Bowdoin Science Journal

Chemistry and Biochemistry

The Science of When You Exercise

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People often think the most important aspect of how exercise affects your overall health is how hard you work, how much weight you can lift, or how far you can run. However, two recent studies have uncovered another factor that might be just as important for maximizing health benefits – when you exercise. Multiple studies have looked at the impact of how when you exercise affects your body. For example, one study looked at the impact of exercise timing in mice, focusing on the growth of muscle tissue, while another study looked at a large population of people and how their exercise habits affected sleep quality. Together, these studies show that when exercise takes place matters more than most people believe.

The first study, done by Liu et al. and published in Nature Communications, looked at how timing of exercise in mice affected long-term health (Liu et al., 2025). Mice, like people, have a circadian rhythm, which is a 24-hour internal clock in the body that regulates and affects energy, metabolism, and sleep. Muscles in the body also have internal clocks, which decide when to burn fat or sugar.

In the study, Liu et al. had two groups of mice run at a low intensity and low volume on treadmills at different times of day: one group exercised before sleep and the other exercised right after waking up. Training lasted for several months, and researchers measured the mice’s body weight throughout the study and measured the mice’s strength, endurance, and blood sugar before and after the study was conducted, all of which are indicators of long-term exercise results. The results of the study were quite clear. Mice who exercised before sleep showed increased physical and metabolic improvements after the period of consistent exercise, meaning they gained less fat, had more endurance, and showed better blood sugar control. The group of mice that exercised after waking saw less improvement in these areas (Liu et al., 2025).

The second study, done by Leota et al. and also published in Nature Communications, tracked the health data of over 14,000 human participants using fitness wearables over four million nights of sleep (Leota et al., 2025). The researchers wanted to see whether exercising in the evening, before bedtime, affected sleep quality.

The researchers found that the later and harder people worked out, the more their sleep was affected. When people exercised four or more hours before going to bed, their sleep was normal, regardless of the intensity of the workout. When people exercised two to four hours before going to bed, they took a longer time to fall asleep and slept less. When people exercised two hours or less before going to bed, especially at a high intensity, sleep noticeably got worse. Some took up to over an hour longer to fall asleep, slept about 40 minutes less overall, and had a higher heart rate throughout the night (Leota et al., 2025).

Although the mice study found that exercise before bed improved overall health, the human study found that the closer exercise got to bedtime, the worse sleep became, which is also known to negatively impact recovery and overall health. While these studies may seem contradictory, they actually align upon consideration of the factor of exercise intensity. High-intensity training in the evening negatively affects sleep, while low/moderate-intensity exercise in the evening is beneficial for muscle growth and recovery without impacting sleep.

Although both studies were different, they arrived at the same key conclusion: that the body works best when its internal cycles, like its circadian rhythm, are not disrupted. Exercise, such as heavy lifting or sprinting, activates the body’s sympathetic nervous system, which is the part of the nervous system responsible for the “fight or flight” response. Sleep, along with recovery, lowered heart rate, and relaxation, is activated by the parasympathetic nervous system, otherwise known as the “rest and digest” state. While the activation of the sympathetic nervous system is good for exercise and performance, it is not good when the body needs to sleep. Instead of letting the body settle down, activation of the sympathetic nervous system keeps your body revved up, lessening sleep time and quality, and therefore overall recovery and future performance.

Because of the busyness of daily life, it’s not always possible to perfectly time every workout. Evening workouts are often unavoidable due to the realities of many people’s daily schedules. However, the combination of results from these studies shows that evening workouts aren’t automatically bad for overall health. In fact, they can even improve the benefits of exercise as long as their intensities are adjusted according to their relation to bedtime. If working out in the evening more than four hours before bedtime, high-intensity exercise can take place without risk of impacting sleep quality and physical health. If working out four hours or less before bedtime, it is better to opt for lower-intensity exercise, which will allow you to sleep better and recover more quickly. In the end, both studies show that being slightly more intentional about when and how hard you train can make a real difference in your sleep, recovery, and overall performance.

 

Works Cited

Liu, J., Xiao, F., Choubey, A., Kumar S, U., Wang, Y., Hong, S., Yang, T., Otlu, H. G., Oturmaz, E. S., Loro, E., Sun, Y., Saha, P., Khurana, T. S., Chen, L., Hou, X., & Sun, Z. (2025). Muscle Rev-erb controls time-dependent adaptations to chronic exercise in mice. Nature Communications, 16(1), 5708. https://doi.org/10.1038/s41467-025-60520-y

Leota, J., Presby, D. M., Le, F., Czeisler, M. É., Mascaro, L., Capodilupo, E. R., Wiley, J. F., Drummond, S. P. A., Rajaratnam, S. M. W., & Facer-Childs, E. R. (2025). Dose-response relationship between evening exercise and sleep. Nature Communications, 16(1), 3297. https://doi.org/10.1038/s41467-025-58271-x

Co-pyrolysis of Biomass and RDF for Waste to Energy Conversion

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One of the primary concerns regarding fossil fuels today is not only their massive environmental impact but their persistent dominance in the energy field. Growing waste, pollution and energy consumption and demand all prompt the search for alternative, renewable energy sources, for example, biomass. Biomass waste includes agricultural residues, such as crops, crop residues, animal waste, and food scraps. All of these can be thermochemically converted into fuel, chemicals, and other biobased materials for various applications, simultaneously reducing the amount of waste going into landfills. Biomasses are also widely available, have high moisture and volatile matter content, presence of alkali metals in ash, and display a wide range of different physical and chemical properties.  

Refuse Derived Fuel (RDF) is another example of waste with high energy potential. RDF is mainly composed of plastic waste, paper, textiles, and wood, containing high organic matter content, giving ita high calorific value. RDF is a fuel produced from municipal solid waste that has been processed to remove non-combustible materials, like metals, glass, and other inorganic materials, leading to relativelystable chemical properties and low moisture content. In return, this gives it a high energy potential. RDF also has a higher energy content than raw municipal solid waste, making it a more efficient fuel source. Itcan be easily transported and stored, making it a convenient fuel source for energy generation in the cement industry or in energy plants. However, the direct combustion of RDF can be potentially unsafe, causing the emission of hazardous substances.  

 Magdziarz et al., 2024 examines the co-conversion of biomass and RDF, specifically through a process called pyrolysis. Pyrolysis is a thermochemical conversion process carried out in an oxygen-free atmosphere (typically in nitrogen or argon) at a temperature above 300–400 ◦C. This leads to the production of three main products: syngas, pyro-oil (liquid or “bio-oil”), and pyro-char (solid or “bio-char”). Thedistribution of product yields depends directly on the conditions of the process (operational parameters) including the temperature, heating rate, residence time of the volatiles, the particle size of the feedstock, type of feedstock or biomass, etc. The syngas may be useful in generating heat and electricity, while the solid bio-char may be useful as a soil applicant, aiding in carbon sequestration, water retention, and nutrient availability. However, the main focus of this study was to improve the quality and quantity of produced bio-oil, which can be used as a renewable alternative to fossil fuels.  

Co-pyrolysis of biomass and RDF was considered a “good solution”, as it helps reduce deposited waste and improves the quality of bio-oil produced by overcoming some of the challenges associated with the pyrolysis of biomass alone, such as poor bio-oil quality due to the presence of impurities. Additionally, the process supports the development of circular economy principles by reducing the dependenceof fossil fuel resources. Previous studies focused on co-pyrolysis of biomass and plastics as opposed to RDF and found that minimizing the concentration of complex liquid compounds and heavy hydrocarbons improved the quality of syngas and liquid products. The addition of catalysts further improved bio-oil quality by increasing the content of hydrocarbons and reducing the content of oxygenated compounds in bio-oil. Pyrolysis of pure RDF can be problematic due to the formation of tar, wax, and other volatile organic compounds, causing equipment damage, reducing product quality, and increasing emissions.  

Additionally, Magdziarz et al., 2024 investigated two agricultural biomass feedstocks, rye straw (RS) and agriculture grass (AG), along with RDF, mainly composed of plastics. The pyrolysis process was conducted at 600 ◦C under a nitrogen atmosphere with a mass sample of 1 gram and residence time of 3 minutes. First, the pyrolysis of raw feedstocks was conducted to collect and analyze the properties of solid, liquid, and gas products. Then, co-pyrolysis experiments were conducted to investigate the impact of RDF addition on the properties of products with mixtures of 75:25 and 50:50 weight-percentage ratios (biomass to RDF mass ratio). Respectively, the samples were named: 75RS-25RDF, 75AG-25RDF, 50RS-50RDF, and 50AG-50RDF. RS and AG have similar physical and chemical properties, but AG containsa higher ash content and, consequently, lower volatile matter. Ash content and volatile matter both can influence the yield of products, as ash can catalyze undesirable secondary reactions (char oxidation or tar formation), reducing bio-oil yield, and higher volatile matter content generally correlates with the higher yield of gaseous products. The study analyzed the composition of volatile matter released during the pyrolysis process for both feedstocks and for the mixtures of biomass and RDF.  

In the case of the RDF sample, there were over 300 chemical compounds, while the biomass samples released about half as many chemical compounds. Therefore, the released analytes, especially forRDF, may be considered highly complex mixtures composed of compounds with different volatility.

Atomic Share for Biomass Samples by Percentage

For RS and AG as seen in the table above, the main group of compounds were oxygen compounds. Meanwhile, for RDF, hydrocarbons were the dominant volatile products, and the very low oxygen content for RDF (<2.85 weight%) resulted in a negligible CO2 content, unlike the biomass samples. For the four mixtures of biomass and RDF (75RS-25RDF, 75AG-25RDF, 50RS-50RDF, and 50AG-50RDF), the percentages of the groups of volatile compounds released were compared to the values estimated based on the linear model.


Atomic Share for Varying Mixtures of Biomass Samples by Percentage

In all four samples, the hydrocarbons and their oxygen derivatives were the dominant group of compounds released during co-pyrolysis. The release of hydrocarbons is arguablybeneficial for increasing the application potential of volatile pyrolysis products that can be a type of alternative fuel. Hydrocarbons can enhance the energy value of the fuel and after additional treatment, can be used as by-products to value-added materials. The study also noted that the observed share of hydrocarbons released during pyrolysis was significantly higher than calculated from the linear model, which correlated with the addition of RDF to the biomass samples. The increased percentage of hydrocarbons also correlated with a simultaneous decrease in the relative share of other groups of compounds, especially oxygen compounds, as well as significantly lower CO2 content than expected from the linear model’s calculation.  

Yields of Bio-char and Bio-oil for Varying Mixtures of Biomass Samples

The yields of the bio-char and bio-oil phases are presented in Figure 5 above. The char yield for AG was higher (27.3%) than for RS (21.2%). The addition of 50% RDF to biomass decreased the char yields to 16.2% and 13.2%, respectively. Bio-oil yield was higher for RS (35.9%) than for AG (29.9%). Results from previous studies also show higher bio-oil yields and lower bio-char yieldsas RDF percentage increased. As predicted, co-pyrolysis of RDF with biomass gave a better synergetic effect for RS than for AG with the RS samples producing a higher ratio of bio-oil than the AG samples.The gas yield was calculated by the formula, 100% – char yield – liquid yield, and the pure RS and AG samples had similar gas yields at around 40%. The presence of RDF did not significantly influence gas yield for AG, but for RS (50RS-50RDF) decreased the yield by 13%. Gas yields consisted mainly of CO, CO2, H2, and CH4. The calorific value of gas from RS pyrolysis was higher than for AG. The addition of RDF for both biomasses (50RS-50RDF and 50AG-50RDF) decreased the content of CO and H2 and simultaneously increased the amount of CO2 and CH4 product. However, the study mentions that the gas yields from co-pyrolysis were not a concern, as the main goal was to obtain bio-oil. 

The main conclusions for the study were that for mixtures of biomass and RDF the content of oxygen in volatiles was significantly reduced, while the content of hydrocarbons was increased, and co-pyrolysis of biomass and RDF confirmed the benefits of RDF addition, which positively influenced product yields and quality. The co-pyrolysis of the AG and RS (waste materials) with RDF offers another method to contribute to circular economics and sustainable waste management. Co-pyrolysis of biomass and RDF may potentially be effective ways to convert waste into energy and produce useful bio-char, bio-oil, and even various gaseous products. Future studies should focus on the type of feedstock used and various parameters of the pyrolysis process to ensure that the process is as efficient, sustainable, and environmentally friendly as possible.  

 

References

Magdziarz, A., Jerzak, W., Wądrzyk, M., & Sieradzka, M. (2024). Benefits from co-pyrolysis of biomass and refuse derived fuel for biofuels production: Experimental investigations. Renewable Energy, 230, 120808. https://doi.org/10.1016/j.renene.2024.120808

MMOF Hydrogels: A New Tool in Aquatic Dye Removal

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Every year, over 280,000 tons of synthetic dyes are introduced into aquatic environments as wastage from textile mills. This significant amount of runoff accounts for the augmentation of environmental contamination in several countries, including China, and can have detrimental effects on aquatic life. For example, decreased red blood cell count has been observed in mosquitofish, and liver degeneration in Mozambique tilapia (Dutta et al. 2024).

Previous studies have attempted to use polyacrylamide hydrogels to selectively remove contaminants from an environment. However, the process of creating these hydrogels was found to be too complex and therefore impractical for real-world applications (He et al. 2021). Cheng et al. describe a sodium alginate hydrogel with increased selectivity to a pollutant, malachite green (MG) dye, and heightened adsorptive properties through enhancement with magnetic and MOF materials. 

Metal-organic frameworks, or MOFs, are a class of crystalline materials that are made up of a metal ion or cluster and organic linkers. They are extremely porous (~90% free volume) and have extremely high internal surface areas (beyond 6000m^2/g) (Zhou, Long, Yaghi. 2012). These properties, along with the adjustability of their composition, have made MOFs of interest for applications as high-capacity adsorbents for pollutants.

To create their MOF, the researchers dissolved two metal solids, FeCl3·6H2O & FeCl2·4H2O, in water and ethanol, centrifuged, and collected Fe3O4 nanoparticles. They then added another hydrated metal, ZrOCl2·8H2O, and TCPP (the organic linker) to the solution, washed with DMF solvent to dissolve the metals and linkers, and obtained their MOF: Fe3O4@MOF-545 with an average particle size of 1100nm.

Structure of a Zr-based MOF-545
Figure 1. Zr-based MOF-545. Adapted from 2024 Chen et al.

 

Next, they created a solution of their MOF, 4.2% sodium alginate, TEMED, and acrylamide to form the polyacrylamide hydrogel. The resulting solution was added drop-by-drop to a CaCl2 solution to form microspheres and stirred magnetically for an hour to obtain the MMOF hydrogel (magnetic MOF hydrogel). The researchers used scanning electron microscopy to characterize the MMOF hydrogel and found that the MMOF hydrogel had a microporous structure and clear surface grooves, enhancing its surface area and adsorptive capacity. (Figure 2)

Scanning electron microscopy of the MMOF hydrogel. The surface grooves and external and internal porous structure are visible.
Figure 2. (A) SEM image of MMOF hydrogel. (B-C) Notable grooves are seen on the surface of the MMOF hydrogel. Adapted from 2025 Cheng et al.

To confirm the heightened performance of the MMOF hydrogel, the researchers compared its dye adsorption and selectivity for MG dye compared to a magnetic hydrogel and a pure hydrogel.  The resulting MMOF hydrogel was found to be a significantly more effective adsorptive agent for MG dye than the other types of hydrogels (Figure 3), further showing the effectiveness of MOFs in increasing adsorption. The MMOF hydrogel also displayed enhanced selectivity to MG dye when applied to the surface of aquatic tissues in situ (Figure 4). 

 

Picture of hydrogel, MOF hydrogel, and MMOF hydrogel placed in solution containing MG dye. The container with MMOF hydrogel is the only one that became clear with no blue color left over, showing the higher adsorption rate of the MMOF hydrogel. The graph to the right of the image further supports this as MMOF hydrogel adsorption rate is over 90%.
Figure 3. Adsorption rate of MMOF hydrogel compared to magnetic hydrogel and hydrogel. MMOF hydrogel displayed greater MG dye adsorption than the magnetic hydrogel and hydrogel. Adapted from 2025 Cheng et al.

 

MMOF hydrogels placed on fish tissue with MG and other dyes on the surface. The hydrogels fully remove the MG dye.
Figure 4. MMOF hydrogel selectivity tested through application of fish tissue containing MG, acridine yellow, methylene blue, carmine, and crystal violet dyes. MMOF hydrogel shown to selectively remove MG dye from environment when in proximity to other dyes. Adapted from 2025 Cheng et al.

Cheng et al. then tested MMOF hydrogels with different characteristics to find material and environmental conditions for optimal adsorption. They found that sodium alginate concentration and MOF:hydrogel weight ratio were associated with the adsorptive capacity of the MMOF hydrogels. The optimal sodium alginate concentration was found to be 4.2%, and the optimal MOF:hydrogel weight ratio was found to be 12.

The researchers also tested the MMOF hydrogel in different environmental conditions to determine its limitations and where it performed best. They observed that the MMOF hydrogels showed the greatest adsorption at an MG dye concentration of 100mg/L (Figure 5A). This is due to the increased competition of MG molecules for adsorption sites on the surface of the MMOF hydrogel at higher concentrations. They also found that adsorption plateaued at MMOF hydrogel weight concentrations higher than 20mg/mL (Figure 5B) due to the adsorption sites on the hydrogel reaching equilibrium. Additionally, adsorption was highest at an MG solution pH of 6 (Figure 5C). At lower pH, H+ ions would compete with MG by due to the negatively charged functional group on the MMOF hydrogel. At higher pH, the carboxyl group on the MMOF hydrogel is ionized, decreasing the adsorption rate of MG dye. The adsorption rate of MG dye by the MMOF hydrogel was also found to show little decrease after 25 days of storage at 60ºC, indicating the strong stability of the material. 

Image containing Graphs A, B, C.A: Conc. vs adsorption rate. Adsorption rate peaks at conc of 100mg/L B: MMOF hydrogel weight concentration vs adsorption rate. adsorption rate peaks at 20mg/ml C: pH vs adsorption rate. Adsorption rate peaks at pH 6.
Figure 5. (A) MMOF hydrogel MG dye adsorption rate peaked at MG concentration of 100 mg/L. (B) Adsorption remains almost the same at MMOF hydrogel weight concentrations of 20mg/L and higher. (C) When the concentration of the MG solution is 100 mg/mL, the pH of the MG solution alters the adsorptive capacity of the MMOF hydrogel with the highest adsorption being observed at pH 6. Adapted from 2025 Cheng et al.

In their work, Cheng et al. have successfully created stable and easy-to-replicate MMOF hydrogels showing high adsorptive capacity and selectivity to MG dye for aquatic tissue in situ. The easily modifiable structure of MOFS also opens the door to the production of MMOF hydrogels selective to other dyes as well. This research has great potential applications for the pretreatment of aquatic products like fish before they reach the market. If automated and integrated into the screening processes of aquatic products, these MMOF hydrogels could strengthen quality control and increase the safety of products that are entering the market.

 

References

Chen, H., Brubach, J.-B., Tran, N.-H., Robinson, A. L., Ferdaous Ben Romdhane, Mathieu Frégnaux, Francesc Penas-Hidalgo, Solé-Daura, A., Mialane, P., Fontecave, M., Dolbecq, A., & Mellot-Draznieks, C. (2024). Zr-Based MOF-545 Metal–Organic Framework Loaded with Highly Dispersed Small Size Ni Nanoparticles for CO2 Methanation. ACS Applied Materials & Interfaces, 16(10), 12509–12520. https://doi.org/10.1021/acsami.3c18154

Cheng, L., Lu, Y., Li, P., Sun, B., & Wu, L. (2025). Metal–Organic Framework (MOF)-Embedded Magnetic Polysaccharide Hydrogel Beads as Efficient Adsorbents for Malachite Green Removal. Molecules, 30(7), 1560–1560. https://doi.org/10.3390/molecules30071560‌

Dutta, S., Adhikary, S., Bhattacharya, S., Roy, D., Chatterjee, S., Chakraborty, A., Banerjee, D., Ganguly, A., Nanda, S., & Rajak, P. (2024). Contamination of textile dyes in aquatic environment: Adverse impacts on aquatic ecosystem and human health, and its management using bioremediation. Journal of Environmental Management, 353(120103), 120103. https://doi.org/10.1016/j.jenvman.2024.120103‌

Zhou, H.-C., Long, J. R., & Yaghi, O. M. (2012). Introduction to Metal–Organic Frameworks. Chemical Reviews, 112(2), 673–674. https://doi.org/10.1021/cr300014x










Floating Systems: Jellyfish and Evolving Nervous Systems

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Jellyfish are just one species within the phylum cnidaria. A phylum is a broad level of taxonomic classification that includes many different species, with cnidaria additionally including coral and anemones. Cnidaria provides comparative neuroscience information due to the simple behaviors that the species within the phylum exhibit. Despite their shared phylum that creates nerve cells with similar properties, the species have dramatically different nervous systems, allowing for unique perspectives on the diversity, origins, and evolution of neural systems within species (Cunningham et al., 2024). Comparative neuroscience information is the study of nervous systems across a variety of animal species. Through this research, the evolutionary changes in the brain’s structure can be examined, allowing scientists to see how differences in nervous systems shape certain behaviors (Miller et al., 2019). Neuroscience researchers can use an all-optical interrogation, in which they study and manipulate neural systems using light, upon these species, allowing them to image and photograph the neuronal networks in the creature for further examination. 

Fig 1. Photo of Clytia hemisphaerica (Clytia Hemisphaerica Medusa – 13673149 ❘ Science Photo Library, n.d.)

Jellyfish are major contributors to ocean ecosystems. Their reproductive, foraging, and defensive behaviors all uniquely impact the ecosystem at large. What is notable about jellyfish, however, is that these behaviors are shaped out of decentralized, regenerative nervous systems. Rather than the creature being controlled by the neurons in its brain, the jellyfish’s neurons are spread throughout the body (“Thinking without a Centralized Brain,” n.d.). This allows the various parts of its body to have a role in controlling and processing information. Additionally, the nervous system itself has the ability to repair and restore itself, allowing damaged nerves to be replaced by new ones (Gaskill, 2018). 

Jellyfish are the most complicated species of Cnidaria, due to various behaviors that demonstrate their higher level functioning compared to other species in the phylum. They have the ability to move in 3-dimensions, capture and consume other creatures, and the ability to escape from predators and other potential threats. Notably, jellyfish also exhibit courtship behaviors and sleep states, despite lacking a central brain. These behaviors are  due to their sensory structures, made up by two nervous systems: one which controls their swimming and another that controls all other behaviors. The jellyfish’s nervous systems can respond to each other, despite the lack of a central controller (Cunningham et al., 2024). 

A recent scientific investigation conducted at Caltech by Anderson et al. sought to explore how the jellyfish can be used to conduct neuroscience research. Clytia hemisphaerica is a species of jellyfish that has recently been adopted into a genetic neuroscience model. It has previously been used as a model to study evolution, embryology, regeneration, and other fields. This species of jellyfish is a particularly useful model for neuroscience research because its genome is already sequenced and assembled from the birth of the creature, with whole-animal single-celled Ribonucleic Acid (RNA) sequences formed within the species. Rather than using multiple animals to sequence the RNA, Clytia hemisphaerica has the capability to provide the necessary amounts of cells needed to be examined. Using multiplexed single-cell RNA sequencing, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run (Chari et al., 2021). Clytia hemisphaerica is the only jellyfish whose RNA sequences are being used to rapidly develop genomic tools. These tools can be tested and utilized by researchers, allowing them to explore brain function and neurological disorders through this model (Cunningham et al., 2024).

The last common ancestor of Clytia hemisphaerica was a hydrozoan jellyfish, which are able to perform specific behaviors even if certain body parts are detached from the body. Hydrozoan jellyfish, notably, have the ability to cycle back and forth between various stages of their life–allowing them to live for large expanses of time. When the body parts exist in an intact organism, they also have the ability to perform more complex behaviors. These include different feeding behaviors and mechanisms. The swimming behavior of the Clytia hemisphaerica also reveals key information about the neuromechanics behind different behaviors of jellyfish. As an example, although jellyfish spend a majority of their lives swimming, there are periods where they may start and stop. These periods are only exhibited when there is food passing or defensive behaviors are exhibited. When these behaviors are examined, neuroscientists can ponder and develop further conclusions about multi-sensory integration, motor control, and the mechanisms that underlie behavioral states (Cunningham et al., 2024). Figure 1

Fig 2. The Evolution, Life Cycle, and Genetic Tools of Clytia hemisphaerica (Cunningham et al., 2024)

Through using neural population imaging, in which researchers have the ability to monitor large groups of neurons through calcium and voltage imaging, on the whole-organism scale through the Clytia hemisphaerica, emergent properties of function networks can be uncovered (Zhu et al., 2022). Without this model, scientists would have to use traditional single-cell unit recordings, requiring using fine tools just to see the individual activity of a single neutron, or anatomical studies, which would not provide the same amount of potential discoveries that new techniques with Clytia hemisphaerica provide. Through using this species as a model, researchers can uncover more knowledge and data about nervous system evolution and function, particularly for neural regeneration.

Neural regeneration is particularly important in the treatment of injury and disease in the nervous system. It aids in cognitive recovery following neurodegeneration, helping rebuild neurons and nervous tissue (Steward et al., 2013). Through neural regeneration, the nervous system may regain its functions, allowing for betterment of quality of life. By continuing to examine species capable of neural regeneration, we may learn to apply this to the human nervous system, allowing us to move forward in curing traumatic brain injuries and degeneration of the brain and its abilities (Neuroregeneration – an Overview | Sciencedirect Topics, n.d.).

 

 

 

 

 

References:

Chari, T., Weissbourd, B., Gehring, J., Ferraioli, A., Leclère, L., Herl, M., Gao, F., Chevalier, S., Copley, R. R., Houliston, E., Anderson, D. J., & Pachter, L. (2021). Whole animal multiplexed single-cell rna-seq reveals plasticity of clytia medusa cell types. bioRxiv. https://doi.org/10.1101/2021.01.22.427844

Cunningham, K., Anderson, D. J., & Weissbourd, B. (2024). Jellyfish for the study of nervous system evolution and function. Current Opinion in Neurobiology, 88, 102903. https://doi.org/10.1016/j.conb.2024.102903

Gaskill, M. (2018, November 20). No brain? For jellyfish, no problem | blog | nature | pbs. Nature. https://www.pbs.org/wnet/nature/blog/no-brain-for-jellyfish-no-problem/

Miller, C. T., Hale, M. E., Okano, H., Okabe, S., & Mitra, P. (2019). Comparative principles for next-generation neuroscience. Frontiers in Behavioral Neuroscience, 13. https://doi.org/10.3389/fnbeh.2019.00012

Neuroregeneration—An overview | sciencedirect topics. (n.d.). Retrieved April 27, 2025, from https://www.sciencedirect.com/topics/neuroscience/neuroregeneration

Steward, M. M., Sridhar, A., & Meyer, J. S. (2013). Neural regeneration. Current Topics in Microbiology and Immunology, 367, 163–191. https://doi.org/10.1007/82_2012_302

Thinking without a centralized brain: The intelligence of the octopus. (n.d.). WHYY. Retrieved April 27, 2025, from https://whyy.org/segments/thinking-without-a-centralized-brain-the-intelligence-of-the-octopus/

Zhu, F., Grier, H. A., Tandon, R., Cai, C., Agarwal, A., Giovannucci, A., Kaufman, M. T., & Pandarinath, C. (2022). A deep learning framework for inference of single-trial neural population dynamics from calcium imaging with sub-frame temporal resolution. Nature Neuroscience, 25(12), 1724–1734. https://doi.org/10.1038/s41593-022-01189-0

Identification of Underlying Apoptotic Pathways in MCF-7 Breast Cancer Cells via CRISPRa Upregulation of HtrA2/Omi

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This experiment investigated a possible candidate for cancer treatment utilizing a cell’s own function for programmed cell death. The purpose of this study was to determine if upregulation of the apoptotic gene HtrA2/Omi in breast cancer cells would lead to increased apoptosis in the cells. Previous literature had described upregulation of apoptotic pathways as a possible viable mechanism for cancer treatment. However, this study did not find significant results to support these claims. 

Breast cancer, one of the most prevalent forms of cancer in the world, disproportionately affects women in the United States. On average, 13 percent of women in the United States will be diagnosed with breast cancer at some point during their lifetime (Breast Cancer Facts and Statistics 2023). Every year, 42,000 women die from breast cancer in the United States, with 240,000 more diagnosed with breast cancer (Basic Information About Breast Cancer 2023). 

Cells undergo a highly regulated process of programmed cell death called apoptosis that allows for natural development and growth of the organism. Through apoptosis, organisms are able to destroy surplus, infected, and damaged cells. Cancerous tumors develop when the apoptosis function of a cell is not working properly, resulting in a malignant cell that can grow and divide uncontrollably into a tumor. As apoptosis pathways can be induced non-surgically, it is a highly effective method used to control or terminate malignant cancer cells. By utilizing the cell’s own mechanism for death, research for cancer treatment has identified apoptosis as a way to target malignant tumors (Pfeffer et al., 2018). 

Research has shown that apoptosis is induced by overexpressing certain genes. HtrA2/Omi is a gene that induces apoptosis when overexpressed in the cell. When released from the mitochondria, HtrA2 inhibits the function of an apoptosis inhibitor, effectively inducing cell death (Suzuki et al., 2001). These data suggest that modulating and upregulating HtrA2 expression shows promising findings in enhancing apoptosis in breast cancer. 

CRISPR-Cas9 is a type of cellular biotechnology which can be used to study the manipulation of genomes by either adding, deleting, or altering genetic material in specific locations. This tool can be used to overexpress the HtrA2 gene in order to induce cell death. The process of CRISPR-Cas9 involves using sgRNA (a single guide RNA) with an enzyme to act as a gene-editing tool and introduce mutations into a desired target sequence in the genome. In order to modulate the HtrA2 gene, this experiment will require CRISPRa, a variant of CRISPR that uses a protein (dCas9) and transcriptional effector. The sgRNA navigates to the genome locus, guiding the dCas9. The dCas9 is unable to make a cut, so the effector instead activates the desired downstream gene expression (“Chapter 2: CRISPRa,” n.d.). This experiment will use CRISPRa technology to upregulate the HtrA2/Omi gene, which will inhibit the X chromosome-linked inhibitor of apoptosis, inducing either caspase-dependent cell death or Caspase-3 independent cell death in MCF-7 cells.

The pilot study for this experiment was conducted to determine the optimal level of Lipofectamine – which is a reagent that can be used for an efficient transfection without causing the cells to undergo apoptosis. The Lipofectamine concentration was varied to identify the fold change it would create in the expression of the target gene, HtrA2/Omi. After statistical analyses, researchers found no statistically significant correlation between the HtrA2/Omi gene expression and the Lipofectamine concentration in this experiment.

Fig. 1. After the transfection, qPCR was conducted on the control, 100% Lipofectamine, 75% Lipofectamine with sgRNA, and 75% Lipofectamine without sgRNA. The average Ct values were calculated and graphed.

Overall, the results from conducting quantitative PCR (qPCR), which shows how much of the HtrA2 was transfected, demonstrated extreme variance, indicating that there may have been errors that significantly affected these results. One possible error was that qPCR was conducted as cells were undergoing apoptosis, which would skew the results as mRNA is destroyed in cells as they die, leaving fragments behind. Another error observed throughout this experiment was high cell confluence (number of cells covering the adherent surface). Much of this experiment was conducted with cells at 100% or almost 100% confluence, which means it is possible that the concentrations of Lipofectamine that were predicted to cause efficient transfection did not work because the reagent could not enter the cells. Ultimately, it was found that a cell seeding concentration of 1*104 cells/mL worked best with regard to transformation, but the experiment still did not yield statistically significant results.

Fig. 2. For the pilot experiment, mCherry plasmid was transfected in MCF-7 cells. The following ZOE images showed the images of MCF-7 before transfection under different fluorescence as well as the merged image of both green and red fluorescence.

 

References

ATCC. (n.d.). MCF-7. ATCC. Retrieved November 17, 2021, from https://www.atcc.org/products/htb-22

Breast cancer facts and statistics, 2023. (n.d.). https://www.breastcancer.org/facts-statistics

Siegel, R. L., Miller, K. D., Fuchs, H., & Jemal, A. (2021). Cancer Statistics, 2021. CA: A Cancer Journal for Clinicians, 71(1), 7–33. https://doi.org/10.3322/caac.21654

Basic Information About Breast Cancer, 2023. https://www.cdc.gov/cancer/breast/basic_info

Pfeffer, C. M., & Singh, A. T. K. (2018). Apoptosis: A Target for Anticancer Therapy. International Journal of Molecular Sciences, 19(2), 448. https://doi.org/10.3390/ijms19020448

Suzuki Y, Imai Y, Nakayama H, Takahashi K, Takio K, Takahashi R. A serine protease, HtrA2, is released from the mitochondria and interacts with XIAP, inducing cell death. Mol Cell. 2001 Sep;8(3):613-21. doi: 10.1016/s1097-2765(01)00341-0. PMID: 11583623.

Hu, Q., Myers, M., Fang, W., Yao, M., Brummer, G., Hawj, J., Smart, C., Berkland, C., & Cheng, N. (2019). Role of ALDH1A1 and HTRA2 expression in CCL2/CCR2-mediated breast cancer cell growth and invasion. Biology open, 8(7), bio040873. https://doi.org/10.1242/bio.040873

Camarillo, Ignacio G., et al. “4 – Low and High Voltage Electrochemotherapy for Breast Cancer:

An in Vitro Model Study.” ScienceDirect, Woodhead Publishing, 1 Jan. 2014. www.sciencedirect.com/science/article/abs/pii/B9781907568152500042.

Rouhimoghadam M, Safarian S, Carroll JS, Sheibani N, Bidkhori G. Tamoxifen-Induced Apoptosis of MCF-7 Cells via GPR30/PI3K/MAPKs Interactions: Verification by ODE Modeling and RNA Sequencing. Front Physiol. 2018 Jul 11;9:907. doi: 10.3389/fphys.2018.00907. PMID: 30050469; PMCID: PMC6050429.

Mooney, L. M., Al-Sakkaf, K. A., Brown, B. L., & Dobson, P. R. (2002). Apoptotic mechanisms in T47D and MCF-7 human breast cancer cells. British journal of cancer, 87(8), 909–917. https://doi.org/10.1038/sj.bjc.6600541

Suzuki, Y., Takahashi-Niki, K., Akagi, T. et al. Mitochondrial protease Omi/HtrA2 enhances caspase activation through multiple pathways. Cell Death Differ 11, 208–216 (2004). https://doi.org/10.1038/sj.cdd.440134

Chapter 2: CRISPRa and CRISPRi. (n.d.). In A Comprehensive Guide on CRISPR Methods. https://www.synthego.com/guide/crispr-methods/crispri-

Better Bonds and New Molecules

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Keywords – chemical bonds, covalent bonds, ionic bonds, ions, free radicals, dissociation, synthesis, stimuli, heterolysis

Free radicals are typically atoms that are most commonly found in diatomic molecules (for example, Oxygen) that are not bonded, so they tend to bond to the first available molecule and are therefore very unpredictable. Free radicals are atoms with unpaired electrons attached. They are commonly found in the body or in the environment. Having unpaired electrons means that they are volatile and can randomly bond to other molecules, creating toxic compounds if they become too abundant. 

By contrast, ions are atoms with charges that create much more predictable bonds in nature. Like free radicals, ions have a different number of electrons (negatively charged parts) than protons (positively charged parts). However, ions have paired electrons and occur more naturally in the body. Ions are essential for communication between cells.

The synthetic breakdown – or dissociation – of molecules in solutions or bodily environments often releases free radicals instead of ions. This new study explores the possibility of using energy differently to reduce the release of free radicals in synthetic dissociation. The replacement of free radicals with ions will reduce harm to the body, as well as the environment. This opens up new possibilities for the creation of new medicines and more efficient biofuels.

Heterolysis results in the release of ions rather than free radicals. The Nuerberger and Breder lab conducted experiments that center around the understanding that many molecules can not be dissociated into their respective atomic contents via heterolysis, a process that involves breaking molecular bonds by using two different energetic stimuli rather than one (for example, light and heat rather than one or the other). The challenge here is to balance the use of heat and light to efficiently break down molecules without harmful byproducts like free radicals.

This procedure begins with determining the lambda-max value, which is the optimal wavelength of light that will maximize the absorbance in a certain molecule, for the molecules PhSe, PhSe+, and PhSe- (Breder, 2024). These are charged compounds consisting of a Selenium atom attached to a phenyl group, or a six-Carbon ring with five attached Hydrogen atoms. These molecules were selected to mimic the complexity and size of many biological molecules found in the body.

Next, the researchers determined the amount of energy that could be absorbed from a light source with the calculated lambda-max wavelength. This data was obtained through the use of absorbance sensors, which shine a broad spectrum of light with various wavelengths and can detect which wavelengths are blocked the most by dissolved particles. All substances have a lambda-max value, which is why we are able to see in color. Even samples that appear to be colorless have a slight color to them. The lambda-max value of a sample will typically correspond to its complementary color in the red-blue-green system (for example, the lambda-max value for a green substance will correspond to a shade of purple light).

Once the lambda-max values were determined for each substance, the researchers calculated how much energy was contained in the absorbed light. This value was subtracted from the known amount of energy required to break the Se-C (Selenium-Carbon) bonds. The remaining energy was supplemented in the form of heat, and the molecules in turn dissociated with a much higher frequency of ions and atoms with paired electrons than free radicals (Breder, 2024). Researchers were able to quantify the difference in ion dissociation from free radicals by determining experimental lambda-max values after exposure to the light and heat stimuli and comparing those of the ion products and of the free radical products. (see Figure 1 for comparison)

Figure 1. Comparison of average energy levels required to separate atoms via homolysis vs. heterolysis (Breder, 2024). 

 

This experiment demonstrates that the combined use of heat and light stimuli to dissociate molecules results in safer byproducts for the human body and the environment. This means that more diverse molecules can be created without extensive energy usage. This leap in chemistry expands into the biological and environmental fields of research, allowing for more complex and efficient medicines, implants, biofuels, plastic replacements, and more to be created.

This research has broad implications in the research world. In environmental sciences, the creation of biofuels can require several steps of synthesizing and dissociating molecules to achieve specific formulas and structures. The knowledge of how to minimize the release of volatile materials during this process is vital to ensuring that living organisms in nearby ecosystems are not harmed by the creation of more renewable fuels.

In medicine, a similar dilemma occurs with the creation of new drugs. While medicinal compounds are synthesized in controlled lab environments, their individual chemical formulas may be counterproductive in that they favor the release of free radicals in the body once administered into such an uncontrolled environment. In addition to reducing the abundance of free radicals in the synthesis of new materials, the knowledge of how to more efficiently construct and break apart molecules opens up new possibilities for entirely unique drug compounds. Ideally, many of these will serve the same functions but will be less structurally in favor of releasing free radicals into the body.

Works Cited

Sayre, Hannah J., and Harsh Bhatia. “Innovative Way to Break Chemical Bonds Broadens Horizons for Making Molecules.” Nature, vol. 632, no. 8025, Nature Portfolio, Aug. 2024, pp. 508–9, https://doi.org/10.1038/d41586-024-02437-y. Accessed 10 Oct. 2024.

Tiefel, Anna F., et al. “Unimolecular Net Heterolysis of Symmetric and Homopolar σ-Bonds.” Nature, vol. 632, no. 8025, Aug. 2024, pp. 550–56, https://doi.org/10.1038/s41586-024-07622-7.

From Milk to Malignancy – Breast Cancer and its Metabolic Implications 

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The annual rise of cancer cases has created a high demand for new innovative treatments and has made cancer a prominent topic in the scientific community. According to the American Cancer Society (ACS), approximately 20 million new cancer cases were diagnosed worldwide in 2022, leading to 9.7 million deaths [1]. It is expected that by 2050, cancer cases will reach 35 million, largely due to population growth [1]. While significant advancements have been made in cancer research, the complexity of different cancer types presents challenges. 

One of the most prevalent forms is breast cancer, which, in 2022, was the second most common cancer in the U.S., with 2.3 million new cases, predominantly affecting women [2]. Unlike many cancers, breast cancer is not a single disease but a collection of subtypes characterized by distinct clinical, morphological, and molecular features. This heterogeneity makes it challenging to study and treat effectively. A recent study published in Nature Metabolism explores the metabolic differences between normal mammary cells and breast cancer cells [4]. Understanding these metabolic processes could pave the way for new, targeted therapies. Researchers have identified specific metabolic vulnerabilities in mammary epithelial cells, which line the breast tissue.

 

Figure 1. Non-tumorigenic Mammary Gland Components. A diagram of a non-tumorigenic mammary gland showing a cluster of alveoli containing luminal and basal cells. Luminal cells line the milk ducts and alveoli and are responsible for milk secretion during lactation. Basal cells are believed to play a role in transporting milk to the nipple during lactation. Source: Created in BioRender, [4], [10], [11].

In the normal mammary gland, various types of cells carry out specific functions, one of which is the progenitor cells. These progenitor cells generate distinct alveolar structures that continuously form in the adult breast, and their activity is crucial for maintaining normal mammary homeostasis [5]. Progenitor cells are located in the luminal compartment [6], which is also home to the luminal cells. The luminal cells play a key role in lactation by lining the milk ducts and alveoli, where they secrete milk (Figure 1)[7]. In contrast, basal cells are located around the luminal cells and are believed to function during lactation by helping to transport milk to the nipple (Figure 1)[7]. Although these mammalian epithelial cells (luminal and basal cells) are important to the function of normal mammary glands, these also serve as a tumour cell of origin [4].

In their study, Mahendralingam et al. used mass spectrometry to analyze the metabolic profiles of normal human mammary cells [8]. They discovered that luminal progenitor cells primarily rely on oxidative phosphorylation for energy, whereas basal cells depend more on glycolysis [4]. This distinction is crucial because oxidative phosphorylation is an efficient, oxygen-dependent process that generates substantial energy, while glycolysis, though faster, is less efficient and does not require oxygen — a pathway often favored by cancer cells to support rapid growth [9]. Targeting these distinct energy pathways could lead to more effective treatments for different breast cancer subtypes.

However, a new discovery was that breast cancer cells appear to adopt the metabolic programs of their cells of origin [4,9]. This complicates treatment since the cancer cells may still be vulnerable to metabolic pathways that are important for normal cell function. As a result, treatments designed to target specific metabolic pathways might not work as expected, since the cancer cells might behave similarly to the healthy cells from which they originated. 

The results from Mahendralingam et al. can form a basis for future metabolic studies that may lead to specific anti-tumoral drug therapies designed to treat specific breast cancer subtypes. This type of research lays a foundation for targeted approaches but further studies are needed to assess how findings, such as this one, can translate into clinical practice. As breast cancer continues to rise, understanding the complexity is more important than ever. 

 

Work Cited: 

  1. Global Cancer Facts & Figures. (n.d.). Retrieved October 27, 2024, from https://www.cancer.org/research/cancer-facts-statistics/global-cancer-facts-and-figures.html
  2. Global cancer burden growing, amidst mounting need for services. (n.d.). Retrieved October 27, 2024, from https://www.who.int/news/item/01-02-2024-global-cancer-burden-growing–amidst-mounting-need-for-services
  3. Sánchez López de Nava, A., & Raja, A. (2024). Physiology, Metabolism. In StatPearls. StatPearls Publishing. http://www.ncbi.nlm.nih.gov/books/NBK546690/
  4. Alfonso-Pérez, T., Baonza, G., & Martin-Belmonte, F. (2021). Breast cancer has a new metabolic Achilles’ heel. Nature Metabolism, 3(5), 590–592. https://doi.org/10.1038/s42255-021-00394-8
  5. Tharmapalan, P., Mahendralingam, M., Berman, H. K., & Khokha, R. (2019). Mammary stem cells and progenitors: Targeting the roots of breast cancer for prevention. The EMBO Journal, 38(14), e100852. https://doi.org/10.15252/embj.2018100852
  6. Tornillo, G., & Smalley, M. J. (2015). ERrrr…Where are the Progenitors? Hormone Receptors and Mammary Cell Heterogeneity. Journal of Mammary Gland Biology and Neoplasia, 20(1–2), 63–73. https://doi.org/10.1007/s10911-015-9336-1
  7. New Paradigm for Mammary Glands. (n.d.). Massachusetts General Hospital. Retrieved December 8, 2024, from https://www.massgeneral.org/cancer-center/clinician-resources/advances/new-paradigm-for-mammary-glands
  8. Mahendralingam, M. J., Kim, H., McCloskey, C. W., Aliar, K., Casey, A. E., Tharmapalan, P., Pellacani, D., Ignatchenko, V., Garcia-Valero, M., Palomero, L., Sinha, A., Cruickshank, J., Shetty, R., Vellanki, R. N., Koritzinsky, M., Stambolic, V., Alam, M., Schimmer, A. D., Berman, H. K., … Khokha, R. (2021). Mammary epithelial cells have lineage-rooted metabolic identities. Nature Metabolism, 3(5), 665–681. https://doi.org/10.1038/s42255-021-00388-6
  9. ZHENG, J. (2012). Energy metabolism of cancer: Glycolysis versus oxidative phosphorylation (Review). Oncology Letters, 4(6), 1151–1157. https://doi.org/10.3892/ol.2012.928
  10. Fig. 3 Stem cell in glandular and stratified epithelia. A A schematic… (n.d.). ResearchGate. Retrieved December 7, 2024, from https://www.researchgate.net/figure/Stem-cell-in-glandular-and-stratified-epithelia-A-A-schematic-model-depicting-the_fig3_374804603
  11. Model of normal mammary gland structure. This tissue is composed of… (n.d.). ResearchGate. Retrieved December 8, 2024, from https://www.researchgate.net/figure/Model-of-normal-mammary-gland-structure-This-tissue-is-composed-of-ducts-which-are_fig1_357239665

Engineered Nanoparticles Enable Selective Gene Therapy in Brain Tumors

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Inborn protective mechanisms present challenges for therapies targeting cancers of the brain. Engineered nanoparticles permit the selective delivery of CRISPR-Cas9 to glioblastoma tumors.

Glioblastoma accounts for almost half of all cancerous tumors originating in the brain.1 Even with maximum safe treatment, the median survival period for patients is less than 1.5 years.2 However, survival varies widely by age, from a 0.9% 5-year survival rate for patients over 75 years old to an 18.2% 5-year survival rate for patient 0-19 years old.3 Nevertheless, the overall 5-year survival rate remains low at 5%2 and novel therapies are urgently needed for glioblastoma treatment. Zou et al. present a highly specific CRISPR-Cas9-based gene therapy for glioblastoma.4

Gene therapies offer an attractive treatment for cancers. The goal of gene therapy is to mutate or remove deleterious DNA sequences such that they are unable to be transcribed and translated into functioning proteins. In the most prevalent technique, CRISPR-Cas9, single guide RNA (sgRNA) identifies and binds to the target DNA sequence. It then recruits Cas9 proteins to excise parts of the target DNA sequence. Mutations are generated as the cell tries to repair the damaged DNA.5

While a powerful tool, researchers have struggled to effectively deliver CRISPR-Cas9 to their cellular target. Delivery is particularly complex in brain tumors such as glioblastoma. Traditionally medications are trafficked through the body and delivered to their target through the bloodstream. However, the brain is a more complex and protected system. Primarily, selective delivery of therapeutics to tumor cells is necessary to protect neuronal function. Moreover, the brain is separated from the blood stream by a thin layer of cells termed the blood-brain barrier (BBB). The BBB allows for selective permeation of compounds into the brain, shielding neurons from toxins while permitting the passage of essential nutrients.6 Previous studies have sought to transport CRISPR-Cas9 therapies across the BBB using viruses as delivery capsules7 or circumvent the BBB altogether via intercranial injection of therapeutics.8 Yet these methods carry risk, either an immune response to the viral vector or complications from the invasive injection.

Zou et al. sought to resolve the issues of specific cell targeting and BBB permeability in CRISPR-Cas9 delivery by encapsulating the gene editing complex within a nanoparticle. The researchers chose to target Polo-like kinase 1 (PLK1) using CRISPR-Cas9 gene therapy. PLK1 is an attractive for selective gene therapy due to its higher overexpression by glioblastoma cells and by the proliferative glioblastoma subtype in particular.9 Moreover, inhibition of PLK1 has been shown to reduce tumor growth and induce cell death.9

The researchers encapsulated Cas9 and sgPLK1 in a neutrally charged nanoparticle for delivery. The small size of nanoparticles, which are measured in nanometers, allow for easy transport through the bloodstream and uptake by cells. Taking advantage of the high expression of lipoprotein receptor-related protein-1 (LRP-1) on both BBB endothelial cells and glioblastoma tumor cells, they decorated the nanocapsule surface with LRP-1 ligand angiopep-2 peptide to facilitate selective uptake by BBB and glioblastoma cells (Figure 1). Zou and her colleagues bound the nanoparticle together with disulfide bonds as an added layer of selectivity for glioblastoma cell delivery. In the high glutathione environment of a glioblastoma cell, the nanoparticle dissolves, releasing its contents. However, glutathione concentrations are lower in BBB endothelial cells and healthy neurons, reducing the dissolution of the nanoparticles and leaving healthy DNA alone.

 

Figure 1. Nanoparticles enable permeation of the blood brain barrier (BBB) and selective delivery of the CRISPR/Cas9 system to glioblastoma (GBM) cells. Angiopep-2 peptides, which decorate the nanoparticle’s surface, bind with lipoprotein receptor-related protein-1 (LRP-1) overexpressed on BBB and GBM cells. Following uptake into GBM cells, the nanoparticles dissolve in the high glutathione environment, releasing the Cas9 nuclease and single guide RNA (sgRNA) targeting Polo-like kinase 1 (PLK-1) genes. Zou et al. demonstrated the selective mutation of PLK-1 induced apoptosis in GBM cells with minimal off-target effects.

 

Through Cas9/sgPLK1 delivery by nanoparticle, Zou et al. demonstrated a 53% reduction in expression of the targeted gene in vitro. PLK1 gene editing was cell selective, with negligible genetic mutation in the healthy surrounding brain tissue. While nanoparticles with and without disulfide cross-linking were capable of gene editing, the disulfide cross-linked nanoparticle induced almost 400% more mutations. Glioblastoma cells treated with disulfide cross-linked nanoparticles were also over 3 times more likely to undergo apoptosis cell death. Mice grafted with patient glioblastoma tumors treated with Cas9/sgPLK1 nanocapsules experienced an almost 3-fold extension in life expectancy, suggesting this treatment as a viable anti-glioblastoma therapy.5

Yet in order to be effectively applied as a cancer therapy, the efficiency of this nanoparticle delivery system must be increased. In mouse glioblastoma models, Zou et al. only achieved a maximum accumulation of 12% and effected a 38% knockdown of PLK1.5 Despite their low magnitude, these values are far greater than similar gene therapy treatments currently studied, suggesting nanoparticles present an innovation in the delivery of CRISPR-Cas9 to difficult to access tumors.

In addition to the improved efficacy over existing systems, the work of Zou et al. opens the door for less invasive administration of treatment. In contrast to previous gene therapies administered directly to the tumor through intercranial injection, the BBB penetration and tumor-specific accumulation of the nanoparticles may permit systemic administration. Zou et al. injected the nanoparticles intravenously, but treatment may even be given as a pill taken orally, eliminating any surgical intervention. Moreover, due to their modular design, the engineered nanoparticles may be adapted as targeted treatments for other tumors. Exchanging the angiopep-2 peptides for another ligand would facilitate uptake by cells expressing the corresponding receptor. The load carried within the nanoparticle could be altered to contain a different sgRNA targeting a new gene or another therapeutic entirely as a complementary treatment. Nanoparticle delivery systems like that studied by Zou et al. contains many layers of selectivity, offering hope for effective delivery of treatment to previously inaccessible tumors.

 

Works Cited:

  1. Wirsching, H.-G. & Weller, M. Glioblastoma. in Malignant Brain Tumors : State-of-the-Art Treatment (eds. Moliterno Gunel, J., Piepmeier, J. M. & Baehring, J. M.) 265–288 (Springer International Publishing, Cham, 2017). doi:10.1007/978-3-319-49864-5_18.
  2. Delgado-López, P. D. & Corrales-García, E. M. Survival in glioblastoma: a review on the impact of treatment modalities. Clin Transl Oncol 18, 1062–1071 (2016).
  3. Ostrom, Q. T. et al. CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2007–2011. Neuro Oncol 16, iv1–iv63 (2014).
  4. Lino, C. A., Harper, J. C., Carney, J. P. & Timlin, J. A. Delivering CRISPR: a review of the challenges and approaches. Drug Delivery 25, 1234–1257 (2018).
  5. Zou, Y. et al. Blood-brain barrier–penetrating single CRISPR-Cas9 nanocapsules for effective and safe glioblastoma gene therapy. Sci Adv 8, eabm8011.
  6. Dotiwala, A. K., McCausland, C. & Samra, N. S. Anatomy, Head and Neck: Blood Brain Barrier. in StatPearls (StatPearls Publishing, Treasure Island (FL), 2024).
  7. Song, R. et al. Selection of rAAV vectors that cross the human blood-brain barrier and target the central nervous system using a transwell model. Molecular Therapy Methods & Clinical Development 27, 73–88 (2022).
  8. Lee, B. et al. Nanoparticle delivery of CRISPR into the brain rescues a mouse model of fragile X syndrome from exaggerated repetitive behaviours. Nat Biomed Eng 2, 497–507 (2018).
  9. Lee, C. et al. Polo-Like Kinase 1 Inhibition Kills Glioblastoma Multiforme Brain Tumor Cells in Part Through Loss of SOX2 and Delays Tumor Progression in Mice. Stem Cells 30, 1064–1075 (2012).

The Melting Arctic’s Impact on the Gulf of Maine

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Recent observation and nutrient analysis in the Gulf of Maine has found that within the past 50 years nutrient sources have become more limited, impacting the entire ecosystem. The Gulf of Maine receives nutrient-rich waters from the continental slope that enters through the Northeast Channel, north of Georges Bank (figure 1). These continental slope waters originate off southern Newfoundland and travel into the Gulf of Maine passing by Labrador and the Scotian Shelf, all the while accumulating and retaining its high concentration of nutrients. Nutrients from this water source, such as nitrate and silicate that exist in excess within continental slope water, make the Gulf of Maine a highly productive area. Nitrate is of particular interest as it is often the limiting nutrient. In other words, nitrate is often scarce in an ecosystem and therefore is the nutrient that puts a cap on the accumulation of biomass such as phytoplankton. However, recent observation and nutrient analysis in the Gulf of Maine has found that within the past 50 years nutrient sources have become more limited, impacting the entire ecosystem.  

              Figure 1. Map of Gulf of Maine

Since the 1970s, studies have shown a notable decrease in the abundance of nitrate in the Gulf of Maine. Along with this change, the deep waters in the Gulf of Maine have become cooler and less salty. In 2010, Townsend et al suggested  that these changes all originate from the accelerating melting of ice in the Arctic. Since salt does not freeze, when water freezes in the Arctic, the ice it forms is made of freshwater. As this freshwater melts at a faster rate than the Earth has previously seen, it changes the salinity of the water, making it fresher and therefore less dense. Deep ocean circulation is based on density and so with this change in density, comes a change in the way water circulates the planet. 

Given the changes in densities of water in the Arctic, a new source of water from the bottom of the Atlantic ocean carrying far less nutrients now supplies the Gulf of Maine.  With the changes in deep ocean circulation patterns, now water entering the Gulf of Maine passes closer to the bottom of the ocean. As this water passes the ocean floor, microbes in the sediment remove nitrogen from the water (for use as a nutrient), a process called denitrification. While this benefits ecosystems at the bottom of the deep ocean, by the time the water reaches the Gulf of Maine, much of the nitrate in the water has already been used. 

The Gulf of Maine will become less productive as ecosystems are supplied with low concentrations of nitrate for long periods of time. Phytoplankton, the first step of the food web, absorb these nutrients and use them for growth. Once phytoplankton are less abundant, animals that rely on them for food will begin to struggle. As nitrogen deficiency continues up the food chain, it will eventually reach the larger fish upon which we in Maine rely on for our food. The gradual loss of nitrogen rich waters to the Gulf of Maine is not only a sad reminder of climate change’s far reaching consequences, but also presents a growing issue for the fishing industry in Maine which relies on the productivity of the water. 

 

 

Work Cited

Townsend, D. W., Pettigrew, N. R., Thomas, M. A., Neary, M. G., McGillicuddy, D. J., & O’Donnell, J. (2015). Water masses and nutrient sources to the Gulf of Maine. Journal of Marine Research, 73(3), 93–122. doi:10.1357/002224015815848811

Fine-tuning of Chemotherapeutic Drug Reactions through Ruthenium Organic Complexes

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The development of cancer treatment reagents aims at optimizing the reactivity of the reagent with the cellular DNA while reducing the reactivity with other bodily sites. This is in order to maximize cytotoxicity to cancer cells while reducing the side effects associated with chemotherapy (Wang, 2005).

Organometallic complexes, organic compounds with one or more metallic central atoms, have been used to control the release of compounds involved in key biological reactions (Renfrew, 2014). In the context of cancer chemotherapy, cisplatin complexes have been successfully developed to react with guanosine 5’ monophosphate, or GMP, as a potential binding site in the cell’s DNA, while avoiding the reactions associated with side effects (Dasari, 2014 & Reedjik, 2003).

The development of chemotherapeutic reagents requires the fine-tuning of the ligand substitution reactions that the organometallic complex can undergo. Ligand substitution reactions are reactions where one or more of the substituents bonded to the metal atom in the organometallic complex are replaced by a compound from the surrounding environment. An example is shown in the figure below.

Fig 1. Example of an organometallic complex undergoing a ligand substitution reaction. When dissolved in pyridine, the chromium complex, [Cr(TPP)(Br)(H2O)], reacts with the solvent, and two of its ligands (Br and OH2) are replaced by pyridine compounds (Py) (Okada, 2012). 

In a 2005 study, a group of chemists tested multiple ligand-substitution reactions of Ruthenium (Ru) complexes to test the possibility of the development of a competitor for cisplatin in chemotherapy (Wang, 2005). The Ruthenium complex studied have “stool”-like structures with an arene upper part and a tetrahedral Ruthenium compound which contains the leaving group. The researchers use X-ray crystallography and other characterization methods to identify the structure of every ruthenium complex involved in the study.

Fig 2. The structure of the Ruthenium organometallic complexes tested in the study. The basic structure is shown on the upper left. The “arene” can be any of the structures shown, while the leaving group, X, can be any of the structures shown as well as a halide or pseudohalide (Wang, 2005). 

Given the high concentration of chloride anions in the bloodstream and the intercellular fluid, the substitution of X by chloride is a main mechanism by which the reagent is lost before it can attack cancer cells (Wang, 2005). Previous research has shown that hydrolysis (substitution of X by a water molecule) is an essential activation step in the reagent’s reaction with GMP (Chen, 2003). The researchers thus investigated how the choice of the arene and the leaving group within the ruthenium complex can affect the reaction rates such that the reagent is cytotoxic but is inactive before reaching its target site. 

The reaction rate with chloride was established by dissolving the complexes in a 104mM NaCl solution, mimicking the high-chloride media within the body, and monitoring the formation of the substitution reaction product using the same characterization methods involved in the identification of the complexes.

The hydrolysis rate was established by allowing the aqueous solutions of the complexes to equilibrate for 24-48 hours at 37°C, mimicking body temperature. The formation of the hydrolysis product was monitored using the same characterization methods. The reaction equilibria were determined using high-performance liquid chromatography. 

The reaction with GMP is believed to be the final step in the reagent’s activityagainst cancer cells. The reaction rate was established by dissolving 0.5mM of each complex in a 0.5mM aqueous GMP solution. The product formation rate was determined using the same methods as the other reactions.

The researchers summarized their key resultsin the table below:

The data show that complex 13, for example, has a faster reaction rate with chloride than GMP, and will, therefore, be lost before attacking cancer cells if it were to be used as a chemotherapyreagent. Data shows that complexes 15 and 17, on the other hand, react faster with water and GMP than chloride, which makes them more suitable for chemotherapy. Complex 1 can undergo hydrolysis and react with GMP at a relatively high rate. A key finding in this research is that complex 21 can bind to GMP without undergoing hydrolysis, skipping a previously thought required first step. 

The overall cytotoxicity of each complex was compared to cisplatin by determining the concentration of the complex which caused at least 50% inhibition in the growth of ovarian cancer cells, IC50 values. As previous research predicted, high hydrolysis rates correlated with high cytotoxicity (Chen, 2003). Cisplatin has IC50 = 0.6µM; chemotherapy reagents are considered to have good cytotoxic activity if they have IC50 < 18µM. Some of the same complexes discussed above, with the exception of complex 17 and 21 had IC50 values competitive with cisplatin (IC50 < 6µM). Furthermore, the studied Ru complexes exhibited cytotoxicity towards cisplatin-resistant ovarian cancer cells (Wang, 2005).

Overall, the results show that the rates of the reactions involved in chemotherapy can be fine tuned by the choice of the ligand within the ruthenium complex. These results can be used in the future development of novel chemotherapy reagents.  

Work Cited:

Chen, H., Parkinson, J. A., Morris, R. E., & Sadler, P. J. (2003). Highly selective binding of organometallic ruthenium ethylenediamine complexes to nucleic acids: novel recognition mechanisms. Journal of the American Chemical Society, 125(1), 173-186.

Dasari, S., & Tchounwou, P. B. (2014). Cisplatin in cancer therapy: molecular mechanisms of action. European journal of pharmacology, 740, 364-378.

Okada, K., Sumida, A., Inagaki, R., & Inamo, M. (2012). Effect of the axial halogen ligand on the substitution reactions of chromium (III) porphyrin complex. Inorganica Chimica Acta, 392, 473-477.

Reedijk, J. (2003). New clues for platinum antitumor chemistry: kinetically controlled metal binding to DNA. Proceedings of the National Academy of Sciences, 100(7), 3611-3616.

Renfrew, A. K. (2014). Transition metal complexes with bioactive ligands: mechanisms for selective ligand release and applications for drug delivery. Metallomics, 6(8), 1324-1335.

Wang, F., Habtemariam, A., van der Geer, E. P., Fernández, R., Melchart, M., Deeth, R. J., … & Sadler, P. J. (2005). Controlling ligand substitution reactions of organometallic complexes: Tuning cancer cell cytotoxicity. Proceedings of the National Academy of Sciences, 102(51), 18269-18274.