to determine activation of the different areas of the brain while hearing the sound of the target laser gun as compared to hearing the consistent standard tone. Columbia postdoc Linbi Hong and colleagues in their study, published in PLOS Computational Biology on May 2023, wanted to further understand the interaction between the non-cortical, LC-NE system and the cortical networks using simultaneous recordings of pupillometry which measures changes in pupil diameter and has been used as a marker for LC activity, electroencephalography (EEG) and fMRI in an oddball experiment. 

The study first utilized EEG-informed fMRI analysis to map the neural cascade underlying salience processing and identify the order of specific regions which are activated during the oddball task. The researchers defined areas in the brain to understand the organization of regions involved in salience processing. Next, the researchers wanted to understand the functional connectivity between the distinct cortex regions and the LC-complex (non-cortex regions) during salience processing by analyzing EEG signals at different times during the oddball experiment. It was determined that the prefrontal cortex and dorsal attention network are the main players in processing salient stimuli. 

Next, the researchers characterized the directional interactions between the functional network regions including the cortical and non-cortical regions. Specifically, they determined that non-cortical regions showed significant functional connectivity with dorsal auditory attention networks and salience networks. These results indicate that the non-cortical regions (LC network) are involved in switching between the different cortical networks during salience processing.

Overall, this study identified spatiotemporally the connectivity of different cortical regions to the non-cortical regions (LC complex) in salience processing. The study also provides insights into utilizing noninvasive pupillary response, which measures non-cortical region (LC) activity, in combination with EEG and fMRI signals, which measure cortical activity, as a valid approach to understand connectivity within the different regions in the brain. As a result, these methods could be used to determine any decline in connectivity of the cortical and non-cortical regions which can provide further understanding in neurological diseases such as Alzhiemers in which the LC network is the first region affected. Future studies from this group can provide additional input to how our brains can distinguish important information such as finding your friends in a crowded restaurant and whether this information is captured the same way in diseased conditions. So, next time you look around in a crowded restaurant, you can think, what captures your attention?

Reviewed by: Trang Nguyen, Martina Proietti Onori, Maaike Schilperoort

The Importance of Consistent Sleep for Memory Retrieval at the Neural Level

Sleep helps us remember the details of past events more clearly. When we sleep, neural mechanisms facilitate the consolidation of memories formed during the waking day. Specifically, memories are temporarily stored in a brain structure called the hippocampus. During the consolidation process, memories are replayed and integrated into long-term storage centers in the neocortex of the brain. Poor sleep impairs sleep-based memory consolidation and memory retrieval. In other words, when our sleep is fragmented, our memory is less clear. 

One way to assess the clarity of a memory is to measure neural similarity, or the overlap between patterns of neural activity.  My colleagues and I presented participants with a series of word pairs to remember while we recorded their neural activity using electroencephalography. We used this task to measure neural activity when participants studied (i.e., encoded) and were tested on (i.e., retrieved) the word pairs. The overlap between their neural patterns for a given word pair at study and test is an index of neural similarity.

Interestingly, we found that sleep quality was associated with neural activity for word pairs that were paired differently. When people had more consistent sleep quality from night-to-night (measured with wrist-worn monitors), they had greater neural similarity when they correctly rejected word pairs that were paired differently. For example, if they saw the pair “wing – clock” during the study period and correctly identified “fork – clock” as a different pairing at test, they demonstrated higher neural similarity. 

There were several strengths of the study. We used an objective measure of sleep quality — wrist-worn monitors. We also measured sleep quality for seven nights, which allows for assessing night-to-night sleep variations. Our participants were racially and ethnically diverse people across the adult lifespan. However, our study was limited by its small, convenience-based sample of participants (74 people) and cross-sectional design. We cannot determine if poorer sleep causes lower neural similarity with this data. 

Taken together, our study suggests that memory integrity, or the ability to clearly remember the details of past events, may be linked with consistent sleep patterns. Thus, in addition to sleeping for enough time, sleep consistency also contributes to better memory retrieval. 

Edited by: Trang Nguyen, Pei-Yin Shih

How a molecular structure explains the transport of fatty acids past the blood-brain barrier

The brain and eyes develop through constant circulation of nutrients through the blood-brain and blood-retina barriers. One such nutrient that is essential for development is an omega-3 fatty acid called docosahexaenoic acid (DHA). DHA makes up a fifth of all the fatty acids required on the membranes of cells in the central nervous system. Neither the neurons in the brain nor the cells in the eye are capable of synthesizing DHA by themselves and therefore depend on dietary sources for DNA. Previously, scientists knew from cellular clues that this fatty acid most likely passed through to the blood-brain and blood-retina barriers in the form of lysophophatidylcholine (LPC-DHA) using a molecular channel. This transporter is known as a major facilitator superfamily domain containing 2A, or MFSD2A, with the help of sodium atoms regulating the channel. However, it was not clear how this channel allowed the passing of complex molecules like DHA. A recent study by Dr. Rosemary Cater and colleagues at Columbia University provided precise clues to further show the structure of this channel. 

To investigate the structure of MFSD2A, the authors used a state of the art imaging technique called single-particle cryo-electron microscopy. This is a method of electron microscopy where a beam of electrons is transmitted through a rapidly frozen purified molecule. Because the sample is flash frozen, the molecules trapped in a frozen state can be imaged in their native shape as present in the cell and from multiple angles. By capturing and combining multiple captured 2D images, a 3D structure of the protein can be reconstructed with extreme accuracy. Cryo-electron microscopy is so impactful in biological significance that this method was awarded the 2017 Nobel Prize in Chemistry. found a number of molecular patterns and arrangements of protein chains that make up a full molecule of MFSD2A

Protein structure studies are typically among the most challenging grounds to explore in biology because proteins need to be captured in their native state as present in the cell. Past discoveries of various protein structures have been so instrumental in shaping therapeutic areas that the extent of mechanistic understanding of biological molecules has resulted in recognition by Nobel committees. Most recently, the discovery of the structure of the ribosome opened up fields of exploration into therapeutic interventions into ribosome diseases, some of which can lead to cancer.

To get the best chance at imaging the structure of MFSD2A, the scientists extracted and examined purified versions of this protein obtained from multiple organisms: the zebrafish, the frog, European cattle, the domestic dog, the red junglefowl, mice and humans. Finally, the authors found that the protein obtained from the red junglefowl, which is a rooster species that originates from Southeast Asia, was the most experimentally stable and most alike (73% identity) the human version of MFSD2A. 

Using additional accessory proteins to help with the orientation of MFSD2A, the authors obtained high-quality images, with a resolution of 0.3 nanometer, or 0.3 billionth of a meter. From the imaging data, the authors found that MFSD2A protein itself is about 5 nm wide and 8 nm long. MFSD2A is a transporter protein and like many transporters, it contains repeated bundles of helices made of protein chains that traverse the cell membrane and are connected by a protein chain that loops within the space in the cell. 

Structure of MFSD2A arranged as protein helices (colored cylinders) within the cell membrane along with protein loops that form both in the extracellular space (“Out”) and within the interior, cytoplasmic space (“In”) of the cell. The cytoplasmic loops likely have an important functional role. Figure from Cater et al, 2021.

The cell membrane consists of two layers of lipid molecules, known as the lipid bilayer, that allow entry and exit of materials from the cell. These loops provide the shape to the protein inside the cell such that it appears to provide a large enough cavity opening from the lipid bilayer into the cellular space to allow the target molecules to enter the cell. Amino acids are the building blocks of proteins and the cavity contains amino acids of both water-attracting and water-repelling kind. This property makes it possible for many molecules of differing chemical nature to be able to be accommodated within the cavity. This cavity contains three important regions that allow for the protein to be specific and functional: a charged region, a binding site for sodium atoms and a lipid-specific pocket. The authors speculate that these parts help in establishing the mechanism by which LPC-DHA is transported from the outside into the cell. The multiple protein helices form two protein domains that capture LPC-DHA from outside the cell layer of the blood brain barrier of endothelial cells, then rock over a rotation axis so that now their confirmation switches and finally, they release the protein molecule into the cell. For this activity of movement of LPC-DHA, sodium atoms are absolutely required to allow for the shape change of the protein. Once LPC-DHA enters the barrier cells in this manner, the protein is then transported across to the other side of the cell facing the brain containing neurons. 

The transporter channel MFSD2A changes its shape once it binds sodium atoms in the extracellular space, which helps the transport of LPC-DHA from the blood into the brain space through the barrier of a single line of cells made up of endothelial cells. Figure adapted from Cater et al, 2021.

Humans with mutations in MFSD2A gene have abnormal brain defects such as microcephaly, and disruption of the gene in mice affected neuronal branching and fatty acid composition in the brain. The discovery of the structure of a molecule that mediates uptake of essential nutrients across the blood-brain and eye-brain barriers will help in the delivery of therapies of neurological diseases.

Dr. Rosemary J. Cater is a postdoctoral researcher in the lab of Dr. Filippo Mancia in the Department of Physiology and Cellular Biophysics at Columbia University.

Newborn octopus neurons steadily march towards maturity from around the eyes into the brain

Anyone who watched the movie Arrival would not miss the conspicuous resemblance of the alien Heptapods to some of our own earthly beings – the octopuses. While serving as inspiration for alien creatures in movies, as clairvoyants in soccer World Cup or as savages in classic science fiction and mythology, cephalopods like octopuses and squids have been dubbed as one of the most intelligent creatures on the planet. There is a good reason for why cephalopods, particularly octopuses, have developed such a reputation. Octopuses have a striking organization of brain structure, different from that of any other studied organism. They have the largest nervous system among animals lacking a backbone, comprising a total of nine “brains”. Out of these, one is a major donut-shaped brain that contains ~200 million neurons surrounding the octopus’s food pipe, which is strangely located in the head! This brain communicates behavioral intricacies to the eight so-called mini-brains located within the arms, each containing ~40 million neurons. The central brain is responsible for executing complex behaviors like tool use, ability to plan for the future, shape-shift, camouflage, recognize individuals and solve complex puzzles. While the last common ancestor between octopuses and humans was about 680 million years ago, a recent surprising discovery showed that they both evolved to use the same molecules during development. Scientists discovered that genes that produced the camera-like eye in humans are the same ones that gave rise to the camera-like eye in octopuses. What’s more, these cephalopods have evolved complex brains that show behavioral innovation on par with a small primate.

Comparison between the number of neurons present in the octopus and human brains. The octopus has one major brain and eight “mini-brains” while humans have neurons in the head and the spinal cord.

Despite the potential that the octopus provides for understanding developmental biology, particularly the brain, the molecules that dictate how the mollusk’s brain is built are unknown. The common octopus, Octopus vulgaris, is specifically suited to address this question because it can produce thousands of small and transparent eggs in a single batch and scientists have recently mapped out most of its genes. Using O. vulgaris in studies led by Dr. Astrid Deryckere from Dr. Eve Seuntjens’s lab at KU Leuven in Belgium, the group set out to unravel these molecular mysteries. “If you would think of cephalopods as the primates of the sea, that have evolved a complex nervous system from a far more simple ancestral nervous system, surprisingly little is understood on the morphological and molecular mechanisms driving its development.”, said Dr. Deryckere. They approached the problem in two studies. In the first study, she established a system for controlled embryonic development, which enabled her to care for thousands of eggs without the need for the mother octopus. She used state of the art microscopy and recorded high-resolution images of octopus development from fertilization through hatching. This work from Dr. Deryckere and colleagues can now be used as an elaborate reference for cephalopod embryology. 

O. vulgaris hatchling imaged in 3D at high resolution after labelling DNA (cyan). The same embryo was imaged from different orientations: back view (left), side view (middle) and front view (right). The head is located on top and the arms are at the bottom. Images were produced by Dr. Astrid Deryckere in the lab of Dr. Eve Seuntjens, KU Leuven, Belgium.

In the second study, Dr. Deryckere dug deep into the origins of the octopus brain. She used precise staging to track the precursor cells of neurons, or “neuronal progenitors”, that generate specialized neurons. Intriguingly, these progenitor cells appeared in structures called the lateral lips, that are unrelated to the brain and are located around the eyes. So, it appeared that neurons were first born in these structures and eventually migrated into the central brain – a possibility that prompted the authors to investigate further. They found that hundreds of thousands of neurons were created within octopus embryos even before hatching. To find out what genes are required for this unique way of making neurons, Dr. Deryckere used molecular markers and showed for the first time that newborn neurons travel long-distances to reach their final location in the brain. The results showed that the genes were expressed in the same order that vertebrates like humans do. By closely observing entire embryos in three dimensions during their growth, she found that neurons proceed through maturation while migrating from the lateral lips to an intermediate transition zone that finally leads to the brain. 

Schematic of O. vulgaris embryo, indicating the location of the lateral lip in relation to the food pipe and the eye. Schematic adapted from images in Deryckere et al., 2021.

Using detailed molecular studies, the scientists now show support for the lateral lips harboring newly dividing neuronal cells in the embryo. This is unusual because unlike in human brains and many other organisms, the dividing cells are located outside the central brain. These dividing cells then unwaveringly make their way towards the final destination to maturity in the octopus central brain. “The migration is especially exceptional for invertebrates where neurons usually migrate only a few cell lengths”, noted Dr. Deryckere about the rarity of the observation.

This unique development in the octopus head and its interesting age-dependent arrangement of dividing cells and mature neurons only inspires further reverence for the cephalopod. While it continues to influence characters in pop culture, the glorious octopus and its brain hold even more promise in the real world. The octopus brain’s cognitive ability has galvanized a new age of artificial intelligence, leading to the construction of flexible robotics and prosthetics, but at the same time, is pushing scientists and philosophers to tackle the important question of how an intelligent life form is defined.

Dr. Astrid Deryckere is currently a postdoc in the lab of Maria Tosches in the Department of Biological Sciences at Columbia University. Her focus remains on brain development but she has transitioned to working on an animal with a backbone – the salamander.

New Technology allowing gene switch to study multiple sclerosis

Our genetic blueprint consists of thousands of genes (more than 30,000) with new genes being discovered and added to the growing list. Our genes provide DNA instructions to the protein-making machinery in our bodies. These instructions can influence our health and dictate if we will get debilitating diseases. Have you ever wondered how scientists unlock which genes are responsible for what? For example, does gene A control our hair colour or gene B dictates if we will develop an autoimmune disease such as multiple sclerosis? The answer lies in DNA recombination technology which allows scientists to delete, invert or replace DNA instructions. The technology called Cre-lox recombination relies on the use of an enzyme called Cre recombinase which can bind, cut and recombine DNA at specific sites that are inserted in pairs in the DNA. The Cre-binding site in DNA is called the LoxP sequence that consists of 34 nucleotides DNA sequence made up of two inverted repeats separated by a spacer.  Cre enzymes can recognize these LoxP sequences and edit the stretch of DNA resulting in gene deletion or inversion.

In a recent research article, Dr. Olaya Fernandez Gayol and colleagues use an advanced version of Cre-lox technology called DIO (Double Floxed Inverted Open reading frame) to understand the role of the Interleukin-6 (IL-6) gene in multiple sclerosis (MS). MS is a chronic disease of the brain and spinal cord in which our immune system eats away the myelin sheath around nerves disrupting the communication between the brain and the body. IL-6 is a proinflammatory cytokine known to promote MS. Gayol et al use an experimental mouse model of MS which acutely develops brain inflammation called encephalitis (Encephalo- “the brain” + itis “inflammation”) within 3 weeks of disease induction. This mouse is referred to as EAE (Experimental Acute Encephalomyelitis) which closely mimics human MS disease.  

Scientists have conventionally studied the role of IL6 in EAE mice by irreversibly deleting the IL6 gene in one cell type. However, the results were confounding due to the compensatory expression of IL6 from other cell types. Gayol et al circumvent this problem by wiping out IL6 from all the cells and then recover IL-6 expression specifically in the microglial cells. It is akin to entering a dark room and turning ON a light switch at one corner of the room to clearly see what’s lying there. 

Figure 1.  Cartoon depicting the genetic strategy used by Goyal et al to recover IL6 gene expression exclusively in microglial cells in the mouse brain. Created with

Olaya and the team use the cutting edge DIO method to wipe out IL6 and introduce the inverted form of the IL6 gene which makes this gene non-functional (Figure 1A). This inverted form of the IL6 gene does not produce IL-6 protein and mice carrying the inverted IL-6 gene (referred to as IL6-DIO-KO) are healthy (Figure 1A). As shown in figure 1B, Cre mediated recombination flips the IL6 gene in the correct orientation to make it active. The IL6 gene flipping occurs exclusively in the microglial cells and only upon treatment of mice with tamoxifen (TAM) drug. Mice in which IL-6 expression is active (referred to as IL6-DIO-ON) develop EAE disease (Figure 1B).

The team carefully optimized the duration of tamoxifen treatment in mice. Just 5 days of TAM did not flip the IL6 gene, so they extended the drug treatment to 11 days and found the IL6 gene turned on in all IL6-DIO-ON mice. Olaya says it is important to validate when creating new mouse models. “We used EAE to validate the mouse because it was a model readily available in our lab and IL6KO [deficient] mice happen to be completely resistant to the disease.” Their interesting finding that IL6-DIO-ON with IL6 gene active exclusively in microglia indicate that IL6 made in the brain promotes disease in the EAE mouse model. 

As compared to more traditional methods of generating gene mutation which requires extensive mice breedings or continuous drug treatment, the strategy presented by Olaya and colleagues is labour and cost-effective. Their findings showed that in the absence of IL-6, EAE disease does not develop in mice. On the other hand, turning on the IL-6 gene (like a gene-switch) using DIO technology, mice develop the disease.  Overall, this technology is highly customizable to understand the role of different genes in specific cell types in the disease context. It paves the way to gain a deeper insight and more thorough analysis of different molecular blocks involved in disease.


Dr. Olaya Fernandez Gayol is a postdoctoral research scientist in the Department of Pediatrics and co-president of Columbia University Postdoc Society(CUPS).  She also manages the CUPS Press office that provides postdocs with a platform to publicize their science while improving their science communication skills. 

Follow this blog

Get every new post delivered right to your inbox.