The key to a longer life might be in skipping that midnight snack

Have you ever caved in to the temptation of a snack in the middle of the night that manifested into a quick freezer dive to grab that ice-cream or into a series of quick taps on your food delivery app to get those udon noodles? Suffice it to say that I have been a victim to this thought one too many times. Much to my chagrin, there is an abundance of evidence that suggests that eating during restricted hours of the day or time-restricted feeding (TRF) can slow down decline of bodily functions. Limiting food intake to certain hours of daytime, even if the food is not necessarily nutritious or low in calories, can prevent ageing or even kickstart anti-aging mechanisms in mice and flies with obesity or heart disease. Because ageing was dependent on when the body takes in food, these studies hint at the role of the body’s biological clock, known as circadian rhythms, in regulating health and longevity. In an unexpected new study authored by Columbia postdoc Dr. Matt Ulgherait, flies following time-restricted feeding while also balancing it with an unlimited all-access ad libitum diet, show a significant increase in lifespan. 

By structuring 24 hour day-night periods as cycles of 12 hours of light followed by 12 hours of darkness in a temperature-controlled box, the authors tested various dietary regimens for their effects on lifespan and stumbled upon one regimen that consistently showed longer lifespan along with enhanced health in the flies. This regimen cycled between a 20-hour fast starting at mid-morning (6 hours after lights on) to a 22 hour recovery period of eating ad-libitum on repeat in young flies within 10-40 day post hatching stage of adulthood. However, flies that began this regimen after reaching older age at day 40 did not show enhanced lifespan. In comparison to flies that were allowed access to food ad-libitum on a 24 hour cycle, flies following this particular fasting-feeding regimen showed a 18% increase in female lifespan and 13% increase male lifespan in their young age. Due to the cycling schedule of unlimited food access with periods of fasting, the authors termed this regimen as intermediate time-restricted feeding (iTRF).

Previous studies have shown that caloric restriction through reduced food intake, protein restriction or inhibiting insulin-like signaling can extend lifespan. However, iTRF did not appear to limit flies from eating less and in many cases, resulted in flies eating more during times of food access compared to those in the ad libitum group. Thus, lifespan extension under iTRF did not occur because of limitation in nutrient uptake. Interestingly, an iTRF regimen performed under additional treatments of either dietary protein restriction or inhibited insulin-like signaling, resulted in a marked boost in lifespan compared to iTRF alone. It therefore seems that  independent mechanisms that  can enhance lifespan can be combined to increase lifespan even more. 

While these methods provide ways to extend lifespan through incremental means, some might argue that it would be meaningless to simply survive without long-lasting health benefits. To examine whether the longer-lived flies continued to exhibit youth, scientists measured the fitness of the flies using two well-known age-related tests: the flies’ ability to climb up the plastic vial they are in and how much they accumulate in their tissues aggregates of aging proteins – polyubiquitin and p62. When compared to the ad libitum group, iTRF flies climbed much faster and had fewer polyubiquitin and p62 aggregates in the flight muscles, even after they reached an age beyond 40 days of hatching. While the gut microbiome was shown to dictate proclivity for disease and thus have an effect on lifespan, the gut tissue in iTRF flies remained healthier with more normal cells, even when the gut microbiome was depleted with antibiotics. Therefore, the flies appeared to be in optimal health conditions with fewer aging markers in addition to longer survival, demonstrating yet again that aging slowed down due to better functioning of organs.

The dietary regimen under iTRF only controls the timing of feeding but not the nutritional intake, which provided clues to the authors that perhaps the body’s natural biological clock had something to do with iTRF-mediated lifespan. The biological clock in flies consists of proteins that are also present in other organisms all the way from fungi to humans. The main molecular parts of the core circadian clock include the proteins ‘Clock’ (Clk) and ‘Cycle’ (Cyc) which activate the genes period (per) and timeless (tim), which in turn inhibit Clk and Cyc. This process is called a feedback loop which takes all of 24 hours to complete in both flies and humans, and this is how our bodies respond to light-dark cycles. Flies undergoing iTRF showed enhanced expression of Clk in the daytime and of per and tim at night time. The authors then explored the feeding behavior and metabolism of circadian clock genetic mutants undergoing iTRF and found that neither the 20 hour long fasting period nor dietary restriction in their food altered their feeding behavior when compared to normal flies under iTRF. Yet, the extended lifespan was completely missing in Clk, per and tim mutants undergoing iTRF. Even the improved health seen with an iTRF regimen through better climbing ability and less aging-protein aggregation was abolished in per mutants compared to normal flies. Shifting the iTRF cycle by 12 hours with a fasting period during the daytime abolished the occurrence of an extended lifespan. In the altered regimen, while the same cycle was now only shifted by half a day, eating at night time while fasting during the day just did not work. This discovery showed that there could be a deep link between the body’s biological timer and when during the day food is eaten that determines both longevity and well-being. 

Because shifting the fasting period to daytime did not show any benefits, the authors checked whether genes that activate during fasting are also linked to the biological clock. In fact, Dr. Ulgherait and group had already shown that disrupting tim and per genes in the gut, which is where food is processed, caused an increase in lifespan. But, iTRF included periods of starvation that could trigger different metabolic processes. Starvation induces cellular mechanisms to degrade and recycle its molecules in a process called autophagy. Interestingly, genes encoding two autophagy proteins, Atg1 and Atg8a, which are also present in humans, showed peak levels in the night time with enhanced peaks in flies under iTRF. During autophagy, there is an increased activity of cell organelles called lysosomes that contain digestive enzymes needed to break down cellular parts. The authors found that normal flies fasting under iTRF showed higher Atg1 and Atg8a expression along with more lysosomal activity but period mutants failed to do so. Using some more genetic tricks, the authors found that manipulating the level of autophagy to go up or down directly showed an effect on iTRF-mediated lifespan.

Finally, to explore the link between iTRF-mediated lifespan and autophagy, the authors used genetic tools to increase night-specific levels of Atg1 and Atg8a. In a surprising revelation, flies with night-specific expression of Atg1 and Atg8a showed an increase in lifespan, even when these flies did not undergo fasting and were fed ad libitum. Subjecting these genetically altered flies to iTRF did not additionally increase their lifespan, suggesting to the authors that circadian enhancement of cellular degradation under an all-access diet provides the same beneficial effects as fasting done under the stricter regimen of iTRF. Flies with night-specific enhanced autophagy also showed better neuromuscular and gut health on an all-access diet. Therefore, clock-dependent enhancement of the biological recycling machinery can mimic the lifespan extension mediated by iTRF.

 

Now of course large genetic manipulations are not yet a consideration in humans but this study provides a potentially powerful yet simple change in dietary strategy that could just somehow slow down aging. Aging increases risk of mortality and disease but imagine a food intake regimen translatable from this study into humans that can help improve overall neuromuscular and gut health. So, while technology has indeed made it so much easier than before to have food at our doorstep in a few phone taps in the middle of the night, perhaps restricting the hours of when we eat can really help us live healthier lives. This study now makes me reconsider the famous quote by Woody Allen in the context of food, “You can live to be a hundred if you give up all the things that make you want to live to be a hundred”.

Dr. Matt Ulgherait is a postdoctoral researcher in the lab of Dr. Mimi Shirasu-Hiza in the department of Genetics & Development at Columbia University. Dr. Ulgherait and his colleagues also recently showed that removing the expression of the period gene from the gut tissue was sufficient to cause an increase in lifespan.

Magic under the microscope

Researchers design an accessible, straightforward technique to characterize moiré systems – a class of materials built by placing slightly misaligned atomic monolayers on top of each other. Under certain conditions, such moiré structures exhibit exotic physical phenomena absent in the individual units that conform them.

A moiré pattern is an interference effect that arises when two grids are superimposed. It can be observed in the wrinkles of a mesh shirt and it is responsible for the fringes that appear when taking a picture of a computer screen. Moiré patterns are present in art and fashion, and in the last few years their effect in two-dimensional materials has entailed a revolution in physics.

Two-dimensional materials are those that are less than a nanometer thick. The first one to be isolated was graphene, a single-layer of carbon atoms (see Fig. 1a). Such discovery opened a whole new field of research and many labs around the world started making their own stacks – structures with two-dimensional materials placed on top of each other. If one were to place one of those layers slightly misaligned with the one below, a moiré pattern would emerge. This interference effect can be visualized in Fig. 1b. The small circles represent the carbon atoms that form a crystalline lattice (an ordered structure) on each graphene layer. The top layer is rotated with respect to the bottom one and, as a consequence, a periodicity larger than the atomic lattice emerges as highlighted in Fig. 1b.

In 2018, the field of condensed matter physics was stirred up: such moiré materials, at a very specific misalignment value called the magic angle, exhibit electronic states of matter that are not present in the individual layers, such as superconductivity or magnetism. The emergence of those electronic phases is a consequence of the moiré pattern and its direct visualization is critical for their understanding. There are a few techniques, including transmission electron microscopy and scanning tunneling microscopy that allow for this, but they require complex setups that do not necessarily work for any material, which has significantly slowed down the progress in the field. McGilly and colleagues show a new and simple technique based on piezoresponse force microscopy to visualize moiré patterns.

A piezoresponse force microscope consists of a sharp metallic tip brought into contact with the material under study –  in this case, the moiré system (see Fig. 1c). Piezoresponsive materials are those that undergo a mechanical deformation in the presence of an electric field. In the microscope, the sample moves a small amount when a voltage is applied across it and the tip follows the motion. Such tip motion is measured as a voltage which is amplified to detectable values. The tip is then moved around the sample and the process is repeated on every pixel of a selected region, producing a map of the sample’s deformation.

a. Graphene atomic lattice. Each ball represents a carbon atom. b. Twisted graphene bilayers. The three main stacking configurations are shown (AA, AB and domain wall). The moiré unit cell is highlighted. c. Microscope tip in contact with the graphene bilayer d. The strain on the graphene layer bends the chemical bonds between the atoms from in-plane (left) to a mixed in-plane/out-of-plane character (right).

In principle, it was not obvious that a moiré pattern would be detectable with the microscope. When moiré patterns form, it creates a repetitive set of individual units that are called unit cells (highlighted region in Fig. 1b). Each unit cell is formed by regions with different atomic three-dimensional configurations, called sites. In the case of graphene, those sites are called AA and AB which stands for how the atoms from each layer lie on top of each other (see insets in Fig. 1b). The AB regions (also called domains) are separated by domain walls, as highlighted in Fig. 1b. McGilly and colleagues show that the voltage signal detected with the microscope is localized on the domain walls.

When the moiré pattern forms, the atomic layers relax to accommodate it and the layer wrinkles along the domain wall (see right panel in Fig. 1d). Since the microscope is not sensitive to such small deformation, the origin of the detected signal must be electronic. Flat graphene layers have planar bonds, as shown in the left panel of Fig. 1d. However, the curvature of the wrinkle bends the atomic bonds on the graphene layer, which in turn causes an asymmetric distribution of the charge in the vertical direction and gives rise to an out-of-plane polarization (P), which is responsible for the signal measured in the microscope.

The technique designed by McGilly and colleagues has been proven extremely useful for the advancement of the field due to the simplicity of the method and the fact that it allows imaging of any moiré pattern, independently of the nature of the individual units that conform it – that is, whether they are metals, semiconductors or insulators. Being able to image moiré patterns with such an accessible technique will help improve the fabrication process, and having uniform samples is critical since strain gradients can significantly alter the states of matter that emerge in moiré materials.

 

Dr. Leo McGilly is a Postdoctoral Research Fellow in the Physics Department at Columbia University.

How Bouldering keeps urban communities in shape

So, you too enjoy this amazing sport, where people climb over comparatively short distances without any tools, such as ropes or harnesses? Amazing! But, to quote a famous British ensemble, now for something completely different. Today we want to talk about a more serious and urgent topic: flood risks. The recent flood in the New York City area convincingly showed us the risk of flooding in (highly) populated urban areas. Climate change and socioeconomic developments keep on increasing this risk further and further.

Flooding in NYC
Figure 1: Strong rain in New York City transformed parts of it into Venice’s little brother, with less romance but at least 43 death cases.

The United Nations have formulated in their 2030 Agenda for Sustainable Development 17 goals to »[…] stimulate action over the next fifteen years in areas of critical importance for humanity and the planet«. Goal number 11 is »sustainable cities and communities«. But, to properly address a risk it is necessary to adequately analyze and describe it. Current approaches for urban risk analysis mostly lack two important factors: First, they are mainly qualitative but not quantitative. That means, they accurately describe the what of a risk but not how much. We probably all can agree that the information that the biggest crocodile ever found in nature was longer than the biggest giraffe ever was high is much more impressive than the statement, crocodiles can become really big. This demonstrates why quantitative statements are important.

The second problem they do not address properly is the prediction of urban development. They project city growth rather arbitrarily, seldomly incorporating geographical, social or economic factors associated with urbanization. While predictions are difficult, especially about the future, some information exists which can be used as a guide about most probable development cases.

Dr. Mona Hemmati and colleagues tackled both these problems by developing a framework for understanding the interactions between urbanization and flood risks. To do so, they combined four main components: an urban growth module, a hazard module, a risk assessment module and a policy implementation module. The urban growth module is used to achieve a more realistic urban development prediction and the hazard module to generate floodplains. For the risk assessment module the two previous modules are combined while the policy implementation module is used to implement nonstructural strategies, such as for example development zones or taxation variations.

For the framework development the City of Boulder, Colorado, has been chosen as a testbed. Various data such as size, shape, surrounding area or density distribution of the city has been gathered by different sources and used as input parameters for their model.

Their urban growth model has four key features which are used to predict the urbanization process, divided into residential, industrial and commercial & mixed-used occupation. They divide the urban area and surroundings into equally sized cells, the so-called cell space, creating a 2D spatial grid. Each cell can have a cell state, which describes if the cell is developed or not. The neighbourhood of a cell is a factor which can either have an attractive or repulsive effect on the surrounding cells and the transition potential represents the probability of a cell state change for the next time step, defined by different development factors. For the hazard module a development by the Federal Emergency Management Agency was used. With this different floodplains characteristics can be calculated for various flood scenarios, such as for 5, 10, etc. year return period. The risk assessment module measures the damage to physical infrastructure and caused by economic and social disruptions as expected annual damage (EAD) in $US. Last, the policy implementation module takes into account nonstructural flood mitigation measures. Structural measures, such as for example dams, aim at controlling the hazard and keeping the flood out, while nonstructural measures, such as for example land acquisition or public awareness programmes aim at reducing the exposure to hazard.

Using this framework, they tested two different policies against both the current development policy of the city as well as no policy at all. For the first policy they defined low-risk zones and disallowed development and high-risk zones, while for the second they defined socioeconomic incentives, such as for example placing school and places of entertainment in low-risk zones. The interesting result was, that from the four tested cases, Boulder’s current development policy showed the worst result in terms of growth inside the floodplains and therefore long-term costs. Even uncontrolled development was better, while the best policy was the zoning policy, closely followed by the incentive policy.

It can be summarised that while their model still contained many educated guesses and assumptions and for example neglected the influence of the growth module onto the hazard module it can be considered a huge step forward in comparison to purely qualitative models based on random development. The testbed Boulder showed it can be directly applied to community planners in assisting the mitigation of risks due to future hazards, bringing the science out of their ivory tower into the heart of modern society: The city itself.

Dr. Mona Hemmati is a Postdoctoral Research Scientist in the department for Ocean and Climate Physics at the Lamont-Doherty Earth Observatory (LDEO) of Columbia University.

The Different Perceptions of Cultural Appropriation

The term cultural appropriation, is by far a familiar one. It is defined as situations where a person associated with one group uses cultural elements from another group. These elements can include cultural items like “symbols, genres, expressions, technology and artifacts”. While the term is widely used, actual empirical data surrounding the perception of cultural appropriation is limited. In a recent publication, Dr. Ariel Mosley, a Columbia postdoc, and Dr. Biernat venture into the perception of cultural appropriation. To understand how cultural appropriation is perceived by different groups, Dr. Mosley utilizes an approach of a majority and a minority group in the same community and identifies how each group views different actions as cultural appropriation. 

This study uses multiple examples of cultural appropriation (Figure) to identify the perception of appropriation (whether the example is actually cultural appropriation), perception of harm (whether the appropriation can be harmful to the group the cultural aspect was borrowed from), perception of intent (whether the appropriation was done purposefully), and distinctiveness threat (whether the appropriation threatened cultural aspects that allow the minority group to be distinct from the majority group).

To fully identify the perception of cultural appropriation, this study was divided into five sub-studies. Studies one through three focused on the perception of appropriation, harm and intent, study four focused on manipulating distinctiveness threat, and study five focused on fully crossing the actor and race. They recruited an equal number of adults that either identified as Black or White Americans, with White Americans being considered representative of the majority group and Black Americans representative of the minority group. For studies one through three, the authors set out to answer whether Black Americans or White Americans would have higher perceptions of appropriation, harm, intent, and distinctiveness threat. They used a design where the participants would read scenarios, adopted from social media and news clips, of potential cultural appropriation. In these scenarios the perpetrator, the person doing the appropriating, could be either white or black. The participants were asked to review six possible cases of cultural appropriation (Figure). Throughout the three studies they found that Black participants perceived more cases of appropriation than White participants when the perpetrator was White. In a similar pattern, Black participants saw the scenarios as more harmful, and with intent when the perpetrator was White. When the perpetrator was Black neither White participants nor Black participants saw the scenario as appropriation. Black participants also overall felt an increased distinctiveness threat when compared to White participants. These findings supported Dr. Mosley and Dr. Biernats’ original hypothesis of cultural appropriation being more likely to be perceived when perceivers were members of the minority group.

Since in studies one through three, Black participants felt an increased distinctiveness threat, Dr. Mosley and Dr. Beirnat wanted to see whether increased distinctiveness threat in particular could alter the perception of cultural appropriation. To test this the authors primed the participants in a fourth study for increased distinctiveness threat and focused on one scenario category, “hairstyle” (Figure). They primed the participants to either have increased distinctiveness of threat by having them read, “The Disappearing Color Line in America” or normal distinctiveness of threat by having them read, “The Geography and Climate in America”. Black participants were widely unaffected by the priming with the results mimicking studies one through three, but for White participants, those that were primed for distinctiveness of threat saw the White perpetrators’ actions as cultural appropriation. These results indicated that the level of distinctiveness threat experienced increases the perception of cultural appropriation.

Figure: Detailed depiction of the study designs and categories of cultural appropriation.

Then in study five, to reassure their results, the authors paired a perpetrator with a product that was distinctly part of the participant’s culture. The previous four studies used an item/product that was outside of the perpetrator’s culture, but not necessarily an item belonging to the participant’s culture.  Here they used an item/product that was explicitly part of the participant’s culture. The perpetrator was either a White waiter serving culturally Black cuisines or a Black waiter serving culturally White cuisines. Mimicking their previous studies, they found that Black volunteers were more likely to see cultural appropriation when the waiter was White.

Overall, their study indicated that majority and minority groups perceive cultural appropriation differently, with the minority group being more sensitive to actions that can be perceived as appropriative. They also found that harm and intent correlated with appropriation leading them to the conclusion that both perceptions are part of the appropriation construct. These findings supported their initial hypothesis that power relations and social constructs affect the perception of cultural appropriation and added empirical data to a topic often spoken about but yet understudied.

While Dr. Mosley and Dr. Beirnat have added a significant amount of empirical information on how cultural appropriation is perceived, there is still more to explore. Future studies could expand on how cultural appropriation affects multiple other groups including individuals across different races, sexual orientations, genders and individuals with disabilities. 

 

Dr. Ashley Mosley is a Post-Doctoral Research Scientist in the Department of Psychology at Columbia University. Her research focuses on social cognition, social identity and intergroup biases. More information about Dr. Mosley can be found on her website.

What happens when macrophages refuse to eat the dead?

Macrophages, a type of immune cells, are an integral part of our body’s defense system. The term macrophage comes from two Greek words – makro meaning big and phagien meaning eat, which makes them the “big eaters”. And boy, do they love to eat! Some things that they like to chomp on include bacteria and other foreign substances, dying and dead cells, and cancer cells, thus, acting as the body’s cleanup system. This process of eating is not only important for defending against foreign pathogens but is also essential for cleaning up cell debris and maintaining normal bodily functions.

Macrophages typically encapsulate their food by surrounding it with cell extensions, then engulf it and digest it. Check out some cool videos of macrophages eating some bacteria here. This process of eating is typically called “phagocytosis”. However, the term for macrophages eating dying cells is called “efferocytosis”. This term is derived from the Latin word efferre which translates to “take to the grave” or “to bury”. When this mechanism of disposal of cellular corpses goes wrong, the rotting dead cells can lead to inflammation that damages the surrounding tissue. This can lead to many diseases, including coronary artery disease, chronic obstructive pulmonary disease, cystic fibrosis, and rheumatoid arthritis. In a recent publication from the Tabas lab, Dr. Kasikara and Columbia postdoc Dr. Schilperoort explore the molecular mechanisms that underlie impaired efferocytosis and how that leads to the formation of dangerous plaques in the arteries that supply blood to your heart. The buildup of these plaques leads to a condition called coronary artery disease which remains the leading cause of deaths in the United States, causing about 1 in 4 deaths.

Significant advances in genomic sequencing in the past few years have led to the discovery of several mutations that are often correlated with the occurrence of coronary artery disease in patients. One of these mutations is in a gene encoding a protein called PHACTR1. However, because the mutation is present in a part of the gene outside of where the protein-coding sequence lies, it was unclear if this mutation disrupted efferocytosis by disrupting the function of PHACTR1. PHACTR1 regulates the ability of various cell types to expand, contract, and move. While the ability of macrophages to execute these motions is required to engulf or eat cells, whether PHACTR1 is involved in this process in macrophages and thereby macrophage efferocytosis was not known. In this study, the authors made two important discoveries. Firstly, they found that PHACTR1 is essential for macrophage efferocytosis. Secondly, they found that the mutation decreases the expression levels of PHACTR1. The authors investigated more and established that PHACTR1 is important for maintaining an activated version of a motor protein called myosin which is required for cellular movement. Thus, lower levels of PHACTR1 hamper the ability of macrophages to eat dead cells by disrupting cellular movement. This contributes to the buildup of dying cells in our arteries and a consequent increase in the risk of heart attack and stroke.

Fig 1. Model depicting the relationship between efferocytosis and risk of coronary artery disease. Reduced levels of efferocytosis lead to insufficient clearance of dead cells and consequent plaque formation in the arteries. Figure adapted from Kasikara, JCI 2021.

The results from this study provide novel insights into the role of PHACTR1, myosin, and other associated proteins in the pathogenesis and progression of coronary artery disease. Before this study was performed, we only knew that there was a correlation between an increased risk of heart disease and a mutation in PHACTR1 gene. The authors performed rigorous experiments and demonstrated that the mutation changes PHACTR1 production and that this causes heart disease. This information is extremely valuable as it provides a basis for designing future therapies. For example, increasing PHACTR1 production artificially may be an effective strategy for treating coronary artery disease. As defective macrophage efferocytosis is also involved in the pathogenesis of many other diseases, this study has direct implications for the discovery of new treatment paradigms for these diseases as well.

Ancestry connects non-cancer causing mutations in cancer patients

The cause of cancer as a disease has been partly attributed to genetics across a diverse range of populations. However, it is unclear whether cancer patients carry additional genetic mutations, also known as variants, in non-cancer causing genes and if these variants are evolutionarily related. Because ancestry-specific variants were more recently generated in evolutionary time, they could have been easily missed in analyses where all patients were cumulatively analyzed without consideration for ancestry. A recent concept proposed by geneticists suggests that people are more likely to develop or be protected from diseases based on recently acquired mutations and are less so due to more distant mutations. This is an interesting theory that scientists can now test using genome information from more than 10,000 cancer patients whose ancestries are known. So far, how mutations affect gene expression – whether they completely abolish the expression of gene products (e.g. protein) or result in the creation of a misshapen protein, have only been reported for variants present in patients with European ancestry. The remaining ancestries are yet to be explored.

 

Advances in sequencing technology have made it easier for researchers to access genome sequencing information under clinical settings and for healthcare providers to share personalized diagnoses as part of ‘genomic medicine’ to patients. Using publicly available genome sequencing data for cancer patients, Dr. Xiao Fan and colleagues analyzed the variants in non-cancer causing genes and in “medically actionable” genes in 10,389 cancer patients. The authors found 1.46 billion mutations, which were then filtered through rigorous quality testing of sequencing information followed by expert geneticist review, resulting in a final total reliable set of 2,920 non-cancer related pathogenic and likely pathogenic variants. About 750 of these variants were harbored on average within a quarter of the cancer cases, no matter the heritage. A surprising majority (~27%) of the total variants were displayed in patients with European ancestry, followed sequentially by Latinx/Native American (15%), African American (13%) and East Asian (12%) patients.

 

Because genetic mutations can affect expression of proteins, the authors then dug deep into the variant data to examine whether these variants behaved in an expected manner on a molecular level. When genes contain mutations that cause the protein it encodes to be a shorter version of itself, the mutation is referred to cause a protein “truncation”. Sometimes, a truncating mutation in a gene can trigger a decrease in expression at the messenger RNA (mRNA) level even before the mRNA is used to make the protein. To find out if the variants that produced truncated gene products underwent changes at the mRNA level, the authors measured the gene expression levels of such variants. Of the variants that showed a meaningful difference in gene expression compared to non-cancer patients, a large majority of variants showed a decrease in expression. This result indicated to the authors that truncation-causing variants often work at the mRNA level even before the cells spend energy to make the disease-associated proteins. The authors then examined the behavior of gene variants that do not cause truncations but rather cause just a single swap in the gene sequence, known as “missense” variants. Missense mutations typically only cause a change in one or two building blocks of the protein but do not affect the abundance of the protein itself. Surprisingly, the authors found that the missense variants in their data are unusually regulated in the cancer patients at the mRNA level resulting in a decrease in gene, and therefore, protein expression. This is an uncommon observation, making the authors speculate that missense variants are perhaps controlled by gene-expression independent mechanisms within the cancer patients’ cells.

This study provides a testament to the power of genomic medicine that can be used to complement conventional medical treatment. With a strong sample of ~10,000 cancer patients, this report stands as one of the most comprehensive studies that considers race and ancestry in its analysis. While genomic profiling is becoming more common in medical diagnoses, this study further provides a reason for understanding diseases and invention of medicine based on race, ethnicity and genetic heritage.

Identifying a potential risk factor for alcohol abuse among victims of violence in childhood

Half of all children in the United States have been physically assaulted in their lifetime, according to a 2014 study. This finding is alarming, especially considering that childhood maltreatment and abuse can lead to numerous negative mental health outcomes. 

Researchers and medical professionals around the globe often focus on adverse childhood experiences and their detrimental effects on development. Experiencing threat and violence is frequently correlated with a decreased ability to effectively handle negative emotions and heightened emotional reactivity relative to those who have not experienced such trauma. For instance, a typical situation such as having your toy taken away by a peer in school might invoke an explosive, angry response from a child who has been a victim of abuse. Moreover, research demonstrates that children who have faced abuse are also more likely than others to interpret ambiguous actions (such as a classmate accidentally bumping into them in the hallway) as confrontational.

How might those who’ve experienced violence in their childhood, and also have trouble dealing with negative emotions, respond to everyday stressors (i.e. getting through hard homework sets or dealing with long waits for customer service on the phone)? Dr. Charlotte Heleniak and her colleagues studied this response, called distress tolerance, in a newly published paper.

Levels of distress tolerance vary among different individuals. Someone with low distress tolerance is extraordinarily uncomfortable in situations where they’re facing a challenging obstacle, upset, or experiencing negative emotions that can make it hard to persist in the face of difficulty. They have a harder time working through these difficult events compared to people with higher distress tolerance. Research also shows that people with low distress tolerance may find it necessary to escape bad feelings by seeking immediate relief. This relief can often take the form of substance abuse. 

Additionally, while little research has been done, distress tolerance may make an individual more vulnerable to other mental health problems such anxiety and depression. Because of this, Dr. Heleniak’s team examined whether low distress tolerance is associated with these two mental illnesses, as well as alcohol abuse.

teens drinking
Image from Pixabay

Propensity toward problematic alcohol use in adolescents involves many environmental risk factors such as sociodemographic factors and parental drinking behavior. These can be difficult or impossible to address therapeutically. However, if distress tolerance is indeed tied to substance abuse, this may offer a clearer path toward crafting a psychological intervention. 

Dr. Heleniak and her colleagues studied 287 16- to 17-year-old participants across a broad range of socioeconomic backgrounds. They asked the teens about previous violence exposure in their personal life, and assessed depression, anxiety, and alcohol use. Four months later, they reassessed these parameters.

To examine the teens’ distress tolerance, the researchers used a measure called the Paced Auditory Serial Addition Task, which measures a person’s persistence on a difficult task. The sooner a participant decides to terminate the task, the lower their distress tolerance. The team found that those teens who experienced a heighted amount of violence did indeed have lower distress tolerance. At the initial time point, lower levels of distress tolerance were not associated with any of the three psychopathologies (i.e. alcohol abuse, anxiety, depression).

However, the researchers found that low distress tolerance predicted alcohol abuse from the first time point to the second, about 4 months later. Low distress tolerance was not associated with anxiety or depression at either of the two time points of data collection.

Figure 1. Teens who experienced more abuse and violence had lower distress tolerance. Four months after the initial assessment, teens who had low distress tolerance were even more likely to have developed problematic drinking behaviors.

Based on their findings, Dr. Heleniak and her team conclude that researchers could potentially pinpoint distress tolerance as a way to target teens’ problematic use of alcohol, especially those who have experienced violence. Indeed, therapeutic programs aimed at improving distress tolerance already exist. The authors explain that treatments such as Dialectical Behavior Therapy (DBT) and mindfulness practices may be particularly useful. 

Given that teen alcohol abuse may continue into adulthood and lead to dependency issues later in life, the findings of this study could go a long way to helping those adolescents who struggle with both addiction issues and an abusive past.

If you or someone you know is experiencing substance dependency problems, SAMHSA (1-800-662-HELP) is a free, confidential, resource available 24/7 365-days a year.

Charlotte Heleniak is a postdoctoral scientist in the Developmental Affective Neuroscience Lab at Columbia University. She received her Ph.D. in Child Clinical Psychology from the University of Washington. She focuses on how childhood adversity impacts emotion regulation and social cognition in ways that predict adolescent psychopathology. This research has earned her awards from the National Institute of Mental Health and the Doris Duke Charitable Foundation, as well as the Sparks Early Career Grant from the American Psychological Foundation.

Shedding light on transfers in soccer – from a physicist’s point of view

Ever wondered about the connection between sports, architecture and molecular physics? These three distinctive fields come together when we talk about fullerenes. Fullerenes are a modification of carbon with some very interesting properties. The most outstanding one is their structure: They are hollow spheres made up of several penta- and hexagons, resembling a cage. The most famous fullerene C60 (Fig. 1a) actually looks very similar to the traditional pattern of a soccer ball (Fig. 1b). Fullerenes are named after the American architect Richard Buckminster Fuller who is famous for his constructions of geodesic domes, very similar to the fullerenes structure (Fig. 1c). Therefore fullerenes are commonly referred to as Buckminster Fullerenes or Bucky Balls. Fullerenes can build a unique molecular structure where atoms, molecules or even other small clusters are bound inside of the cage. These molecules are called endohedral molecules, with Ho3[email protected]80 (Fig. 1d) being an example introduced later in this text.

3D structure of fullerenes in comparison with a soccer ball and a geodesic dome
a) The carbon cage structure (grey) of C60 with the typical pentagons (orange) and hexagons (purple). b) The same structure can also be found in a classical design of a soccer ball. c) The Biosphère in Montreal, designed by R. B. Buckminster. d) The molecule used in the study, Ho3[email protected]80.

Endohedral molecules have gained some attention in biochemical research for two reasons. First, they are considered excellent vehicles to transport drug molecules to specific locations and release the cage’s content by an externally triggered mechanism. Second, they could be applied in radiotherapy, since the ability to carry metal atoms inside allows them to release a large amount of electrons which cause very localised cell damage, especially to cancer cells.

One mechanism which is expected to play an important role for these two applications is the so-called intermolecular coulombic decay (ICD, not to be confused with the International Classification of Diseases). In an atom, electrons are bound to the nucleus in so-called shells which layer above each other like an onion (a property they share with ogres). To remove an electron from its shell one has to supply energy to it, the closer to the nucleus the shell is, the more energy is needed. A common way of supplying this energy is to shine high-energetic light onto the atoms, either ultraviolet (UV) or even X-rays. If an electron is removed from an atom, we call the remaining atom an ion. If an inner electron is removed, a vacancy or “free spot” in that shell is created. Such ions are called excited.

Speaking from personal experience, excitement tends to decay quickly (citation needed), which also holds true for ions. Within an ion, an electron from a higher shell “falls down” (decays) into the vacancy of the inner shell. By doing so it has to give up the difference in energy between the two shells. One way to give up its energy is by emitting a photon, meaning shining light. This effect is used for example in neon bulbs. If the two involved shells are far enough from each other, the electron can transfer its energy to another electron which is then removed from its shell. This process is called the Auger effect (Fig. 2a). Within molecules another process can happen: The decaying electron can transfer its energy onto an electron of another atom in the molecule which then gets removed from its shell (Fig. 2b). This is the aforementioned ICD.

scheme of the auger effect and ICD in molecules and endohedral fullerenes
a) Schematic of the Auger effect. b) ICD in a normal molecule. c) ICD in an endohedral molecule.

Unfortunately, ICD in endohedral molecules (Fig. 2c) has, even though theoretically predicted, not been discovered. Well, until recently. Dr. Razib Obaid and colleagues set up an experiment at the Advanced Light Source (ALS) in Berkeley, one of the world’s brightest UV and X-ray light source facilities in the world. They used the UV light to radiate the molecule Ho3[email protected]80 (a molecule consisting of three holmium and one nitrogen atom, trapped in a cage of 80 carbon atoms). The result was the production of ions and electrons, which the researchers measured together with their energy distribution. Additionally, they measured the relation of the particle’s production time. Putting these measurements together, they were able for the first time to demonstrate ICD in endohedral molecules. This required not only a clever experimental setup, but also a lot of theoretical effort. The complexity of the experiment and its analysis derives from the fact that ICD involves multiple atoms with many electrons. This makes the measured spectra resulting from  such experiments difficult to disentangle and complicates the assignment of each individual process.

With the first clear observation of ICD in endohedral fullerenes, demonstrating the existence of the proposed mechanism, the researchers have opened the door to further research on the application of the process as a drug delivery system and its influence in the propagation of radiation induced molecular damage in biomolecules.

Dr. Razib Obaid is currently a postdoc at RARAF Radiological Research Accelerator Facility located at the Nevis Laboratory of Columbia University, lead by Dr. David J. Brenner.

Images:

Figure 1b: Derived from Football (soccer ball).svg. (2020, September 23). Wikimedia Commons. Retrieved 23:10, August 30, 2021

Figure 1c: Biosphere, Montreal.jpg. (2020, October 26). Wikimedia Commons,. Retrieved 23:11, August 30, 2021

Over the brainbow with a new PAL

Brains come in a variety of sizes. Several orders of magnitude separate the convoluted human brain from that of the fruit fly. But no matter the configuration, neuroscientists strive to study neurons in further and further detail, ideally at the single-cell level. However, consistently identifying individual neurons is not an easy endeavor; in most organisms there are so many neurons that even when labelled with colored tags we can’t see the forest for the trees.

Enter Caenorhabditis elegans, a worm with only 302 neurons. This tiny transparent worm comes in handy for scientists because they can easily follow the fate of any of its cells from the embryonic stage to adulthood. However, despite the somewhat predetermined developmental paths, the exact spatial location of each cell is slightly variable. Therefore, studies examining individual cell identities are doomed if they rely exclusively on relative position within each group of neurons.

In their recent paper, Dr. Eviatar Yemini and colleagues introduce a solution to this problem in the form of deterministic fluorescent labelling of all 302 neurons of the worm C. elegans. Their approach, NeuroPAL (a neuronal polychromatic atlas of landmarks), produces the same pattern of colors across worms, which makes a fundamental improvement to previous similar techniques like Brainbow that produce random patterns.

The first challenge they faced was determining how many distinguishable colors they needed to correctly identify all neurons. Fortunately, the neurons of this worm are dispersed over its whole body, grouped in 11 different clusters, so they didn’t need all 302 to be labelled with distinct colors. The biggest of these ganglia contains roughly 30 neurons, so aiming for a range of colors around that number was enough. How do you get those colors? One could achieve a sizable palette by using just a few different fluorescent markers or “fluorophores” that are detectable at different intensities. However, selecting the final fluorophores wouldn’t have happened without a great example of scientific collaboration. Dr. Yemini had been struggling with the colors blending together until he contacted a colleague who told him about a new fluorophore, and this ended up being the missing puzzle piece he needed to achieve all the distinguishable fluorophores. Once they had carefully selected the three distinct markers, a clever trick of imaging them in red, blue and green, allowed them to obtain a whole RGB palette of colors.

The next step was to achieve the different levels of each fluorophore for each neuron in a consistent way across worms by changing the signal driving the fluorophores’ expression. Starting from a list of 133 previously published genes with different patterns of neuronal expression, Dr. Yemini tried them all, painstakingly narrowing down the list to 41 winners by a process of iterative trial and error, checking the resulting color combinations and whether the neurons could be distinguished at each step. This process alone spanned more than two years, and required deep dives into the literature and some expert judgement calls: “in one rather desperate case, I guessed the expression from the behavioral phenotype and, very luckily, was approximately right” Dr. Yemini says.

Once they achieved the final combination of colors, they had finally created a genetically modified worm that could pass on this colorful and robust pattern for many generations.

A fluorescent image of a NeuroPAL worm with distinct labelling of each neuron
A NeuroPAL worm with deterministic fluorescent labelling of its 302 neurons. Notice that the head, on the left, has a much higher density of neurons, which had previously complicated the task of identifying them. Courtesy of Dr. Yemini.

NeuroPAL is not only a technical feat in and of itself, but was also a creative outlet for Dr. Yemini, who enjoyed the highly collaborative art-meets-science project:

“In high school, I had to choose between applying to art school or following what I thought was a more traditional route. I loved the artistic process, I’d taken many art classes and even managed to score a scholarship for an after-school art program at SUNY Purchase. But I let luck guide my fate and ended up taking the non-artistic route. I really miss that part of me. The process of making NeuroPAL has felt like a taste of a part of me that I’d lost.”

So what do you do after you create a tool that allows you to unambiguously identify all neurons? You use it to explore more questions! Dr. Yemini and his colleagues applied their shiny new worms to study many old questions in the field. For example, they leveraged the individual cell identification to refine whole-brain activity imaging, with which scientists previously had the issue of being unable to determine neuronal identity. They succeeded in recording responses to different chemical stimuli, both attractive and repulsive, confirming previous results and adding new neurons to the response pathways, thus unraveling more complex neuronal networks. On the whole, they show that this new tool can be used for exploring a variety of questions in C. elegans.

Sped-up video of a NeuroPAL worm responding to a stimulus. The cells that are activated by the stimulus shine more brightly and are identifiable by their underlying color.

You might be thinking, “This is all very cool, but what does a tiny transparent worm have to do with me?” While studying C. elegans in itself can shine light on some basic biological processes, it can also open the door to discoveries in more complex organisms and those more similar in neural organization to humans. Indeed, the authors suggest that this approach to unequivocally label cells could be translated to other models that are widely used in biomedical research, such as the fruit fly, fish and even mice. We still have a long way to go before we can create an entire rodent with a consistent pattern of shiny cells, but local labelling may be a more attainable goal. And eventually, this research will help us distinguish the trees from the forest.

Dr. Eviatar Yemini  is an Adjunct Associate Research Scientist in the Department of Biological Sciences at Columbia University (Hobert lab). He will be starting his own lab at the University of Massachusetts Medical School in January 2022. Reach out to him for exciting job opportunities!

Beneath The Surface Of Healing Wounds

With an average weight of ~12 kg and surface area of ~2m², skin is the largest organ of the body and is made up of three layers: epidermis, dermis, and hypodermis. Epidermis, the outermost layer, is composed of densely packed epithelial cells. Under the epidermis lies the dermis, which mainly contains blood vessels, hair follicles and sweat glands. The third layer, the hypodermis, is composed of loose connective and fatty tissue (Fig. 1). Given its large area and exposure to external elements, the skin is susceptible to injury, ranging from minor bruises to cuts, lacerations, and tears. The skin’s response to insults like these is a process well-known as wound healing, which occurs in three stages: inflammation, proliferation, and tissue remodeling. These stages work together in an overlapping sequential manner to ensure complete wound healing. A failure in any of the normal wound healing stages leads to chronic wounding and aberrant scar formation as seen in burn injuries and scar tissue formations. A delay in wound healing can result in increased infections and permanent tissue damage as seen in patients with diabetes.

Fig.1. Schematic representation of the layers of skin.

During inflammation, there is an influx of immune cells to clear invading microbes and cell debris at the site of injury. This is followed by  the proliferation phase during which there is an increase in the production of epithelial cells  that will migrate to the outer edge of the site of injury to repair the wound and restore it back to its uninjured state.  An essential step in wound healing is the mobilization of stem cells for the formation of new epithelial cells. Skin stem cells are found in the basal layer of the epidermis and in the bulge area of hair follicles. Epidermal stem cells are actively involved in replenishing cells as skin undergoes normal homeostasis as well as during wound repair. Stem cells in the hair follicles, on the other hand have periodic patterns of rest and activity during hair growth. Following injury, however, hair follicular stem cells are also involved in rebuilding the epidermis to seal the open wound.

Interactions between the immune cells during the inflammation stage and stem cells during the proliferation stage of wound healing are important for efficient tissue repair to take place. Cytokines are signaling molecules produced by cells that are required for cell-cell communication to stimulate cell migration towards the site of injury. Molecular and cellular mechanisms to address the role of cytokines in mediating interactions between immune cells and stem cells during wound healing remain unexplained.

In a previous study, Pedro Lee and colleagues observed that mice that lacked the interleukin -1 receptor (IL-1R) for IL-1 cytokine had a delayed wound healing response. In the skin, IL-1 is released by damaged keratinocytes (keratin producing cells present in nails, hair and skin). and dysregulation of IL-1 has been associated with a number of skin diseases. Pedro Lee, Rupali Gund and colleagues conducted the current study to understand the mechanism behind delayed wound healing in IL-1R mutant mice. They analyzed the molecular and cellular interactions during wound healing using a genetically engineered mouse model in which the entire skin mimics the biological response of wound healing. This mouse model, which lacks the caspase 8 gene in the epidermis, exhibits a wound healing response even in the absence of injury, thereby providing the researchers with a large number of stem cells participating in a wound healing process. The authors studied the structure of tissues and gene expression patterns in the skin of these mice. The researcher additionally performed assays to analyze proliferation of cells by growing cells in the lab from the genetically engineered model and the mice lacking IL-1R. The researchers found that IL-1 mediates wound healing through activation of stem cell proliferation in two possible ways. The first is by activating dermal fibroblasts that will activate the epidermal stem cell to cover up the open wound (Fig.2.A). The second is the activation of a population of immune cells called gamma delta T(γδT)-cells. These cells in turn activate the resting stem cells found in the hair follicles. These activated stem cells then migrate from the hair follicle towards the site of the injury for wound healing. The researchers also found that IL-1 interacts with another cytokine, IL-7, and together they work to increase the number of active gamma delta T cells in wounded skin and secrete growth factors (Fig.2.B) thereby increasing the population of stem cells promoting wound healing.

Fig.2. Schematic of cytokine mediated interactions between cell types during wound healing. A. IL-1 mediated interactions between dermal fibroblasts and epidermal stem cells. B. IL-1 mediated interaction between immune cells (γδT) and stem cells. Image adapted from Lee, Gund et al., 2017

Normal wound healing is an important and complex physiological process to ensure timely healing to maintain skin integrity. It requires coordinated interactions between various factors, cells and cytokines at each healing stage. Lee, Gund and colleagues have identified a novel role for immune cells (γδT-cells) in tissue repair in addition to their well-established role of fighting infections. The ability of γδT cells to respond to IL-1 and, in turn, secrete growth factors that promote stem cell reparative activity expands the kind of functions that immune cells can perform in tissues in addition to their common role in immunity. Stem cell therapy and regenerative medicine shows great potential in the field of wound healing and skin regeneration.

This study reveals how immune cells communicate with stem cells during tissue repair and identifies new cellular interactions that can be targeted to prevent diseases in which wound healing is impaired. Such therapies will preclude need for invasive surgical interventions and skin graft procedures as a treatment for chronic wounds.

Dr. Rupali Gund is a postdoctoral research scientist in the department of dermatology at Columbia University Irving Medical Centre. Her research focuses on studying mechanisms in skin autoimmune diseases and finding new ways to design therapies to improve patient’s quality of life.